Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013266.1 Corchorus olitorius cultivar O-4 contig13299, 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: 54072
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:290 original size:21 final size:21
Alignment explanation
Indices: 264--308 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
254 CGATTCTGTT
*
264 TCAACCTTCATGG-GGTCGACA
1 TCAACCTTCAAGGAGGTCGA-A
285 TCAACCTTCAAGGAGGTCGAA
1 TCAACCTTCAAGGAGGTCGAA
306 TCA
1 TCA
309 GAAACTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
TCAACCTTCAAGGAGGTCGAA
Found at i:6000 original size:3 final size:3
Alignment explanation
Indices: 5992--6024 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5982 TTCTAGTATA
5992 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6025 ATATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11102 original size:2 final size:2
Alignment explanation
Indices: 11095--11129 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11085 GAGTCAAGAC
11095 AT AT AT AT AT 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 AT AT AT AT AT A
11130 ATGCAGGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12395 original size:2 final size:2
Alignment explanation
Indices: 12388--12418 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12378 AAACTTACTT
12388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12419 TAAACCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22794 original size:196 final size:198
Alignment explanation
Indices: 22460--22853 Score: 729
Period size: 196 Copynumber: 2.0 Consensus size: 198
22450 GGAAGTTGTG
* * *
22460 AGGCGCAAGCTTGATTGGGAGCTGTGCAGCAGTGTTGATCGTGATGAGAGGAGGCAAGCCATTTG
1 AGGCGCAAGCTTGATTGGGAGCTATGCAGCAGCGTTGATCATGATGAGAGGAGGCAAGCCATTTG
22525 TTTGTGAGATGGTTTGAGTGTTTGTATTGAGGAGTGTTTGGGAGGATGAAGAAGATTGTGAGCCA
66 TTTGTGAGATGGTTTGAGTGTTTGTATTGAGGAGTGTTTGGGAGGATGAAGAAGATTGTGAGCCA
*
22590 GACATGTTGATGAAGAAAGGAAGAAGAAA-TTTGATTTTCGAGAG-AAGAGAAAAAAAAATCTGG
131 GACATGTTGATGAAGAAAGGAAGAAGAAATTTTGATTTTCGAAAGAAAGAGAAAAAAAAATCTGG
22653 TTT
196 TTT
22656 AGGCGCAAGCTTGATTGGGAGCTATGCAGCAGCGTTGATCATGATGAGAGGAGGCAAGCCATTTG
1 AGGCGCAAGCTTGATTGGGAGCTATGCAGCAGCGTTGATCATGATGAGAGGAGGCAAGCCATTTG
*
22721 TTTGTGAGATGGTTTGAGTGTTTGTATTGAGGAGTGTTTGGGAGGATGAAGAAGATTGTGAGCTA
66 TTTGTGAGATGGTTTGAGTGTTTGTATTGAGGAGTGTTTGGGAGGATGAAGAAGATTGTGAGCCA
22786 GACATGTTGATGAAGAAAGGAAGAAGAAATTTTGATTTTCGAAAGAAAGAGAAAAAAAAATCTGG
131 GACATGTTGATGAAGAAAGGAAGAAGAAATTTTGATTTTCGAAAGAAAGAGAAAAAAAAATCTGG
22851 TTT
196 TTT
22854 TGGATATTAT
Statistics
Matches: 191, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
196 155 0.81
197 14 0.07
198 22 0.12
ACGTcount: A:0.31, C:0.08, G:0.33, T:0.28
Consensus pattern (198 bp):
AGGCGCAAGCTTGATTGGGAGCTATGCAGCAGCGTTGATCATGATGAGAGGAGGCAAGCCATTTG
TTTGTGAGATGGTTTGAGTGTTTGTATTGAGGAGTGTTTGGGAGGATGAAGAAGATTGTGAGCCA
GACATGTTGATGAAGAAAGGAAGAAGAAATTTTGATTTTCGAAAGAAAGAGAAAAAAAAATCTGG
TTT
Found at i:32834 original size:21 final size:22
Alignment explanation
Indices: 32808--32848 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
32798 AGGAAATTTA
*
32808 TTTTATT-TTTTATTTTTTTCG
1 TTTTATTATTTGATTTTTTTCG
32829 TTTTATTATTTGATTTTTTT
1 TTTTATTATTTGATTTTTTT
32849 TATTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (22 bp):
TTTTATTATTTGATTTTTTTCG
Found at i:32839 original size:17 final size:16
Alignment explanation
Indices: 32813--32862 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
32803 ATTTATTTTA
32813 TTTTTTATTTTTTTCG
1 TTTTTTATTTTTTTCG
**
32829 TTTTATTATTTGATT--
1 TTTT-TTATTTTTTTCG
32844 TTTTTTATTTTTTTCG
1 TTTTTTATTTTTTTCG
32860 TTT
1 TTT
32863 GTTAATTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
16 7 0.26
17 8 0.30
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTTTCG
Found at i:34621 original size:424 final size:423
Alignment explanation
Indices: 33814--34660 Score: 1247
Period size: 424 Copynumber: 2.0 Consensus size: 423
33804 TTTATTTTTA
*
33814 CCATTTTACAATTTAATTAAAAAAACTTATAAAGTTTTTAAAAAATAAAAAGAAGAGTAATAGGC
1 CCATTTTACAATTTAATTAAAAAAACTTATAAAGTTTTTAAAAAATAAAAAGAAGAGTAACAGGC
* * *
33879 AATTATTTCATTTGACTTATAAAGTTAGACGAGTCAATCGGGCGGGTTGGATGAGTTTCAGATTT
66 AATTATTTCATTTGACTTATAAAGTTAGACGAGTCAATCGGGCGGGTTGGACGAGGTTCAGATTC
**
33944 AGGTCATCTAAATACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTCGGGTTTCAGCTCAT
131 AGGTCATCTAAATACAAATCAAATGAGGCAGGTAATTTTCTCAAGACATTCGGGTTTCAGCTCAT
* * * * *
34009 CTAGATTCAGGAAATTCGGGTCTCGGGAATGTTGGGTCTAGGGTCAAGCAGGTTCGGGTTTTGGC
196 CTAGATTCAGGAAATTCAGGTCTCGGGAATGCTAGGTCTAGGGTCAAGCAGGTTCGAGTTTTGAC
* *
34074 CTCAGGTCACTCAGGTTATGGGTCATTTGAGTTTTGGATTTTTCGGGTATAGGACTCGGATTCAA
261 CTCAGGTCACTCAGGTTATGGGTCATTTGAGTTTCGGATTTTTCGGGTATAGGACTCAGATTCAA
* *
34139 TTGCGATTTTATTAAATAAAACATGATTTTAGTTTATAATATTCTTGGATCATTCGGGTAAACTA
326 TTGCGATTTTATTAAATAAAACATAATTTTAGTTTATAATATTCTTAGATCATTCGGGTAAACTA
* * * *
34204 CTCGGATTATTCGGACTACGGGTTTGTCGGGCC
391 CTCGAATTATTCAGACTACAGATTTGTCGGGCC
34237 CCATTTTACTAATTTAATTAAAAAAAAACTTATAAAGTTTTT-AAAAATAAAAAGAAGAGTAACA
1 CCATTTTAC-AATTTAATT--AAAAAAACTTATAAAGTTTTTAAAAAATAAAAAGAAGAGTAACA
* *
34301 TGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTCAATCGGGCGGGTTGGACG-GGTTC-GA
63 GGCAATTATTTCATTTGACTTATAAAGTTAGACGAGTCAATCGGGCGGGTTGGACGAGGTTCAGA
* **
34364 GTTCGGGTCATCTAGGTACAAATCAAATGAGGCAGGTAATTTTCTCAAGACATTCGGGTTTC-GA
128 -TTCAGGTCATCTAAATACAAATCAAATGAGGCAGGTAATTTTCTCAAGACATTCGGGTTTCAG-
* * * ** *
34428 CTCATTTAGGTTCA-GATCATTCAGGTCTCGGGTCTGCTAGGTCTAGGGTC-AGACGGGTTCGAG
191 CTCATCTAGATTCAGGA-AATTCAGGTCTCGGGAATGCTAGGTCTAGGGTCAAG-CAGGTTCGAG
** *
34491 TTTTGACCTCAGGTCACTTGGGTTATGGGTCATTTGAGTTTCGGGTTTTTCGGGTATAGGACTCA
254 TTTTGACCTCAGGTCACTCAGGTTATGGGTCATTTGAGTTTCGGATTTTTCGGGTATAGGACTCA
* *
34556 GATTCAATTGGGATTTTATTAAATAAAACATAATTTTAGTTTATAATATTCTTAGATCTTTCGGG
319 GATTCAATTGCGATTTTATTAAATAAAACATAATTTTAGTTTATAATATTCTTAGATCATTCGGG
* * *
34621 TTAACTTCTCGAATTATTCAGCCTACAGATTTGTCGGGCC
384 TAAACTACTCGAATTATTCAGACTACAGATTTGTCGGGCC
34661 TACATAGGAT
Statistics
Matches: 379, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
423 16 0.04
424 268 0.71
425 74 0.20
426 21 0.06
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (423 bp):
CCATTTTACAATTTAATTAAAAAAACTTATAAAGTTTTTAAAAAATAAAAAGAAGAGTAACAGGC
AATTATTTCATTTGACTTATAAAGTTAGACGAGTCAATCGGGCGGGTTGGACGAGGTTCAGATTC
AGGTCATCTAAATACAAATCAAATGAGGCAGGTAATTTTCTCAAGACATTCGGGTTTCAGCTCAT
CTAGATTCAGGAAATTCAGGTCTCGGGAATGCTAGGTCTAGGGTCAAGCAGGTTCGAGTTTTGAC
CTCAGGTCACTCAGGTTATGGGTCATTTGAGTTTCGGATTTTTCGGGTATAGGACTCAGATTCAA
TTGCGATTTTATTAAATAAAACATAATTTTAGTTTATAATATTCTTAGATCATTCGGGTAAACTA
CTCGAATTATTCAGACTACAGATTTGTCGGGCC
Found at i:36050 original size:24 final size:21
Alignment explanation
Indices: 35964--36056 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 21
35954 TTGTACTCGG
*
35964 CGAGCATTCTTCATTCACGCT
1 CGAGCATTCTTCATTCGCGCT
* *
35985 CGGCGGGCATTCTTCATTTGCGCT
1 ---CGAGCATTCTTCATTCGCGCT
* *
36009 CGAGCATTTTTCGCTTCGCGACCT
1 CGAGCATTCTTC-ATTCGCG--CT
36033 CGAGTCATTCTTCATTCGCGCT
1 CGAG-CATTCTTCATTCGCGCT
36055 CG
1 CG
36057 GCGAGAGTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
21 10 0.18
22 9 0.16
24 30 0.54
25 7 0.12
ACGTcount: A:0.13, C:0.32, G:0.22, T:0.33
Consensus pattern (21 bp):
CGAGCATTCTTCATTCGCGCT
Found at i:36260 original size:25 final size:25
Alignment explanation
Indices: 36232--36310 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
36222 TCGAGAAGCA
*
36232 TTCTCTGCTTTGCACTCGACGAGCG
1 TTCTCTGCTTTGCACTCGGCGAGCG
* *
36257 TTCTAC-GCTTTGCGCTCGGCGAGCA
1 TTCT-CTGCTTTGCACTCGGCGAGCG
*
36282 TTCT-T-CGTTTGGCACTCGGTGAGCG
1 TTCTCTGC-TTT-GCACTCGGCGAGCG
36307 TTCT
1 TTCT
36311 ACGCTTCGCG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 3 0.07
25 39 0.89
26 1 0.02
ACGTcount: A:0.10, C:0.29, G:0.27, T:0.34
Consensus pattern (25 bp):
TTCTCTGCTTTGCACTCGGCGAGCG
Found at i:36435 original size:25 final size:25
Alignment explanation
Indices: 36398--36448 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
36388 TGGGGATCTA
* *
36398 CGCTTTGCGCTCGGCGAGCGTTCTC
1 CGCTTGGCACTCGGCGAGCGTTCTC
36423 CGCTTGGCACTCGGCGAGCGTTCTC
1 CGCTTGGCACTCGGCGAGCGTTCTC
36448 C
1 C
36449 TCTCACGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.06, C:0.37, G:0.31, T:0.25
Consensus pattern (25 bp):
CGCTTGGCACTCGGCGAGCGTTCTC
Found at i:36682 original size:25 final size:25
Alignment explanation
Indices: 36645--36792 Score: 61
Period size: 25 Copynumber: 6.0 Consensus size: 25
36635 TGAGGATCTA
* *
36645 CGCTTTGCGCTCGACGAGCGTTCTC
1 CGCTTCGCACTCGACGAGCGTTCTC
* **
36670 CGCTTGGCACTCGGTG-GTCGTTCTC
1 CGCTTCGCACTCGACGAG-CGTTCTC
* * * *
36695 CGCTTCGCATTC-AGCGAGTGTTGTA
1 CGCTTCGCACTCGA-CGAGCGTTCTC
* * * *
36720 C-ATTTGCGA-TCGGCGATCGTTCTC
1 CGCTTCGC-ACTCGACGAGCGTTCTC
* * * *
36744 CGTTTGGCACTCGACAAGCGTTCTA
1 CGCTTCGCACTCGACGAGCGTTCTC
* * *
36769 CGCTTCACATTCGGCGAGCGTTCT
1 CGCTTCGCACTCGACGAGCGTTCT
36793 ACATTTGCGA
Statistics
Matches: 86, Mismatches: 30, Indels: 14
0.66 0.23 0.11
Matches are distributed among these distances:
24 16 0.19
25 69 0.80
26 1 0.01
ACGTcount: A:0.12, C:0.30, G:0.27, T:0.30
Consensus pattern (25 bp):
CGCTTCGCACTCGACGAGCGTTCTC
Found at i:36773 original size:74 final size:74
Alignment explanation
Indices: 36648--36809 Score: 191
Period size: 74 Copynumber: 2.2 Consensus size: 74
36638 GGATCTACGC
* * *** * *
36648 TTTGCGCTCGACGAGCGTTCTCCGCTTGGCACTCGGTGGTCGTTCTCCGCTTCGCATTCAGCGAG
1 TTTGCGATCGGCGAGCGTTCTCCGCTTGGCACTCGCAAGTCGTTCTACGCTTCACATTCAGCGAG
* *
36713 TGTTGTACA
66 CGTTCTACA
* * *
36722 TTTGCGATCGGCGATCGTTCTCCGTTTGGCACTCGACAAG-CGTTCTACGCTTCACATTCGGCGA
1 TTTGCGATCGGCGAGCGTTCTCCGCTTGGCACTCG-CAAGTCGTTCTACGCTTCACATTCAGCGA
36786 GCGTTCTACA
65 GCGTTCTACA
*
36796 TTTGCGATTGGCGA
1 TTTGCGATCGGCGA
36810 ATGTTCTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 73 0.99
75 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.27, T:0.31
Consensus pattern (74 bp):
TTTGCGATCGGCGAGCGTTCTCCGCTTGGCACTCGCAAGTCGTTCTACGCTTCACATTCAGCGAG
CGTTCTACA
Found at i:37007 original size:25 final size:25
Alignment explanation
Indices: 36971--37018 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
36961 TCTACATTTT
* *
36971 GCACTCGTCGAGCATTCTCCGCTTG
1 GCACTCGGCGAGCATTCTACGCTTG
*
36996 GCACTCGGCGAGCGTTCTACGCT
1 GCACTCGGCGAGCATTCTACGCT
37019 CCGCGCTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.12, C:0.35, G:0.27, T:0.25
Consensus pattern (25 bp):
GCACTCGGCGAGCATTCTACGCTTG
Found at i:37016 original size:110 final size:111
Alignment explanation
Indices: 36779--37016 Score: 338
Period size: 111 Copynumber: 2.2 Consensus size: 111
36769 CGCTTCACAT
* * *
36779 TCGGCGAGCGTTCTACATTTGCGATTGGCGAATGTTCTTTACTCACGGGGAGCATTCTCCTCTCC
1 TCGGCGAGCGTTCTACGTTTGCGATTGACGAATGTTCTCTACTCACGGGGAGCATTCTCCTCTCC
* * *
36844 TTGGGGATATACGCTTTGCGCTCAGCGAGCATTCTCCGCTTGGCAT
66 TTGGGGATATACACTTTGCACTCAGCGAGCATTCTCCGCTTGGCAC
* * *
36890 TCAGCGAGCGTTCTACGTTTGCGATTGACGATTGTTCTCCT-CTCACGGGGAGTATTCTCCTCTC
1 TCGGCGAGCGTTCTACGTTTGCGATTGACGAATGTTCT-CTACTCACGGGGAGCATTCTCCTCTC
* *
36954 CTT-GGGATCTACATTTTGCACTC-GTCGAGCATTCTCCGCTTGGCAC
65 CTTGGGGATATACACTTTGCACTCAG-CGAGCATTCTCCGCTTGGCAC
37000 TCGGCGAGCGTTCTACG
1 TCGGCGAGCGTTCTACG
37017 CTCCGCGCTC
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 52 0.46
111 59 0.52
112 1 0.01
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (111 bp):
TCGGCGAGCGTTCTACGTTTGCGATTGACGAATGTTCTCTACTCACGGGGAGCATTCTCCTCTCC
TTGGGGATATACACTTTGCACTCAGCGAGCATTCTCCGCTTGGCAC
Found at i:37134 original size:134 final size:135
Alignment explanation
Indices: 36901--37149 Score: 378
Period size: 134 Copynumber: 1.9 Consensus size: 135
36891 CAGCGAGCGT
* * * *
36901 TCTACGTTTGCGATTGACGATTGTTCTCCTCTCACGGGGAGTATTCTCCTCTCCTTGGGATCTAC
1 TCTACATTTGCGATAGACGATTGTTCTCCTCTCACGGGGAGCATTCTCCTCTCCTTGGGATATAC
* **
36966 ATTTTGCACTCGTCGAGCATTCTCCGCTTGGCACTCGGCGAGCGTTCTACGCTCCGCGCTCGACG
66 ACTTTGCACTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGTTCTACGCTCCGCGCTCGACG
37031 AACGC
131 AACGC
*
37036 TCTACATTTGCGATCAG-CGATTGTTCTCCTCTCAC-GGGAGCATTCTCCT-TTCTTGGGTATAT
1 TCTACATTTGCGAT-AGACGATTGTTCTCCTCTCACGGGGAGCATTCTCCTCTCCTTGGG-ATAT
*
37098 ACACTTTGCGCTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGTTCTAC
64 ACACTTTGCACTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGTTCTAC
37150 CTTTGCAATC
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
133 7 0.07
134 64 0.62
135 31 0.30
136 1 0.01
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.31
Consensus pattern (135 bp):
TCTACATTTGCGATAGACGATTGTTCTCCTCTCACGGGGAGCATTCTCCTCTCCTTGGGATATAC
ACTTTGCACTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGTTCTACGCTCCGCGCTCGACG
AACGC
Found at i:37147 original size:25 final size:24
Alignment explanation
Indices: 37113--37172 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
37103 TTGCGCTCAA
* *
37113 CGAGCATTCTCCGCTTGGCACTCGG
1 CGAGCGTTCTCC-CTTGGCAATCGG
* *
37138 CGAGCGTTCTACCTTTGCAATCGG
1 CGAGCGTTCTCCCTTGGCAATCGG
*
37162 CGATCGTTCTC
1 CGAGCGTTCTC
37173 TTCTCACCGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.13, C:0.33, G:0.25, T:0.28
Consensus pattern (24 bp):
CGAGCGTTCTCCCTTGGCAATCGG
Found at i:37171 original size:109 final size:111
Alignment explanation
Indices: 37036--37258 Score: 270
Period size: 111 Copynumber: 2.0 Consensus size: 111
37026 CGACGAACGC
* * * *
37036 TCTACATTTGCGATCAGCGATTGTTCTCCTCTCA-CGGGAGCATTCTCCT-TTCTTGGGTATATA
1 TCTACATTTGCAATCAGCGATCGTTCTCCTCTCACCGGGAGCATTCTCCTCTACTTGGGGATATA
37099 CACTTTGCGCTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGT
66 CACTTTGCGCTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGT
* * * * *
37145 TCTACCTTTGCAATCGGCGATCGTTCTCTTCTCACCGGGAGCATTCTCCTCTACTTGGGGATTTG
1 TCTACATTTGCAATCAGCGATCGTTCTCCTCTCACCGGGAGCATTCTCCTCTACTTGGGGATATA
** * ** ** * *
37210 CGTTTTGTGCTCGGCGAGTGTTCTCCGCTTGGTACTCGGCGATCGT
66 CACTTTGCGCTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGT
37256 TCT
1 TCT
37259 CCGCTTGGCA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
109 29 0.31
110 15 0.16
111 50 0.53
ACGTcount: A:0.13, C:0.29, G:0.24, T:0.34
Consensus pattern (111 bp):
TCTACATTTGCAATCAGCGATCGTTCTCCTCTCACCGGGAGCATTCTCCTCTACTTGGGGATATA
CACTTTGCGCTCAACGAGCATTCTCCGCTTGGCACTCGGCGAGCGT
Found at i:37257 original size:25 final size:25
Alignment explanation
Indices: 37219--37458 Score: 148
Period size: 25 Copynumber: 9.7 Consensus size: 25
37209 GCGTTTTGTG
* * * *
37219 CTCGGCGAGTGTTCTCCGCTTGGTA
1 CTCGACGAGCGTTCTACGCTTGGCA
* * *
37244 CTCGGCGATCGTTCTCCGCTTGGCA
1 CTCGACGAGCGTTCTACGCTTGGCA
*
37269 CTCGACGAGCGTTCTACGCTTTGCA
1 CTCGACGAGCGTTCTACGCTTGGCA
* * * * * *
37294 TTCGGCGAACGTTTTAC-TTTTGCGA
1 CTCGACGAGCGTTCTACGCTTGGC-A
* * *
37319 -TCGAAGATCGTTCTCCGCTTGGCA
1 CTCGACGAGCGTTCTACGCTTGGCA
* *
37343 CTCGACGAGCGTTCTACGCTTCGTA
1 CTCGACGAGCGTTCTACGCTTGGCA
* * *
37368 TTCGACGAGCGTTCTAC-ATTTGCGA
1 CTCGACGAGCGTTCTACGCTTGGC-A
** *
37393 -TCGTTGATCGTTCT-CGGCTTGGCA
1 CTCGACGAGCGTTCTAC-GCTTGGCA
* **
37417 CTCGCCGAGCGTTCTACGCTCCGCA
1 CTCGACGAGCGTTCTACGCTTGGCA
* *
37442 TTCGGCGAGCGTTCTAC
1 CTCGACGAGCGTTCTAC
37459 ATTTGCGATC
Statistics
Matches: 167, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.01
24 32 0.19
25 133 0.80
26 1 0.01
ACGTcount: A:0.13, C:0.30, G:0.26, T:0.30
Consensus pattern (25 bp):
CTCGACGAGCGTTCTACGCTTGGCA
Found at i:37342 original size:74 final size:74
Alignment explanation
Indices: 37250--37482 Score: 349
Period size: 74 Copynumber: 3.1 Consensus size: 74
37240 GGTACTCGGC
* * * *
37250 GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTTGCATTCGGCGAACGTTTTACTTTT
1 GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTCGCATTCGGCGAGCGTTCTACATTT
37315 GCGATCGAA
66 GCGATCGAA
* *
37324 GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTCGTATTCGACGAGCGTTCTACATTT
1 GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTCGCATTCGGCGAGCGTTCTACATTT
**
37389 GCGATCGTT
66 GCGATCGAA
* * *
37398 GATCGTTCTCGGCTTGGCACTCGCCGAGCGTTCTACGCTCCGCATTCGGCGAGCGTTCTACATTT
1 GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTCGCATTCGGCGAGCGTTCTACATTT
**
37463 GCGATCGGC
66 GCGATCGAA
37472 GATCGTTCTCC
1 GATCGTTCTCC
37483 TATCACGGTG
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 143 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.31
Consensus pattern (74 bp):
GATCGTTCTCCGCTTGGCACTCGACGAGCGTTCTACGCTTCGCATTCGGCGAGCGTTCTACATTT
GCGATCGAA
Found at i:37842 original size:123 final size:120
Alignment explanation
Indices: 37579--38013 Score: 396
Period size: 122 Copynumber: 3.6 Consensus size: 120
37569 CATTTGCGAC
* * *
37579 CGCCTGTT-GAGTTGGGCCCCTTGAGGACTTCATCATTCCTCATACTCGGTCAGGGATGG-TCAT
1 CGCCTGTTGGCGTTGGGCCCCTT-AGGGCTTCATTATTCC-CATACTCGGTCAGGGATGGTTC-T
* * * * * * *
37642 TGTCGATTGCCTGCCGGTC-GAGGCCATACTAGGTTGAGCTTGG-CCTTGCCTGATCGCT
63 TGCCGATCGCCTGCC-GTCGGGGGCCATACTTGGTCGAGGTTGGTTCTTGCC-GATCGCT
* * * *
37700 CGCCTGTTGGCATTAGGCCCTTTGAGGGCTTCATTAATTCCCATACTCGGTCAAAGG-TGGTTCT
1 CGCCTGTTGGCGTTGGGCCCCTT-AGGGCTTCATT-ATTCCCATACTCGGTC-AGGGATGGTTCT
* * *
37764 TGCCGATCGCCTGTCGATCGGGGGCCATACTTGGTCGAGGTCGGTTCTTGCCGATCGTT
63 TGCCGATCGCCTGCCG-TCGGGGGCCATACTTGGTCGAGGTTGGTTCTTGCCGATCGCT
* * * *
37823 CGCCAGTTGGCGTTGGG-CCC------CTTC-GT-TTCCCATTCTCGGTCAGGGATGTTTCTTGC
1 CGCCTGTTGGCGTTGGGCCCCTTAGGGCTTCATTATTCCCATACTCGGTCAGGGATGGTTCTTGC
37879 CGATCGCCTGCCTGTCGGGGGCCCATACTTGGTCGAGGTTGGTTCTTGCCGATCGCT
66 CGATCGCCTGCC-GTCGGGGG-CCATACTTGGTCGAGGTTGGTTCTTGCCGATCGCT
** * *
37936 CG-CTGATTGGCGTTGGGCCCCTTAGGGGCTTCATCTCCTCCCATACTTGGTCAGGGATGGTTCG
1 CGCCTG-TTGGCGTTGGGCCCCTTA-GGGCTTCAT-TATTCCCATACTCGGTCAGGGATGGTTCT
* *
38000 TGACGATCACCTGC
63 TGCCGATCGCCTGC
38014 TAGTTGGGCA
Statistics
Matches: 255, Mismatches: 37, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
111 3 0.01
112 43 0.17
113 47 0.18
114 4 0.02
115 4 0.02
121 13 0.05
122 51 0.20
123 50 0.20
124 40 0.16
ACGTcount: A:0.12, C:0.28, G:0.30, T:0.30
Consensus pattern (120 bp):
CGCCTGTTGGCGTTGGGCCCCTTAGGGCTTCATTATTCCCATACTCGGTCAGGGATGGTTCTTGC
CGATCGCCTGCCGTCGGGGGCCATACTTGGTCGAGGTTGGTTCTTGCCGATCGCT
Found at i:37950 original size:113 final size:112
Alignment explanation
Indices: 37737--37958 Score: 324
Period size: 113 Copynumber: 2.0 Consensus size: 112
37727 GCTTCATTAA
*
37737 TTCCCATACTCGGTCAAAGGTGGTTCTTGCCGATCGCCTGTCGATCGGGGGCCATACTTGGTCGA
1 TTCCCATACTCGGTCAAAGGTGGTTCTTGCCGATCGCCTGCCGATCGGGGGCCATACTTGGTCGA
*
37802 GGTCGGTTCTTGCCGATCGTTCGCCAGTTGGCGTTGGGCCCCTTCGT
66 GGTCGGTTCTTGCCGATCGCTCGCCAGTTGGCGTTGGGCCCCTTCGT
* * *
37849 TTCCCATTCTCGGTC-AGGGATGTTTCTTGCCGATCGCCTGCCTG-TCGGGGGCCCATACTTGGT
1 TTCCCATACTCGGTCAAAGG-TGGTTCTTGCCGATCGCCTGCC-GATCGGGGG-CCATACTTGGT
* *
37912 CGAGGTTGGTTCTTGCCGATCGCTCG-CTGATTGGCGTTGGGCCCCTT
63 CGAGGTCGGTTCTTGCCGATCGCTCGCCAG-TTGGCGTTGGGCCCCTT
37959 AGGGGCTTCA
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
111 3 0.03
112 43 0.43
113 53 0.54
ACGTcount: A:0.09, C:0.29, G:0.31, T:0.31
Consensus pattern (112 bp):
TTCCCATACTCGGTCAAAGGTGGTTCTTGCCGATCGCCTGCCGATCGGGGGCCATACTTGGTCGA
GGTCGGTTCTTGCCGATCGCTCGCCAGTTGGCGTTGGGCCCCTTCGT
Found at i:47638 original size:12 final size:12
Alignment explanation
Indices: 47621--47650 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
47611 TAATCACAAT
47621 AATTAAATTTTA
1 AATTAAATTTTA
47633 AATTAAATTTTA
1 AATTAAATTTTA
47645 AATTAA
1 AATTAA
47651 TTAGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTAAATTTTA
Found at i:48925 original size:28 final size:28
Alignment explanation
Indices: 48885--48941 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
48875 AAAATTATTT
48885 ATCTATACATTGGGAATA-CTCTATGACA
1 ATCTATACATTGGGAATAGCT-TATGACA
48913 ATCTATACATTGGGAATAGCTTATGACA
1 ATCTATACATTGGGAATAGCTTATGACA
48941 A
1 A
48942 CTTTGGGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (28 bp):
ATCTATACATTGGGAATAGCTTATGACA
Found at i:48992 original size:28 final size:28
Alignment explanation
Indices: 48939--48992 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
48929 TAGCTTATGA
* *
48939 CAACTTTGGGTGTCAAAGTATTATTTGC
1 CAACTTTCGGTGTCAAAGTATAATTTGC
48967 CAACTTTCGGTGTCAAAAG-ATAATTT
1 CAACTTTCGGTGTC-AAAGTATAATTT
48993 ACCGTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (28 bp):
CAACTTTCGGTGTCAAAGTATAATTTGC
Found at i:49165 original size:41 final size:41
Alignment explanation
Indices: 49065--49258 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 41
49055 GTAATTCAAG
* * * ***
49065 GTGACAATTTCTAGTGTCAACA-GTAATTATAATTTACTGGA
1 GTGACAACTTCTGGTGTCAA-AGGTAATTTTAATTTACCAAA
*
49106 GTAAC-ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
*
49146 GTGACAACTTCTGGTGTCAAAAGGTAATTTTAATTTACCAAG
1 GTGACAACTTCTGGTGTC-AAAGGTAATTTTAATTTACCAAA
* * * *
49188 GTGACAACTTTTAGTGTCAGCA-GTAATTTTAATTTACTAAA
1 GTGACAACTTCTGGTGTCA-AAGGTAATTTTAATTTACCAAA
*
49229 GTGACAACTTCTGGTGTGAAAGGTAATTTT
1 GTGACAACTTCTGGTGTCAAAGGTAATTTT
49259 CAATATTATT
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 32 0.25
41 58 0.45
42 39 0.30
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (41 bp):
GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
Found at i:50199 original size:130 final size:131
Alignment explanation
Indices: 50003--50252 Score: 421
Period size: 130 Copynumber: 1.9 Consensus size: 131
49993 AATATATTTT
* * *
50003 AAAAATTCTAACATATCTAACTTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTAT
1 AAAAATTCTAACATATATAAC-GTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
* *
50068 AAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATC
65 AAGGATATTATATTTAATTAAATAAAAATAGAGGTTTTAGTTGAGCAAAACTATAAAAGTATATC
50133 TA
130 TA
* *
50135 AAAAATTCTAATATATATAA-GTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATA
1 AAAAATTCTAACATATATAACGTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
50199 AGGATATTATATTTAATTAAATAAAAATAGAGGTTTTAGTTGAGCAAAACTATA
66 AGGATATTATATTTAATTAAATAAAAATAGAGGTTTTAGTTGAGCAAAACTATA
50253 TAAAAATTTA
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
130 93 0.84
132 18 0.16
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (131 bp):
AAAAATTCTAACATATATAACGTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
AGGATATTATATTTAATTAAATAAAAATAGAGGTTTTAGTTGAGCAAAACTATAAAAGTATATCT
A
Found at i:52251 original size:17 final size:17
Alignment explanation
Indices: 52225--52264 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
52215 TTTAGTTATT
* *
52225 TTATTATTTGACTATAC
1 TTATTTTTTGACTATAA
52242 TTATTTTTTGACTATAA
1 TTATTTTTTGACTATAA
52259 TTATTT
1 TTATTT
52265 ATTATTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (17 bp):
TTATTTTTTGACTATAA
Found at i:52475 original size:29 final size:30
Alignment explanation
Indices: 52439--52496 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
52429 AGAAAGAGGC
52439 TGAGGCTGCTCGGATGTATAGGG-GAGGGT
1 TGAGGCTGCTCGGATGTATAGGGAGAGGGT
*
52468 TGAGGCTGCTCGGATGTATTGGGAGAGGG
1 TGAGGCTGCTCGGATGTATAGGGAGAGGG
52497 AGGCTGCCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.17, C:0.10, G:0.48, T:0.24
Consensus pattern (30 bp):
TGAGGCTGCTCGGATGTATAGGGAGAGGGT
Found at i:52801 original size:20 final size:20
Alignment explanation
Indices: 52776--52817 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
52766 TATTATGTGA
*
52776 TATTATAAATTGAAATTAAT
1 TATTATAAATTGAAATAAAT
52796 TATTATAAATTGAAATAAAT
1 TATTATAAATTGAAATAAAT
52816 TA
1 TA
52818 AATAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATTATAAATTGAAATAAAT
Done.