Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006793.1 Hibiscus syriacus cultivar Beakdansim tig00017222_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: 75875
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:4110 original size:31 final size:31
Alignment explanation
Indices: 4075--4143 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
4065 AAGTTAATTT
* *
4075 TTAATTTGATCTCTAAAGTTTAGATAAAATC
1 TTAATTTGATCCCTAAACTTTAGATAAAATC
* *
4106 TTAATTTGATCCCTAAACTTTATATAAAATG
1 TTAATTTGATCCCTAAACTTTAGATAAAATC
4137 TTAATTT
1 TTAATTT
4144 AACCTTTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (31 bp):
TTAATTTGATCCCTAAACTTTAGATAAAATC
Found at i:14324 original size:30 final size:31
Alignment explanation
Indices: 14281--14345 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
14271 TATAATTTAT
* *
14281 ATTTGATCATTAATATTTA-TTTATTTGATCA
1 ATTTGATCATTAAT-TTTATTTTAATTGATAA
*
14312 ATTTGGTC-TTAATTTTATTTTAATTGATAA
1 ATTTGATCATTAATTTTATTTTAATTGATAA
14342 ATTT
1 ATTT
14346 AATTCTCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 4 0.13
30 19 0.63
31 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.57
Consensus pattern (31 bp):
ATTTGATCATTAATTTTATTTTAATTGATAA
Found at i:14740 original size:20 final size:20
Alignment explanation
Indices: 14715--14758 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
14705 TTTGTTCACG
14715 GAATGTAAAATTACCAATGA
1 GAATGTAAAATTACCAATGA
*
14735 GAATGTAAGATTACCAATGA
1 GAATGTAAAATTACCAATGA
14755 GAAT
1 GAAT
14759 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (20 bp):
GAATGTAAAATTACCAATGA
Found at i:14767 original size:20 final size:20
Alignment explanation
Indices: 14721--14767 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14711 CACGGAATGT
**
14721 AAAATTACCAATGAGAATGT
1 AAAATTACCAATGAGAATAA
*
14741 AAGATTACCAATGAGAATAA
1 AAAATTACCAATGAGAATAA
14761 AAAATTA
1 AAAATTA
14768 TTAGGGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAATTACCAATGAGAATAA
Found at i:15019 original size:33 final size:34
Alignment explanation
Indices: 14956--15019 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
14946 TTAATTTATA
**
14956 TATATTTTTTTAAAAAATTTAAATTCATAAAATT
1 TATATTTTTTTAAAAAATTTAAAAACATAAAATT
* *
14990 TATATTTTTTTACAAAA-TTAAAAAGATAAA
1 TATATTTTTTTAAAAAATTTAAAAACATAAA
15020 TAGGTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 10 0.38
34 16 0.62
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (34 bp):
TATATTTTTTTAAAAAATTTAAAAACATAAAATT
Found at i:15988 original size:15 final size:16
Alignment explanation
Indices: 15968--15997 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15958 CAAAATACAA
15968 TATTCCC-AGTAATCC
1 TATTCCCTAGTAATCC
15983 TATTCCCTAGTAATC
1 TATTCCCTAGTAATC
15998 TTACATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (16 bp):
TATTCCCTAGTAATCC
Found at i:17713 original size:27 final size:27
Alignment explanation
Indices: 17683--17740 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
17673 GTTGTACAAT
* *
17683 TAAATGTAAAATTAAAGTTTAATGTTA
1 TAAATGTAAAACTAAAATTTAATGTTA
*
17710 TAAATGTATAACTAAAATTTAATGTTA
1 TAAATGTAAAACTAAAATTTAATGTTA
17737 TAAA
1 TAAA
17741 CGAGTCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.40
Consensus pattern (27 bp):
TAAATGTAAAACTAAAATTTAATGTTA
Found at i:21584 original size:74 final size:74
Alignment explanation
Indices: 21353--21631 Score: 293
Period size: 74 Copynumber: 3.7 Consensus size: 74
21343 AACAAATCAA
* * * *
21353 AGCTTAAATTAAGGAAACAAGT-AGTGAAACAAATACTATAAT-AATTCTATATATATTATTAAT
1 AGCTTAAATTAAGGAAACATGTGAG-GAAACAAATATTATAATGATTTC-ATATAT-TTA--AAA
**
21416 AGTTAAACACCAAAC-AT
61 AACT-AA-ACC--ACTAT
* * * *
21433 AGCTTAAATT-AGGGAA-A-GTGAAGAAACAAATATTATAATAATTTTATATA-TTAAAAAACTA
1 AGCTTAAATTAAGGAAACATGTGAGGAAACAAATATTATAATGATTTCATATATTTAAAAAACTA
21494 AACCACTAT
66 AACCACTAT
* * * *
21503 AGCTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAATGACTCCATATATTTAAAAAACTA
1 AGCTTAAATTAAGGAAACATGTGAGGAAACAAATATTATAATGATTTCATATATTTAAAAAACTA
21568 AACCACTAT
66 AACCACTAT
*
21577 AGCTTAAATTAAGGAAACATGTGAGAAAACAAATATTATAATGATTTCATATATT
1 AGCTTAAATTAAGGAAACATGTGAGGAAACAAATATTATAATGATTTCATATATT
21632 ATATATTTTT
Statistics
Matches: 171, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
69 2 0.01
70 12 0.07
71 8 0.05
72 3 0.02
73 30 0.18
74 70 0.41
75 3 0.02
77 23 0.13
78 5 0.03
79 5 0.03
80 10 0.06
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.29
Consensus pattern (74 bp):
AGCTTAAATTAAGGAAACATGTGAGGAAACAAATATTATAATGATTTCATATATTTAAAAAACTA
AACCACTAT
Found at i:22859 original size:49 final size:48
Alignment explanation
Indices: 22753--22876 Score: 169
Period size: 49 Copynumber: 2.6 Consensus size: 48
22743 TTTATCTCCA
* * * *
22753 CTTACTCTGAAGGGAATATCACATCTTGGGAAAGAGAGGCCTGTTTCG
1 CTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAGAGACATGTTCCG
22801 CTTACTCTGAAGGGAATATCAGATCTT-GGAAAGAGAGATACATGTTCCG
1 CTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAGAG--ACATGTTCCG
* *
22850 TTTACTCTGAAGAGAATATCAGATCTT
1 CTTACTCTGAAGGGAATATCAGATCTT
22877 ACAGGAGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 10 0.15
48 26 0.38
49 32 0.47
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (48 bp):
CTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAGAGACATGTTCCG
Found at i:25853 original size:70 final size:73
Alignment explanation
Indices: 25772--25935 Score: 190
Period size: 75 Copynumber: 2.3 Consensus size: 73
25762 AATATCAAAC
* * * * * *
25772 ATAGCATAAATTAGGGAAAT-TAGAGAAACAAATATTATAATAATTCTATATA-TT-AAAAAACT
1 ATAGCTTAAATTAAGGAAATGTAGAGAAACAAATAATATAACAACTCCATATATTTAAAAAAACT
*
25834 AAATCACT
66 AAACCACT
* * * *
25842 ATAGCTTAAATTAAAGAAACATGTGGGGAAACAAATAATATAACGACTCCATATATTTAAAAAAA
1 ATAGCTTAAATT-AAGGAA-ATGTAGAGAAACAAATAATATAACAACTCCATATATTTAAAAAAA
25907 CTAAACCACT
64 CTAAACCACT
25917 ATAGCTTAAATTAAGGAAA
1 ATAGCTTAAATTAAGGAAA
25936 CATGTGGAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
70 11 0.14
71 4 0.05
72 2 0.03
73 26 0.34
74 7 0.09
75 27 0.35
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (73 bp):
ATAGCTTAAATTAAGGAAATGTAGAGAAACAAATAATATAACAACTCCATATATTTAAAAAAACT
AAACCACT
Found at i:25884 original size:73 final size:73
Alignment explanation
Indices: 25794--25974 Score: 238
Period size: 75 Copynumber: 2.5 Consensus size: 73
25784 AGGGAAATTA
* *
25794 GAGAAACAAATATTATAATAATTCTATATATTAAAAAACTAAATCACTATAGCTTAAATTAAAGA
1 GAGAAACAAATATTATAATGATTCTATATATTAAAAAACTAAACCACTATAGCTTAAATTAAAGA
25859 AACATGTG
66 AACATGTG
* * * * * *
25867 GGGAAACAAATAATATAACGACTCCATATATTTAAAAAAACTAAACCACTATAGCTTAAATTAAG
1 GAGAAACAAATATTATAATGATTCTATATA-TT-AAAAAACTAAACCACTATAGCTTAAATTAAA
25932 GAAACATGTG
64 GAAACATGTG
* *
25942 GAAAAACATATATTATAATGATT-TCATATATTA
1 GAGAAACAAATATTATAATGATTCT-ATATATTA
25975 TATATATTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
73 25 0.28
74 4 0.04
75 61 0.68
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.29
Consensus pattern (73 bp):
GAGAAACAAATATTATAATGATTCTATATATTAAAAAACTAAACCACTATAGCTTAAATTAAAGA
AACATGTG
Found at i:28021 original size:72 final size:72
Alignment explanation
Indices: 27929--28086 Score: 205
Period size: 72 Copynumber: 2.2 Consensus size: 72
27919 CAGACAATAT
* * *
27929 TCGGACAAGGAAGCCGAAGACACACCACAAACTGA-AAACGAAACCTGATATTCGGTCCACAACA
1 TCGGACAAGGAAACCAAAGACACACCACAAACTGATAAACGAAACCCGATATTCGGTCCA-AACA
27993 AAC-AACGG
65 AACTAA-GG
* * * *
28001 TCGGACAAGGAAACCAAAGACACACCACAAACTGATAAATGAAACCCGATTTTCGGTTCAAACAG
1 TCGGACAAGGAAACCAAAGACACACCACAAACTGATAAACGAAACCCGATATTCGGTCCAAACAA
28066 ACTAAGG
66 ACTAAGG
*
28073 TC-GACATGGAAACC
1 TCGGACAAGGAAACC
28087 GATGAGTTGC
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 11 0.14
72 43 0.57
73 22 0.29
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (72 bp):
TCGGACAAGGAAACCAAAGACACACCACAAACTGATAAACGAAACCCGATATTCGGTCCAAACAA
ACTAAGG
Found at i:43254 original size:35 final size:34
Alignment explanation
Indices: 43208--43319 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
43198 AAAACAATCC
*
43208 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
43243 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * *
43278 TCAATTACATTCTAAAACCTAAATTCTAAAATATT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
43313 TCAATTT
1 TCAATTT
43320 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.91
36 5 0.07
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:44424 original size:35 final size:34
Alignment explanation
Indices: 44376--44487 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
44366 AAAAAGACAT
* *
44376 AAATTGAAGTATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
44411 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
44446 AAATTGAATTACTTTGGAATTTGTGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTG-GGTTTAGAATG
44481 AAATTGA
1 AAATTGA
44488 GGATTGTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 66 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:46395 original size:3 final size:3
Alignment explanation
Indices: 46387--46413 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
46377 CTGATTGTAG
46387 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
46414 TACTCTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:50476 original size:22 final size:22
Alignment explanation
Indices: 50448--50524 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
50438 TCTCTCACTC
* *
50448 TCTCCGGCGATATTCGTCCACA
1 TCTCCGGCGACATTCGTCCCCA
* *
50470 TCTCCGGCGACATCCATCCCCA
1 TCTCCGGCGACATTCGTCCCCA
50492 TCTCCGGCGACATTCGTCCCCA
1 TCTCCGGCGACATTCGTCCCCA
*
50514 TATCCGGCGAC
1 TCTCCGGCGAC
50525 CTCCCTCCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.17, C:0.43, G:0.18, T:0.22
Consensus pattern (22 bp):
TCTCCGGCGACATTCGTCCCCA
Found at i:56086 original size:15 final size:16
Alignment explanation
Indices: 56066--56099 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56056 ACACATATAC
56066 ATTTATCA-TGAACAT
1 ATTTATCAGTGAACAT
*
56081 ATTTATCAGTGATCAT
1 ATTTATCAGTGAACAT
56097 ATT
1 ATT
56100 ATTATCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTTATCAGTGAACAT
Found at i:58561 original size:44 final size:44
Alignment explanation
Indices: 58512--58615 Score: 156
Period size: 44 Copynumber: 2.3 Consensus size: 44
58502 TGGTATATGG
*
58512 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
*
58556 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
58600 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
58616 TAAAATATTG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
44 46 0.84
45 2 0.04
46 7 0.13
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (44 bp):
TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:59430 original size:42 final size:42
Alignment explanation
Indices: 59363--59486 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 42
59353 CCCCACTTTT
* * *
59363 TCATTGAATCGATTCTTCAGTTCGACACCGAGATCCATCACC
1 TCATTGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
* *
59405 TCATCT-AGTCGATTCTCCACTTCGACACTGAGATCCATCACC
1 TCAT-TGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
* * *
59447 TGATTGAGTCGATTATACACCTCGACACCGAGATCCATCA
1 TCATTGAGTCGATTCTACACTTCGACACCGAGATCCATCA
59487 TATCATCGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.97
43 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (42 bp):
TCATTGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
Found at i:59699 original size:21 final size:21
Alignment explanation
Indices: 59658--59720 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
59648 TGATGCATGG
* *
59658 CGTGATGAGGTAG-GGTCTTTA
1 CGTGGTGAGGTAGTTGT-TTTA
59679 CGTGGTGAGGTAGTTGTTTTA
1 CGTGGTGAGGTAGTTGTTTTA
*
59700 CATGGTGAGGTAGTTGTTTTA
1 CGTGGTGAGGTAGTTGTTTTA
59721 TGTGACGAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.17, C:0.06, G:0.37, T:0.40
Consensus pattern (21 bp):
CGTGGTGAGGTAGTTGTTTTA
Found at i:59730 original size:21 final size:21
Alignment explanation
Indices: 59685--59731 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
59675 TTTACGTGGT
**
59685 GAGGTAGTTGTTTTACATGGT
1 GAGGTAGTTGTTTTACATGAC
**
59706 GAGGTAGTTGTTTTATGTGAC
1 GAGGTAGTTGTTTTACATGAC
59727 GAGGT
1 GAGGT
59732 CGGTGCTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.04, G:0.36, T:0.40
Consensus pattern (21 bp):
GAGGTAGTTGTTTTACATGAC
Found at i:60061 original size:21 final size:21
Alignment explanation
Indices: 60031--60078 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
60021 AAGCCTGATC
*
60031 CACCTACCATTATTCAGGATT
1 CACCTCCCATTATTCAGGATT
*
60052 CACCTCCCATTGTTCAGGATT
1 CACCTCCCATTATTCAGGATT
60073 CACCTC
1 CACCTC
60079 TTATCGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.31
Consensus pattern (21 bp):
CACCTCCCATTATTCAGGATT
Found at i:60087 original size:21 final size:21
Alignment explanation
Indices: 60043--60155 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
60033 CCTACCATTA
*
60043 TTCAGGATTCACCTCCCATTG
1 TTCAGGATTCACCTCCCATCG
**
60064 TTCAGGATTCACCTCTTATCG
1 TTCAGGATTCACCTCCCATCG
* ** *
60085 TTCAAGAGAC-CCATCCCATTG
1 TTCAGGATTCACC-TCCCATCG
* ** *
60106 TTCAAGAGCCTCCTCCCATCG
1 TTCAGGATTCACCTCCCATCG
* * *
60127 TTCAAGAATCCCCTCCCATCG
1 TTCAGGATTCACCTCCCATCG
60148 TTCAGGAT
1 TTCAGGAT
60156 CCACATTCAA
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 2 0.03
21 70 0.95
22 2 0.03
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (21 bp):
TTCAGGATTCACCTCCCATCG
Found at i:60103 original size:42 final size:42
Alignment explanation
Indices: 60056--60159 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
60046 AGGATTCACC
* **
60056 TCCCATTGTTCAGGATTCACCTCTTATCGTTCAAGAGA-CCCA
1 TCCCATTGTTCAGGATCCACCTCCCATCGTTCAAGA-ATCCCA
* * * *
60098 TCCCATTGTTCAAGAGCCTCCTCCCATCGTTCAAGAATCCCC
1 TCCCATTGTTCAGGATCCACCTCCCATCGTTCAAGAATCCCA
*
60140 TCCCATCGTTCAGGATCCAC
1 TCCCATTGTTCAGGATCCAC
60160 ATTCAATACT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.22, C:0.37, G:0.13, T:0.28
Consensus pattern (42 bp):
TCCCATTGTTCAGGATCCACCTCCCATCGTTCAAGAATCCCA
Found at i:62459 original size:24 final size:24
Alignment explanation
Indices: 62408--62459 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
62398 ATCTGAGTAT
** *
62408 TGACCAAGATCAAATTTCGGGTAT
1 TGACCAAGATCAAATTTCGAATAC
*
62432 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAATTTCGAATAC
62456 TGAC
1 TGAC
62460 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
TGACCAAGATCAAATTTCGAATAC
Found at i:63388 original size:20 final size:20
Alignment explanation
Indices: 63363--63457 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
63353 AACAATTCGT
63363 GTTGCGAAAAAGAAAATCGA
1 GTTGCGAAAAAGAAAATCGA
* *
63383 GTTGCGAAAAATG-AATTCGT
1 GTTGCGAAAAA-GAAAATCGA
**
63403 GTTGCGAATTCA-AAAATCGA
1 GTTGCGAA-AAAGAAAATCGA
* *
63423 GTTGCGAAATTA-AAAATCGT
1 GTTGCGAAA-AAGAAAATCGA
*
63443 GTTGTGAAAAAGAAA
1 GTTGCGAAAAAGAAA
63458 TATGTGTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 56 0.95
21 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.24
Consensus pattern (20 bp):
GTTGCGAAAAAGAAAATCGA
Found at i:63400 original size:40 final size:39
Alignment explanation
Indices: 63356--63457 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 39
63346 ATACCCAAAC
63356 AATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAA-AA
1 AATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAATAA
**
63394 TGAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAATTAA
1 --AATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAAA-TAA
* *
63436 AAATCGTGTTGTGAAAAAGAAA
1 AATTCGTGTTGCGAAAAAGAAA
63458 TATGTGTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
39 1 0.02
40 48 0.92
41 1 0.02
42 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (39 bp):
AATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAATAA
Found at i:63429 original size:60 final size:62
Alignment explanation
Indices: 63363--63492 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 62
63353 AACAATTCGT
*
63363 GTTGCGAAA-AAGAAAATCGAGTTGCGAAAAATG-AAT-TCGTGTTGCG-AA-T-TCAAAAATCG
1 GTTGCGAAATAA-AAAATCGAGTTGCGAAAAA-GAAATAT-GTGTTACGAAATTGTC-AAAATCG
63422 A
62 A
* * *
63423 GTTGCGAAATTAAAAATCGTGTTGTGAAAAAGAAATATGTGTTACGAAATTGTCAAAATCGA
1 GTTGCGAAATAAAAAATCGAGTTGCGAAAAAGAAATATGTGTTACGAAATTGTCAAAATCGA
63485 GTTGCGAA
1 GTTGCGAA
63493 TTTGACTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
59 1 0.02
60 36 0.60
61 4 0.07
62 17 0.28
63 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (62 bp):
GTTGCGAAATAAAAAATCGAGTTGCGAAAAAGAAATATGTGTTACGAAATTGTCAAAATCGA
Found at i:63510 original size:20 final size:20
Alignment explanation
Indices: 63485--63534 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
63475 TCAAAATCGA
*
63485 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
63505 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
63525 CTTGCGAATT
1 GTTGCGAATT
63535 CCAAATTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:69439 original size:16 final size:16
Alignment explanation
Indices: 69414--69454 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
69404 TCAAGAACTT
69414 GAAAAGAAATCAAAAG
1 GAAAAGAAATCAAAAG
*
69430 GAAAATAAATCAAAAG
1 GAAAAGAAATCAAAAG
69446 GAAAAGAAA
1 GAAAAGAAA
69455 CTTCGAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (16 bp):
GAAAAGAAATCAAAAG
Done.