Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007778.1 Hibiscus syriacus cultivar Beakdansim tig00110061_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: 85116
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:287 original size:45 final size:46
Alignment explanation
Indices: 217--304 Score: 160
Period size: 45 Copynumber: 1.9 Consensus size: 46
207 TGTATGTATA
*
217 TTTATGTTGAGGTCATTGTATTTTAATGTTATTTATACTTAAGCAG
1 TTTATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAGCAG
263 TTTATGTTGA-GTCATTGTACTTTAATGTTATTTATACTTAAG
1 TTTATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAG
305 TAGGATATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 31 0.76
46 10 0.24
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (46 bp):
TTTATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAGCAG
Found at i:314 original size:45 final size:46
Alignment explanation
Indices: 219--315 Score: 151
Period size: 45 Copynumber: 2.1 Consensus size: 46
209 TATGTATATT
* **
219 TATGTTGAGGTCATTGTATTTTAATGTTATTTATACTTAAGCAGTT
1 TATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAGCAGGA
*
265 TATGTTGA-GTCATTGTACTTTAATGTTATTTATACTTAAGTAGGA
1 TATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAGCAGGA
310 TATGTT
1 TATGTT
316 TTTTTATTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 39 0.83
46 8 0.17
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (46 bp):
TATGTTGAGGTCATTGTACTTTAATGTTATTTATACTTAAGCAGGA
Found at i:831 original size:16 final size:15
Alignment explanation
Indices: 810--841 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
800 ATTTTTTCGC
810 TATTTCCATTCGTATT
1 TATTTCCATT-GTATT
826 TATTTCCATTGTATT
1 TATTTCCATTGTATT
841 T
1 T
842 CTTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (15 bp):
TATTTCCATTGTATT
Found at i:2892 original size:14 final size:16
Alignment explanation
Indices: 2858--2896 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
2848 GATCAATATT
*
2858 TTTGCATCTATCTGTA
1 TTTGCATCTATCTGAA
2874 TTTGCATCT-T-TGAA
1 TTTGCATCTATCTGAA
2888 TTTGCATCT
1 TTTGCATCT
2897 GCATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 1 0.05
16 9 0.41
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (16 bp):
TTTGCATCTATCTGAA
Found at i:4222 original size:17 final size:17
Alignment explanation
Indices: 4200--4252 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
4190 GATAAAAGCA
*
4200 AAGAAAAAGAGCAAAAG
1 AAGAAAAAGAACAAAAG
4217 AAGAAAAA-AATC-AAAG
1 AAGAAAAAGAA-CAAAAG
4233 -A-AAAAAGAACAAAA-
1 AAGAAAAAGAACAAAAG
4247 AAGAAA
1 AAGAAA
4253 TAAAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
14 6 0.20
15 7 0.23
16 8 0.27
17 9 0.30
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (17 bp):
AAGAAAAAGAACAAAAG
Found at i:4232 original size:30 final size:31
Alignment explanation
Indices: 4191--4258 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
4181 CAAGGCGAGG
*
4191 ATAAAAGCAAAG-AAAAAGAGCAAAAGAAGAA
1 ATAAAAGCAAAGAAAAAAGAACAAAA-AAGAA
*
4222 A-AAAATCAAAGAAAAAAGAACAAAAAAGAA
1 ATAAAAGCAAAGAAAAAAGAACAAAAAAGAA
4252 ATAAAAG
1 ATAAAAG
4259 AAAATAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (31 bp):
ATAAAAGCAAAGAAAAAAGAACAAAAAAGAA
Found at i:5486 original size:37 final size:36
Alignment explanation
Indices: 5419--5564 Score: 143
Period size: 36 Copynumber: 4.0 Consensus size: 36
5409 ATAAAGTGTC
* *
5419 GTCTCGCTAGAGACAAGTTT-TCT-AAAACAAATTTT
1 GTCTCGCTTGAGAC-ATTTTCTCTAAAAACAAATTTT
* * *
5454 GGCTCTCTTGAGATAGTTTTCTCTAAAAACAAATTTT
1 GTCTCGCTTGAGACA-TTTTCTCTAAAAACAAATTTT
* * * *
5491 GTCTCGCTTGAGACAATTTCTCTCAAAGCAAATTTC
1 GTCTCGCTTGAGACATTTTCTCTAAAAACAAATTTT
*
5527 GTCTCGCTTGAGACATTTTTTCTTTAAAACACAAATTT
1 GTCTCGCTTGAGACA--TTTTCTCTAAAA-ACAAATTT
5565 AGAAGTTGCT
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
34 1 0.01
35 13 0.15
36 35 0.39
37 24 0.27
38 9 0.10
39 7 0.08
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
GTCTCGCTTGAGACATTTTCTCTAAAAACAAATTTT
Found at i:5497 original size:72 final size:75
Alignment explanation
Indices: 5419--5564 Score: 183
Period size: 73 Copynumber: 2.0 Consensus size: 75
5409 ATAAAGTGTC
* * *
5419 GTCTCGCTAGAGACAAGTTT-TCT-AAAACAAATTTTGGCTCTCTTGAGATA-GTTTTCTCTAAA
1 GTCTCGCTAGAGACAA-TTTCTCTCAAAACAAATTTCGGCTCGCTTGAGACATGTTTTCTCTAAA
5481 A-ACAAATTTT
65 ACACAAATTTT
* * * * *
5491 GTCTCGCTTGAGACAATTTCTCTCAAAGCAAATTTCGTCTCGCTTGAGACATTTTTTCTTTAAAA
1 GTCTCGCTAGAGACAATTTCTCTCAAAACAAATTTCGGCTCGCTTGAGACATGTTTTCTCTAAAA
5556 CACAAATTT
66 CACAAATTT
5565 AGAAGTTGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
71 3 0.05
72 18 0.29
73 22 0.35
74 11 0.18
75 8 0.13
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (75 bp):
GTCTCGCTAGAGACAATTTCTCTCAAAACAAATTTCGGCTCGCTTGAGACATGTTTTCTCTAAAA
CACAAATTTT
Found at i:5631 original size:30 final size:30
Alignment explanation
Indices: 5595--5718 Score: 108
Period size: 30 Copynumber: 3.9 Consensus size: 30
5585 CAAAATTTAT
5595 AACCTTTGAGATAGTTTCTCGTGAAACACC
1 AACCTTTGAGATAGTTTCTCGTGAAACACC
* *
5625 AACCTTTGAGATTGTTTCTCTTGAAACA--
1 AACCTTTGAGATAGTTTCTCGTGAAACACC
* *
5653 AATTTTGTCTCCCTTGAGACAGTTTCTCGTGAAACACC
1 AA--------CCTTTGAGATAGTTTCTCGTGAAACACC
* *
5691 AACCTTTGAGATTGTTTCTCTTGAAACA
1 AACCTTTGAGATAGTTTCTCGTGAAACA
5719 AGTTTTATCT
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
28 2 0.03
30 48 0.65
36 22 0.30
38 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (30 bp):
AACCTTTGAGATAGTTTCTCGTGAAACACC
Found at i:5653 original size:66 final size:65
Alignment explanation
Indices: 5600--5886 Score: 335
Period size: 66 Copynumber: 4.3 Consensus size: 65
5590 TTTATAACCT
* *
5600 TTGAGATAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCC
1 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCT-C
5665 C
65 C
*
5666 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAGTTTTATCTCA
1 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTC-
5731 C
65 C
* * * * *
5732 TTGAGACAATTTCTC-TGAAACACCAACCTTTGAGATTGTTTCCCTTGAAATAAGTTTTGTCTCC
1 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCT-C
5796 C
65 C
* ** * * ** *
5797 TTGA-ACAGTTTCTCTTGAAACAAAAAAAACCTTTGAGATTGTTTCCCTTAAAACACGTTTTTTC
1 TTGAGACAGTTTCTCGTGAAAC---ACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATC
5861 TCTC
63 TC-C
* *
5865 TTGAGACGGTTTCTCTTGAAAC
1 TTGAGACAGTTTCTCGTGAAAC
5887 CATCATTCCT
Statistics
Matches: 198, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
64 9 0.05
65 56 0.28
66 76 0.38
67 1 0.01
68 40 0.20
69 16 0.08
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (65 bp):
TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCC
Found at i:5790 original size:131 final size:132
Alignment explanation
Indices: 5600--5886 Score: 398
Period size: 131 Copynumber: 2.2 Consensus size: 132
5590 TTTATAACCT
* *
5600 TTGAGATAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCC
1 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCC
** * *
5665 CTTGAGACAGTTTCTCGTGAAAC-ACCAACCTTTGAGATTGTTTCTCTTGAAACAAGTTTTATCT
66 CTTGA-ACAGTTTCTCGTGAAACAAAAAACCTTTGAGATTGTTTCCCTTAAAACAAGTTTTATCT
5729 CAC
130 CAC
* * *
5732 TTGAGACAATTTCTC-TGAAACACCAACCTTTGAGATTGTTTCCCTTGAAATAAGTTTTGTCTCC
1 TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCC
* * *
5796 CTTGAACAGTTTCTCTTGAAACAAAAAAAACCTTTGAGATTGTTTCCCTTAAAACACGTTTTTTC
66 CTTGAACAGTTTCTCGTGAAAC--AAAAAACCTTTGAGATTGTTTCCCTTAAAACAAGTTTTATC
*
5861 TCTC
129 TCAC
* *
5865 TTGAGACGGTTTCTCTTGAAAC
1 TTGAGACAGTTTCTCGTGAAAC
5887 CATCATTCCT
Statistics
Matches: 136, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
130 16 0.12
131 51 0.38
132 13 0.10
133 50 0.37
134 6 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (132 bp):
TTGAGACAGTTTCTCGTGAAACACCAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCC
CTTGAACAGTTTCTCGTGAAACAAAAAACCTTTGAGATTGTTTCCCTTAAAACAAGTTTTATCTC
AC
Found at i:7893 original size:30 final size:30
Alignment explanation
Indices: 7823--7879 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
7813 CAAAATTTTG
7823 TTTGCTATTTTAGTCCTTTAAATTTCTATT
1 TTTGCTATTTTAGTCCTTTAAATTTCTATT
* *
7853 TTTGCTATTTTAGTTCTTTAAGTTTCT
1 TTTGCTATTTTAGTCCTTTAAATTTCT
7880 GTTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (30 bp):
TTTGCTATTTTAGTCCTTTAAATTTCTATT
Found at i:13759 original size:60 final size:59
Alignment explanation
Indices: 13680--13825 Score: 136
Period size: 60 Copynumber: 2.4 Consensus size: 59
13670 TGAATGTTTA
* * *
13680 AAAAGTTGGGGACCAATTT-AGAATGA-AGGTCATAGTTT-GGAGATGAAATTAAAATATTC
1 AAAAGTTGAGGACCAATTTAAG-ATGATA-ATCATAGTTTAGG-GATAAAATTAAAATATTC
* * *
13739 AAAAGTTTGAGGACTAATTTAAGATGATAATCATAGTTTAGGGATAAAATTAGAATATTT
1 AAAAG-TTGAGGACCAATTTAAGATGATAATCATAGTTTAGGGATAAAATTAAAATATTC
* * * *
13799 AAAAATTTAAGATCCAATTTAAAATGA
1 AAAAGTTGAGGA-CCAATTTAAGATGA
13826 AGAACATACT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
59 10 0.14
60 56 0.79
61 5 0.07
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (59 bp):
AAAAGTTGAGGACCAATTTAAGATGATAATCATAGTTTAGGGATAAAATTAAAATATTC
Found at i:16640 original size:21 final size:21
Alignment explanation
Indices: 16596--16663 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 21
16586 ATTAATATTA
16596 TTATATTATATA-ATATTACAAT
1 TTATATTATATATAT-TTAC-AT
16618 TTATATTATATATATTTACAT
1 TTATATTATATATATTTACAT
16639 TTATA-TAT-TATATTTACAT
1 TTATATTATATATATTTACAT
16658 TT-TATT
1 TTATATT
16664 TTGTTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.05
19 14 0.32
20 3 0.07
21 7 0.16
22 16 0.36
23 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATTATATATATTTACAT
Found at i:16652 original size:19 final size:19
Alignment explanation
Indices: 16602--16659 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
16592 ATTATTATAT
*
16602 TATATAATA-TTACAATTTA
1 TATATTATATTTAC-ATTTA
16621 TATTATATATATTTACATTTA
1 TA-TAT-TATATTTACATTTA
16642 TATATTATATTTACATTT
1 TATATTATATTTACATTT
16660 TATTTTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 15 0.43
20 6 0.17
21 10 0.29
22 4 0.11
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTATATTTACATTTA
Found at i:17749 original size:3 final size:3
Alignment explanation
Indices: 17737--17776 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
17727 CACTTATATA
*
17737 TAT T-T TAT TAT TAT TAT TAT TAT TAC TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T
17777 GTTTAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17874 original size:19 final size:21
Alignment explanation
Indices: 17836--17874 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17826 TTTGTGTATA
17836 TATATTATTTATTATTTCTTC
1 TATATTATTTATTATTTCTTC
17857 TATATTATTT-TT-TTTCTT
1 TATATTATTTATTATTTCTT
17875 GAATTGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (21 bp):
TATATTATTTATTATTTCTTC
Found at i:23345 original size:12 final size:12
Alignment explanation
Indices: 23328--23352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23318 ATTACATAAG
23328 ATACAACCAACA
1 ATACAACCAACA
23340 ATACAACCAACA
1 ATACAACCAACA
23352 A
1 A
23353 ACCACCCCAA
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:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (12 bp):
ATACAACCAACA
Found at i:27005 original size:314 final size:314
Alignment explanation
Indices: 26428--27073 Score: 1057
Period size: 314 Copynumber: 2.1 Consensus size: 314
26418 CTTGACATAC
*
26428 TTGTTTGGTTAGTGAGTTTAACTTGTAGTTTCCTTTATGATTCCTATTGCTCTTGTTGGTGACCA
1 TTGTTTGGTTAGTGAGTTTAACTTGTAGTTTCCTTTATGATTCCTATTGCTCATGTTGGTGACCA
* * * *
26493 TAAATACTAGAATTTCAAGTGAAGACTCTTCAATTGGGTTCAGAAATAGGATCTACCTAGAATTT
66 TAAATACTAGAATTTCAACTGAACACTCTTCAATTGGGTTCAGAAATAGAATCTACCAAGAATTT
26558 TGATTTGTGAAAATTCATTAGTAAGGCCTGCCATGTTCTACTTTATTCCCTGTAAAGCCATAGTA
131 TGATTTGTGAAAATTCATTAGTAAGGCCTGCCATGTTCTACTTTATTCCCTGTAAAGCCATAGTA
* * *
26623 TCCTATCTTGTAATACACCTTTCTCACCCTTTTTGGTGGTTGAAGTTGTAGACATATGGCCTTAC
196 TCCTATCTGGTAATACACCTTTCTAACCCTTTTCGGTGGTTGAAGTTGTAGACATATGGCCTTAC
* *
26688 ATTGCCTTGAAAATTTCTTTTAGAGACAGTTACACTAATTCTTTCTGGAATTGT
261 ATTGCCTTGAAAATTTCCTTTAGAGACAGTTACACTAATTCTTACTGGAATTGT
*
26742 TTGTTTGGTTAGTGAGTTTAACTTGTGGTTTCCTTTATGATTCCTATTGCTCATGTTGGTGACCA
1 TTGTTTGGTTAGTGAGTTTAACTTGTAGTTTCCTTTATGATTCCTATTGCTCATGTTGGTGACCA
* * * *
26807 TTAATACTTGAATTTCAACTGGACACTCTTCAATTGGGTTCAGAAATCGAATCTACCAAGAATTT
66 TAAATACTAGAATTTCAACTGAACACTCTTCAATTGGGTTCAGAAATAGAATCTACCAAGAATTT
*
26872 TGATTTGTGAAAATTCCTTAGTAAGGCCTGCCATGTTCTACTTTATTCCCTGTAAAGCCATAGTA
131 TGATTTGTGAAAATTCATTAGTAAGGCCTGCCATGTTCTACTTTATTCCCTGTAAAGCCATAGTA
* *
26937 TTCCTATCTGGTAATACACC-TT-TAACCCTTTTCGGTGGTTGACGTTGTAGACATATATTGCC-
196 -TCCTATCTGGTAATACACCTTTCTAACCCTTTTCGGTGGTTGAAGTTGTAGAC--ATATGGCCT
26999 TACATTGCCTTGAAAATTTCCTTTAGAGACAGTTACACTAATTCTTACTGGAATTGT
258 TACATTGCCTTGAAAATTTCCTTTAGAGACAGTTACACTAATTCTTACTGGAATTGT
* *
27056 TTG-TTGTTTAGTGGGTTT
1 TTGTTTGGTTAGTGAGTTT
27074 CAATAATAAG
Statistics
Matches: 309, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
313 40 0.13
314 244 0.79
315 25 0.08
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (314 bp):
TTGTTTGGTTAGTGAGTTTAACTTGTAGTTTCCTTTATGATTCCTATTGCTCATGTTGGTGACCA
TAAATACTAGAATTTCAACTGAACACTCTTCAATTGGGTTCAGAAATAGAATCTACCAAGAATTT
TGATTTGTGAAAATTCATTAGTAAGGCCTGCCATGTTCTACTTTATTCCCTGTAAAGCCATAGTA
TCCTATCTGGTAATACACCTTTCTAACCCTTTTCGGTGGTTGAAGTTGTAGACATATGGCCTTAC
ATTGCCTTGAAAATTTCCTTTAGAGACAGTTACACTAATTCTTACTGGAATTGT
Found at i:33454 original size:20 final size:20
Alignment explanation
Indices: 33411--33456 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
33401 GAGTGTGGCG
* *
33411 GCGGACGGCGGCAGCAGACG
1 GCGGGCGGCGGCAGCAGACA
* *
33431 GCGGGCGGCGGCAGCGGCCA
1 GCGGGCGGCGGCAGCAGACA
33451 GCGGGC
1 GCGGGC
33457 AACAGACGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.54, T:0.00
Consensus pattern (20 bp):
GCGGGCGGCGGCAGCAGACA
Found at i:39256 original size:15 final size:15
Alignment explanation
Indices: 39238--39296 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
39228 TAATCGGTTT
39238 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
39253 CGGTTTTTTTTAAAAAAAAC
1 CGG----TTTT-AAAAAAAC
*
39273 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
39288 CGATTTTAA
1 CGGTTTTAA
39297 TATTCCGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 18 0.50
16 3 0.08
19 4 0.11
20 11 0.31
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:39258 original size:21 final size:20
Alignment explanation
Indices: 39240--39277 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39230 ATCGGTTTCG
39240 GTTTT-AAAAAAACCGGTTT
1 GTTTTAAAAAAAACCGGTTT
*
39259 TTTTTAAAAAAAACCGGTT
1 GTTTTAAAAAAAACCGGTT
39278 ATAAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
GTTTTAAAAAAAACCGGTTT
Found at i:39493 original size:21 final size:21
Alignment explanation
Indices: 39469--39518 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
39459 CTTAGGGAAT
39469 CGATTCCCTATGAGAGGAAAC
1 CGATTCCCTATGAGAGGAAAC
**
39490 CGATTCCCTATGAGAGGGTAC
1 CGATTCCCTATGAGAGGAAAC
39511 CGATTCCC
1 CGATTCCC
39519 CCATGCTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (21 bp):
CGATTCCCTATGAGAGGAAAC
Found at i:39735 original size:13 final size:13
Alignment explanation
Indices: 39714--39768 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
39704 AAGTTCGATA
*
39714 AATTCAAATACTT
1 AATTGAAATACTT
39727 AATTGAAATACTT
1 AATTGAAATACTT
* *
39740 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
39754 AATTGAAATACTT
1 AATTGAAATACTT
39767 AA
1 AA
39769 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:39850 original size:32 final size:33
Alignment explanation
Indices: 39754--39852 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
39744 AACTCAACAT
* * *
39754 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39787 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39820 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39852 A
1 A
39853 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:39871 original size:21 final size:21
Alignment explanation
Indices: 39847--39886 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39837 ACTTCAAGTT
39847 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
39868 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
39887 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:56113 original size:31 final size:31
Alignment explanation
Indices: 56091--56199 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
56081 ATAGATTCCG
* *
56091 AAGAACTTAGGTAATCAGTCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
56122 AAGAACATAGGTAAACAGTCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
*
56153 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
56184 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
56200 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCA
Found at i:56820 original size:18 final size:19
Alignment explanation
Indices: 56784--56820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
56774 TTTCATTTAG
56784 GGGGAATCGATACACCCCCA
1 GGGGAATCGATA-ACCCCCA
56804 GGGGAATCGAT-ACCCCC
1 GGGGAATCGATAACCCCC
56821 TGAACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (19 bp):
GGGGAATCGATAACCCCCA
Found at i:60545 original size:31 final size:31
Alignment explanation
Indices: 60522--60630 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
60512 ATAGATTCCG
* *
60522 AAGAACCTAGGTAATCAGTCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
60553 AAGAACATAGGTAAACAGTCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
*
60584 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
60615 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
60631 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCA
Found at i:61817 original size:18 final size:18
Alignment explanation
Indices: 61794--61833 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
61784 GAGAAGAAGA
61794 TGAAGAAGAGAATTGCTT
1 TGAAGAAGAGAATTGCTT
61812 TGAAGAAGAGAATTGCTT
1 TGAAGAAGAGAATTGCTT
61830 TGAA
1 TGAA
61834 TCTTATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (18 bp):
TGAAGAAGAGAATTGCTT
Found at i:62443 original size:31 final size:31
Alignment explanation
Indices: 62407--62465 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
62397 AACTTAAAAG
*
62407 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
62438 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
62466 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:62512 original size:40 final size:40
Alignment explanation
Indices: 62458--62607 Score: 157
Period size: 40 Copynumber: 3.8 Consensus size: 40
62448 TACTGAAATT
62458 TAAAT-AATCCATACAACTACAATAATAAATTATTTAAAA
1 TAAATAAATCCATACAACTACAATAATAAATTATTTAAAA
* * ***
62497 TAAATCAATCCATACAACTACAATAATAAATCAATCTATATTT
1 TAAATAAATCCATACAACTACAATAATAAAT-TAT-T-TAAAA
* * *
62540 TAAAATAAATCAAT-CTA-TAC--TAATAAGTTATTTAAAA
1 T-AAATAAATCCATACAACTACAATAATAAATTATTTAAAA
62577 TAAATAAATCCATACAACTACAATAATAAAT
1 TAAATAAATCCATACAACTACAATAATAAAT
62608 CAATCCATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
36 11 0.13
37 5 0.06
38 4 0.05
39 7 0.08
40 39 0.45
41 2 0.02
42 4 0.05
43 5 0.06
44 10 0.11
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (40 bp):
TAAATAAATCCATACAACTACAATAATAAATTATTTAAAA
Found at i:62525 original size:26 final size:26
Alignment explanation
Indices: 62495--62616 Score: 76
Period size: 26 Copynumber: 4.6 Consensus size: 26
62485 AATTATTTAA
62495 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* * **
62521 AATAAATCAAT-C-TA-TATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
*
62543 AATAAATCAATCTATACTAA-TA-AGTTATTT
1 AATAAATCAATCCATAC-AACTACA---A--T
*
62573 AAAATAAATAAATCCATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
62601 AATAAATCAATCCATA
1 AATAAATCAATCCATA
62617 TTTTAAAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 28
0.65 0.09 0.25
Matches are distributed among these distances:
22 11 0.15
23 4 0.06
24 5 0.07
25 2 0.03
26 27 0.38
27 1 0.01
28 1 0.01
30 1 0.01
31 2 0.03
32 17 0.24
33 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.30
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:62580 original size:54 final size:54
Alignment explanation
Indices: 62521--63300 Score: 352
Period size: 54 Copynumber: 14.4 Consensus size: 54
62511 CAACTACAAT
* *
62521 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAGTTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* *** * * * *
62575 AATAAATAAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* *
62623 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* * * * * * ** * **
62677 AATAAATCAATCTATA-CTAATAAATTATTTAAAATA-AATCAATCCA-TATTTTAA
1 AATAAATCAATCCATATTTTA-AAATAAATCAATCTATACT-AATAAATTA-TTTAA
*
62731 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCTATACTAATAAATTATTTAA
*
62795 AATAAATCAATCCATATTTTAAAATAAATCAATCTATATTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* ** * ** * ** *
62849 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCTATACTAATAAATTATTTAA
** ** *
62905 AATCCATACAAATAAAT-TATTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* * * * * *
62961 AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAA
* * * * * *
63015 AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAA
* *
63069 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
** * * * * * *
63123 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CCACA-CAACTA--CAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCTATACTA-ATAAATTATTTAA
*
63180 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* * * *
63235 AATAAATCAATTCATA--CT--AATAAAT-TAT-T-TA-AAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA-TTTAA
63282 AATAAATCAATCCATATTT
1 AATAAATCAATCCATATTT
63301 ATAATAATTT
Statistics
Matches: 555, Mismatches: 112, Indels: 123
0.70 0.14 0.16
Matches are distributed among these distances:
46 9 0.02
47 27 0.05
48 29 0.05
49 9 0.02
50 22 0.04
52 16 0.03
53 16 0.03
54 251 0.45
55 29 0.05
56 12 0.02
57 21 0.04
58 51 0.09
59 12 0.02
60 14 0.03
62 1 0.00
63 1 0.00
64 29 0.05
65 6 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
Found at i:62595 original size:80 final size:80
Alignment explanation
Indices: 62480--62634 Score: 283
Period size: 80 Copynumber: 1.9 Consensus size: 80
62470 ACAACTACAA
* *
62480 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAA
1 TAATAAATTATTTAAAATAAATAAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
62545 TAAATCAATCTATAC
66 TAAATCAATCTATAC
*
62560 TAATAAGTTATTTAAAATAAATAAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
1 TAATAAATTATTTAAAATAAATAAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
62625 TAAATCAATC
66 TAAATCAATC
62635 CATATTTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.33
Consensus pattern (80 bp):
TAATAAATTATTTAAAATAAATAAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
TAAATCAATCTATAC
Found at i:62626 original size:22 final size:22
Alignment explanation
Indices: 62601--62660 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
62591 CAACTACAAT
62601 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
62623 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
62645 AATAAATCAATCCATA
1 AATAAATCAATCCATA
62661 CAAATAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:62669 original size:22 final size:21
Alignment explanation
Indices: 62572--62669 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 21
62562 ATAAGTTATT
* *
62572 TAAAATAAATAAATCCATACAA
1 TAAAATAAATAAATCAAT-CCA
*
62594 CTACAAT-AATAAATCAATCCA
1 -TAAAATAAATAAATCAATCCA
***
62615 TATTTTAAAATAAATCAATCCA
1 TAAAAT-AAATAAATCAATCCA
***
62637 TATTTTAAAATAAATCAATCCA
1 TAAAAT-AAATAAATCAATCCA
62659 TACAAATAAAT
1 TA-AAATAAAT
62670 TATTTAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 3 0.05
21 2 0.03
22 52 0.83
23 6 0.10
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATAAATAAATCAATCCA
Found at i:62679 original size:14 final size:14
Alignment explanation
Indices: 62662--62715 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
62652 CAATCCATAC
62662 AAATAAATTATTTA
1 AAATAAATTATTTA
*
62676 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
62693 CTAATAAATTATTTA
1 -AAATAAATTATTTA
62708 AAATAAAT
1 AAATAAAT
62716 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:62679 original size:32 final size:32
Alignment explanation
Indices: 62640--63273 Score: 536
Period size: 32 Copynumber: 22.4 Consensus size: 32
62630 CAATCCATAT
*
62640 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
62672 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62704 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62726 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62758 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62790 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
62812 TTTAAAATAAATCAATCTATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
62844 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
62874 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
62892 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
62924 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62956 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
62988 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63010 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63042 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* ** *
63064 TTTAAAATAAATCAATTCATA-TTTTAAAA--
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63093 -------TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63118 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
63150 TTTAAAATAAATCAATCCACAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
63180 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63198 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
63230 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
63262 TTTAAAATAAAT
1 TTTAAAATAAAT
63274 TATTTTAAAA
Statistics
Matches: 501, Mismatches: 20, Indels: 162
0.73 0.03 0.24
Matches are distributed among these distances:
20 2 0.00
22 105 0.21
23 14 0.03
24 8 0.02
25 1 0.00
26 40 0.08
27 1 0.00
28 12 0.02
29 1 0.00
30 5 0.01
31 10 0.02
32 302 0.60
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:62716 original size:86 final size:86
Alignment explanation
Indices: 62618--63138 Score: 715
Period size: 86 Copynumber: 6.2 Consensus size: 86
62608 CAATCCATAT
62618 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
*
62683 TCAATCTATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
*
62704 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
62769 TCAATCCATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
* **
62790 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
*
62855 TCAATCCATAC-AACTACA--A
66 TCAATCCATACTAA-TAAATTA
62874 --T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
*
62935 TCAATCGATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
* * * ** * * *
62956 TTTAAAATAAATCAATCCATA--CT--AATAAATTATTTAAAATAAATCAATCCATATTTTAAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAAT---TA-TTTAAAA
63017 TAAATCAATCCATACTAATAAATTA
62 TAAATCAATCCATACTAATAAATTA
63042 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT---T-C--AT--A-T-TTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
63097 TCAATCCATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
63118 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
63139 CTAATAAATT
Statistics
Matches: 395, Mismatches: 24, Indels: 42
0.86 0.05 0.09
Matches are distributed among these distances:
76 53 0.13
78 1 0.00
80 70 0.18
81 2 0.01
82 21 0.05
84 5 0.01
85 4 0.01
86 229 0.58
88 1 0.00
90 9 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (86 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
TCAATCCATACTAATAAATTA
Found at i:62730 original size:22 final size:22
Alignment explanation
Indices: 62704--62746 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62694 TAATAAATTA
62704 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
62726 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
62747 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:62755 original size:22 final size:22
Alignment explanation
Indices: 62706--62754 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
62696 ATAAATTATT
**
62706 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
62728 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
62751 TAAA
1 TAAA
62755 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:62816 original size:22 final size:22
Alignment explanation
Indices: 62790--62834 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
62780 TAATAAATTA
62790 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
62812 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
62834 T
1 T
62835 AATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:62841 original size:22 final size:22
Alignment explanation
Indices: 62788--62840 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
62778 ACTAATAAAT
62788 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
* *
62809 TATTTTAAAATAAATCAATCTA
1 TATTATAAAATAAATCAATCCA
62831 TATTAATAAA
1 TATT-ATAAA
62841 TTATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:62921 original size:22 final size:22
Alignment explanation
Indices: 62848--62921 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
62838 AAATTATTTA
*
62848 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
62873 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
62895 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
62918 AAAT
1 AAAT
62922 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:63014 original size:22 final size:22
Alignment explanation
Indices: 62988--63030 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62978 TAATAAATTA
62988 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
63010 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
63031 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:63039 original size:22 final size:22
Alignment explanation
Indices: 62990--63038 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
62980 ATAAATTATT
**
62990 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
63012 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
63035 TAAA
1 TAAA
63039 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:63115 original size:22 final size:22
Alignment explanation
Indices: 63042--63106 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
63032 TAATAAATTA
63042 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
63064 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
63086 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
63107 CTAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:63227 original size:22 final size:22
Alignment explanation
Indices: 63152--63226 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
63142 ATAAATTATT
* *
63152 TAAAATAAATCAATCCACACAA
1 TAAAATAAATCAATCCATATAA
**
63174 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
63200 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
63223 TAAA
1 TAAA
63227 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:63256 original size:18 final size:18
Alignment explanation
Indices: 63203--63259 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
63193 CATATTTTAA
*
63203 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
63221 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
63235 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
63253 AATAAAT
1 AATAAAT
63260 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:63274 original size:46 final size:47
Alignment explanation
Indices: 63221--63369 Score: 162
Period size: 51 Copynumber: 3.1 Consensus size: 47
63211 AATCCATACT
63221 AATAAATTA-TTTAAAATAAATCAATTCATACTAATAAATTA-TTTAA
1 AATAAATTATTTTAAAATAAATCAATTCATA-TAATAAATTATTTTAA
* *
63267 AATAAATTATTTTAAAATAAATCAATCCATATTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATTC--A--TATAATAAATTATTTTAA
* * * * *
63318 AGTAAATTATTTTATAATAAAT-TATT-TTAAAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATTCATATAATAAATTATTTTAA
63363 AATAAAT
1 AATAAAT
63370 AACCTTATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
45 22 0.25
46 9 0.10
47 17 0.20
49 1 0.01
50 11 0.13
51 27 0.31
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (47 bp):
AATAAATTATTTTAAAATAAATCAATTCATATAATAAATTATTTTAA
Found at i:63282 original size:15 final size:15
Alignment explanation
Indices: 63221--63369 Score: 140
Period size: 15 Copynumber: 9.5 Consensus size: 15
63211 AATCCATACT
63221 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
63235 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
63253 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
63267 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
63282 AATAAATCAATCCATATTTAT
1 AATAAAT---T--AT-TTTAA
*
63303 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
63318 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
63333 AATAAATTATTTTAA
1 AATAAATTATTTTAA
63348 AATAAATTATTTTAA
1 AATAAATTATTTTAA
63363 AATAAAT
1 AATAAAT
63370 AACCTTATTA
Statistics
Matches: 110, Mismatches: 14, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
14 16 0.15
15 66 0.60
16 4 0.04
17 3 0.03
18 9 0.08
20 2 0.02
21 10 0.09
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:63405 original size:81 final size:80
Alignment explanation
Indices: 63195--63369 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 80
63185 AATCAATCCA
* * * *
63195 TATTTTAAAATAAATCAATCC--A-TACTAATAAATTA-TTTAAAATAAATCAATTCATACTAAT
1 TATTTTAAAATAAATCAATCCATATTAATAATAAATTATTTTAAAGTAAAT-TATT-TTA-TAAT
63256 AAATTATTTAAAATAAAT
63 AAATTATTTAAAATAAAT
* *
63274 TATTTTAAAATAAATCAATCCATATTTATAATAATTTATTTTAAAGTAAATTATTTTATAATAAA
1 TATTTTAAAATAAATCAATCCATATTAATAATAAATTATTTTAAAGTAAATTATTTTATAATAAA
63339 TTATTTTAAAATAAAT
66 TTA-TTTAAAATAAAT
63355 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
63370 AACCTTATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
79 21 0.25
80 10 0.12
81 30 0.35
82 13 0.15
83 11 0.13
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (80 bp):
TATTTTAAAATAAATCAATCCATATTAATAATAAATTATTTTAAAGTAAATTATTTTATAATAAA
TTATTTAAAATAAAT
Found at i:66131 original size:33 final size:34
Alignment explanation
Indices: 66089--66152 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
66079 TGCTTGTACT
66089 TTATTTATTTT-TATGTT-TTTATTTTAATTATTG
1 TTATTTATTTTCTATGTTATTT-TTTTAATTATTG
66122 TTATTTATTTTCTATGTTATTTTTTTAATTA
1 TTATTTATTTTCTATGTTATTTTTTTAATTA
66153 GTACCTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 11 0.38
34 15 0.52
35 3 0.10
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (34 bp):
TTATTTATTTTCTATGTTATTTTTTTAATTATTG
Found at i:78842 original size:7 final size:7
Alignment explanation
Indices: 78830--78888 Score: 118
Period size: 7 Copynumber: 8.4 Consensus size: 7
78820 TTTAGTGATC
78830 GAAAAGG
1 GAAAAGG
78837 GAAAAGG
1 GAAAAGG
78844 GAAAAGG
1 GAAAAGG
78851 GAAAAGG
1 GAAAAGG
78858 GAAAAGG
1 GAAAAGG
78865 GAAAAGG
1 GAAAAGG
78872 GAAAAGG
1 GAAAAGG
78879 GAAAAGG
1 GAAAAGG
78886 GAA
1 GAA
78889 GTCTTGAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:81762 original size:47 final size:47
Alignment explanation
Indices: 81665--81762 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
81655 AAAATAAAGA
* * *
81665 AAAAATCGAAGGAATATGGAAATCAGGGACTAAATCGCAAAACTGTC
1 AAAAATCGAAGGAAAATGGAAATCAGGGACTAAATCGCAAAACAGCC
* *
81712 AAAAATTGAAGGAAAATGGAAATCAGGGACTAAATCGCAAATCAGCC
1 AAAAATCGAAGGAAAATGGAAATCAGGGACTAAATCGCAAAACAGCC
81759 AAAA
1 AAAA
81763 TTTCAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.15
Consensus pattern (47 bp):
AAAAATCGAAGGAAAATGGAAATCAGGGACTAAATCGCAAAACAGCC
Found at i:83983 original size:32 final size:32
Alignment explanation
Indices: 83933--83993 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
83923 GGTACAATCT
* *
83933 ATTTTATTAAAAAATAAAATTTTTAATTATTA
1 ATTTTATTAAAAAATAAAACTTTAAATTATTA
** *
83965 ATTTTATTATTAATTAAAACTTTAAATTA
1 ATTTTATTAAAAAATAAAACTTTAAATTA
83994 GATGTTTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTTATTAAAAAATAAAACTTTAAATTATTA
Found at i:84175 original size:28 final size:30
Alignment explanation
Indices: 84107--84177 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 30
84097 GATATTATAT
* **
84107 TATTATATCAATAAAAATATTTTAATTTTTA
1 TATTATA-AAATAAAAATATTTTAACCTTTA
*
84138 AATTAT-AAATAAAAATA-TTT-ACCTTTA
1 TATTATAAAATAAAAATATTTTAACCTTTA
84165 TATTATAAAATAA
1 TATTATAAAATAA
84178 GTTATTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 10 0.29
28 9 0.26
29 10 0.29
31 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
TATTATAAAATAAAAATATTTTAACCTTTA
Found at i:84935 original size:15 final size:15
Alignment explanation
Indices: 84917--84993 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 15
84907 ATTGCTTTAT
84917 GTTCAGGTACTTTCA
1 GTTCAGGTACTTTCA
* * *
84932 GTTCAGCTTATTTTCG
1 GTTCAG-GTACTTTCA
84948 GTTCAGGTTAC-TTCA
1 GTTCAGG-TACTTTCA
* * *
84963 GTTCAGCTTATTTTCG
1 GTTCAG-GTACTTTCA
84979 GTTCAGGTTACTTTC
1 GTTCAGG-TACTTTC
84994 GACTTAACTA
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
15 17 0.37
16 29 0.63
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (15 bp):
GTTCAGGTACTTTCA
Found at i:84951 original size:16 final size:16
Alignment explanation
Indices: 84927--84994 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
84917 GTTCAGGTAC
*
84927 TTTCAGTTCAGCTTAT
1 TTTCGGTTCAGCTTAT
*
84943 TTTCGGTTCAGGTTA-
1 TTTCGGTTCAGCTTAT
* *
84958 CTTCAGTTCAGCTTAT
1 TTTCGGTTCAGCTTAT
* *
84974 TTTCGGTTCAGGTTAC
1 TTTCGGTTCAGCTTAT
84990 TTTCG
1 TTTCG
84995 ACTTAACTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 12 0.29
16 30 0.71
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (16 bp):
TTTCGGTTCAGCTTAT
Found at i:84952 original size:31 final size:32
Alignment explanation
Indices: 84917--84993 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 32
84907 ATTGCTTTAT
84917 GTTCAGG-TACTTTCAGTTCAGCTTATTTTCG
1 GTTCAGGTTACTTTCAGTTCAGCTTATTTTCG
84948 GTTCAGGTTAC-TTCAGTTCAGCTTATTTTCG
1 GTTCAGGTTACTTTCAGTTCAGCTTATTTTCG
84979 GTTCAGGTTACTTTC
1 GTTCAGGTTACTTTC
84994 GACTTAACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 38 0.86
32 6 0.14
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (32 bp):
GTTCAGGTTACTTTCAGTTCAGCTTATTTTCG
Done.