Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015576.1 Corchorus capsularis cultivar CVL-1 contig15597, 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: 21230
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1096 original size:26 final size:26
Alignment explanation
Indices: 1025--1096 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
1015 AAAGTGGACT
*
1025 TAAAATGACTAAAATGCCCTTGAATG
1 TAAAATGACCAAAATGCCCTTGAATG
* * *
1051 TGCAAATGGCCAAAATGCCCTT-AGTG
1 T-AAAATGACCAAAATGCCCTTGAATG
1077 TAAAGATGACCAAAATGCCC
1 TAAA-ATGACCAAAATGCCC
1097 CTAGGTGACC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 17 0.45
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (26 bp):
TAAAATGACCAAAATGCCCTTGAATG
Found at i:1415 original size:56 final size:56
Alignment explanation
Indices: 1342--1471 Score: 181
Period size: 56 Copynumber: 2.3 Consensus size: 56
1332 CTGAAATTTA
* * *
1342 AGAAAAATGATCGTCTTCGACCAACTTGAGTAACTACTAAAAACTACTGGAAACTG
1 AGAAAGATGACCGTCTTCGACCAACTTGAGTAACTACTAAAAACTACTGAAAACTG
* * **
1398 AGAAAGATGACCGTCTTCGATCAACTTGAGTAACTACTTAAAACTGTTGAAAACTG
1 AGAAAGATGACCGTCTTCGACCAACTTGAGTAACTACTAAAAACTACTGAAAACTG
1454 -GAAAGGATGACCGTCTTC
1 AGAAA-GATGACCGTCTTC
1472 AGTCTAAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 4 0.06
56 62 0.94
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (56 bp):
AGAAAGATGACCGTCTTCGACCAACTTGAGTAACTACTAAAAACTACTGAAAACTG
Found at i:1680 original size:58 final size:58
Alignment explanation
Indices: 1466--2026 Score: 418
Period size: 58 Copynumber: 9.4 Consensus size: 58
1456 AAGGATGACC
* * * * *
1466 GTCTTCAGTCTAAATCTAAAAAGCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
1 GTCTTCAGCCTCATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* * * * * *
1524 GTCTTAAACCTTAATGCATGTTAAATCTTTCAAGAACTGTCTTCAGATCCATCTATGAGCT
1 GTCTTCAGCC-TCATTC-T-TAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* *
1585 GTCTT-AGCCTCTTTCTTGAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
1 GTCTTCAGCCTCATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* *
1642 GTCTTCAGCCTCTTTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTGTGAGCT
1 GTCTTCAGCCTCATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* * * * * * * *
1700 GTCTTCAGTCTCACTT-TTAAATACCATTGAGGAACTGTCTTCAAACCCACCT-TCGCGAACT
1 GTCTTCAGCCTCA-TTCTTAAA-ATCTTTCAGGAACTGTCTTCAGATCCATCTAT---GAGCT
** * * * * * *
1761 GTCTTCAGATTCACTCTT-AAATACTTTTTAGGATCCGTCTTCAGAACCCAT-TATTGTGAACT
1 GTCTTCAGCCTCATTCTTAAAAT-C-TTTCAGGAACTGTCTTCAG-ATCCATCTA---TGAGCT
* * * * * * *
1823 GTCTTCAG-ATCCACTCTTAAATACCTTTTAGGAATTGTCTTCAGAATCCATCTTTATAAACT
1 GTCTTCAGCCT-CATTCTTAAA-ATCTTTCAGGAACTGTCTTCAG-ATCCATC--TATGAGCT
* * * *
1885 GTCTTCAGTCTGAATT-TTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCT
1 GTCTTCAGCCT-CATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* * * * * *
1943 ATCTTCAGTCTCAATT-TTCAAATCTTTTAGGAACTGTCTTCGGATCCATCTGTGAGCT
1 GTCTTCAGCCTC-ATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
* * *
2001 ATCTTCAGCCTCAATCGTAAAATCTT
1 GTCTTCAGCCTCATTCTTAAAATCTT
2027 CAGAACCATT
Statistics
Matches: 417, Mismatches: 60, Indels: 52
0.79 0.11 0.10
Matches are distributed among these distances:
57 46 0.11
58 152 0.36
59 34 0.08
60 15 0.04
61 95 0.23
62 65 0.16
63 6 0.01
64 1 0.00
65 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.37
Consensus pattern (58 bp):
GTCTTCAGCCTCATTCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCT
Found at i:1775 original size:61 final size:62
Alignment explanation
Indices: 1656--1928 Score: 206
Period size: 62 Copynumber: 4.5 Consensus size: 62
1646 TCAGCCTCTT
* * * * * *
1656 TCTTAAA-ATCTTTCAGGAACTGTCTTCAG-ATCCA-TCT-GTGAGCTGTCTTCAG-TCTCAC
1 TCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCACTATCGCGAACTGTCTTCAGAT-TCAC
* * *
1714 TTTTAAATACCATTGAGGAACTGTCTTCA-AACCCACCT-TCGCGAACTGTCTTCAGATTCAC
1 TCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCA-CTATCGCGAACTGTCTTCAGATTCAC
* * * * * * *
1775 TCTTAAATACTTTTTAGGATCCGTCTTCAGAACCCATTATTGTGAACTGTCTTCAGATCCAC
1 TCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCACTATCGCGAACTGTCTTCAGATTCAC
* * **** * *
1837 TCTTAAATACCTTTTAGGAATTGTCTTCAGAATCCATCT-TTATAAACTGTCTTCAG-TCTGAA
1 TCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCA-CTATCGCGAACTGTCTTCAGAT-TCAC
* *
1899 TTTTAAA-ATCTTTTAGGAACTGTCTTCAGA
1 TCTTAAATACCTTTTAGGAACTGTCTTCAGA
1929 TCCATCTGTG
Statistics
Matches: 174, Mismatches: 31, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
58 6 0.03
59 22 0.13
60 1 0.01
61 64 0.37
62 80 0.46
63 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (62 bp):
TCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCACTATCGCGAACTGTCTTCAGATTCAC
Found at i:1913 original size:123 final size:120
Alignment explanation
Indices: 1466--1993 Score: 351
Period size: 118 Copynumber: 4.4 Consensus size: 120
1456 AAGGATGACC
* * * * *
1466 GTCTTCAGTCTAAATC-TAAAAAGCTTTCAGGAACTGTCTTCAG-ATCCATC--TATGAGCTGTC
1 GTCTTCAGTCTCACTCTTAAATACCTTTCAGGAACTGTCTTCAGAATCCATCTTTATGAACTGTC
* ** * * * * *
1527 TTAAACCTTAATGCATGTT-AAATCTTTCAAGAACTGTCTTCAG-ATCCATCTATGAGCT
66 TTCAGTC-TAAT---T-TTAAAATCTTTTAGGAACTGTCTTCAGAACCCATCTGTGAACT
* ** *
1585 GTCTT-AGCCTCTTTCTTGAAAT--CTTTCAGGAACTGTCTTCAG-ATCCATC--TATGAGCTGT
1 GTCTTCAGTCTCACTCTT-AAATACCTTTCAGGAACTGTCTTCAGAATCCATCTTTATGAACTGT
* ** * * *
1644 CTTCAGCCTCTTTCTTAAAATCTTTCAGGAACTGTCTTCAG-ATCCATCTGTGAGCT
65 CTTCAGTCTAATT-TTAAAATCTTTTAGGAACTGTCTTCAGAACCCATCTGTGAACT
* * * * * ***
1700 GTCTTCAGTCTCACTTTTAAATACCATTGAGGAACTGTCTTCA-AACCCACCTTCGCGAACTGTC
1 GTCTTCAGTCTCACTCTTAAATACCTTTCAGGAACTGTCTTCAGAATCCATCTTTATGAACTGTC
* * * * *
1764 TTCAGAT-TCACTCTT-AAATACTTTTTAGGATCCGTCTTCAGAACCCATTATTGTGAACT
66 TTCAG-TCT-AATTTTAAAAT-C-TTTTAGGAACTGTCTTCAGAACCCA-T-CTGTGAACT
* * *
1823 GTCTTCAGATC-CACTCTTAAATACCTTTTAGGAATTGTCTTCAGAATCCATCTTTATAAACTGT
1 GTCTTCAG-TCTCACTCTTAAATACCTTTCAGGAACTGTCTTCAGAATCCATCTTTATGAACTGT
* *
1887 CTTCAGTCTGAATTTTAAAATCTTTTAGGAACTGTCTTCAG-ATCCATCTGTGAGCT
65 CTTCAGTCT-AATTTTAAAATCTTTTAGGAACTGTCTTCAGAACCCATCTGTGAACT
* * * * *
1943 ATCTTCAGTCTCAATTTTCAAAT--CTTTTAGGAACTGTCTTC-GGATCCATCT
1 GTCTTCAGTCTCACTCTT-AAATACCTTTCAGGAACTGTCTTCAGAATCCATCT
1994 GTGAGCTATC
Statistics
Matches: 330, Mismatches: 57, Indels: 45
0.76 0.13 0.10
Matches are distributed among these distances:
114 3 0.01
115 46 0.14
116 8 0.02
117 24 0.07
118 62 0.19
119 41 0.12
120 39 0.12
121 9 0.03
122 5 0.02
123 61 0.18
124 28 0.08
125 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (120 bp):
GTCTTCAGTCTCACTCTTAAATACCTTTCAGGAACTGTCTTCAGAATCCATCTTTATGAACTGTC
TTCAGTCTAATTTTAAAATCTTTTAGGAACTGTCTTCAGAACCCATCTGTGAACT
Found at i:3185 original size:25 final size:25
Alignment explanation
Indices: 3157--3206 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
3147 GTCCCATCCA
3157 TTTT-CATTTTCTCATTAGTCCTATT
1 TTTTGCATTTTCTCATTAGT-CTATT
*
3182 TTTTGCATTTTCTCATTGGTCTATT
1 TTTTGCATTTTCTCATTAGTCTATT
3207 AGTCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.14, C:0.18, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTTGCATTTTCTCATTAGTCTATT
Found at i:3844 original size:33 final size:33
Alignment explanation
Indices: 3807--3948 Score: 230
Period size: 33 Copynumber: 4.3 Consensus size: 33
3797 TTCTTTTCAC
** *
3807 CCAAAACAGAATTATTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
3840 CCAAAACAGAATTATTTGTAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
3873 CCAAAACAGAATTATTTGCAATGTTATGATTAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
3906 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
3939 CCAAAACAGA
1 CCAAAACAGA
3949 TTTGTTTTCA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 102 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:4011 original size:33 final size:33
Alignment explanation
Indices: 3974--4078 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
3964 ATTAGCATCC
*
3974 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
4007 AAAACGGATTTAGTGTCATTGCAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
4040 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
4073 AAAACA
1 AAAACA
4079 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:6786 original size:33 final size:31
Alignment explanation
Indices: 6749--6822 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
6739 TTTTTTTCAC
** *
6749 CCAAAACAGTCCTATTTTCAATGCTATGATCAA
1 CCAAAACAGAACTATTTGCAA--CTATGATCAA
*
6782 CCAAAACAGAATTATTTGCAACTATGATCAA
1 CCAAAACAGAACTATTTGCAACTATGATCAA
6813 CCAAAACAGA
1 CCAAAACAGA
6823 TTTGTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 20 0.54
33 17 0.46
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.24
Consensus pattern (31 bp):
CCAAAACAGAACTATTTGCAACTATGATCAA
Found at i:6918 original size:33 final size:33
Alignment explanation
Indices: 6815--6919 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
6805 ATGATCAACC
** * *
6815 AAAACAGATTT-GTTTTCATCACAATTAGCATCC
1 AAAACAGATTTAG-TTTCATCACAAACAACATCT
*
6848 AAAACAGATTTAGTTTCATCACAAACAA-AACT
1 AAAACAGATTTAGTTTCATCACAAACAACATCT
*
6880 CAAAACAGATTTAGTATCATCACAAACAACATCT
1 -AAAACAGATTTAGTTTCATCACAAACAACATCT
6914 AAAACA
1 AAAACA
6920 CTCTTTGCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 2 0.03
33 56 0.90
34 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACATCT
Found at i:17746 original size:27 final size:27
Alignment explanation
Indices: 17675--17738 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
17665 GGTCACCTAC
17675 GGGCATTTTGGTCATTTTTACATTCAG
1 GGGCATTTTGGTCATTTTTACATTCAG
*
17702 GGGCATTTTGGTCATTTTTGCATTCAG
1 GGGCATTTTGGTCATTTTTACATTCAG
17729 GGGCATTTTG
1 GGGCATTTTG
17739 ATAATTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.44
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTACATTCAG
Found at i:19294 original size:24 final size:24
Alignment explanation
Indices: 19267--19320 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
19257 CTAGCTTCTA
*
19267 ACAAAAAAGAC-TCTTTCTTTTCAC
1 ACAAAAAAGACAT-TTTCTTTGCAC
* * *
19291 ACAAGAATGTCATTTTCTTTGCAC
1 ACAAAAAAGACATTTTCTTTGCAC
19315 ACAAAA
1 ACAAAA
19321 GGATTCACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (24 bp):
ACAAAAAAGACATTTTCTTTGCAC
Found at i:20066 original size:36 final size:36
Alignment explanation
Indices: 20019--20137 Score: 158
Period size: 36 Copynumber: 3.4 Consensus size: 36
20009 TCTTTTCTGG
* *
20019 ATTAAGCTCTTTATTGACCTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
20055 ATTAAGTTCTTTATT---CT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
* *
20087 ATTAAG-CCTTTTATTGACTTCACTTAATTACCCTGA
1 ATTAAGTTC-TTTATTGACCTCACTTAATTACCCTGA
20123 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
20138 TTACTTAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
33 2 0.03
35 1 0.01
36 41 0.57
37 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
Found at i:20081 original size:32 final size:32
Alignment explanation
Indices: 20040--20147 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
20030 TATTGACCTC
*
20040 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCT
*
20072 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT--C-T
*
20107 CACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCT
20140 ACTTAATT
1 ACTTAATT
20148 TCCTTTCCTA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 34 0.52
33 1 0.02
34 1 0.02
35 1 0.02
36 27 0.41
37 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCT
Found at i:20104 original size:68 final size:68
Alignment explanation
Indices: 20019--20147 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
20009 TCTTTTCTGG
*
20019 ATTAAGCTCTTTATTGACCTCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
1 ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
20084 TGA
66 TGA
* *
20087 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGCTC-TTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATT
20148 TCCTTTCCTA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 1 0.02
68 56 0.98
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:20262 original size:37 final size:36
Alignment explanation
Indices: 20174--20422 Score: 225
Period size: 37 Copynumber: 6.9 Consensus size: 36
20164 AGCCTGTGTC
* * **
20174 TTTTTACTTAATTTCCTTGAAATTAATTCAG-TCTT
1 TTTTTACCTAATTTCCTTGAAACTAAGCCAGCTCTT
* * * *
20209 TCCTTTACCTAATTTCCTTGAAATTAAGCGAGGCTTTT
1 T-TTTTACCTAATTTCCTTGAAACTAAGCCA-GCTCTT
* *
20247 TTTTTACCTAGTTTCCTTGAAACTAAGCCAATCTCTT
1 TTTTTACCTAATTTCCTTGAAACTAAGCC-AGCTCTT
* *
20284 TTTTTACCTAGTTTCCTTGAAACTAAGCCAATCTCTT
1 TTTTTACCTAATTTCCTTGAAACTAAGCC-AGCTCTT
* * * *
20321 TTTTCTACCTAGTTTCCTAGAAACTAGGCCAG-TCCT
1 TTTT-TACCTAATTTCCTTGAAACTAAGCCAGCTCTT
* * * *
20357 TTTTTACTTAATTCCCTTGAAATTAAGCCAG-TCTA
1 TTTTTACCTAATTTCCTTGAAACTAAGCCAGCTCTT
* * *
20392 TCTTTACCTAATTTCCTTGAAATTAAACCAG
1 TTTTTACCTAATTTCCTTGAAACTAAGCCAG
20423 TTTTTTATCA
Statistics
Matches: 181, Mismatches: 28, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
35 51 0.28
36 31 0.17
37 71 0.39
38 28 0.15
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTTTACCTAATTTCCTTGAAACTAAGCCAGCTCTT
Found at i:20284 original size:75 final size:74
Alignment explanation
Indices: 20212--20386 Score: 228
Period size: 75 Copynumber: 2.4 Consensus size: 74
20202 CAGTCTTTCC
* * * *
20212 TTTACCTAATTTCCTTGAAATTAAGCGAGGCT-TTTTTTTTACCTAGTTTCCTTGAAACTAAGCC
1 TTTACCTAATTTCCTTGAAATTAAGCCAAGCTCTTTTTTCTACCTAGTTTCCTAGAAACTAAGCC
20276 AATCTCTTTT
66 AATCTC-TTT
* * * *
20286 TTTACCTAGTTTCCTTGAAACTAAGCCAATCTCTTTTTTCTACCTAGTTTCCTAGAAACTAGGCC
1 TTTACCTAATTTCCTTGAAATTAAGCCAAGCTCTTTTTTCTACCTAGTTTCCTAGAAACTAAGCC
*
20351 AGTC-CTTT
66 AATCTCTTT
* *
20359 TTTACTTAATTCCCTTGAAATTAAGCCA
1 TTTACCTAATTTCCTTGAAATTAAGCCA
20387 GTCTATCTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 27 0.31
74 28 0.32
75 32 0.37
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (74 bp):
TTTACCTAATTTCCTTGAAATTAAGCCAAGCTCTTTTTTCTACCTAGTTTCCTAGAAACTAAGCC
AATCTCTTT
Found at i:20444 original size:11 final size:11
Alignment explanation
Indices: 20430--20604 Score: 129
Period size: 11 Copynumber: 15.6 Consensus size: 11
20420 CAGTTTTTTA
20430 TCAGTCTAATT
1 TCAGTCTAATT
**
20441 TCAGTCTTCTT
1 TCAGTCTAATT
* *
20452 TCAATCTGATT
1 TCAGTCTAATT
*
20463 TCAGTTTAATT
1 TCAGTCTAATT
*
20474 ATCAGTCT-TTT
1 -TCAGTCTAATT
20485 TCAGTCTAATT
1 TCAGTCTAATT
* *
20496 TCAGTCTGATC
1 TCAGTCTAATT
20507 TCAGT-TGAATT
1 TCAGTCT-AATT
**
20518 ATCAGTCTTTTT
1 -TCAGTCTAATT
20530 TCAGTCTAATT
1 TCAGTCTAATT
* **
20541 TCAGTTTTCTTT
1 TCAG-TCTAATT
**
20553 TCAGTCTTCTT
1 TCAGTCTAATT
*
20564 TCAGTTTAATT
1 TCAGTCTAATT
**
20575 ATCAGTCTTTTT
1 -TCAGTCTAATT
20587 TCAGTCTAATT
1 TCAGTCTAATT
20598 TCAGTCT
1 TCAGTCT
20605 TCTTTTCAGC
Statistics
Matches: 124, Mismatches: 33, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
10 8 0.06
11 86 0.69
12 29 0.23
13 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:20485 original size:57 final size:55
Alignment explanation
Indices: 20420--20609 Score: 215
Period size: 57 Copynumber: 3.6 Consensus size: 55
20410 GAAATTAAAC
20420 CAGT-TTTTTATCAGTCTAATTTCAGTCTTCTTTCAATCTGATTTCAGTTTAATTAT
1 CAGTCTTTTT-TCAGTCTAATTTCAGTCTTCTTTC-ATCTGATTTCAGTTTAATTAT
* *
20476 CAGTC-TTTTTCAGTCTAATTTCAG----------TCTGATCTCAGTTGAATTAT
1 CAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTCATCTGATTTCAGTTTAATTAT
* **
20520 CAGTCTTTTTTCAGTCTAATTTCAGTTTTCTTTTCAGTCTTCTTTCAGTTTAATTAT
1 CAGTCTTTTTTCAGTCTAATTTCAGTCTTC-TTTCA-TCTGATTTCAGTTTAATTAT
20577 CAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTT
1 CAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTT
20610 TCAGCTTTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
44 23 0.20
45 19 0.17
55 15 0.13
56 11 0.10
57 45 0.40
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.52
Consensus pattern (55 bp):
CAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTCATCTGATTTCAGTTTAATTAT
Found at i:20487 original size:44 final size:44
Alignment explanation
Indices: 20427--20543 Score: 162
Period size: 44 Copynumber: 2.6 Consensus size: 44
20417 AACCAGTTTT
* ** * *
20427 TTATCAGTCTAATTTCAGTCTTCTTTCAATCTGATTTCAGTTTAA
1 TTATCAGTCT-TTTTCAGTCTAATTTCAATCTGATCTCAGTTGAA
*
20472 TTATCAGTCTTTTTCAGTCTAATTTCAGTCTGATCTCAGTTGAA
1 TTATCAGTCTTTTTCAGTCTAATTTCAATCTGATCTCAGTTGAA
20516 TTATCAGTCTTTTTTCAGTCTAATTTCA
1 TTATCAGTC-TTTTTCAGTCTAATTTCA
20544 GTTTTCTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 37 0.57
45 28 0.43
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (44 bp):
TTATCAGTCTTTTTCAGTCTAATTTCAATCTGATCTCAGTTGAA
Found at i:20557 original size:34 final size:33
Alignment explanation
Indices: 20430--20604 Score: 154
Period size: 34 Copynumber: 5.2 Consensus size: 33
20420 CAGTTTTTTA
* * * *
20430 TCAGTCTAATTTCAGTCTTCTTTCAATCTGATT
1 TCAGTCTAATTTCAGTTTTTTTTCAGTCTTATT
* * *
20463 TCAGTTTAATTATCAG-TCTTTTTCAGTCTAATT
1 TCAGTCTAATT-TCAGTTTTTTTTCAGTCTTATT
* * ** * *
20496 TCAGTCTGATCTCAGTTGAATTATCAGTCTTTTT
1 TCAGTCTAATTTCAGTT-TTTTTTCAGTCTTATT
*
20530 TCAGTCTAATTTCAGTTTTCTTTTCAGTCTTCTT
1 TCAGTCTAATTTCAGTTTT-TTTTCAGTCTTATT
* * *
20564 TCAGTTTAATTATCAGTCTTTTTTCAGTCTAATT
1 TCAGTCTAATT-TCAGTTTTTTTTCAGTCTTATT
20598 TCAGTCT
1 TCAGTCT
20605 TCTTTTCAGC
Statistics
Matches: 112, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
32 4 0.04
33 31 0.28
34 70 0.62
35 7 0.06
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (33 bp):
TCAGTCTAATTTCAGTTTTTTTTCAGTCTTATT
Found at i:20558 original size:23 final size:22
Alignment explanation
Indices: 20461--20570 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 22
20451 TTCAATCTGA
* *
20461 TTTCAGTTTAATTATCAG-TCTT
1 TTTCAGTCTAATT-TCAGTTTTT
* **
20483 TTTCAGTCTAATTTCAGTCTGA
1 TTTCAGTCTAATTTCAGTTTTT
* *
20505 TCTCAGT-TGAATTATCAGTCTTT
1 TTTCAGTCT-AATT-TCAGTTTTT
20528 TTTCAGTCTAATTTCAGTTTTCT
1 TTTCAGTCTAATTTCAGTTTT-T
**
20551 TTTCAGTCTTCTTTCAGTTT
1 TTTCAGTCTAATTTCAGTTT
20571 AATTATCAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.07
22 29 0.41
23 36 0.51
24 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (22 bp):
TTTCAGTCTAATTTCAGTTTTT
Found at i:20579 original size:23 final size:22
Alignment explanation
Indices: 20528--20609 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
20518 ATCAGTCTTT
** **
20528 TTTCAGTCTAATTTCAGTTTTCT
1 TTTCAGTCTTCTTTCAG-TTTAA
20551 TTTCAGTCTTCTTTCAGTTTAA
1 TTTCAGTCTTCTTTCAGTTTAA
* *
20573 TTATCAGTCTTTTTTCAGTCTAA
1 TT-TCAGTCTTCTTTCAGTTTAA
20596 TTTCAGTCTTCTTT
1 TTTCAGTCTTCTTT
20610 TCAGCTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.17, C:0.18, G:0.09, T:0.56
Consensus pattern (22 bp):
TTTCAGTCTTCTTTCAGTTTAA
Found at i:20641 original size:57 final size:56
Alignment explanation
Indices: 20514--20624 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 56
20504 ATCTCAGTTG
*
20514 AATTATCAGTCTTTTTTCAGTCTAATTTCAGTTTTCTTTTCAGTCTTCTTTCAGTTT
1 AATTATCAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTTCAGTCTTCTTTCA-TTT
20571 AATTATCAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTTCAG-CTT-TTTC-TTT
1 AATTATCAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTTCAGTCTTCTTTCATTT
20624 A
1 A
20625 CCTAGTTTCC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
53 4 0.08
55 4 0.08
56 3 0.06
57 42 0.79
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (56 bp):
AATTATCAGTCTTTTTTCAGTCTAATTTCAGTCTTCTTTTCAGTCTTCTTTCATTT
Done.