Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002682.1 Hibiscus syriacus cultivar Beakdansim tig00005545_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: 63757
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:12085 original size:42 final size:42
Alignment explanation
Indices: 11940--12370 Score: 399
Period size: 42 Copynumber: 10.2 Consensus size: 42
11930 AAGGTAATTA
* * *
11940 GCGGTGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * ** *
11983 GTGGCGTTTGTTCCAAAAAACGACATTATAGATCTCGATCTTTT
1 GCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCT-GACCTTTT
* * *
12027 GCGGCGTTTGTT-CAAAAATGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
12068 ACGGCGTTTGTTCCAAAAACACCGCTATAGATCTAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
*
12110 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* ** * * *
12152 GCGGAGTTAATTCC-AAAACGTCGCCATAGATTTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
** * * *
12193 GCGGTATTTATTCCAAAAATGCCGCTATAAATCTTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
* * *
12236 GCGGCGTTTGTTCC---AATGCCGCTATAAATCTCGACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
*** * * *
12276 GCGGCGTTTGTT-CAAAAATTATCGCTTTAGGTGTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAA-CGCCGCTATAGATCT-GACCTTTT
*
12319 GCGGCGTTTGTTACAAAAACGCCGCTATAGGTAT-TGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATA-G-ATCTGACCTTTT
12362 GCGGCGTTT
1 GCGGCGTTT
12371 ATAGAGCTTG
Statistics
Matches: 319, Mismatches: 56, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.01
40 35 0.11
41 53 0.17
42 104 0.33
43 99 0.31
44 25 0.08
45 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:12193 original size:83 final size:84
Alignment explanation
Indices: 11940--12370 Score: 372
Period size: 83 Copynumber: 5.1 Consensus size: 84
11930 AAGGTAATTA
* * *
11940 GCGGTGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTTGTGGCGTTTGTTCCAAAAAACG
1 GCGGTGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC-AAAAACG
** * *
12005 ACATTATAGATCTCGATCTTTT
64 ACGCTATAGAT-TTGACCTTTT
* * * * *
12027 GCGGCGTTTGTT-CAAAAATGCCGTTATAGGTCTGACCTTTTACGGCGTTTGTTCCAAAAAC-AC
1 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGA-
* * *
12090 CGCTATAGATCTAACTTTTT
65 CGCTATAGATTTGACCTTTT
* ** *
12110 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGAGTTAATTCC-AAAACGTC
1 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGAC
*
12174 GCCATAGATTTGACCTTTT
66 GCTATAGATTTGACCTTTT
* * * * * *
12193 GCGGTATTTATTCCAAAAATGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC---AATGC
1 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGA
* * *
12255 CGCTATAAATCTCGACTTTTT
65 CGCTATAGAT-TTGACCTTTT
* *** * * * *
12276 GCGGCGTTTGTT-CAAAAATTATCGCTTTAGGTGTCGACCTTTTGCGGCGTTTGTTACAAAAACG
1 GCGGTGTTTGTTCCAAAAA-CGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACG
* *
12340 CCGCTATAGGTATTGACCTTTT
64 ACGCTATAGAT-TTGACCTTTT
*
12362 GCGGCGTTT
1 GCGGTGTTT
12371 ATAGAGCTTG
Statistics
Matches: 277, Mismatches: 57, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
82 18 0.06
83 113 0.41
84 70 0.25
85 36 0.13
86 30 0.11
87 10 0.04
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (84 bp):
GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGAC
GCTATAGATTTGACCTTTT
Found at i:12537 original size:20 final size:21
Alignment explanation
Indices: 12493--12544 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
12483 GGCGCTTAGG
12493 AAACGCCGCTATAGGACTAAA
1 AAACGCCGCTATAGGACTAAA
*
12514 AAACACCGCTATAGGACT-AA
1 AAACGCCGCTATAGGACTAAA
12534 AAACGCCGCTA
1 AAACGCCGCTA
12545 AAAGCCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.13
Consensus pattern (21 bp):
AAACGCCGCTATAGGACTAAA
Found at i:13203 original size:29 final size:29
Alignment explanation
Indices: 13137--13199 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
13127 TGTAGCGGTT
*
13137 AAAAATATTCGTTCATTTATGGTATTGGT
1 AAAAATATTCGTTCATTTATGGTATTGGA
* *
13166 TAAAATATTCGTTCATTTATGGTGTT-GA
1 AAAAATATTCGTTCATTTATGGTATTGGA
13194 AAAAAT
1 AAAAAT
13200 TATTTGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (29 bp):
AAAAATATTCGTTCATTTATGGTATTGGA
Found at i:16475 original size:29 final size:29
Alignment explanation
Indices: 16424--16535 Score: 170
Period size: 29 Copynumber: 3.8 Consensus size: 29
16414 CTTGACCCGA
16424 TGACATTTTGAGAATTATTTTTGAAAAATG
1 TGACATTTTGAGAATTA-TTTTGAAAAATG
* *
16454 TGATATTTTGGGAATTATTTTGAAAAATG
1 TGACATTTTGAGAATTATTTTGAAAAATG
* *
16483 TGACATTCTGAGAATTATTTTGAAAAAGG
1 TGACATTTTGAGAATTATTTTGAAAAATG
*
16512 TGACATTTTGGGAATTATTTTGAA
1 TGACATTTTGAGAATTATTTTGAA
16536 TGTAGACTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 59 0.80
30 15 0.20
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.42
Consensus pattern (29 bp):
TGACATTTTGAGAATTATTTTGAAAAATG
Found at i:16525 original size:58 final size:59
Alignment explanation
Indices: 16424--16535 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 59
16414 CTTGACCCGA
* * *
16424 TGACATTTTGAGAATTATTTTTGAAAAATGTGATATTTTGGGAATTATTTTGAAAAATG
1 TGACATTCTGAGAATTATTTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAATG
16483 TGACATTCTGAGAATTA-TTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAA
1 TGACATTCTGAGAATTATTTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAA
16536 TGTAGACTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
58 34 0.68
59 16 0.32
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.42
Consensus pattern (59 bp):
TGACATTCTGAGAATTATTTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAATG
Found at i:16593 original size:11 final size:11
Alignment explanation
Indices: 16577--16605 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16567 TTGACCGGCT
16577 TTAAACGGCCA
1 TTAAACGGCCA
16588 TTAAACGGCCA
1 TTAAACGGCCA
16599 TTAAACG
1 TTAAACG
16606 ACCTTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (11 bp):
TTAAACGGCCA
Found at i:17502 original size:32 final size:31
Alignment explanation
Indices: 17428--17512 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
17418 CTAATGTGAC
* * *
17428 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
**
17459 TCTCGGGTAGGCCCTACGGCCCTAAGAT-ATGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCA--T
*
17491 TCTTAGGTAGGCCCCACGGCCC
1 TCTTAGGTAGGCCCTACGGCCC
17513 CGAAATCTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.02
31 23 0.52
32 20 0.45
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:17621 original size:26 final size:26
Alignment explanation
Indices: 17568--17621 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
17558 AGGGTAACTC
* *
17568 TTTTATGGGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
17594 TTTTATGAGATTTACTGTACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
17620 TT
1 TT
17622 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:18206 original size:18 final size:18
Alignment explanation
Indices: 18143--18207 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
18133 TGTCAACGAA
*
18143 TTTAAAATTATTAAAAAT
1 TTTAAAAATATTAAAAAT
*
18161 TTT-AAAATTTTAAAAACAT
1 TTTAAAAATATT-AAAA-AT
* *
18180 TTGAAAAATATTAAAATT
1 TTTAAAAATATTAAAAAT
18198 TTTAAAAATA
1 TTTAAAAATA
18208 CAAATATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.16
18 17 0.45
19 8 0.21
20 7 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTAAAAATATTAAAAAT
Found at i:20214 original size:14 final size:14
Alignment explanation
Indices: 20182--20224 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
20172 TAATTATGAA
*
20182 AAATATATATTAAT
1 AAATATATATTTAT
*
20196 TAATATATATTTAT
1 AAATATATATTTAT
*
20210 AAATAAAATATTTAT
1 AAAT-ATATATTTAT
20225 TTATTTAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATATATTTAT
Found at i:20350 original size:20 final size:20
Alignment explanation
Indices: 20315--20354 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20305 TAAATAAATA
*
20315 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
20336 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
20355 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:21866 original size:3 final size:3
Alignment explanation
Indices: 21846--21905 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
21836 TTTGGGCCTG
* *
21846 TAA T-A TAA TAA -AA TTAA TAA TAA AAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
21890 -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
21906 ATAAAACAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 8 0.17
3 38 0.79
4 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:21867 original size:12 final size:12
Alignment explanation
Indices: 21850--21906 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 12
21840 GGCCTGTAAT
21850 ATAATAAAATTA
1 ATAATAAAATTA
21862 ATAATAAAAATAATA
1 ATAAT-AAAAT--TA
*
21877 ATAATAATATTA
1 ATAATAAAATTA
*
21889 A-AACAAAA-TA
1 ATAATAAAATTA
21899 ATAATAAA
1 ATAATAAA
21907 TAAAACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 3 0.08
11 10 0.27
12 8 0.22
13 5 0.14
14 4 0.11
15 7 0.19
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATTA
Found at i:22268 original size:113 final size:113
Alignment explanation
Indices: 22139--23231 Score: 1929
Period size: 113 Copynumber: 9.6 Consensus size: 113
22129 AGAATCATGC
22139 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
22204 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCA
65 TATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
22253 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
22318 ATGAACTC-ACCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGA-CCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
22366 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
22431 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGTG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
22479 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
22544 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
22592 AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
22657 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
22706 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
22771 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
22819 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
22884 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
22932 AAAAGTTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
22997 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
23046 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
23111 ATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* * *
23159 AAAAGTTGAACAAGTTCTTCGCATTATGAACTTCTTCTTTCTTCTTCAGACGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
23224 ATGAACTC
66 ATGAACTC
23232 TTCCAGAAAT
Statistics
Matches: 944, Mismatches: 31, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
113 717 0.76
114 227 0.24
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:22764 original size:340 final size:340
Alignment explanation
Indices: 22139--23231 Score: 1940
Period size: 340 Copynumber: 3.2 Consensus size: 340
22129 AGAATCATGC
*
22139 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
22204 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCAAAAAG-TTGAACAAG
65 TATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAG
*
22267 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC-ACCCT
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA-CCT
*
22331 GGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAA
193 GGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAA
*
22396 CTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATC
258 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATC
*
22461 GAATGATGAATTCAAGTG
323 GAATGATGAATTCAAGCG
22479 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
22544 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAGTT
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAGTT
22609 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
*
22674 AATGCTGATCCATCGAATGATGAATTCAAGCGAAAATTTGAACAAGTTCTTCTCATTATGAACTT
196 AATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
*
22739 CTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
22804 TGATGAATTCAAGCG
326 TGATGAATTCAAGCG
*
22819 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
22884 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAGTT
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAGTT
*
22949 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
* *
23014 AATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
196 AATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
*
23079 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
23144 TGATGAATTCAAGCG
326 TGATGAATTCAAGCG
* * * *
23159 AAAAGTTGAACAAGTTCTTCGCATTATGAACTTCTTCTTTCTTCTTCAGACGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
23224 ATGAACTC
66 ATGAACTC
23232 TTCCAGAAAT
Statistics
Matches: 725, Mismatches: 25, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
339 104 0.14
340 620 0.86
341 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (340 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
AATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
TGATGAATTCAAGCG
Found at i:23057 original size:453 final size:453
Alignment explanation
Indices: 22139--23231 Score: 1958
Period size: 453 Copynumber: 2.4 Consensus size: 453
22129 AGAATCATGC
22139 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
22204 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCAAAAAGTTGAACAAGT
66 TATGAACTCGAC-CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGT
*
22268 TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCACCCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCACCCTGG
22333 CAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
195 CAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
*
22398 TCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGA
260 TCTTATTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGA
*
22463 ATGATGAATTCAAGTGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAG
325 ATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAG
*
22528 ATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
390 ATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
*
22592 AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
22657 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAATTTGAACAAGTT
66 TATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
*
22722 CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA-CCTGG
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-ACCCTGG
*
22786 TAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
195 CAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
22851 TCTTATTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGA
260 TCTTATTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGA
* *
22916 ATGATGAATTCAAGCGAAAAGTTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
325 ATGATGAATTCAAGCGAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCA
22981 GATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
389 GATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
*
23046 AAAAG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23110 TATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
66 TATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
* * *
23175 CTTCGCATTATGAACTTCTTCTTTCTTCTTCAGACGAGTTCTTCTCATTATGAACTC
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
23232 TTCCAGAAAT
Statistics
Matches: 614, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
453 502 0.82
454 112 0.18
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (453 bp):
AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCACCCTGGC
AATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
CTTATTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
Found at i:23692 original size:22 final size:22
Alignment explanation
Indices: 23667--23721 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
23657 GATAAAGCTT
*
23667 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
23689 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
23711 TCATCTTTGAA
1 TCATCTTTGAA
23722 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:24931 original size:75 final size:75
Alignment explanation
Indices: 24785--24944 Score: 182
Period size: 75 Copynumber: 2.1 Consensus size: 75
24775 AGGATGATAT
*
24785 GGCTTTCAGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATACCTCAACATTCTTTATTC
1 GGCTTTCAGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATA-CTCAACATTCTTGATTC
*
24850 TGATTGAAA-G
65 TAATTGAAATG
* * * * * *
24860 GGTTTTCAGCATGCCCCAACATTTTGCTGATATAAATGTTCAGAATATA-TCGACATT-TCTGAT
1 GGCTTTCAGCATGCCCCAACA-TTGGCTAATACAAATGTTCA-AAAATACTCAACATTCT-TGAT
*
24923 TTTAATTGAAATG
63 TCTAATTGAAATG
24936 GGCTTTCAG
1 GGCTTTCAG
24945 TCTGCCCTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
74 1 0.01
75 39 0.55
76 26 0.37
77 5 0.07
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (75 bp):
GGCTTTCAGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATACTCAACATTCTTGATTCT
AATTGAAATG
Found at i:28335 original size:9 final size:9
Alignment explanation
Indices: 28321--28394 Score: 69
Period size: 9 Copynumber: 8.1 Consensus size: 9
28311 TTCAATTTTC
28321 TTTTTTCTT
1 TTTTTTCTT
28330 TTTTTT-TAT
1 TTTTTTCT-T
* *
28339 TTCTTTCCT
1 TTTTTTCTT
*
28348 TTTTTTCCT
1 TTTTTTCTT
28357 TTTTTTCTT
1 TTTTTTCTT
*
28366 TTTTCCTCTT
1 TTTT-TTCTT
*
28376 TTTTTTCCT
1 TTTTTTCTT
*
28385 TTTTTCCTT
1 TTTTTTCTT
28394 T
1 T
28395 CTTTGCTGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
8 1 0.02
9 44 0.83
10 8 0.15
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:28358 original size:28 final size:28
Alignment explanation
Indices: 28321--28389 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
28311 TTCAATTTTC
*
28321 TTTTTT-CTTTTTTT-TTATTTCTTTCCT
1 TTTTTTCCTTTTTTTCTTATTTC-CTCCT
* *
28348 TTTTTTCCTTTTTTTCTTTTTTCCTCTT
1 TTTTTTCCTTTTTTTCTTATTTCCTCCT
28376 TTTTTTCCTTTTTT
1 TTTTTTCCTTTTTT
28390 CCTTTCTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.16
28 25 0.68
29 6 0.16
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTTTCCTTTTTTTCTTATTTCCTCCT
Found at i:28366 original size:36 final size:35
Alignment explanation
Indices: 28321--28394 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
28311 TTCAATTTTC
28321 TTTTTTCTTTTTT-T-TTATTTCTTTCCTTTTTTTCCT
1 TTTTTTCTTTTTTCTCTT-TTT-TTTCC-TTTTTTCCT
28357 TTTTTTCTTTTTTCCTCTTTTTTTTCCTTTTTTCCT
1 TTTTTTCTTTTTT-CTCTTTTTTTTCCTTTTTTCCT
28393 TT
1 TT
28395 CTTTGCTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 24 0.69
37 5 0.14
38 4 0.11
39 2 0.06
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (35 bp):
TTTTTTCTTTTTTCTCTTTTTTTTCCTTTTTTCCT
Found at i:28391 original size:8 final size:8
Alignment explanation
Indices: 28342--28394 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
28332 TTTTTATTTC
28342 TTTCCTTTT
1 TTTCC-TTT
28351 TTTCCTTT
1 TTTCCTTT
*
28359 TTTTCTTT
1 TTTCCTTT
28367 TTTCCTCTTTTT
1 TTT-C-C--TTT
28379 TTTCCTTT
1 TTTCCTTT
28387 TTTCCTTT
1 TTTCCTTT
28395 CTTTGCTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 24 0.63
9 5 0.13
10 2 0.05
11 1 0.03
12 6 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCCTTT
Found at i:28421 original size:26 final size:28
Alignment explanation
Indices: 28377--28431 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
28367 TTTCCTCTTT
28377 TTTTTCCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCCTTTTTTCCTTTCTTTGCTGGA
*
28405 TTTTT-CTTTTTT-CTTTCTTTGTTGGA
1 TTTTTCCTTTTTTCCTTTCTTTGCTGGA
28431 T
1 T
28432 GAGTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 14 0.54
27 7 0.27
28 5 0.19
ACGTcount: A:0.04, C:0.16, G:0.11, T:0.69
Consensus pattern (28 bp):
TTTTTCCTTTTTTCCTTTCTTTGCTGGA
Found at i:31745 original size:14 final size:14
Alignment explanation
Indices: 31711--31764 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
31701 CATAAAAATA
* *
31711 CAAATGCAAAGATG
1 CAAATGTAAATATG
31725 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
31740 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
31754 TAAATGTAAAT
1 CAAATGTAAAT
31765 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:31891 original size:14 final size:14
Alignment explanation
Indices: 31872--31898 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31862 TTAATGCATG
31872 ATGTAAATGTAAAA
1 ATGTAAATGTAAAA
31886 ATGTAAATGTAAA
1 ATGTAAATGTAAA
31899 TACAAACGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
ATGTAAATGTAAAA
Found at i:33863 original size:45 final size:48
Alignment explanation
Indices: 33812--33902 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
33802 TAAATTGTCT
*
33812 CTATTA-TTAGAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATC
1 CTATTATTTA-AAATTATAATAATGAAAAATATATATTAATTTATAATC
*
33857 CTATTATTTTAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTA-TTTAAAATTATAATAATGAAAAATATATATTAATTTATA
33903 TATATTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 6 0.15
46 6 0.15
47 5 0.13
48 12 0.31
49 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (48 bp):
CTATTATTTAAAATTATAATAATGAAAAATATATATTAATTTATAATC
Found at i:34025 original size:20 final size:19
Alignment explanation
Indices: 33986--34027 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
33976 TTTCTTTGAT
33986 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
34005 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
34025 ATT
1 ATT
34028 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:34138 original size:120 final size:120
Alignment explanation
Indices: 33895--34131 Score: 288
Period size: 120 Copynumber: 2.0 Consensus size: 120
33885 AATATATATT
* * *
33895 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAGAACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGAACTTCCAG
* * *
33958 GTGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
** *
34013 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGA-TATCC
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GAACT-TCC
* ** * *
34077 AGTTATTTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAAC
64 AGGTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
34131 A
1 A
34132 TGATTAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
118 19 0.19
119 27 0.27
120 39 0.39
121 16 0.16
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGAACTTCCAG
GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:34159 original size:20 final size:20
Alignment explanation
Indices: 34124--34163 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
34114 TAAATAAATA
*
34124 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
34145 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
34164 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:35927 original size:20 final size:20
Alignment explanation
Indices: 35899--36018 Score: 152
Period size: 20 Copynumber: 5.9 Consensus size: 20
35889 TAATTGAAAA
* *
35899 TCGCATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
35919 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
35939 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
35959 TCGCATTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
35979 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
36001 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
36019 AATTCGTTGC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 70 0.80
21 1 0.01
22 16 0.18
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:35971 original size:60 final size:61
Alignment explanation
Indices: 35899--36018 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 61
35889 TAATTGAAAA
* * *
35899 TCGCATTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCAGTTCG-CGTTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTT-GTCGTTGCGATTTTCCATT
35959 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATA-TCTACAGTTGTCGTTGCGATTTTCCA
36019 AATTCGTTGC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
60 31 0.57
61 1 0.02
62 22 0.41
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (61 bp):
TCGCATTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTTGTCGTTGCGATTTTCCATT
Found at i:36007 original size:22 final size:22
Alignment explanation
Indices: 35982--36045 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
35972 TTCCAGTTCG
35982 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
36004 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
36023 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
36045 C
1 C
36046 CGTCGGGTCG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 10 0.32
20 5 0.16
21 5 0.16
22 11 0.35
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:36035 original size:41 final size:41
Alignment explanation
Indices: 35922--36045 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 41
35912 TTCCATTTCG
* * *
35922 CGTTGCGATTTTCCAGTTCGCGTTGCGAT--TTTCCA-TT-T
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
*
35960 CGCATTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTTGT
1 CG--TTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
36004 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGT
36045 C
1 C
36046 CGTCGGGTCG
Statistics
Matches: 76, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
38 2 0.03
40 27 0.36
41 23 0.30
42 16 0.21
43 5 0.07
44 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:36077 original size:6 final size:6
Alignment explanation
Indices: 36047--36104 Score: 88
Period size: 6 Copynumber: 10.3 Consensus size: 6
36037 ACAGTTGTCC
36047 GTCG-G GTCG-G GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
36091 GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GT
36105 AATACGTGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 19 0.37
6 33 0.63
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.29
Consensus pattern (6 bp):
GTCGTG
Found at i:36265 original size:41 final size:41
Alignment explanation
Indices: 36220--36317 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
36210 GACATTGTAG
* *
36220 ACTATCGCAACGCGAAATGGAAAATCGAAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGAAACGCAATTTTCA
*
36261 ACTATCGCAACGCGAAATGGAAAATCGCAACGCAATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGAAACGCAATTTTCA
36302 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
36318 TTTGCGATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGAAACGCAATTTTCA
Found at i:36275 original size:21 final size:21
Alignment explanation
Indices: 36251--36316 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
36241 AAATCGAAAT
36251 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** *
36272 GCGAAATGGAA-AATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
36292 GCAATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
36313 GCGA
1 GCGA
36317 ATTTGCGATA
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:36289 original size:20 final size:20
Alignment explanation
Indices: 36223--36293 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
36213 ATTGTAGACT
36223 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * ** ** *
36243 ATCGAAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
36264 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
36284 ATCGCAACGC
1 ATCGCAACGC
36294 AATTTTCAAC
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:36474 original size:19 final size:20
Alignment explanation
Indices: 36450--36488 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36440 TTATTTTCTC
*
36450 ATAATAAT-ATTAAAACAAA
1 ATAATAATAAATAAAACAAA
36469 ATAATAATAAATAAAACAAA
1 ATAATAATAAATAAAACAAA
36489 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAATAATAAATAAAACAAA
Found at i:40809 original size:21 final size:21
Alignment explanation
Indices: 40785--40825 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40775 TTTTTCAAAA
40785 ATACTTTAAAAAAT-ATTTTTT
1 ATACTTT-AAAAATCATTTTTT
*
40806 ATACTTTTAAAATCATTTTT
1 ATACTTTAAAAATCATTTTT
40826 CAAAAGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
ATACTTTAAAAATCATTTTTT
Found at i:41933 original size:23 final size:21
Alignment explanation
Indices: 41890--41952 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
41880 CCGAAACTCG
* * *
41890 AGCTCGATTGAAACTCAATTCC
1 AGCTCGTTTG-AACTCGATTCA
41912 AGCTCGACTTTGAACTCGATTCA
1 AGCTCG--TTTGAACTCGATTCA
41935 AGCTCGTTTGAAGCTCGA
1 AGCTCGTTTGAA-CTCGA
41953 AGAGGGGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 15 0.43
24 3 0.09
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (21 bp):
AGCTCGTTTGAACTCGATTCA
Found at i:43396 original size:7 final size:7
Alignment explanation
Indices: 43372--43418 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
43362 GGATTTAGGT
*
43372 TTTAGGG
1 TTTATGG
43379 TTTA-GG
1 TTTATGG
*
43385 TTTTATGA
1 -TTTATGG
43393 TTTATGG
1 TTTATGG
*
43400 TTTGTGG
1 TTTATGG
43407 TTTATGG
1 TTTATGG
43414 TTTAT
1 TTTAT
43419 TGCAAAGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 31 0.91
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.57
Consensus pattern (7 bp):
TTTATGG
Found at i:43396 original size:14 final size:14
Alignment explanation
Indices: 43362--43402 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
43352 TCACATAATT
43362 GGATTTAGGTTTTA
1 GGATTTAGGTTTTA
*
43376 GGGTTTAGGTTTTA
1 GGATTTAGGTTTTA
*
43390 TGATTTATGGTTT
1 GGATTTA-GGTTT
43403 GTGGTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (14 bp):
GGATTTAGGTTTTA
Found at i:43499 original size:14 final size:14
Alignment explanation
Indices: 43482--43527 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
43472 TATGGTTCAT
*
43482 GGTTTATGATTTAG
1 GGTTTAGGATTTAG
*
43496 GGTTTAGGGTTTAG
1 GGTTTAGGATTTAG
* *
43510 GATTTAGGTTTTAG
1 GGTTTAGGATTTAG
43524 GGTT
1 GGTT
43528 CATTACAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (14 bp):
GGTTTAGGATTTAG
Found at i:43499 original size:21 final size:21
Alignment explanation
Indices: 43469--43527 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
43459 GGTAAGTATA
* * *
43469 ATTTATGGTTCATGGTTTATG
1 ATTTAGGGTTCAGGGTTTAGG
*
43490 ATTTAGGGTTTAGGGTTTAGG
1 ATTTAGGGTTCAGGGTTTAGG
* *
43511 ATTTAGGTTTTAGGGTT
1 ATTTAGGGTTCAGGGTT
43528 CATTACAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.49
Consensus pattern (21 bp):
ATTTAGGGTTCAGGGTTTAGG
Found at i:43501 original size:7 final size:7
Alignment explanation
Indices: 43491--43527 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
43481 TGGTTTATGA
43491 TTTAGGG
1 TTTAGGG
43498 TTTAGGG
1 TTTAGGG
*
43505 TTTAGGA
1 TTTAGGG
*
43512 TTTAGGT
1 TTTAGGG
43519 TTTAGGG
1 TTTAGGG
43526 TT
1 TT
43528 CATTACAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:43628 original size:10 final size:11
Alignment explanation
Indices: 43574--43635 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
43564 GTATTATAGA
43574 ATTTTTAATAT
1 ATTTTTAATAT
43585 ATTTTT-A-A-
1 ATTTTTAATAT
43593 ATTTTT-ATA-
1 ATTTTTAATAT
* *
43602 ATTATCAATAGT
1 ATTTTTAATA-T
43614 ATATTTTAATAT
1 AT-TTTTAATAT
43626 ATTTTTAATA
1 ATTTTTAATA
43636 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.17
9 6 0.14
10 4 0.10
11 14 0.33
12 5 0.12
13 6 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:45286 original size:20 final size:20
Alignment explanation
Indices: 45263--45300 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45253 CCTCCTATTT
*
45263 TGCGTTTGATTATTTTCCCC
1 TGCGTTAGATTATTTTCCCC
*
45283 TGCGTTAGATTCTTTTCC
1 TGCGTTAGATTATTTTCC
45301 TAGTAAGATT
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:0.11, C:0.24, G:0.16, T:0.50
Consensus pattern (20 bp):
TGCGTTAGATTATTTTCCCC
Found at i:58381 original size:19 final size:19
Alignment explanation
Indices: 58357--58399 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
58347 GATGTGGATA
*
58357 TGAGTGCCTATAGATAAGG
1 TGAGTGCCTACAGATAAGG
*
58376 TGAGTGCCTACAGTTAAGG
1 TGAGTGCCTACAGATAAGG
58395 TGAGT
1 TGAGT
58400 AGTAGATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.28
Consensus pattern (19 bp):
TGAGTGCCTACAGATAAGG
Found at i:60961 original size:14 final size:15
Alignment explanation
Indices: 60942--60970 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60932 TGACCAGCAT
60942 AATAAA-ATTTTTTA
1 AATAAACATTTTTTA
60956 AATAAACATTTTTTA
1 AATAAACATTTTTTA
60971 TGAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAACATTTTTTA
Found at i:62695 original size:22 final size:20
Alignment explanation
Indices: 62654--62695 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
62644 TGTTATTTTT
*
62654 ATATTTAATTATTTATGATA
1 ATATTTAATAATTTATGATA
62674 ATATTTGAATAATTTAATGATA
1 ATATTT-AATAATTT-ATGATA
62696 GAGATCTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATATTTAATAATTTATGATA
Done.