Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007048.1 Hibiscus syriacus cultivar Beakdansim tig00018274_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: 78589
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:965 original size:64 final size:62
Alignment explanation
Indices: 897--1093 Score: 215
Period size: 61 Copynumber: 3.1 Consensus size: 62
887 TTTACTAAGA
*
897 GTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGACTT
1 GTGCATCGATGCAT-AA-TGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGAATT
* * *
961 GTGCATCGATGCA-AATGCATTCGATGTTTCATAA-AGCCCTGAGTGCATCAATGCATG-GTAT
1 GTGCATCGATGCATAATGCATTCGATGTTTCAAAATAG-CCTGAGTGCATCGATGCATGAAT-T
** *
1022 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGAAT
1 GTGCATCGATGCAT--AATGCATTCGATGTTTCAAAATA-GCC-TGAGTGCATCGATGCATGAAT
1085 T
62 T
1086 GGTGCATC
1 -GTGCATC
1094 AGTGTATCAC
Statistics
Matches: 114, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
60 3 0.03
61 51 0.45
62 2 0.02
63 4 0.04
64 44 0.39
65 10 0.09
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGAATT
Found at i:2284 original size:23 final size:23
Alignment explanation
Indices: 2252--2312 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
2242 ACCCTCACGT
2252 GGGGGTATCGGTACCCATTC-AA
1 GGGGGTATCGGTACCCATTCAAA
2274 GGAGGGTATCGGTACCCATTCAAA
1 GG-GGGTATCGGTACCCATTCAAA
*
2298 GGGGGTATCGATACC
1 GGGGGTATCGGTACC
2313 TCTTGCACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 2 0.06
23 30 0.83
24 4 0.11
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (23 bp):
GGGGGTATCGGTACCCATTCAAA
Found at i:14428 original size:3 final size:3
Alignment explanation
Indices: 14422--14467 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
14412 GTGGAGGAGA
* *
14422 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCA TCA TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
14468 TTTTTCCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:14628 original size:20 final size:20
Alignment explanation
Indices: 14599--14636 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14589 TTTGGTTTAC
*
14599 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
14619 GGAATATAAGATTACCAG
1 GGAATATAAGATTACCAG
14637 GTAATAGGAT
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:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:14838 original size:2 final size:2
Alignment explanation
Indices: 14831--14861 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14821 TCATAAAATT
14831 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 T
14862 TTTTACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18272 original size:16 final size:16
Alignment explanation
Indices: 18251--18282 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18241 CAAATAAGTA
18251 TTTAGGGTTGTTAAAC
1 TTTAGGGTTGTTAAAC
18267 TTTAGGGTTGTTAAAC
1 TTTAGGGTTGTTAAAC
18283 CAAGGAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
TTTAGGGTTGTTAAAC
Found at i:20312 original size:15 final size:16
Alignment explanation
Indices: 20292--20336 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
20282 TTATCTTCAC
20292 TTAAAAATATATTTT-
1 TTAAAAATATATTTTA
20307 TTAAAAA-ATATTTTAA
1 TTAAAAATATATTTT-A
*
20323 TTTAAAATATATTT
1 TTAAAAATATATTT
20337 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 6 0.23
17 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATATATTTTA
Found at i:20337 original size:16 final size:15
Alignment explanation
Indices: 20295--20338 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
20285 TCTTCACTTA
20295 AAAATATATTT-TTT
1 AAAATATATTTATTT
*
20309 AAAAAATATTTTAATTT
1 AAAATATA-TTT-ATTT
20326 AAAATATATTTAT
1 AAAATATATTTAT
20339 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 3 0.12
17 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATATATTTATTT
Found at i:20341 original size:2 final size:2
Alignment explanation
Indices: 20329--20397 Score: 67
Period size: 2 Copynumber: 36.0 Consensus size: 2
20319 TTAATTTAAA
* *
20329 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20369 CA- AT GA- AT -T AT AT AT AT AT AT AT AT AT AT
1 -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
20398 TTCTTATCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
1 5 0.09
2 50 0.89
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20594 original size:29 final size:29
Alignment explanation
Indices: 20562--20684 Score: 97
Period size: 29 Copynumber: 4.2 Consensus size: 29
20552 ATTTTGAAAA
20562 TTAAGATAAGAATAAATTATATTTTTAAG
1 TTAAGATAAGAATAAATTATATTTTTAAG
* * * *
20591 TTAAAATAAGAGTAAAATATACTTTTAAG
1 TTAAGATAAGAATAAATTATATTTTTAAG
* * * * *
20620 TGAAGATGATATTAAAATATATATTTTTATG
1 TTAAGATAAGAAT-AAAT-TATATTTTTAAG
* * *
20651 -TAAAATGAGAATAAA-TATATTTAATAAG
1 TTAAGATAAGAATAAATTATATTT-TTAAG
20679 TTAAGA
1 TTAAGA
20685 AAAGTAAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
27 7 0.10
28 3 0.04
29 40 0.56
30 11 0.15
31 10 0.14
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (29 bp):
TTAAGATAAGAATAAATTATATTTTTAAG
Found at i:20720 original size:28 final size:28
Alignment explanation
Indices: 20663--20724 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
20653 AAATGAGAAT
20663 AAATATATTTAATAAGTTAAGAAAAGTA
1 AAATATATTTAATAAGTTAAGAAAAGTA
*
20691 AAATATAATTTTAA-AAGTTAAGAATA-TA
1 AAATAT-A-TTTAATAAGTTAAGAAAAGTA
20719 AAATAT
1 AAATAT
20725 TATAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 14 0.45
29 12 0.39
30 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATATATTTAATAAGTTAAGAAAAGTA
Found at i:20740 original size:86 final size:87
Alignment explanation
Indices: 20570--20740 Score: 199
Period size: 86 Copynumber: 2.0 Consensus size: 87
20560 AATTAAGATA
* *
20570 AGAATAAATTATATTTTTAAGTTAAAATAAGAGTAAAATATACTTTTAAGTGAAGATGATATTAA
1 AGAATAAATTATATTTATAAGTTAAAATAAGAGTAAAATATAATTTTAAGTGAAGA-GATATTAA
** *
20635 AATATATATTTTTATGTAAAATG
65 AATATATAAATTTAAGTAAAATG
* *
20658 AGAATAAA-TATATTTAATAAGTTAAGA-AA-AGTAAAATATAATTTTAAAAGTTAAGA-ATA-T
1 AGAATAAATTATATTT-ATAAGTTAAAATAAGAGTAAAATATAATTTT--AAGTGAAGAGATATT
20718 AAAATATTATAAATTTAAGTAAA
63 AAAATA-TATAAATTTAAGTAAA
20741 GTGTTTATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
85 7 0.10
86 31 0.43
87 9 0.12
88 25 0.35
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.37
Consensus pattern (87 bp):
AGAATAAATTATATTTATAAGTTAAAATAAGAGTAAAATATAATTTTAAGTGAAGAGATATTAAA
ATATATAAATTTAAGTAAAATG
Found at i:26903 original size:27 final size:28
Alignment explanation
Indices: 26873--26932 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
26863 TAGGTAATTT
*
26873 ATTTTATTTATATATTAGGGTTC-AAAA
1 ATTTTATTCATATATTAGGGTTCGAAAA
*
26900 ATTTTATTCATATATTAGGGTTCGAATA
1 ATTTTATTCATATATTAGGGTTCGAAAA
26928 ATTTT
1 ATTTT
26933 TGAATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (28 bp):
ATTTTATTCATATATTAGGGTTCGAAAA
Found at i:27128 original size:23 final size:23
Alignment explanation
Indices: 27084--27128 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
27074 ATGGTTTATA
** **
27084 TAGTTAGTTTTTTTTGTTTAAAT
1 TAGTTAGTTAGTTTTGGGTAAAT
27107 TAGTTAGTTAGTTTTGGGTAAA
1 TAGTTAGTTAGTTTTGGGTAAA
27129 ACTATTTAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (23 bp):
TAGTTAGTTAGTTTTGGGTAAAT
Found at i:28558 original size:21 final size:22
Alignment explanation
Indices: 28524--28633 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 22
28514 CCACAACTCG
*
28524 TAATTTTCACCGAAGTG-CCACA
1 TAATTGTC-CCGAAGTGACCACA
* *
28546 TAATTATCCCGAA-TGACCATA
1 TAATTGTCCCGAAGTGACCACA
*
28567 TAGGTT-TGCACCGAAGTG-CCACA
1 TA-ATTGT-C-CCGAAGTGACCACA
28590 TAATTGTCCCGAA-TGACCACA
1 TAATTGTCCCGAAGTGACCACA
*
28611 TAATTGTCCCAAAG-GACCACA
1 TAATTGTCCCGAAGTGACCACA
28632 TA
1 TA
28634 GAACCCTCGA
Statistics
Matches: 74, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.05
21 43 0.58
22 13 0.18
23 12 0.16
24 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (22 bp):
TAATTGTCCCGAAGTGACCACA
Found at i:29254 original size:2 final size:2
Alignment explanation
Indices: 29247--29277 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29237 CTCATATCAT
29247 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 T
29278 CAATGCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35053 original size:22 final size:22
Alignment explanation
Indices: 35028--35087 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
35018 TTTAATAACC
35028 GGTCAACGCCGGTCAAAGTTCT
1 GGTCAACGCCGGTCAAAGTTCT
*
35050 GGTCAATGCCGGTCAAAGTTCT
1 GGTCAACGCCGGTCAAAGTTCT
*
35072 AGTCAACGCCGGTCAA
1 GGTCAACGCCGGTCAA
35088 CAGTGGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.22
Consensus pattern (22 bp):
GGTCAACGCCGGTCAAAGTTCT
Found at i:44603 original size:4 final size:4
Alignment explanation
Indices: 44594--45212 Score: 1086
Period size: 4 Copynumber: 154.8 Consensus size: 4
44584 GATTAATCAG
44594 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44642 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44690 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44738 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44786 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44834 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44882 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44930 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
44978 ATAC ATAC ATAC ATAC ATAC -TATC ATTATC AT-C ATTCAC AT-C CTTC
1 ATAC ATAC ATAC ATAC ATAC ATA-C A-TA-C ATAC A-T-AC ATAC ATAC
* * * * *
45024 TTAT TTAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45072 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT--
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
45118 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45166 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
45213 TATATATACT
Statistics
Matches: 594, Mismatches: 12, Indels: 18
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.00
3 6 0.01
4 577 0.97
5 2 0.00
6 7 0.01
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:45758 original size:169 final size:169
Alignment explanation
Indices: 45479--45799 Score: 624
Period size: 169 Copynumber: 1.9 Consensus size: 169
45469 ACTGAAGTGC
45479 CACATAATTGTCCCAAAGGACCATATAGGTTTGCATCGAAAGACCATGTAGAACCCTCGACTCTT
1 CACATAATTGTCCCAAAGGACCATATAGGTTTGCATCGAAAGACCATGTAGAACCCTCGACTCTT
45544 AGCATGCCAACTATACCCCTAGCTCTCATCACATAACATGGGCATTATCATTTATTTTTGTCACA
66 AGCATGCCAACTATACCCCTAGCTCTCATCACATAACATGGGCATTATCATTTATTTTTGTCACA
45609 TATTCACATAGTCACACAAATAGGTTTGCATCACATAGT
131 TATTCACATAGTCACACAAATAGGTTTGCATCACATAGT
*
45648 CACATAATTGTCCCAAAGGACCATATAGGTTTGCATCGAAGGACCATGTAGAACCCTCGACTCTT
1 CACATAATTGTCCCAAAGGACCATATAGGTTTGCATCGAAAGACCATGTAGAACCCTCGACTCTT
45713 AGCATGCCAACTATACCCCTAGCTCTCATCACATAACATGGGCATTATCATTTATTTTTGTCACA
66 AGCATGCCAACTATACCCCTAGCTCTCATCACATAACATGGGCATTATCATTTATTTTTGTCACA
*
45778 TATTCACATAGTCACGCAAATA
131 TATTCACATAGTCACACAAATA
45800 ATCACATAAC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 150 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (169 bp):
CACATAATTGTCCCAAAGGACCATATAGGTTTGCATCGAAAGACCATGTAGAACCCTCGACTCTT
AGCATGCCAACTATACCCCTAGCTCTCATCACATAACATGGGCATTATCATTTATTTTTGTCACA
TATTCACATAGTCACACAAATAGGTTTGCATCACATAGT
Found at i:49519 original size:32 final size:32
Alignment explanation
Indices: 49478--49539 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
49468 AGAAAAAAAT
*
49478 GTAACGCATGGTGTTCCATGCGCCAAGCATAG
1 GTAACGCATGGTGCTCCATGCGCCAAGCATAG
*
49510 GTAACGCATGGTGCTCCATGCGCCATGCAT
1 GTAACGCATGGTGCTCCATGCGCCAAGCAT
49540 TGGGGTGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (32 bp):
GTAACGCATGGTGCTCCATGCGCCAAGCATAG
Found at i:54912 original size:17 final size:17
Alignment explanation
Indices: 54878--54922 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
54868 CCATTCCCTT
* *
54878 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
54894 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
54911 TCATTCGAGAAA
1 TCTTTCGAGAAA
54923 CAAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:58942 original size:77 final size:76
Alignment explanation
Indices: 58790--58942 Score: 166
Period size: 77 Copynumber: 2.0 Consensus size: 76
58780 AAAAAATATT
**
58790 ATTTAATTAATTCAAATTAAACATCCATTAAAGACTTATAATCTGAATTACAATTTTTAATGTTT
1 ATTTAATTAATTCAAATTAAACATCCATTAAAGACTTATAATCAAAATTACAATTTTTAATGTTT
*
58855 ATTTAAACTATC
66 ACTT-AACTATC
* * * * * * *
58867 ATTTAATT-ATTCCGAATTAAATATCGATTAAAAGAGTTATTATCAAAATTACATTCTTTTAATT
1 ATTTAATTAATT-CAAATTAAACATCCATT-AAAGACTTATAATCAAAATTACAAT-TTTTAATG
58931 TTTACTT-ACTAT
63 TTTACTTAACTAT
58943 ATTCGGGATA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
76 3 0.05
77 27 0.43
78 20 0.32
79 13 0.21
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (76 bp):
ATTTAATTAATTCAAATTAAACATCCATTAAAGACTTATAATCAAAATTACAATTTTTAATGTTT
ACTTAACTATC
Found at i:63277 original size:28 final size:28
Alignment explanation
Indices: 63246--63308 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
63236 GGTATACATA
*
63246 GTATAGTATAATTTTTATATTAAATATT
1 GTATAGTATAATTTTCATATTAAATATT
* * *
63274 GTATATTATAGTTTTCATATTAGATATT
1 GTATAGTATAATTTTCATATTAAATATT
*
63302 ATATAGT
1 GTATAGT
63309 TTTGATGTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (28 bp):
GTATAGTATAATTTTCATATTAAATATT
Found at i:63294 original size:21 final size:21
Alignment explanation
Indices: 63269--63326 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
63259 TTTATATTAA
63269 ATATTGTATATTATAGTTTTC
1 ATATTGTATATTATAGTTTTC
*
63290 ATATTAG-ATATTATATAGTTTTG
1 ATATT-GTATA-T-TATAGTTTTC
*
63313 AT-GTGTATATTATA
1 ATATTGTATATTATA
63327 AAGTATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 6 0.19
23 11 0.35
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (21 bp):
ATATTGTATATTATAGTTTTC
Found at i:66518 original size:3 final size:3
Alignment explanation
Indices: 66510--66577 Score: 93
Period size: 3 Copynumber: 22.3 Consensus size: 3
66500 CCATTTGTTT
66510 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* *
66556 A-A CAAA ATA ATA ATA GTA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA A
66578 ATTAAAATAG
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.02
3 54 0.92
4 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:66835 original size:40 final size:41
Alignment explanation
Indices: 66732--66843 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 41
66722 TTAGTTGTTG
* **
66732 GGGACGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAA
1 GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCG--T-A
* * * * *
66776 GGG-TGACACGGTTCCTACGTGATGAGGAAATCTGGTCG-A
1 GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCGTA
66815 GGGATGACACTGCTCATACGTGATGAAGA
1 GGGATGACACTGCTCATACGTGATGAAGA
66844 GTTCTTGGCC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
39 4 0.07
40 21 0.38
43 27 0.49
44 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (41 bp):
GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCGTA
Found at i:67021 original size:129 final size:131
Alignment explanation
Indices: 66771--67125 Score: 511
Period size: 129 Copynumber: 2.7 Consensus size: 131
66761 GTTCGGGTCG
* * *
66771 TCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACT-GCTCATACG
1 TCTAGGGGTGACAC-GCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACA-TGGCTCATACG
* *
66835 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
63 -GATGAAGAGTTC-TAGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGC
66900 TGGTTA
126 TGGTTA
*
66906 TCTAGGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTC-GGGATGACATGGCTCATAC-GA
1 TCTAGGGGTGACAC-GCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACATGGCTCATACGGA
* *
66969 TGAAGAGTTCT-GCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGTCTGGT
65 TGAAGAGTTCTAGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGT
67033 TA
130 TA
* *
67035 TCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGAGATGACACGGCTCATACGT
1 TCTAGGGGTGACACG-CTCCTACGTGATGAGGAGATCTGGTCAGG-GATGACATGGCTCATACG-
67100 GATGAAGAGTTCTAGCCATCTTTAGG
63 GATGAAGAGTTCTAGCCATCTTTAGG
67126 GATAATGATT
Statistics
Matches: 202, Mismatches: 11, Indels: 15
0.89 0.05 0.07
Matches are distributed among these distances:
128 1 0.00
129 90 0.45
130 3 0.01
131 28 0.14
132 1 0.00
133 30 0.15
134 12 0.06
135 37 0.18
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (131 bp):
TCTAGGGGTGACACGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACATGGCTCATACGGAT
GAAGAGTTCTAGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTT
A
Found at i:67458 original size:29 final size:29
Alignment explanation
Indices: 67406--67480 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
67396 GAGACAAAAC
* **
67406 TTTGTTTCAAAATAAACAAACTCAAAGA-T
1 TTTGTTTCAAAAGAAA-TGACTCAAAGACT
*
67435 TTTGGTTTCAAAAGAAATGACTCACAGACT
1 TTT-GTTTCAAAAGAAATGACTCAAAGACT
*
67465 TTTGTTTCAAGAGAAA
1 TTTGTTTCAAAAGAAA
67481 CAAACTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAATGACTCAAAGACT
Found at i:67503 original size:32 final size:30
Alignment explanation
Indices: 67406--67542 Score: 127
Period size: 30 Copynumber: 4.5 Consensus size: 30
67396 GAGACAAAAC
* *
67406 TTTGTTTCAAAATAAACAAACTCAAAGAT-
1 TTTGTTTCAAGAGAAACAAACTCAAAGATA
* ** *
67435 TTTGGTTTCAAAAGAAA-TGACTCACAGACT-
1 TTT-GTTTCAAGAGAAACAAACTCAAAGA-TA
67465 TTTGTTTCAAGAGAAACAAACTCAAAGATAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGAT--A
* * *
67497 TTTGTTTCAAGGGAAACAATCTCAAAGATG
1 TTTGTTTCAAGAGAAACAAACTCAAAGATA
*
67527 TTTGTTTTAAGAGAAA
1 TTTGTTTCAAGAGAAA
67543 TTGTCTCAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
29 24 0.27
30 38 0.43
32 27 0.30
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (30 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATA
Found at i:67689 original size:63 final size:61
Alignment explanation
Indices: 67494--67726 Score: 191
Period size: 64 Copynumber: 3.6 Consensus size: 61
67484 ACTCAAAGAT
* * * * *
67494 AAATTTGTTTCAAGGGAAACA-ATCTCAAAGATGTTTGTTTTAAGAGAAATTGTCTCAAAAGAGA
1 AAATTTGTTTCAA--AAAACATA-CTCAAAGA--TTT-TTTCAAAAGAAACTGTATCAAAAGAGA
67558 CA
60 CA
* * * * *
67560 AACATTTGTTTTCATAAAAC-GACTTAAAGATTTTTATTCAAAAGGAACTGTCTCAAAAGAGACA
1 AA-ATTTG-TTTCAAAAAACATACTCAAAGA-TTTT-TTCAAAAGAAACTGTATCAAAAGAGACA
* * *
67624 AAATTGTGTTTCCAAAAAACATACTCAAAGATTCTTTCAAAAGAAACTTTATCGAAAGAGACA
1 AAATT-TGTTT-CAAAAAACATACTCAAAGATTTTTTCAAAAGAAACTGTATCAAAAGAGACA
*
67687 AAATTTTGTTATCAAAGAAATATACTCAAAGATTTTTTCA
1 AAA-TTTGTT-TCAAA-AAACATACTCAAAGATTTTTTCA
67727 TTTTGTTTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
63 42 0.30
64 65 0.47
65 15 0.11
66 7 0.05
67 5 0.04
68 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (61 bp):
AAATTTGTTTCAAAAAACATACTCAAAGATTTTTTCAAAAGAAACTGTATCAAAAGAGACA
Found at i:67730 original size:37 final size:37
Alignment explanation
Indices: 67689--67760 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
67679 AAGAGACAAA
*
67689 ATTTTGTTATCAA-AGAAATATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAAGAGAAACATACTCAAAGATTTTTTC
* *
67726 ATTTTGTTTTAAGTGAAACATACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTT
67761 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTTTC
Found at i:67734 original size:100 final size:99
Alignment explanation
Indices: 67630--67819 Score: 226
Period size: 100 Copynumber: 1.9 Consensus size: 99
67620 GACAAAATTG
* *
67630 TGTTTCCAA-AAAACATACTCAAAGATTCTTTCAA-AAGAAACTTTATCGAA-AGAGACAAAATT
1 TGTTT-CAAGAAAACATACTCAAAGATT-TTTCAAGAA-AAACTGTATC-AAGAGAAACAAAATT
*
67692 TTGTTATC-AAAGAAATATACTCAAAGATTTTTTCATTT
62 TTGTT-TCAAAAGAAATAGACTCAAAGATTTTTTCATTT
* * * * *
67730 TGTTTTAAGTGAAACATACTCAAAGATTTTTCAAGAAAATCTGTCTCAAGAGAAACAAAGTTTTG
1 TGTTTCAAG-AAAACATACTCAAAGATTTTTCAAGAAAAACTGTATCAAGAGAAACAAAATTTTG
67795 TTTCAAAAGAAATAGACTCAAAGAT
65 TTTCAAAAGAAATAGACTCAAAGAT
67820 CCTTTATTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
99 6 0.08
100 52 0.68
101 19 0.25
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (99 bp):
TGTTTCAAGAAAACATACTCAAAGATTTTTCAAGAAAAACTGTATCAAGAGAAACAAAATTTTGT
TTCAAAAGAAATAGACTCAAAGATTTTTTCATTT
Found at i:67969 original size:35 final size:35
Alignment explanation
Indices: 67891--68011 Score: 109
Period size: 35 Copynumber: 3.4 Consensus size: 35
67881 TTTGGAAAAT
* * *
67891 TATCTCAAGTGAGACAACATTGTTTTTTTAGAGAAAT
1 TATCTCAAGCGAGACAAAATTG--TTTTTAGAGAAAC
* * *
67928 TGTCTCAAACGAGACAAAATTGTTTTTAGGGAAAC
1 TATCTCAAGCGAGACAAAATTGTTTTTAGAGAAAC
* * *
67963 TATCTCATGCGAGACAAAGTTTGTTTTGAGA-AAAC
1 TATCTCAAGCGAGACAAA-ATTGTTTTTAGAGAAAC
* *
67998 GATCTCAAGTGAGA
1 TATCTCAAGCGAGA
68012 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 41 0.60
36 9 0.13
37 18 0.26
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (35 bp):
TATCTCAAGCGAGACAAAATTGTTTTTAGAGAAAC
Found at i:68127 original size:106 final size:103
Alignment explanation
Indices: 67991--68301 Score: 374
Period size: 104 Copynumber: 3.0 Consensus size: 103
67981 GTTTGTTTTG
* *
67991 AGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
1 AGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
* *
68056 AATGAAAAATGTCTCAAATGAGACGAATTTTATTTTGAA
66 AAGGAAAAATGTCTCAAACGAGACGAATTTTATTTT-AA
* * * * * *
68095 AGAAATAACAATCTCAATTGAGATTAATTTTGTTTCAA-GTGAATCAAATTCAAAATTTGTA-TG
1 AG-AA-AACAATCTCAAATGAGATCAACTTTGTTT-AATGTGAAACAAATTCGAAATTTGTATTC
* * * * * *
68158 TCAAAGGAAAAAAATGTCTCAAGCAAGACGGAGTTTGTTTTTA
63 TCAAAGG--AAAAATGTCTCAAACGAGACGAATTTTATTTTAA
* *
68201 AGAAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
1 AGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
*
68266 AAGGAAAAATGTCTCAAACGAGAAAGAATTTTATTT
66 AAGGAAAAATGTCTCAAACGAG-ACGAATTTTATTT
68302 CTCAAATGTG
Statistics
Matches: 170, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
103 18 0.11
104 56 0.33
105 19 0.11
106 49 0.29
107 28 0.16
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (103 bp):
AGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
AAGGAAAAATGTCTCAAACGAGACGAATTTTATTTTAA
Found at i:68247 original size:104 final size:103
Alignment explanation
Indices: 67974--68284 Score: 376
Period size: 106 Copynumber: 3.0 Consensus size: 103
67964 ATCTCATGCG
* * *
67974 AGACAAAGTTTG-TTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAAT
1 AGACGAAGTTTGTTTTTAAGAAAACGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAAT
* **
68038 TCGAAATTTGTATTCTCAAATGAAAAATGTCTCAAATG
66 TCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACA
* * * * * * * *
68076 AGACGAATTTTATTTTGAAAGAAATAACAATCTCAATTGAGATTAATTTTGTTTCAA-GTGAATC
1 AGACGAAGTTTGTTTT-TAAG-AA-AACGATCTCAAATGAGATCAACTTTGTTT-AATGTGAAAC
* * *
68140 AAATTCAAAATTTGTA-TGTCAAAGGAAAAAAATGTCTCAAGCA
62 AAATTCGAAATTTGTATTCTCAAAGG--AAAAATGTCTCAAACA
* *
68183 AGACGGAGTTTGTTTTTAAGAAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAAT
1 AGACGAAGTTTGTTTTTAAGAAAACGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAAT
68248 TCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAAC
66 TCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAAC
68285 GAGAAAGAAT
Statistics
Matches: 171, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
102 9 0.05
103 19 0.11
104 47 0.27
105 19 0.11
106 49 0.29
107 28 0.16
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (103 bp):
AGACGAAGTTTGTTTTTAAGAAAACGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAAT
TCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACA
Found at i:75319 original size:51 final size:50
Alignment explanation
Indices: 75228--75352 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 50
75218 TTAGCAGTAA
* **
75228 AGCGCG-CCCCT-CACCGCGTTATACGATGATTTGGCACCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGT-GGGTAT
* * *
75277 AGTGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGGGTAT
* *
75327 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
75353 CTGTATATCT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 5 0.08
50 34 0.52
51 26 0.40
ACGTcount: A:0.16, C:0.34, G:0.31, T:0.18
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGGGTAT
Found at i:75504 original size:12 final size:10
Alignment explanation
Indices: 75463--75503 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
75453 TTTATCACAC
75463 CAAATTCTCT
1 CAAATTCTCT
75473 CAAATTCTCT
1 CAAATTCTCT
75483 -AAATTTCTCT
1 CAAA-TTCTCT
*
75493 CAAATACTCT
1 CAAATTCTCT
75503 C
1 C
75504 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:75538 original size:15 final size:15
Alignment explanation
Indices: 75518--75567 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
75508 AAGGTATATT
75518 TTATATATTTTACTA
1 TTATATATTTTACTA
75533 TTATAT-TTTTACTTA
1 TTATATATTTTAC-TA
75548 TT-TAATATTTTACTA
1 TTAT-ATATTTTACTA
*
75563 ATATA
1 TTATA
75568 ATTCTTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 7 0.23
15 16 0.53
16 7 0.23
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATATTTTACTA
Found at i:75569 original size:16 final size:16
Alignment explanation
Indices: 75522--75569 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
75512 TATATTTTAT
*
75522 ATATTTTACTATTAT-
1 ATATTTTACTAATATA
* *
75537 AT-TTTTACTTATTTA
1 ATATTTTACTAATATA
75552 ATATTTTACTAATATA
1 ATATTTTACTAATATA
75568 AT
1 AT
75570 TCTTTTGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 13 0.50
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTACTAATATA
Done.