Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016289.1 Corchorus capsularis cultivar CVL-1 contig16310, 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: 53903
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:674 original size:10 final size:10
Alignment explanation
Indices: 659--688 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
649 TCGCATGGAG
659 CAACCGGCCA
1 CAACCGGCCA
669 CAACCGGCCA
1 CAACCGGCCA
679 CAACCGGCCA
1 CAACCGGCCA
689 TCGCATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (10 bp):
CAACCGGCCA
Found at i:15462 original size:41 final size:41
Alignment explanation
Indices: 15409--15493 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
15399 GTTCATGTTT
* *
15409 TTTCTTTTTATCTCACCTAGGGTTTA-ATATGTTTTTTGAGGG
1 TTTCTTTTTATCTCACCTAAGGTTTATAT-TGTTTGTT-AGGG
*
15451 TTTC-TTTTATCTCATCTAAGGTTTATATTGTTTGTTAGGG
1 TTTCTTTTTATCTCACCTAAGGTTTATATTGTTTGTTAGGG
15491 TTT
1 TTT
15494 GGGTTTCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 7 0.18
41 26 0.67
42 6 0.15
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (41 bp):
TTTCTTTTTATCTCACCTAAGGTTTATATTGTTTGTTAGGG
Found at i:17852 original size:26 final size:25
Alignment explanation
Indices: 17823--17875 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 25
17813 TGCTCTTGTC
17823 ATCGAACCGAATGGCATCTTCAAAGG
1 ATCGAA-CGAATGGCATCTTCAAAGG
17849 AT----CGAATGGCATCTTCAAAGG
1 ATCGAACGAATGGCATCTTCAAAGG
17870 ATCGAA
1 ATCGAA
17876 TGGCATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
21 21 0.91
26 2 0.09
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (25 bp):
ATCGAACGAATGGCATCTTCAAAGG
Found at i:17854 original size:21 final size:21
Alignment explanation
Indices: 17830--17884 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
17820 GTCATCGAAC
17830 CGAATGGCATCTTCAAAGGAT
1 CGAATGGCATCTTCAAAGGAT
17851 CGAATGGCATCTTCAAAGGAT
1 CGAATGGCATCTTCAAAGGAT
17872 CGAATGGCATCTT
1 CGAATGGCATCTT
17885 AATGGCATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (21 bp):
CGAATGGCATCTTCAAAGGAT
Found at i:18033 original size:30 final size:30
Alignment explanation
Indices: 17993--18051 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17983 TGTCTTCAAG
17993 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
18023 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
18052 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:18472 original size:33 final size:33
Alignment explanation
Indices: 18430--18571 Score: 239
Period size: 33 Copynumber: 4.3 Consensus size: 33
18420 TTCTTTTCAC
* **
18430 CCAAAACAGAATTATTTTCAATATTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
18463 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
18496 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
18529 CCAAAACAGAATTATTTGCAATGTTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
18562 CGAAAACAGA
1 CCAAAACAGA
18572 TTTGTTTTCA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 104 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:18599 original size:66 final size:66
Alignment explanation
Indices: 18430--18604 Score: 208
Period size: 66 Copynumber: 2.7 Consensus size: 66
18420 TTCTTTTCAC
* ** *
18430 CCAAAACAGAATTATTTTCAATATTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
18495 A
66 A
* * * *
18496 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGTTATGATCA
1 CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
18561 A
66 A
* * * * * *
18562 CGAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACAGA
1 CCAAAACAGAATTATTTGCAAT-ACAATGAGCAACCAAAACAGA
18605 TTTAGTATCA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 2 0.02
66 93 0.98
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
A
Found at i:18634 original size:33 final size:33
Alignment explanation
Indices: 18597--18701 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
18587 ATTAGCATCC
* *
18597 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTGTCATCGCAAACAACACTT
* * *
18630 AAAACAAATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTGTCATCGCAAACAACACTT
** *
18663 AAATTAGGTTTAGTGTCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTGTCATCGCAAACAACACT-T
18696 AAAACA
1 AAAACA
18702 CTCTCTTCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCGCAAACAACACTT
Found at i:20089 original size:5 final size:5
Alignment explanation
Indices: 20079--20109 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
20069 TTCTGGTCGA
20079 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
20110 ATTTTTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:20216 original size:8 final size:8
Alignment explanation
Indices: 20188--20221 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
20178 GAATCGGCTA
20188 TGAATTTT
1 TGAATTTT
*
20196 TGAAGTTTC
1 TGAA-TTTT
20205 TGAATTTT
1 TGAATTTT
20213 TGAATTTT
1 TGAATTTT
20221 T
1 T
20222 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:24186 original size:37 final size:37
Alignment explanation
Indices: 24136--24209 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
24126 AAATATTGCA
24136 ATTGATACTTGAAACAAAGTTAAGTATAAAATTCATC
1 ATTGATACTTGAAACAAAGTTAAGTATAAAATTCATC
24173 ATTGATACTTGAAACAAAGTTAAGTATAAAATTCATC
1 ATTGATACTTGAAACAAAGTTAAGTATAAAATTCATC
24210 CAAATATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (37 bp):
ATTGATACTTGAAACAAAGTTAAGTATAAAATTCATC
Found at i:25122 original size:133 final size:134
Alignment explanation
Indices: 24972--25239 Score: 529
Period size: 134 Copynumber: 2.0 Consensus size: 134
24962 GATTAATAGC
24972 AAAAAATGAATACCCACAAACAAAAATAAAAACTACAATTGATTAGTCTAAAGAG-AAAAAAAAA
1 AAAAAATGAATACCCACAAACAAAAATAAAAACTACAATTGATTAGTCTAAAGAGAAAAAAAAAA
25036 GCCATTTAAGAGCCTCACCATAGAATTTACCATTAAAGATTGTAGCCTCACCATCGCTGCTTTTA
66 GCCATTTAAGAGCCTCACCATAGAATTTACCATTAAAGATTGTAGCCTCACCATCGCTGCTTTTA
25101 AAAT
131 AAAT
25105 AAAAAATGAATACCCACAAACAAAAATAAAAACTACAATTGATTAGTCTAAAGAGAAAAAAAAAA
1 AAAAAATGAATACCCACAAACAAAAATAAAAACTACAATTGATTAGTCTAAAGAGAAAAAAAAAA
25170 GCCATTTAAGAGCCTCACCATAGAATTTACCATTAAAGATTGTAGCCTCACCATCGCTGCTTTTA
66 GCCATTTAAGAGCCTCACCATAGAATTTACCATTAAAGATTGTAGCCTCACCATCGCTGCTTTTA
25235 AAAT
131 AAAT
25239 A
1 A
25240 TGAACAAAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 55 0.41
134 79 0.59
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (134 bp):
AAAAAATGAATACCCACAAACAAAAATAAAAACTACAATTGATTAGTCTAAAGAGAAAAAAAAAA
GCCATTTAAGAGCCTCACCATAGAATTTACCATTAAAGATTGTAGCCTCACCATCGCTGCTTTTA
AAAT
Found at i:25874 original size:21 final size:21
Alignment explanation
Indices: 25831--25870 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25821 TCCTTTCTGC
25831 AACAAAGAAAGTAATAGAACA
1 AACAAAGAAAGTAATAGAACA
25852 AACAAA-AAA-TAATGAGAAC
1 AACAAAGAAAGTAAT-AGAAC
25871 CAAAAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (21 bp):
AACAAAGAAAGTAATAGAACA
Found at i:30596 original size:16 final size:16
Alignment explanation
Indices: 30572--30604 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30562 GACATCCAAA
30572 CCAGCAGCTCACTTGT
1 CCAGCAGCTCACTTGT
*
30588 CCAGTAGCTCACTTGT
1 CCAGCAGCTCACTTGT
30604 C
1 C
30605 GTCGTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.27
Consensus pattern (16 bp):
CCAGCAGCTCACTTGT
Found at i:30625 original size:12 final size:12
Alignment explanation
Indices: 30608--30634 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30598 ACTTGTCGTC
30608 GTCTTCCATCGA
1 GTCTTCCATCGA
30620 GTCTTCCATCGA
1 GTCTTCCATCGA
30632 GTC
1 GTC
30635 CTAGCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.33, G:0.19, T:0.33
Consensus pattern (12 bp):
GTCTTCCATCGA
Found at i:38543 original size:49 final size:49
Alignment explanation
Indices: 37777--38532 Score: 932
Period size: 49 Copynumber: 15.5 Consensus size: 49
37767 ACTTGCCTTT
* ** * *
37777 CGTCTGGAAAGGGCATTTTGGGAAA-AGCAGGT-AAAATAAGTGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* ** * *
37824 CGTTTGGGAAGGGCGCTTTGGGAAATAGCAAGCGAAGATAAACGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * *
37873 CGTCCGGGAAGGGCTCTTTGGGAAATAGCAAGTAAAAACAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* **
37922 TGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGCGAAAATAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * *
37971 CATCTGGGAAGGGCGCTTTGGGAAATAGCAAAT-AAAATAAGTGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* *
38019 CGTTTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAGTGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * * *
38068 TGTTTGGGAAGGGTGCTTTGGGAAATAGCAAGT-AAAATAAGTGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * * * * *
38116 CGTCT-GGAATGGTGTTTTGGGAGATAGCACGTAAAAATGAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* *
38164 CGTCTAGGAAGGGCGCTTTAGGAAATAGCAAGTAAAAAATAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT-AAAAATAAATGGCTTC
* ** * *
38214 CGTCTAGGAAGGGCATTTTGGGGAGATAGCAAGCAAAAATAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTT-GGGAAATAGCAAGTAAAAATAAATGGCTTC
* * * * **
38264 CGTCTGGGAAGGGTGTTTTGGGGAGATAACAAGCGAAAATAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTT-GGGAAATAGCAAGTAAAAATAAATGGCTTC
38314 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT-AAAATAAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * * *
38362 CGTGTGGGTAGGGCGCTTTGGGAAATAGCAAGT-AAAATAAGTGGCTTT
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * * *
38410 CGTCTGGGAAGGGCGCTTTGGGAGATAGCAAGCAAAGATGAATGGCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
* * *
38459 CGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATGAATGCCTTC
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
*
38508 CGTCTGGGAAGGGCGTTTTGGGAAA
1 CGTCTGGGAAGGGCGCTTTGGGAAA
38533 AAGTAGGTAA
Statistics
Matches: 621, Mismatches: 80, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
47 44 0.07
48 173 0.28
49 283 0.46
50 110 0.18
51 11 0.02
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (49 bp):
CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTTC
Found at i:38543 original size:146 final size:145
Alignment explanation
Indices: 37777--38543 Score: 948
Period size: 146 Copynumber: 5.2 Consensus size: 145
37767 ACTTGCCTTT
* ** *
37777 CGTCTGGAAAGGGCATTTTGGGAAA-AGCAGGTAAAATAAGTGGCTTCCGTTTGGGAAGGGCGCT
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAGGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGCT
* * * * *
37841 TTGGGAAATAGCAAGCGAAGATAAACGGCTTCCGTCCGGGAAGGGCTCTTTGGGAAATAGCAAGT
66 TTGGGAGATAGCAAGC-AAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT
*
37906 AAAAACAAATGGCTTC
130 AAAAATAAATGGCTTC
* * *
37922 TGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGCG-AAAATAAATGGCTTCCATCTGGGAAGGGCG
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGC-AG-GTAAAATAAGTGGCTTCCGTCTGGGAAGGGCG
* ** * *
37986 CTTTGGGAAATAGCAAATAAAATAAGTGGCTTCCGTTTGGGAAGGGCGCTTTGGGAAATAGCAAG
64 CTTTGGGAGATAGCAAGCAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAG
*
38051 TAAAAATAAGTGGCTTC
129 TAAAAATAAATGGCTTC
* * * * * * *
38068 TGTTTGGGAAGGGTGCTTTGGGAAATAGCAAGTAAAATAAGTGGCTTCCGTCT-GGAATGGTGTT
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAGGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGCT
* * * * *
38132 TTGGGAGATAGCACGTAAAAATGAATGGCTTCCGTCTAGGAAGGGCGCTTTAGGAAATAGCAAGT
66 TTGGGAGATAGCAAG-CAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT
38197 AAAAAATAAATGGCTTC
130 -AAAAATAAATGGCTTC
* ** * ** * *
38214 CGTCTAGGAAGGGCATTTTGGGGAGATAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGTG
1 CGTCTGGGAAGGGCGCTTT-GGGAAATAGC-AGGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCG
* *
38279 TTTTGGGGAGATAACAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCA
64 CTTT-GGGAGATAGCAAGC-AAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCA
38344 AGT-AAAATAAATGGCTTC
127 AGTAAAAATAAATGGCTTC
* * * *
38362 CGTGTGGGTAGGGCGCTTTGGGAAATAGCAAGTAAAATAAGTGGCTTTCGTCTGGGAAGGGCGCT
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAGGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGCT
* *
38427 TTGGGAGATAGCAAGCAAAGATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGT
66 TTGGGAGATAGCAAGCAAA-ATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT
* *
38492 AAAAATGAATGCCTTC
130 AAAAATAAATGGCTTC
* * *
38508 CGTCTGGGAAGGGCGTTTTGGGAAAAAGTAGGTAAA
1 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAGGTAAA
38544 GACTGAAAAT
Statistics
Matches: 532, Mismatches: 77, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
144 24 0.05
145 139 0.26
146 188 0.35
147 63 0.12
148 50 0.09
149 12 0.02
150 56 0.11
ACGTcount: A:0.31, C:0.13, G:0.32, T:0.24
Consensus pattern (145 bp):
CGTCTGGGAAGGGCGCTTTGGGAAATAGCAGGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGCT
TTGGGAGATAGCAAGCAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTA
AAAATAAATGGCTTC
Found at i:39528 original size:17 final size:16
Alignment explanation
Indices: 39502--39535 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
39492 CCCAAGCCGT
39502 ACTTCTCTTCTTCCTC
1 ACTTCTCTTCTTCCTC
39518 ACTTCCTCTTCTTCCTC
1 ACTT-CTCTTCTTCCTC
39535 A
1 A
39536 ATCCACGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (16 bp):
ACTTCTCTTCTTCCTC
Found at i:42946 original size:22 final size:21
Alignment explanation
Indices: 42904--42946 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42894 AAATTACCTT
*
42904 TTAATGGACACATGAATCAAA
1 TTAATGGACAAATGAATCAAA
42925 TTAATCGGACAAATAGAA-CAAA
1 TTAAT-GGACAAAT-GAATCAAA
42947 GAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 11 0.58
23 3 0.16
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (21 bp):
TTAATGGACAAATGAATCAAA
Found at i:45601 original size:60 final size:60
Alignment explanation
Indices: 45483--45607 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
45473 TTATTGAGAA
* * * ** *
45483 ATTTTCACAAATGTTATGACCCTATTTGACCAAATTAAAAGCATGGGCTCTTATTTAAGC
1 ATTTTCACAAACGTTAGGACCCTATTTGACCAAATTAAAAGCATAGGCTCAAAATTAAGC
* *
45543 ATTTTCACATACGTTAGGCCCCTATTTGACCAAATTAAAAGCATAAGGC-CAAAATTAAGC
1 ATTTTCACAAACGTTAGGACCCTATTTGACCAAATTAAAAGCAT-AGGCTCAAAATTAAGC
45603 ATTTT
1 ATTTT
45608 TGCACATGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 53 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (60 bp):
ATTTTCACAAACGTTAGGACCCTATTTGACCAAATTAAAAGCATAGGCTCAAAATTAAGC
Found at i:45908 original size:46 final size:47
Alignment explanation
Indices: 45814--45914 Score: 177
Period size: 47 Copynumber: 2.2 Consensus size: 47
45804 TGTGTAATCC
*
45814 ATTTCAATATCATGTTCATGAGTAGCAAAAAAAAAGTGTATGTATGT
1 ATTTCAATATAATGTTCATGAGTAGCAAAAAAAAAGTGTATGTATGT
45861 ATTTCAATATAATGTTCATGAGTAGCAAAAAAAAA-TGTATGTATGT
1 ATTTCAATATAATGTTCATGAGTAGCAAAAAAAAAGTGTATGTATGT
*
45907 ATTACAAT
1 ATTTCAAT
45915 TACGCTCCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
46 18 0.35
47 34 0.65
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (47 bp):
ATTTCAATATAATGTTCATGAGTAGCAAAAAAAAAGTGTATGTATGT
Found at i:48475 original size:215 final size:215
Alignment explanation
Indices: 48104--48536 Score: 796
Period size: 215 Copynumber: 2.0 Consensus size: 215
48094 CATTAGATAA
* *
48104 ATAATCCAATAAAAGTATTAGTTTATGGAGAATGGGCCCCACAGAATAGTAACTTTTTCACAAAG
1 ATAATCCAATAAAAGTATTAGTTTATGGAGAATGGACCCCACAAAATAGTAACTTTTTCACAAAG
48169 TTCCCAAAATACCCTCAAGCATCAATCCAGATAACAAAAAACCAAGCATGAAAGTACCAAAATAC
66 TTCCCAAAATACCCTCAAGCATCAATCCAGATAACAAAAAACCAAGCATGAAAGTACCAAAATAC
48234 CCCTCCCCATTTATTCTTCAAGTCATGAGAAGAGTTGGTTGGGTTGGTTTTTTCGTACTTTCATA
131 CCCTCCCCATTTATTCTTCAAGTCATGAGAAGAGTTGGTTGGGTTGGTTTTTTCGTACTTTCATA
*
48299 TCCTCTTTTTATTGTTTTTT
196 TCCTCTTTTTATTGTTTTGT
48319 ATAATCCAATAAAAGTATTAGTTTATGGAGAATGGACCCCACAAAATAGTAACTTTTTCACAAAG
1 ATAATCCAATAAAAGTATTAGTTTATGGAGAATGGACCCCACAAAATAGTAACTTTTTCACAAAG
* *
48384 TTCCCAAAATACCCTCAAGCATCAATCCAGATAACAAAAAAATCGAGCATGAAAGTA-CAAAATA
66 TTCCCAAAATACCCTCAAGCATCAATCCAGATAAC-AAAAAACCAAGCATGAAAGTACCAAAATA
*
48448 CCCCTCCCCATTTATTCTTCAAGTCATGAGAAGAGTTGGTTGGGTTGGTTTTTTGGTACTTTCAT
130 CCCCTCCCCATTTATTCTTCAAGTCATGAGAAGAGTTGGTTGGGTTGGTTTTTTCGTACTTTCAT
48513 ATCCTCTTTTTATTGTTTTGT
195 ATCCTCTTTTTATTGTTTTGT
48534 ATA
1 ATA
48537 TATATCCTCT
Statistics
Matches: 211, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
215 192 0.91
216 19 0.09
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (215 bp):
ATAATCCAATAAAAGTATTAGTTTATGGAGAATGGACCCCACAAAATAGTAACTTTTTCACAAAG
TTCCCAAAATACCCTCAAGCATCAATCCAGATAACAAAAAACCAAGCATGAAAGTACCAAAATAC
CCCTCCCCATTTATTCTTCAAGTCATGAGAAGAGTTGGTTGGGTTGGTTTTTTCGTACTTTCATA
TCCTCTTTTTATTGTTTTGT
Found at i:48542 original size:27 final size:27
Alignment explanation
Indices: 48511--48568 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
48501 TGGTACTTTC
48511 ATATCCTCTTTTTATTGTTTTGTATAT
1 ATATCCTCTTTTTATTGTTTTGTATAT
*
48538 ATATCCTCTTTTTATTGTTTTGTGTAT
1 ATATCCTCTTTTTATTGTTTTGTATAT
48565 ATAT
1 ATAT
48569 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.10, G:0.09, T:0.62
Consensus pattern (27 bp):
ATATCCTCTTTTTATTGTTTTGTATAT
Found at i:49804 original size:2 final size:2
Alignment explanation
Indices: 49797--49826 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49787 CTCTTAATTC
49797 AT AT AT AT AT AT 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
49827 GTAGAAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52286 original size:22 final size:22
Alignment explanation
Indices: 52258--52304 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
52248 ATTTATTCAT
52258 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
52280 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
52302 TAT
1 TAT
52305 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:52300 original size:11 final size:11
Alignment explanation
Indices: 52258--52300 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
52248 ATTTATTCAT
*
52258 TATTAATTAAC
1 TATTAATTAGC
*
52269 TATTAATTAGA
1 TATTAATTAGC
52280 TATTAATTAGC
1 TATTAATTAGC
52291 TATTAATTAG
1 TATTAATTAG
52301 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:53686 original size:2 final size:2
Alignment explanation
Indices: 53681--53711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53671 TAATAGTGTG
53681 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
53712 TACTATTGTT
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:53756 original size:13 final size:13
Alignment explanation
Indices: 53740--53766 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53730 AATAATAATC
53740 AAAAAATCATCAA
1 AAAAAATCATCAA
53753 AAAAAATCATCAA
1 AAAAAATCATCAA
53766 A
1 A
53767 TCAGAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATCATCAA
Found at i:53802 original size:21 final size:21
Alignment explanation
Indices: 53778--53838 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
53768 CAGAAAAGTG
53778 AAAAGAAAAAGAAA-AAAAAAC
1 AAAAG-AAAAGAAATAAAAAAC
53799 AAAAGAAAAGAAATAAAAAAC
1 AAAAGAAAAGAAATAAAAAAC
* **
53820 -TAATCAAAGAAATAAAAAA
1 AAAAGAAAAGAAATAAAAAA
53839 GGAAGAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.67
21 12 0.33
ACGTcount: A:0.80, C:0.05, G:0.08, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAGAAATAAAAAAC
Found at i:53848 original size:20 final size:20
Alignment explanation
Indices: 53784--53848 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
53774 AGTGAAAAGA
*
53784 AAAAGAAA-AAAAAACAAAAG
1 AAAAGAAATAAAAAAC-GAAG
* *
53804 AAAAGAAATAAAAAACTAAT
1 AAAAGAAATAAAAAACGAAG
* *
53824 CAAAGAAATAAAAAAGGAAG
1 AAAAGAAATAAAAAACGAAG
53844 AAAAG
1 AAAAG
53849 TCAAATCAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 30 0.81
21 7 0.19
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.06
Consensus pattern (20 bp):
AAAAGAAATAAAAAACGAAG
Done.