Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004269.1 Hibiscus syriacus cultivar Beakdansim tig00009363_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: 130192
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9053 original size:34 final size:36
Alignment explanation
Indices: 9009--9102 Score: 158
Period size: 34 Copynumber: 2.7 Consensus size: 36
8999 GACCAAGGAT
9009 GACCAAGGATCGGTTCATGCATGGGGCACTC-GGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
*
9044 GACC-AGGATCGATTCATGCAT-GGGCACTCGGGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
9078 GACCAAGGATCGGTTCATGCATGGG
1 GACCAAGGATCGGTTCATGCATGGG
9103 AGAATGGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
33 8 0.15
34 24 0.44
35 20 0.37
36 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.18
Consensus pattern (36 bp):
GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
Found at i:9216 original size:29 final size:29
Alignment explanation
Indices: 9183--9267 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
9173 AGCAGGGGAT
* * **
9183 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
9212 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
9241 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
9268 GCTACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:19354 original size:64 final size:62
Alignment explanation
Indices: 19269--19428 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
19259 TTGTTTAAGG
* * * *
19269 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TT-AATA-AAAACATCGAATAAGATTTA
* * *
19333 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAATAAAAACATCGAATAAGATTTA
*
19396 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
19429 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
62 1 0.01
63 32 0.38
64 48 0.57
65 2 0.02
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (62 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAATAAAAACATCGAATAAGATTTA
Found at i:21008 original size:145 final size:147
Alignment explanation
Indices: 20811--21121 Score: 547
Period size: 145 Copynumber: 2.1 Consensus size: 147
20801 GAGTCGAGGG
20811 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTC-GTGGAACATGTGTGAAGTCTTGAAAGACACAT
20876 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
64 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
20941 TATGACACTACGGTGCAAT
129 TATGACACTACGGTGCAAT
*
20960 TCTACGCGGTCTTTCGGG-ATATATATATTC-TGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TCTACGCGGTCCTTCGGGAATATATATATTCGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
*
21023 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
*
21088 TGGCACTACGGTGCAAT
131 TGACACTACGGTGCAAT
21105 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
21122 TGCAATTATA
Statistics
Matches: 157, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
144 1 0.01
145 127 0.81
147 12 0.08
149 17 0.11
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
TGACACTACGGTGCAAT
Found at i:21122 original size:23 final size:23
Alignment explanation
Indices: 21089--21133 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21079 ATTATTATAT
*
21089 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
21112 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
21134 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:29619 original size:21 final size:21
Alignment explanation
Indices: 29559--29619 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
29549 CGTTGACATC
* *
29559 ATAAATTATTACATTAATATT
1 ATAAATTACTAAATTAATATT
* *
29580 ATGAATCACCATAAA--AATATT
1 ATAAATTA-C-TAAATTAATATT
29601 ATAAATTACTAAATTAATA
1 ATAAATTACTAAATTAATA
29620 CCGTAACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 22 0.73
23 3 0.10
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAATTACTAAATTAATATT
Found at i:39327 original size:23 final size:23
Alignment explanation
Indices: 39301--39364 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
39291 CAGCTCATAT
39301 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
39324 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
39347 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
39365 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:39551 original size:103 final size:103
Alignment explanation
Indices: 39380--39592 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
39370 TAATGTCCAT
* * *
39380 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
39445 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
39483 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
39548 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
39586 AAGGACC
1 AAGGACC
39593 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:44312 original size:31 final size:30
Alignment explanation
Indices: 44277--44386 Score: 115
Period size: 31 Copynumber: 3.8 Consensus size: 30
44267 TTATCATTTC
44277 CAATACTAGTGGATTGAGCATTATTAACATT
1 CAATACTAGTGGATTGAGCATTATT-ACATT
* *
44308 CAATACTAATTGA-TGAGCATTA-T-C---
1 CAATACTAGTGGATTGAGCATTATTACATT
44332 CAATACTAGTGGATTGAGCATTATTACCATT
1 CAATACTAGTGGATTGAGCATTATTA-CATT
* * *
44363 TAATACTAGTTGAATGAGCATTAT
1 CAATACTAGTGGATTGAGCATTAT
44387 CCAACACTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
24 11 0.17
25 9 0.14
26 1 0.02
27 1 0.02
28 1 0.02
29 1 0.02
30 9 0.14
31 32 0.49
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (30 bp):
CAATACTAGTGGATTGAGCATTATTACATT
Found at i:44355 original size:55 final size:56
Alignment explanation
Indices: 44271--44416 Score: 224
Period size: 55 Copynumber: 2.6 Consensus size: 56
44261 GCAAAATTAT
44271 CATT-TCCAATACTAGTGGATTGAGCATTATTAACATTCAATACTAATTG-ATGAG
1 CATTATCCAATACTAGTGGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
* * *
44325 CATTATCCAATACTAGTGGATTGAGCATTATTACCATTTAATACTAGTTGAATGAG
1 CATTATCCAATACTAGTGGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
* * *
44381 CATTATCCAACACTAGTAGATTGAGCATTATCAACA
1 CATTATCCAATACTAGTGGATTGAGCATTATTAACA
44417 ATAGTGACAT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 4 0.05
55 42 0.51
56 37 0.45
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (56 bp):
CATTATCCAATACTAGTGGATTGAGCATTATTAACATTCAATACTAATTGAATGAG
Found at i:44772 original size:12 final size:12
Alignment explanation
Indices: 44755--44779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44745 TATTACCCGA
44755 CCTGTTTTCAAC
1 CCTGTTTTCAAC
44767 CCTGTTTTCAAC
1 CCTGTTTTCAAC
44779 C
1 C
44780 TGATCTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CCTGTTTTCAAC
Found at i:44787 original size:16 final size:16
Alignment explanation
Indices: 44768--44818 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
44758 GTTTTCAACC
44768 CTGTTTTCAACCTGAT
1 CTGTTTTCAACCTGAT
**
44784 CTGTTTTCAACCTGCC
1 CTGTTTTCAACCTGAT
* *
44800 CTGTTTTTAACCTTAT
1 CTGTTTTCAACCTGAT
44816 CTG
1 CTG
44819 ATATTTACCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.16, C:0.27, G:0.12, T:0.45
Consensus pattern (16 bp):
CTGTTTTCAACCTGAT
Found at i:45089 original size:23 final size:24
Alignment explanation
Indices: 45055--45104 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
45045 ATTCAAAGGA
*
45055 AAATTAATATAGTTTACTTTATAT
1 AAATTAATATAGTTTAATTTATAT
45079 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
45102 AAA
1 AAA
45105 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:45279 original size:7 final size:7
Alignment explanation
Indices: 45267--45297 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
45257 TCTATTTATA
45267 TTAGGGT
1 TTAGGGT
45274 TTAGGGT
1 TTAGGGT
45281 TTAGGGT
1 TTAGGGT
*
45288 TTAGAGT
1 TTAGGGT
45295 TTA
1 TTA
45298 TATATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:45606 original size:14 final size:14
Alignment explanation
Indices: 45583--45629 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
45573 TTATATTAGG
* *
45583 GTTTAGGGTTTATA
1 GTTTAAGGTTTAAA
45597 GTTTAAGGTTTAAA
1 GTTTAAGGTTTAAA
* *
45611 ATTTAAGGTTTAGA
1 GTTTAAGGTTTAAA
45625 GTTTA
1 GTTTA
45630 TATATATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
GTTTAAGGTTTAAA
Found at i:45919 original size:14 final size:14
Alignment explanation
Indices: 45902--45955 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
45892 AAAGTTTATG
*
45902 GTTTATGGTTTAAT
1 GTTTATGGTTTAAA
45916 GTTTATGGTTTAAA
1 GTTTATGGTTTAAA
* * *
45930 GTTTAGGGTGTATA
1 GTTTATGGTTTAAA
*
45944 GTTTATGATTTA
1 GTTTATGGTTTA
45956 GGGTTTAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
GTTTATGGTTTAAA
Found at i:45933 original size:21 final size:21
Alignment explanation
Indices: 45890--45934 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45880 TCCATTTACA
**
45890 TTAAAGTTTATGGTTTATGGT
1 TTAAAGTTTATGGTTTAAAGT
*
45911 TTAATGTTTATGGTTTAAAGT
1 TTAAAGTTTATGGTTTAAAGT
45932 TTA
1 TTA
45935 GGGTGTATAG
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:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TTAAAGTTTATGGTTTAAAGT
Found at i:45963 original size:7 final size:7
Alignment explanation
Indices: 45895--45962 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
45885 TTACATTAAA
45895 GTTTATG
1 GTTTATG
45902 GTTTATG
1 GTTTATG
45909 GTTTAAT-
1 GTTT-ATG
45916 GTTTATG
1 GTTTATG
**
45923 GTTTAAA
1 GTTTATG
*
45930 GTTTAGG
1 GTTTATG
* *
45937 GTGTATA
1 GTTTATG
45944 GTTTATG
1 GTTTATG
* *
45951 ATTTAGG
1 GTTTATG
45958 GTTTA
1 GTTTA
45963 GAATTTCTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
6 2 0.04
7 43 0.91
8 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.51
Consensus pattern (7 bp):
GTTTATG
Found at i:46459 original size:7 final size:7
Alignment explanation
Indices: 46421--46470 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
46411 TATGGTTCAT
46421 GGTTTAG
1 GGTTTAG
*
46428 GATTTAG
1 GGTTTAG
*
46435 GGTTTAA
1 GGTTTAG
* * *
46442 TGTGTAT
1 GGTTTAG
46449 GGTTTAG
1 GGTTTAG
46456 GGTTTAG
1 GGTTTAG
46463 GGTTTAG
1 GGTTTAG
46470 G
1 G
46471 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:46537 original size:2 final size:2
Alignment explanation
Indices: 46526--46623 Score: 189
Period size: 2 Copynumber: 49.5 Consensus size: 2
46516 ATAGTGTTTC
46526 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46609 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
46624 CTATTGATTA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 94 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46713 original size:15 final size:16
Alignment explanation
Indices: 46679--46720 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
46669 TAATATAAAT
46679 TATAATTTATAAACTA
1 TATAATTTATAAACTA
* *
46695 TATAGTTTATACA-TA
1 TATAATTTATAAACTA
46710 TATAATTTATA
1 TATAATTTATA
46721 TACATACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TATAATTTATAAACTA
Found at i:47010 original size:17 final size:19
Alignment explanation
Indices: 46961--47012 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 19
46951 TTTTCTATTC
46961 CCTCTAAATTTCTCAATTTT
1 CCTCTAAA-TTCTCAATTTT
46981 CCTCTAAATTCTCAA-TTT
1 CCTCTAAATTCTCAATTTT
*
46999 CC-CTATATTCTCAA
1 CCTCTAAATTCTCAA
47013 AAATTTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 11 0.35
18 5 0.16
19 7 0.23
20 8 0.26
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (19 bp):
CCTCTAAATTCTCAATTTT
Found at i:47166 original size:25 final size:24
Alignment explanation
Indices: 47138--47191 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
47128 TTAATATAAA
*
47138 TTATAGTTTATAAACTATATATTTT
1 TTATAGTTTATAAA-TATATAGTTT
*
47163 TTATAGTTTATACATATATAGTTT
1 TTATAGTTTATAAATATATAGTTT
*
47187 ATATA
1 TTATA
47192 TATATAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
TTATAGTTTATAAATATATAGTTT
Found at i:47184 original size:15 final size:14
Alignment explanation
Indices: 47164--47285 Score: 81
Period size: 15 Copynumber: 8.1 Consensus size: 14
47154 ATATATTTTT
47164 TATAGTTTATACATA
1 TATAGTTTATA-ATA
47179 TATAGTTTATATATA
1 TATAGTTTATA-ATA
47194 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
47209 CATAATTTAT-ATA
1 TATAGTTTATAATA
47222 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
47240 TATAGTTTATAATATAAA
1 TATAGTTTAT-A-AT--A
47258 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
47271 TATAATTTAT-ATA
1 TATAGTTTATAATA
47284 TA
1 TA
47286 AACTTATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
12 1 0.01
13 22 0.25
14 2 0.02
15 32 0.36
16 6 0.07
17 8 0.09
18 18 0.20
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:47192 original size:13 final size:13
Alignment explanation
Indices: 47164--47285 Score: 65
Period size: 13 Copynumber: 9.2 Consensus size: 13
47154 ATATATTTTT
47164 TATAGTTTATACATA
1 TATAGTTTAT--ATA
47179 TATAGTTTATATATA
1 TATAG-TT-TATATA
*
47194 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
47209 CATAATTTATATA
1 TATAGTTTATATA
*
47222 TATAGCTTATA-A
1 TATAGTTTATATA
47234 TA-A--TTATATA
1 TATAGTTTATATA
* * *
47244 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
47258 TATAGTTTATATA
1 TATAGTTTATATA
*
47271 TATAATTTATATA
1 TATAGTTTATATA
47284 TA
1 TA
47286 AACTTATATT
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 4 0.05
13 35 0.42
14 8 0.10
15 24 0.29
16 2 0.02
17 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:47260 original size:18 final size:18
Alignment explanation
Indices: 47216--47275 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
47206 AAACATAATT
* *
47216 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
47234 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
47252 TATAAATATAGTTTATATA
1 TATAAATATAGTTTATA-A
47271 TATAA
1 TATAA
47276 TTTATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.78
19 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:51219 original size:17 final size:17
Alignment explanation
Indices: 51193--51233 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
51183 CAAATACAAA
*
51193 GAGGAGAGGGAGGACTG
1 GAGGAAAGGGAGGACTG
51210 GAGGAAAGGGAGGACTG
1 GAGGAAAGGGAGGACTG
51227 GAGGAAA
1 GAGGAAA
51234 AGCGGAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.54, T:0.05
Consensus pattern (17 bp):
GAGGAAAGGGAGGACTG
Found at i:65846 original size:6 final size:6
Alignment explanation
Indices: 65835--65861 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
65825 GGGTACAACC
65835 GAAAAT GAAAAT GAAAAT GAAAAT GAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAA
65862 GAATAAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (6 bp):
GAAAAT
Found at i:66551 original size:2 final size:2
Alignment explanation
Indices: 66544--66622 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
66534 GTAATACATT
66544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66623 TTAAAAAAGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70160 original size:30 final size:30
Alignment explanation
Indices: 70126--70222 Score: 185
Period size: 30 Copynumber: 3.2 Consensus size: 30
70116 CCCGAATGAC
70126 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
70156 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
70186 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
70216 CTGTCCA
1 CTATCCA
70223 TATGTTCCTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:71028 original size:21 final size:21
Alignment explanation
Indices: 70986--71028 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
70976 TTTCTGGGTT
* * *
70986 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
71007 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
71028 A
1 A
71029 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:71088 original size:65 final size:66
Alignment explanation
Indices: 70986--71156 Score: 211
Period size: 67 Copynumber: 2.6 Consensus size: 66
70976 TTTCTGGGTT
* * *
70986 AGGGGAATCGGTACCCATTCAAGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGC
1 AGGGGAATCGGTACCC--CCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGC
71050 TAG
64 TAG
* * * *
71053 AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTT
1 AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTA
71118 G
66 G
* *
71119 AGGGGAATCGATA-CCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA--GGGGGAACCGATACCCCC
71157 ATGAGAAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 29 0.32
66 30 0.33
67 33 0.36
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (66 bp):
AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTA
G
Found at i:71557 original size:30 final size:30
Alignment explanation
Indices: 71523--71581 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
71513 GTTATATGAG
* *
71523 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
71553 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
71582 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:71853 original size:23 final size:22
Alignment explanation
Indices: 71792--71860 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
71782 TCCTTATGGA
71792 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
71814 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
71836 CAATTCTACGGGGCACTTCGGTG
1 CAATTCTAC-GGGCACTTCGGTG
71859 CA
1 CA
71861 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 31 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:74014 original size:21 final size:21
Alignment explanation
Indices: 73984--74028 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
73974 TGTTGTTCGT
*
73984 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
74005 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
74026 TTG
1 TTG
74029 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:75789 original size:13 final size:13
Alignment explanation
Indices: 75771--75816 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
75761 CACATAATTG
75771 GGTTTTGGGTTTA
1 GGTTTTGGGTTTA
75784 GGTTTTGGGTTTTA
1 GGTTTTGGG-TTTA
75798 GGTTTAT-GGTTTA
1 GGTTT-TGGGTTTA
75811 GGTTTT
1 GGTTTT
75817 AAGGTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.03
13 18 0.58
14 11 0.35
15 1 0.03
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.57
Consensus pattern (13 bp):
GGTTTTGGGTTTA
Found at i:75793 original size:20 final size:21
Alignment explanation
Indices: 75768--75824 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
75758 TATCACATAA
* * *
75768 TTGGGTTTTGGGTTTAGGTTT
1 TTGGGTTTTAGGTTTATGGTT
75789 -TGGGTTTTAGGTTTATGG-T
1 TTGGGTTTTAGGTTTATGGTT
*
75808 TTAGGTTTTAAGGTTTA
1 TTGGGTTTT-AGGTTTA
75825 GAGTTCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 22 0.73
21 7 0.23
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.54
Consensus pattern (21 bp):
TTGGGTTTTAGGTTTATGGTT
Found at i:75817 original size:14 final size:14
Alignment explanation
Indices: 75778--75825 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
75768 TTGGGTTTTG
*
75778 GGTTTAGGTTTT-G
1 GGTTTAGGTTTTAA
*
75791 GGTTTTAGG-TTTAT
1 GG-TTTAGGTTTTAA
75805 GGTTTAGGTTTTAA
1 GGTTTAGGTTTTAA
75819 GGTTTAG
1 GGTTTAG
75826 AGTTCATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
GGTTTAGGTTTTAA
Found at i:76343 original size:11 final size:11
Alignment explanation
Indices: 76329--76389 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
76319 ATTATAGAAA
76329 TTTTAATATAT
1 TTTTAATATAT
76340 TTTTAA-A-AT
1 TTTTAATATAT
76349 TTTATAAT-TAT
1 TTT-TAATATAT
*** *
76360 CAATAATGTAT
1 TTTTAATATAT
76371 TTTTAATATAT
1 TTTTAATATAT
76382 TTTTAATA
1 TTTTAATA
76390 ATGCAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:78470 original size:14 final size:15
Alignment explanation
Indices: 78440--78470 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
78430 AAATAAAAGT
78440 AAGAATGAGATAGAA
1 AAGAATGAGATAGAA
78455 AAGAATGAGA-AGAA
1 AAGAATGAGATAGAA
78469 AA
1 AA
78471 TGAAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (15 bp):
AAGAATGAGATAGAA
Found at i:81172 original size:21 final size:21
Alignment explanation
Indices: 81146--81190 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
81136 GATTTCTGGG
* *
81146 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
81167 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
81188 CAA
1 CAA
81191 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:82591 original size:14 final size:14
Alignment explanation
Indices: 82572--82599 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
82562 GAAAAGAAGC
82572 TATGTGATACGTGA
1 TATGTGATACGTGA
82586 TATGTGATACGTGA
1 TATGTGATACGTGA
82600 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:82885 original size:149 final size:149
Alignment explanation
Indices: 82700--83014 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
82690 GAGTCGAGGG
*
82700 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAATATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
82765 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
82830 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
82849 TCTACGCGGTCCTTCGGGATATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* **
82914 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
82979 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
82998 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
83015 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:83015 original size:23 final size:23
Alignment explanation
Indices: 82982--83026 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
82972 ATTTTTATAT
*
82982 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
83005 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
83027 AGCTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:86929 original size:2 final size:2
Alignment explanation
Indices: 86922--86950 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
86912 AAATCCATGC
86922 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86951 TACCTGAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101249 original size:37 final size:37
Alignment explanation
Indices: 101173--101249 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
101163 TTTTTATATT
*
101173 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
101210 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
101247 TTT
1 TTT
101250 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:101431 original size:20 final size:20
Alignment explanation
Indices: 101395--101432 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101385 ATCATATTCC
**
101395 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
101415 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
101433 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:102944 original size:20 final size:20
Alignment explanation
Indices: 102900--103237 Score: 214
Period size: 20 Copynumber: 16.6 Consensus size: 20
102890 AATGACCAAT
*
102900 AAAATCGCAACGCGATATA-
1 AAAATCGCAACGCGATTTAG
102919 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
102939 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
102959 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
102979 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
103000 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
103023 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
103043 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
103063 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
103083 AGAGTCGCAACGCGGTCTAGAAG
1 AAAATCGCAACGCGAT-T--TAG
* * *
103106 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
103126 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
103146 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
103166 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
103186 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
103206 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
103226 AAAATCGCAACG
1 AAAATCGCAACG
103238 GTCAAAAGAA
Statistics
Matches: 259, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
19 18 0.07
20 198 0.76
21 15 0.06
22 1 0.00
23 27 0.10
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:103078 original size:40 final size:40
Alignment explanation
Indices: 103004--103235 Score: 248
Period size: 40 Copynumber: 5.7 Consensus size: 40
102994 GCTTCCAAGT
* *
103004 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* *
103047 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * * *
103087 TCGCAACGCGGTCTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * * * *
103130 TCGCAATGCGACTGAGAGAATCGCAACGCGATTTATAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * *
103170 TCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
103210 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAATGCGATTTAGAGAATCGCAA
103236 CGGTCAAAAG
Statistics
Matches: 162, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 111 0.69
41 2 0.01
42 4 0.02
43 45 0.28
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:103116 original size:83 final size:82
Alignment explanation
Indices: 103004--103237 Score: 292
Period size: 83 Copynumber: 2.9 Consensus size: 82
102994 GCTTCCAAGT
* *
103004 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGA-TTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAATC
* *
103069 GCAATGCGATTGAGAGAG
65 GCAACGCGATTGAGAGAA
* * * *
103087 TCGCAACGCGGTCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGAT-TAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAATC
* *
103152 GCAACGCGATTTATAGAA
65 GCAACGCGATTGAGAGAA
* * * * * *
103170 TCGCAATGCGATT-G-AGAGAATCGCAACGCGATTTAGAGAATCGCAACGCGATTTAGAAAATCG
1 TCGCAACGCGATTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAATCG
103233 CAACG
66 CAACG
103238 GTCAAAAGAA
Statistics
Matches: 130, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
80 46 0.35
81 1 0.01
82 2 0.02
83 81 0.62
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (82 bp):
TCGCAACGCGATTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAATCG
CAACGCGATTGAGAGAA
Found at i:103236 original size:40 final size:40
Alignment explanation
Indices: 102900--103237 Score: 238
Period size: 40 Copynumber: 8.3 Consensus size: 40
102890 AATGACCAAT
*
102900 AAAATCGCAACGCGATAT-A-AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TGAGAGAATCGCAACGCGATTTAG
** *** * **
102939 AAAATCGCAACGTTAAAAAGAAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGAT--TTAG
* *
102979 AAAATCGCAACGCGAGCTTCCA-AG-TTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA--TT-GAGAGAATCGCAACGCGATTT---AG
* * * *
103023 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * * * *
103063 AGAATCGCAATGCGATTGAGAGAGTCGCAACGCGGTCTAGAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGAT-T--TAG
* * * * *
103106 AAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * * * *
103146 AGAATCGCAACGCGATTTATAGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* *
103186 AGAATCGCAACGCGATTTAGAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
103226 AAAATCGCAACG
1 AAAATCGCAACG
103238 GTCAAAAGAA
Statistics
Matches: 238, Mismatches: 44, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.00
39 15 0.06
40 143 0.60
41 10 0.04
42 7 0.03
43 46 0.19
44 16 0.07
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
Found at i:103336 original size:6 final size:6
Alignment explanation
Indices: 103325--103374 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
103315 GACACGTATT
103325 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
103372 ACC
1 ACC
103375 CGAGACGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:104077 original size:6 final size:6
Alignment explanation
Indices: 104061--104162 Score: 183
Period size: 6 Copynumber: 17.5 Consensus size: 6
104051 TCTCGTCTCG
104061 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
104108 GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCG- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
104154 GGTCGT GGT
1 GGTCGT GGT
104163 AATACGTGTC
Statistics
Matches: 94, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.16
6 79 0.84
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:104094 original size:29 final size:30
Alignment explanation
Indices: 104061--104162 Score: 183
Period size: 29 Copynumber: 3.5 Consensus size: 30
104051 TCTCGTCTCG
104061 GGTCG-GGTCGTGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGT
104090 GGTCGTGGTCGTGGTCGTGGTCGT-GTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGT
104119 GGTCGTGGTCGTGGTCGTGGTCG-GGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGT
104148 GGTCGTGGTCGTGGT
1 GGTCGTGGTCGTGGT
104163 AATACGTGTC
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
29 53 0.75
30 18 0.25
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (30 bp):
GGTCGTGGTCGTGGTCGTGGTCGTGGTCGT
Found at i:104273 original size:20 final size:20
Alignment explanation
Indices: 104250--104567 Score: 192
Period size: 20 Copynumber: 15.6 Consensus size: 20
104240 TTCTTTTGAC
104250 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
104270 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
104290 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
104310 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
104330 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
104350 CATTGCGATTTTCTTCTAGATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
104373 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
104393 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
104413 CATTGCGATTTTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
104433 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
104456 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
104477 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
104495 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
104517 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
104537 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
104556 CGTTGCGATTTT
1 CGTTGCGATTTT
104568 ATTGGTCATT
Statistics
Matches: 239, Mismatches: 48, Indels: 23
0.77 0.15 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 172 0.72
21 14 0.06
22 6 0.03
23 28 0.12
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:104296 original size:40 final size:40
Alignment explanation
Indices: 104252--104442 Score: 220
Period size: 40 Copynumber: 4.7 Consensus size: 40
104242 CTTTTGACCG
* * *
104252 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * * *
104292 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * *
104332 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAGATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGATTCTC-TC-A-ATCGCA
* * *
104375 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
104415 TTGCGATTTTATCAATCGCATTGCGATT
1 TTGCGATTCTCTCAATCGCATTGCGATT
104443 TTCTTCTAAA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 93 0.72
41 3 0.02
42 2 0.02
43 31 0.24
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:104392 original size:83 final size:82
Alignment explanation
Indices: 104252--104463 Score: 266
Period size: 83 Copynumber: 2.6 Consensus size: 82
104242 CTTTTGACCG
* * * * * *
104252 TTGCGATTTTCTAAATCGCGTTGCGATTCTC-TC-AATCGCATTGCGATTCTATAAATCGCGTTG
1 TTGCGATTTTCTCAATCGCATTGCGATTTTCTTCTAATCGCGTTGCGACTCTATAAATCGCATTG
* * *
104315 CGATTCTCTCAGTCGCA
66 CGATTCTATAAATCGCA
* * * *
104332 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAGATCGCGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTTTCTCAATCGCATTGCGATTTTCTTCTA-ATCGCGTTGCGACTCTATAAATCGCATT
104397 GCGATTCTATAAATCGCA
65 GCGATTCTATAAATCGCA
*
104415 TTGCGATTTTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTTTCTCAATCGCATTGCGATTTTCTTCT-AATCGCGTTGCGA
104464 ACTTGGAAGC
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
80 26 0.23
81 2 0.02
82 1 0.01
83 82 0.73
84 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (82 bp):
TTGCGATTTTCTCAATCGCATTGCGATTTTCTTCTAATCGCGTTGCGACTCTATAAATCGCATTG
CGATTCTATAAATCGCA
Found at i:104557 original size:19 final size:20
Alignment explanation
Indices: 104517--104567 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
104507 TTCTTTTTAA
*
104517 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
104537 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
104556 CGTTGCGATTTT
1 CGTTGCGATTTT
104568 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:105242 original size:20 final size:22
Alignment explanation
Indices: 105219--105258 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
105209 TATTATTTAT
105219 ATTTGTT-TATATT-TATAAAG
1 ATTTGTTATATATTATATAAAG
105239 ATTTGTTATATATTATATAA
1 ATTTGTTATATATTATATAA
105259 CATATTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
ATTTGTTATATATTATATAAAG
Found at i:110458 original size:20 final size:20
Alignment explanation
Indices: 110433--110470 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
110423 CACCTGTTAA
*
110433 AGAATGCATCGATGCACTAT
1 AGAATGCACCGATGCACTAT
110453 AGAATGCACCGATGCACT
1 AGAATGCACCGATGCACT
110471 TCAATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAATGCACCGATGCACTAT
Found at i:111188 original size:18 final size:18
Alignment explanation
Indices: 111165--111200 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
111155 GAGGGTCTAC
111165 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
111183 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
111201 TGTGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:115090 original size:25 final size:24
Alignment explanation
Indices: 115047--115099 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
115037 TTAACAAAAA
*
115047 ATATTTTTTAAAATCAAAATTTAT
1 ATATTTTTTAAAATCAAAATTTAG
*
115071 ATATTTTATTTAAATCAAAATTTAG
1 ATATTTT-TTAAAATCAAAATTTAG
115096 ATAT
1 ATAT
115100 AATATGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATTTTTTAAAATCAAAATTTAG
Found at i:115109 original size:25 final size:25
Alignment explanation
Indices: 115057--115109 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
115047 ATATTTTTTA
* ** *
115057 AAATCAAAATTTATATATTTTATTT
1 AAATCAAAATTTAGATATAATATGT
115082 AAATCAAAATTTAGATATAATATGT
1 AAATCAAAATTTAGATATAATATGT
115107 AAA
1 AAA
115110 AATTTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
AAATCAAAATTTAGATATAATATGT
Found at i:127771 original size:18 final size:19
Alignment explanation
Indices: 127731--127774 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
127721 GTTTCGCAAT
*
127731 TTTATTAATTAATATAAAA
1 TTTATTAATAAATATAAAA
*
127750 -TTATTTATAAAT-TAAAA
1 TTTATTAATAAATATAAAA
127767 TTTATTAA
1 TTTATTAA
127775 GTTAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTAATAAATATAAAA
Done.