Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002169.1 Hibiscus syriacus cultivar Beakdansim tig00004425_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: 81575
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:964 original size:20 final size:20
Alignment explanation
Indices: 930--967 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
920 AATATATAAA
**
930 AAATTATAATTTATTTTTTG
1 AAATTATAAAATATTTTTTG
950 AAATTATAAAATATTTTT
1 AAATTATAAAATATTTTT
968 AAAATATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
AAATTATAAAATATTTTTTG
Found at i:7168 original size:21 final size:18
Alignment explanation
Indices: 7123--7157 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7113 AAAATGAATG
*
7123 ATAA-ATTCAGTTAAAAA
1 ATAATATTCAGATAAAAA
7140 ATAATATTCAGATAAAAA
1 ATAATATTCAGATAAAAA
7158 TTATGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAATATTCAGATAAAAA
Found at i:22173 original size:15 final size:15
Alignment explanation
Indices: 22150--22179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22140 TGTTTTGATC
22150 AAAAATTAAAACATT
1 AAAAATTAAAACATT
*
22165 AAAAGTTAAAACATT
1 AAAAATTAAAACATT
22180 CTAAACAAAA
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:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAACATT
Found at i:22938 original size:16 final size:16
Alignment explanation
Indices: 22855--22939 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
22845 CGTTCATTTA
22855 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
22869 ATAAACGAACACGAAT
1 ATAAATGAACACGAAC
**
22885 ATAAACAAACACGAAC
1 ATAAATGAACACGAAC
22901 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
22917 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
22933 ATAAATG
1 ATAAATG
22940 GACATAAACG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 56 0.89
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:24101 original size:24 final size:24
Alignment explanation
Indices: 24061--24122 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
24051 AGATTGGTTA
*
24061 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
24085 AGCATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
24109 AACATAATCGAACG
1 AACATAATCGAACG
24123 TTCACGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:26000 original size:20 final size:20
Alignment explanation
Indices: 25964--26001 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25954 TTGAAAACTT
*
25964 AAATATTGTATTTAATAAAA
1 AAATATTGTATTAAATAAAA
25984 AAATATTGCTA-TAAATAA
1 AAATATTG-TATTAAATAA
26002 TATTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATATTGTATTAAATAAAA
Found at i:27343 original size:23 final size:23
Alignment explanation
Indices: 27317--27361 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27307 TACGTGAAAC
27317 TAAA-AAAAATCTTAGAGTTTTTT
1 TAAATAAAAATCTTA-AGTTTTTT
* *
27340 TAAATAATAATTTTAAGTTTTT
1 TAAATAAAAATCTTAAGTTTTT
27362 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TAAATAAAAATCTTAAGTTTTTT
Found at i:32491 original size:8 final size:8
Alignment explanation
Indices: 32471--32519 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
32461 ATTTCCATCT
*
32471 TTAAAAAA
1 TTAAATAA
32479 TTAAATAA
1 TTAAATAA
*
32487 ATAAA-ATA
1 TTAAATA-A
32495 TTAAAATAA
1 TT-AAATAA
32504 TTAAATAA
1 TTAAATAA
32512 TTAAATAA
1 TTAAATAA
32520 AAATACTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
7 1 0.03
8 27 0.77
9 6 0.17
10 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TTAAATAA
Found at i:33774 original size:48 final size:48
Alignment explanation
Indices: 33698--33796 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
33688 ATTGCAGAAG
* *
33698 GAATTAGTAAGTAGAAGAGAGATTATGGAACAAGATCTAGACAAGGTA
1 GAATCAGTAAGCAGAAGAGAGATTATGGAACAAGATCTAGACAAGGTA
33746 GAATCAGTAAGCAGAAGAGAGATTATGGAACAAGATCTAGACAAGGTA
1 GAATCAGTAAGCAGAAGAGAGATTATGGAACAAGATCTAGACAAGGTA
33794 GAA
1 GAA
33797 ACAGAAACGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.18
Consensus pattern (48 bp):
GAATCAGTAAGCAGAAGAGAGATTATGGAACAAGATCTAGACAAGGTA
Found at i:33810 original size:48 final size:48
Alignment explanation
Indices: 33710--33812 Score: 172
Period size: 48 Copynumber: 2.1 Consensus size: 48
33700 ATTAGTAAGT
* *
33710 AGAAGAGAGATTATGGAACAAGATCTAGACAAGGTAGAATCAGTAAGC
1 AGAAGAGAGATTATGGAACAAGATCTAGACAAGGTAGAAACAGAAAGC
33758 AGAAGAGAGATTATGGAACAAGATCTAGACAAGGTAGAAACAGAAA-C
1 AGAAGAGAGATTATGGAACAAGATCTAGACAAGGTAGAAACAGAAAGC
33805 GAGAAGAG
1 -AGAAGAG
33813 CGCAAGTACA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.49, C:0.10, G:0.28, T:0.14
Consensus pattern (48 bp):
AGAAGAGAGATTATGGAACAAGATCTAGACAAGGTAGAAACAGAAAGC
Found at i:37485 original size:19 final size:19
Alignment explanation
Indices: 37461--37497 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37451 ATGACCAACA
*
37461 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
37480 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
37498 CAGTATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:37626 original size:41 final size:41
Alignment explanation
Indices: 37581--37677 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
37571 GCGATTTTAG
*
37581 AAAATTGCAATGCGAATATGTA-AATCGCAACGCGATAATAC
1 AAAATCGCAATGCGAATATG-ACAATCGCAACGCGATAATAC
* * * *
37622 AAAATCGCAACGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGAATATGACAATCGCAACGCGATAATAC
*
37663 AAAATGGCAATGCGA
1 AAAATCGCAATGCGA
37678 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (41 bp):
AAAATCGCAATGCGAATATGACAATCGCAACGCGATAATAC
Found at i:37628 original size:21 final size:21
Alignment explanation
Indices: 37602--37678 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
37592 GCGAATATGT
37602 AAATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
**
37623 AAATCGCAACGCGATTCTGAC-
1 AAATCGCAACGCGATAAT-ACA
*
37644 -TATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
* *
37664 AAATGGCAATGCGAT
1 AAATCGCAACGCGAT
37679 TTTCCAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGATAATACA
Found at i:37718 original size:19 final size:19
Alignment explanation
Indices: 37694--37764 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
37684 AAATTTACGT
37694 TAGTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
* *
37713 TAGTCCAAGTTACGATGCGA
1 TAGTCCAAATT-CGTTGCGA
** *
37733 TTTTTCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
*
37752 TAGTCCAAGTTCG
1 TAGTCCAAATTCG
37765 CGTTGCGATT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 26 0.65
20 14 0.35
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (19 bp):
TAGTCCAAATTCGTTGCGA
Found at i:37748 original size:39 final size:40
Alignment explanation
Indices: 37699--37776 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 40
37689 TACGTTAGTC
37699 CAAATTCGTTGCGATAGTCCAAGTT-ACGATGCGATTTTT
1 CAAATTCGTTGCGATAGTCCAAGTTCACGATGCGATTTTT
* *
37738 CAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTT
1 CAAATTCGTTGCGATAGTCCAAGTTCACGATGCGATTTT
37777 GGAAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (40 bp):
CAAATTCGTTGCGATAGTCCAAGTTCACGATGCGATTTTT
Found at i:38223 original size:19 final size:19
Alignment explanation
Indices: 38196--38237 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
38186 TATTTTGGAT
*
38196 TTTTCACTATCGCAACACA
1 TTTTAACTATCGCAACACA
*
38215 TTTTAACTATTGCAACACA
1 TTTTAACTATCGCAACACA
38234 TTTT
1 TTTT
38238 TCAAAATCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:39376 original size:2 final size:2
Alignment explanation
Indices: 39369--39403 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39359 ATTATATCAT
39369 TA TA 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 TA TA T
39404 TAATGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44706 original size:14 final size:14
Alignment explanation
Indices: 44687--44715 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44677 TTAAATTTAA
44687 TATAAAAGAAATTT
1 TATAAAAGAAATTT
44701 TATAAAAGAAATTT
1 TATAAAAGAAATTT
44715 T
1 T
44716 GGTTCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TATAAAAGAAATTT
Found at i:46373 original size:42 final size:42
Alignment explanation
Indices: 46306--46444 Score: 192
Period size: 42 Copynumber: 3.3 Consensus size: 42
46296 TGAATATTAT
* *
46306 TGATGTTGATTT-TATTTAGACTTATTAAGACTTATTAGTGTTA
1 TGATGTT-ATTTAT-TTTAGACTTATTGAGACTTAATAGTGTTA
* * *
46349 TGATGTTATTTATTTTAAACTTATTGAGATTTAATGGTGTTA
1 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTA
46391 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTA
1 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTA
46433 TTG-TGTTATTTA
1 -TGATGTTATTTA
46445 AAGGTGTAGC
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
42 76 0.88
43 10 0.12
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.53
Consensus pattern (42 bp):
TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTA
Found at i:51046 original size:462 final size:462
Alignment explanation
Indices: 50181--51554 Score: 2595
Period size: 462 Copynumber: 3.0 Consensus size: 462
50171 GATATATTAC
* * *
50181 CGGAAATGTCATTACCTCCATTTCCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAAATGC
1 CGGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGC
50246 CCTTAATTTTTTTCTTTCAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
66 CCTTAATTTTTTTCTTTCAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
*
50311 TAAATTACAAATTTATCTTTAAACTATTTTAGATTTACAAAAAAAAAGTCTATAATTAAAATTTT
131 TAAATTACAAATTTATCTTTAAACTATTTTAGATTTA-TAAAAAAAAGTCTATAATTAAAATTTT
50376 ATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTT
195 ATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTT
50441 TGTAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTCC
260 TGTAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTCC
50506 AACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTTT
325 AACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTTT
50571 TATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAAGGGTATT
390 TATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAAGGGTATT
50636 GTTAAACA
455 GTTAAACA
50644 CGGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGC
1 CGGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGC
* *
50709 CCTTAATTTTTTTCTTTCAAAAATATCATTCTTCTGTCATTTAATAATAAAAATTCTACGAATGT
66 CCTTAATTTTTTTCTTTCAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
*
50774 TAAATTACAAATTTATCTTTAATCTATTTTAGATTTATAAAAAAAAGTCTATAATTAAAATTTTA
131 TAAATTACAAATTTATCTTTAAACTATTTTAGATTTATAAAAAAAAGTCTATAATTAAAATTTTA
*
50839 TATGAAGTTCAGGGATTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTTT
196 TATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTTT
*
50904 CTAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTCCA
261 GTAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTCCA
50969 ACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTT
326 ACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTT
*
51034 ATTCTTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAAGGGTATTG
391 ATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAAGGGTATTG
51099 TTAAACA
456 TTAAACA
* *
51106 CAGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGT
1 CGGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGC
*
51171 CCTTAATTTTTTTCTTTAAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
66 CCTTAATTTTTTTCTTTCAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
51236 TAAATTACAAATTTATCTTTAAACTATTTTAGATTTATAAAAAAAAAGTCTATAATTAAAATTTT
131 TAAATTACAAATTTATCTTTAAACTATTTTAGATTTAT-AAAAAAAAGTCTATAATTAAAATTTT
*
51301 ATATGAAGTTCAGGGGTTAAAATAAAATTTTACCTTTTTATTAAACCTTTTTATATTTTTAATTT
195 ATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTT
51366 TGTAAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTC
260 TGT-AAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTC
51431 CAACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTT
324 CAACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTT
51496 TTATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAA
389 TTATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAA
51555 TACAACATTC
Statistics
Matches: 889, Mismatches: 20, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
462 453 0.51
463 252 0.28
464 184 0.21
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (462 bp):
CGGAAATGTCAATACCTCCATTTTCTTAGGTATTGTTAGATTACCGGCGTTTTGGACTAAATTGC
CCTTAATTTTTTTCTTTCAAAAATATCCTTCTTCTGTCATTTAATAATAAAAATTCTACGAAGGT
TAAATTACAAATTTATCTTTAAACTATTTTAGATTTATAAAAAAAAGTCTATAATTAAAATTTTA
TATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTTATTAAACCTTTTTATATTTTTAATTTT
GTAAAAAAATTATATAAATTTTATGAATTTAATTTTTTTTAAAGAAAATATAAAAATATTTTCCA
ACTTGTTAAAAAAATAAATATATAACAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTT
ATTCCTTTAACCAAACACGGTAATCTTACATTCTTGCAAAATCAACCAAATACAAAAGGGTATTG
TTAAACA
Found at i:51637 original size:20 final size:19
Alignment explanation
Indices: 51612--51653 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
51602 TTTGGTTCAC
51612 GAAATGTAAGATTACCAGTA
1 GAAATGTAAGATTACCA-TA
51632 GAAATGTAAGATTACCATA
1 GAAATGTAAGATTACCATA
51651 GAA
1 GAA
51654 TAGGATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (19 bp):
GAAATGTAAGATTACCATA
Found at i:51719 original size:35 final size:35
Alignment explanation
Indices: 51680--51792 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 35
51670 GTTATATTTT
51680 GTGTTTGGTTAGTTTAGCAGGAATGTAAGATTATC
1 GTGTTTGGTTAGTTTAGCAGGAATGTAAGATTATC
* ** *
51715 GTG-TT--TT-G-TTA-AAGGAATAAAAGATTATTG
1 GTGTTTGGTTAGTTTAGCAGGAATGTAAGATTA-TC
* ** *
51745 GAATGTATATTTGGTTTAGCAGGAATGTAAGATTATC
1 G--TGTTTGGTTAGTTTAGCAGGAATGTAAGATTATC
51782 GTGTTTGGTTA
1 GTGTTTGGTTA
51793 AAGGAATAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 18
0.64 0.15 0.21
Matches are distributed among these distances:
29 13 0.23
30 5 0.09
31 1 0.02
32 4 0.07
33 1 0.02
34 2 0.04
35 11 0.20
36 1 0.02
37 5 0.09
38 13 0.23
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.41
Consensus pattern (35 bp):
GTGTTTGGTTAGTTTAGCAGGAATGTAAGATTATC
Found at i:51731 original size:29 final size:29
Alignment explanation
Indices: 51706--51809 Score: 82
Period size: 29 Copynumber: 3.3 Consensus size: 29
51696 GCAGGAATGT
51706 AAGATTATCGTGTTTTGTTAAAGGAATAA
1 AAGATTATCGTGTTTTGTTAAAGGAATAA
* * **
51735 AAGATTATTGGAATGTATATTTGGTTTAGCAGGAATGT
1 AAGATTA-TCG--TG--T-TTT-G-TTA-AAGGAATAA
*
51773 AAGATTATCGTGTTTGGTTAAAGGAATAA
1 AAGATTATCGTGTTTTGTTAAAGGAATAA
51802 AAGATTAT
1 AAGATTAT
51810 TGGAATGTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
29 21 0.37
30 5 0.09
31 1 0.02
32 4 0.07
33 1 0.02
34 1 0.02
35 5 0.09
36 1 0.02
37 5 0.09
38 13 0.23
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (29 bp):
AAGATTATCGTGTTTTGTTAAAGGAATAA
Found at i:51762 original size:67 final size:67
Alignment explanation
Indices: 51691--51824 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
51681 TGTTTGGTTA
*
51691 GTTTAGCAGGAATGTAAGATTATCGTGTTTTGTTAAAGGAATAAAAGATTATTGGAATGTATATT
1 GTTTAGCAGGAATGTAAGATTATCGTGTTTGGTTAAAGGAATAAAAGATTATTGGAATGTATATT
51756 TG
66 TG
51758 GTTTAGCAGGAATGTAAGATTATCGTGTTTGGTTAAAGGAATAAAAGATTATTGGAATGTATATT
1 GTTTAGCAGGAATGTAAGATTATCGTGTTTGGTTAAAGGAATAAAAGATTATTGGAATGTATATT
51823 TG
66 TG
51825 ATCAAATTGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (67 bp):
GTTTAGCAGGAATGTAAGATTATCGTGTTTGGTTAAAGGAATAAAAGATTATTGGAATGTATATT
TG
Found at i:56306 original size:36 final size:37
Alignment explanation
Indices: 56246--56318 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
56236 ATAGATTTTA
*
56246 ATTTTAATAATAAAAAATGAATATT-TTTAATAGAAAC
1 ATTTTAATAAT-AAAAATGAATATTAATTAATAGAAAC
56283 ATTTTAATGAAT-AAAATGAATATTAATTAATAGAAA
1 ATTTTAAT-AATAAAAATGAATATTAATTAATAGAAA
56319 TAAGATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 12 0.36
37 18 0.55
38 3 0.09
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (37 bp):
ATTTTAATAATAAAAATGAATATTAATTAATAGAAAC
Found at i:56780 original size:31 final size:27
Alignment explanation
Indices: 56733--56791 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 27
56723 GAATAAATTA
56733 TATGTTTAATACTTTAACTATAATTTTTGT
1 TATGTTTAATACTTTAA-T-T-ATTTTTGT
56763 TATGTTTTAATTA-TTTAATTATTTTTGT
1 TATG-TTTAA-TACTTTAATTATTTTTGT
56791 T
1 T
56792 TTAAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 9 0.33
29 1 0.04
30 5 0.19
31 10 0.37
32 2 0.07
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (27 bp):
TATGTTTAATACTTTAATTATTTTTGT
Found at i:57458 original size:6 final size:6
Alignment explanation
Indices: 57449--57645 Score: 225
Period size: 6 Copynumber: 33.0 Consensus size: 6
57439 AATTCCCCTT
* * * *
57449 TTCTTC TTCTTC TTCTCC TTCTTC TTCTCC TTCTTC TCCTTC TCCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * * *
57497 TCCTTC TCCTTC TTCCTC TTCTCC TTCTTC CTCTTC -TCTTC TCCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
57544 TTCCTC TTCTCC TTCTCC TTCTCC TTCTTC TTCTTC CTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
57592 TTCTTC CTCTTC TTCTTC TTCTTC TTCCTC TTCTTC CTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
57640 TTCTTC
1 TTCTTC
57646 CTCCTATAAT
Statistics
Matches: 165, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
5 5 0.03
6 160 0.97
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (6 bp):
TTCTTC
Found at i:57471 original size:15 final size:15
Alignment explanation
Indices: 57449--57645 Score: 194
Period size: 15 Copynumber: 13.6 Consensus size: 15
57439 AATTCCCCTT
*
57449 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTCC
*
57464 TCCTTCTTCTTCTCC
1 TTCTTCTTCTTCTCC
*
57479 TTCTTCTCCTTCTCC
1 TTCTTCTTCTTCTCC
57494 TTC-TC--CTTCTCC
1 TTCTTCTTCTTCTCC
*
57506 TTCTTCCTCTTCTCC
1 TTCTTCTTCTTCTCC
*
57521 TTCTTCCTCTTCT-C
1 TTCTTCTTCTTCTCC
*
57535 TTCTCCTTC-T-TCC
1 TTCTTCTTCTTCTCC
*
57548 -TCTTCTCCTTCTCC
1 TTCTTCTTCTTCTCC
* *
57562 TTCTCCTTCTTCTTC
1 TTCTTCTTCTTCTCC
* *
57577 TTCCTCTTCTTCTTC
1 TTCTTCTTCTTCTCC
* *
57592 TTCTTCCTCTTCTTC
1 TTCTTCTTCTTCTCC
57607 TTCTTCTTCTTC-CTC
1 TTCTTCTTCTTCTC-C
* *
57622 TTCTTCCTCTTCTTC
1 TTCTTCTTCTTCTCC
57637 TTCTTCTTC
1 TTCTTCTTC
57646 CTCCTATAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 18
0.80 0.10 0.09
Matches are distributed among these distances:
12 17 0.11
13 5 0.03
14 13 0.08
15 118 0.77
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCTTCTTCTTCTCC
Found at i:59548 original size:30 final size:30
Alignment explanation
Indices: 59502--59570 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
59492 ATTAAAAAAA
** *
59502 ATATTAAATATTAAAAAT-T-AATTTAATTT
1 ATATTAAATAAAAAAAATCTAAATATAA-TT
59531 ATACTTAAATAAAAAAAATCTAAATATAATT
1 ATA-TTAAATAAAAAAAATCTAAATATAATT
59562 ATATTAAAT
1 ATATTAAAT
59571 GATATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 19 0.56
31 6 0.18
32 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATTAAATAAAAAAAATCTAAATATAATT
Found at i:62542 original size:20 final size:20
Alignment explanation
Indices: 62517--62572 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
62507 TGGTTCACGG
62517 AATGTAAGATTATCAGTAAA
1 AATGTAAGATTATCAGTAAA
* ***
62537 AATGTAAGATTACCAGTGGG
1 AATGTAAGATTATCAGTAAA
*
62557 AATATAAGATTATCAG
1 AATGTAAGATTATCAG
62573 GGAATAGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.29
Consensus pattern (20 bp):
AATGTAAGATTATCAGTAAA
Found at i:62797 original size:33 final size:34
Alignment explanation
Indices: 62734--62798 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
62724 AAAATATTTA
*
62734 TATATTTTCTTTAAAAAATTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAATTAAAATCATAAAATT
*
62768 TATATTTT-TTTACAAAATTGAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAATT-AAAATCATAAAA
62799 AAGGTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (34 bp):
TATATTTTCTTTAAAAAATTAAAATCATAAAATT
Found at i:64098 original size:18 final size:18
Alignment explanation
Indices: 64075--64176 Score: 77
Period size: 18 Copynumber: 5.8 Consensus size: 18
64065 GTGGTTGCTT
64075 CTCCTCTTCCTTCTTCTC
1 CTCCTCTTCCTTCTTCTC
**
64093 CTCCTC-T--TTCTTGGC
1 CTCCTCTTCCTTCTTCTC
* *
64108 CTCTTCTTCCTTCTTCGC
1 CTCCTCTTCCTTCTTCTC
*
64126 CTCCTCTTCCTTCTT-TGG
1 CTCCTCTTCCTTCTTCT-C
* * * *
64144 TTCTTCTTCCTTCTTGTG
1 CTCCTCTTCCTTCTTCTC
*
64162 TTCCTCTTCCTTCTT
1 CTCCTCTTCCTTCTT
64177 GTGTTCTTCT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.16
16 1 0.01
17 1 0.01
18 55 0.80
19 1 0.01
ACGTcount: A:0.00, C:0.40, G:0.07, T:0.53
Consensus pattern (18 bp):
CTCCTCTTCCTTCTTCTC
Found at i:64140 original size:36 final size:35
Alignment explanation
Indices: 64079--64192 Score: 128
Period size: 36 Copynumber: 3.3 Consensus size: 35
64069 TTGCTTCTCC
* *
64079 TCTTCCTTCTTCTCCTCCTC-T--TTCTTGGCCTCT
1 TCTTCCTTCTTCGCCTCCTCTTCCTTCTTGG-TTCT
64112 TCTTCCTTCTTCGCCTCCTCTTCCTTCTTTGGTTCT
1 TCTTCCTTCTTCGCCTCCTCTTCCTTC-TTGGTTCT
**
64148 TCTTCCTTCTT-GTGTTCCTCTTCCTTCTTGTGTTCT
1 TCTTCCTTCTTCG-CCTCCTCTTCCTTCTTG-GTTCT
64184 TCTTCCTTC
1 TCTTCCTTC
64193 ATCGATACTA
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
33 19 0.27
34 1 0.01
35 4 0.06
36 43 0.61
37 4 0.06
ACGTcount: A:0.00, C:0.38, G:0.08, T:0.54
Consensus pattern (35 bp):
TCTTCCTTCTTCGCCTCCTCTTCCTTCTTGGTTCT
Found at i:64177 original size:18 final size:18
Alignment explanation
Indices: 64127--64192 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
64117 CTTCTTCGCC
64127 TCCTCTTCCTTCTT-TGGT
1 TCCTCTTCCTTCTTGT-GT
*
64145 TCTTCTTCCTTCTTGTGT
1 TCCTCTTCCTTCTTGTGT
64163 TCCTCTTCCTTCTTGTGT
1 TCCTCTTCCTTCTTGTGT
*
64181 TCTTCTTCCTTC
1 TCCTCTTCCTTC
64193 ATCGATACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 43 0.98
19 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.09, T:0.58
Consensus pattern (18 bp):
TCCTCTTCCTTCTTGTGT
Found at i:65220 original size:16 final size:16
Alignment explanation
Indices: 65196--65228 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
65186 TCTAATTAAT
65196 AATTATTGTAATTTGTA
1 AATTATTGTAA-TTGTA
65213 AATT-TTGTAATTGTA
1 AATTATTGTAATTGTA
65228 A
1 A
65229 TAGTGAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
AATTATTGTAATTGTA
Found at i:67545 original size:31 final size:30
Alignment explanation
Indices: 67510--67596 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
67500 TCAATAAAGT
*
67510 TTAAAAAACTATAAAATACTTATTAAATTTA
1 TTAAAATACTATAAAATA-TTATTAAATTTA
* *
67541 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATACTATAAAA-TATTATTAAATTTA
67572 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATACTATAAAAT-ATTATTA
67597 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAAATACTATAAAATATTATTAAATTTA
Found at i:67560 original size:19 final size:21
Alignment explanation
Indices: 67521--67563 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
67511 TAAAAAACTA
*
67521 TAAAATACTTATTAAATTTAT
1 TAAAATACTTATTAAAATTAT
67542 TAAAATA-TTA-TAAAATTAT
1 TAAAATACTTATTAAAATTAT
67561 TAA
1 TAA
67564 TAAATTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATACTTATTAAAATTAT
Found at i:68349 original size:2 final size:2
Alignment explanation
Indices: 68337--68415 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
68327 ATCTATCGTT
*
68337 TA TA TA CA 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 TA TA TA
68379 TA TA TA 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 TA TA TA T
68416 CCTTAAAATG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.