Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005927.1 Hibiscus syriacus cultivar Beakdansim tig00013915_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: 407020
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:291335 original size:20 final size:20
Alignment explanation
Indices: 291310--291354 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
291300 CCCCCTGCTC
*
291310 ATGCTCCTCCAGTACCGCGA
1 ATGCTCCTCCAGTACCGCCA
291330 ATGCTCCTCCAGTACCGCCA
1 ATGCTCCTCCAGTACCGCCA
291350 ATGCT
1 ATGCT
291355 AATTCTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.40, G:0.18, T:0.22
Consensus pattern (20 bp):
ATGCTCCTCCAGTACCGCCA
Found at i:306818 original size:18 final size:18
Alignment explanation
Indices: 306795--306831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
306785 TTATACTTTC
*
306795 ATTTTCCTTGTCTTCAAT
1 ATTTTCCTTCTCTTCAAT
*
306813 ATTTTCCTTCTTTTCAAT
1 ATTTTCCTTCTCTTCAAT
306831 A
1 A
306832 CATTTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTTCCTTCTCTTCAAT
Found at i:321096 original size:61 final size:61
Alignment explanation
Indices: 321025--321139 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
321015 GAAGGTGGAT
* *
321025 ACGACCTTATGTATCA-TGTCCGAATTAGCACTAT-AGCGTAAGCTTAGTGTAGGTGGTGGGA
1 ACGACCTTATGTAT-ATTATCCGAATTAGCACTATGA-CGTAAGCTTAGTGCAGGTGGTGGGA
* *
321086 ACGACCTTATGTGTATTATCCGGATTAGCACTATGACGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATATTATCCGAATTAGCACTATGACGTAAGCTTAGTGCAGGT
321140 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 1 0.02
61 46 0.96
62 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATATTATCCGAATTAGCACTATGACGTAAGCTTAGTGCAGGTGGTGGGA
Found at i:321313 original size:45 final size:45
Alignment explanation
Indices: 321249--321384 Score: 236
Period size: 45 Copynumber: 3.0 Consensus size: 45
321239 GTAACCATGC
321249 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
321294 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
321339 AAATAAGATTACGAGCTTATGGGATAAATGGTAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
321384 A
1 A
321385 GAAATTTTAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:326350 original size:13 final size:13
Alignment explanation
Indices: 326334--326366 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
326324 GTCAACGAGT
*
326334 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
326347 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
326360 CGGGTCG
1 CGGGTCG
326367 TGATCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:326389 original size:10 final size:10
Alignment explanation
Indices: 326371--326412 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
326361 GGGTCGTGAT
326371 CGGTC-AAAC
1 CGGTCAAAAC
326380 CGGTCAAAAC
1 CGGTCAAAAC
*
326390 CGGT-TAAAC
1 CGGTCAAAAC
326399 CGGTCAAAAC
1 CGGTCAAAAC
326409 CGGT
1 CGGT
326413 TTCTAGCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:326413 original size:19 final size:19
Alignment explanation
Indices: 326371--326413 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
326361 GGGTCGTGAT
*
326371 CGGTCAAACCGGTCAAAAC
1 CGGTTAAACCGGTCAAAAC
326390 CGGTTAAACCGGTCAAAAC
1 CGGTTAAACCGGTCAAAAC
326409 CGGTT
1 CGGTT
326414 TCTAGCGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (19 bp):
CGGTTAAACCGGTCAAAAC
Found at i:333605 original size:10 final size:10
Alignment explanation
Indices: 333585--333639 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
333575 ACGGGTCGTG
333585 ACCGGTC-AA
1 ACCGGTCAAA
333594 ACCGGTCAAA
1 ACCGGTCAAA
333604 ACCGGTTCAAA
1 ACCGG-TCAAA
*
333615 ACCGGT-TAA
1 ACCGGTCAAA
333624 ACCGGTCAAA
1 ACCGGTCAAA
*
333634 ATCGGT
1 ACCGGT
333640 TTCCAGCGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
9 15 0.38
10 15 0.38
11 10 0.25
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:333615 original size:11 final size:11
Alignment explanation
Indices: 333592--333640 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
333582 GTGACCGGTC
333592 AAACCGG-TCA
1 AAACCGGTTCA
333602 AAACCGGTTCA
1 AAACCGGTTCA
333613 AAACCGGTT--
1 AAACCGGTTCA
333622 AAACCGG-TCA
1 AAACCGGTTCA
*
333632 AAATCGGTT
1 AAACCGGTT
333641 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.21
10 13 0.38
11 13 0.38
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:333640 original size:19 final size:20
Alignment explanation
Indices: 333592--333640 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
333582 GTGACCGGTC
*
333592 AAACCGGTCAAAACCGGTTCA
1 AAACCGGT-TAAACCGGTTCA
333613 AAACCGGTTAAACCGG-TCA
1 AAACCGGTTAAACCGGTTCA
*
333632 AAATCGGTT
1 AAACCGGTT
333641 TCCAGCGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
21 8 0.31
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
AAACCGGTTAAACCGGTTCA
Found at i:344100 original size:24 final size:24
Alignment explanation
Indices: 344071--344132 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
344061 GAGATATCAA
*
344071 AAATCAAAACAGAATTCAAATAAG
1 AAATCAAAACAGAATCCAAATAAG
* * * * *
344095 ATATCATAACAAAATCCATATTAG
1 AAATCAAAACAGAATCCAAATAAG
*
344119 AAATCAGAACAGAA
1 AAATCAAAACAGAA
344133 ATTATATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (24 bp):
AAATCAAAACAGAATCCAAATAAG
Found at i:354264 original size:24 final size:24
Alignment explanation
Indices: 354237--354282 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
354227 CGGATCATAT
354237 ATCAGAACAGATTCCAGGTCAGGA
1 ATCAGAACAGATTCCAGGTCAGGA
*
354261 ATCAGAATAGATTCCAGGTCAG
1 ATCAGAACAGATTCCAGGTCAG
354283 ATGTCATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGATTCCAGGTCAGGA
Found at i:359277 original size:54 final size:54
Alignment explanation
Indices: 359209--359694 Score: 657
Period size: 54 Copynumber: 9.0 Consensus size: 54
359199 TACATTTTTT
*
359209 CCGTATTGGCACTATGTGTGTAACCCACATAATTCATAATGAGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * * *
359263 CCGCATTGGCACTATGTGTTCAACACACATAATTCATAATGAGTCTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* *
359317 CCGTATTGGCACTATTTGTGCAACCCACATAATTCATAACGAGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * ** * *
359371 TCGTATTGACACTATGTGTGCAACCCATGTAATTCATAACGAGTCTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * ** * *
359425 TCGTATTGACACTATGTGTGCAACCCACGCAATTCATAACGAGTTCATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
** * *
359479 CCGTATTGGCACTATGTGTGCAACCCATGTAATTCATAATGAGTTCATGGATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * *
359533 CTGTATTGGCACTATGTGTGCATCCCACATAATTCATAATGACTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * * * *
359587 CGGTATTGGCACTATGTGTGAAACCCACGTAATTCATAATTAGTTAATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * * *
359641 CGGTATTAGCACTATGTGTGTAACCCATATAATTCATAATGAGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
359695 TTATATTGGA
Statistics
Matches: 385, Mismatches: 47, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 385 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (54 bp):
CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
Found at i:367812 original size:20 final size:21
Alignment explanation
Indices: 367778--367827 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
367768 AGTTAAAGAA
* *
367778 GTATCGATA-ATAAGATGCAG
1 GTATCGATACATAAGAGGAAG
367798 GTATCGATACA-AAGAGGAAG
1 GTATCGATACATAAGAGGAAG
*
367818 GTATTGATAC
1 GTATCGATAC
367828 CGTAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (21 bp):
GTATCGATACATAAGAGGAAG
Found at i:368328 original size:54 final size:54
Alignment explanation
Indices: 368234--368656 Score: 504
Period size: 54 Copynumber: 7.8 Consensus size: 54
368224 ATGTATTATT
* * * *
368234 GTATTGGCAATATGTGTGTAACCAACATAATTCATAATGAGTTTATGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* * * * * *
368288 ATATTAGAACTATGAGTGCAACCCACGTAGTTCATAATGAGTTTGTGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* * *
368342 GTATTGGCCTCTATGTGTGCAACCCATGCAATTCATAATGAGTTTATGAATTACC
1 GTATTGG-CACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* *
368397 GTATTGGCACTATGTGTGCAACCTATGTAATTCATAATGAGTTTATGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* ** * *
368451 ATATTGGCACTATGTGTGCAATACACGTAATTCATAATGATTTTATGAATTATC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* * * *
368505 GTATTGGCACGATTTGTGCAACCCACATAATTCATAATAAGTTTATGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* * * * * *
368559 ATATTGGCAATATGTGTGCAACCCACGTAATTCACACTAACTTTATGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
* * * * * *
368613 GTTTTGGAACTATGTGTGCAAAACAACATAATTTATAATGAGTT
1 GTATTGGCACTATGTGTGC-AACCCACGTAATTCATAATGAGTT
368657 GTAATATTCA
Statistics
Matches: 309, Mismatches: 58, Indels: 3
0.84 0.16 0.01
Matches are distributed among these distances:
54 246 0.80
55 63 0.20
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (54 bp):
GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACC
Found at i:368435 original size:163 final size:162
Alignment explanation
Indices: 368234--368656 Score: 540
Period size: 163 Copynumber: 2.6 Consensus size: 162
368224 ATGTATTATT
* * *
368234 GTATTGGCAATATGTGTGTAACCAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACT
1 GTATTGGCAATATGTGTGCAACCAACGTAATTCATAATGAGTTTATGAATTACCATATTGGAACT
* * * * * *
368299 ATGAGTGCAACCCACGTAGTTCATAATGAGTTTGTGAATTACCGTATTGGCCTCTATGTGTGCAA
66 ATGTGTGCAACACACGTAATTCATAATGAGTTTATGAATTACCGTATTGG-CACGATGTGTGCAA
** *
368364 CCCATGCAATTCATAATGAGTTTATGAATTACC
130 CCCACACAATTCATAATAAGTTTATGAATTACC
* * * *
368397 GTATTGGCACTATGTGTGCAACCTATGTAATTCATAATGAGTTTATGAATTACCATATTGGCACT
1 GTATTGGCAATATGTGTGCAACCAACGTAATTCATAATGAGTTTATGAATTACCATATTGGAACT
* * * *
368462 ATGTGTGCAATACACGTAATTCATAATGATTTTATGAATTATCGTATTGGCACGATTTGTGCAAC
66 ATGTGTGCAACACACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCACGATGTGTGCAAC
*
368527 CCACATAATTCATAATAAGTTTATGAATTACC
131 CCACACAATTCATAATAAGTTTATGAATTACC
* * * * * * * *
368559 ATATTGGCAATATGTGTGCAACCCACGTAATTCACACTAACTTTATGAATTACCGTTTTGGAACT
1 GTATTGGCAATATGTGTGCAACCAACGTAATTCATAATGAGTTTATGAATTACCATATTGGAACT
* * *
368624 ATGTGTGCAAAACAACATAATTTATAATGAGTT
66 ATGTGTGCAACAC-ACGTAATTCATAATGAGTT
368657 GTAATATTCA
Statistics
Matches: 223, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
162 106 0.48
163 117 0.52
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (162 bp):
GTATTGGCAATATGTGTGCAACCAACGTAATTCATAATGAGTTTATGAATTACCATATTGGAACT
ATGTGTGCAACACACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCACGATGTGTGCAAC
CCACACAATTCATAATAAGTTTATGAATTACC
Found at i:369444 original size:54 final size:54
Alignment explanation
Indices: 369373--369877 Score: 584
Period size: 54 Copynumber: 9.4 Consensus size: 54
369363 TTCATTGAGA
* * * *
369373 TGCACAC-TAGTGCCTATACGGTCATTCGTAAACATATTATGAATTCCAT-GGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
* * * *
369425 T-CACACATAAAGTGCCTATACGGTCGTTCATCAATATATGATGAATTTCGTGGAT
1 TGCACACAT--AGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
** * *
369480 TGCACACATAGTGCCTATACTATCGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
*
369534 TGCACACATAGTGCCTATACGGTCATTCATCAACATACGATGAATTTCATGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
* ** * * * *
369588 TGCATACATAGTGCCTATACGGTTTTTCAACAATAAATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
** *
369642 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
* * * * * * *
369696 AGCACACATTGTGCATATACGGTCGTTCATCAACATATGACGAATTCCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
* ** *
369750 TGCACACCTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
*** * * ** *
369804 TGCACACATAGTGCCTATATAATCATTCATCAACATATGATGAATTACTTACGC
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
*
369858 TGTACACATAGTGCCTATAC
1 TGCACACATAGTGCCTATAC
369878 TACACATATT
Statistics
Matches: 392, Mismatches: 56, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
51 5 0.01
52 2 0.01
54 375 0.96
55 3 0.01
56 7 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCATGGGT
Found at i:369647 original size:162 final size:162
Alignment explanation
Indices: 369373--369877 Score: 694
Period size: 162 Copynumber: 3.1 Consensus size: 162
369363 TTCATTGAGA
* * *
369373 TGCACAC-TAGTGCCTATACGGTCATTCGTAAACATATTATGAATTCCAT-GGTT-CACACATAA
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCATGGGTTGCACACAT--
* *
369435 AGTGCCTATACGGTCGTTCATCAATATATGATGAATTTCGTGGATTGCACACATAGTGCCTATAC
64 AGTGCCTATACGGTTGTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATAC
369500 TATCGTTCATCAACATATGATGAATTTCGTGGGT
129 TATCGTTCATCAACATATGATGAATTTCGTGGGT
* * *
369534 TGCACACATAGTGCCTATACGGTCATTCATCAACATACGATGAATTTCATGGGTTGCATACATAG
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCATGGGTTGCACACATAG
* * * **
369599 TGCCTATACGGTTTTTCAACAATAAATGATGAATTTCGTGGGTTGCACACATAGTGCCTATACGG
66 TGCCTATACGGTTGTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATACTA
*
369664 TTGTTCATCAACATATGATGAATTTCGTGGGT
131 TCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * * * *
369696 AGCACACATTGTGCATATACGGTCGTTCATCAACATATGACGAATTCCGTGGGTTGCACACCTAG
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCATGGGTTGCACACATAG
*
369761 TGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATA-TA
66 TGCCTATACGGTTGTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATACT-
* * * ** *
369825 ATCATTCATCAACATATGATGAATTACTTACGC
130 ATCGTTCATCAACATATGATGAATTTCGTGGGT
*
369858 TGTACACATAGTGCCTATAC
1 TGCACACATAGTGCCTATAC
369878 TACACATATT
Statistics
Matches: 299, Mismatches: 41, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
161 7 0.02
162 282 0.94
163 4 0.01
164 6 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (162 bp):
TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCATGGGTTGCACACATAG
TGCCTATACGGTTGTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATACTA
TCGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:370342 original size:18 final size:18
Alignment explanation
Indices: 370319--370362 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
370309 TTCCTTATAG
370319 TATCGATACCCTCATCAA
1 TATCGATACCCTCATCAA
*
370337 TATCGATACCCTCATCAG
1 TATCGATACCCTCATCAA
370355 TATCGATA
1 TATCGATA
370363 TTGTTCATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (18 bp):
TATCGATACCCTCATCAA
Found at i:376073 original size:14 final size:14
Alignment explanation
Indices: 376040--376080 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
376030 AATGGATGTA
376040 TAATAAA-AAAG-T
1 TAATAAATAAAGAT
*
376052 TAAAAAATAAAGAT
1 TAATAAATAAAGAT
376066 TAATAAATAATAGAT
1 TAATAAATAA-AGAT
376081 AAAGATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 4 0.17
14 10 0.42
15 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (14 bp):
TAATAAATAAAGAT
Found at i:382562 original size:16 final size:17
Alignment explanation
Indices: 382538--382571 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
382528 CTATTTCATA
*
382538 TTAACTATTAATTATAT
1 TTAACTATTAACTATAT
382555 TTAA-TATTAACTATAT
1 TTAACTATTAACTATAT
382571 T
1 T
382572 ATGAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAACTATTAACTATAT
Found at i:390811 original size:55 final size:55
Alignment explanation
Indices: 390727--390957 Score: 331
Period size: 55 Copynumber: 4.2 Consensus size: 55
390717 TACACTATGC
*
390727 GTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTCTGT
1 GTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
* * * *
390782 GTGCAAAACTAAAAAATT-AGTATTAAGTTTATGAATTTCCGTATGGGTACTGTGT
1 GTGCAAAACTAAGAAATTCA-TAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
* *
390837 GTGCAAAAGTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCATTGTGT
1 GTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
* * * *
390892 GTGTAAAACTAAGAAATTCATAATAAATTTATTAATTTAT-GTATTGGCACTGTGT
1 GTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATGGGCACTGTGT
390947 GTGCAAAACTA
1 GTGCAAAACTA
390958 TATATTTATA
Statistics
Matches: 155, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
54 1 0.01
55 152 0.98
56 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (55 bp):
GTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
Found at i:395962 original size:95 final size:92
Alignment explanation
Indices: 395809--395984 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 92
395799 GGGTATCGAT
* * *
395809 ATAAAAGGGAAAGTATCGATACCATGGATCCAGAATGCCAAAATGGTATCGATACTGAAAAGGAG
1 ATAAAAGAGAAAGTATCGATACCATGCATCCAAAATGCCAAAATGGTATCGATACTGAAAAGGAG
*
395874 TATCGATTCCATAGTAAAGTTGTATCA
66 TATCGATACCATAGTAAAGTTGTATCA
* *
395901 ATAATAAGAGAAAGGTATCGATACCATGCATCACAAAATG-TAGAAATGGTATCGATACTGAAAG
1 ATAA-AAGAGAAA-GTATCGATACCATGCATC-CAAAATGCCA-AAATGGTATCGATACTGAAAA
* *
395965 GGGGTATCGGTACCATAGTA
62 GGAGTATCGATACCATAGTA
395985 TATAAGTATC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
92 4 0.06
93 7 0.10
94 18 0.25
95 43 0.60
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (92 bp):
ATAAAAGAGAAAGTATCGATACCATGCATCCAAAATGCCAAAATGGTATCGATACTGAAAAGGAG
TATCGATACCATAGTAAAGTTGTATCA
Found at i:396422 original size:55 final size:54
Alignment explanation
Indices: 396352--396523 Score: 227
Period size: 55 Copynumber: 3.1 Consensus size: 54
396342 CTATGCGTTA
*
396352 AAAACTAAGAAATTCATATCAAGTTTATGAATTTCCATATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAT-AAGTTTATGAATTTTCATATGGGCACTGTGTGTGC
* * ** *
396407 AAAACTAAGAAATTCAAAATAACTTTATGAATTTTTGTATGGGTACTGTGTGTGC
1 AAAACTAAGAAATTC-ATATAAGTTTATGAATTTTCATATGGGCACTGTGTGTGC
* * * *
396462 TAAACTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGACATTGTGTGTGC
1 AAAACTAAGAAATTCAT-ATAAGTTTATGAATTTTCATATGGGCACTGTGTGTGC
396517 AAAACTA
1 AAAACTA
396524 TAGATTTATA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
54 1 0.01
55 95 0.96
56 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (54 bp):
AAAACTAAGAAATTCATATAAGTTTATGAATTTTCATATGGGCACTGTGTGTGC
Found at i:397778 original size:20 final size:20
Alignment explanation
Indices: 397753--397796 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
397743 GATTTTATTG
397753 AGCCCGAAAGGACATCACTA
1 AGCCCGAAAGGACATCACTA
* *
397773 AGCCCGAAAGGACTTCACTG
1 AGCCCGAAAGGACATCACTA
397793 AGCC
1 AGCC
397797 AAACTCTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.32, G:0.23, T:0.11
Consensus pattern (20 bp):
AGCCCGAAAGGACATCACTA
Found at i:402405 original size:20 final size:20
Alignment explanation
Indices: 402380--402417 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
402370 GTCGTTTGGC
402380 CTTATGGTATCGATACTAAG
1 CTTATGGTATCGATACTAAG
402400 CTTATGGTATCGATACTA
1 CTTATGGTATCGATACTA
402418 CTATGTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
CTTATGGTATCGATACTAAG
Found at i:403895 original size:92 final size:92
Alignment explanation
Indices: 403581--403909 Score: 288
Period size: 93 Copynumber: 3.6 Consensus size: 92
403571 TGATTTATAT
* ** *
403581 GAACTAAAGAGGTTAACTTATCCAAGTTGTTACATTGAG-GGATGGATGTTTGAATAGCATTCAA
1 GAACTAAAGAGGTTAACTTATCCAAGTTGTTACATT-AGTGGATGGAAGTTT-AATAATATTGAA
* *
403645 ATGCCTTAACTAAACACTTTGATGTTTAC
64 ATGACTTAACTAAACACTTTGATGTGTAC
* * * * * ** *
403674 -AGACTAAAGAGGTTATCTTTTCTAAGTTATTAC-TCTAATAAATGGAAGTTTAAATAATGTTGA
1 GA-ACTAAAGAGGTTAACTTATCCAAGTTGTTACAT-TAGTGGATGGAAGTTT-AATAATATTGA
* * *
403737 AATGACTGAACAAAACACTTTGATGTGTAT
63 AATGACTTAACTAAACACTTTGATGTGTAC
* * * * * * * *
403767 GGACTAAATAGGTTAACTTATCCAAATTCTTTCATTAGTGGGTGAAAGTTTAACTATTATTGAAA
1 GAACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAGTGGATGGAAGTTTAA-TAATATTGAAA
* *
403832 TGTCTTAACTACA-ACTTTGATGTGTAC
65 TGACTTAACTAAACACTTTGATGTGTAC
* * * * *
403859 GAACTGAGGAGGTTAACTTATCCAAGTTGTTACATTAATGCATAGAAGTTT
1 GAACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAGTGGATGGAAGTTT
403910 TATAGCATTG
Statistics
Matches: 180, Mismatches: 50, Indels: 13
0.74 0.21 0.05
Matches are distributed among these distances:
92 57 0.32
93 122 0.68
94 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (92 bp):
GAACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAGTGGATGGAAGTTTAATAATATTGAAAT
GACTTAACTAAACACTTTGATGTGTAC
Found at i:404289 original size:92 final size:93
Alignment explanation
Indices: 403963--404348 Score: 318
Period size: 93 Copynumber: 4.2 Consensus size: 93
403953 AAACATATTT
* ** * * * * **
403963 ACTAAACCCTTTGATGTTTACAAAATAAATAGGTTAACTTATCCAAGTTTTTATATTAAGGGATG
1 ACTAAACACTTTGATGTTTACGGACTAAAGAGGTTAACTTATCCATGTTGTTATATTAATAGATG
* * **
404028 GATGATTGAA-TAGCGTTGAAAT--ATCATA
66 GAAG-TTTAACTAATGTTGAAATGAAT--TA
* * * * * * *
404056 ACTAAATACGTTGATGTTTACAGACTAAAGAGGTAAACTTATCCAAGTTGTTATTTTGATAGATG
1 ACTAAACACTTTGATGTTTACGGACTAAAGAGGTTAACTTATCCATGTTGTTATATTAATAGATG
* *
404121 GAAGTTTAAGTAATGTTGAAATGACTTA
66 GAAGTTTAACTAATGTTGAAATGAATTA
* *
404149 ACTAAACACTTTGATGTTTATGGACTAAAGA-GTTCAACTTATCCATGTTGTTATAATAATAGAT
1 ACTAAACACTTTGATGTTTACGGACTAAAGAGGTT-AACTTATCCATGTTGTTATATTAATAGAT
* * *
404213 GGTAGTTTGACTAGCT-TTGAAATGAATTA
65 GGAAGTTTAACTA-ATGTTGAAATGAATTA
** * * * *
404242 AC-ATCCACTTTGATGTTTAGGGACTAAGGAGGTTAACTTATCCATGTTGTTATATTAATGGATT
1 ACTAAACACTTTGATGTTTACGGACTAAAGAGGTTAACTTATCCATGTTGTTATATTAATAGATG
* ** * **
404306 AAAGTTTGAA-TAACATTTAAATGTTTTA
66 GAAGTTT-AACTAATGTTGAAATGAATTA
404334 ACTAAACACTTTGAT
1 ACTAAACACTTTGAT
404349 TGATGCCATC
Statistics
Matches: 236, Mismatches: 48, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
92 76 0.32
93 158 0.67
94 1 0.00
95 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (93 bp):
ACTAAACACTTTGATGTTTACGGACTAAAGAGGTTAACTTATCCATGTTGTTATATTAATAGATG
GAAGTTTAACTAATGTTGAAATGAATTA
Found at i:406104 original size:21 final size:21
Alignment explanation
Indices: 406063--406104 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
406053 AAACATTTTA
* *
406063 TTATTATATATTAAAATATTT
1 TTATTATATATAAAAAAATTT
406084 TTATT-TATATAAACAAAATTT
1 TTATTATATATAAA-AAAATTT
406105 AATGGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTATATATAAAAAAATTT
Done.