Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004941.1 Hibiscus syriacus cultivar Beakdansim tig00011111_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: 61844
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:450 original size:2 final size:2
Alignment explanation
Indices: 443--478 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
433 TTCTTTTTAG
443 AT AT AT 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 AT AT AT
479 CTTCAATGTT
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):
AT
Found at i:2813 original size:28 final size:29
Alignment explanation
Indices: 2769--2877 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
2759 CTAGTGGAAA
*
2769 TACCTAATTTTCAAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
2798 TACCT-ATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
2826 TACCTAATTTTCCAATATTCAATGACCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
2856 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
2878 ATTCAATGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
28 27 0.36
29 31 0.41
30 18 0.24
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:2833 original size:57 final size:58
Alignment explanation
Indices: 2769--2877 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 58
2759 CTAGTGGAAA
*
2769 TACCTAATTTTCAAATATTCAATGAGCA-TTACCT-ATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCAAATATTCAATGACCATTTACCTAATTTTCCAATA-TCAATGAGCAT
*
2826 TACCTAATTTTCCAATATTCAATGACCATTTACCTAATTTTCCAATATCAAT
1 TACCTAATTTTCAAATATTCAATGACCATTTACCTAATTTTCCAATATCAAT
2878 ATTCAATGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
57 26 0.54
58 11 0.23
59 11 0.23
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (58 bp):
TACCTAATTTTCAAATATTCAATGACCATTTACCTAATTTTCCAATATCAATGAGCAT
Found at i:3482 original size:31 final size:31
Alignment explanation
Indices: 3447--3540 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
3437 AATTTGGTGA
3447 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
3478 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
3509 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
3540 A
1 A
3541 AACTCTTGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:8192 original size:29 final size:29
Alignment explanation
Indices: 8156--8265 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
8146 CTAGTGGAAA
8156 TACCTAATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
8185 TACCTAATTTTCCAATATTCAATGAACAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
8214 TACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
8244 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
8266 ATTCAATGAG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 60 0.77
30 18 0.23
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:16724 original size:21 final size:21
Alignment explanation
Indices: 16698--16742 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16688 GATTTCTGGG
* *
16698 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
16719 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
16740 CAA
1 CAA
16743 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:17442 original size:21 final size:22
Alignment explanation
Indices: 17413--17456 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17403 GTTGTATGAT
17413 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
17434 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
17456 A
1 A
17457 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:18515 original size:149 final size:149
Alignment explanation
Indices: 18334--18637 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
18324 GAGTCGAGGG
18334 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
18399 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
18464 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
18483 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
18548 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
18613 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
18632 TCTACG
1 TCTACG
18638 GGGCACTTCG
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:18660 original size:23 final size:23
Alignment explanation
Indices: 18616--18660 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18606 ATCATTATAT
*
18616 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
18639 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
18661 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:21815 original size:21 final size:21
Alignment explanation
Indices: 21791--21835 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21781 GATTTCTGGG
* *
21791 CAAGGGAAATCGGTACCCATT
1 CAAGGGAAACCGATACCCATT
* *
21812 CAAGGGGAACCGATACCCCTT
1 CAAGGGAAACCGATACCCATT
21833 CAA
1 CAA
21836 ACGACAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGAAACCGATACCCATT
Found at i:22438 original size:18 final size:18
Alignment explanation
Indices: 22415--22449 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22405 CTAGGAGATT
22415 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
22433 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
22450 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:22535 original size:21 final size:22
Alignment explanation
Indices: 22506--22549 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22496 GTTGTATGAT
22506 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
22527 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
22549 A
1 A
22550 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:23700 original size:149 final size:149
Alignment explanation
Indices: 23430--23733 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
23420 GAGTCGAGGG
23430 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
23495 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
23560 TATGGTACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
23579 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
23644 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
23709 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
23728 TCTACG
1 TCTACG
23734 GGGCACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:23756 original size:23 final size:23
Alignment explanation
Indices: 23712--23756 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23702 ATCATTATAT
*
23712 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
23735 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
23757 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:31141 original size:11 final size:10
Alignment explanation
Indices: 31116--31173 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 10
31106 TAAAAGGTTG
*
31116 AAAAGTTGAA
1 AAAAATTGAA
31126 AAAAATTAGAA
1 AAAAATT-GAA
31137 TAAAAATTG-A
1 -AAAAATTGAA
31147 AAAAATTGAA
1 AAAAATTGAA
*
31157 AATAATGTTGAA
1 AA-AA-ATTGAA
31169 AAAAA
1 AAAAA
31174 CGTGTAGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.20
10 10 0.25
11 8 0.20
12 14 0.35
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (10 bp):
AAAAATTGAA
Found at i:31171 original size:22 final size:22
Alignment explanation
Indices: 31116--31173 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
31106 TAAAAGGTTG
31116 AAAAGTTGAAAAAAATTAGAAT
1 AAAAGTTGAAAAAAATTAGAAT
*
31138 AAAAATTG-AAAAAATT-GAA-
1 AAAAGTTGAAAAAAATTAGAAT
31157 AATAATGTTGAAAAAAA
1 AA-AA-GTTGAAAAAAA
31174 CGTGTAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 11 0.35
22 13 0.42
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (22 bp):
AAAAGTTGAAAAAAATTAGAAT
Found at i:31459 original size:16 final size:16
Alignment explanation
Indices: 31359--31463 Score: 61
Period size: 16 Copynumber: 6.3 Consensus size: 16
31349 ATATATGTAT
* *
31359 AATAATAATAATATAA
1 AATAATAAAAATAGAA
* *
31375 AATAATAATAAAGACAA
1 AATAATAA-AAATAGAA
* *
31392 AAGACTAAAAA-AGAAA
1 AATAATAAAAATAG-AA
* *
31408 AATAATATAATATAATAA
1 AATAATA-AAAAT-AGAA
*
31426 TAATGAATAAAAA-CGAA
1 -AAT-AATAAAAATAGAA
31443 AATAATAAAAATAGAA
1 AATAATAAAAATAGAA
31459 AATAA
1 AATAA
31464 AAAGAAAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
15 9 0.13
16 29 0.43
17 16 0.24
18 2 0.03
19 7 0.10
20 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (16 bp):
AATAATAAAAATAGAA
Found at i:31463 original size:35 final size:35
Alignment explanation
Indices: 31373--31472 Score: 82
Period size: 35 Copynumber: 2.9 Consensus size: 35
31363 ATAATAATAT
* * *
31373 AAAATAATAATAA-AGACAA-AAGACTAAAAAAGA
1 AAAATAATAAAAATAGAAAATAAGAATAAAAAAGA
* * *
31406 AAAATAATATAATATA-ATAATAATGAATAAAAACG-
1 AAAATAATA-AAAATAGAAAATAA-GAATAAAAAAGA
* *
31441 AAAATAATAAAAATAGAAAATAAAAAGAAAAA
1 AAAATAATAAAAATAGAAAATAAGAATAAAAA
31473 TACACTTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
33 9 0.17
34 17 0.32
35 18 0.34
36 9 0.17
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (35 bp):
AAAATAATAAAAATAGAAAATAAGAATAAAAAAGA
Found at i:33385 original size:98 final size:98
Alignment explanation
Indices: 33205--33829 Score: 1069
Period size: 98 Copynumber: 6.3 Consensus size: 98
33195 GCGTTGTTCC
*
33205 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GATATTGTTTATTGACAACCAGCGGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
33266 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
33299 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCATCGGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
33364 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
33397 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCATCGGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
33462 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
33495 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTATTTATTGACAACCAGCGGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
33560 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
33593 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGTGGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
33658 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
33691 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA-T------TGTTTATTGACAAC
* *
33756 CAGCGGTCCCTTCGCCGTGAAGTCGAACTTGCGTTGTCTG
59 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
33796 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
33830 ACTCTGGGTA
Statistics
Matches: 507, Mismatches: 13, Indels: 11
0.95 0.02 0.02
Matches are distributed among these distances:
94 35 0.07
98 387 0.76
99 1 0.00
105 84 0.17
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (98 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:33800 original size:105 final size:106
Alignment explanation
Indices: 33632--33835 Score: 356
Period size: 105 Copynumber: 1.9 Consensus size: 106
33622 AATTGGCCCT
* * *
33632 GAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTCGAACTTGCGTTGTCTGGAGTCC
*
33697 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGA
*
33738 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTCGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTCGAACTTGCGTTGTCTGGAGTCC
33802 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
66 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
33836 GGTAAAACCT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 89 0.96
106 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTCGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGA
Found at i:34521 original size:18 final size:18
Alignment explanation
Indices: 34498--34532 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34488 TGAACCCACC
*
34498 TTATTTTCTCTTCTTTTA
1 TTATTTTCTCCTCTTTTA
*
34516 TTATTTTTTCCTCTTTT
1 TTATTTTCTCCTCTTTT
34533 TCTTTTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTCTCCTCTTTTA
Found at i:47379 original size:5 final size:5
Alignment explanation
Indices: 47366--47398 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
47356 AAGGAAAAAG
*
47366 AAACG AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAA
47399 AGGTCCTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:53036 original size:177 final size:181
Alignment explanation
Indices: 52740--53105 Score: 634
Period size: 177 Copynumber: 2.0 Consensus size: 181
52730 CAAACATGAG
52740 TACAATCGAACGTGATCTTCATAAGCATGTTTTATGTCCCTTTTCTTTCTTAGCTAAACTGCTTC
1 TACAATCGAACGTGATCTTCATAAGCATGTTTTATGTCCCTTTTCTTTCTTAGCTAAACTGCTTC
52805 TCAAAGTTTTCTTCCTCTTACAAACTTGTATTCTTCTTATTTAGTCAG-ATATATATA-AGGATC
66 TCAAAGTTTTCTTCCTCTTACAAACTTGTATTCTTCTTATTTAGTCAGAATATATATACAGGATC
52868 AATGAAC-AT-AACATATGCAGTTGTTAGGCTTTCAAAATT-AAACAATTCT
131 AATGAACAATCAACATATGCAGTTGTTA-GCTTTCAAAATTAAAACAATTCT
52917 TACAATCGAACGTGATCTTCATAAGCATGTTTTATGTCCCTTTTCTTTCTTAGCTAAACTGCTTC
1 TACAATCGAACGTGATCTTCATAAGCATGTTTTATGTCCCTTTTCTTTCTTAGCTAAACTGCTTC
52982 TCAAAGTTTTCTTCCTCTTACAAACTTGTATTCTTCTTATTTAGTCAGATATATATATATAGCAG
66 TCAAAGTTTTCTTCCTCTTACAAACTTGTATTCTTCTTATTTAGTCAG--A-ATATATATA-CAG
53047 GATCAATGAACATAATCAACATATGCAGTTGTTAGCTTTCAAAATTAAAACAATTCT
127 GATCAATGAAC--AATCAACATATGCAGTTGTTAGCTTTCAAAATTAAAACAATTCT
53104 TA
1 TA
53106 ATTTTTATTT
Statistics
Matches: 178, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
177 113 0.63
181 9 0.05
183 13 0.07
186 14 0.08
187 29 0.16
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.40
Consensus pattern (181 bp):
TACAATCGAACGTGATCTTCATAAGCATGTTTTATGTCCCTTTTCTTTCTTAGCTAAACTGCTTC
TCAAAGTTTTCTTCCTCTTACAAACTTGTATTCTTCTTATTTAGTCAGAATATATATACAGGATC
AATGAACAATCAACATATGCAGTTGTTAGCTTTCAAAATTAAAACAATTCT
Found at i:54571 original size:13 final size:13
Alignment explanation
Indices: 54553--54586 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
54543 CTTACCAAGA
54553 AAAGAAAATTAGG
1 AAAGAAAATTAGG
54566 AAAGAAAATTAGG
1 AAAGAAAATTAGG
*
54579 AGAGAAAA
1 AAAGAAAA
54587 AGTTAGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (13 bp):
AAAGAAAATTAGG
Found at i:55143 original size:3 final size:3
Alignment explanation
Indices: 55135--55161 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55125 TAAGTAATAT
55135 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
55162 AAGTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:57584 original size:63 final size:63
Alignment explanation
Indices: 57485--57613 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
57475 ATGAGCCGCC
57485 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
1 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
57548 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
1 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
57611 ACT
1 ACT
57614 TTGGACGTCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (63 bp):
ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
Found at i:58775 original size:71 final size:71
Alignment explanation
Indices: 58654--58854 Score: 368
Period size: 71 Copynumber: 2.8 Consensus size: 71
58644 CATTCATTCA
* * *
58654 TTCATTTACACTAACATTCCCCTTGCAACCTTCAACTTCAAACCTCCTTCAAAACTCAAATTGAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
58719 CTAATG
66 CTAATG
58725 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
58790 CTAATG
66 CTAATG
58796 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTC-AAACTCAAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAA
58855 CTGATCTTCT
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 9 0.07
71 118 0.93
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (71 bp):
TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
CTAATG
Done.