Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012217.1 Corchorus capsularis cultivar CVL-1 contig12238, 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: 33594
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:420 original size:188 final size:188
Alignment explanation
Indices: 103--480 Score: 738
Period size: 188 Copynumber: 2.0 Consensus size: 188
93 TCACATTATA
103 ATTAGTACAGATTACTATTTTATTTATTATTTATTTAAATTAATTAACATATGATAAATGATAAT
1 ATTAGTACAGATTACTATTTTATTTATTATTTATTTAAATTAATTAACATATGATAAATGATAAT
168 TATTTGAAATTAAATTTATGGAAGTTAAATTCATTTTATGTATTTTTATTATATTGAAATATATT
66 TATTTGAAATTAAATTTATGGAAGTTAAATTCATTTTATGTATTTTTATTATATTGAAATATATT
*
233 TATTATTCCATTTATATATTATAAATTAAATTAAATAATTTAGTTATACAACTAATTT
131 TATTATTCAATTTATATATTATAAATTAAATTAAATAATTTAGTTATACAACTAATTT
291 ATTAGTACAGATTACTATTTTATTTATTATTTATTTAAATTAATTAACATATGATAAATGATAAT
1 ATTAGTACAGATTACTATTTTATTTATTATTTATTTAAATTAATTAACATATGATAAATGATAAT
356 TATTTGAAATTAAATTTATGGAAGTTAAATTCATTTTATGTATTTTTATTATATTGAAATATATT
66 TATTTGAAATTAAATTTATGGAAGTTAAATTCATTTTATGTATTTTTATTATATTGAAATATATT
*
421 TATTATTCAATTTATATATTATAAATTAAATTAAATAATTTAGTTATACAATTAATTT
131 TATTATTCAATTTATATATTATAAATTAAATTAAATAATTTAGTTATACAACTAATTT
479 AT
1 AT
481 ACCATACTAT
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 188 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (188 bp):
ATTAGTACAGATTACTATTTTATTTATTATTTATTTAAATTAATTAACATATGATAAATGATAAT
TATTTGAAATTAAATTTATGGAAGTTAAATTCATTTTATGTATTTTTATTATATTGAAATATATT
TATTATTCAATTTATATATTATAAATTAAATTAAATAATTTAGTTATACAACTAATTT
Found at i:3052 original size:3 final size:3
Alignment explanation
Indices: 3044--3071 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3034 TACTTGATAT
3044 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3072 CTCAATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7946 original size:15 final size:16
Alignment explanation
Indices: 7920--7961 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
7910 TGGAACTGAA
7920 GGAAACATTTAAGTAT
1 GGAAACATTTAAGTAT
7936 GGAAA-ATTTAAGTAT
1 GGAAACATTTAAGTAT
7951 GGAAACATTTA
1 GGAAACATTTA
7962 GTTACGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (16 bp):
GGAAACATTTAAGTAT
Found at i:9990 original size:58 final size:58
Alignment explanation
Indices: 9901--10326 Score: 581
Period size: 58 Copynumber: 7.3 Consensus size: 58
9891 CAATAACGAT
* * *
9901 CGAGCATCCCTTGGTCGCACAG-CCAAGTGGGCATCCCCCACTCATGTAATAAGAAAAC
1 CGAGCATCCCTCGGTCACACGGCCCAA-TGGGCATCCCCCACTCATGTAATAAGAAAAC
*
9959 CGAGCATCCCTCGGTCACATGGCCCAATGGGCAT-CCCCACTCATGTAATAAGAAAAC
1 CGAGCATCCCTCGGTCACACGGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
* *
10016 CGAGCATCTCTCGGTCACACAG-CCAAGTGGGCATCCCCCACTCATGTAATAAGAAAAC
1 CGAGCATCCCTCGGTCACACGGCCCAA-TGGGCATCCCCCACTCATGTAATAAGAAAAC
* * *
10074 CGAGCATCCCTCGGTCACACAGCCCAAGTGGGCATCCCCCACTCATGCAATAAGAGAAC
1 CGAGCATCCCTCGGTCACACGGCCCAA-TGGGCATCCCCCACTCATGTAATAAGAAAAC
* * * *
10133 CGAGCATCCCTCGGTCACACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAGAAT
1 CGAGCATCCCTCGGTCACACGGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
* *
10191 CGAGCATCCCTCGGTCACATGGCCCAATGGGCATCCCCCACTCATGTAATAA-ATAAAT
1 CGAGCATCCCTCGGTCACACGGCCCAATGGGCATCCCCCACTCATGTAATAAGA-AAAC
* * * * * *
10249 CGAGCATCCCTCGGTCACATGGCCCAATGGGCATCCCCCACACGTGCAAGAAGAAAAA
1 CGAGCATCCCTCGGTCACACGGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
* *
10307 CAAGCATCCCTTGGTCACAC
1 CGAGCATCCCTCGGTCACAC
10327 AACCTAAAAT
Statistics
Matches: 337, Mismatches: 25, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
56 4 0.01
57 50 0.15
58 219 0.65
59 64 0.19
ACGTcount: A:0.29, C:0.35, G:0.20, T:0.16
Consensus pattern (58 bp):
CGAGCATCCCTCGGTCACACGGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
Found at i:10184 original size:117 final size:116
Alignment explanation
Indices: 9901--10327 Score: 590
Period size: 117 Copynumber: 3.7 Consensus size: 116
9891 CAATAACGAT
* * *
9901 CGAGCATCCCTTGGTCGCACAGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAACCGAGCAT
1 CGAGCATCCCTCGGTCACACAGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACCGAGCAT
**
9966 CCCTCGGTCACATGGCCCAATGGGCAT-CCCCACTCATGTAATAAGAAAAC
66 CCCTCGGTCACACAGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
* *
10016 CGAGCATCTCTCGGTCACACAGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAACCGAGCAT
1 CGAGCATCCCTCGGTCACACAGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACCGAGCAT
* *
10081 CCCTCGGTCACACAGCCCAAGTGGGCATCCCCCACTCATGCAATAAGAGAAC
66 CCCTCGGTCACACAGCCCAA-TGGGCATCCCCCACTCATGTAATAAGAAAAC
* * * *
10133 CGAGCATCCCTCGGTCACACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAGAATCGAGCAT
1 CGAGCATCCCTCGGTCACACAGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACCGAGCAT
** *
10198 CCCTCGGTCACATGGCCCAATGGGCATCCCCCACTCATGTAATAA-ATAAAT
66 CCCTCGGTCACACAGCCCAATGGGCATCCCCCACTCATGTAATAAGA-AAAC
** * * * * *
10249 CGAGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACAAGCA
1 CGAGCATCCCTCGGTCACACAG-CCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACCGAGCA
*
10313 TCCCTTGGTCACACA
65 TCCCTCGGTCACACA
10328 ACCTAAAATG
Statistics
Matches: 279, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
115 81 0.29
116 97 0.35
117 101 0.36
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.16
Consensus pattern (116 bp):
CGAGCATCCCTCGGTCACACAGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACCGAGCAT
CCCTCGGTCACACAGCCCAATGGGCATCCCCCACTCATGTAATAAGAAAAC
Found at i:10791 original size:29 final size:29
Alignment explanation
Indices: 10737--10847 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
10727 AAAAAAAAAG
**
10737 GTGGTAGTACGCCC-CCAAAGTTCAAGAA
1 GTGGTAGTACGCCCTCCAAAGAGCAAGAA
*
10765 GTGGTAGTACTCCCTCCAAAGAGCAAGAA
1 GTGGTAGTACGCCCTCCAAAGAGCAAGAA
** * *
10794 GTGGTAGTACGCCCTATAAA-ACTCACGAA
1 GTGGTAGTACGCCCTCCAAAGA-GCAAGAA
*
10823 GTGGTAGTACTCCCTCCAAAG-GCAA
1 GTGGTAGTACGCCCTCCAAAGAGCAA
10848 AAAATACCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.24
29 51 0.76
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (29 bp):
GTGGTAGTACGCCCTCCAAAGAGCAAGAA
Found at i:10806 original size:57 final size:57
Alignment explanation
Indices: 10737--10847 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
10727 AAAAAAAAAG
* **
10737 GTGGTAGTACGCCC-CCAAAGTTCAAGAAGTGGTAGTACTCCCTCCAAAGAGCAAGAA
1 GTGGTAGTACGCCCTACAAAACTCAAGAAGTGGTAGTACTCCCTCCAAAG-GCAAGAA
* *
10794 GTGGTAGTACGCCCTATAAAACTCACGAAGTGGTAGTACTCCCTCCAAAGGCAA
1 GTGGTAGTACGCCCTACAAAACTCAAGAAGTGGTAGTACTCCCTCCAAAGGCAA
10848 AAAATACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 18 0.38
58 30 0.62
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (57 bp):
GTGGTAGTACGCCCTACAAAACTCAAGAAGTGGTAGTACTCCCTCCAAAGGCAAGAA
Found at i:10945 original size:29 final size:29
Alignment explanation
Indices: 10912--10982 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
10902 AAGGGGCAAG
**
10912 AAGTGGTAGTACTCCCTCCAAAGTTCACA
1 AAGTGGTAGTACTCCCTCCAAAACTCACA
*
10941 AAGTGGTAGTACTCCCTCCAAAACTCACG
1 AAGTGGTAGTACTCCCTCCAAAACTCACA
10970 AAGTGGTAGTACT
1 AAGTGGTAGTACT
10983 ACCCCAAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (29 bp):
AAGTGGTAGTACTCCCTCCAAAACTCACA
Found at i:11027 original size:149 final size:147
Alignment explanation
Indices: 10727--10998 Score: 386
Period size: 149 Copynumber: 1.8 Consensus size: 147
10717 GAGCAGATGC
**
10727 AAAAAAAAAGGTGGTAGTACGCCCCCAAAGTTCAAGAAGTGGTAGTACTCCCTCCAAAGAGCAAG
1 AAAAAAAAAGGTGGTAGTACGCCCCCAAAGGGCAAGAAGTGGTAGTACTCCCTCCAAAGAGCAAG
* * *
10792 AAGTGGTAGTACGCCCTATAAAACTCACGAAGTGGTAGTACTCCCTCCAAAGGCAAAAAATACCA
66 AAGTGGTAGTACGCCCTACAAAACTCACGAAGTGGTAGTACTACCTCCAAAAGCAAAAAATACCA
*
10857 AGTCAGGGGAAACCCAA
131 AGTCAGCGGAAACCCAA
* **
10874 AAAAAAGAAAGGGTGGTAGTACGCCCCCAAGGGGCAAGAAGTGGTAGTACTCCCTCCAAAGTTCA
1 AAAAAA-AAA-GGTGGTAGTACGCCCCCAAAGGGCAAGAAGTGGTAGTACTCCCTCCAAAGAGCA
* *
10939 CA-AAGTGGTAGTACTCCCTCCAAAACTCACGAAGTGGTAGTACTACC-CCAAGATAGCAAA
64 -AGAAGTGGTAGTACGCCCTACAAAACTCACGAAGTGGTAGTACTACCTCCAA-A-AGCAAA
10999 GTGGAAGCAC
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
147 6 0.05
148 7 0.06
149 91 0.83
150 6 0.05
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (147 bp):
AAAAAAAAAGGTGGTAGTACGCCCCCAAAGGGCAAGAAGTGGTAGTACTCCCTCCAAAGAGCAAG
AAGTGGTAGTACGCCCTACAAAACTCACGAAGTGGTAGTACTACCTCCAAAAGCAAAAAATACCA
AGTCAGCGGAAACCCAA
Found at i:11247 original size:29 final size:28
Alignment explanation
Indices: 11109--11492 Score: 388
Period size: 27 Copynumber: 14.0 Consensus size: 28
11099 GGAGCACGCT
* **
11109 CACCATGTTGGAC-GAGCGTTGTACATC
1 CACCATTTTGGACAGAGCGCCGTACATC
* *
11136 CATCATCTTGGA-AGAAAAGCGCCGTACAT-
1 CACCATTTTGGACAG---AGCGCCGTACATC
* *
11165 --CCATCTTGGAAGAGAGCGCCGTACATC
1 CACCATTTTGG-ACAGAGCGCCGTACATC
11192 CACCATTTTGGAC-GAGCGCCGTACATC
1 CACCATTTTGGACAGAGCGCCGTACATC
*
11219 CACCATATTGGACGAGAGCGCCGTACATC
1 CACCATTTTGGAC-AGAGCGCCGTACATC
**
11248 CACCATTTTGGAC-GAGCGCTATACATC
1 CACCATTTTGGACAGAGCGCCGTACATC
11275 CACCATTTTGGAC-GAGCGCCGTACATC
1 CACCATTTTGGACAGAGCGCCGTACATC
* *
11302 CACTATTTTGGAC-GAGCGCCGTGCATC
1 CACCATTTTGGACAGAGCGCCGTACATC
*
11329 CACTATTTTGGAC-GAGCGCCGTACATC
1 CACCATTTTGGACAGAGCGCCGTACATC
11356 CACCATTTTGGAC-GAGCGCCGTACA--
1 CACCATTTTGGACAGAGCGCCGTACATC
* * * *
11381 -ACTATCTTGGAAGAGAGCGTCGTACA--
1 CACCATTTTGG-ACAGAGCGCCGTACATC
11407 -ACCATTTTGGACATGAGCGCCGTACATC
1 CACCATTTTGGACA-GAGCGCCGTACATC
*
11435 CACCATTTTGGACGAGAGCGCTGTACATC
1 CACCATTTTGGAC-AGAGCGCCGTACATC
* *
11464 CACCATCTTGGAAGAGAGCGCCGTACATC
1 CACCATTTTGG-ACAGAGCGCCGTACATC
11493 AATCTTGGAA
Statistics
Matches: 309, Mismatches: 29, Indels: 36
0.83 0.08 0.10
Matches are distributed among these distances:
24 8 0.03
25 3 0.01
26 42 0.14
27 157 0.51
28 2 0.01
29 85 0.28
30 12 0.04
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (28 bp):
CACCATTTTGGACAGAGCGCCGTACATC
Found at i:11363 original size:81 final size:80
Alignment explanation
Indices: 11109--11475 Score: 379
Period size: 83 Copynumber: 4.5 Consensus size: 80
11099 GGAGCACGCT
* ** * * *
11109 CACCATGTTGGACGAGCGTTGTACATCCATCATCTTGGAAGAAAAGCGCCGT-A--CATCCATCT
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGACG---AGCGCCGTCATCCA-CCATTT
*
11171 TGGAAGAGAGCGCCGTACATC
62 TGG-A-CGAGCGCCGTACATC
*
11192 CACCATTTTGGACGAGCGCCGTACATCCACCATATTGGACGAGAGCGCCGTACATCCACCATTTT
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGAC--GAGCGCCGT-CATCCACCATTTT
**
11257 GGACGAGCGCTATACATC
63 GGACGAGCGCCGTACATC
* * *
11275 CACCATTTTGGACGAGCGCCGTACATCCACTATTTTGGACGAGCGCCGTGCATCCACTATTTTGG
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGACGAGCGCCGT-CATCCACCATTTTGG
11340 ACGAGCGCCGTACATC
65 ACGAGCGCCGTACATC
* * * * *
11356 CACCATTTTGGACGAGCGCCGTACA---ACTATCTTGGAAGAGAG-CGTCGTACAACCATTTTGG
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGACGAGCGCCGTCAT-CCACCATTTTGG
11417 ACATGAGCGCCGTACATC
65 AC--GAGCGCCGTACATC
*
11435 CACCATTTTGGACGAGAGCGCTGTACATCCACCATCTTGGA
1 CACCATTTTGGAC--GAGCGCCGTACATCCACCATCTTGGA
11476 AGAGAGCGCC
Statistics
Matches: 246, Mismatches: 24, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
76 2 0.01
77 15 0.06
78 14 0.06
79 27 0.11
81 73 0.30
82 8 0.03
83 84 0.34
84 12 0.05
85 9 0.04
86 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (80 bp):
CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGACGAGCGCCGTCATCCACCATTTTGGA
CGAGCGCCGTACATC
Found at i:11511 original size:110 final size:105
Alignment explanation
Indices: 11109--11505 Score: 422
Period size: 110 Copynumber: 3.6 Consensus size: 105
11099 GGAGCACGCT
* ** * *
11109 CACCATGTTGGACGAGCGTTGTACATCCATCATCTTGGAAGAAAAGCGCCGTACATCCATCTTGG
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGAAG---AGCGCCGTACATCAATCTTGG
11174 AAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACATC
63 AAGAGAGCGCCGTACA--CACCATTTTGGACGAGCGCCGTACATC
* * * ** *
11219 CACCATATTGGACGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTATACATCCACCATTTT
1 CACCATTTTGGAC--GAGCGCCGTACATCCACCATCTTGGAAGAGCGCCGTACAT-CA--ATCTT
* * *
11284 GG-A-CGAGCGCCGTACATCCACTATTTTGGACGAGCGCCGTGCATC
61 GGAAGAGAGCGCCGTACA--CACCATTTTGGACGAGCGCCGTACATC
* * * * *
11329 CACTATTTTGGACGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACAACTATCTTGGAAG
1 CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGAAGAGCGCCGTACATCAATCTTGGAAG
*
11394 AGAGCGTCGTACA-ACCATTTTGGACATGAGCGCCGTACATC
66 AGAGCGCCGTACACACCATTTTGGAC--GAGCGCCGTACATC
*
11435 CACCATTTTGGACGAGAGCGCTGTACATCCACCATCTTGGAAGAGAGCGCCGTACATCAATCTTG
1 CACCATTTTGGAC--GAGCGCCGTACATCCACCATCTTGG-A-AGAGCGCCGTACATCAATCTTG
11500 GAAGAG
62 GAAGAG
11506 GGCGTCATAC
Statistics
Matches: 244, Mismatches: 30, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
104 11 0.05
105 6 0.02
106 26 0.11
107 12 0.05
108 60 0.25
109 11 0.05
110 88 0.36
111 1 0.00
112 29 0.12
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (105 bp):
CACCATTTTGGACGAGCGCCGTACATCCACCATCTTGGAAGAGCGCCGTACATCAATCTTGGAAG
AGAGCGCCGTACACACCATTTTGGACGAGCGCCGTACATC
Found at i:11540 original size:55 final size:54
Alignment explanation
Indices: 11369--11541 Score: 158
Period size: 55 Copynumber: 3.1 Consensus size: 54
11359 CATTTTGGAC
* * * *
11369 GAGCGCCGTACAACTATCTTGGAAGAGAGCGTCGTA--CAACCATTTTGGACAT
1 GAGCGCCGTACATCAATCTTGGAAGAGAGCGTCGTACCCAACCATCTTGGAAAT
* *
11421 GAGCGCCGTACATCCACCATTTTGGACGAGAGCG-CTGTACATCC-ACCATCTTGGAAGA-
1 GAGCGCCGTACAT-CA--ATCTTGGAAGAGAGCGTC-GTAC--CCAACCATCTTGGAA-AT
* *
11479 GAGCGCCGTACATCAATCTTGGAAGAGGGCGTCATACGCCAACCATCTTGGAAAT
1 GAGCGCCGTACATCAATCTTGGAAGAGAGCGTCGTAC-CCAACCATCTTGGAAAT
*
11534 GGGCGCCG
1 GAGCGCCG
11542 CATGCCCACC
Statistics
Matches: 97, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
52 12 0.12
53 1 0.01
54 4 0.04
55 52 0.54
56 1 0.01
57 2 0.02
58 23 0.24
59 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (54 bp):
GAGCGCCGTACATCAATCTTGGAAGAGAGCGTCGTACCCAACCATCTTGGAAAT
Found at i:11591 original size:25 final size:26
Alignment explanation
Indices: 11534--11601 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
11524 TCTTGGAAAT
*
11534 GGGCGCCGCATGCCCACCATAACAAGA
1 GGGCGCCGCACGCCCACCAT-ACAAGA
** *
11561 AAGCGCCGCGCGCCCACCAT-CAAGA
1 GGGCGCCGCACGCCCACCATACAAGA
*
11586 GGGCGCCGTACGCCCA
1 GGGCGCCGCACGCCCA
11602 TTGTCGGGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
25 17 0.52
27 16 0.48
ACGTcount: A:0.25, C:0.41, G:0.28, T:0.06
Consensus pattern (26 bp):
GGGCGCCGCACGCCCACCATACAAGA
Found at i:11687 original size:19 final size:20
Alignment explanation
Indices: 11663--11700 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
11653 ATGACCGCGA
11663 AGCGGTAGTACGC-CCCAAT
1 AGCGGTAGTACGCTCCCAAT
11682 AGCGGTAGTACGCTCCCAA
1 AGCGGTAGTACGCTCCCAA
11701 CGACCACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
AGCGGTAGTACGCTCCCAAT
Found at i:11722 original size:28 final size:28
Alignment explanation
Indices: 11682--11753 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
11672 ACGCCCCAAT
*
11682 AGCGGTAGTACGCTCCCAACGACCACGA
1 AGCGGTAGTACGCTCCCAACGACCACAA
* *
11710 AGCGGTAGTACGCTCCCAATGACCGCAA
1 AGCGGTAGTACGCTCCCAACGACCACAA
*
11738 AGCGATAGTACGCTCC
1 AGCGGTAGTACGCTCC
11754 AAAAGCGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.33, G:0.25, T:0.14
Consensus pattern (28 bp):
AGCGGTAGTACGCTCCCAACGACCACAA
Found at i:11760 original size:19 final size:19
Alignment explanation
Indices: 11736--11776 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
11726 CAATGACCGC
*
11736 AAAGCGATAGTACGCTCCA
1 AAAGCGATAGAACGCTCCA
*
11755 AAAGCGGTAGAACGCTCCA
1 AAAGCGATAGAACGCTCCA
11774 AAA
1 AAA
11777 AAAAATCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAGCGATAGAACGCTCCA
Found at i:19087 original size:11 final size:11
Alignment explanation
Indices: 19071--19100 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19061 TTGTTTTTTA
19071 TTTTTGTTTCG
1 TTTTTGTTTCG
*
19082 TTTTTGTTTTG
1 TTTTTGTTTCG
19093 TTTTTGTT
1 TTTTTGTT
19101 ACGCTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTCG
Found at i:20517 original size:61 final size:62
Alignment explanation
Indices: 20436--20581 Score: 213
Period size: 61 Copynumber: 2.4 Consensus size: 62
20426 AAGTGTTTAA
* * * * * * *
20436 AAAAAAAACTCAAACTAAATATAGCGGCGTTTTGATGCCGCTATATTTAAGGGATTTTTTTT
1 AAAAAAATCTCAAATTAAATATAACGGCATTTAGACGCCGCTATATTTAAAGGATTTTTTTT
*
20498 -AAAAATTCTCAAATTAAATATAACGGCATTTAGACGCCGCTATATTTAAAGGATTTTTTTT
1 AAAAAAATCTCAAATTAAATATAACGGCATTTAGACGCCGCTATATTTAAAGGATTTTTTTT
20559 AAAAAAATCTCAAATTAAATATA
1 AAAAAAATCTCAAATTAAATATA
20582 TTTAAAGGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 53 0.72
62 21 0.28
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (62 bp):
AAAAAAATCTCAAATTAAATATAACGGCATTTAGACGCCGCTATATTTAAAGGATTTTTTTT
Found at i:21062 original size:16 final size:15
Alignment explanation
Indices: 21016--21062 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
21006 AAAAAAAGAA
21016 AGAAGTATAAAATTTC
1 AGAA-TATAAAATTTC
21032 AG-ATATAGAAA-TTC
1 AGAATATA-AAATTTC
21046 AGAACTATAAAATTTC
1 AGAA-TATAAAATTTC
21062 A
1 A
21063 TGTAAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.33
15 8 0.30
16 10 0.37
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (15 bp):
AGAATATAAAATTTC
Done.