Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001382.1 Hibiscus syriacus cultivar Beakdansim tig00002697_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: 88965
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10258 original size:29 final size:30
Alignment explanation
Indices: 10216--10275 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
10206 CTTGTACTAC
10216 TCAAATTACATAAATTCCATGTTTT-CTGA
1 TCAAATTACATAAATTCCATGTTTTCCTGA
*
10245 TCAAATTACATAAATTTCATGTTTTCCTGA
1 TCAAATTACATAAATTCCATGTTTTCCTGA
10275 T
1 T
10276 AACTATAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
TCAAATTACATAAATTCCATGTTTTCCTGA
Found at i:12677 original size:26 final size:27
Alignment explanation
Indices: 12645--12711 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
12635 TTTCCCTTGT
12645 AGTGTAAAATGACCAAAATGCCCCTAA
1 AGTGTAAAATGACCAAAATGCCCCTAA
* **
12672 AG-GTAAAATAAGTAAAATGCCCCTAA
1 AGTGTAAAATGACCAAAATGCCCCTAA
12698 AGTGTAAAATGACC
1 AGTGTAAAATGACC
12712 TAAAGTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.19
Consensus pattern (27 bp):
AGTGTAAAATGACCAAAATGCCCCTAA
Found at i:12715 original size:17 final size:18
Alignment explanation
Indices: 12683--12717 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12673 GGTAAAATAA
*
12683 GTAAAATGCCCCTAAAGT
1 GTAAAATGCACCTAAAGT
12701 GTAAAATG-ACCTAAAGT
1 GTAAAATGCACCTAAAGT
12718 ATATTCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (18 bp):
GTAAAATGCACCTAAAGT
Found at i:15750 original size:32 final size:32
Alignment explanation
Indices: 15714--15800 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
15704 TAGATCTTCC
15714 CCTAGTTTCTCTCGAACACTAAGGATCTATAA
1 CCTAGTTTCTCTCGAACACTAAGGATCTATAA
* **
15746 CCTAGTTTCTCTTGAGTACTAAGGATCTATAA
1 CCTAGTTTCTCTCGAACACTAAGGATCTATAA
*
15778 CCTAGTTTCTCTCGAACAATAAG
1 CCTAGTTTCTCTCGAACACTAAG
15801 CAATCTACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (32 bp):
CCTAGTTTCTCTCGAACACTAAGGATCTATAA
Found at i:15898 original size:48 final size:47
Alignment explanation
Indices: 15842--15938 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 47
15832 CTCATACAAT
15842 CTTAAGTAATTAAGTACAATGAGAAAAACAAATAGATAAACGCAAAAA
1 CTTAAGTAATTAAGTACAATGAGAAAAA-AAATAGATAAACGCAAAAA
*
15890 CTTAAGTAATTAAGTACAATGAGAAAAAAAATAGATAAACTCAAAAA
1 CTTAAGTAATTAAGTACAATGAGAAAAAAAATAGATAAACGCAAAAA
15937 CT
1 CT
15939 CAAATCATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 20 0.42
48 28 0.58
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.21
Consensus pattern (47 bp):
CTTAAGTAATTAAGTACAATGAGAAAAAAAATAGATAAACGCAAAAA
Found at i:24287 original size:32 final size:32
Alignment explanation
Indices: 24203--24287 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
24193 GATCCTCCCT
* * *
24203 TAGTTTCCCTCGAACACTAAAGATCTATAACC
1 TAGTTTCTCTTGAACACTAAGGATCTATAACC
* *
24235 TAGTTTTTCTTGAGCACTAAGGATCTATAACC
1 TAGTTTCTCTTGAACACTAAGGATCTATAACC
24267 TAGTTTCTCTTGAACACTAAG
1 TAGTTTCTCTTGAACACTAAG
24288 CAATCTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (32 bp):
TAGTTTCTCTTGAACACTAAGGATCTATAACC
Found at i:39055 original size:30 final size:31
Alignment explanation
Indices: 38998--39055 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
38988 ACTTTTGATA
* * *
38998 AATATATATACATATATTACTACATATAATT
1 AATATATAAACATATATAACTAAATATAATT
*
39029 AATAT-TAAACATCTATAACTAAATATA
1 AATATATAAACATATATAACTAAATATA
39056 TATAAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (31 bp):
AATATATAAACATATATAACTAAATATAATT
Found at i:41587 original size:29 final size:27
Alignment explanation
Indices: 41502--41644 Score: 81
Period size: 29 Copynumber: 4.9 Consensus size: 27
41492 TTTTTTTATT
* *
41502 AAAATTATATATACTAATACT-TAATTTC
1 AAAATTATATATA-AAATA-TATATTTTC
* * *
41530 AAAACTATAATATATAATATGTACTTATTTCC
1 AAAA-T-T-ATATATAAAATATA--TATTTTC
*
41562 AAAACTCTATATATAAAATATATATTTTTT
1 AAAA-T-TATATATAAAATATATA-TTTTC
* *
41592 AAAATTATATATATAATACACTATTTTC
1 AAAATTATATATAAAATATA-TATTTTC
*
41620 AAAAATTATATATATATATATATAT
1 -AAAATTATATATA-AAATATATAT
41645 ATATATATAC
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
28 21 0.24
29 23 0.26
30 14 0.16
31 19 0.21
32 12 0.13
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (27 bp):
AAAATTATATATAAAATATATATTTTC
Found at i:41633 original size:2 final size:2
Alignment explanation
Indices: 41626--41653 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41616 TTTCAAAAAT
41626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41654 CTACATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41635 original size:31 final size:31
Alignment explanation
Indices: 41502--41637 Score: 83
Period size: 28 Copynumber: 4.5 Consensus size: 31
41492 TTTTTTTATT
* * *
41502 AAAATTATATATA-CTAATAC-TTAATTTC-
1 AAAATTATATATATATAATACACTATTTTCA
* * *
41530 AAAACTATA-ATATATAATATGTACTTATTTCCA
1 AAAATTATATATATATAATA--CAC-TATTTTCA
* * **
41563 AAACTCTATATATA-A-AATATA-TATTTTTT
1 AAAAT-TATATATATATAATACACTATTTTCA
41592 AAAA-T-TATATATATAATACACTATTTTCA
1 AAAATTATATATATATAATACACTATTTTCA
41621 AAAATTATATATATATA
1 AAAATTATATATATATA
41638 TATATATATA
Statistics
Matches: 80, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
26 6 0.08
27 5 0.06
28 18 0.22
29 18 0.22
30 1 0.01
31 12 0.15
32 5 0.06
33 7 0.09
34 5 0.06
35 3 0.04
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.43
Consensus pattern (31 bp):
AAAATTATATATATATAATACACTATTTTCA
Found at i:42730 original size:255 final size:255
Alignment explanation
Indices: 42266--42727 Score: 577
Period size: 255 Copynumber: 1.8 Consensus size: 255
42256 ATTTTTCATT
* *
42266 TTCCACGAATATCATATGAAAACACCATGCCCGGAGGTCTTATAGATGGCCCGGAGGACTTATCA
1 TTCCACGAATATCATACGAAAACACCATGCCCGGAGGTCTTATAGATGGCCCAGAGGACTTATCA
* ** * * * * *
42331 TATTGCTCAAAAGACTTACAGATGACTTGGTGGATTTGATCCTCATGCTCGGAATACTACTGATG
66 TATTGCTCAAAAGACTTACAGATAACCCGGAGGATTTAATCATCATGATCGGAAGACTACTGATG
* * * * * *
42396 TCATAGAGAACTTACTCATTTTGGAAACATTCTACTAGGTAAGAAACTTTGAAAATCACTTTTTT
131 ACATAGAGAACTTACTAACTTTGAAAACATTCTACTAGGAAAGAAACTTTGAAAATCACTTTCTT
*
42461 ACTTTTCAAAAATTTCATTTTTTGAAAATCAAATAAGAAACTTTGAAAATCACTTTCTCA
196 ACTATTCAAAAATTTCATTTTTTGAAAATCAAATAAGAAACTTTGAAAATCACTTTCTCA
* * * * *
42521 TTCCATGAATGTCATACGAAAACATCATGCCTGGAGGTCTTATAGATGGTCCAGAGGACTTATCA
1 TTCCACGAATATCATACGAAAACACCATGCCCGGAGGTCTTATAGATGGCCCAGAGGACTTATCA
* ** * * *
42586 TCTTGCTTGAAAGACTTACAGATAACCCGGAGGATTTAATCATCATGATTGGAAGATTTATTGAT
66 TATTGCTCAAAAGACTTACAGATAACCCGGAGGATTTAATCATCATGATCGGAAGA-CTACTGAT
* * * * **
42651 GAC-TCGGAGGACTTACTAACTTTGAAAATATTCTACTAGGAAAGAAACTTTCG-TAATTGCTTT
130 GACAT-AGAGAACTTACTAACTTTGAAAACATTCTACTAGGAAAGAAACTTT-GAAAATCACTTT
42714 CTTACTATTCAAAA
193 CTTACTATTCAAAA
42728 TTTTAAAAAA
Statistics
Matches: 170, Mismatches: 34, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
255 103 0.61
256 66 0.39
257 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (255 bp):
TTCCACGAATATCATACGAAAACACCATGCCCGGAGGTCTTATAGATGGCCCAGAGGACTTATCA
TATTGCTCAAAAGACTTACAGATAACCCGGAGGATTTAATCATCATGATCGGAAGACTACTGATG
ACATAGAGAACTTACTAACTTTGAAAACATTCTACTAGGAAAGAAACTTTGAAAATCACTTTCTT
ACTATTCAAAAATTTCATTTTTTGAAAATCAAATAAGAAACTTTGAAAATCACTTTCTCA
Found at i:50476 original size:7 final size:7
Alignment explanation
Indices: 50464--50514 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
50454 GTCAAAGAAA
50464 GTCAACG
1 GTCAACG
50471 GTCAACG
1 GTCAACG
50478 GTC-ACG
1 GTCAACG
50484 GTCAACG
1 GTCAACG
50491 GTCAACG
1 GTCAACG
50498 GTCAACG
1 GTCAACG
50505 GTCAACG
1 GTCAACG
50512 GTC
1 GTC
50515 GGGTCAACAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.14
7 37 0.86
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:50533 original size:17 final size:17
Alignment explanation
Indices: 50511--50555 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
50501 AACGGTCAAC
50511 GGTCGGGTCAACAGTCG
1 GGTCGGGTCAACAGTCG
50528 GGTCGGGTCAACAGTCG
1 GGTCGGGTCAACAGTCG
50545 GGTCGGGTCAA
1 GGTCGGGTCAA
50556 ACCGGTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCAACAGTCG
Found at i:50571 original size:10 final size:10
Alignment explanation
Indices: 50552--50639 Score: 103
Period size: 9 Copynumber: 9.1 Consensus size: 10
50542 TCGGGTCGGG
50552 TCAAACCGGT
1 TCAAACCGGT
*
50562 TCAGACCGG-
1 TCAAACCGGT
50571 TCAAACCGGT
1 TCAAACCGGT
*
50581 TCAGACCGG-
1 TCAAACCGGT
50590 TCAAACCGGT
1 TCAAACCGGT
*
50600 TCGAACCGG-
1 TCAAACCGGT
50609 TCAAACCGGT
1 TCAAACCGGT
*
50619 TCAAAACTGG-
1 TC-AAACCGGT
50629 TCAAACCGGT
1 TCAAACCGGT
50639 T
1 T
50640 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
9 30 0.46
10 29 0.45
11 6 0.09
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:50574 original size:19 final size:19
Alignment explanation
Indices: 50550--50639 Score: 137
Period size: 19 Copynumber: 4.7 Consensus size: 19
50540 AGTCGGGTCG
50550 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
50569 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
50588 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
50607 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
50627 GGTCAAACCGGTT
1 GGTCAAACCGGTT
50640 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 50 0.76
20 15 0.23
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:57763 original size:7 final size:7
Alignment explanation
Indices: 57751--57816 Score: 125
Period size: 7 Copynumber: 9.6 Consensus size: 7
57741 GTCAAAGAAA
57751 GTCAACG
1 GTCAACG
57758 GTCAACG
1 GTCAACG
57765 GTC-ACG
1 GTCAACG
57771 GTCAACG
1 GTCAACG
57778 GTCAACG
1 GTCAACG
57785 GTCAACG
1 GTCAACG
57792 GTCAACG
1 GTCAACG
57799 GTCAACG
1 GTCAACG
57806 GTCAACG
1 GTCAACG
57813 GTCA
1 GTCA
57817 GGTCGGGTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.10
7 52 0.90
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:57827 original size:17 final size:17
Alignment explanation
Indices: 57805--57862 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
57795 AACGGTCAAC
* *
57805 GGTCAACGGTCAGGTCG
1 GGTCAACAGTCGGGTCG
57822 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
57839 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
57856 GGTCAAC
1 GGTCAAC
57863 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:57880 original size:19 final size:19
Alignment explanation
Indices: 57856--57926 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
57846 AGTCGGGTCG
*
57856 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
57875 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
57894 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
57914 GGTCAAACCGGTT
1 GGTCAAACCGGTT
57927 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:57894 original size:10 final size:10
Alignment explanation
Indices: 57858--57926 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
57848 TCGGGTCGGG
*
57858 TCAACCCGGT
1 TCAAACCGGT
*
57868 TCAGACCGG-
1 TCAAACCGGT
57877 TCAAACCGGT
1 TCAAACCGGT
*
57887 TCAGACCGG-
1 TCAAACCGGT
57896 TCAAACCGGT
1 TCAAACCGGT
*
57906 TCAAAACTGG-
1 TC-AAACCGGT
57916 TCAAACCGGT
1 TCAAACCGGT
57926 T
1 T
57927 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:60094 original size:20 final size:22
Alignment explanation
Indices: 60046--60099 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
60036 ATCATCATAT
60046 GGTATCGATACCTCAACACTATA
1 GGTATCGATA-CTCAACACTATA
*
60069 -GTATCGATACTCATC-CTA-A
1 GGTATCGATACTCAACACTATA
60088 GGTATCGATACT
1 GGTATCGATACT
60100 GCCATAATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 5 0.17
22 9 0.31
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (22 bp):
GGTATCGATACTCAACACTATA
Found at i:65791 original size:27 final size:26
Alignment explanation
Indices: 65754--65809 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
65744 TTTTGATAAA
* *
65754 ATTTATATACATATAATATTAC-ATAT
1 ATTTATATACACAT-ATATAACTATAT
65780 ATTTAATATACACATATATAACTATAT
1 ATTT-ATATACACATATATAACTATAT
65807 ATT
1 ATT
65810 AAAAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTATATACACATATATAACTATAT
Found at i:72365 original size:22 final size:24
Alignment explanation
Indices: 72340--72397 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
72330 ACTTATTTCC
* *
72340 AAAACTATATAT-ATA-ATTTTTT
1 AAAACTATATATAATACACTATTT
*
72362 AAAATTATATATAATACACTATTT
1 AAAACTATATATAATACACTATTT
*
72386 CAAACTATATAT
1 AAAACTATATAT
72398 CACTATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 11 0.38
23 3 0.10
24 15 0.52
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAACTATATATAATACACTATTT
Found at i:72431 original size:48 final size:46
Alignment explanation
Indices: 72341--72450 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 46
72331 CTTATTTCCA
* *
72341 AAACTATATATATAATTTTTTAAAATTATATATAATACACTATTTC
1 AAACTATATATATAATATTTTAAAATTATAAATAATACACTATTTC
* * *
72387 AAACTATATATCACT-ATATTTTAACATTATAGAATACTATACTATTT-
1 AAACTATATAT-A-TAATATTTTAAAATTATA-AATAATACACTATTTC
*
72434 ATA-TATATATAT-ATATT
1 AAACTATATATATAATATT
72451 CTATATATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
44 6 0.11
45 1 0.02
46 18 0.33
47 17 0.31
48 13 0.24
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (46 bp):
AAACTATATATATAATATTTTAAAATTATAAATAATACACTATTTC
Found at i:75407 original size:17 final size:17
Alignment explanation
Indices: 75385--75433 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
75375 AATGTTTCTG
75385 AGGAATTGGAAT-TGTGA
1 AGGAATTGGAATCTGT-A
*
75402 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTA
75419 AGGAATTGGAATCTG
1 AGGAATTGGAATCTG
75434 AATATGAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 27 0.90
18 3 0.10
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.29
Consensus pattern (17 bp):
AGGAATTGGAATCTGTA
Found at i:76101 original size:25 final size:25
Alignment explanation
Indices: 76073--76121 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
76063 AGAAAAGACA
*
76073 TAAAAAAAAAAAACAAGATAAAAAT
1 TAAAAAAAAAAAACAACATAAAAAT
* * *
76098 TAAATAAAATAAAGAACATAAAAA
1 TAAAAAAAAAAAACAACATAAAAA
76122 ACAAAAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (25 bp):
TAAAAAAAAAAAACAACATAAAAAT
Found at i:76152 original size:18 final size:19
Alignment explanation
Indices: 76129--76193 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
76119 AAAACAAAAG
*
76129 AAATAAA-ATAATGAAGAA
1 AAATAAAGATAATGAAGCA
* * *
76147 AAATAAATAAAAT-AATCA
1 AAATAAAGATAATGAAGCA
*
76165 AAATAAAGATAACG-AGCA
1 AAATAAAGATAATGAAGCA
76183 AAATAAA-ATAA
1 AAATAAAGATAA
76194 AAATAAGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.11
18 30 0.79
19 4 0.11
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.17
Consensus pattern (19 bp):
AAATAAAGATAATGAAGCA
Found at i:76226 original size:21 final size:22
Alignment explanation
Indices: 76130--76219 Score: 60
Period size: 22 Copynumber: 3.9 Consensus size: 22
76120 AAACAAAAGA
76130 AATAAAATAATGAAGAAAAAT-A-
1 AATAAAATAA--AAGAAAAATAAG
*
76152 AATAAAATAATCAAAATAAAGATAACG
1 AATAAAATAA--AAGA-AAA-ATAA-G
** *
76179 AGCAAAATAAAATAAAAATAAG
1 AATAAAATAAAAGAAAAATAAG
76201 AATAAAAT-AAAGAAAAATA
1 AATAAAATAAAAGAAAAATA
76220 CTAATAATTG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
21 10 0.18
22 21 0.38
23 7 0.13
24 5 0.09
25 4 0.07
27 8 0.15
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (22 bp):
AATAAAATAAAAGAAAAATAAG
Found at i:76248 original size:4 final size:4
Alignment explanation
Indices: 76239--76321 Score: 53
Period size: 4 Copynumber: 19.5 Consensus size: 4
76229 GTATATACAT
* * *
76239 AATA AATA AATA AATA AATA AATA AACA AGAGA AA-A ATACA AATGAA
1 AATA AATA AATA AATA AATA AATA AATA A-ATA AATA A-ATA AAT--A
*
76286 AATA AATA TATA AATAA AACTA ATATA AA-A AATA AA
1 AATA AATA AATA AAT-A AA-TA A-ATA AATA AATA AA
76322 ATAAGAAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
3 5 0.08
4 41 0.63
5 13 0.20
6 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:76324 original size:62 final size:62
Alignment explanation
Indices: 76230--76352 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 62
76220 CTAATAATTG
* * *
76230 TATATACATAATAAATAAATAAATAAATAAATAA-ACAA-GAGAAAAATACAAATGAAAATAAA
1 TATATAAATAATAAATAAATAAATAAATAAATAAGAAAAGGA-AAAAAAACAAAT-AAAATAAA
*
76292 TATATAAATAA-AACTAATATAAA-AAATAAAATAAGAAAAGGAAAAAAAACAAATAAAATAA
1 TATATAAATAATAAATAA-ATAAATAAAT-AAATAAGAAAAGGAAAAAAAACAAATAAAATAA
76353 GAAAAATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
61 9 0.17
62 28 0.53
63 14 0.26
64 2 0.04
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.20
Consensus pattern (62 bp):
TATATAAATAATAAATAAATAAATAAATAAATAAGAAAAGGAAAAAAAACAAATAAAATAAA
Found at i:80419 original size:22 final size:20
Alignment explanation
Indices: 80391--80431 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
80381 ATAACTATGT
80391 TAAAAATATATAAAATTATTAA
1 TAAAAAT-T-TAAAATTATTAA
*
80413 TAAAAATTTGAAATTATTA
1 TAAAAATTTAAAATTATTA
80432 CTTATGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAAAATTTAAAATTATTAA
Found at i:80905 original size:6 final size:6
Alignment explanation
Indices: 80894--80921 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
80884 TTATTAGATT
80894 AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAAT
80922 AATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:81648 original size:20 final size:21
Alignment explanation
Indices: 81604--81653 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
81594 AAATACTTTT
81604 GTATCGATACTGAATCGCTGA
1 GTATCGATACTGAATCGCTGA
81625 GTATCGATACTGAA-C-CTCGA
1 GTATCGATACTGAATCGCT-GA
81645 GTATCGATA
1 GTATCGATA
81654 TTCCTATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 12 0.43
21 14 0.50
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (21 bp):
GTATCGATACTGAATCGCTGA
Found at i:84547 original size:40 final size:40
Alignment explanation
Indices: 84492--84570 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
84482 AGGTTTATAG
* *
84492 TACACTTTGGTGTATATGGTGGGCACGACCTTATGTGTAT
1 TACACTTCGATGTATATGGTGGGCACGACCTTATGTGTAT
84532 TACACTTCGATGTATATGGTGGGCACGACCTTATGTGTA
1 TACACTTCGATGTATATGGTGGGCACGACCTTATGTGTA
84571 GCACTACGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (40 bp):
TACACTTCGATGTATATGGTGGGCACGACCTTATGTGTAT
Found at i:84769 original size:44 final size:44
Alignment explanation
Indices: 84675--84829 Score: 215
Period size: 44 Copynumber: 3.5 Consensus size: 44
84665 GTAAGCATGC
**
84675 AAATAAGCTTACGAGCTTATGG-A-ATAATGACAAGTATATAGTA
1 AAATAAGCTTACGAGCTTATGGTACA-AATGGTAAGTATATAGTA
* *
84718 AAGTAAGCTTACGAGCTTACGGTACAAATGGTAAGTATATAGTA
1 AAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATATAGTA
* *
84762 AAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATTTTGATA
1 AAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATATAG-TA
*
84807 AAATAAGCTTACGAGTTTATGGT
1 AAATAAGCTTACGAGCTTATGGT
84830 TAATAAATGG
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 20 0.20
44 55 0.55
45 25 0.25
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATATAGTA
Done.