Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004800.1 Hibiscus syriacus cultivar Beakdansim tig00010815_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: 110959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3148 original size:29 final size:31
Alignment explanation
Indices: 3116--3175 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
3106 AAACTTTGAA
3116 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3145 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3176 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:10887 original size:15 final size:15
Alignment explanation
Indices: 10867--10896 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10857 AAAACCGTTT
10867 TTTTTTTAAAACCGA
1 TTTTTTTAAAACCGA
*
10882 TTTTTTTCAAACCGA
1 TTTTTTTAAAACCGA
10897 AACCGGTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (15 bp):
TTTTTTTAAAACCGA
Found at i:18374 original size:29 final size:28
Alignment explanation
Indices: 18291--18374 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
18281 ATATAGAAGG
* *
18291 TTTTTTATTATTTTAATATTTAAAATTTAAT
1 TTTTGTATTATTTT--TATTTAAAA-TTAAA
* *
18322 TTTTGTATTATATTTT-TATGAAATTAAGA
1 TTTTGTATTAT-TTTTATTTAAAATTAA-A
18351 TTTTGTATTATTTTTATTTAAAAT
1 TTTTGTATTATTTTTATTTAAAAT
18375 ATTGTGATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.18
29 22 0.50
30 1 0.02
31 10 0.23
32 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTTGTATTATTTTTATTTAAAATTAAA
Found at i:18882 original size:29 final size:30
Alignment explanation
Indices: 18849--18906 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
18839 GTGTGTTTTT
* *
18849 CAGTTTAATGTCTAATG-TTTATTTCGTTC
1 CAGTTTAATGCCTAACGTTTTATTTCGTTC
*
18878 CAGTTTGATGCCTAACGTTTTATTTCGTT
1 CAGTTTAATGCCTAACGTTTTATTTCGTT
18907 AATCAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (30 bp):
CAGTTTAATGCCTAACGTTTTATTTCGTTC
Found at i:21886 original size:20 final size:20
Alignment explanation
Indices: 21863--21912 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
21853 CAACGCGAAC
*
21863 TCCAATTTCGTAACCCATTT
1 TCCAATTTCGTAACCCAGTT
21883 TCCAATTTCGTAACCCAGTT
1 TCCAATTTCGTAACCCAGTT
21903 TCCAATTTCG
1 TCCAATTTCG
21913 CAACGCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.38
Consensus pattern (20 bp):
TCCAATTTCGTAACCCAGTT
Found at i:21953 original size:20 final size:20
Alignment explanation
Indices: 21930--22010 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
21920 AATTTGTAAA
21930 TCGCAACAC-ATAAGTCAAAT
1 TCGCAACACGAT-AGTCAAAT
*
21950 TCGCATCACGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
* *
21970 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGATAGTCAAAT
*
21990 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
22010 T
1 T
22011 GGCTTGTCGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
20 51 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:21974 original size:40 final size:40
Alignment explanation
Indices: 21930--22010 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
21920 AATTTGTAAA
* *
21930 TCGCAACACATAAGTCAAATTCGCATCACGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACGATAGTCAAAT
*
21970 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACGATAGTCAAAT
22010 T
1 T
22011 GGCTTGTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.21
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACACGATAGTCAAAT
Found at i:22734 original size:13 final size:13
Alignment explanation
Indices: 22716--22748 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
22706 CAACTGTCCT
22716 TAGCTTGTATTTA
1 TAGCTTGTATTTA
22729 TAGCTTGTATTTA
1 TAGCTTGTATTTA
22742 TAGCTTG
1 TAGCTTG
22749 GAATGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (13 bp):
TAGCTTGTATTTA
Found at i:22849 original size:14 final size:14
Alignment explanation
Indices: 22811--22849 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
22801 AAAGTCAAAT
22811 TCGCAACGCG-AAA
1 TCGCAACGCGAAAA
22824 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
22838 TCGCAACGCGAA
1 TCGCAACGCGAA
22850 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:23101 original size:64 final size:66
Alignment explanation
Indices: 22961--23136 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 66
22951 AATTTAAAAC
*
22961 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTTTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
23026 A
66 A
* * *
23027 AACAAATCAACTTTTACAAATCAATTAAATAAGC-AAAAAATAGTTCTTATTT-CTTCATC-AAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTAC-ACATCAAAT
23089 TA
65 TA
23091 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
23137 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
64 17 0.18
65 22 0.23
66 33 0.34
68 4 0.04
69 15 0.15
70 6 0.06
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
A
Found at i:24140 original size:11 final size:11
Alignment explanation
Indices: 24126--24158 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
24116 TAATCAAAAT
24126 ACAATATAAGA
1 ACAATATAAGA
24137 ACAATATAAGA
1 ACAATATAAGA
*
24148 AGAATATAAGA
1 ACAATATAAGA
24159 CTTACCACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (11 bp):
ACAATATAAGA
Found at i:26851 original size:14 final size:14
Alignment explanation
Indices: 26832--26881 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
26822 TGCGATTTTC
*
26832 ATTTTCACGTTGCG
1 ATTTTCATGTTGCG
*
26846 ATTTTCGTGTTGCG
1 ATTTTCATGTTGCG
**
26860 ATTTTGGTGTTGCG
1 ATTTTCATGTTGCG
26874 ATTTTCAT
1 ATTTTCAT
26882 TTTCGTGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.50
Consensus pattern (14 bp):
ATTTTCATGTTGCG
Found at i:27532 original size:20 final size:20
Alignment explanation
Indices: 27405--27520 Score: 169
Period size: 20 Copynumber: 5.8 Consensus size: 20
27395 TTGTGTTTCA
* *
27405 CGTTGTGAATTTAACTATCG
1 CGTTGCGAATTTGACTATCG
*
27425 CGTTGCGAATTTGGCTATCG
1 CGTTGCGAATTTGACTATCG
*
27445 CGTTGCGAATTTGGCTATCG
1 CGTTGCGAATTTGACTATCG
* *
27465 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
*
27485 TGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
27505 CGTTGCGAATTTGACT
1 CGTTGCGAATTTGACT
27521 TCTGTGTTGC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:27547 original size:20 final size:20
Alignment explanation
Indices: 27524--27572 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
27514 TTTGACTTCT
27524 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
*
27544 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAAATTC
*
27564 GCGTTGCGA
1 GTGTTGCGA
27573 AATTGGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (20 bp):
GTGTTGCGATTTACAAATTC
Found at i:27548 original size:60 final size:60
Alignment explanation
Indices: 27426--27573 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 60
27416 TAACTATCGC
* * * *
27426 GTTGCGAATTTGGCTATCGCGTTGCGAATTTGGCTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACATTCGT
*
27486 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC--ATTCGT
*
27546 GTTGCG-ATTT-ACAGATTCGCGTTGCGAA
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAA
27574 ATTGGAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
58 4 0.05
59 11 0.14
60 62 0.81
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACATTCGT
Found at i:27552 original size:40 final size:40
Alignment explanation
Indices: 27406--27539 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
27396 TGTGTTTCAC
* * * * *
27406 GTTGTGAATTTAACTATCGCGTTGCGAATTTGGCTATC-GC
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACT-TCTGT
* * *
27446 GTTGCGAATTTGGCTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGT
*
27486 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGT
27526 GTTGCG-ATTT-ACAA
1 GTTGCGAATTTGACAA
27540 ATTCGTGTTG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
38 3 0.04
39 5 0.06
40 76 0.90
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGT
Found at i:27609 original size:20 final size:21
Alignment explanation
Indices: 27538--27613 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 21
27528 TGCGATTTAC
* * *
27538 AAATTCGTGTTGCG-ATTTAC
1 AAATTCGCGTTGCGAAATTAG
* *
27558 AGATTCGCGTTGCGAAATTGG
1 AAATTCGCGTTGCGAAATTAG
*
27579 AAATT-GGGTTGCGAAATTAG
1 AAATTCGCGTTGCGAAATTAG
*
27599 -AGTTCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
27614 TTTGAGATCA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 34 0.77
21 7 0.16
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (21 bp):
AAATTCGCGTTGCGAAATTAG
Found at i:27627 original size:19 final size:20
Alignment explanation
Indices: 27586--27628 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
27576 TGGAAATTGG
* *
27586 GTTGCGAAATTAGAGTTCGC
1 GTTGCGAAATTAGAGATCAC
*
27606 GTTGCG-AATTTGAGATCAC
1 GTTGCGAAATTAGAGATCAC
27625 GTTG
1 GTTG
27629 TAAATTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (20 bp):
GTTGCGAAATTAGAGATCAC
Found at i:28345 original size:23 final size:23
Alignment explanation
Indices: 28309--28353 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28299 CTGAATGATT
*
28309 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
28332 CAGTGTTGAATGATTCAGCAAA
1 CAGTGCTGAATGATTCAGCAAA
28354 GATACATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:28464 original size:15 final size:16
Alignment explanation
Indices: 28426--28466 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28416 ACAGAGCCTC
28426 TGAATCATTCAACATT
1 TGAATCATTCAACATT
* *
28442 TGAATCATTCAGCGTT
1 TGAATCATTCAACATT
28458 T-AATCATTC
1 TGAATCATTC
28467 TGGAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:30212 original size:21 final size:21
Alignment explanation
Indices: 30188--30229 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
30178 TGAACAGTTC
30188 GCTAAATGTTCGATTCATTTA
1 GCTAAATGTTCGATTCATTTA
30209 GCTAAATGTTCGATTCATTTA
1 GCTAAATGTTCGATTCATTTA
30230 CATGTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
GCTAAATGTTCGATTCATTTA
Found at i:32127 original size:17 final size:18
Alignment explanation
Indices: 32079--32134 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
32069 ATAATGAAAC
* *
32079 ATAAAATAATCATTAAAA
1 ATAAAATAATTATTTAAA
*
32097 ATAAAATAATTATTTTAA
1 ATAAAATAATTATTTAAA
*
32115 ATTAAAT-ATTATTTAAA
1 ATAAAATAATTATTTAAA
32132 ATA
1 ATA
32135 TTATATATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAATAATTATTTAAA
Found at i:35036 original size:11 final size:10
Alignment explanation
Indices: 34982--35049 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
34972 AAAGAGATGA
34982 TATTTTTA--
1 TATTTTTATT
*
34990 TATTTATATT
1 TATTTTTATT
*
35000 ATATTTTTGTT
1 -TATTTTTATT
* *
35011 GAATTTTATT
1 TATTTTTATT
*
35021 CATTTTTATT
1 TATTTTTATT
35031 GTATTTTTATT
1 -TATTTTTATT
35042 TATTTTTA
1 TATTTTTA
35050 AAAAGAGTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
8 7 0.15
10 23 0.49
11 17 0.36
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (10 bp):
TATTTTTATT
Found at i:35049 original size:31 final size:29
Alignment explanation
Indices: 34982--35049 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 29
34972 AAAGAGATGA
*
34982 TATTTTTATATTTATATTATATTTTTGTT
1 TATTTTTATATTTATATTATATTTTTATT
* * * *
35011 GAATTTTATTCATTTTTATTGTATTTTTATT
1 TATTTTTA-T-ATTTATATTATATTTTTATT
35042 TATTTTTA
1 TATTTTTA
35050 AAAAGAGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
31 23 0.77
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (29 bp):
TATTTTTATATTTATATTATATTTTTATT
Found at i:37876 original size:23 final size:24
Alignment explanation
Indices: 37830--37880 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
37820 GATATATATA
* *
37830 TTTTTATTTAATATTAAAATTTAT
1 TTTTTACTTAATAATAAAATTTAT
*
37854 TTTTTACTTAATAATATAA-TTAT
1 TTTTTACTTAATAATAAAATTTAT
37877 TTTT
1 TTTT
37881 ATGTATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTACTTAATAATAAAATTTAT
Found at i:45562 original size:2 final size:2
Alignment explanation
Indices: 45555--45580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45545 AAAGCTAATA
45555 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
45581 TTCAGCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55296 original size:28 final size:29
Alignment explanation
Indices: 55244--55302 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
55234 CCTCCAGGAG
*
55244 GGGTCATAAAACTCTGTGACGGTGGC-AA
1 GGGTCATAAAACTCGGTGACGGTGGCGAA
55272 GGGTCATAAAAC-CAGGTGA-GAGTGGCGAA
1 GGGTCATAAAACTC-GGTGACG-GTGGCGAA
55301 GG
1 GG
55303 CGGCATCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.07
28 21 0.78
29 4 0.15
ACGTcount: A:0.31, C:0.15, G:0.37, T:0.17
Consensus pattern (29 bp):
GGGTCATAAAACTCGGTGACGGTGGCGAA
Found at i:56184 original size:2 final size:2
Alignment explanation
Indices: 56177--56209 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56167 ATTGACTTTT
56177 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
56210 GTCATTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:56600 original size:18 final size:18
Alignment explanation
Indices: 56577--56649 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
56567 ACTGAATATT
*
56577 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
56595 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
56614 TTGTTCCAAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
56633 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
56650 GTTTATCCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 2 0.04
20 14 0.31
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:56631 original size:38 final size:38
Alignment explanation
Indices: 56588--56669 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
56578 GTCCCGAATG
* *
56588 ACCACTATGTCCCGAAGGACCACTGATTGTTCCAAAGA
1 ACCACTATGTCCCGAAGGACCACTGATTATCCCAAAGA
* * *
56626 ACCACTATGTCCTGAAGGACCACTGTTTATCCCAAAGG
1 ACCACTATGTCCCGAAGGACCACTGATTATCCCAAAGA
56664 ACCACT
1 ACCACT
56670 GATAATCCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (38 bp):
ACCACTATGTCCCGAAGGACCACTGATTATCCCAAAGA
Found at i:56677 original size:20 final size:20
Alignment explanation
Indices: 56640--56678 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56630 CTATGTCCTG
* *
56640 AAGGACCACTGTTTATCCCA
1 AAGGACCACTGATAATCCCA
56660 AAGGACCACTGATAATCCC
1 AAGGACCACTGATAATCCC
56679 TCGACTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (20 bp):
AAGGACCACTGATAATCCCA
Found at i:58825 original size:25 final size:24
Alignment explanation
Indices: 58791--58862 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
58781 ATATCTGCAA
58791 AAAAAATTAAATAAATAAAATATT
1 AAAAAATTAAATAAATAAAATATT
58815 AAAAAACTTAAATAAATTAAAA-A-T
1 AAAAAA-TTAAATAAA-TAAAATATT
*
58839 AAAATATTAAATATAATAAAATAT
1 AAAAAATTAAATA-AATAAAATAT
58863 ACCTTAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
23 12 0.29
24 15 0.36
25 10 0.24
26 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAAATTAAATAAATAAAATATT
Found at i:58911 original size:10 final size:10
Alignment explanation
Indices: 58896--58932 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
58886 ATAAGAATAT
58896 TTGAGAGAAG
1 TTGAGAGAAG
* *
58906 TTGAGAGTAT
1 TTGAGAGAAG
58916 TTGAGAGAAG
1 TTGAGAGAAG
58926 TTGAGAG
1 TTGAGAG
58933 GATTTGGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:58916 original size:20 final size:20
Alignment explanation
Indices: 58893--58938 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
58883 AATATAAGAA
58893 TATTTGAGAGAAGTTGAGAG
1 TATTTGAGAGAAGTTGAGAG
58913 TATTTGAGAGAAGTTGAGAG
1 TATTTGAGAGAAGTTGAGAG
*
58933 GATTTG
1 TATTTG
58939 GTGTGATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (20 bp):
TATTTGAGAGAAGTTGAGAG
Found at i:62002 original size:32 final size:32
Alignment explanation
Indices: 61961--62023 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
61951 AAGCATCTAG
61961 TAGCACTATCAAAACTGTATTTGATCATCGAA
1 TAGCACTATCAAAACTGTATTTGATCATCGAA
61993 TAGCACTATCAAAACTGTATTTGATCATCGA
1 TAGCACTATCAAAACTGTATTTGATCATCGA
62024 GAACAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TAGCACTATCAAAACTGTATTTGATCATCGAA
Found at i:64129 original size:17 final size:18
Alignment explanation
Indices: 64107--64154 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
64097 ATATGGAATT
*
64107 AGATTCCAATTCC-TGAC
1 AGATTCCAATTCCTTCAC
64124 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
64142 ATATTCCAATTCC
1 AGATTCCAATTCC
64155 CTCATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.33
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:64762 original size:16 final size:16
Alignment explanation
Indices: 64737--64767 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64727 CCGCCGAACC
*
64737 TCCACTCGACCTCACT
1 TCCACCCGACCTCACT
64753 TCCACCCGACCTCAC
1 TCCACCCGACCTCAC
64768 CTCAACCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.55, G:0.06, T:0.19
Consensus pattern (16 bp):
TCCACCCGACCTCACT
Found at i:65294 original size:35 final size:35
Alignment explanation
Indices: 65243--65354 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
65233 AAAACATTCC
* *
65243 TCAACTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
65278 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
65313 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
65348 TCAATTT
1 TCAATTT
65355 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:66525 original size:34 final size:34
Alignment explanation
Indices: 66415--66526 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
66405 AAAAAAGACA
* *
66415 GAAATTGAAGTATTTCAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
*
66450 GTAATTGAATTATTTTAGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
*
66485 GAAATTGAATTATTTTGGAATTTGTGGTTTA-AAT
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
66519 GAAATTGA
1 GAAATTGA
66527 GGATTGTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
34 12 0.17
35 55 0.79
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:72549 original size:24 final size:24
Alignment explanation
Indices: 72472--72561 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
72462 TCCGACTTGA
* *
72472 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
72495 ATTCTGATATGATA-TTGGCATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
72518 ATTATGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
72542 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
72562 TTGAATTATG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
23 30 0.57
24 23 0.43
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:78123 original size:24 final size:24
Alignment explanation
Indices: 78046--78135 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
78036 TCCGACTTGA
* *
78046 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
78069 ATTCTGATATGATA-TTGGCATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
78092 ATTATGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
78116 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
78136 TTGAATTATG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
23 30 0.57
24 23 0.43
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:84240 original size:9 final size:10
Alignment explanation
Indices: 84213--84242 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
84203 ACTTGATAGA
84213 ATTAAAAGAAT
1 ATTAAAA-AAT
84224 ATTAAAAAAT
1 ATTAAAAAAT
84234 ATTAAAAAA
1 ATTAAAAAA
84243 ACAGACTCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
ATTAAAAAAT
Found at i:89754 original size:17 final size:18
Alignment explanation
Indices: 89722--89755 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89712 AATTATATAT
89722 AATTATAATAAAAAATTA
1 AATTATAATAAAAAATTA
*
89740 AATTA-AATTAAAAATT
1 AATTATAATAAAAAATT
89756 CATTTAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTATAATAAAAAATTA
Found at i:93140 original size:17 final size:18
Alignment explanation
Indices: 93115--93157 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
93105 GGAATCATTT
*
93115 TAAAAATTAA-TTAAAAA
1 TAAATATTAATTTAAAAA
93132 TAAATATTAATTTAAAAA
1 TAAATATTAATTTAAAAA
*
93150 TAATTATT
1 TAAATATT
93158 TTAATAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATTAATTTAAAAA
Found at i:95243 original size:2 final size:2
Alignment explanation
Indices: 95236--95268 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
95226 AAAGAACATA
95236 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 A
95269 ATCACCGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:99982 original size:10 final size:9
Alignment explanation
Indices: 99948--100058 Score: 50
Period size: 10 Copynumber: 11.6 Consensus size: 9
99938 TAATTTTATT
99948 TTTTTATAA
1 TTTTTATAA
*
99957 TTCTTT-TGAT
1 TT-TTTAT-AA
99967 TTTTTATAA
1 TTTTTATAA
99976 CTTTTTATAA
1 -TTTTTATAA
*
99986 TTTTATGTAA
1 TTTT-TATAA
*
99996 TTATTT-TATG
1 TT-TTTATA-A
100006 TTTTTGATAA
1 TTTTT-ATAA
*
100016 -GTTTAT-A
1 TTTTTATAA
*
100023 TTTTAATAA
1 TTTTTATAA
100032 TTTTTAATAA
1 TTTTT-ATAA
100042 TTATTCTATAA
1 TT-TT-TATAA
100053 TATTTT
1 T-TTTT
100059 TTAAATAATC
Statistics
Matches: 78, Mismatches: 9, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 24 0.31
10 32 0.41
11 13 0.17
12 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:102087 original size:16 final size:16
Alignment explanation
Indices: 102066--102099 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
102056 TGTTATTAAA
*
102066 AATATTATTATTTTTT
1 AATATTAATATTTTTT
102082 AATATTAATATTTTTT
1 AATATTAATATTTTTT
102098 AA
1 AA
102100 CATTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTAATATTTTTT
Found at i:103180 original size:24 final size:26
Alignment explanation
Indices: 103156--103205 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
103146 ATATATTATT
103156 ATAA-AATAATATCACGA-CAACATTAA
1 ATAATAATAATATCAC-ATCAACATT-A
103182 ATAATAATAATATCACATCAACAT
1 ATAATAATAATATCACATCAACAT
103206 CATCTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (26 bp):
ATAATAATAATATCACATCAACATTA
Found at i:104353 original size:59 final size:59
Alignment explanation
Indices: 104208--104353 Score: 154
Period size: 59 Copynumber: 2.4 Consensus size: 59
104198 AACATAGTAA
* * *
104208 ATAGTC-GGGTGACCATTTTGTTATTTTTAATAGTCGAGGGATTCAACAAATCAACTCCTT
1 ATAGTCAGGG-GACCATTTTG-TACTTTTAATAGTCGAGGGACTCAACAAAGCAACTCCTT
* * * * *
104268 ATAATCAGGGAACCATTTTATAACTTTTAATAGTTGA-GGACTCAACAAAGCAA-TATCTT
1 ATAGTCAGGGGACCATTTTGT-ACTTTTAATAGTCGAGGGACTCAACAAAGCAACT-CCTT
104327 ATAGTCAGGGGACCATTTGTGTACTTT
1 ATAGTCAGGGGACCATTT-TGTACTTT
104354 ACTCATATAT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
58 1 0.01
59 39 0.55
60 28 0.39
61 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (59 bp):
ATAGTCAGGGGACCATTTTGTACTTTTAATAGTCGAGGGACTCAACAAAGCAACTCCTT
Found at i:104574 original size:19 final size:20
Alignment explanation
Indices: 104541--104632 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 20
104531 CTAGACCAAC
*
104541 TAATTTAA-GTTTAAAGTAT
1 TAATTTAATATTTAAAGTAT
*
104560 T-ATTTAATATTTAAAAT-T
1 TAATTTAATATTTAAAGTAT
* *
104578 TTATTTATTTATTT-AAGTATT
1 TAATTTA-ATATTTAAAGTA-T
104599 TAGATTTAAT-TTTAAAGT-T
1 TA-ATTTAATATTTAAAGTAT
*
104618 TAATTTGATATTTAA
1 TAATTTAATATTTAA
104633 TTTTTTTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
18 14 0.24
19 24 0.41
20 8 0.14
21 7 0.12
22 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATTTAATATTTAAAGTAT
Found at i:109623 original size:28 final size:29
Alignment explanation
Indices: 109583--109641 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
109573 CAGGTTTCGG
109583 ATCTATATACCTACACAAATCAT-ACACA
1 ATCTATATACCTACACAAATCATAACACA
109611 ATCTATATACCTACACAAATCATAACACA
1 ATCTATATACCTACACAAATCATAACACA
109640 AT
1 AT
109642 GTAAACTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (29 bp):
ATCTATATACCTACACAAATCATAACACA
Found at i:110695 original size:124 final size:124
Alignment explanation
Indices: 110475--110722 Score: 442
Period size: 124 Copynumber: 2.0 Consensus size: 124
110465 GAGCTGCAGC
*
110475 GGTAGTAATAGACGGTGTTCAGGTTCAAGGGGCCGATAACGGCGTCATGAATTTGACCGGATTTG
1 GGTAGTAATAGACGGTGTTCAGGTTCAAGGGACCGATAACGGCGTCATGAATTTGACCGGATTTG
110540 TATAGAAGATAACGATAGGAAGACGAAGTCCCAGTTACAGAGTTGGTGTATACCTTTGG
66 TATAGAAGATAACGATAGGAAGACGAAGTCCCAGTTACAGAGTTGGTGTATACCTTTGG
* *
110599 GGTAGTAATAGACGGTGTTCGGGTTCAAGGGACCGATAACGGGGTCATGAATTTGACCGGATTTG
1 GGTAGTAATAGACGGTGTTCAGGTTCAAGGGACCGATAACGGCGTCATGAATTTGACCGGATTTG
* * *
110664 TATAGAAGATAACGATAGGAAGATGATGTCCCAGTTACAGAGTTGGTGTATGCCTTTGG
66 TATAGAAGATAACGATAGGAAGACGAAGTCCCAGTTACAGAGTTGGTGTATACCTTTGG
110723 AGATGTACCG
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (124 bp):
GGTAGTAATAGACGGTGTTCAGGTTCAAGGGACCGATAACGGCGTCATGAATTTGACCGGATTTG
TATAGAAGATAACGATAGGAAGACGAAGTCCCAGTTACAGAGTTGGTGTATACCTTTGG
Done.