Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013495.1 Corchorus capsularis cultivar CVL-1 contig13516, 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: 54534
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1810 original size:141 final size:141
Alignment explanation
Indices: 1543--1868 Score: 528
Period size: 141 Copynumber: 2.3 Consensus size: 141
1533 TGATTACATC
1543 ATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATTTTT
1 ATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATTTTT
* * *
1608 TTGGTAACATAATTACTTATTGATTTATTTATTTATGATAATTTTTTTGGTGGCGATTTTATGGT
66 TTGGTAACATAATTACTAATTGATTTATTTATTTATGATAATTTTTTTGGTAGCCATTTTATGGT
*
1673 AAAATTATATA
131 AAAATTAAATA
* *
1684 ATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAATTTATTTTT
1 ATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATTTTT
* *
1749 TTGGTAACATAATTACTAATTGATTTATTTCTTTATGTTAATTTTTTTTGGTAGCCA-TTTATGG
66 TTGGTAACATAATTACTAATTGATTTATTTATTTATGATAA-TTTTTTTGGTAGCCATTTTATGG
*
1813 TAAAATTAAATT
130 TAAAATTAAATA
* **
1825 ATTATCAATCAATTAGGACTTTGATTGGCAAAATTAACTAACGA
1 ATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGA
1869 TCACTAACTT
Statistics
Matches: 171, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 158 0.92
142 13 0.08
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (141 bp):
ATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATTTTT
TTGGTAACATAATTACTAATTGATTTATTTATTTATGATAATTTTTTTGGTAGCCATTTTATGGT
AAAATTAAATA
Found at i:1952 original size:125 final size:126
Alignment explanation
Indices: 1842--2092 Score: 324
Period size: 129 Copynumber: 1.9 Consensus size: 126
1832 ATCAATTAGG
1842 ACTTTGATTGGCAAA-ATTAACTAACGATCACTAACTTGATTCATTTATTTATTTAGCATGTTCA
1 ACTTTGATTGG-AAATATTAACTAA-G--CACTAACTTGATTCATTTATTTATTTAGCATGTTCA
* *
1906 ATCAATTTATTTTTTTGCTAACGTAATTACTAAATGGTTCATTTATTTATGGCAAAATTGTAGGA
62 ATCAATTTATTTTTTTGCTAACATAATTACTAAATGATTCATTTA-TTAT-GCAAAATTGTAGGA
1971 GTA
125 G-A
* * * * *
1974 ACTTTGATTGGAAATATTGACTTAGGACTAACTTGGTTCATTTATTTATTTAGCATGTTGAATCA
1 ACTTTGATTGGAAATATTAACTAAGCACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCA
* **
2039 ATTTATTTTTTTGCTAATATAATTACTATTTGATTCATTTATTTATGGCAAAAT
66 ATTTATTTTTTTGCTAACATAATTACTAAATGATTCATTTA-TTAT-GCAAAAT
2093 GTAATAATCA
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
129 86 0.80
131 4 0.04
132 18 0.17
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (126 bp):
ACTTTGATTGGAAATATTAACTAAGCACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCA
ATTTATTTTTTTGCTAACATAATTACTAAATGATTCATTTATTATGCAAAATTGTAGGAGA
Found at i:2172 original size:28 final size:30
Alignment explanation
Indices: 2114--2181 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 30
2104 CAATCAGTTA
2114 TAACTTTGATTGGCAAAGTTAATTAACGAC
1 TAACTTTGATTGGCAAAGTTAATTAACGAC
**
2144 TAACTTTTTTTGGC-AA-TTAATTAACGAC
1 TAACTTTGATTGGCAAAGTTAATTAACGAC
2172 TAA-TTTGATT
1 TAACTTTGATT
2182 CACTAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.15
28 15 0.44
29 2 0.06
30 12 0.35
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (30 bp):
TAACTTTGATTGGCAAAGTTAATTAACGAC
Found at i:2189 original size:28 final size:28
Alignment explanation
Indices: 2114--2189 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 28
2104 CAATCAGTTA
2114 TAACTTTGATTGGCA-AAGTTAATTAACGAC
1 TAACTTTGATT--CACAA-TTAATTAACGAC
** **
2144 TAACTTTTTTTGGCAATTAATTAACGAC
1 TAACTTTGATTCACAATTAATTAACGAC
2172 TAA-TTTGATTCACTAATT
1 TAACTTTGATTCAC-AATT
2190 TATTTTTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
27 6 0.17
28 19 0.53
29 2 0.06
30 9 0.25
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (28 bp):
TAACTTTGATTCACAATTAATTAACGAC
Found at i:3865 original size:30 final size:30
Alignment explanation
Indices: 3831--3889 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3821 TCAACTAATT
*
3831 AATCAATCAAAAGTAATTAATATATTTCCC
1 AATCAACCAAAAGTAATTAATATATTTCCC
* *
3861 AATCAACCTAAAGTAATTAATTTATTTCC
1 AATCAACCAAAAGTAATTAATATATTTCC
3890 TTTTGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (30 bp):
AATCAACCAAAAGTAATTAATATATTTCCC
Found at i:3876 original size:190 final size:194
Alignment explanation
Indices: 3506--3887 Score: 567
Period size: 190 Copynumber: 2.0 Consensus size: 194
3496 TAGGGTTATT
* * * *
3506 TTAGTAATTAAAAGCTAAATGGCATTAATGTTACTTTATTGTAATTGATCAAAATTTTCATTTTA
1 TTAGTAATTAAAAGCTAAATAGCATTAATGTTAATTGATTGTAATTAATCAAAATTTTCATTTTA
3571 ACAATTAATTAAATAGAATTTTATTACAAATCGATTTTAATTGATCAAATTATTCAAAAATCAAC
66 ACAATTAATTAAATAGAA-TTTATTACAAATCGATTTTAATTGATCAAATTATT-AAAAATCAAC
* *
3636 TATTTAATAAATAAAAAGAAATTAATATATTTCCTAATCAACCTAAAGTAA-TAATTAATTTAAT
129 TAATTAATAAATAAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTTAAT
3700 A
194 A
* *
3701 TTAGTAATTAACAA-CTAAATAGCATTAATTTTAATTGATTGTAATTAATTAAAATTTTCA-TTT
1 TTAGTAATTAA-AAGCTAAATAGCATTAATGTTAATTGATTGTAATTAATCAAAATTTTCATTTT
* * *
3764 AACAATTAATTAAATAGAA-TTATTACTAATTGATTTTAATTGATCAAATTATT-GAAATCAACT
65 AACAATTAATTAAATAGAATTTATTACAAATCGATTTTAATTGATCAAATTATTAAAAATCAACT
* * * *
3827 AATTAATCAATCAAAAGTAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTT
130 AATTAATAAATAAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTT
3888 CCTTTTGTCC
Statistics
Matches: 170, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
190 54 0.32
191 9 0.05
192 32 0.19
194 22 0.13
195 51 0.30
196 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (194 bp):
TTAGTAATTAAAAGCTAAATAGCATTAATGTTAATTGATTGTAATTAATCAAAATTTTCATTTTA
ACAATTAATTAAATAGAATTTATTACAAATCGATTTTAATTGATCAAATTATTAAAAATCAACTA
ATTAATAAATAAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTTAATA
Found at i:4952 original size:30 final size:30
Alignment explanation
Indices: 4918--4976 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
4908 TCAACTAATT
*
4918 AATCAATCAAAAGAAATTAATATATTTCCC
1 AATCAACCAAAAGAAATTAATATATTTCCC
* * *
4948 AATCAACCTAAAGTAATTAATTTATTTCC
1 AATCAACCAAAAGAAATTAATATATTTCC
4977 TTTTTTCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (30 bp):
AATCAACCAAAAGAAATTAATATATTTCCC
Found at i:4954 original size:189 final size:194
Alignment explanation
Indices: 4594--4974 Score: 646
Period size: 189 Copynumber: 2.0 Consensus size: 194
4584 TAGGGTTATT
* * *
4594 TTAGTAATTAACATCTAAATGGCATTAATGTTAATTGATTGTAATTGATCAAAATTTTCATTTTA
1 TTAGTAATTAACAACTAAATAGAATTAATGTTAATTGATTGTAATTGATCAAAATTTTCATTTTA
4659 ACAATTAATTAAATAGAATTTTATTACAAATTGATTTTAATTGATCAAATTATTCAAAAATCAAC
66 ACAATTAATTAAATAGAA-TTTATTACAAATTGATTTTAATTGATCAAATTATTC-AAAATCAAC
*
4724 TAATTAATCAATCAAAAGAAATTAATATATTTCCTAATCAACCTAAAGTAA-TAATTAATTTAAT
129 TAATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTTAAT
4788 A
194 A
*
4789 TTAGTAATTAACAACTAAATAGAATTAATTTTAATTGATTGTAATTGATCAAAATTTTCA-TTTA
1 TTAGTAATTAACAACTAAATAGAATTAATGTTAATTGATTGTAATTGATCAAAATTTTCATTTTA
*
4853 ACAATTAATT-AATAGAA-TTATTACTAATTGATTTTAATTGATCAAATTATTC-AAATCAACTA
66 ACAATTAATTAAATAGAATTTATTACAAATTGATTTTAATTGATCAAATTATTCAAAATCAACTA
*
4915 ATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTT
131 ATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTT
4975 CCTTTTTTCT
Statistics
Matches: 178, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
189 58 0.33
190 9 0.05
191 34 0.19
193 7 0.04
194 14 0.08
195 56 0.31
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (194 bp):
TTAGTAATTAACAACTAAATAGAATTAATGTTAATTGATTGTAATTGATCAAAATTTTCATTTTA
ACAATTAATTAAATAGAATTTATTACAAATTGATTTTAATTGATCAAATTATTCAAAATCAACTA
ATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTAATTTAATA
Found at i:7549 original size:30 final size:30
Alignment explanation
Indices: 7515--7604 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
7505 ACTAATTAAT
*
7515 CAATCAACCTAAAGTAATTAATATATTTTC
1 CAATCAACCTAAAGTAATTAATATATTTCC
*
7545 CAATCAATCTAAAGTAATTAATATATTTCC
1 CAATCAACCTAAAGTAATTAATATATTTCC
*
7575 CAATCAACCTAAAGTAATTAATTTATTTCC
1 CAATCAACCTAAAGTAATTAATATATTTCC
7605 TTTTGTCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (30 bp):
CAATCAACCTAAAGTAATTAATATATTTCC
Found at i:7636 original size:2 final size:2
Alignment explanation
Indices: 7629--7673 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
7619 CTCAGTTTTA
7629 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
7672 AT
1 AT
7674 GATTACACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7659 original size:23 final size:23
Alignment explanation
Indices: 7629--7676 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
7619 CTCAGTTTTA
7629 ATATATATATATATATATATATG
1 ATATATATATATATATATATATG
7652 ATATATATATATATATATATATG
1 ATATATATATATATATATATATG
7675 AT
1 AT
7677 TACACATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATATATATATATATATATATG
Found at i:12330 original size:19 final size:20
Alignment explanation
Indices: 12301--12340 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
12291 ATTTTTAAGT
12301 AAAAATATAATA-TATAAATA
1 AAAAATATAATAGTA-AAATA
12321 AAAAAT-TAATAGTAAAATA
1 AAAAATATAATAGTAAAATA
12340 A
1 A
12341 TTAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATATAATAGTAAAATA
Found at i:12344 original size:15 final size:15
Alignment explanation
Indices: 12319--12351 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12309 AATATATAAA
12319 TAAAAAATTAA-TAG
1 TAAAAAATTAATTAG
12333 TAAAATAATTAATTAG
1 TAAAA-AATTAATTAG
12349 TAA
1 TAA
12352 CCGGATTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
TAAAAAATTAATTAG
Found at i:13163 original size:177 final size:178
Alignment explanation
Indices: 12901--13223 Score: 501
Period size: 177 Copynumber: 1.8 Consensus size: 178
12891 AAGGTGATTT
*
12901 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAACTTA
* * *
12966 ATGTTTCAAGTATCAAAAATGCTACCGAAA-AATTTGTTGTTTCGATTAACG-GAATAGACGGT-
66 ATGTTTCAAGTATAAAAAATGCTACC-AAAGAATTAGTTGTTTCGATTAACGAAAATAGACGGTC
13028 TCACTTAATATTATATAACTTTTGTTCCAGATGTCTGATTGAGATTATTC
130 T-ACTTAATATTATATAACTTTTGTTCCAGATGTCTGATTGAGATTATTC
* * * *
13078 AAGTGTCTTTTGAAAGGTTGTTCCATGATCTACACCTTTCATGAAGGACTCGAAAACTAAACTTA
1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAACTTA
* *
13143 ATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAGACGGTC
66 ATGTTTCAA-GTATAAAAAATGCTACCAAAGAATTAGTTGTTTCGATTAACGAAAATAGACGGTC
13207 TACTTAATATTATATAA
130 TACTTAATATTATATAA
13224 TTTATGCTTA
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
176 8 0.06
177 97 0.73
178 26 0.20
179 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAACTTA
ATGTTTCAAGTATAAAAAATGCTACCAAAGAATTAGTTGTTTCGATTAACGAAAATAGACGGTCT
ACTTAATATTATATAACTTTTGTTCCAGATGTCTGATTGAGATTATTC
Found at i:15685 original size:15 final size:15
Alignment explanation
Indices: 15665--15696 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15655 CCCGCTTGCT
15665 AAAAAATTTTTTGGC
1 AAAAAATTTTTTGGC
*
15680 AAAAAATTTTTTTGC
1 AAAAAATTTTTTGGC
15695 AA
1 AA
15697 TGGAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (15 bp):
AAAAAATTTTTTGGC
Found at i:15891 original size:103 final size:102
Alignment explanation
Indices: 15610--15915 Score: 344
Period size: 103 Copynumber: 3.0 Consensus size: 102
15600 TTTGCTACAG
* * * * *
15610 ATTTTGCCACGAAATTAATTTTCGTGACAAATTTAAATTTGAATTCCCGCTTGCTAAAAAATTTT
1 ATTTTG-CATGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTTGCTCAAATATTTT
* * * *
15675 TTGGCAAAA-AATTTTTTTGCAATGGAAATTACTACAAA
65 GTGCCAAAATAA-ATTTTTGCAACGGAAATTACTACAAA
* * ** * ** ** *
15713 CTTTTGCAGTGAATTTAGTTTTTTATAAGGAATTAAAATTTGAATTTTCGCTCGCTCAAATATTT
1 ATTTTGCA-TGAATTTA-ATTTTCGTGACAAATTAAAATTTGAATTCCCGCTTGCTCAAATATTT
** * *
15778 TGCACCAAAATAAATTTTTGCGACAGAAATTACTACAAA
64 TGTGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
15817 ATTTTGCGATGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTTGCTCAAATATTTT
1 ATTTTGC-ATGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTTGCTCAAATATTTT
*
15882 GTGCCAAAATAAATTGTTGCAACGGAAATTACTA
65 GTGCCAAAATAAATTTTTGCAACGGAAATTACTA
15916 TAGAAAATCC
Statistics
Matches: 161, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
102 2 0.01
103 79 0.49
104 77 0.48
105 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (102 bp):
ATTTTGCATGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTTGCTCAAATATTTTG
TGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
Found at i:24181 original size:22 final size:22
Alignment explanation
Indices: 24156--24197 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24146 TTACACCAGG
24156 CAAAAAAAAAGTTAGTTCACAC
1 CAAAAAAAAAGTTAGTTCACAC
* *
24178 CAAAAAAAAATTTTGTTCAC
1 CAAAAAAAAAGTTAGTTCAC
24198 CAGCCACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (22 bp):
CAAAAAAAAAGTTAGTTCACAC
Found at i:34561 original size:25 final size:25
Alignment explanation
Indices: 34533--34580 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
34523 TGGATGTTCA
34533 CTTTGAATGACAT-GTTAGGGTTTGG
1 CTTT-AATGACATAGTTAGGGTTTGG
* *
34558 CTTTCATGTCATAGTTAGGGTTT
1 CTTTAATGACATAGTTAGGGTTT
34581 AGCCTTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (25 bp):
CTTTAATGACATAGTTAGGGTTTGG
Found at i:38169 original size:19 final size:20
Alignment explanation
Indices: 38131--38169 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38121 GCTTGGTACC
* *
38131 TTTGCTTCCAAATTTCAATT
1 TTTGCTACCAAATCTCAATT
38151 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
38170 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTGCTACCAAATCTCAATT
Found at i:43290 original size:15 final size:15
Alignment explanation
Indices: 43270--43328 Score: 73
Period size: 16 Copynumber: 3.8 Consensus size: 15
43260 ATTGGGCAGG
*
43270 TTCGGGTTCGGATAC
1 TTCGGGTTCGGGTAC
*
43285 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTA-C
*
43301 TTCGGGTTCGGGTTC
1 TTCGGGTTCGGGTAC
43316 TGTCGGGTTCGGG
1 T-TCGGGTTCGGG
43329 CTCGGATCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 14 0.37
16 24 0.63
ACGTcount: A:0.05, C:0.17, G:0.41, T:0.37
Consensus pattern (15 bp):
TTCGGGTTCGGGTAC
Found at i:43310 original size:6 final size:6
Alignment explanation
Indices: 43301--43371 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
43291 TTCGGGTATT
* * *
43301 TTCGGG TTCGGG TTC-TG -TCGGG TTCGGG CTC-GG ATCGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
**
43346 TTCGGG CCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTC
43372 ACTTTCGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 41 0.77
ACGTcount: A:0.01, C:0.23, G:0.46, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:43340 original size:17 final size:16
Alignment explanation
Indices: 43302--43350 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 16
43292 TCGGGTATTT
*
43302 TCGGGTTCGGGTTCTG
1 TCGGGTTCGGGTTCGG
*
43318 TCGGGTTCGGGCTCGG
1 TCGGGTTCGGGTTCGG
43334 ATCGGGTTCGGGTTCGG
1 -TCGGGTTCGGGTTCGG
43351 GCCCGGGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.02, C:0.20, G:0.47, T:0.31
Consensus pattern (16 bp):
TCGGGTTCGGGTTCGG
Found at i:43348 original size:23 final size:23
Alignment explanation
Indices: 43318--43371 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
43308 TCGGGTTCTG
*
43318 TCGGGTTCGGGCTCGGATCGGGT
1 TCGGGTTCGGGCCCGGATCGGGT
*
43341 TCGGGTTCGGGCCCGGGTCGGGT
1 TCGGGTTCGGGCCCGGATCGGGT
43364 TCGGGTTC
1 TCGGGTTC
43372 ACTTTCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.02, C:0.24, G:0.48, T:0.26
Consensus pattern (23 bp):
TCGGGTTCGGGCCCGGATCGGGT
Found at i:44151 original size:22 final size:22
Alignment explanation
Indices: 44113--44198 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 22
44103 GATCTCGGGC
*
44113 TCGGGTCGGGTTTGGGTTTGGGT
1 TCGGG-CGGGTTCGGGTTTGGGT
44136 TCGGGCGGGTTCGGGTTTGGGT
1 TCGGGCGGGTTCGGGTTTGGGT
** *
44158 T-GTCTCGGGTTCAGGTATTTTCGGGT
1 TCG-GGCGGGTTC-GG--GTTT-GGGT
44184 TCGGGCGGGTTCGGG
1 TCGGGCGGGTTCGGG
44199 ACGTTGACTT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
21 1 0.02
22 24 0.48
23 7 0.14
25 5 0.10
26 12 0.24
27 1 0.02
ACGTcount: A:0.02, C:0.14, G:0.49, T:0.35
Consensus pattern (22 bp):
TCGGGCGGGTTCGGGTTTGGGT
Found at i:46644 original size:33 final size:33
Alignment explanation
Indices: 46602--46668 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
46592 CCATAGGACT
46602 TGAGTACAAACACGAGAGCACAAGTCAAAGGTA
1 TGAGTACAAACACGAGAGCACAAGTCAAAGGTA
46635 TGAGTACAAACACGAGAGCACAAGTCAAAGGTA
1 TGAGTACAAACACGAGAGCACAAGTCAAAGGTA
46668 T
1 T
46669 AAGCACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAGTACAAACACGAGAGCACAAGTCAAAGGTA
Found at i:47545 original size:33 final size:33
Alignment explanation
Indices: 47503--47574 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
47493 GTTGTTTGCA
* * *
47503 ATGACACTAAATCTGTTTTAAATGTTATTTGTG
1 ATGAAACTAAATCTGTTTTAAATGCTAATTGTG
**
47536 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTAAATGCTAATTGTG
47569 ATGAAA
1 ATGAAA
47575 ACAATTATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (33 bp):
ATGAAACTAAATCTGTTTTAAATGCTAATTGTG
Found at i:47619 original size:33 final size:33
Alignment explanation
Indices: 47572--47693 Score: 172
Period size: 33 Copynumber: 3.7 Consensus size: 33
47562 AATTGTGATG
* *
47572 AAAACAATTATGTTTTGGTTGAACATAGCATTA
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* *
47605 AAAATAATTCTGTTTTGGTTGATCATAGCATTG
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* **
47638 CAAATAATTCTGTTTTGGTTGATTATAGCATTA
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
*
47671 AAAATAATTCTGTTTTGGGTGAA
1 AAAATAATTCTGTTTTGGTTGAA
47694 AAGAAAGAGA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (33 bp):
AAAATAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:48103 original size:30 final size:30
Alignment explanation
Indices: 48067--48125 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
48057 CAAGGGGGAG
*
48067 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATACG-CCAAGGACTTATCATGGAA
48097 GGAATGATACGCCAAGGACTTATCATGGA
1 GGAATGATACGCCAAGGACTTATCATGGA
48126 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (30 bp):
GGAATGATACGCCAAGGACTTATCATGGAA
Found at i:52066 original size:26 final size:26
Alignment explanation
Indices: 51995--52068 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
51985 TAGGGTCATC
51995 CAAGGGTATTTTGGTCATTTTCACAT
1 CAAGGGTATTTTGGTCATTTTCACAT
* *
52021 CATAGGGGCATTTTGATCATTCTTGCAC-T
1 CA-A-GGGTATTTTGGTCATT-TT-CACAT
52050 -AAGGGTATTTTGGTCATTT
1 CAAGGGTATTTTGGTCATTT
52069 GCATATTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 1 0.03
26 16 0.40
27 2 0.05
28 15 0.38
29 3 0.08
30 3 0.08
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (26 bp):
CAAGGGTATTTTGGTCATTTTCACAT
Found at i:52212 original size:16 final size:16
Alignment explanation
Indices: 52191--52246 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
52181 TTGGCATTTT
52191 TTGCATCTCAATATTC
1 TTGCATCTCAATATTC
* * *
52207 TTGCATTTTGGC-ATTTTT
1 TTGCA-TCT--CAATATTC
52225 TTGCATCTCAATATTC
1 TTGCATCTCAATATTC
52241 TTGCAT
1 TTGCAT
52247 TTCAGTCACA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 1 0.03
16 15 0.50
17 4 0.13
18 9 0.30
19 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50
Consensus pattern (16 bp):
TTGCATCTCAATATTC
Found at i:52221 original size:33 final size:34
Alignment explanation
Indices: 52179--52248 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
52169 TGATGTGTAC
52179 TTTTGGCA-TTTTTTGCATCTCAATATTCTTGCA
1 TTTTGGCATTTTTTTGCATCTCAATATTCTTGCA
52212 TTTTGGCATTTTTTTGCATCTCAATATTCTTGCA
1 TTTTGGCATTTTTTTGCATCTCAATATTCTTGCA
52246 TTT
1 TTT
52249 CAGTCACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (34 bp):
TTTTGGCATTTTTTTGCATCTCAATATTCTTGCA
Done.