Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007269.1 Hibiscus syriacus cultivar Beakdansim tig00019272_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: 110681
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7113 original size:27 final size:27
Alignment explanation
Indices: 7093--7285 Score: 316
Period size: 27 Copynumber: 7.1 Consensus size: 27
7083 GCCACCACCA
* *
7093 AACAACATGGGAAGAATGCCACCCAAC
1 AACAACATGGGAGGGATGCCACCCAAC
*
7120 AACAACATGGGAAGGATGCCACCCAAC
1 AACAACATGGGAGGGATGCCACCCAAC
7147 AACAACATGGGAGGGATGCCACCCAAC
1 AACAACATGGGAGGGATGCCACCCAAC
7174 AACAACATGGGAGGGATGCCACCCAAC
1 AACAACATGGGAGGGATGCCACCCAAC
7201 AACAACATGGGAGGGATGCCACCCAAC
1 AACAACATGGGAGGGATGCCACCCAAC
* *
7228 AACAACATGGGAAGGATGCCA-CCACC
1 AACAACATGGGAGGGATGCCACCCAAC
*
7254 AAACAACATGGGAGGGATGCCACCAAAC
1 -AACAACATGGGAGGGATGCCACCCAAC
7282 AACA
1 AACA
7286 TGGGGAATAT
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
26 4 0.03
27 150 0.96
28 3 0.02
ACGTcount: A:0.40, C:0.29, G:0.23, T:0.07
Consensus pattern (27 bp):
AACAACATGGGAGGGATGCCACCCAAC
Found at i:9476 original size:50 final size:50
Alignment explanation
Indices: 9405--9501 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
9395 TGTATGTATG
9405 TACATGCATACATAGTTTGCTTAGACTTTGCCTCCATTTAAACAGTTACA
1 TACATGCATACATAGTTTGCTTAGACTTTGCCTCCATTTAAACAGTTACA
*
9455 TACATGCATACATAGTTTGCTTAGACTTTGCCTCTATTTAAACAGTT
1 TACATGCATACATAGTTTGCTTAGACTTTGCCTCCATTTAAACAGTT
9502 CTCTGGTGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (50 bp):
TACATGCATACATAGTTTGCTTAGACTTTGCCTCCATTTAAACAGTTACA
Found at i:12470 original size:39 final size:39
Alignment explanation
Indices: 12416--12490 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
12406 ATGAATCGAC
*
12416 GAATACTCCATCCCTGATGCTGAATAAGGACCGGTATCT
1 GAATACTCCATCCCTGAGGCTGAATAAGGACCGGTATCT
*
12455 GAATATTCCATCCCTGAGGCTGAATAAGGACCGGTA
1 GAATACTCCATCCCTGAGGCTGAATAAGGACCGGTA
12491 GATACTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (39 bp):
GAATACTCCATCCCTGAGGCTGAATAAGGACCGGTATCT
Found at i:19452 original size:301 final size:301
Alignment explanation
Indices: 18910--19512 Score: 1179
Period size: 301 Copynumber: 2.0 Consensus size: 301
18900 GAATACAGAC
18910 ACCAAAGACGGTTGAAGTACATGGCAGAAAGTTCAGGTCGGCAATGAATTGGTACAAGCAAGAGC
1 ACCAAAGACGGTTGAAGTACATGGCAGAAAGTTCAGGTCGGCAATGAATTGGTACAAGCAAGAGC
18975 ACCTTTACAAGTTCAACACCACCGGAAAAAGGCCACTGGTATTATACAAGTAAACTGTTAAGTAC
66 ACCTTTACAAGTTCAACACCACCGGAAAAAGGCCACTGGTATTATACAAGTAAACTGTTAAGTAC
19040 ACCAACACTCAACAAATTGCAGCACAAGATCAAGAAGCAACCGACAAATCACTGGTATACTTAAC
131 ACCAACACTCAACAAATTGCAGCACAAGATCAAGAAGCAACCGACAAATCACTGGTATACTTAAC
19105 AAAATACTTGTTCTCACATCATTAGGATCATCATTGAAACAAGAACCCACTCAGAAAGTCCATGA
196 AAAATACTTGTTCTCACATCATTAGGATCATCATTGAAACAAGAACCCACTCAGAAAGTCCATGA
19170 TATTGGGGCATTCTACAAAATTTTCACATTGAACAAACCAG
261 TATTGGGGCATTCTACAAAATTTTCACATTGAACAAACCAG
*
19211 ACCAAAGACGGTTGAAGTACATGGCAGAAAGTTCAGGTCGGCAATGCATTGGTACAAGCAAGAGC
1 ACCAAAGACGGTTGAAGTACATGGCAGAAAGTTCAGGTCGGCAATGAATTGGTACAAGCAAGAGC
19276 ACCTTTACAAGTTCAACACCACCGGAAAAAGGCCACTGGTATTATACAAGTAAACTGTTAAGTAC
66 ACCTTTACAAGTTCAACACCACCGGAAAAAGGCCACTGGTATTATACAAGTAAACTGTTAAGTAC
*
19341 ACCAACACTCAACAGATTGCAGCACAAGATCAAGAAGCAACCGACAAATCACTGGTATACTTAAC
131 ACCAACACTCAACAAATTGCAGCACAAGATCAAGAAGCAACCGACAAATCACTGGTATACTTAAC
*
19406 GAAATACTTGTTCTCACATCATTAGGATCATCATTGAAACAAGAACCCACTCAGAAAGTCCATGA
196 AAAATACTTGTTCTCACATCATTAGGATCATCATTGAAACAAGAACCCACTCAGAAAGTCCATGA
19471 TATTGGGGCATTCTACAAAATTTTCACATTGAACAAACCAG
261 TATTGGGGCATTCTACAAAATTTTCACATTGAACAAACCAG
19512 A
1 A
19513 GAAACCTTGG
Statistics
Matches: 299, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 299 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (301 bp):
ACCAAAGACGGTTGAAGTACATGGCAGAAAGTTCAGGTCGGCAATGAATTGGTACAAGCAAGAGC
ACCTTTACAAGTTCAACACCACCGGAAAAAGGCCACTGGTATTATACAAGTAAACTGTTAAGTAC
ACCAACACTCAACAAATTGCAGCACAAGATCAAGAAGCAACCGACAAATCACTGGTATACTTAAC
AAAATACTTGTTCTCACATCATTAGGATCATCATTGAAACAAGAACCCACTCAGAAAGTCCATGA
TATTGGGGCATTCTACAAAATTTTCACATTGAACAAACCAG
Found at i:22194 original size:24 final size:24
Alignment explanation
Indices: 22162--22265 Score: 163
Period size: 24 Copynumber: 4.3 Consensus size: 24
22152 AGCACCCAAC
* * *
22162 CCACCATAGCCGGTTGAACCTGGT
1 CCACCATAGCCAGCTGGACCTGGT
* *
22186 CCACCATAGCCGGTTGGACCTGGT
1 CCACCATAGCCAGCTGGACCTGGT
22210 CCACCATAGCCAGCTGGACCTGGT
1 CCACCATAGCCAGCTGGACCTGGT
22234 CCACCATAGCCAGCTGGACCTGGT
1 CCACCATAGCCAGCTGGACCTGGT
22258 CCACCATA
1 CCACCATA
22266 CGGACCAACA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.18
Consensus pattern (24 bp):
CCACCATAGCCAGCTGGACCTGGT
Found at i:32301 original size:10 final size:10
Alignment explanation
Indices: 32286--32310 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32276 GTACTTAAGT
32286 GGGACGGGTA
1 GGGACGGGTA
32296 GGGACGGGTA
1 GGGACGGGTA
32306 GGGAC
1 GGGAC
32311 AGTCGCCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.60, T:0.08
Consensus pattern (10 bp):
GGGACGGGTA
Found at i:34832 original size:16 final size:16
Alignment explanation
Indices: 34813--34846 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34803 AATCAACATG
*
34813 AATCGAAAGTAAACTA
1 AATCGAAAATAAACTA
*
34829 AATCGAAAATAACCTA
1 AATCGAAAATAAACTA
34845 AA
1 AA
34847 CTGAAAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.18
Consensus pattern (16 bp):
AATCGAAAATAAACTA
Found at i:36704 original size:14 final size:14
Alignment explanation
Indices: 36685--36711 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36675 GTGTTTATCT
36685 TATTTTGATCATTA
1 TATTTTGATCATTA
36699 TATTTTGATCATT
1 TATTTTGATCATT
36712 TGCATTATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TATTTTGATCATTA
Found at i:40042 original size:24 final size:22
Alignment explanation
Indices: 39997--40041 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
39987 TAATATATTT
39997 TATATTTTTAATAATTAAATAA
1 TATATTTTTAATAATTAAATAA
40019 TATA-TTTTAATAATATAAA-AA
1 TATATTTTTAATAAT-TAAATAA
40040 TA
1 TA
40042 AAAATTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTTTTAATAATTAAATAA
Found at i:52070 original size:26 final size:26
Alignment explanation
Indices: 52040--52092 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52030 TTTAATTCGA
*
52040 TTAATTTCAATTATTGATATTTTATT
1 TTAATTTCAATTATTGAAATTTTATT
* * *
52066 TTAATTTTAATTTTTTAAATTTTATT
1 TTAATTTCAATTATTGAAATTTTATT
52092 T
1 T
52093 AATGACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTAATTTCAATTATTGAAATTTTATT
Found at i:55745 original size:23 final size:24
Alignment explanation
Indices: 55719--55764 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
55709 ATAATGATCT
55719 AAATATATGATC-TATCATAAATA
1 AAATATATGATCTTATCATAAATA
55742 AAATATATGATCTTATCATAAAT
1 AAATATATGATCTTATCATAAAT
55765 TATAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATGATCTTATCATAAATA
Found at i:56047 original size:18 final size:18
Alignment explanation
Indices: 56024--56063 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
56014 CTTAAATGTT
56024 TAAATAAAATTTCAAA-AA
1 TAAATAAAATTT-AAATAA
56042 TAAATAAAATTTAAATAA
1 TAAATAAAATTTAAATAA
56060 TAAA
1 TAAA
56064 GTTAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATAAAATTTAAATAA
Found at i:60483 original size:49 final size:49
Alignment explanation
Indices: 60426--60520 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
60416 TGAGGGGAAA
60426 TTCTAACATTTTACTCTCATGTATAAATATATTGAAGTTGTTCATTAAT
1 TTCTAACATTTTACTCTCATGTATAAATATATTGAAGTTGTTCATTAAT
60475 TTCTAACATTTTACTCTCATGTATAAATATATTGAAGTTGTTCATT
1 TTCTAACATTTTACTCTCATGTATAAATATATTGAAGTTGTTCATT
60521 TAAAAGAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (49 bp):
TTCTAACATTTTACTCTCATGTATAAATATATTGAAGTTGTTCATTAAT
Found at i:63357 original size:58 final size:58
Alignment explanation
Indices: 63265--63390 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
63255 ACCCAACCCG
*
63265 GTGATATTTTGGGAATTATTTTGAAAAAGATGACATTTTGGGAA-TTTTCTTAAAAACA
1 GTGATATTTTGAGAATTATTTTGAAAAAGATGACATTTTGGGAATTTTTCTTAAAAA-A
* * * * * *
63323 GTGATATTTTGATAATTATTTTTAAAATGTTGACATTTTGGGAATTTTTTTTAAAAAT
1 GTGATATTTTGAGAATTATTTTGAAAAAGATGACATTTTGGGAATTTTTCTTAAAAAA
63381 GTGATATTTT
1 GTGATATTTT
63391 TGAAATTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 49 0.82
59 11 0.18
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (58 bp):
GTGATATTTTGAGAATTATTTTGAAAAAGATGACATTTTGGGAATTTTTCTTAAAAAA
Found at i:63397 original size:29 final size:29
Alignment explanation
Indices: 63265--63399 Score: 123
Period size: 29 Copynumber: 4.7 Consensus size: 29
63255 ACCCAACCCG
* *
63265 GTGATATTTTGGGAATTATTTTGAAAAA-
1 GTGATATTTTGGGAATTTTTTTTAAAAAT
* * *
63293 GATGACATTTTGGGAA-TTTTCTTAAAAACA
1 G-TGATATTTTGGGAATTTTTTTTAAAAA-T
** *
63323 GTGATATTTTGATAATTATTTTT-AAAAT
1 GTGATATTTTGGGAATTTTTTTTAAAAAT
*
63351 GTTGACATTTTGGGAATTTTTTTTAAAAAT
1 G-TGATATTTTGGGAATTTTTTTTAAAAAT
* *
63381 GTGATATTTTTGAAATTTT
1 GTGATATTTTGGGAATTTT
63400 CGAATGTGGA
Statistics
Matches: 84, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
28 11 0.13
29 61 0.73
30 12 0.14
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.47
Consensus pattern (29 bp):
GTGATATTTTGGGAATTTTTTTTAAAAAT
Found at i:64466 original size:26 final size:26
Alignment explanation
Indices: 64413--64466 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
64403 AAGGTAACTC
* *
64413 TTTTATGGGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
64439 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
64465 TT
1 TT
64467 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:71762 original size:26 final size:26
Alignment explanation
Indices: 71709--71762 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
71699 AAGGTAACTC
* *
71709 TTTTATGGGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
71735 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
71761 TT
1 TT
71763 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:73881 original size:21 final size:21
Alignment explanation
Indices: 73808--73882 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
73798 CAGTTTCTAG
* *
73808 ATTCGCAACGCGATTTTGACT-
1 ATTCGCAATGCGATTTT-CCTA
* * *
73829 A-TCGCATTTCGATTTTCCAA
1 ATTCGCAATGCGATTTTCCTA
**
73849 ATTCGCGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTTCCTA
73870 ATTCGCAATGCGA
1 ATTCGCAATGCGA
73883 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
21 28 0.67
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCCTA
Found at i:73897 original size:20 final size:20
Alignment explanation
Indices: 73872--74044 Score: 260
Period size: 20 Copynumber: 8.7 Consensus size: 20
73862 TTTTCCTAAT
*
73872 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* **
73892 TCGCAATGTAAATACGTAAA
1 TCGCAACGCGAATACGTAAA
73912 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
73932 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
73952 TCGCAACGCGAATACATAAA
1 TCGCAACGCGAATACGTAAA
73972 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
73992 TCGCAACGCGAAT-C-TGACTA
1 TCGCAACGCGAATACGT-A-AA
74012 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
74032 TCGCAACGCGAAT
1 TCGCAACGCGAAT
74045 CTGACTATAG
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 134 0.96
21 2 0.01
22 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:74057 original size:20 final size:20
Alignment explanation
Indices: 73991--74097 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
73981 GAATACGTAA
73991 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
*
74011 ATCGCAACGCGAATAC-GTA-A
1 ATCGCAACGCGAAT-CTG-ACT
74031 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
* * *
74051 ATAGCAACGAGATTCTGACT
1 ATCGCAACGCGAATCTGACT
* * *
74071 GTCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATCTGACT
74091 ATCGCAA
1 ATCGCAA
74098 TACTGAATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.03
20 71 0.95
21 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:74068 original size:60 final size:60
Alignment explanation
Indices: 73902--74079 Score: 202
Period size: 60 Copynumber: 3.0 Consensus size: 60
73892 TCGCAATGTA
* * * *
73902 AATACGTAAATCGCAACGCGAATACGTAAATCGCAACGCGAATAC-GTA-AATCGCAACGCG
1 AATACATAAATCGCAACGCGAATACGTAAATAGCAACGAGAAT-CTG-ACTATCGCAACGCG
* *
73962 AATACATAAATCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCG
1 AATACATAAATCGCAACGCGAATACGTAAATAGCAACGAGAATCTGACTATCGCAACGCG
* * * *
74022 AATACGTAAATCGCAACGCGAAT-C-TGACTATAGCAACGAGATTCTGACTGTCGCAACG
1 AATACATAAATCGCAACGCGAATACGT-A-AATAGCAACGAGAATCTGACTATCGCAACG
74080 AGATTCTGAC
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 101 0.95
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (60 bp):
AATACATAAATCGCAACGCGAATACGTAAATAGCAACGAGAATCTGACTATCGCAACGCG
Found at i:74079 original size:40 final size:40
Alignment explanation
Indices: 73902--74062 Score: 204
Period size: 40 Copynumber: 4.0 Consensus size: 40
73892 TCGCAATGTA
* *
73902 AATACGTAAATCGCAACGCGAATAC-GTA-AATCGCAACGCG
1 AATACGTAAATCGCAACGCGAAT-CTG-ACTATCGCAACGAG
* *
73942 AATACGTAAATCGCAACGCGAATACAT-A-AATCGCAACGCG
1 AATACGTAAATCGCAACGCGAAT-C-TGACTATCGCAACGAG
*
73982 AATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCG
1 AATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAG
*
74022 AATACGTAAATCGCAACGCGAATCTGACTATAGCAACGAG
1 AATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAG
74062 A
1 A
74063 TTCTGACTGT
Statistics
Matches: 114, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 111 0.97
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (40 bp):
AATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAG
Found at i:74990 original size:24 final size:24
Alignment explanation
Indices: 74939--74992 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
74929 GTATTCGAAA
**
74939 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAAAC
* *
74963 TTTGATCTTGGTCAATACTCAAAT
1 TTTGATCTTGGTCAATACCCAAAC
74987 TTTGAT
1 TTTGAT
74993 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAAAC
Found at i:76438 original size:22 final size:22
Alignment explanation
Indices: 76376--76441 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
76366 TGACCGTGAA
* *
76376 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* * *
76398 TGATATCGTTGAAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
76420 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
76442 GGATGTCGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:76660 original size:20 final size:20
Alignment explanation
Indices: 76644--76729 Score: 136
Period size: 20 Copynumber: 4.3 Consensus size: 20
76634 CAGATTCGTG
*
76644 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
76664 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
**
76684 TTATGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
76704 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATTCGCA
76724 TTGCGA
1 TTGCGA
76730 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:76749 original size:21 final size:21
Alignment explanation
Indices: 76719--76771 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
76709 ATTTATGTAT
*
76719 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
76740 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
76761 TCGCAATGCGA
1 TCGCAATGCGA
76772 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:77545 original size:35 final size:37
Alignment explanation
Indices: 77474--77546 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
77464 GTTGAAAAAT
* *
77474 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
77511 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
77546 A
1 A
77547 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:80491 original size:208 final size:208
Alignment explanation
Indices: 80133--80537 Score: 684
Period size: 208 Copynumber: 1.9 Consensus size: 208
80123 CCCGTGTTCA
* * * *
80133 TAAGAGTACTGGTGTTTGTATTGTCTGTTATATGTGTAAACTGTTTATTACCAATCGGTAGGTTA
1 TAAGAGTACTGGTATTTGTATTGTCTGTCATAGGTGTAAACTGTTTATTACCAATCAGTAGGTTA
* *
80198 GATTTTTATGATACATTAAGGGAGAATTCTGTGCATTCTGCTTTTAGCTGTATTTCTTTTTTTAA
66 GATTTTTATGATACATTAAGGGAGAATTCTGTGCATTCTGCTTTTAGCTGTACTTCTTTCTTTAA
* * *
80263 TTATATGTTAATGTTTTACTTTTTAAGGAGGGATATCACTAATCTATATTTAAGAAACTTGTGTT
131 TTATATGTTAATGTTTTACTTTTTAAGGAGAGATACCACTAATCTATATTTAAGAAACTCGTGTT
80328 TAAAGGTAATGCG
196 TAAAGGTAATGCG
80341 TAAGAGTACTGGTATTTGTATTGTCTGTCATAGGTGTAAACTGTTTATTACCAATCAGTAGGTTA
1 TAAGAGTACTGGTATTTGTATTGTCTGTCATAGGTGTAAACTGTTTATTACCAATCAGTAGGTTA
* *
80406 GATTTTTATGATACATTAAGGGAGAATTCTGTGCATTCTGCTTTTAGCTTTGCTTCTTTCTTTAA
66 GATTTTTATGATACATTAAGGGAGAATTCTGTGCATTCTGCTTTTAGCTGTACTTCTTTCTTTAA
* * *
80471 TTATATGTTAATGTTTTACTTTTTAGGGAGAGATGCCACTAATCTATATTTGAGAAACTCGTGTT
131 TTATATGTTAATGTTTTACTTTTTAAGGAGAGATACCACTAATCTATATTTAAGAAACTCGTGTT
80536 TA
196 TA
80538 TGGAAAGTAC
Statistics
Matches: 183, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
208 183 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (208 bp):
TAAGAGTACTGGTATTTGTATTGTCTGTCATAGGTGTAAACTGTTTATTACCAATCAGTAGGTTA
GATTTTTATGATACATTAAGGGAGAATTCTGTGCATTCTGCTTTTAGCTGTACTTCTTTCTTTAA
TTATATGTTAATGTTTTACTTTTTAAGGAGAGATACCACTAATCTATATTTAAGAAACTCGTGTT
TAAAGGTAATGCG
Found at i:92510 original size:2 final size:2
Alignment explanation
Indices: 92505--92544 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
92495 AAAATAAAAT
92505 TA TA TA TA TA TA 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 TA TA TA TA TA TA
92545 CACAATTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:102880 original size:22 final size:22
Alignment explanation
Indices: 102855--102906 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
102845 TTTTCATTTT
* *
102855 TTTAATATTTTATAAATTTATC
1 TTTAATATTTCATAAATTTACC
*
102877 TTTAAAATTTCATAAATTTACC
1 TTTAATATTTCATAAATTTACC
102899 TTTAATAT
1 TTTAATAT
102907 AAAAGTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATATTTCATAAATTTACC
Found at i:104320 original size:36 final size:36
Alignment explanation
Indices: 104264--104350 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
104254 ATTAAAAATT
* *
104264 ATTATATATATATATATATAATATTAATAAATTTAA
1 ATTAAATATATATACATATAATATTAATAAATTTAA
* *
104300 ATTAAAT-TAATATACATATAATATTTATATATTTAA
1 ATTAAATAT-ATATACATATAATATTAATAAATTTAA
*
104336 TTTAAATATATATAC
1 ATTAAATATATATAC
104351 CCGACCCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.02
36 42 0.95
37 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTAAATATATATACATATAATATTAATAAATTTAA
Found at i:109136 original size:19 final size:20
Alignment explanation
Indices: 109104--109143 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
109094 AGAAGGTTGG
109104 TTTTTTAAATATATATATAA
1 TTTTTTAAATATATATATAA
*
109124 TTTTTTAAA-ATATATTTAA
1 TTTTTTAAATATATATATAA
109143 T
1 T
109144 ACATGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTTAAATATATATATAA
Done.