Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007701.1 Hibiscus syriacus cultivar Beakdansim tig00109912_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: 173251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9730 original size:28 final size:28
Alignment explanation
Indices: 9676--9731 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
9666 GAGGTAAGGG
* * *
9676 TTAGAGTTTATGGTTTAAGATTAATGAT
1 TTAGAGTTTAGGGCTTAAGAGTAATGAT
9704 TTAGAGTTTAGGGCTT-AGAGTACATGAT
1 TTAGAGTTTAGGGCTTAAGAGTA-ATGAT
9732 GATGCGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (28 bp):
TTAGAGTTTAGGGCTTAAGAGTAATGAT
Found at i:19031 original size:51 final size:50
Alignment explanation
Indices: 18921--19031 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 50
18911 GTATTAAGAG
* * * *
18921 CTACATTTTTTTATTTTATTCACTTATATTGGTGTGTATGTGTTAAGTGT
1 CTACATTTTTTTATTTTATTCACTTACATTGATGTATATGAGTTAAGTGT
* *
18971 -TACAATTTTTTATTTTATTTACTTACATTGATGTAAATATGAGTTAAGT-T
1 CTACATTTTTTTATTTTATTCACTTACATTGATGT--ATATGAGTTAAGTGT
19021 CTACATTTTTT
1 CTACATTTTTT
19032 GCAGTATGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
49 30 0.59
50 1 0.02
51 20 0.39
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (50 bp):
CTACATTTTTTTATTTTATTCACTTACATTGATGTATATGAGTTAAGTGT
Found at i:21306 original size:18 final size:19
Alignment explanation
Indices: 21264--21306 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
21254 TTTGGTTCAC
21264 GGAATGTAAGATTACCAGTT
1 GGAATGTAAGATTACCAG-T
21284 GGAATGTAAGATTACCA-T
1 GGAATGTAAGATTACCAGT
21302 GGAAT
1 GGAAT
21307 AAGATTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGT
Found at i:21311 original size:16 final size:18
Alignment explanation
Indices: 21264--21313 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
21254 TTTGGTTCAC
21264 GGAATGTAAGATTACCAGTT
1 GGAA-GTAAGATTACCAG-T
21284 GGAATGTAAGATTACCA-T
1 GGAA-GTAAGATTACCAGT
21302 GGAA-TAAGATTA
1 GGAAGTAAGATTA
21314 ATGGGAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.27
18 5 0.17
20 17 0.57
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGT
Found at i:27015 original size:41 final size:44
Alignment explanation
Indices: 26974--27057 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
26964 CATTAAAATA
26974 ATATTA-TTAA-TTAATAATATTTTATTATTTATTAAAAAATAAT
1 ATATTAGTTAACTT-ATAATATTTTATTATTTATTAAAAAATAAT
* * *
27017 ATATTAGTTAACTTATTATTTTTTATTATTTATTAATAAAT
1 ATATTAGTTAACTTATAATATTTTATTATTTATTAAAAAAT
27058 TAAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 6 0.17
44 28 0.78
45 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (44 bp):
ATATTAGTTAACTTATAATATTTTATTATTTATTAAAAAATAAT
Found at i:37335 original size:8 final size:8
Alignment explanation
Indices: 37322--37347 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
37312 CAAGAGTTGT
37322 AAGCATTC
1 AAGCATTC
37330 AAGCATTC
1 AAGCATTC
37338 AAGCATTC
1 AAGCATTC
37346 AA
1 AA
37348 CAAGCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (8 bp):
AAGCATTC
Found at i:39457 original size:23 final size:23
Alignment explanation
Indices: 39431--39475 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39421 CACCACAGCT
*
39431 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
39454 CGTAGAATTGCACTGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
39476 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:45165 original size:36 final size:36
Alignment explanation
Indices: 45118--45457 Score: 545
Period size: 36 Copynumber: 9.4 Consensus size: 36
45108 TAAGGTGAAT
* *
45118 AAGTCGAACGGAAGGATGCATTGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
*
45154 AAGTCGAACGGAAGGATGCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
*
45190 AAGTCGAACGGAAGGATGCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
45226 AAGTCGAACGGAAGGAGGCATCGACACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
45262 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
45298 AAGTCGAACGGAAGGAACCATCGACACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
45334 AAGTCGAACGGAAAGAAGCATCGGCACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* * *
45370 AAGTCGAACGGAATGAACCATCGACACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
**
45406 AAGTCGAACGGAAGGAAGCATTAGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
45442 AAGTCGAACGGAAGGA
1 AAGTCGAACGGAAGGA
45458 TGTATTGCAC
Statistics
Matches: 284, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 284 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.18
Consensus pattern (36 bp):
AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
Found at i:50616 original size:18 final size:17
Alignment explanation
Indices: 50581--50622 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
50571 AAAATATATT
* *
50581 TTGATGATCAAAATGAA
1 TTGATGCTCAAAACGAA
50598 TTGATGCTCAAAAACGAA
1 TTGATGCTC-AAAACGAA
50616 TTGATGC
1 TTGATGC
50623 AAAGCGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (17 bp):
TTGATGCTCAAAACGAA
Found at i:52681 original size:16 final size:15
Alignment explanation
Indices: 52660--52705 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
52650 TATGTGCAAC
52660 TTAAAAAAAGACAAA
1 TTAAAAAAAGACAAA
52675 GTT-AAAAAAGAACAAA
1 -TTAAAAAAAG-ACAAA
*
52691 TAAAAAAAAG-CAAA
1 TTAAAAAAAGACAAA
52705 T
1 T
52706 AAATTGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 14 0.52
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.13
Consensus pattern (15 bp):
TTAAAAAAAGACAAA
Found at i:52694 original size:14 final size:14
Alignment explanation
Indices: 52663--52708 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
52653 GTGCAACTTA
52663 AAAAAAG-ACAAAGTT
1 AAAAAAGAACAAA--T
52678 AAAAAAGAACAAAT
1 AAAAAAGAACAAAT
52692 AAAAAA-AAGCAAAT
1 AAAAAAGAA-CAAAT
52706 AAA
1 AAA
52709 TTGAATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.07
14 15 0.52
15 7 0.24
16 5 0.17
ACGTcount: A:0.76, C:0.07, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAAGAACAAAT
Found at i:52696 original size:15 final size:15
Alignment explanation
Indices: 52661--52708 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
52651 ATGTGCAACT
52661 TAAAAAAAG-ACAAA
1 TAAAAAAAGAACAAA
*
52675 GTTAAAAAAGAACAAA
1 -TAAAAAAAGAACAAA
*
52691 TAAAAAAA-AGCAAA
1 TAAAAAAAGAACAAA
52705 TAAA
1 TAAA
52709 TTGAATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.31
15 15 0.52
16 5 0.17
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.10
Consensus pattern (15 bp):
TAAAAAAAGAACAAA
Found at i:53342 original size:38 final size:41
Alignment explanation
Indices: 53300--53384 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 41
53290 AAACTACAAA
* **
53300 ATTTAATAAAATAAAAT-AATTTTTGATTT-AT-CTAAATT
1 ATTTAATAAAATAAAATAAATATTAAATTTGATCCTAAATT
53338 ATTTAATAAAATAAAATAAATATTAAATTTGATCCTAAATT
1 ATTTAATAAAATAAAATAAATATTAAATTTGATCCTAAATT
53379 ATTTAA
1 ATTTAA
53385 AATACTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
38 17 0.41
39 9 0.22
40 2 0.05
41 13 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (41 bp):
ATTTAATAAAATAAAATAAATATTAAATTTGATCCTAAATT
Found at i:56731 original size:17 final size:17
Alignment explanation
Indices: 56709--56742 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56699 ATTTTAAAAA
56709 TTCAAACTCAAATTCCG
1 TTCAAACTCAAATTCCG
56726 TTCAAACTCAAATTCCG
1 TTCAAACTCAAATTCCG
56743 AATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (17 bp):
TTCAAACTCAAATTCCG
Found at i:57236 original size:16 final size:16
Alignment explanation
Indices: 57212--57249 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
57202 ATTAAACTCT
* *
57212 AAATCTAAAAAAAGTA
1 AAATATAAAAAAACTA
57228 AAATATAAAAAAACTA
1 AAATATAAAAAAACTA
57244 AAATAT
1 AAATAT
57250 GAAAGACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATATAAAAAAACTA
Found at i:57776 original size:19 final size:20
Alignment explanation
Indices: 57735--57776 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
57725 GGACCGGTTG
*
57735 AAAATCGGAAAAAACTAGGA
1 AAAATCGGAAAAAACTAGAA
57755 AAAATC-GAAAAAA-TCAGAA
1 AAAATCGGAAAAAACT-AGAA
57774 AAA
1 AAA
57777 CCGCCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.65
20 6 0.30
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (20 bp):
AAAATCGGAAAAAACTAGAA
Found at i:58712 original size:2 final size:2
Alignment explanation
Indices: 58701--58740 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
58691 ATTTTGCATT
58701 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58741 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62256 original size:33 final size:33
Alignment explanation
Indices: 62219--62296 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
62209 ACACTATCAG
*
62219 TCGAGTCAGTAGGGCCAAGGAAAGCACCACCAT
1 TCGAGTCAGTAGGGCCAAGGAAAGAACCACCAT
* *
62252 TCGAGTCAGTAGGGCCAAGGGAGGAACCACCAT
1 TCGAGTCAGTAGGGCCAAGGAAAGAACCACCAT
* *
62285 TCAAGTTAGTAG
1 TCGAGTCAGTAG
62297 ATCCAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.15
Consensus pattern (33 bp):
TCGAGTCAGTAGGGCCAAGGAAAGAACCACCAT
Found at i:62310 original size:31 final size:32
Alignment explanation
Indices: 62222--62310 Score: 90
Period size: 33 Copynumber: 2.8 Consensus size: 32
62212 CTATCAGTCG
* * * *
62222 AGTCAGTAGGGCCAAGGAAAGCACCACCATTCG
1 AGTCAGTAGAGCCAAGG-AGGAACCACCATTCA
*
62255 AGTCAGTAGGGCCAAGGGAGGAACCACCATTCA
1 AGTCAGTAGAGCCAA-GGAGGAACCACCATTCA
* *
62288 AGTTAGTAGATCCAA-GAGGAACC
1 AGTCAGTAGAGCCAAGGAGGAACC
62311 TGTTCAATCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.16
33 39 0.80
34 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.28, T:0.13
Consensus pattern (32 bp):
AGTCAGTAGAGCCAAGGAGGAACCACCATTCA
Found at i:63158 original size:21 final size:21
Alignment explanation
Indices: 63132--63176 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
63122 GATTTCTGGG
* *
63132 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
63153 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
63174 CAA
1 CAA
63177 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:64673 original size:149 final size:149
Alignment explanation
Indices: 64493--64956 Score: 885
Period size: 149 Copynumber: 3.1 Consensus size: 149
64483 GAGTCGAGGG
64493 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
64558 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
64623 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
64642 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
64707 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
64772 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
64791 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
64856 ATTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
64921 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTGCAAT
64940 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
64957 TGCAATTATA
Statistics
Matches: 311, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.00
149 310 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:64957 original size:23 final size:23
Alignment explanation
Indices: 64924--64968 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
64914 ATCATTATAT
*
64924 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* *
64947 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTACAATTATACG
64969 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:68245 original size:21 final size:21
Alignment explanation
Indices: 68219--68263 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
68209 GATTTCTGGG
* *
68219 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
68240 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
68261 CAA
1 CAA
68264 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:69855 original size:149 final size:149
Alignment explanation
Indices: 69585--70048 Score: 867
Period size: 149 Copynumber: 3.1 Consensus size: 149
69575 GAGTCGAGGG
69585 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
69650 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATTTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
69715 TATGGCACTACGATGCAAT
131 TATGGCACTACGGTGCAAT
69734 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
69799 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
69864 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
69883 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
69948 ATTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
70013 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTGCAAT
70032 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
70049 TGCAATTATA
Statistics
Matches: 309, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
148 1 0.00
149 308 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:70049 original size:23 final size:23
Alignment explanation
Indices: 70016--70060 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
70006 ATCATTATAT
*
70016 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* *
70039 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTACAATTATACG
70061 AGATGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:84537 original size:22 final size:22
Alignment explanation
Indices: 84519--84592 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 22
84509 AGAGGGAATT
84519 GATACCCCCTTGAAGGGGAACC
1 GATACCCCCTTGAAGGGGAACC
* *
84541 GATTCCCCCTTTGAAGGGGAACT
1 GATACCCCC-TTGAAGGGGAACC
* *
84564 GATTCCCCC-T--AGGGGAATC
1 GATACCCCCTTGAAGGGGAACC
84583 GATACCCCCT
1 GATACCCCCT
84593 GGGGTTCTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.33
21 1 0.02
22 8 0.18
23 21 0.47
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.20
Consensus pattern (22 bp):
GATACCCCCTTGAAGGGGAACC
Found at i:84554 original size:23 final size:23
Alignment explanation
Indices: 84523--84573 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
84513 GGAATTGATA
84523 CCCCC-TTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
*
84545 CCCCCTTTGAAGGGGAACTGATT
1 CCCCCTTTGAAGGGGAACCGATT
84568 CCCCCT
1 CCCCCT
84574 AGGGGAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:84590 original size:19 final size:19
Alignment explanation
Indices: 84555--84596 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
84545 CCCCCTTTGA
*
84555 AGGGGAACTGATTCCCCCT
1 AGGGGAACTGATACCCCCT
84574 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
84593 -GGGG
1 AGGGG
84597 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGGGAACTGATACCCCCT
Found at i:87324 original size:20 final size:20
Alignment explanation
Indices: 87295--87344 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
87285 GGAGGGAACC
87295 GATT-CCCCCAAGGGGTACT
1 GATTCCCCCCAAGGGGTACT
87314 GATTCCCCCCAAGGGGTACT
1 GATTCCCCCCAAGGGGTACT
87334 GATTCCCCCCA
1 GATTCCCCCCA
87345 CTGTACAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20
Consensus pattern (20 bp):
GATTCCCCCCAAGGGGTACT
Found at i:95092 original size:2 final size:2
Alignment explanation
Indices: 95087--95113 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95077 TTTGGGCCAA
95087 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
95114 CACTATAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95244 original size:36 final size:36
Alignment explanation
Indices: 95197--95265 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
95187 GGTTAGCCTG
95197 TCACTATTGGTAGGAGTGTTGCATAAATTATTCACA
1 TCACTATTGGTAGGAGTGTTGCATAAATTATTCACA
*
95233 TCACTATTGGTAGGTGTGTTGCATAAATTATTC
1 TCACTATTGGTAGGAGTGTTGCATAAATTATTC
95266 TTCGTAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (36 bp):
TCACTATTGGTAGGAGTGTTGCATAAATTATTCACA
Found at i:101058 original size:168 final size:169
Alignment explanation
Indices: 100780--101110 Score: 475
Period size: 168 Copynumber: 1.9 Consensus size: 169
100770 CAACAACTCA
* * * * *
100780 GTTGACAGATGCATGGATTCTTGATTCAGGATGCTCTTATCATATAACGCTTAACAAAGAGTGGT
1 GTTGACAAATGCAAGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
* *
100845 TTTCGACATACATGTCAGTTAATTCTGGTTCTGTCTATTTAGGTGATGAAAGATGTTGCAATATT
66 TTTCGACATACAAGTCAGTTAATTCTAGTTCTGTCTATTTAGGTGATGAAAGATGTTGCAATATT
* * *
100910 GTTTGTA-TGAAGTCAGAATTAAGATGTATAATAGTATT
131 ATTGGTAGTGAAGTCAAAATTAAGATGTATAATAGTATT
**
100948 GTTGACAAATGCAAGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACATGGAGTGGT
1 GTTGACAAATGCAAGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
* * ** *
101013 TTTCGATATACAAGTCAGTTAATTTTAGTTCTGTCTATTTAGGTGATGGCAGGTGTTGCAATATT
66 TTTCGACATACAAGTCAGTTAATTCTAGTTCTGTCTATTTAGGTGATGAAAGATGTTGCAATATT
101078 ATTGGTATTGGTGAAGTCAAAATTAAGATGTAT
131 ATTGGTA---GTGAAGTCAAAATTAAGATGTAT
101111 GATGATATTG
Statistics
Matches: 142, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
168 121 0.85
172 21 0.15
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (169 bp):
GTTGACAAATGCAAGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
TTTCGACATACAAGTCAGTTAATTCTAGTTCTGTCTATTTAGGTGATGAAAGATGTTGCAATATT
ATTGGTAGTGAAGTCAAAATTAAGATGTATAATAGTATT
Found at i:107060 original size:23 final size:23
Alignment explanation
Indices: 107034--107113 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
107024 CTCGTATAAA
*
107034 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
107057 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
* * *
107080 TGAACTGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
107103 TGCACCGAAGT
1 TGCACCGAAGT
107114 TCCATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:108849 original size:64 final size:63
Alignment explanation
Indices: 108762--108923 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 63
108752 CCCTTAACAT
* * *
108762 GTGCATCGATGCACTACCC-ATGCATCGATACACAA-AGCACCTTCGATGTTT-TAATCTTAAGG
1 GTGCATCGATGCACT-CCCTATGCATCGATGCACAATAGCA--TTCGATATTTCCAATCTTAAGG
108824 G
63 G
* * * *
108825 GATGTATCGATGCACTCCCTATGCATCGATGCACTAATTGCATTCGATATTTCCATTTTTAAGGG
1 G-TGCATCGATGCACTCCCTATGCATCGATGCAC-AATAGCATTCGATATTTCCAATCTTAAGGG
* *
108890 GTGCATCGATGCACTTCCTGTGCATCGATGCACA
1 GTGCATCGATGCACTCCCTATGCATCGATGCACA
108924 CTGAACAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
63 5 0.06
64 64 0.76
65 12 0.14
66 3 0.04
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCACTCCCTATGCATCGATGCACAATAGCATTCGATATTTCCAATCTTAAGGG
Found at i:110236 original size:20 final size:19
Alignment explanation
Indices: 110207--110247 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
110197 TAAACTCAAT
*
110207 CATTTTCATTTATTTATTC
1 CATTTTCATTTATTCATTC
110226 CATTATTCATTTATTCATTC
1 CATT-TTCATTTATTCATTC
110246 CA
1 CA
110248 AATTGAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (19 bp):
CATTTTCATTTATTCATTC
Found at i:112275 original size:23 final size:23
Alignment explanation
Indices: 112244--112323 Score: 133
Period size: 23 Copynumber: 3.5 Consensus size: 23
112234 CTCGTATAAA
* * *
112244 TGCAACGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
112267 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
112290 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
112313 TGCACCGAAGT
1 TGCACCGAAGT
112324 TCCATATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:126505 original size:164 final size:168
Alignment explanation
Indices: 126234--126566 Score: 629
Period size: 164 Copynumber: 2.0 Consensus size: 168
126224 GTGGACGGTT
126234 CTTTTATCTTTGTTATGCTGTTCGGCTTCCAAATCCCGAGTCATTTATAGGATTGTTATACCTCT
1 CTTTTATCTTTGTTATGCTGTTCGGCTTCCAAATCCCGAGTCATTTATAGGATTGTTATACCTCT
126299 TGTACAAGTTACTGTTGCGAAAGACGGCTATCGGATAGAGC-AAAT-CAACTGATAATTTGAGAA
66 TGTACAAGTTACTGTTGCGAAAGACGGCTATCGGATAGAGCAAAATCCAACTGATAATTTGAGAA
126362 AAT-AAAATGAAGATAAAAGAGACACAAAA-TTACGTG
131 AATAAAAATGAAGATAAAAGAGACACAAAATTTACGTG
126398 CTTTTATCTTTGTTATGCTGTTCGGCTTCCAAATCCCGAGTCATTTATAGGATTGTTATACCTCT
1 CTTTTATCTTTGTTATGCTGTTCGGCTTCCAAATCCCGAGTCATTTATAGGATTGTTATACCTCT
126463 TGTACAAGTTACTGTTGCGAAAGACGGCTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGA
66 TGTACAAGTTACTGTTGCGAAAGACGGCTATCGGATAGAGCAAAATC-CAACTGATAATTTGAGA
126528 AAATAAAAATGAAGATAAAAGAGACACAAAATTTACGTG
130 AAATAAAAATGAAGATAAAAGAGACACAAAATTTACGTG
126567 AAAAACCCCT
Statistics
Matches: 164, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
164 106 0.65
165 4 0.02
167 21 0.13
168 26 0.16
169 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (168 bp):
CTTTTATCTTTGTTATGCTGTTCGGCTTCCAAATCCCGAGTCATTTATAGGATTGTTATACCTCT
TGTACAAGTTACTGTTGCGAAAGACGGCTATCGGATAGAGCAAAATCCAACTGATAATTTGAGAA
AATAAAAATGAAGATAAAAGAGACACAAAATTTACGTG
Found at i:130713 original size:19 final size:20
Alignment explanation
Indices: 130689--130728 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
130679 ATATCTCCTT
130689 AGATGTCTTTTT-CTCCTCG
1 AGATGTCTTTTTCCTCCTCG
130708 AGATGTCTTTTTCCTCCTCG
1 AGATGTCTTTTTCCTCCTCG
130728 A
1 A
130729 TGCTTGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.12, C:0.28, G:0.15, T:0.45
Consensus pattern (20 bp):
AGATGTCTTTTTCCTCCTCG
Found at i:131737 original size:4 final size:4
Alignment explanation
Indices: 131730--131775 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
131720 TCTATCTATC
* * * *
131730 TAGA TAGA TAGA TATA TAGA TAGA TACA TAAA TAAA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
131776 AGTAGTAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (4 bp):
TAGA
Found at i:131751 original size:16 final size:16
Alignment explanation
Indices: 131730--131786 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
131720 TCTATCTATC
*
131730 TAGATAGATAGATATA
1 TAGATAGATAGATAAA
*
131746 TAGATAGATACATAAA
1 TAGATAGATAGATAAA
* *
131762 TAAATAGATAGATAAG
1 TAGATAGATAGATAAA
131778 TAG-TAGATA
1 TAGATAGATA
131787 TGTCCATCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
15 6 0.17
16 29 0.83
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.28
Consensus pattern (16 bp):
TAGATAGATAGATAAA
Found at i:136083 original size:28 final size:23
Alignment explanation
Indices: 136020--136071 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
136010 TAGTAAATAT
*
136020 TGAACTTATAACCTAAATAAGAA
1 TGAAATTATAACCTAAATAAGAA
136043 TGAAATTATAACCTAAATAAGAA
1 TGAAATTATAACCTAAATAAGAA
136066 TGAAAT
1 TGAAAT
136072 GTGTTAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (23 bp):
TGAAATTATAACCTAAATAAGAA
Found at i:155857 original size:399 final size:396
Alignment explanation
Indices: 155120--156315 Score: 2056
Period size: 399 Copynumber: 3.0 Consensus size: 396
155110 CAAGTTAGGT
* *
155120 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGATAGTCACTCTCAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGT-GGTAGGGTAGTCACTCTTAAAATTTTAAAA
* *
155185 TTATTATATATTTAAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAGAA
65 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTTGTCTCTCTAGAA
* * *
155250 TTTTATAAGTTTAAGTTCACACACCTGAAATTTTATAAGTTCAAGTTCACACCTTCGACATAAAA
130 TTTTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACCTT-AACATAAAA
* *
155315 TCATGCATTCCTCCCTGTGTTTGTTTCTTATAATATATTTCAATATGAGCCTTTCAAAACGATAT
194 TCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATAT
* *
155380 TATTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATATTCGAC
259 TGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGAC
*
155445 CCATACGTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
324 CCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
*
155510 GTCTTTCC
389 GTCCTTCC
155518 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTAGGTAGGGTAGTCACTCTTAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGT-GGTAGGGTAGTCACTCTTAAAATTTTAAAA
155583 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTTATTGAAAATATACTTTTGTCTCTCTAGA
65 TTATTATATATTTCAAAAATTTTCTATTTA-TTTTTTATTGAAAATATACTTTTGTCTCTCTAGA
155648 ATTTTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACTCTTAACATAAA
129 ATTTTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACAC-CTTAACATAAA
155713 ATCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATA
193 ATCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATA
* *
155778 TTGTTTTGGAAAGATTGTTCGTATTCTAAAACAGCATCGTTTTGATTATCTAGTTTGATGTTCGA
258 TTGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGA
155843 CCCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTT
323 CCCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTT
*
155908 GGTCCTTCT
388 GGTCCTTCC
*
155917 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGATAGGGCAGTCACTCTTAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGG-TAGGGTAGTCACTCTTAAAATTTTAAAA
** *
155982 TTATTATATATTTCAAATTTTTTCTATTTATTTTTTATTGAAAATATA-TTTTCGTCTCTCTATA
65 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTT-GTCTCTCTAGA
* *
156046 ATTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAATTCATGTTCACACCCTTAACATAAA
129 ATTTTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACA-CCTTAACAT-AA
*
156111 AATCATGCATTTCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGAT
192 AATCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGAT
*
156176 ATTGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCAAGTATGATGTTCG
257 ATTGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCG
* *
156241 ACCCATACCTAAACTAGATCCACAACCAAGA--TGTGTTTGAAATCTTTGGATAAATTTTAATTT
322 ACCCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTT
156304 TGGTCCTTCC
387 TGGTCCTTCC
156314 GC
1 GC
156316 CTTTCTAACT
Statistics
Matches: 762, Mismatches: 30, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
397 46 0.06
398 179 0.23
399 534 0.70
400 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (396 bp):
GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGTAGGGTAGTCACTCTTAAAATTTTAAAAT
TATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTTGTCTCTCTAGAAT
TTTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACCTTAACATAAAATC
ATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATATTG
TTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGACCC
ATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTGGT
CCTTCC
Found at i:161406 original size:2 final size:2
Alignment explanation
Indices: 161401--161438 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
161391 CGTGTGTGTG
161401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
161439 TTTATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:161551 original size:16 final size:16
Alignment explanation
Indices: 161532--161571 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
161522 CATCGATTTA
161532 CTCTTACAGTCGACAC
1 CTCTTACAGTCGACAC
*
161548 CTCTTACAGTGGACAC
1 CTCTTACAGTCGACAC
*
161564 CTCCTACA
1 CTCTTACA
161572 CCCCATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (16 bp):
CTCTTACAGTCGACAC
Found at i:161826 original size:28 final size:29
Alignment explanation
Indices: 161785--161857 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
161775 CTTTATAAAG
* *
161785 TTTAATTTAATTAAATTGAGTT-AAAAAA
1 TTTAAATTATTTAAATTGAGTTAAAAAAA
*
161813 TTTAAGTTATTTAAA--GAGTTAAAAAAA
1 TTTAAATTATTTAAATTGAGTTAAAAAAA
*
161840 TTCTAAATTATTTGAATT
1 TT-TAAATTATTTAAATT
161858 AATAAGTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
28 24 0.65
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTAAATTATTTAAATTGAGTTAAAAAAA
Found at i:162006 original size:2 final size:2
Alignment explanation
Indices: 161999--162039 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
161989 AACATATAAG
161999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
162040 TCTTTCCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:163307 original size:29 final size:31
Alignment explanation
Indices: 163230--163307 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
163220 AGAGAAAAAC
* *
163230 AAAAACTTAAGGGATT-AAATAGCAAAAGAA
1 AAAAAATTAAAGGATTAAAATAGCAAAAGAA
* * *
163260 AAAAAATTAAAGTACTAAAATAGC-ATA-AA
1 AAAAAATTAAAGGATTAAAATAGCAAAAGAA
*
163289 TAAAAATTAAAGGATTAAA
1 AAAAAATTAAAGGATTAAA
163308 GTAGAAAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 18 0.46
30 14 0.36
31 7 0.18
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.21
Consensus pattern (31 bp):
AAAAAATTAAAGGATTAAAATAGCAAAAGAA
Found at i:164019 original size:2 final size:2
Alignment explanation
Indices: 164012--164039 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
164002 ACCCATTTTC
164012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
164040 TTGAAAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:164578 original size:17 final size:17
Alignment explanation
Indices: 164556--164588 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
164546 AATTGCAATC
164556 AAAATACTAA-ATTAAGT
1 AAAATAC-AATATTAAGT
164573 AAAATACAATATTAAG
1 AAAATACAATATTAAG
164589 AGTCTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAATACAATATTAAGT
Found at i:166896 original size:20 final size:21
Alignment explanation
Indices: 166871--166963 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
166861 TTTTCCCAAT
*
166871 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
166891 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
166912 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
166932 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
166953 TCGCAATGCGA
1 TCGCAATGCGA
166964 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:166916 original size:41 final size:41
Alignment explanation
Indices: 166871--166963 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
166861 TTTTCCCAAT
166871 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
166912 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
166953 TCGCAATGCGA
1 TCGCAATGCGA
166964 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:166976 original size:41 final size:41
Alignment explanation
Indices: 166890--167024 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
166880 GAATAAGTAA
* *
166890 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
166931 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
166972 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
167013 TTCGCAACGCGA
1 ATCGCAACGCGA
167025 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:166977 original size:20 final size:20
Alignment explanation
Indices: 166952--167046 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
166942 AATTGGGAAA
*
166952 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
166972 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
166993 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
167013 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
167033 TTCGCAACGCGATA
1 ATCGCAACGCGATA
167047 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:167274 original size:21 final size:22
Alignment explanation
Indices: 167234--167276 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
167224 CACTCTCTCA
167234 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
167256 CCCATCTCCGGCG-AATCCGTC
1 CCCATCTCCGACGAAATCCGTC
167277 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:167563 original size:20 final size:20
Alignment explanation
Indices: 167538--167575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
167528 CGATTCTCTC
167538 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
167558 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
167576 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:168920 original size:18 final size:18
Alignment explanation
Indices: 168899--168943 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
168889 TCCACTTCGG
*
168899 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
168917 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
168935 GAGCCATCA
1 GAGCCATCA
168944 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:169444 original size:20 final size:20
Alignment explanation
Indices: 169419--169464 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
169409 TAGTTTACTT
169419 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* *
169439 TCGCAACGCGAAAATGGCTA
1 TCGCAACACGAAAATGACTA
169459 TCGCAA
1 TCGCAA
169465 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:169469 original size:20 final size:20
Alignment explanation
Indices: 169427--169490 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
169417 TTTCGCAACA
*
169427 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAATG
*
169447 CGAAAATGGCTATCGCAATG
1 CGAAAATGACTATCGCAATG
**
169467 CG-AAATGAAAATCGCAATG
1 CGAAAATGACTATCGCAATG
169486 CGAAA
1 CGAAA
169491 TGAAATCGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 16 0.42
20 22 0.58
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
CGAAAATGACTATCGCAATG
Found at i:169480 original size:19 final size:19
Alignment explanation
Indices: 169458--169539 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
169448 GAAAATGGCT
169458 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
169477 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
169495 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
169509 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
169528 ATCGCAATGCGA
1 ATCGCAATGCGA
169540 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
14 10 0.19
16 4 0.07
18 10 0.19
19 30 0.56
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:169583 original size:19 final size:19
Alignment explanation
Indices: 169546--169654 Score: 121
Period size: 19 Copynumber: 5.7 Consensus size: 19
169536 GCGATTTGTG
169546 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
169564 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
169583 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
169602 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
169622 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
169641 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
169655 AAGTAAACTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.17
19 36 0.46
20 29 0.37
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:169652 original size:39 final size:38
Alignment explanation
Indices: 169546--169654 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
169536 GCGATTTGTG
**
169546 TTTCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCA
* ***
169583 TTTCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCATTT-CGCGTTGCGATAGTCA
* *
169622 TTTCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TTTCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
169655 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
37 12 0.21
38 5 0.09
39 37 0.65
40 3 0.05
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (38 bp):
TTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCA
Found at i:171523 original size:13 final size:14
Alignment explanation
Indices: 171491--171525 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
171481 ATTGTTTAAT
171491 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
171505 TGATTTGTAAATG-
1 TGATTTGTAAAAGA
171518 TGATTTGT
1 TGATTTGT
171526 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:171658 original size:33 final size:33
Alignment explanation
Indices: 171613--171727 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 33
171603 AAAATAGACT
* ***
171613 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
171646 ATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CGAGA--AA
*
171683 ATTGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
171716 ATCGCATTGCGA
1 ATCGCAATGCGA
171728 TTCTCGTTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 33 0.49
35 8 0.12
37 26 0.39
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:171686 original size:18 final size:18
Alignment explanation
Indices: 171644--171701 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
171634 CGCAACGAGA
*
171644 AAATCGCAATGCGAAATG
1 AAATTGCAATGCGAAATG
171662 AAAATTGCAATGCGAAATG
1 -AAATTGCAATGCGAAATG
171681 AAATTGCAATGCGAAATG
1 AAATTGCAATGCGAAATG
171699 AAA
1 AAA
171702 ATCGCAACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 21 0.55
19 17 0.45
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (18 bp):
AAATTGCAATGCGAAATG
Found at i:171715 original size:19 final size:19
Alignment explanation
Indices: 171642--171708 Score: 109
Period size: 19 Copynumber: 3.6 Consensus size: 19
171632 ATCGCAACGA
171642 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
171661 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
171680 G-AAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
171698 GAAAATCGCAA
1 GAAAATCGCAA
171709 CGAGAAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.40
19 27 0.60
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:171782 original size:20 final size:20
Alignment explanation
Indices: 171732--171782 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
171722 TTGCGATTCT
*
171732 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCG
171752 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
171772 CGTTGCGATAG
1 CGTTGCGATAG
171783 TCAATGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:172851 original size:24 final size:24
Alignment explanation
Indices: 172824--172870 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
172814 CGAAATTTTC
*
172824 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACACGGACTTTGATA
*
172848 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
172871 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Done.