Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012726.1 Corchorus capsularis cultivar CVL-1 contig12747, 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: 44900
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:11861 original size:22 final size:22
Alignment explanation
Indices: 11843--12034 Score: 67
Period size: 22 Copynumber: 8.8 Consensus size: 22
11833 AACATTTTTG
11843 CTCTTACTGATTATTATTTTAC
1 CTCTTACTGATTATTATTTTAC
* *
11865 CTTTTACTGATTACT-TTTTAC
1 CTCTTACTGATTATTATTTTAC
* * ** * *
11886 TATTTTACTCTTTACTGA--TAAC
1 -CTCTTACTGATTA-TTATTTTAC
** *
11908 CTTCTTACTTTTTACTGATTTTTA-
1 C-TCTTACTGATTA-TTA-TTTTAC
** *
11932 CTCTTTACTGATTACCATTTT-G
1 CTC-TTACTGATTATTATTTTAC
**
11954 CTCTTACTGATTA-CCTTTTAC
1 CTCTTACTGATTATTATTTTAC
** *
11975 C-CTTTACTGATTACCATTTT-G
1 CTC-TTACTGATTATTATTTTAC
**
11996 CTCTTACTGATTACCATTTTAC
1 CTCTTACTGATTATTATTTTAC
*
12018 CTTTTACTGATTATTAT
1 CTCTTACTGATTATTAT
12035 CACTTTTTAC
Statistics
Matches: 132, Mismatches: 24, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.05
21 45 0.34
22 67 0.51
23 3 0.02
24 9 0.07
25 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (22 bp):
CTCTTACTGATTATTATTTTAC
Found at i:11879 original size:29 final size:29
Alignment explanation
Indices: 11846--11967 Score: 79
Period size: 29 Copynumber: 4.1 Consensus size: 29
11836 ATTTTTGCTC
*
11846 TTACTGATTATTATTTTAC-CTTTTACTGA
1 TTACTGATTACTATTTTACTC-TTTACTGA
**
11875 TTACTTTTTACTATTTTACTCTTTACTGA
1 TTACTGATTACTATTTTACTCTTTACTGA
* ** * **
11904 TAACCTTCTTACT-TTTTACTGATTTTTACTCT
1 TTA-CTGATTACTATTTTAC---TCTTTACTGA
* *
11936 TTACTGATTACCATTTTGCTC-TTACTGA
1 TTACTGATTACTATTTTACTCTTTACTGA
11964 TTAC
1 TTAC
11968 CTTTTACCCT
Statistics
Matches: 71, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
28 9 0.13
29 33 0.46
30 9 0.13
31 6 0.08
32 14 0.20
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (29 bp):
TTACTGATTACTATTTTACTCTTTACTGA
Found at i:12050 original size:35 final size:35
Alignment explanation
Indices: 12006--12165 Score: 124
Period size: 35 Copynumber: 4.7 Consensus size: 35
11996 CTCTTACTGA
*
12006 TTACCATTTTACCTTTTACTGATTATTATCACTTT
1 TTACGATTTTACCTTTTACTGATTATTATCACTTT
* *
12041 TTACGATTTTA-CTCTTTACTGATTACCTTCTTACTTT
1 TTACGATTTTACCT-TTTACTGATTA--TTATCACTTT
* **
12078 TTACTGA--TTACCATTTTAC----TCTTA-C-C-GA
1 TTAC-GATTTTACC-TTTTACTGATTATTATCACTTT
* *
12106 TTACCATTTTACCTTTTACTGATTATTCTCACTTT
1 TTACGATTTTACCTTTTACTGATTATTATCACTTT
*
12141 TTACGATTTTACTTTTTACTGATTA
1 TTACGATTTTACCTTTTACTGATTA
12166 CCATTTTACT
Statistics
Matches: 95, Mismatches: 15, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
27 1 0.01
28 10 0.11
29 6 0.06
31 2 0.02
32 3 0.03
33 2 0.02
34 3 0.03
35 44 0.46
36 3 0.03
37 18 0.19
38 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (35 bp):
TTACGATTTTACCTTTTACTGATTATTATCACTTT
Found at i:12066 original size:22 final size:21
Alignment explanation
Indices: 12041--12382 Score: 235
Period size: 22 Copynumber: 16.1 Consensus size: 21
12031 TTATCACTTT
12041 TTACGATTTTACTCTTTACTGA
1 TTAC-ATTTTACTCTTTACTGA
* *
12063 TTACCTTCTTACTTTTTACTGA
1 TTACATT-TTACTCTTTACTGA
*
12085 TTACCATTTTACTC-TTACCGA
1 TTA-CATTTTACTCTTTACTGA
12106 TTACCATTTTAC-CTTTTACTGA
1 TTA-CATTTTACTC-TTTACTGA
* *
12128 TT--ATTCTCACTTTTTAC-G-
1 TTACATT-TTACTCTTTACTGA
*
12146 ----ATTTTACTTTTTACTGA
1 TTACATTTTACTCTTTACTGA
*
12163 TTACCATTTTACTTTTTACTGA
1 TTA-CATTTTACTCTTTACTGA
*
12185 TTACCATTTTACTTTTTACTGA
1 TTA-CATTTTACTCTTTACTGA
* *
12207 TTGCTATTTTAC-CATTTTGCT-A
1 TTAC-ATTTTACTC--TTTACTGA
** *
12229 TTACAAATTAC-CTTTTACTAA
1 TTACATTTTACTC-TTTACTGA
12250 TTACTATTTTACTCTTTACTGA
1 TTAC-ATTTTACTCTTTACTGA
* *
12272 TTACCTTCTTACTTTTTACTGA
1 TTACATT-TTACTCTTTACTGA
12294 TTACCATTTTACTCTTTACTGA
1 TTA-CATTTTACTCTTTACTGA
* * * *
12316 TTACCATTTTGC-CCTCACCGA
1 TTA-CATTTTACTCTTTACTGA
12337 TTACTATTTTACTCTTTACTGA
1 TTAC-ATTTTACTCTTTACTGA
* *
12359 TTACCTTCTTACTTTTTACTGA
1 TTACATT-TTACTCTTTACTGA
12381 TT
1 TT
12383 TTTACTCTTT
Statistics
Matches: 263, Mismatches: 33, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
15 10 0.04
16 4 0.02
19 4 0.02
20 16 0.06
21 51 0.19
22 166 0.63
23 12 0.05
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
TTACATTTTACTCTTTACTGA
Found at i:12100 original size:100 final size:100
Alignment explanation
Indices: 11861--12325 Score: 508
Period size: 100 Copynumber: 4.5 Consensus size: 100
11851 GATTATTATT
** ** * * *
11861 TTACCTTTTACTGATTACTTTTTACTATTTTACTCTTTACTGATAACC-TTCTTACTTTTTACTG
1 TTACCTTTTACTTTTTACTGATTACCATTTTACTC-TTACTGATTACCATT-TTACCTTTTACTG
* * * *
11925 ATTTTTACTCTTTACTGATTACCATTTTGCTC-TTACTGA
64 ATTATTACTC---ACTTATTACGATTTTACTCTTTACTGA
** *
11964 TTACCTTTTACCCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGAT
1 TTACCTTTTACTTTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCTTTTACTGAT
*
12029 TATTA-TCACTTTTTACGATTTTACTCTTTACTGA
66 TATTACTCACTTATTACGATTTTACTCTTTACTGA
*
12063 TTACCTTCTTACTTTTTACTGATTACCATTTTACTCTTACCGATTACCATTTTACCTTTTACTGA
1 TTACCTT-TTACTTTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCTTTTACTGA
* *
12128 TTATT-CTCACTTTTTACGATTTTACTTTTTACTGA
65 TTATTACTCACTTATTACGATTTTACTCTTTACTGA
* * * *
12163 TTACCATTTTACTTTTTACTGATTACCATTTTACTTTTTACTGATTGCTATTTTACCATTTTGCT
1 TTACC-TTTTACTTTTTACTGATTACCATTTTAC-TCTTACTGATTACCATTTTACC-TTTTACT
* * *
12228 -ATTACAAATTACCTTTTACTAATTACTATTTTACTCTTTACTGA
63 GATT----ATTA-C--TCACTTATTACGATTTTACTCTTTACTGA
12272 TTACCTTCTTACTTTTTACTGATTACCATTTTACTCTTTACTGATTACCATTTT
1 TTACCTT-TTACTTTTTACTGATTACCATTTTACTC-TTACTGATTACCATTTT
12326 GCCCTCACCG
Statistics
Matches: 313, Mismatches: 32, Indels: 28
0.84 0.09 0.08
Matches are distributed among these distances:
98 15 0.05
99 14 0.04
100 117 0.37
101 25 0.08
102 35 0.11
103 30 0.10
105 3 0.01
107 1 0.00
108 3 0.01
109 70 0.22
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (100 bp):
TTACCTTTTACTTTTTACTGATTACCATTTTACTCTTACTGATTACCATTTTACCTTTTACTGAT
TATTACTCACTTATTACGATTTTACTCTTTACTGA
Found at i:12156 original size:15 final size:15
Alignment explanation
Indices: 12136--12208 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
12126 GATTATTCTC
12136 ACTTTTTACGATTTT
1 ACTTTTTACGATTTT
12151 ACTTTTTACTGA--TT
1 ACTTTTTAC-GATTTT
* *
12165 ACCATTTTAC-TTTTT
1 A-CTTTTTACGATTTT
** *
12180 ACTGATTACCATTTT
1 ACTTTTTACGATTTT
12195 ACTTTTTACTGATT
1 ACTTTTTAC-GATT
12209 GCTATTTTAC
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
14 8 0.19
15 30 0.70
16 5 0.12
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.56
Consensus pattern (15 bp):
ACTTTTTACGATTTT
Found at i:12253 original size:87 final size:88
Alignment explanation
Indices: 12149--12382 Score: 289
Period size: 87 Copynumber: 2.7 Consensus size: 88
12139 TTTTACGATT
* * * * *
12149 TTACTTTTTACTGATTACCATTTTACTTTTTACTGATTACCATT-TTACTTTTTACTGATTGCTA
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACC-TTCTTACTTTTTACTGATTACCA
*
12213 TTTTAC-CATTTTGCT-ATTA-CAAA
65 TTTTACTC--TTTACTGATTACCAAA
*
12236 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACCAT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACCAT
**
12301 TTTACTCTTTACTGATTACCATT
66 TTTACTCTTTACTGATTACCAAA
* * * *
12324 TTGCC-CTCACCGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATT
12383 TTTACTCTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
86 7 0.05
87 115 0.89
88 7 0.05
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (88 bp):
TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACCAT
TTTACTCTTTACTGATTACCAAA
Found at i:12442 original size:40 final size:42
Alignment explanation
Indices: 12398--12490 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
12388 TCTTTACCGA
*
12398 TTTACTGATTGCTTCTTTTACTCTT-ACT-TTTAATTAC-CAT
1 TTTACTGATTACTTCTTTTACT-TTGACTCTTTAATTACTCAT
*
12438 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTGAT
1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
*
12480 TTCACTGATTA
1 TTTACTGATTA
12491 ATCTCTTGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.04
40 24 0.51
41 9 0.19
42 12 0.26
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (42 bp):
TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
Found at i:12505 original size:41 final size:38
Alignment explanation
Indices: 12419--12505 Score: 86
Period size: 41 Copynumber: 2.2 Consensus size: 38
12409 CTTCTTTTAC
* * *
12419 TCTT-ACTTTTAATTACCATTTTACTGATTACTTCTTT
1 TCTTGACTTTTAATTACCATTTCACTGATTAATTCTTG
*
12456 TACTTTGACTCTTTAATTACTGATTTCACTGATTAATCTCTTG
1 T-C-TTGACT-TTTAATTAC-CATTTCACTGATTAAT-TCTTG
12499 TCTTGAC
1 TCTTGAC
12506 CCTTCATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
37 1 0.03
38 1 0.03
39 2 0.05
40 3 0.08
41 14 0.35
42 14 0.35
43 5 0.12
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.52
Consensus pattern (38 bp):
TCTTGACTTTTAATTACCATTTCACTGATTAATTCTTG
Found at i:13304 original size:2 final size:2
Alignment explanation
Indices: 13297--13321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13287 CATTTGCTTA
13297 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 A
13322 CATTCTAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22875 original size:156 final size:155
Alignment explanation
Indices: 22568--22932 Score: 368
Period size: 156 Copynumber: 2.3 Consensus size: 155
22558 GAGTTTCTCA
* * *
22568 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AA
*
22633 TTTTGCCAAGGATCTTAGAGTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTC
65 TTTTGCCAAGGATCTTAGAGTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTC
* * * *
22698 CCCTTGATGGTGAACTAGGTTTCTCT
130 CCCTCGATAGAGAACTAGGTTTCACT
* * * * *
22724 CC-CTGAGTTGTCCTTAAATGAAAACCTAACATAAGTTTTTCATTCTAAGTC-CAACGAAGTTG-
1 CCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
* * *
22786 ATTTTCCGCC-AGTAGA-CTTATATTAT-CACCATAAGGCTATGCGAAAAAA-TCTAAGTAAAAC
64 ATTTT--GCCAAG--GATCTTAGAGTATCCA-CATAAGACTATG-GAAAAAATTCTAAGTAAAAC
* * * *
22847 CGAACT-CTCTACGATAGAGAAGTTGGTTTGACT
123 CGAACTCCCCT-CGATAGAGAACTAGGTTTCACT
* * *
22880 CCTCAAATTGTCCTTAACTGAAAAAACTAGCATAAGTTTTTTATACTAAGTCT
1 CCTCAAATTGTCCTTAAATG-AAAAACTAGCATAAGTTTTTCATTCTAAGTCT
22933 GTTTGAGATG
Statistics
Matches: 170, Mismatches: 27, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
154 5 0.03
155 11 0.06
156 117 0.69
157 37 0.22
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (155 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTGCCAAGGATCTTAGAGTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCC
CCTCGATAGAGAACTAGGTTTCACT
Found at i:24831 original size:12 final size:12
Alignment explanation
Indices: 24814--24868 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
24804 TTAATACAGG
24814 TATCGACGGATA
1 TATCGACGGATA
24826 TATCGAACGGATA
1 TATCG-ACGGATA
*
24839 TATTGACGGATA
1 TATCGACGGATA
*
24851 TATCGATGGATA
1 TATCGACGGATA
24863 TATCGA
1 TATCGA
24869 GGTATCGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:24852 original size:25 final size:24
Alignment explanation
Indices: 24818--24865 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
24808 TACAGGTATC
24818 GACGGATATATCGAACGGATATATT
1 GACGGATATATCG-ACGGATATATT
*
24843 GACGGATATATCGATGGATATAT
1 GACGGATATATCGACGGATATAT
24866 CGAGGTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (24 bp):
GACGGATATATCGACGGATATATT
Found at i:29317 original size:24 final size:25
Alignment explanation
Indices: 29284--29336 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
29274 GCATACCTGC
*
29284 GAGATTGAACCCAACGAAAGCCAAA
1 GAGATTGAACCCAAAGAAAGCCAAA
29309 GAGA-TGAACCCAAAGAAAGCCAAA
1 GAGATTGAACCCAAAGAAAGCCAAA
29333 GAGA
1 GAGA
29337 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.51, C:0.21, G:0.23, T:0.06
Consensus pattern (25 bp):
GAGATTGAACCCAAAGAAAGCCAAA
Found at i:30251 original size:10 final size:10
Alignment explanation
Indices: 30228--30282 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
30218 TGAGGTATTC
*
30228 ATAAGACTTA
1 ATAAGCCTTA
*
30238 ATAAGCCTTT
1 ATAAGCCTTA
*
30248 ATAAGCCTTC
1 ATAAGCCTTA
*
30258 ATAAGACTTA
1 ATAAGCCTTA
* *
30268 ATAATCCTTG
1 ATAAGCCTTA
30278 ATAAG
1 ATAAG
30283 ATTGAATGAG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (10 bp):
ATAAGCCTTA
Found at i:30261 original size:20 final size:20
Alignment explanation
Indices: 30228--30307 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
30218 TGAGGTATTC
* * *
30228 ATAAGACTTAATAAGCCTTT
1 ATAAGCCTTAATAAGACTTA
*
30248 ATAAGCCTTCATAAGACTTA
1 ATAAGCCTTAATAAGACTTA
* *
30268 ATAATCCTTGATAAGA-TTGA
1 ATAAGCCTTAATAAGACTT-A
* *
30288 ATGAGCCTAAATAAGACTTA
1 ATAAGCCTTAATAAGACTTA
30308 TAATTAGCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
19 2 0.04
20 44 0.92
21 2 0.04
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (20 bp):
ATAAGCCTTAATAAGACTTA
Found at i:30261 original size:30 final size:30
Alignment explanation
Indices: 30225--30282 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
30215 TTATGAGGTA
*
30225 TTCATAAGACTTAATAAGCCTTTATAAGCC
1 TTCATAAGACTTAATAAGCCTTGATAAGCC
*
30255 TTCATAAGACTTAATAATCCTTGATAAG
1 TTCATAAGACTTAATAAGCCTTGATAAG
30283 ATTGAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (30 bp):
TTCATAAGACTTAATAAGCCTTGATAAGCC
Found at i:32580 original size:75 final size:75
Alignment explanation
Indices: 32488--32637 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
32478 TTTTGTATTG
32488 TAGAGCCACCCTCATGCTAATAAGGCCTTCCCTCATTATGATGCATTTCCACACATCTTTGGCAG
1 TAGAGCCACCCTCATGCTAATAAGGCCTTCCCTCATTATGATGCATTTCCACACATCTTTGGCAG
32553 TGATTCAGCA
66 TGATTCAGCA
32563 TAGAGCCACCCTCATGCTAATAAGGCCTTCCCTCATTATGATGCATTTCCACACATCTTTGGCAG
1 TAGAGCCACCCTCATGCTAATAAGGCCTTCCCTCATTATGATGCATTTCCACACATCTTTGGCAG
32628 TGATTCAGCA
66 TGATTCAGCA
32638 AAAGGAGCAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (75 bp):
TAGAGCCACCCTCATGCTAATAAGGCCTTCCCTCATTATGATGCATTTCCACACATCTTTGGCAG
TGATTCAGCA
Found at i:44280 original size:13 final size:13
Alignment explanation
Indices: 44262--44335 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 13
44252 TAGTAGAGTC
44262 ATGGTTTTCAAAA
1 ATGGTTTTCAAAA
44275 ATGGTTTTCAAAAGAGA
1 ATGGTTTTC--AA-A-A
*
44292 GTCATGATTTTCAAAA
1 ---ATGGTTTTCAAAA
*
44308 ATGTTTTTCAAAA
1 ATGGTTTTCAAAA
*
44321 ATGTTTTTCAAAA
1 ATGGTTTTCAAAA
44334 AT
1 AT
44336 AATAATAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 36 0.69
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
20 8 0.15
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (13 bp):
ATGGTTTTCAAAA
Found at i:44303 original size:33 final size:33
Alignment explanation
Indices: 44256--44320 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
44246 TTGGAATAGT
*
44256 AGAGTCATGGTTTTCAAAAATGGTTTTCAAAAG
1 AGAGTCATGATTTTCAAAAATGGTTTTCAAAAG
*
44289 AGAGTCATGATTTTCAAAAATGTTTTTCAAAA
1 AGAGTCATGATTTTCAAAAATGGTTTTCAAAA
44321 ATGTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (33 bp):
AGAGTCATGATTTTCAAAAATGGTTTTCAAAAG
Found at i:44320 original size:12 final size:13
Alignment explanation
Indices: 44299--44335 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
44289 AGAGTCATGA
44299 TTTTCAAAAATGT
1 TTTTCAAAAATGT
44312 TTTTCAAAAATGT
1 TTTTCAAAAATGT
44325 TTTTCAAAAAT
1 TTTTCAAAAAT
44336 AATAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:44341 original size:3 final size:3
Alignment explanation
Indices: 44333--44369 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
44323 GTTTTTCAAA
*
44333 AAT AAT AAT AAT AAT AAT AAT -AT AA- AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44370 TTTTGAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:44677 original size:6 final size:6
Alignment explanation
Indices: 44666--44693 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44656 AAGTGCAAAA
44666 AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
44694 GTGGAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATC
Done.