Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006433.1 Corchorus capsularis cultivar CVL-1 contig06454, 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: 79839
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:182 original size:73 final size:73
Alignment explanation
Indices: 1--191 Score: 323
Period size: 73 Copynumber: 2.6 Consensus size: 73
1 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAACAAT-AAA-GCTTAATTCAGGGTAATTA
1 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAACAATAAAAGGCTTAATTCAGGGTAATTA
64 AGTGGAGT
66 AGTGGAGT
*
72 CAATAAAGAACTTAATCTAAAAAGAGATTAAATAAAACAATAAAAGGCTTAATTCAGGGTAATTA
1 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAACAATAAAAGGCTTAATTCAGGGTAATTA
137 AGTGGAGT
66 AGTGGAGT
* * * *
145 CATTAAAGAACTTAATCTAAAAAGAGATTAGGCAAAACAGTAAAAGG
1 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAACAATAAAAGG
192 GCTTGATTTA
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
71 40 0.36
72 3 0.03
73 69 0.62
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.24
Consensus pattern (73 bp):
CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAACAATAAAAGGCTTAATTCAGGGTAATTA
AGTGGAGT
Found at i:3650 original size:12 final size:13
Alignment explanation
Indices: 3633--3663 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3623 GAGGCAACCC
3633 AATTTTAA-TTTT
1 AATTTTAATTTTT
3645 AATTTTAATTTTT
1 AATTTTAATTTTT
3658 AATTTT
1 AATTTT
3664 CTAACTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTTAATTTTT
Found at i:3659 original size:7 final size:6
Alignment explanation
Indices: 3633--3663 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3623 GAGGCAACCC
3633 AATTTT AATTTT AATTTT AATTTTT AATTTT
1 AATTTT AATTTT AATTTT AA-TTTT AATTTT
3664 CTAACTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
AATTTT
Found at i:11174 original size:26 final size:26
Alignment explanation
Indices: 11143--11264 Score: 131
Period size: 26 Copynumber: 4.7 Consensus size: 26
11133 TCGCACATAA
11143 GAGGTCACGTGTGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * * *
11169 GAGGTCACGTGTTGCAGGTATCCGTTG
1 GAGGTCACGTG-TGGAGTTGTACGTTG
11196 GAGGTCACGTGTGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * *
11222 GAGATCACGTGTGGGGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACGTTG
*
11248 GAGGTCATGTGTGGAGT
1 GAGGTCACGTGTGGAGT
11265 GCCAGCTGGC
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.03
26 53 0.68
27 21 0.27
28 2 0.03
ACGTcount: A:0.16, C:0.15, G:0.40, T:0.30
Consensus pattern (26 bp):
GAGGTCACGTGTGGAGTTGTACGTTG
Found at i:11223 original size:53 final size:52
Alignment explanation
Indices: 11143--11264 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
11133 TCGCACATAA
* *
11143 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGTTGCAGGT-ATCCGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTG-TG-AGGTCATACGTTG
* *
11196 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGAGGTCATACGTTG
*
11248 GAGGTCATGTGTGGAGT
1 GAGGTCACGTGTGGAGT
11265 GCCAGCTGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 3 0.05
52 24 0.38
53 36 0.57
ACGTcount: A:0.16, C:0.15, G:0.40, T:0.30
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGAGGTCATACGTTG
Found at i:23125 original size:59 final size:59
Alignment explanation
Indices: 23058--23231 Score: 312
Period size: 59 Copynumber: 2.9 Consensus size: 59
23048 AACCTGAGAC
*
23058 CTTGCTTAAGGAAAACAAGTGTCAAATCACTTGAACCAACCACTTGTAGGTCTGACGAT
1 CTTGCTTAAGGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTGACGAT
*
23117 CTTGCTTAAGGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTAACGAT
1 CTTGCTTAAGGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTGACGAT
* *
23176 CTTACTTAAAGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTGAC
1 CTTGCTTAAGGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTGAC
23232 TGTAACTTAA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 110 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (59 bp):
CTTGCTTAAGGAAAACAAGTGTCAAACCACTTGAACCAACCACTTGTAGGTCTGACGAT
Found at i:26527 original size:60 final size:59
Alignment explanation
Indices: 26453--26611 Score: 194
Period size: 60 Copynumber: 2.7 Consensus size: 59
26443 GACGTTAGAC
* * **
26453 CCTTATTTGAGCATTTTCGATAACGTTATGCCTTTATTTGGCCAAATTAAAAGATCAGA
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCAGA
* *
26512 TCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTAACCAAATTAAAAGATCGGA
1 -CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCAGA
* * * *
26572 CCTTTATTTGAACATTTT-GACAAACATTAGGCTCTTATTT
1 CC-TTATTTGAGCATTTTCGA-TAACGTTAGGCCCTTATTT
26612 GAACAATTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.05
60 82 0.95
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCAGA
Found at i:28740 original size:156 final size:155
Alignment explanation
Indices: 28359--28742 Score: 380
Period size: 156 Copynumber: 2.5 Consensus size: 155
28349 GAGCTTCTCA
28359 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTG-ATGAGCTGAAA
** * * *
28424 TTTTGCCAAGGGACTTAGAATATCCACATAATACTATGCAAAAAATTCTAAGTAAAACTGAGCTT
65 TTTCACCAAGAGACTTAGAATATCCACATAAGACTATGCAAAAAATTCTAAGTAAAACCGAGCTT
* * * *
28489 CCCTTGGTAGTGAACTAGGTTTCTCT
130 CCCTAGATAGAGAACTAGGTTTCACT
* * * * * **
28515 CC-CCAAGTGGTCCTTAAATGAAAAACAAGCATAAGTTTTTCATTCTATGTCCGACAAGGCT-AA
1 CCTCAAACT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGATGA-GCTGAA
* * * * **
28578 TTTTTCACC-AGTAGACTTAGATTATCCCCATAAGGCTATGGGAAAAATTCTAAGTAAAACCGAG
64 -ATTTCACCAAG-AGACTTAGAATATCCACATAAGACTATGCAAAAAATTCTAAGTAAAACCGAG
* * * *
28642 C-TCTCTAGCATAGAGAAGTTGGTTTGACT
127 CTTCCCTAG-ATAGAGAACTAGGTTTCACT
* * * * * * *
28671 CCTCAAACTGTCCTTAACTAAAAAACTAGTATAAGTTTTTCATACTAAGTCTGTTTGAGATGACA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTG-ATGAGCTGAAA
28736 TTTCACC
65 TTTCACC
28743 TAGATGACCT
Statistics
Matches: 179, Mismatches: 41, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
155 15 0.08
156 158 0.88
157 6 0.03
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (155 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGATGAGCTGAAAT
TTCACCAAGAGACTTAGAATATCCACATAAGACTATGCAAAAAATTCTAAGTAAAACCGAGCTTC
CCTAGATAGAGAACTAGGTTTCACT
Found at i:32007 original size:12 final size:12
Alignment explanation
Indices: 31990--32021 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31980 AAGCATGTTG
31990 ATAGTATTTTCA
1 ATAGTATTTTCA
32002 ATAGTATTTTCA
1 ATAGTATTTTCA
*
32014 ATTGTATT
1 ATAGTATT
32022 GAAAAGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (12 bp):
ATAGTATTTTCA
Found at i:33303 original size:48 final size:47
Alignment explanation
Indices: 33220--33357 Score: 186
Period size: 48 Copynumber: 2.9 Consensus size: 47
33210 CGGGGTCCGA
* * * * *
33220 AAAGACCAAGTTTGGCCGAAGGATTTCTGATTCACATGGAAGTGAGG
1 AAAGACCAACTTGGGTCGAACGATTTCTGACTCACATGGAAGTGAGG
* *
33267 AAAGACCAACTTGGGTTGGAACGATTTTTGACTCACATGGAAGTGAGG
1 AAAGACCAACTTGGG-TCGAACGATTTCTGACTCACATGGAAGTGAGG
* *
33315 AAAGACCAACTTGGGTCGAAGGATTGCTGACTCACATGGAAGT
1 AAAGACCAACTTGGGTCGAACGATTTCTGACTCACATGGAAGT
33358 TGTCAATTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 37 0.47
48 42 0.53
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (47 bp):
AAAGACCAACTTGGGTCGAACGATTTCTGACTCACATGGAAGTGAGG
Found at i:33411 original size:16 final size:15
Alignment explanation
Indices: 33388--33446 Score: 91
Period size: 15 Copynumber: 3.7 Consensus size: 15
33378 ATTGAAATGC
33388 TGAAAAGTTGTAAAT
1 TGAAAAGTTGTAAAT
33403 TGAAAAAGTTGTAAAAGT
1 TG-AAAAGTTGT-AAA-T
33421 TGAAAAGTTGTAAAT
1 TGAAAAGTTGTAAAT
33436 TGAAAAGTTGT
1 TGAAAAGTTGT
33447 TGGAGTGCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
15 14 0.34
16 12 0.29
17 12 0.29
18 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (15 bp):
TGAAAAGTTGTAAAT
Found at i:33445 original size:23 final size:22
Alignment explanation
Indices: 33357--33446 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 22
33347 CACATGGAAG
* *
33357 TTGTCAATTGAAAAGTTGTGAA
1 TTGTAAATTGAAAAGTTGTAAA
33379 TTG-AAATGCTGAAAAGTTGTAAA
1 TTGTAAAT--TGAAAAGTTGTAAA
* *
33402 TTGAAAAAGTTGTAAAAGTTGAAAA
1 TTG-TAAA-TTG-AAAAGTTGTAAA
33427 GTTGTAAATTGAAAAGTTGT
1 -TTGTAAATTGAAAAGTTGT
33447 TGGAGTGCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.05
22 3 0.05
23 24 0.43
24 5 0.09
25 17 0.30
26 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.33
Consensus pattern (22 bp):
TTGTAAATTGAAAAGTTGTAAA
Found at i:33527 original size:38 final size:38
Alignment explanation
Indices: 33476--33608 Score: 185
Period size: 38 Copynumber: 3.5 Consensus size: 38
33466 AGCAATCGAA
33476 AACTGCTGAAAGATAACCTGTTTCCAGTCGATCTTGAT
1 AACTGCTGAAAGATAACCTGTTTCCAGTCGATCTTGAT
* * * *
33514 AACTGTTGAAAGATGACCTGTTTCCAGTCGAACTTGAC
1 AACTGCTGAAAGATAACCTGTTTCCAGTCGATCTTGAT
* * *
33552 AAGTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
1 AACTGCTGAAAGATAACCTGTTTCCAGTCGATCTTGAT
* *
33590 AATTGTTGAAAGATAACCT
1 AACTGCTGAAAGATAACCT
33609 TTGATAATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 83 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (38 bp):
AACTGCTGAAAGATAACCTGTTTCCAGTCGATCTTGAT
Found at i:33623 original size:22 final size:24
Alignment explanation
Indices: 33585--33630 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
33575 CCAGTCAATC
33585 TTGATAATTGTTGAAAGATAACCT
1 TTGATAATTGTTGAAAGATAACCT
*
33609 TTGATAA-T-TTGAAAGATGACCT
1 TTGATAATTGTTGAAAGATAACCT
33631 ATTTCTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (24 bp):
TTGATAATTGTTGAAAGATAACCT
Found at i:33662 original size:98 final size:98
Alignment explanation
Indices: 33510--33962 Score: 746
Period size: 98 Copynumber: 4.6 Consensus size: 98
33500 CAGTCGATCT
* * *
33510 TGATAACTGTTGAAAGATGACCTGTTTCCAGTCGAA-CTTGACAAGTGCTGAAAGATGACCTGTT
1 TGATAA-T-TTGAAAGATGACCTGTTTCCAGTC-AATCTTGATAACTGTTGAAAGATGACCTGTT
*
33574 TCCAGTCAATCTTGATAATTGTTGAAAGATAACCTT
63 TCCAGTCAATCTTGATAATTGTTGAAAGATAACCTC
* * * * *
33610 TGATAATTTGAAAGATGACCTATTTCTAGTCAATCTTAAAAAGTGTTGAAAGATGACCTGTTTCC
1 TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTGTTTCC
*
33675 AGTCAATCTTAATAATTGTTGAAAGATAACCTC
66 AGTCAATCTTGATAATTGTTGAAAGATAACCTC
*
33708 TGATAATTTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCTGTTTCC
1 TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTGTTTCC
33773 AGTCAATCTTGATAATTGTTGAAAGATAACCTC
66 AGTCAATCTTGATAATTGTTGAAAGATAACCTC
* *
33806 TGATAATTTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACATGTTTCC
1 TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTGTTTCC
*
33871 AGTCGATCTTGATAATTGTTGAAAGATAACCTC
66 AGTCAATCTTGATAATTGTTGAAAGATAACCTC
33904 TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCT
1 TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCT
33963 CTGATAATTT
Statistics
Matches: 334, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
97 2 0.01
98 325 0.97
99 1 0.00
100 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (98 bp):
TGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTGTTTCC
AGTCAATCTTGATAATTGTTGAAAGATAACCTC
Found at i:33668 original size:38 final size:38
Alignment explanation
Indices: 33617--33706 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
33607 CTTTGATAAT
*
33617 TTGAAAGATGACCTATTTCTAGTCAATCTTAAAAAGTG
1 TTGAAAGATGACCTATTTCCAGTCAATCTTAAAAAGTG
* * *
33655 TTGAAAGATGACCTGTTTCCAGTCAATCTTAATAATTG
1 TTGAAAGATGACCTATTTCCAGTCAATCTTAAAAAGTG
*
33693 TTGAAAGATAACCT
1 TTGAAAGATGACCT
33707 CTGATAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (38 bp):
TTGAAAGATGACCTATTTCCAGTCAATCTTAAAAAGTG
Found at i:33722 original size:60 final size:60
Alignment explanation
Indices: 33655--34022 Score: 293
Period size: 60 Copynumber: 5.9 Consensus size: 60
33645 TTAAAAAGTG
* * *
33655 TTGAAAGATGACCTGTTTCCAGTCAATCTTAATAATTGTTGAAAGATAACCTCTGATAAT
1 TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTCTGATAAT
* * *
33715 TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCTGTTTCCAGTCAAT
1 TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACC--TCT-GA-T-AAT
* *** *
33780 CTTGATA-AT----TGTTGAAAGAT-AACCTCTGATAA-T-TTGAAAGATGACCTGTTTCCAGTC
1 -TTGAAAGATGACCTGTTTCCAG-TCAATCT-TGATAACTGTTGAAAGATGACC----T-C--T-
33837 GATCTTGATAACT
55 GA---T-A--A-T
* * * *
33850 GTTGAAAGATGACATGTTTCCAGTCGATCTTGATAATTGTTGAAAGATAACCTCTGATAAT
1 -TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTCTGATAAT
33911 TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTCTGATAAT
1 TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTCTGATAAT
* * **
33971 TTGAAAGATGACCTTTTTCCGGTCGGTCTTGATAACTGTTGAAAGATGACCT
1 TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCT
34023 GTTTCCAGTC
Statistics
Matches: 249, Mismatches: 33, Indels: 52
0.75 0.10 0.16
Matches are distributed among these distances:
60 164 0.66
61 11 0.04
62 12 0.05
63 1 0.00
64 2 0.01
65 9 0.04
66 5 0.02
67 2 0.01
68 2 0.01
69 2 0.01
70 6 0.02
71 3 0.01
72 1 0.00
74 7 0.03
75 10 0.04
76 12 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (60 bp):
TTGAAAGATGACCTGTTTCCAGTCAATCTTGATAACTGTTGAAAGATGACCTCTGATAAT
Found at i:33758 original size:38 final size:37
Alignment explanation
Indices: 33708--33804 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 37
33698 AGATAACCTC
*
33708 TGATAAT-TTGAAAGATGACCTGTTTCCAGTCGATCT
1 TGATAATGTTGAAAGATGACCTGTTTCCAGTCAATCT
33744 TGATAACTGTTGAAAGATGACCTGTTTCCAGTCAATCT
1 TGATAA-TGTTGAAAGATGACCTGTTTCCAGTCAATCT
*
33782 TGATAATTGTTGAAAGATAACCT
1 TGATAA-TGTTGAAAGATGACCT
33805 CTGATAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 6 0.11
37 1 0.02
38 49 0.88
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (37 bp):
TGATAATGTTGAAAGATGACCTGTTTCCAGTCAATCT
Found at i:33819 original size:22 final size:24
Alignment explanation
Indices: 33782--33826 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
33772 CAGTCAATCT
33782 TGATAATTGTTGAAAGATAACCTC
1 TGATAATTGTTGAAAGATAACCTC
*
33806 TGATAA-T-TTGAAAGATGACCT
1 TGATAATTGTTGAAAGATAACCT
33827 GTTTCCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (24 bp):
TGATAATTGTTGAAAGATAACCTC
Found at i:33853 original size:158 final size:157
Alignment explanation
Indices: 33655--34022 Score: 438
Period size: 158 Copynumber: 2.3 Consensus size: 157
33645 TTAAAAAGTG
* * * * * *
33655 TTGAAAGATGACCTGTTTCCAGTCAATCTTAATAATTGTTGAAAGATAACCTCTGAT-AATTTGA
1 TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCTCT-ATCAAGTCGA
* *** * *
33719 -AAGATGACCTGTTTCCAG-TCGATCT-TGATAACTGTTGAAAGATGACCTGTTTCCAGTCAATC
65 CAAGAT-AACTGTTGAAAGAT-AACCTCTGATAA-T-TTGAAAGATGACCTGTTTCCAGTCAATC
*
33781 TTGATAATTGTTGAAAGATAACCTCTGATAAT
126 TTGATAACTGTTGAAAGATAACCTCTGATAAT
* * * *
33813 TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACATGTTTCCAGTCGAT
1 TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCTCTATCAAGTCGA-
** *
33878 CTTGATAATTGTTGAAAGATAACCTCTGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGA
65 CAAGATAACTGTTGAAAGATAACCTCTGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGA
*
33943 TAACTGTTGAAAGATGACCTCTGATAAT
130 TAACTGTTGAAAGATAACCTCTGATAAT
* * *
33971 TTGAAAGATGACCTTTTTCCGGTCGGTCTTGATAACTGTTGAAAGATGACCT
1 TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCT
34023 GTTTCCAGTC
Statistics
Matches: 180, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
157 1 0.01
158 158 0.88
159 11 0.06
160 10 0.06
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (157 bp):
TTGAAAGATGACCTGTTTCCAGTCGATCTTGATAACTGTTGAAAGATGACCTCTATCAAGTCGAC
AAGATAACTGTTGAAAGATAACCTCTGATAATTTGAAAGATGACCTGTTTCCAGTCAATCTTGAT
AACTGTTGAAAGATAACCTCTGATAAT
Found at i:33856 original size:38 final size:37
Alignment explanation
Indices: 33806--33902 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 37
33796 AGATAACCTC
33806 TGATAAT-TTGAAAGATGACCTGTTTCCAGTCGATCT
1 TGATAATGTTGAAAGATGACCTGTTTCCAGTCGATCT
*
33842 TGATAACTGTTGAAAGATGACATGTTTCCAGTCGATCT
1 TGATAA-TGTTGAAAGATGACCTGTTTCCAGTCGATCT
*
33880 TGATAATTGTTGAAAGATAACCT
1 TGATAA-TGTTGAAAGATGACCT
33903 CTGATAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 6 0.11
37 1 0.02
38 48 0.87
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (37 bp):
TGATAATGTTGAAAGATGACCTGTTTCCAGTCGATCT
Found at i:33917 original size:22 final size:24
Alignment explanation
Indices: 33880--33924 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
33870 CAGTCGATCT
33880 TGATAATTGTTGAAAGATAACCTC
1 TGATAATTGTTGAAAGATAACCTC
*
33904 TGATAA-T-TTGAAAGATGACCT
1 TGATAATTGTTGAAAGATAACCT
33925 GTTTCCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (24 bp):
TGATAATTGTTGAAAGATAACCTC
Found at i:33976 original size:22 final size:24
Alignment explanation
Indices: 33940--33984 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
33930 CAGTCAATCT
33940 TGATAACTGTTGAAAGATGACCTC
1 TGATAACTGTTGAAAGATGACCTC
33964 TGATAA-T-TTGAAAGATGACCT
1 TGATAACTGTTGAAAGATGACCT
33985 TTTTCCGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.67
23 1 0.05
24 6 0.29
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (24 bp):
TGATAACTGTTGAAAGATGACCTC
Found at i:35480 original size:12 final size:12
Alignment explanation
Indices: 35463--35488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35453 TTTCATTCAC
35463 TTTTGATTTGAA
1 TTTTGATTTGAA
35475 TTTTGATTTGAA
1 TTTTGATTTGAA
35487 TT
1 TT
35489 ATTTGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTTGATTTGAA
Found at i:35800 original size:14 final size:13
Alignment explanation
Indices: 35781--35828 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
35771 ACCCGAAACC
35781 TTTTGAAAACTCAT
1 TTTTGAAAAC-CAT
*
35795 TTTTGAAAACCTT
1 TTTTGAAAACCAT
*
35808 TTCTTGAAAACAAT
1 TT-TTGAAAACCAT
35822 TTTTGAA
1 TTTTGAA
35829 TAATGTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:37590 original size:19 final size:18
Alignment explanation
Indices: 37566--37601 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37556 TGAAGATTTC
37566 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
37585 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
37602 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:38875 original size:15 final size:16
Alignment explanation
Indices: 38855--38888 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38845 GATTGCTTTC
*
38855 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
38870 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
38886 TTA
1 TTA
38889 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:43335 original size:13 final size:13
Alignment explanation
Indices: 43315--43346 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43305 ATGATTATGC
43315 ATAA-TGCAATTT
1 ATAAGTGCAATTT
43327 ATAAGTGCAATTT
1 ATAAGTGCAATTT
43340 ATAAGTG
1 ATAAGTG
43347 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (13 bp):
ATAAGTGCAATTT
Found at i:44593 original size:28 final size:28
Alignment explanation
Indices: 44561--44619 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
44551 TGTTTTTTTA
* *
44561 TATCTCTTTCATTGCATTAAAAAACTGT
1 TATCTCTATCATTGCATTAAAAAACTAT
*
44589 TA--TCTATCATTGCATTAGAAAACTAT
1 TATCTCTATCATTGCATTAAAAAACTAT
44615 TATCT
1 TATCT
44620 ATGATGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 23 0.88
28 3 0.12
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (28 bp):
TATCTCTATCATTGCATTAAAAAACTAT
Found at i:44599 original size:26 final size:26
Alignment explanation
Indices: 44569--44621 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
44559 TATATCTCTT
*
44569 TCATTGCATTAAAAAACTGTTATCTA
1 TCATTGCATTAAAAAACTATTATCTA
*
44595 TCATTGCATTAGAAAACTATTATCTA
1 TCATTGCATTAAAAAACTATTATCTA
44621 T
1 T
44622 GATGTCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (26 bp):
TCATTGCATTAAAAAACTATTATCTA
Found at i:45195 original size:57 final size:57
Alignment explanation
Indices: 45122--45271 Score: 205
Period size: 56 Copynumber: 2.7 Consensus size: 57
45112 CCTTTTAATC
* * * * *
45122 CTTTTACTCTTCTTAGTTTAATTACTCTTGAATTAAACTATCTATTGTTTACTCTTT
1 CTTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATCTACTATATACTCCTT
* *
45179 CTTTTACTCTTTTTAGTTTAATTACTC-TGAATTAAACTGTCTACTATATATTCCTT
1 CTTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATCTACTATATACTCCTT
* *
45235 CTTTTACTCTTTCTAGTTTAATTA-TTTTGAATTAAAC
1 CTTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAC
45272 CAGTTTACTG
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
55 1 0.01
56 56 0.67
57 26 0.31
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (57 bp):
CTTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATCTACTATATACTCCTT
Found at i:45354 original size:32 final size:31
Alignment explanation
Indices: 45315--45488 Score: 233
Period size: 32 Copynumber: 5.5 Consensus size: 31
45305 TTTTCTATTG
*
45315 CTTTTACTCTTACTTCATTCTGCTGATTACTT
1 CTTTTACTTTTACTTCATT-TGCTGATTACTT
* * *
45347 ATTTTACTTTTACTCCACTTT-CATGACTACTT
1 CTTTTACTTTTACTTCA-TTTGC-TGATTACTT
*
45379 CTTTCACTTTTACTTCACTTTGCTGATTACTT
1 CTTTTACTTTTACTTCA-TTTGCTGATTACTT
45411 CTTTTACTTTTACTTCATTTTGCTGATTACTT
1 CTTTTACTTTTACTTCA-TTTGCTGATTACTT
45443 CTTTTACTTTTACTTCATTTTGCTGATTACTT
1 CTTTTACTTTTACTTCA-TTTGCTGATTACTT
*
45475 CTGTTACTTTTACT
1 CTTTTACTTTTACT
45489 CTTTTATTTT
Statistics
Matches: 128, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
31 1 0.01
32 124 0.97
33 3 0.02
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.55
Consensus pattern (31 bp):
CTTTTACTTTTACTTCATTTGCTGATTACTT
Found at i:45408 original size:17 final size:17
Alignment explanation
Indices: 45388--45475 Score: 103
Period size: 16 Copynumber: 5.4 Consensus size: 17
45378 TCTTTCACTT
*
45388 TTACTTCACTTTGCTGA
1 TTACTTCATTTTGCTGA
* *
45405 TTACTTC-TTTTACT-T
1 TTACTTCATTTTGCTGA
45420 TTACTTCATTTTGCTGA
1 TTACTTCATTTTGCTGA
* *
45437 TTACTTC-TTTTACT-T
1 TTACTTCATTTTGCTGA
45452 TTACTTCATTTTGCTGA
1 TTACTTCATTTTGCTGA
45469 TTACTTC
1 TTACTTC
45476 TGTTACTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
15 14 0.24
16 23 0.40
17 21 0.36
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.57
Consensus pattern (17 bp):
TTACTTCATTTTGCTGA
Found at i:45435 original size:96 final size:96
Alignment explanation
Indices: 45315--45488 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
45305 TTTTCTATTG
45315 CTTTTACTCTTACTTCATTCTGCTGATTACTTATTTTACTTTTACTCCACTTT-CATGACTACTT
1 CTTTTACTCTTACTTCATTCTGCTGATTACTTATTTTACTTTTACTCCACTTTGC-TGACTACTT
45379 CT-TTCACTTTTACTTCACTTTGCTGATTACTT
65 CTGTT-ACTTTTACTTCACTTTGCTGATTACTT
* * * * * *
45411 CTTTTACTTTTACTTCATTTTGCTGATTACTTCTTTTACTTTTACTTCATTTTGCTGATTACTTC
1 CTTTTACTCTTACTTCATTCTGCTGATTACTTATTTTACTTTTACTCCACTTTGCTGACTACTTC
45476 TGTTACTTTTACT
66 TGTTACTTTTACT
45489 CTTTTATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
96 67 0.96
97 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.55
Consensus pattern (96 bp):
CTTTTACTCTTACTTCATTCTGCTGATTACTTATTTTACTTTTACTCCACTTTGCTGACTACTTC
TGTTACTTTTACTTCACTTTGCTGATTACTT
Found at i:45518 original size:36 final size:35
Alignment explanation
Indices: 45401--45574 Score: 180
Period size: 36 Copynumber: 5.1 Consensus size: 35
45391 CTTCACTTTG
* *
45401 CTGATTACTTCTTTTACTTTTA--C-TTCATTTTG
1 CTGATTACTTCTTTTACTTTTACTCTTTTATTTTA
* *
45433 CTGATTACTTCTTTTACTTTTA--C-TTCATTTTG
1 CTGATTACTTCTTTTACTTTTACTCTTTTATTTTA
*
45465 CTGATTACTTCTGTTACTTTTACTCTTTTATTTTTA
1 CTGATTACTTCTTTTACTTTTACTCTTTTA-TTTTA
* * * *
45501 CTGATTAGTTCTTTTACTTCTACTATTTTACTTTCA
1 CTGATTACTTCTTTTACTTTTACTCTTTTA-TTTTA
* *
45537 CTGATTACTTCTTTTACTCTTGCTCTTTTACTTTTA
1 CTGATTACTTCTTTTACTTTTACTCTTTTA-TTTTA
45573 CT
1 CT
45575 AATTTAATTT
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
32 53 0.43
34 1 0.01
35 3 0.02
36 66 0.54
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.59
Consensus pattern (35 bp):
CTGATTACTTCTTTTACTTTTACTCTTTTATTTTA
Found at i:45548 original size:72 final size:67
Alignment explanation
Indices: 45315--45574 Score: 214
Period size: 64 Copynumber: 3.9 Consensus size: 67
45305 TTTTCTATTG
* * * * * *
45315 CTTTTACTCTTACTTCA-TTCTGCTGATTACTTATTTTACTTTTACTC---CACTTT-CATGACT
1 CTTTTACTTTTACTTCATTTC-ACTGATTACTTCTTTTACTTTTACTCTTTTATTTTAC-TGATT
45375 ACTT
64 ACTT
* * * *
45379 CTTTCACTTTTACTTCACTTT-GCTGATTACTTCTTTTACTTTTA--C-TTCATTTTGCTGATTA
1 CTTTTACTTTTACTTCA-TTTCACTGATTACTTCTTTTACTTTTACTCTTTTATTTTACTGATTA
45440 CTT
65 CTT
** *
45443 CTTTTACTTTTACTTCATTTTGCTGATTACTTCTGTTACTTTTACTCTTTTATTTTTACTGATTA
1 CTTTTACTTTTACTTCATTTCACTGATTACTTCTTTTACTTTTACTCTTTTA-TTTTACTGATTA
*
45508 GTT
65 CTT
* * * *
45511 CTTTTACTTCTACTATTTTACTTTCACTGATTACTTCTTTTACTCTTGCTCTTTTACTTTTACT
1 CTTTTACTT-T--TACTTCA-TTTCACTGATTACTTCTTTTACTTTTACTCTTTTA-TTTTACT
45575 AATTTAATTT
Statistics
Matches: 164, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 88 0.54
65 1 0.01
66 3 0.02
67 3 0.02
68 22 0.13
69 1 0.01
71 5 0.03
72 37 0.23
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.57
Consensus pattern (67 bp):
CTTTTACTTTTACTTCATTTCACTGATTACTTCTTTTACTTTTACTCTTTTATTTTACTGATTAC
TT
Found at i:46145 original size:40 final size:40
Alignment explanation
Indices: 46062--46145 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
46052 TTTACTCCCT
* * *
46062 CTCTTAATTATCAATTTACTAATCAATCCTTCTGCTTTAA
1 CTCTTAACTATCAATTTACTAATCAATCCTTCTACCTTAA
* * *
46102 CTCTTAACTATCAATTTACTGATTAATCCTT-TCACCTTGA
1 CTCTTAACTATCAATTTACTAATCAATCCTTCT-ACCTTAA
46142 CTCT
1 CTCT
46146 AAATTACTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44
Consensus pattern (40 bp):
CTCTTAACTATCAATTTACTAATCAATCCTTCTACCTTAA
Found at i:49518 original size:30 final size:30
Alignment explanation
Indices: 49482--49556 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
49472 AGAGGATGCC
* **
49482 ATCGCACAAGACCGGCCATTGCATGGAG-GG
1 ATCGCACAAGACCGGCCATGGCATGG-GCCA
*
49512 ATCGCACATGACCGGCCATGGCATGGGCCA
1 ATCGCACAAGACCGGCCATGGCATGGGCCA
49542 ATCGCACAAGACCGG
1 ATCGCACAAGACCGG
49557 GCACAAGCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.27, C:0.31, G:0.31, T:0.12
Consensus pattern (30 bp):
ATCGCACAAGACCGGCCATGGCATGGGCCA
Found at i:52097 original size:33 final size:33
Alignment explanation
Indices: 52000--52104 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
51990 TTGCAAAGAG
* * *
52000 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGATACTAAATC
** *
52033 TAATTT-GAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGTGATGATACTAAATC
52066 TGTTTTAGGTGTTGTTTGTGATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGATACTAAATC
52099 TGTTTT
1 TGTTTT
52105 GGATGCTAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 59 0.97
34 1 0.02
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.47
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGATACTAAATC
Found at i:52118 original size:33 final size:32
Alignment explanation
Indices: 52048--52140 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 32
52038 TGAGTGTTGT
* * **
52048 TTGTGATGACACTAAATCTGTTTTAGGTGTTGT
1 TTGTGATGAAACTAAATCTGTTTT-GGTGCTAA
*
52081 TTGTGATGATACTAAATCTGTTTTGGATGCTAA
1 TTGTGATGAAACTAAATCTGTTTTGG-TGCTAA
52114 TTGTGATGAAAAC-AAATCTGTTTTGGT
1 TTGTGATG-AAACTAAATCTGTTTTGGT
52141 TGATCATAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
32 3 0.06
33 47 0.89
34 3 0.06
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (32 bp):
TTGTGATGAAACTAAATCTGTTTTGGTGCTAA
Found at i:52118 original size:66 final size:66
Alignment explanation
Indices: 52000--52137 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
51990 TTGCAAAGAG
* ** *
52000 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATG-ACACTAAA
1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGCTAATTGTGATGAAAAC-AAA
52064 TC
65 TC
* * * **
52066 TGTTTTAGGTGTTGTTTGTGATGATACTAAATCTGTTTTG-GATGCTAATTGTGATGAAAACAAA
1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAG-TGCTAATTGTGATGAAAACAAA
52130 TC
65 TC
52132 TGTTTT
1 TGTTTT
52138 GGTTGATCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 1 0.02
66 57 0.93
67 3 0.05
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (66 bp):
TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGCTAATTGTGATGAAAACAAAT
C
Found at i:52167 original size:66 final size:66
Alignment explanation
Indices: 52097--52226 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 66
52087 TGATACTAAA
* * * *
52097 TCTGTTTTGGATGCTAATTGTGA-TGAAAACAAATCTGTTTTGGTTGATCATAGCATTGCAAATA
1 TCTGTTTTGGATGATAATAG-CATTGAAAACAAATCTGTTTTGGTTGATCATAGCATTGAAAATA
52161 AT
65 AT
* * * * * *
52163 TCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGTTTGATCATAGCATTGAAAATA
1 TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGATCATAGCATTGAAAATA
52227 GGACTGTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (66 bp):
TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGATCATAGCATTGAAAATAA
T
Found at i:52237 original size:33 final size:33
Alignment explanation
Indices: 52130--52226 Score: 176
Period size: 33 Copynumber: 2.9 Consensus size: 33
52120 TGAAAACAAA
52130 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
52163 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* *
52196 TCTGTTTTGTTTGATCATAGCATTGAAAATA
1 TCTGTTTTGGTTGATCATAGCATTGCAAATA
52227 GGACTGTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:55876 original size:13 final size:16
Alignment explanation
Indices: 55842--55871 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55832 TTTTTGTGAT
55842 CTCTTTCTTTTTTAGG
1 CTCTTTCTTTTTTAGG
55858 CTCTTT-TTTTTTAG
1 CTCTTTCTTTTTTAG
55872 TCTTTATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.67
Consensus pattern (16 bp):
CTCTTTCTTTTTTAGG
Found at i:59820 original size:11 final size:11
Alignment explanation
Indices: 59804--59837 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
59794 GAAGTTCGTG
59804 TTTTGAAGATT
1 TTTTGAAGATT
*
59815 TTTTGAAGATA
1 TTTTGAAGATT
*
59826 TTTTGAAAATT
1 TTTTGAAGATT
59837 T
1 T
59838 GAAGACAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (11 bp):
TTTTGAAGATT
Found at i:65535 original size:12 final size:13
Alignment explanation
Indices: 65513--65539 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65503 ATAGAAGATG
65513 GCATAATTTTTTC
1 GCATAATTTTTTC
65526 GCATAATTTTTTC
1 GCATAATTTTTTC
65539 G
1 G
65540 AAAATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (13 bp):
GCATAATTTTTTC
Found at i:66724 original size:11 final size:10
Alignment explanation
Indices: 66706--66739 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
66696 GAAGTTCGTG
66706 TTTTGAAGAT
1 TTTTGAAGAT
66716 TTCTTGAAGAT
1 TT-TTGAAGAT
66727 ATTTTGAAGAT
1 -TTTTGAAGAT
66738 TT
1 TT
66740 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:70991 original size:127 final size:127
Alignment explanation
Indices: 70765--70993 Score: 363
Period size: 127 Copynumber: 1.8 Consensus size: 127
70755 TTAAAAGGTA
* *
70765 TGGGGCCCCTCCACATTCTGGTAGGAACTTCCACAAGTCAAGAACCGTGACTATTTACAATTCTG
1 TGGGGCCCCTCCACATTCTGGTAGGAACTTCCACAAGTCAAGAACCATGACCATTTACAATTCTG
70830 GGAATAATCAAGGCTCTTGGCTTTATGCAAATGATGTGAATGTCATGAATTTATTTAAGATG
66 GGAATAATCAAGGCTCTTGGCTTTATGCAAATGATGTGAATGTCATGAATTTATTTAAGATG
* * * *
70892 TGGGGTCCCTCCACATTTTGGTAGGAACTTCCATAAG-CTAGGAACCATGACCATTTACAATTCT
1 TGGGGCCCCTCCACATTCTGGTAGGAACTTCCACAAGTC-AAGAACCATGACCATTTACAATTCT
*
70956 GTGAATAATC-AGAGCTCTTGGCTTTATGCAAATGATGT
65 GGGAATAATCAAG-GCTCTTGGCTTTATGCAAATGATGT
70994 CATGATGCAT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
126 3 0.03
127 90 0.97
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (127 bp):
TGGGGCCCCTCCACATTCTGGTAGGAACTTCCACAAGTCAAGAACCATGACCATTTACAATTCTG
GGAATAATCAAGGCTCTTGGCTTTATGCAAATGATGTGAATGTCATGAATTTATTTAAGATG
Found at i:71142 original size:35 final size:35
Alignment explanation
Indices: 71096--71179 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
71086 TTGCAAACAT
*
71096 CAAACCATTGTTCTAAGACTAGAAATCAAGGATTA
1 CAAACCATTGTTCTAAGACTAGAAAGCAAGGATTA
** * * * *
71131 CAAACCATTGTTCCGATACTAGGACGCAAGGATTT
1 CAAACCATTGTTCTAAGACTAGAAAGCAAGGATTA
71166 CAAACCATTGTTCT
1 CAAACCATTGTTCT
71180 GAAACTAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (35 bp):
CAAACCATTGTTCTAAGACTAGAAAGCAAGGATTA
Found at i:74425 original size:26 final size:26
Alignment explanation
Indices: 74395--74447 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
74385 TATATCTCTT
*
74395 TCATTGCACTAGAAAACTGTTATCTA
1 TCATTGCACTAGAAAACTATTATCTA
*
74421 TCATTGCATTAGAAAACTATTATCTA
1 TCATTGCACTAGAAAACTATTATCTA
74447 T
1 T
74448 GATGTCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (26 bp):
TCATTGCACTAGAAAACTATTATCTA
Found at i:75020 original size:57 final size:55
Alignment explanation
Indices: 74957--75102 Score: 175
Period size: 56 Copynumber: 2.6 Consensus size: 55
74947 TTTACTCTGA
* * *
74957 TTACTCTTTCTTTTACTCTTCTTAGTTTAATTACTCTTAAATTAAACTATCTATTGT
1 TTACTCTTTCTTTTACTCTT-TTAGTTTAATTAATC-TAAATTAAACTATCTACTAT
* *
75014 TTACTCTTTCTTTTACTCCTTTTAGTTTAATTAATCTGAATTAAACTGTCTACTAT
1 TTACTCTTTCTTTTACT-CTTTTAGTTTAATTAATCTAAATTAAACTATCTACTAT
* * * *
75070 ATATTCCTGCTTTTACTCTTTCTAGTTTAATTA
1 TTACTCTTTCTTTTACTCTTT-TAGTTTAATTA
75103 TTAAACCAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
55 4 0.05
56 40 0.51
57 31 0.40
58 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (55 bp):
TTACTCTTTCTTTTACTCTTTTAGTTTAATTAATCTAAATTAAACTATCTACTAT
Found at i:75190 original size:32 final size:32
Alignment explanation
Indices: 75152--75330 Score: 189
Period size: 32 Copynumber: 5.5 Consensus size: 32
75142 TTTTCTATTG
*
75152 CTTTTACTCTTACTTCATTCTGCTGATTACTT
1 CTTTTACTTTTACTTCATTCTGCTGATTACTT
* *
75184 CTTTTACTTTTACTCCACTT-TGCTGACTACTT
1 CTTTTACTTTTACTTCA-TTCTGCTGATTACTT
* * *
75216 CTTTCACTTTTACTTCACTCTGCTAATTACTT
1 CTTTTACTTTTACTTCATTCTGCTGATTACTT
* *
75248 CTTTTACTTTTACTTCATTTTGTTGATTACTT
1 CTTTTACTTTTACTTCATTCTGCTGATTACTT
* * * * *
75280 CTGTTACTTTTACTCTTTTATTTTTACTGATAACTT
1 CTTTTACTTTTA--C-TTCA-TTCTGCTGATTACTT
75316 CTTTTACTTTTACTT
1 CTTTTACTTTTACTT
75331 TTACTCTTTT
Statistics
Matches: 122, Mismatches: 19, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
31 1 0.01
32 89 0.73
33 4 0.03
34 2 0.02
35 3 0.02
36 23 0.19
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (32 bp):
CTTTTACTTTTACTTCATTCTGCTGATTACTT
Found at i:75323 original size:36 final size:36
Alignment explanation
Indices: 75241--75449 Score: 137
Period size: 36 Copynumber: 5.8 Consensus size: 36
75231 CACTCTGCTA
*
75241 ATTACTTCTTTTACTTTTA--C-TTCATTTTGT--TG
1 ATTACTTCTTTTACTTTTACTCTTTTATTTT-TACTG
*
75273 ATTACTTCTGTTACTTTTACTCTTTTATTTTTACTG
1 ATTACTTCTTTTACTTTTACTCTTTTATTTTTACTG
* *
75309 ATAACTTCTTTTACTTTTA--CTTTTACTCTTTTATTCTTA
1 ATTACTTCTTTTACTTTTACTCTTTTA-T-TTTTA--C-TG
* *** **
75348 ATGACCAATTTT-CGAATTACTTCTTTTACTTTTTATCTG
1 ATTACTTCTTTTAC-TTTTAC-TCTTTTA-TTTTTA-CTG
* * * *
75387 ATTTCTTCTTTTACTTCTGCTCTTTTACTTTTACTG
1 ATTACTTCTTTTACTTTTACTCTTTTATTTTTACTG
*
75423 ATTACTTCTTTTACTTCTACTCTTTTA
1 ATTACTTCTTTTACTTTTACTCTTTTA
75450 CTTCTACTAT
Statistics
Matches: 138, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
32 18 0.13
34 8 0.06
35 8 0.06
36 52 0.38
37 5 0.04
38 9 0.07
39 22 0.16
40 3 0.02
41 5 0.04
42 8 0.06
ACGTcount: A:0.18, C:0.19, G:0.04, T:0.59
Consensus pattern (36 bp):
ATTACTTCTTTTACTTTTACTCTTTTATTTTTACTG
Found at i:75412 original size:14 final size:14
Alignment explanation
Indices: 75393--75466 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 14
75383 TCTGATTTCT
*
75393 TCTTTTACTTCTGC
1 TCTTTTACTTCTAC
*
75407 TCTTTTACTTTTAC
1 TCTTTTACTTCTAC
**
75421 T-GATTAC-T-T-C
1 TCTTTTACTTCTAC
75431 T-T-TTACTTCTAC
1 TCTTTTACTTCTAC
75443 TCTTTTACTTCTAC
1 TCTTTTACTTCTAC
*
75457 TATTTTACTT
1 TCTTTTACTT
75467 TCACTGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 2 0.04
12 3 0.06
13 5 0.10
14 32 0.65
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (14 bp):
TCTTTTACTTCTAC
Found at i:75452 original size:50 final size:50
Alignment explanation
Indices: 75393--75514 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
75383 TCTGATTTCT
* * *
75393 TCTTTTACTTCTGCTCTTTTACTTTTACTGATTACTTCTTTTACT-TCTAC
1 TCTTTTACTTCTACTATTTTACTTTCACTGATTACTTCTTTTACTCT-TAC
*
75443 TCTTTTACTTCTACTATTTTACTTTCACTGATTACTTCTTTTACTCTTGC
1 TCTTTTACTTCTACTATTTTACTTTCACTGATTACTTCTTTTACTCTTAC
*
75493 TCTTTTACTTTTACTAATTTTA
1 TCTTTTACTTCTACT-ATTTTA
75515 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 58 0.89
51 7 0.11
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.58
Consensus pattern (50 bp):
TCTTTTACTTCTACTATTTTACTTTCACTGATTACTTCTTTTACTCTTAC
Found at i:75684 original size:34 final size:34
Alignment explanation
Indices: 75555--75697 Score: 105
Period size: 34 Copynumber: 4.3 Consensus size: 34
75545 TTCTTTTACT
* * * *
75555 TTTTACTCTTAATTACCAACTTACTAATT--TAC
1 TTTTACTCTTAATTACTAATTTTCTAATTACTTC
* ** ** * *
75587 TTTTACTCTTAGTTGTTGGTTTTCTAATTTCTCC
1 TTTTACTCTTAATTACTAATTTTCTAATTACTTC
* *
75621 TTTTACTCTTAATTACTAATTTGCAAATTACTTC
1 TTTTACTCTTAATTACTAATTTTCTAATTACTTC
*
75655 TTTTACTCTT-ATCTACT-ATTTCTCTAATTACCTC
1 TTTTACTCTTAAT-TACTAATTT-TCTAATTACTTC
*
75689 TCTTACTCT
1 TTTTACTCT
75698 GACCCTTAAT
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
32 21 0.25
33 6 0.07
34 58 0.68
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.52
Consensus pattern (34 bp):
TTTTACTCTTAATTACTAATTTTCTAATTACTTC
Found at i:76098 original size:32 final size:32
Alignment explanation
Indices: 76075--76150 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
76065 TTCACCTTGG
76075 CTCTTAATTACTAAGTTACCCTTTTACTTTGA
1 CTCTTAATTACTAAGTTACCCTTTTACTTTGA
*
76107 CTCTTAATTACTAAGTTATCCTTTTACTTTGA
1 CTCTTAATTACTAAGTTACCCTTTTACTTTGA
76139 CTCTTAATTACT
1 CTCTTAATTACT
76151 GATTACTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (32 bp):
CTCTTAATTACTAAGTTACCCTTTTACTTTGA
Done.