Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002612.1 Hibiscus syriacus cultivar Beakdansim tig00005282_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: 87866
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5222 original size:23 final size:24
Alignment explanation
Indices: 5176--5241 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
5166 GAGCTGGTAC
* **
5176 ATTAAATTATATTAATTAGTATATT
1 ATTAAA-TATATTTATTAAAATATT
5201 -TTAAATATATTTATTAAAATATT
1 ATTAAATATATTTATTAAAATATT
*
5224 ATTAGAT-TATTATATTAA
1 ATTAAATATATT-TATTAA
5242 TATTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTAAATATATTTATTAAAATATT
Found at i:5387 original size:27 final size:27
Alignment explanation
Indices: 5325--5410 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 27
5315 TATTAATAAT
5325 TTATTATATATTATTAAAATAT-ATATA
1 TTATT-TATATTATTAAAATATAATATA
* *
5352 ATATCTTATATTATTATAATATAAT-TGA
1 TTAT-TTATATTATTAAAATATAATAT-A
5380 TTATTTATTATAATATTAAAATATAATATA
1 TTATTTA-TAT--TATTAAAATATAATATA
5410 T
1 T
5411 ATTATTAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
27 22 0.46
28 10 0.21
30 15 0.31
31 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTATTTATATTATTAAAATATAATATA
Found at i:5414 original size:95 final size:94
Alignment explanation
Indices: 5230--5414 Score: 202
Period size: 95 Copynumber: 1.9 Consensus size: 94
5220 TATTATTAGA
*
5230 TTATTATATTAATATTAAATATAAATAATATTTCATTATTAATAATTTAATAATATTATTTCTAT
1 TTATTATATTAATATTAAATATAAATAATATTTCATTATTAATAATATAAT-ATATTATTTCTAT
*
5295 GAAATTAATAATATAAATTTTATTAATAAT
65 GAAATTAATAATATAAATTATATTAATAAT
* * *
5325 TTATTATA-TATTATTAAAATATATATAATATCTTATATTATT-ATAATATAAT-TGATTATTTA
1 TTATTATATTAATATT-AAATATAAATAATAT-TT-CATTATTAATAATATAATAT-ATTATTT-
*
5387 TTAT-AATATTAA-AATAT-AATATATATTA
61 CTATGAA-ATTAATAATATAAAT-TATATTA
5415 TTAGAAATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
94 10 0.13
95 42 0.55
96 19 0.25
97 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (94 bp):
TTATTATATTAATATTAAATATAAATAATATTTCATTATTAATAATATAATATATTATTTCTATG
AAATTAATAATATAAATTATATTAATAAT
Found at i:5417 original size:50 final size:49
Alignment explanation
Indices: 5204--5417 Score: 119
Period size: 49 Copynumber: 4.3 Consensus size: 49
5194 GTATATTTTA
* *
5204 AATATAT-TTATTAAAATATTATTAGATTA-TTA-TATTAATATTAAATATAAAT
1 AATATATATTATTATAATATAATT--ATTATTTATTA-TAATATTAAA-AT--AT
* * *
5256 AATATTTCATTATTAATAATTTAATAATATTATTT-CTATGAA-ATTAATAATAT
1 AATATAT-ATTATT-ATAATATAAT--TATTATTTATTAT-AATATTAA-AATAT
* * *
5309 AA-AT-T-TTATTAATAAT-TTATTA-TATATTATTAAAATATATATAATAT
1 AATATATATTATT-ATAATATAATTATTAT-TTATTATAATAT-TAAAATAT
*
5356 -CT-TATATTATTATAATATAATTGATTATTTATTATAATATTAAAATAT
1 AATATATATTATTATAATATAATT-ATTATTTATTATAATATTAAAATAT
5404 AATATATATTATTA
1 AATATATATTATTA
5418 GAAATATTAA
Statistics
Matches: 128, Mismatches: 13, Indels: 44
0.69 0.07 0.24
Matches are distributed among these distances:
45 3 0.02
46 7 0.05
47 15 0.12
48 21 0.16
49 24 0.19
50 13 0.10
51 1 0.01
52 8 0.06
53 4 0.03
54 5 0.04
55 19 0.15
56 7 0.05
57 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (49 bp):
AATATATATTATTATAATATAATTATTATTTATTATAATATTAAAATAT
Found at i:5714 original size:42 final size:42
Alignment explanation
Indices: 5668--5750 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
5658 CAAACACTGG
* *
5668 AAAATATTTTTCGAAAAACGAATTACGTG-AAACAAACACGAA
1 AAAATATTTTCCGAAAAACAAATTAC-TGAAAACAAACACGAA
**
5710 AAAATATTTTCCTTAAAACAAATTACTGAAAACAAACACGA
1 AAAATATTTTCCGAAAAACAAATTACTGAAAACAAACACGA
5751 GATTTCGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.23
Consensus pattern (42 bp):
AAAATATTTTCCGAAAAACAAATTACTGAAAACAAACACGAA
Found at i:19123 original size:21 final size:23
Alignment explanation
Indices: 19097--19144 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
19087 ATTGATATAG
*
19097 TTTACCTTT-TATTTT-AAATAA
1 TTTACCTTTAAATTTTCAAATAA
*
19118 TTTACCTTTAAATTTTCAACTAA
1 TTTACCTTTAAATTTTCAAATAA
19141 TTTA
1 TTTA
19145 TAATTATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTACCTTTAAATTTTCAAATAA
Found at i:21367 original size:14 final size:14
Alignment explanation
Indices: 21350--21385 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
21340 TAAAAACAGA
*
21350 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
21364 AAATTAGAGGAATG
1 AAATTAAAGGAATG
21378 AAATTAAA
1 AAATTAAA
21386 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:26604 original size:20 final size:20
Alignment explanation
Indices: 26575--26636 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
26565 TGTTTTTTAG
* *
26575 TATCGGTACTATTCACACAA
1 TATCGATACTATTCATACAA
*
26595 TATCGATACTATTCATACAG
1 TATCGATACTATTCATACAA
*
26615 TATTGATACTATTCATACAA
1 TATCGATACTATTCATACAA
26635 TA
1 TA
26637 ATATTCATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (20 bp):
TATCGATACTATTCATACAA
Found at i:32894 original size:43 final size:42
Alignment explanation
Indices: 32742--33126 Score: 254
Period size: 42 Copynumber: 9.0 Consensus size: 42
32732 TTGAGTCTTT
** * *
32742 TAATTTTCTTCAATTTTA-TTTTTATCTTAATAATTG-AGACCTC
1 TAATTTT-TTCAATCCTACTTTTTACCTTTATAATTGAAG-CC-C
* * * *
32785 TAATTTTTGT-AACCCTAC-TTTTATCTTTATAATTGAGGCCTT
1 TAATTTTT-TCAATCCTACTTTTTACCTTTATAATTGAAGCC-C
* * * *
32827 TAATTTTTTTAATCCCACTCTTTTACATTTATGATTGATAGCCC
1 TAATTTTTTCAATCCTACT-TTTTACCTTTATAATTGA-AGCCC
32871 TAATTTTTTCAATCCTACTTTTTACCTTTATAATTG-AGCTCC
1 TAATTTTTTCAATCCTACTTTTTACCTTTATAATTGAAGC-CC
* *
32913 TAATTTTTTCAAT-CTCACTTTCTACCTTTATAATTGAGGCCCC
1 TAATTTTTTCAATCCT-ACTTTTTACCTTTATAATTGAAG-CCC
* * *
32956 TAATTTATT-AATCAC-ATTTTTTACCTTTATAATTGAGACCCC
1 TAATTTTTTCAATC-CTACTTTTTACCTTTATAATTGA-AGCCC
* * * *
32998 TGA-TTTTTCAAT-CTCACTTTTTACCTTTAAAATTGAGGACAC
1 TAATTTTTTCAATCCT-ACTTTTTACCTTTATAATTGAAG-CCC
* * **
33040 TAAATTTTTT-AAT-CTCATTTTTTACCTTTATAATTGAGGTCTT
1 T-AATTTTTTCAATCCT-ACTTTTTACCTTTATAATTGAAG-CCC
* * * * *
33083 TAAGTTTTTGAATCGTACTTTTTTACTTTTATAATTTAAGCCC
1 TAATTTTTTCAATCCTAC-TTTTTACCTTTATAATTGAAGCCC
33126 T
1 T
33127 TTAGTTTAAT
Statistics
Matches: 274, Mismatches: 45, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
40 1 0.00
41 10 0.04
42 131 0.48
43 71 0.26
44 58 0.21
45 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (42 bp):
TAATTTTTTCAATCCTACTTTTTACCTTTATAATTGAAGCCC
Found at i:32992 original size:84 final size:81
Alignment explanation
Indices: 32742--33077 Score: 309
Period size: 85 Copynumber: 4.0 Consensus size: 81
32732 TTGAGTCTTT
* * * * * * *
32742 TAATTTTCTTCAATTTTA-TTTTTATCTTAATAATTGAGACCTCTAATTTTTGTAA-CCCTACTT
1 TAATTTT-TTCAATCTCACTTTTTACCTTTATAATTGAGGCC-CTAATTTTT-TAATCCAT-TTT
* *
32805 TTATCTTTATAATTGAGGCCTT
62 TTACCTTTATAATTGA-GCC-C
* * * * * *
32827 TAATTTTTTTAATCCCACTCTTTTACATTTATGATTGATAGCCCTAATTTTTTCAATCCTACTTT
1 TAATTTTTTCAATCTCACT-TTTTACCTTTATAATTGA-GGCCCTAATTTTTT-AATCC-ATTTT
32892 TTACCTTTATAATTGAGCTCC
62 TTACCTTTATAATTGAGC-CC
* *
32913 TAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCCCTAATTTATTAATCACATTTTTT
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGG-CCCTAATTTTTTAATC-CATTTTTT
32978 ACCTTTATAATTGAGACCCC
64 ACCTTTATAATTGAG--CCC
* * *
32998 TGA-TTTTTCAATCTCACTTTTTACCTTTAAAATTGAGGACACTAAATTTTTTAATCTCATTTTT
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGG-CCCT-AATTTTTTAATC-CATTTTT
33062 TACCTTTATAATTGAG
63 TACCTTTATAATTGAG
33078 GTCTTTAAGT
Statistics
Matches: 209, Mismatches: 30, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
84 68 0.33
85 74 0.35
86 45 0.22
87 22 0.11
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (81 bp):
TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCTAATTTTTTAATCCATTTTTTAC
CTTTATAATTGAGCCC
Found at i:38864 original size:17 final size:17
Alignment explanation
Indices: 38837--38869 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
38827 TTATTATATT
38837 AGAATTAAATTTAAAATA
1 AGAATTAAA-TTAAAATA
38855 AGAA-TAAATTAAAAT
1 AGAATTAAATTAAAAT
38870 TAAAATGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
AGAATTAAATTAAAATA
Found at i:39582 original size:21 final size:21
Alignment explanation
Indices: 39558--39623 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
39548 TATCGCAAAT
39558 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*** * ** **
39579 TCGCAAAGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
39599 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
39620 TCGC
1 TCGC
39624 AAAGCGATTT
Statistics
Matches: 28, Mismatches: 16, Indels: 2
0.61 0.35 0.04
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:39630 original size:21 final size:21
Alignment explanation
Indices: 39565--39631 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
39555 AATTCGCGTT
39565 GCGATAGTTGAAAATCGCAAA
1 GCGATAGTTGAAAATCGCAAA
* ** ** ***
39586 GCGAT-TTTCCATTTCGCGTT
1 GCGATAGTTGAAAATCGCAAA
39606 GCGATAGTTGAAAATCGCAAA
1 GCGATAGTTGAAAATCGCAAA
39627 GCGAT
1 GCGAT
39632 TTTCCATTTC
Statistics
Matches: 29, Mismatches: 16, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (21 bp):
GCGATAGTTGAAAATCGCAAA
Found at i:39691 original size:20 final size:20
Alignment explanation
Indices: 39668--39733 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
39658 AAATCGCAAC
39668 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
* * *
39688 GCGATAGTGTACA-GT-GTCGTT
1 GCGAT--TTTCCATTTCG-CGTT
39709 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
39729 GCGAT
1 GCGAT
39734 AGTCTACAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 11 0.31
22 4 0.11
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.39
Consensus pattern (20 bp):
GCGATTTTCCATTTCGCGTT
Found at i:39743 original size:41 final size:41
Alignment explanation
Indices: 39557--39736 Score: 265
Period size: 41 Copynumber: 4.4 Consensus size: 41
39547 CTATCGCAAA
39557 TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
39598 TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
* *
39639 TTCGTGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
* * ***
39680 TTCGCGTTGCGATAG-TGTACAGT-GTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTG-AAAATCG-CAAAGCGATTTTCCAT
39721 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
39737 CTACAGTAAA
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
40 3 0.02
41 125 0.98
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCAT
Found at i:39835 original size:6 final size:6
Alignment explanation
Indices: 39824--39880 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
39814 GACACGTATT
39824 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
39870 A-CACG A-CACG A
1 ACCACG ACCACG A
39881 GACGGCGGCG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.39
6 31 0.61
ACGTcount: A:0.37, C:0.46, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:40273 original size:21 final size:20
Alignment explanation
Indices: 40247--40325 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
40237 TTTAATTTAC
40247 TGTAGACTATCGCAACGACA
1 TGTAGACTATCGCAACGACA
40267 TTGTAGACTATCGCAACG-CGA
1 -TGTAGACTATCGCAACGAC-A
** **
40288 AATAGAAAATCGCAACGACA
1 TGTAGACTATCGCAACGACA
*
40308 CTGTACACTATCGCAACG
1 -TGTAGACTATCGCAACG
40326 CGAGATTTAG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
TGTAGACTATCGCAACGACA
Found at i:40666 original size:24 final size:24
Alignment explanation
Indices: 40640--40685 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
40630 TTTATGTACA
* *
40640 AAAATTTAAAAA-ATTTAAATCAG
1 AAAATATAAAAAGATTGAAATCAG
40663 AAAATATAAAAAGATTGAAATCA
1 AAAATATAAAAAGATTGAAATCA
40686 AAGATCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAAATATAAAAAGATTGAAATCAG
Found at i:41667 original size:29 final size:29
Alignment explanation
Indices: 41612--41672 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
41602 CCTAACTGGC
*
41612 TGAACCGATCAACCCGTTGACTCGACCGT
1 TGAACCGATCAACCCGTTGACTCGACCAT
*
41641 TGAACC-AGTCAACCTGTTGAC-CAGACCAT
1 TGAACCGA-TCAACCCGTTGACTC-GACCAT
41670 TGA
1 TGA
41673 TTTTGACCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (29 bp):
TGAACCGATCAACCCGTTGACTCGACCAT
Found at i:42242 original size:30 final size:30
Alignment explanation
Indices: 42206--42303 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
42196 ATTTCAGTCT
42206 TGACATCTGCATAGGATTAATTCCCCGTTC
1 TGACATCTGCATAGGATTAATTCCCCGTTC
** *
42236 TGACATCCACATAGGATTAATTCCTCGTTC
1 TGACATCTGCATAGGATTAATTCCCCGTTC
* *
42266 TGACATCTGCAT-GATATTAATTCCCTGTTC
1 TGACATCTGCATAG-GATTAATTCCCCGTTC
42296 TGACATCT
1 TGACATCT
42304 ATATGGGACT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 58 0.98
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (30 bp):
TGACATCTGCATAGGATTAATTCCCCGTTC
Found at i:47196 original size:29 final size:29
Alignment explanation
Indices: 47157--47246 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
47147 GACTGAATTA
* *
47157 GTTGAATCGGTCAACCCGTTAACCTGATC
1 GTTGAACCGGTCAACCCGTTAACCTGACC
* * * *
47186 GTTGAACCGGTAAACCAGTTGACTTGACC
1 GTTGAACCGGTCAACCCGTTAACCTGACC
* * * * *
47215 ATTGAACCGATCAACTCGTTGACCCGACC
1 GTTGAACCGGTCAACCCGTTAACCTGACC
47244 GTT
1 GTT
47247 AATCGTTAAC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (29 bp):
GTTGAACCGGTCAACCCGTTAACCTGACC
Found at i:47291 original size:14 final size:13
Alignment explanation
Indices: 47255--47293 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
47245 TTAATCGTTA
*
47255 ACCGTTAACTTTG
1 ACCGTTGACTTTG
*
47268 ACCATTGACTTTG
1 ACCGTTGACTTTG
47281 ATCCGTTGACTTT
1 A-CCGTTGACTTT
47294 TTCTAGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (13 bp):
ACCGTTGACTTTG
Found at i:47775 original size:23 final size:23
Alignment explanation
Indices: 47748--47791 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47738 ATGGTAATAA
*
47748 ATGGATATGTCATT-GCAAATTGG
1 ATGGAAATGTC-TTGGCAAATTGG
47771 ATGGAAATGTCTTGGCAAATT
1 ATGGAAATGTCTTGGCAAATT
47792 AAGTTGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (23 bp):
ATGGAAATGTCTTGGCAAATTGG
Found at i:49254 original size:37 final size:37
Alignment explanation
Indices: 49178--49254 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
49168 TTTTTATATT
*
49178 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
49215 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
49252 TTT
1 TTT
49255 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:49436 original size:20 final size:20
Alignment explanation
Indices: 49400--49437 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49390 ATCCTATTCC
**
49400 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
49420 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
49438 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:49945 original size:20 final size:20
Alignment explanation
Indices: 49916--49958 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
49906 ATTCCACCAC
49916 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
49936 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
49956 ATG
1 ATG
49959 AGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:50340 original size:30 final size:30
Alignment explanation
Indices: 50299--50476 Score: 214
Period size: 30 Copynumber: 5.9 Consensus size: 30
50289 TGTATTTCCG
* * *
50299 ATCTCCATGGGACTAATTCCCCGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
50329 ATCTGCATGGGATTAATTTCCTGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* *
50359 ATCTGCATGGGATTAATTTCCCGTTCTAAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
50389 ATCTGTATGGGATTAGTTCCCCATTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
50419 ATCTGTATGAGATTAGTTCCCCGTTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
50449 ATCTGCATGGGATT-ATATCCCCGTTCTG
1 ATCTGCATGGGATTAAT-TCCCCGTTCTG
50477 TTTATCTGTG
Statistics
Matches: 130, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
29 1 0.01
30 129 0.99
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (30 bp):
ATCTGCATGGGATTAATTCCCCGTTCTGAC
Found at i:51059 original size:15 final size:15
Alignment explanation
Indices: 51031--51073 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
51021 ATGGAAAATA
* *
51031 ATTAATTGAGTTTTT
1 ATTAATTAAATTTTT
51046 ATTAATTAAA-TTTT
1 ATTAATTAAATTTTT
51060 -TTAATTAAATTTTT
1 ATTAATTAAATTTTT
51074 TAATTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.36
14 8 0.32
15 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
ATTAATTAAATTTTT
Found at i:51065 original size:13 final size:13
Alignment explanation
Indices: 51042--51080 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
51032 TTAATTGAGT
51042 TTTTATTAATTAAA
1 TTTT-TTAATTAAA
51056 TTTTTTAATTAAA
1 TTTTTTAATTAAA
51069 TTTTTTAATTAA
1 TTTTTTAATTAA
51081 TGTCGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTAATTAAA
Found at i:55184 original size:31 final size:31
Alignment explanation
Indices: 55086--55176 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
55076 CAATTTAAGG
55086 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
55117 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
55148 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
55177 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:58589 original size:31 final size:31
Alignment explanation
Indices: 58491--58581 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
58481 CAATTTAAGG
58491 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
58522 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
58553 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
58582 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:61983 original size:31 final size:31
Alignment explanation
Indices: 61885--61975 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
61875 CAATTTAAGG
61885 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
61916 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
61947 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
61976 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:65374 original size:31 final size:31
Alignment explanation
Indices: 65276--65366 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
65266 CAATTTAAGG
65276 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
65307 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
65338 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
65367 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:65455 original size:19 final size:19
Alignment explanation
Indices: 65431--65516 Score: 118
Period size: 19 Copynumber: 4.5 Consensus size: 19
65421 AATGGTTTTA
* *
65431 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
* *
65450 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
65469 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
65488 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
65507 TGAACAGTAA
1 TGAACAGTAA
65517 CCCGAGGCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:65648 original size:21 final size:21
Alignment explanation
Indices: 65622--65664 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
65612 ATTTGAATAT
*
65622 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65643 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65664 T
1 T
65665 CCATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:65725 original size:21 final size:21
Alignment explanation
Indices: 65692--65731 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
65682 TTTGAGTAGA
*
65692 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
65714 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
65732 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:68218 original size:2 final size:2
Alignment explanation
Indices: 68052--68210 Score: 121
Period size: 2 Copynumber: 79.5 Consensus size: 2
68042 GGGTGTTACA
*
68052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
68094 AGT AT A- AGT AT AT AA ACT AT AT A- AT AT A- AT AT AT AA ACT AT
1 A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * *
68135 AT AT AT AT AT AT AC AT AT GT AT AT AT GT AT GT AT AA AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * *
68178 A- AT AT AA AC AT AT A- AA AA AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68211 AGTATATAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
1 5 0.04
2 115 0.92
3 5 0.04
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (2 bp):
AT
Found at i:68745 original size:23 final size:22
Alignment explanation
Indices: 68677--68759 Score: 57
Period size: 23 Copynumber: 3.7 Consensus size: 22
68667 TTAAATTATT
* **
68677 AATTAATTATTATATAAAAAATA
1 AATTAATT-TTAAATAATTAATA
68700 AATTAAATTTATAAAT-ATT--TA
1 AATT-AATTT-TAAATAATTAATA
68721 AATTAATTTTAAATAATCTAATAA
1 AATTAATTTTAAATAAT-TAAT-A
*
68745 AATT-ATGTTAAATAA
1 AATTAATTTTAAATAA
68760 ATATATTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.10
20 7 0.14
21 7 0.14
23 17 0.35
24 13 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
AATTAATTTTAAATAATTAATA
Found at i:69055 original size:16 final size:16
Alignment explanation
Indices: 69036--69070 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
69026 TAAGTTAATT
69036 ACATGTCAGGTTCATA
1 ACATGTCAGGTTCATA
* *
69052 ACATGTCAGTTTGATA
1 ACATGTCAGGTTCATA
69068 ACA
1 ACA
69071 GGTCGGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (16 bp):
ACATGTCAGGTTCATA
Found at i:81694 original size:32 final size:32
Alignment explanation
Indices: 81658--81736 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
81648 TCCACACTTT
*
81658 GCATTCTTCACTTTTACTTTGCTCTTATTTCA
1 GCATTATTCACTTTTACTTTGCTCTTATTTCA
* * *
81690 GCATTATTCGCTTATACTTTTCTCTTATTTCA
1 GCATTATTCACTTTTACTTTGCTCTTATTTCA
81722 GCATTATTCA-TTTTA
1 GCATTATTCACTTTTA
81737 TCGTTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 4 0.10
32 37 0.90
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (32 bp):
GCATTATTCACTTTTACTTTGCTCTTATTTCA
Found at i:83586 original size:189 final size:190
Alignment explanation
Indices: 83264--83635 Score: 529
Period size: 188 Copynumber: 2.0 Consensus size: 190
83254 AACAATATCT
* *
83264 TTTAATTTGAAATATTCAAAAGATAAAACTCATTTTACCATTCAAACTTAAATATGTATTATTTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCATTCTACCATTCAAACTTAAATATGTATTATTTT
* * * *
83329 AATTTGAATTAAACAAAAATATATAATTATCTTTAATATTCAAAGTTAAAAAGGTAACAAATACC
66 AACTTGAAATAAACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACC
* * *
83394 -TTTTAAGTTGA-TATATTCAAAA-AGTAATTATCCTACTAATCTTTAAATTAAATAATATA
131 TTTTTAAATTGACT-TATT-AAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
* * * *
83453 TTTAATTTGCAATGGTCAAAAGGT-AAACTCCTTCTACCATTCAAACTTAAATA-GATATTATTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCATTCTACCATTCAAACTTAAATATG-TATTATTT
* * *
83516 TAACTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAATTA
65 TAACTTGAAATAAACAAAAATATATAATTATC-TTTAATATTCAAAATTAAAAAGATAACAAATA
83581 CCTTTTTAAATTGACTTATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA
129 CCTTTTTAAATTGACTTATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA
83636 AATTATCTTT
Statistics
Matches: 162, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
187 1 0.01
188 63 0.39
189 55 0.34
190 42 0.26
191 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (190 bp):
TTTAATTTGAAATAGTCAAAAGATAAAACTCATTCTACCATTCAAACTTAAATATGTATTATTTT
AACTTGAAATAAACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATACC
TTTTTAAATTGACTTATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
Found at i:84784 original size:87 final size:86
Alignment explanation
Indices: 84638--84817 Score: 333
Period size: 87 Copynumber: 2.1 Consensus size: 86
84628 TGCGAAATAT
* *
84638 ATCCATTTGTCGTTGATGTTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
1 ATCCATTTGCCGTTGATATTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
84703 GTAGAATAATAAAAAAAATACA
66 GTAGAATAAT-AAAAAAATACA
84725 ATCCATTTGCCGTTGATATTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
1 ATCCATTTGCCGTTGATATTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
84790 GTAGAATAATAAAAAAATACA
66 GTAGAATAATAAAAAAATACA
84811 ATCCATT
1 ATCCATT
84818 GTTTAGGATT
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 18 0.20
87 73 0.80
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.33
Consensus pattern (86 bp):
ATCCATTTGCCGTTGATATTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
GTAGAATAATAAAAAAATACA
Done.