Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013868.1 Corchorus capsularis cultivar CVL-1 contig13889, 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: 31932
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:116 original size:2 final size:2
Alignment explanation
Indices: 109--160 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
99 GCCATCAACT
*
109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
151 TT TA TA TA TA
1 TA TA TA TA TA
161 ATGGCCATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2388 original size:20 final size:21
Alignment explanation
Indices: 2360--2399 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2350 TTTGGTCTCG
*
2360 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
*
2380 AGTCGTTTGACTCCTTAAGT
1 AGTCATTTGACTCCTTAAGT
2400 TGAACATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:5632 original size:134 final size:134
Alignment explanation
Indices: 5367--5661 Score: 394
Period size: 134 Copynumber: 2.2 Consensus size: 134
5357 CAGAGGCAGA
* * *
5367 GCACAAAGCGGTTGTTTGTTTTTCCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCGATGAGACC
1 GCACCAAGCAGTTG-TTGGTTTTCCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCGATGAGACC
* * * ** * *
5432 AACCTGAGCCATGACCTGTTGATTGTTCATCTGATGGTTAACTTGTCGAAGGGGAAGAGGATCGG
65 AACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGG
5497 GCCGG
130 GCCGG
*
5502 GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTG-CCCCCAAGTCTTTCATCGATGAGACC
1 GCACCAAGCAGTTGTTGGTTTT-CCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCGATGAGACC
* * * * * *
5566 AATCTCAGCCATGACTTGTGGGTTGTTCACCTGATGGTTGACTTGTTGAAAAGGCAGAGCACCGG
65 AACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGG
*
5631 GCTGG
130 GCCGG
*
5636 GCACCAATCAGTTGTTGGTTTTCCCC
1 GCACCAAGCAGTTGTTGGTTTTCCCC
5662 TCCAAGTCTT
Statistics
Matches: 140, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
133 4 0.03
134 109 0.78
135 27 0.19
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (134 bp):
GCACCAAGCAGTTGTTGGTTTTCCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCGATGAGACCA
ACCTCAGCCATGACCTGTGGATTGTTCACCTGATGGTTAACTTGTCGAAAAGGAAGAGCACCGGG
CCGG
Found at i:5943 original size:15 final size:15
Alignment explanation
Indices: 5923--5952 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5913 TCAACCCAGC
5923 AGATCCAAGCGGATT
1 AGATCCAAGCGGATT
*
5938 AGATCCAAGTGGATT
1 AGATCCAAGCGGATT
5953 CTGGCTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (15 bp):
AGATCCAAGCGGATT
Found at i:6945 original size:17 final size:17
Alignment explanation
Indices: 6908--6945 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6898 ATATAGTACC
*
6908 TAGGTAGTATGAGATGC
1 TAGGTAGTATGAGATGA
*
6925 TAGGTAGTATGAGGTGA
1 TAGGTAGTATGAGATGA
6942 TAGG
1 TAGG
6946 CTGCATCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.39, T:0.29
Consensus pattern (17 bp):
TAGGTAGTATGAGATGA
Found at i:7528 original size:156 final size:154
Alignment explanation
Indices: 7291--7654 Score: 369
Period size: 156 Copynumber: 2.3 Consensus size: 154
7281 GAGCTTCTCA
* * * *
7291 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGATCTGAAA
1 CCTCAAAGTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG--A
** * * * * *
7356 ATTTTCCAAAGTACTTAGAATATTTCCAT-GAGACTATGGGAAAAATTCCAAGTGAAACCGTACT
64 ATTTTCCAAAGTACTTAGAATATCACCATAAAG-CTATGGAAAAAAATCCAAGTAAAACCGAACT
* * * *
7420 CCCCTTG-ATGGTGAACTAGGTTTCTCT
128 -CCCTAGCATAGAGAACTAGGTTTCACT
** *
7447 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAATTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTCAAAG-TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
* * *
7509 ATTTTCCACCAGTAGACTTAGATTATCACCATAAAGCTATGGAAAAAAATCTAAGTAAAACCGAA
64 ATTTTCCA-AAGT--ACTTAGAATATCACCATAAAGCTATGGAAAAAAATCCAAGTAAAACCGAA
* * * *
7574 CTCTCTAGCTTAGAGAAGTTGGTTTCACT
126 CTCCCTAGCATAGAGAACTAGGTTTCACT
* *
7603 CCTCAAAGTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATGCTAAGTCT
1 CCTCAAAGTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
7655 GTTTGAGATG
Statistics
Matches: 169, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
153 8 0.05
154 3 0.02
155 9 0.05
156 144 0.85
157 5 0.03
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (154 bp):
CCTCAAAGTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTCCAAAGTACTTAGAATATCACCATAAAGCTATGGAAAAAAATCCAAGTAAAACCGAACTCCC
TAGCATAGAGAACTAGGTTTCACT
Found at i:9304 original size:32 final size:32
Alignment explanation
Indices: 9244--9303 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
9234 AAGAAGTTTA
9244 ATTAAGGATTGAAAAGTAGTTTTTTTTTTGGC
1 ATTAAGGATTGAAAAGTAGTTTTTTTTTTGGC
9276 ATTAA-GATTGAAAAGTAGTTTTTTTTTT
1 ATTAAGGATTGAAAAGTAGTTTTTTTTTT
9304 TTTTTCGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (32 bp):
ATTAAGGATTGAAAAGTAGTTTTTTTTTTGGC
Found at i:9318 original size:35 final size:36
Alignment explanation
Indices: 9263--9331 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
9253 TGAAAAGTAG
* *
9263 TTTTTTTTTTGGCATTAAGATTGAAAAGTAGTTTTT
1 TTTTTTTTTTCGCATCAAGATTGAAAAGTAGTTTTT
*
9299 TTTTTTTTTTCGCA-CAAGATTGAGAAGTAGTTT
1 TTTTTTTTTTCGCATCAAGATTGAAAAGTAGTTT
9332 AGTGTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (36 bp):
TTTTTTTTTTCGCATCAAGATTGAAAAGTAGTTTTT
Found at i:9442 original size:18 final size:20
Alignment explanation
Indices: 9408--9445 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
9398 TATTCACCTC
9408 CCCAAACAAAGAAAATTAAA
1 CCCAAACAAAGAAAATTAAA
9428 CCCAAA-AAA-AAAATTAAA
1 CCCAAACAAAGAAAATTAAA
9446 ATACTAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.68, C:0.18, G:0.03, T:0.11
Consensus pattern (20 bp):
CCCAAACAAAGAAAATTAAA
Found at i:9595 original size:2 final size:2
Alignment explanation
Indices: 9588--9629 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
9578 ATTTACCTTC
9588 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9630 TTTTTTTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9888 original size:2 final size:2
Alignment explanation
Indices: 9883--9913 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
9873 TTAAATTATT
9883 TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
9914 AAAGTACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9983 original size:31 final size:31
Alignment explanation
Indices: 9948--10006 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
9938 ATGTTTTCCG
9948 ATTGTACCCTTATTTTTAAAACATATTTTCA
1 ATTGTACCCTTATTTTTAAAACATATTTTCA
*
9979 ATTGTACCCTTTTTTTTAAAACATATTT
1 ATTGTACCCTTATTTTTAAAACATATTT
10007 CTAAATTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTTCA
Found at i:10141 original size:22 final size:22
Alignment explanation
Indices: 10116--10222 Score: 169
Period size: 22 Copynumber: 4.9 Consensus size: 22
10106 TCCATGAGGA
* *
10116 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
10138 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
*
10160 GGTTACCAAAATTTTATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
10182 AGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
10204 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
10223 GATCAGCTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:10261 original size:22 final size:22
Alignment explanation
Indices: 10093--10276 Score: 118
Period size: 22 Copynumber: 8.3 Consensus size: 22
10083 TATTTTACTT
* *
10093 TGGTTATTATAATTCCAT-GAGG
1 TGGTTATTAAAATTTCATAG-GG
* * * *
10115 AGGTTATCAAAATTCCATAGTG
1 TGGTTATTAAAATTTCATAGGG
** *
10137 TGGTTACCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
** * *
10159 TGGTTACCAAAATTTTATAGTG
1 TGGTTATTAAAATTTCATAGGG
* ** *
10181 TAGTTACCAAAATTTCATAGAG
1 TGGTTATTAAAATTTCATAGGG
** *
10203 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGG
* * *
10225 TCAGCTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGG
*
10249 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGG
10271 TGGTTA
1 TGGTTA
10277 ATTATCACAA
Statistics
Matches: 136, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
22 118 0.87
23 1 0.01
24 17 0.12
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGG
Found at i:10365 original size:22 final size:22
Alignment explanation
Indices: 10315--10436 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
10305 AAAAAGATTT
* *
10315 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
10338 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
10359 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
10380 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * * *
10403 CGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
10425 CAAAATTTCATA
1 CAAAATTTCATA
10437 TGAAGTTTAT
Statistics
Matches: 73, Mismatches: 21, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
21 6 0.08
22 62 0.85
23 5 0.07
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:10525 original size:22 final size:22
Alignment explanation
Indices: 10473--10727 Score: 129
Period size: 22 Copynumber: 11.6 Consensus size: 22
10463 TAAGAAGTAC
*
10473 CAAAATTTAATAGAAG-GA-TAT
1 CAAAATTTCATAG-AGTGATTAT
*
10494 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
* *
10515 CGAAATTTCATAAAGATATGATTAT
1 CAAAATTTCAT--AGA-GTGATTAT
*
10540 CAAAATTT-ATATGA-AGATTAT
1 CAAAATTTCATA-GAGTGATTAT
*
10561 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
* * * * *
10583 TAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
*
10605 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * * *
10627 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGTGATTAT
* *
10649 CAAAATTTTATAAAGATG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
10671 CAAAATTTCATGAAGAG-G-TTAT
1 CAAAATTTCAT--AGAGTGATTAT
* * *
10693 CAAATTTTCA-AAATCTGATTA-
1 CAAAATTTCATAGA-GTGATTAT
10714 CAAAAATTTCATAG
1 C-AAAATTTCATAG
10728 TGGTATTTCT
Statistics
Matches: 178, Mismatches: 35, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.02
20 11 0.06
21 23 0.13
22 112 0.63
23 6 0.03
24 8 0.04
25 14 0.08
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:10553 original size:18 final size:19
Alignment explanation
Indices: 10530--10568 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
10520 TTTCATAAAG
10530 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
10548 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
10569 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:10655 original size:88 final size:87
Alignment explanation
Indices: 10561--10727 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 87
10551 TGAAGATTAT
** * * * *
10561 CAAAATTTCATAGTGTTGTTATTAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCAGAA--GAGGTTATCAAAATTACAAAATCTGATT
10625 ATC-AAAATTTCATAGAGGGGTCAA
64 A-CAAAAATTTCATAGAGGGGTCAA
* * *
10649 CAAAATTTTATAAAGATGTTATCAAAATTTCATGAAGAGGTTATCAAATTTTCAAAATCTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCA-GAAGAGGTTATCAAAATTACAAAATCTGATTA
10714 CAAAAATTTCATAG
65 CAAAAATTTCATAG
10728 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
87 1 0.01
88 64 0.96
90 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (87 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCAGAAGAGGTTATCAAAATTACAAAATCTGATTAC
AAAAATTTCATAGAGGGGTCAA
Found at i:10693 original size:66 final size:65
Alignment explanation
Indices: 10517--10702 Score: 162
Period size: 66 Copynumber: 2.8 Consensus size: 65
10507 GTGATTATCG
* * ** *
10517 AAATTTCATAAAGATATGATTATCAAAATTTATATGAAGA-TTATCAAAATTTCATAGTGTTGTT
1 AAATTTCATAAAG--ATG-TTATCAAAATTT-CATGAAGAGTTATCAAAATTTCATAGAGGGGTC
**
10581 ATTA
62 AACA
* * * *
10585 AAATTTCA-AAGCGAGGTTATCAAAATTACAT-AATGTGATTATCAAAATTTCATAGAGGGGTCA
1 AAATTTCATAA-AGATGTTATCAAAATTTCATGAA-GAG-TTATCAAAATTTCATAGAGGGGTCA
10648 ACA
63 ACA
* *
10651 AAATTTTATAAAGATGTTATCAAAATTTCATGAAGAGGTTATCAAATTTTCA
1 AAATTTCATAAAGATGTTATCAAAATTTCATGAAGA-GTTATCAAAATTTCA
10703 AAATCTGATT
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
63 2 0.02
64 3 0.03
65 11 0.12
66 62 0.66
67 7 0.07
68 9 0.10
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (65 bp):
AAATTTCATAAAGATGTTATCAAAATTTCATGAAGAGTTATCAAAATTTCATAGAGGGGTCAACA
Found at i:10846 original size:19 final size:19
Alignment explanation
Indices: 10810--10874 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
10800 ATGGAGTAAA
* * *
10810 CAAAATTTCAAGGCGGATAC
1 CAAAA-TTCAGGGAGGATAT
10830 CAAAATTCAGGGAGGATAT
1 CAAAATTCAGGGAGGATAT
*
10849 CAAAATTCAGTGAGGATAT
1 CAAAATTCAGGGAGGATAT
10868 CAAAATT
1 CAAAATT
10875 TCATATGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 36 0.88
20 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (19 bp):
CAAAATTCAGGGAGGATAT
Found at i:10893 original size:22 final size:22
Alignment explanation
Indices: 10865--11134 Score: 98
Period size: 22 Copynumber: 12.5 Consensus size: 22
10855 TCAGTGAGGA
10865 TATCAAAATTTCATATGAAGAT
1 TATCAAAATTTCATATGAAGAT
* **
10887 TATCAAATTTTCATAGTTTA-AT
1 TATCAAAATTTCATA-TGAAGAT
* * * *
10909 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGAT
* * *
10931 TATCGAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGAT
* *
10953 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGAT
* ** * * *
10975 TATTAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATATGAAGAT
*
10997 TATCAAAA--T--T-TGTA-AT
1 TATCAAAATTTCATATGAAGAT
*
11013 TATC-AAATTTCATAAGAA-AGT
1 TATCAAAATTTCATATGAAGA-T
* * * *
11034 TATCAAAATTTTATAGGGAGGGT
1 TATCAAAATTTCATA-TGAAGAT
* *
11057 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAGA-T
* *
11080 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGAT
* * *
11102 TATCACAATTTCATGGTG-TGAT
1 TATCAAAATTTCAT-ATGAAGAT
11124 TATCAAAATTT
1 TATCAAAATTT
11135 TAAAGTGTGA
Statistics
Matches: 182, Mismatches: 49, Indels: 34
0.69 0.18 0.13
Matches are distributed among these distances:
15 3 0.02
16 5 0.03
17 3 0.02
18 1 0.01
19 1 0.01
20 4 0.02
21 8 0.04
22 118 0.65
23 38 0.21
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGAT
Found at i:10960 original size:44 final size:44
Alignment explanation
Indices: 10912--11007 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
10902 GTTTAATTTT
* **
10912 CAAAATTTCATAA-GAGGGTTATCGAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAATGA-GGTTATCAAAAAATCATAGGGAGATTAA
* * *
10956 CAAAATTTCATAATGAGGTTATTAAAAAATCATAGGGAGCTTAT
1 CAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGATTAA
11000 CAAAATTT
1 CAAAATTT
11008 GTAATTATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (44 bp):
CAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGATTAA
Found at i:11104 original size:45 final size:45
Alignment explanation
Indices: 11017--11115 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
11007 TGTAATTATC
* *
11017 AAATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGGTTATTA
1 AAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGGTTATTA
* *
11062 AAATTTTAT-AGAAAGATTTATCAAAATTTCATAGCGA-GGTTATCA
1 AAATTTCATAAGAAAG--TTATCAAAATTTCATAGCGAGGGTTATTA
*
11107 CAATTTCAT
1 AAATTTCAT
11116 GGTGTGATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 6 0.13
45 22 0.48
46 18 0.39
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (45 bp):
AAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGGTTATTA
Found at i:11351 original size:22 final size:21
Alignment explanation
Indices: 11326--11378 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
11316 AGGATTCTTG
* *
11326 AAATTCCATAGTACCGTTATCA
1 AAATTTCATAGGA-CGTTATCA
*
11348 AAATTTCATAGGAGGTTATCA
1 AAATTTCATAGGACGTTATCA
11369 AAATTTCATA
1 AAATTTCATA
11379 ATGGGATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATTTCATAGGACGTTATCA
Found at i:11506 original size:2 final size:2
Alignment explanation
Indices: 11499--11547 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
11489 CTAAAACTAG
*
11499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
11542 TA TA TA
1 TA TA TA
11548 AAAGTACGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11607 original size:31 final size:31
Alignment explanation
Indices: 11570--11628 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
11560 TTGTAAAACT
11570 TTTTG-AATCACCCATTATACCCTTATTTAAC
1 TTTTGAAAT-ACCCATTATACCCTTATTTAAC
* *
11601 TTTTGAAATACCTATTATATCCTTATTT
1 TTTTGAAATACCCATTATACCCTTATTT
11629 TTCTAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTGAAATACCCATTATACCCTTATTTAAC
Found at i:12368 original size:23 final size:24
Alignment explanation
Indices: 12336--12381 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
12326 TTCTAATGTG
12336 TAATTATTTTATTTGACTT-ATAAT
1 TAATTATTTTATTTG-CTTGATAAT
*
12360 TAATT-TTTTTTTTGCTTGATAA
1 TAATTATTTTATTTGCTTGATAA
12382 ATGCAACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 12 0.60
24 5 0.25
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (24 bp):
TAATTATTTTATTTGCTTGATAAT
Found at i:13302 original size:123 final size:123
Alignment explanation
Indices: 13166--13409 Score: 470
Period size: 123 Copynumber: 2.0 Consensus size: 123
13156 AACATAAAAA
*
13166 AAAAAAAGACACGAACCAAAATAGACTCAAACCCAAATGACCTGACATTTGAGCCATCCGAACCC
1 AAAAAAAGACACGAACCAAAATAGACTCAAACCCAAATGACCCGACATTTGAGCCATCCGAACCC
13231 AACCCAACCCAACCGACGGAAACAAGTATTTGTTCAACTTCCAAACAGAGTGCAAACC
66 AACCCAACCCAACCGACGGAAACAAGTATTTGTTCAACTTCCAAACAGAGTGCAAACC
*
13289 AAAAAAAGACACGAACCAAAATTGACTCAAACCCAAATGACCCGACATTTGAGCCATCCGAACCC
1 AAAAAAAGACACGAACCAAAATAGACTCAAACCCAAATGACCCGACATTTGAGCCATCCGAACCC
13354 AACCCAACCCAACCGACGGAAACAAGTATTTGTTCAACTTCCAAACAGAGTGCAAA
66 AACCCAACCCAACCGACGGAAACAAGTATTTGTTCAACTTCCAAACAGAGTGCAAA
13410 TGCCGAACTA
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.14
Consensus pattern (123 bp):
AAAAAAAGACACGAACCAAAATAGACTCAAACCCAAATGACCCGACATTTGAGCCATCCGAACCC
AACCCAACCCAACCGACGGAAACAAGTATTTGTTCAACTTCCAAACAGAGTGCAAACC
Found at i:23996 original size:11 final size:10
Alignment explanation
Indices: 23980--24020 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
23970 TTCAATACTG
23980 CTTTTCTTTTT
1 CTTTT-TTTTT
*
23991 CTTTTCTTTT
1 CTTTTTTTTT
24001 CTTTTTTTTT
1 CTTTTTTTTT
24011 CCTTTTTTTT
1 -CTTTTTTTT
24021 GAGAAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:27970 original size:3 final size:3
Alignment explanation
Indices: 27890--27950 Score: 77
Period size: 3 Copynumber: 19.0 Consensus size: 3
27880 TATTATATAT
*
27890 ATA ATA ATA TATA TATA CTA ATCA ATA ATCA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA -ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA
27939 ATA ATA ATA ATA
1 ATA ATA ATA ATA
27951 TGTACCCAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 40 0.75
4 13 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29858 original size:83 final size:84
Alignment explanation
Indices: 29722--29882 Score: 247
Period size: 83 Copynumber: 1.9 Consensus size: 84
29712 TCATGTACAA
29722 AACTATATTCCAAAATAGTAGCAAATTTCCCTTAAATGTCATATTCCAACTTTAATTCC-T-TAT
1 AACTATATTCCAAAATAGTAGCAAATTTCCCTTAAATGTCATATTCCAACTTTAATTCCTTATAT
29785 TCCTTATACAACCCAAACT
66 TCCTTATACAACCCAAACT
* * * *
29804 AACTATATTTCAAAATA-TAGCAAATTTCCCTTATGAATGTCTTTTTCCATCTTTAATTCCTTAT
1 AACTATATTCCAAAATAGTAGCAAATTTCCCTTA--AATGTCATATTCCAACTTTAATTCCTTAT
29868 ATTCCTTATACAACC
64 ATTCCTTATACAACC
29883 AAAAAAATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
81 16 0.23
82 16 0.23
83 22 0.31
84 1 0.01
85 16 0.23
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (84 bp):
AACTATATTCCAAAATAGTAGCAAATTTCCCTTAAATGTCATATTCCAACTTTAATTCCTTATAT
TCCTTATACAACCCAAACT
Done.