Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007349.1 Hibiscus syriacus cultivar Beakdansim tig00019691_pilon, 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: 75873
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:446 original size:4 final size:4
Alignment explanation
Indices: 439--508 Score: 95
Period size: 4 Copynumber: 17.0 Consensus size: 4
429 TGGAAGTAAG
* * *
439 TACA TACA TACA TATA TGCCTA TACA TAAA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA T-AC-A TACA TACA TACA TACA TACA TACA TACA
489 TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA
509 CATGATTGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 55 0.95
5 1 0.02
6 2 0.03
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1232 original size:28 final size:31
Alignment explanation
Indices: 1200--1258 Score: 97
Period size: 28 Copynumber: 2.0 Consensus size: 31
1190 AAATTAAGAC
1200 GTTTTAAGATGTA-T-AAAAGAT-ACCGGAA
1 GTTTTAAGATGTATTAAAAAGATAACCGGAA
1228 GTTTTAAGATGTATTAAAAAGATAACCGGAA
1 GTTTTAAGATGTATTAAAAAGATAACCGGAA
1259 AACGATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.46
29 1 0.04
30 7 0.25
31 7 0.25
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (31 bp):
GTTTTAAGATGTATTAAAAAGATAACCGGAA
Found at i:21977 original size:2 final size:2
Alignment explanation
Indices: 21970--21997 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21960 TTTATTTGGT
21970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21998 ATCGTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22146 original size:34 final size:34
Alignment explanation
Indices: 22108--22172 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
22098 TTTTATTTCG
*
22108 TGTAGAAAAGGAAAGAAATAGAATATATATAAAT
1 TGTAGAAAAAGAAAGAAATAGAATATATATAAAT
*
22142 TGTAGAAAAAGAAATAAATAGAATATATATA
1 TGTAGAAAAAGAAAGAAATAGAATATATATA
22173 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (34 bp):
TGTAGAAAAAGAAAGAAATAGAATATATATAAAT
Found at i:25641 original size:24 final size:24
Alignment explanation
Indices: 25609--25660 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25599 TCAAAATAAT
* * * *
25609 TTTATATTCGTTTGTTTGTGTTTA
1 TTTACATTCGTTCGTTTGTATTCA
25633 TTTACATTCGTTCGTTTGTATTCA
1 TTTACATTCGTTCGTTTGTATTCA
25657 TTTA
1 TTTA
25661 TCATAACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTACATTCGTTCGTTTGTATTCA
Found at i:29437 original size:38 final size:39
Alignment explanation
Indices: 29397--29471 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
29387 TAACATTAAT
*
29397 TTTTTAACG-GA-GTGCTAAAATAAAACT-AAAACTAAAA
1 TTTTTAACGAGAGGTACTAAAATAAAA-TAAAAACTAAAA
*
29434 TTTTTAACGATAGGTACTAAAATAAAATAAAAACTAAA
1 TTTTTAACGAGAGGTACTAAAATAAAATAAAAACTAAA
29472 CTTTAGGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 9 0.27
38 2 0.06
39 22 0.67
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (39 bp):
TTTTTAACGAGAGGTACTAAAATAAAATAAAAACTAAAA
Found at i:30015 original size:93 final size:93
Alignment explanation
Indices: 29856--30048 Score: 350
Period size: 93 Copynumber: 2.1 Consensus size: 93
29846 AGTAAAAGTT
*
29856 TAAAACAGATCAAAACGGATAGTTTAGGTACCAAATGCATAATTTACCCTATAATTAAACAATCA
1 TAAAACGGATCAAAACGGATAGTTTAGGTACCAAATGCATAATTTACCCTATAATTAAACAATCA
29921 AAACTTAGAAGTCATGGCTCTTCTCACA
66 AAACTTAGAAGTCATGGCTCTTCTCACA
* *
29949 TAAAACGGATCAAAACGGGTAGTTTAGGTATCAAATGCATAATTTACCCTATAATTAAACAATCA
1 TAAAACGGATCAAAACGGATAGTTTAGGTACCAAATGCATAATTTACCCTATAATTAAACAATCA
30014 AAACTTAGAAGTCATGGCTCTTCTCACA
66 AAACTTAGAAGTCATGGCTCTTCTCACA
*
30042 TATAACG
1 TAAAACG
30049 TGTACGGTAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (93 bp):
TAAAACGGATCAAAACGGATAGTTTAGGTACCAAATGCATAATTTACCCTATAATTAAACAATCA
AAACTTAGAAGTCATGGCTCTTCTCACA
Found at i:36060 original size:5 final size:5
Alignment explanation
Indices: 36050--36143 Score: 107
Period size: 5 Copynumber: 18.8 Consensus size: 5
36040 TTCGGATATC
* * * * * * *
36050 AACAT AACAT AACAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT AGCAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
* *
36100 AGCAT AGCAT AACAT AACAT AACAT AACAT AACAT AACAT AACA
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACA
36144 GACAAACATA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 87 1.00
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.19
Consensus pattern (5 bp):
AACAT
Found at i:43933 original size:65 final size:64
Alignment explanation
Indices: 43851--44041 Score: 167
Period size: 67 Copynumber: 2.9 Consensus size: 64
43841 TTTGTTTCAA
* * * *
43851 TTTGATCCTTTAAATTTTTATTTATTTATTTTATTTCTTTTAAAATTTAACACTTTTTTCATTTT
1 TTTGAT-CTTTTAATTTTTATTTATTTATTTTATTTATTTTATAATTTAACACTTTTTTC-TTCT
43916 C
64 C
* * *
43917 ATTT-CTCTTTTAATTTTTTTACTTTA-TTATTTT-TTTATTTTCTTAATTTAACCCTTTTTTTC
1 -TTTGATCTTTTAA--TTTTTA-TTTATTTATTTTATTTATTTT-ATAATTTAACAC-TTTTTTC
43979 TTCTC
60 TTCTC
* * *
43984 TTTGAT-TTACTTAATATTTATTTATTTA-TTTATTTATTTTATAATCTAACATTTTTTT
1 TTTGATCTT--TTAATTTTTATTTATTTATTTTATTTATTTTATAATTTAACACTTTTTT
44042 GACTTTTTAG
Statistics
Matches: 101, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
64 6 0.06
65 21 0.21
66 29 0.29
67 30 0.30
68 15 0.15
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (64 bp):
TTTGATCTTTTAATTTTTATTTATTTATTTTATTTATTTTATAATTTAACACTTTTTTCTTCTC
Found at i:44007 original size:4 final size:4
Alignment explanation
Indices: 43998--44022 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
43988 ATTTACTTAA
43998 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
44023 TATAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:44456 original size:52 final size:51
Alignment explanation
Indices: 44387--44499 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
44377 AGGATTATAT
*
44387 TTATTATTTTATTAGGAATTAAGATAGAGTTAAAAACATTACCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGATAGA-ATAAAAACATTACCTTTAGTTTA
* * * * * *
44439 TTATTGTTTTATTAGGAATTATGATAGAATCACAATATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGATAGAATAAAAACATTACCTTTAGTTTA
44490 TTATTATTTT
1 TTATTATTTT
44500 TTGTTCAGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 27 0.51
52 26 0.49
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (51 bp):
TTATTATTTTATTAGGAATTAAGATAGAATAAAAACATTACCTTTAGTTTA
Found at i:47706 original size:17 final size:17
Alignment explanation
Indices: 47663--47714 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
47653 TATACAGTAG
*
47663 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
47680 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
47695 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
47712 AAA
1 AAA
47715 TTTGTCTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:48367 original size:19 final size:20
Alignment explanation
Indices: 48343--48393 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
48333 AATGACCAAT
48343 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
48362 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
48382 AAAATCGCAACG
1 AAAATCGCAACG
48394 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:48387 original size:20 final size:20
Alignment explanation
Indices: 48343--48660 Score: 188
Period size: 20 Copynumber: 15.6 Consensus size: 20
48333 AATGACCAAT
* *
48343 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
48362 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
48382 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
** ***
48402 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
* **
48422 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
48443 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
48466 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
48486 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
48506 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
48526 AGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
48549 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
48569 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
48589 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
48609 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
48629 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
48649 AAAATCGCAACG
1 AAAATCGCAACG
48661 TTAAAAAGAA
Statistics
Matches: 246, Mismatches: 45, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
19 17 0.07
20 187 0.76
21 13 0.05
23 29 0.12
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:48521 original size:40 final size:40
Alignment explanation
Indices: 48468--48658 Score: 238
Period size: 40 Copynumber: 4.7 Consensus size: 40
48458 TTTAGAAGAA
* * *
48468 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
48508 AATCGCAATGCGATTGAGAGATTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* *
48551 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
48591 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
48631 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
48659 CGTTAAAAAG
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 94 0.72
41 3 0.02
42 1 0.01
43 32 0.25
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:48556 original size:83 final size:83
Alignment explanation
Indices: 48446--48658 Score: 288
Period size: 83 Copynumber: 2.6 Consensus size: 83
48436 AGCTTCCAAG
* * * *
48446 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
48511 CGCAATGCGATTGAGAGA
66 CGCAATGCGATTGAGAGA
*
48529 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
* *
48594 CGCAATGCGATTTATAGA
66 CGCAATGCGATTGAGAGA
* * * * * *
48612 ATCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAA
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAA
48659 CGTTAAAAAG
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 27 0.23
81 1 0.01
82 2 0.02
83 86 0.74
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAAT
CGCAATGCGATTGAGAGA
Found at i:48759 original size:6 final size:6
Alignment explanation
Indices: 48748--48993 Score: 440
Period size: 6 Copynumber: 40.5 Consensus size: 6
48738 GACACGTATT
48748 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
48796 ACCACG AACACG TATTACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ----ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48848 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48896 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48944 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48991 ACC
1 ACC
48994 CGAGACGAGA
Statistics
Matches: 234, Mismatches: 2, Indels: 9
0.96 0.01 0.04
Matches are distributed among these distances:
5 5 0.02
6 224 0.96
10 5 0.02
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:49700 original size:6 final size:6
Alignment explanation
Indices: 49684--49757 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
49674 TCTCGTCTCG
49684 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
49731 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
49758 AAATCGTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:49856 original size:20 final size:20
Alignment explanation
Indices: 49790--50029 Score: 255
Period size: 20 Copynumber: 11.4 Consensus size: 20
49780 TTATTTTCAA
49790 CGTTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTC-TC--AATCG
49813 CGTTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTC-TC--AATCG
*
49836 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
*
49856 CGTTGCGATTCTCTTAATCG
1 CGTTGCGATTCTCTCAATCG
*
49876 CGTTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
49896 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
*
49916 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTC-TC--AATCG
*
49939 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
49959 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
49979 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
49999 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTCAATCG
50022 CGTTGCGA
1 CGTTGCGA
50030 ACTTGGAAGC
Statistics
Matches: 196, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
20 122 0.62
21 2 0.01
22 7 0.04
23 65 0.33
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTCAATCG
Found at i:49938 original size:63 final size:63
Alignment explanation
Indices: 49792--49990 Score: 287
Period size: 63 Copynumber: 3.2 Consensus size: 63
49782 ATTTTCAACG
* * * *
49792 TTGCGATTCTCTTCTAAATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGC
1 TTGCGATTCTCTTCTAAATCGCGTTGCGATTCT-ATC--AATCGCATTGCGATTCTATCAATCGC
*
49857 G
63 A
49858 TTGCGATTCTC-T-T-AATCGCGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTTCTAAATCGCGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
* *
49918 TTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTTCTAAATCGCGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
49981 TTGCGATTCT
1 TTGCGATTCT
49991 ATCAATCGCA
Statistics
Matches: 123, Mismatches: 7, Indels: 9
0.88 0.05 0.06
Matches are distributed among these distances:
60 34 0.28
61 1 0.01
62 3 0.02
63 72 0.59
64 1 0.01
65 1 0.01
66 11 0.09
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (63 bp):
TTGCGATTCTCTTCTAAATCGCGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
Found at i:49938 original size:83 final size:83
Alignment explanation
Indices: 49790--50030 Score: 326
Period size: 83 Copynumber: 2.9 Consensus size: 83
49780 TTATTTTCAA
* * * * *
49790 CGTTGCGATTCTCTTCTAAATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTC-TC--A
1 CGTTGCGATTCT-ATC--AATCGCATTGCGATTCT-ATC--AATCGCATTGCGATTCTCTTCTAA
* *
49852 ATCGCGTTGCGATTCTCTTAATCG
60 ATCGCGTTGCGAATCTCTCAATCG
49876 CGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCG
1 CGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCG
49941 TTGCGAATCTCTCAATCG
66 TTGCGAATCTCTCAATCG
* *
49959 CATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 CGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCG
50024 TTGCGAA
66 TTGCGAA
50031 CTTGGAAGCT
Statistics
Matches: 143, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
80 16 0.11
81 2 0.01
82 2 0.01
83 109 0.76
85 2 0.01
86 12 0.08
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (83 bp):
CGTTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCG
TTGCGAATCTCTCAATCG
Found at i:49956 original size:103 final size:103
Alignment explanation
Indices: 49808--50008 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 103
49798 TTCTCTTCTA
* * * *
49808 AATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCGTTGCGATTCTCTTAA
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
*
49873 TCGCGTTGCGATTCTATCAATCGCATTGCGATTCTATC
66 TCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
49911 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
49976 TCGCATTGCGATTCTATCAATCGCATTGCGATT
66 TCGCATTGCGATTCTATCAATCGCATTGCGATT
50009 TTCTTCTAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (103 bp):
AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
TCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
Found at i:50068 original size:20 final size:19
Alignment explanation
Indices: 50043--50096 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
50033 TGGAAGCTCG
50043 CGTTGCGATTTTCTTTTGA
1 CGTTGCGATTTTCTTTTGA
*
50062 CCGTTGCGATTTTCTTTTTTA
1 -CGTTGCGATTTTC-TTTTGA
50083 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
50097 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 26 0.81
21 5 0.16
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.54
Consensus pattern (19 bp):
CGTTGCGATTTTCTTTTGA
Found at i:55700 original size:77 final size:78
Alignment explanation
Indices: 55566--55710 Score: 213
Period size: 77 Copynumber: 1.9 Consensus size: 78
55556 CTTCGAATAG
* *
55566 TCGAAGGACTCAACAAAGTATCACACCTTATAGTCAAGCGGCCGTTTATATACTTTACCCTGATA
1 TCGAAGGACTCAAAAAAGTAT-ACACCTTATAGTCAAGCGGCCGTTTATATACTTTACCCTAATA
55631 TAAATTATTTTTTT
65 TAAATTATTTTTTT
* * *
55645 TCGAGGGACTCAAAAAAGTAT-TACCTTATAGTCGAG-GGACCGTTTATATACTTTACCCTAATA
1 TCGAAGGACTCAAAAAAGTATACACCTTATAGTCAAGCGG-CCGTTTATATACTTTACCCTAATA
55708 TAA
65 TAA
55711 CTTAAGATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
76 2 0.03
77 39 0.65
79 19 0.32
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (78 bp):
TCGAAGGACTCAAAAAAGTATACACCTTATAGTCAAGCGGCCGTTTATATACTTTACCCTAATAT
AAATTATTTTTTT
Found at i:58982 original size:13 final size:13
Alignment explanation
Indices: 58960--59022 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
58950 TAGTACTTAC
*
58960 TATAACAAATAAT
1 TATAATAAATAAT
58973 TATAATAAATAACT
1 TATAATAAATAA-T
*
58987 GTCA-AAAAAATAAT
1 -T-ATAATAAATAAT
*
59001 TATAATAAATAAAA
1 TATAATAAAT-AAT
59015 TATAATAA
1 TATAATAA
59023 TACCCTAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.02
13 18 0.44
14 12 0.29
15 9 0.22
16 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (13 bp):
TATAATAAATAAT
Found at i:59055 original size:21 final size:21
Alignment explanation
Indices: 59031--59070 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
59021 AATACCCTAG
*
59031 ATCATAAACTCTAAGCCTTAA
1 ATCATAAACTCTAAACCTTAA
59052 ATCATAAACTCTAAACCTT
1 ATCATAAACTCTAAACCTT
59071 GAACCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (21 bp):
ATCATAAACTCTAAACCTTAA
Found at i:59520 original size:2 final size:2
Alignment explanation
Indices: 59507--59537 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
59497 TGACTCAAAA
*
59507 AT AT AT AC 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 A
59538 GATAAAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:60718 original size:16 final size:16
Alignment explanation
Indices: 60693--60736 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
60683 AAACAGTTTT
60693 AAATAGTTAAATGATA
1 AAATAGTTAAATGATA
*
60709 AAATATTTAAATGATA
1 AAATAGTTAAATGATA
60725 AAATAGTTAAAT
1 AAATAGTTAAAT
60737 AGAGGATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AAATAGTTAAATGATA
Found at i:61911 original size:27 final size:27
Alignment explanation
Indices: 61856--61911 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
61846 GGACACTTGT
* *
61856 TTGAGAAAAACTGTATAGTTTGGACAC
1 TTGAGAAAAACTGTATAATTTAGACAC
** *
61883 TTGAGAAAAGTTGTATAATTTAGATAC
1 TTGAGAAAAACTGTATAATTTAGACAC
61910 TT
1 TT
61912 ATTATATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (27 bp):
TTGAGAAAAACTGTATAATTTAGACAC
Found at i:65651 original size:60 final size:60
Alignment explanation
Indices: 65557--65717 Score: 173
Period size: 60 Copynumber: 2.7 Consensus size: 60
65547 GATGAATTTG
* ** **
65557 GGGATAAAGTTAGAATATTCAAAAGTTTGGGGACTAATTTAGAAAT-A-GGGTCATAGTTTA
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAG-AATGAGGGGT-ATAGTTTA
* * *
65617 GGGATAAAATTAGAATGCACAAAAGTTTAAGGACTAGTTTAGAATGAGGGGTATAGTTTG
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAGAATGAGGGGTATAGTTTA
** * * *
65677 GGGATAAAATTAGAATATGCAGAAGTTAAAGGACCAATTTA
1 GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTA
65718 ATATGACAGT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
59 3 0.04
60 77 0.92
61 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (60 bp):
GGGATAAAATTAGAATACACAAAAGTTTAAGGACTAATTTAGAATGAGGGGTATAGTTTA
Found at i:67702 original size:2 final size:2
Alignment explanation
Indices: 67695--67730 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
67685 CAACCACTAT
67695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67731 ACACTGCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69070 original size:36 final size:36
Alignment explanation
Indices: 69023--69098 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
69013 TGAAAGCATT
*
69023 TTTAATCATTCATAACTAAACTCTATCAATTCAATA
1 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
69059 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
1 TTTAATCATTCATAACTAAACCCTATCAATTCAATA
69095 TTTA
1 TTTA
69099 TTCTTCTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (36 bp):
TTTAATCATTCATAACTAAACCCTATCAATTCAATA
Found at i:73913 original size:12 final size:12
Alignment explanation
Indices: 73896--73961 Score: 105
Period size: 12 Copynumber: 5.5 Consensus size: 12
73886 CAGTTGTTGG
73896 TGCCAATGTCGA
1 TGCCAATGTCGA
*
73908 TGCCAATGTCGG
1 TGCCAATGTCGA
*
73920 TGCAAATGTCGA
1 TGCCAATGTCGA
*
73932 TGCCAATGTCGG
1 TGCCAATGTCGA
73944 TGCCAATGTCGA
1 TGCCAATGTCGA
73956 TGCCAA
1 TGCCAA
73962 AGATGACGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (12 bp):
TGCCAATGTCGA
Found at i:73927 original size:24 final size:24
Alignment explanation
Indices: 73894--73961 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
73884 TGCAGTTGTT
73894 GGTGCCAATGTCGATGCCAATGTC
1 GGTGCCAATGTCGATGCCAATGTC
*
73918 GGTGCAAATGTCGATGCCAATGTC
1 GGTGCCAATGTCGATGCCAATGTC
73942 GGTGCCAATGTCGATGCCAA
1 GGTGCCAATGTCGATGCCAA
73962 AGATGACGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (24 bp):
GGTGCCAATGTCGATGCCAATGTC
Found at i:74998 original size:2 final size:2
Alignment explanation
Indices: 74991--75062 Score: 75
Period size: 2 Copynumber: 39.0 Consensus size: 2
74981 CCTCCCCGAT
*
74991 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
75031 TA T- TA TT TA TA T- TA TT TA TA T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75063 ATTTATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:75072 original size:6 final size:6
Alignment explanation
Indices: 74990--75072 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
74980 CCCTCCCCGA
* * * *
74990 TTATAT ATATAT ATATAT ATATAT ATAATAT TATATAT TTATA- TTAT-T
1 TTATAT TTATAT TTATAT TTATAT -TTATAT T-TATAT TTATAT TTATAT
* *
75038 TATATTAT TTATAT TAATAT ATATAAT TTATAT TT
1 T-TA-TAT TTATAT TTATAT TTAT-AT TTATAT TT
75073 TTTATATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
5 5 0.08
6 38 0.61
7 17 0.27
8 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATAT
Found at i:75076 original size:28 final size:28
Alignment explanation
Indices: 75028--75092 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
75018 TATTATATAT
*
75028 TTATATTATTTATATTATTTATATT-AA
1 TTATATAATTTATATTATTTATATTAAA
*
75055 TATATATAATTTATATTTTTTATATTAAA
1 T-TATATAATTTATATTATTTATATTAAA
75084 TTATATAAT
1 TTATATAAT
75093 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 30 0.88
29 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATATAATTTATATTATTTATATTAAA
Found at i:75087 original size:19 final size:19
Alignment explanation
Indices: 75026--75089 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
75016 AATATTATAT
*
75026 ATTTATATTATTTATATT-
1 ATTTATATTTTTTATATTA
**
75044 ATTTATA-TTAATATATATA
1 ATTTATATTTTTTATAT-TA
75063 ATTTATATTTTTTATATTA
1 ATTTATATTTTTTATATTA
*
75082 AATTATAT
1 ATTTATAT
75090 AATAAAACCC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 6 0.16
18 8 0.22
19 16 0.43
20 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTATATTTTTTATATTA
Found at i:75093 original size:37 final size:36
Alignment explanation
Indices: 75011--75093 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 36
75001 TATATATATA
*
75011 TATATAATATTATATATTTATATTATTTATATTATT
1 TATATAATATTATATATTTATATTATTTATATTAAT
*
75047 TATATTAATA-TATATAATTTATATTTTTTATATTAAAT
1 TATA-TAATATTATAT-ATTTATATTATTTATATT-AAT
75085 TATATAATA
1 TATATAATA
75094 AAACCCTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 9 0.21
37 27 0.64
38 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TATATAATATTATATATTTATATTATTTATATTAAT
Done.