Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007390.1 Hibiscus syriacus cultivar Beakdansim tig00019904_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: 75715
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5093 original size:25 final size:24
Alignment explanation
Indices: 5065--5112 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
5055 AATAAGACAA
5065 TATATATAATATTAAAACAATATAG
1 TATATATAATATTAAAA-AATATAG
*
5090 TATATATGATATTAAAAAATATA
1 TATATATAATATTAAAAAATATA
5113 TGTTACATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
TATATATAATATTAAAAAATATAG
Found at i:12908 original size:32 final size:32
Alignment explanation
Indices: 12866--12952 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
12856 TGGATCTTCC
12866 CTTAGTTTCTCTCAAACAATAAGGATCTTTAA
1 CTTAGTTTCTCTCAAACAATAAGGATCTTTAA
* *
12898 CTTTGTTTCTCTCAAACACTAAGGATCTTTAA
1 CTTAGTTTCTCTCAAACAATAAGGATCTTTAA
*
12930 CTTAGTTTCTCTCAAATAATAAG
1 CTTAGTTTCTCTCAAACAATAAG
12953 TAATAAACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (32 bp):
CTTAGTTTCTCTCAAACAATAAGGATCTTTAA
Found at i:15615 original size:24 final size:24
Alignment explanation
Indices: 15583--15628 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15573 TACCAGAAAT
15583 GCCACGACAAATTCCTTTGCACTC
1 GCCACGACAAATTCCTTTGCACTC
* *
15607 GCCACGACAAGTTTCTTTGCAC
1 GCCACGACAAATTCCTTTGCAC
15629 ACCTTTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (24 bp):
GCCACGACAAATTCCTTTGCACTC
Found at i:15953 original size:20 final size:22
Alignment explanation
Indices: 15930--15983 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
15920 ACTCGACCCC
15930 GAGTATC-A-GTACTGATTAAT
1 GAGTATCTATGTACTGATTAAT
15950 GAGTATCTATTGGTACTGATTAAT
1 GAGTATCTA-T-GTACTGATTAAT
15974 GAGTATCTAT
1 GAGTATCTAT
15984 TAGGACTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
23 1 0.03
24 21 0.70
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
GAGTATCTATGTACTGATTAAT
Found at i:15991 original size:24 final size:24
Alignment explanation
Indices: 15938--15984 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
15928 CCGAGTATCA
15938 GTACTGATTAATGAGTATCTATTG
1 GTACTGATTAATGAGTATCTATTG
15962 GTACTGATTAATGAGTATCTATT
1 GTACTGATTAATGAGTATCTATT
15985 AGGACTGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (24 bp):
GTACTGATTAATGAGTATCTATTG
Found at i:16436 original size:90 final size:89
Alignment explanation
Indices: 16280--16442 Score: 272
Period size: 90 Copynumber: 1.8 Consensus size: 89
16270 AACACACCCT
*
16280 TTTATAGCCAAGGTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTT
1 TTTATAGCCAAGGTACCCTAATCATATTAGGGTTTAATTATTTCAAATTAATTAAATATATATTT
*
16345 AATTAATTGGAATTTAATAATCAA
66 AATCAATTGGAATTTAATAATCAA
* * *
16369 TTTATATCCAAGTTACCCTAATCATATTAGGGATTTAATTATTTCAAATTAATTAAATCTATATT
1 TTTATAGCCAAGGTACCCTAATCATATTAGGG-TTTAATTATTTCAAATTAATTAAATATATATT
16434 TAATCAATT
65 TAATCAATT
16443 AAAATTAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 30 0.44
90 38 0.56
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (89 bp):
TTTATAGCCAAGGTACCCTAATCATATTAGGGTTTAATTATTTCAAATTAATTAAATATATATTT
AATCAATTGGAATTTAATAATCAA
Found at i:16483 original size:20 final size:20
Alignment explanation
Indices: 16415--16483 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 20
16405 AATTATTTCA
16415 AATTAATTAAATC-TATATTT
1 AATT-ATTAAATCATATATTT
* * * *
16435 AATCAATTAAAATTAAATATTC
1 AAT-TATT-AAATCATATATTT
16457 AGGATTATTAAATCATATATTT
1 A--ATTATTAAATCATATATTT
16479 AATTA
1 AATTA
16484 ACTCTAGATA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 10 0.28
21 4 0.11
22 17 0.47
23 3 0.08
24 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (20 bp):
AATTATTAAATCATATATTT
Found at i:32941 original size:2 final size:2
Alignment explanation
Indices: 32934--32965 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32924 TTTAAGGCCA
32934 AT AT AT AT AT AT 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 AT
32966 CAAATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32980 original size:10 final size:10
Alignment explanation
Indices: 32964--32994 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
32954 ATATATATAT
32964 ATCAAATTAA
1 ATCAAATTAA
*
32974 ATTAAATTAA
1 ATCAAATTAA
32984 ATCAAATTAA
1 ATCAAATTAA
32994 A
1 A
32995 AAAAGCATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (10 bp):
ATCAAATTAA
Found at i:34309 original size:20 final size:20
Alignment explanation
Indices: 34284--34329 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
34274 GCAAATTTGT
* *
34284 AATTCGTAACACATAAGTCA
1 AATTCGCAACACAAAAGTCA
34304 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
34324 AATTCG
1 AATTCG
34330 AAAAGCGCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:34505 original size:22 final size:22
Alignment explanation
Indices: 34480--34530 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
34470 TCACTCTCTT
*
34480 CGGCGACATCCGTCCCCATTTC
1 CGGCGACATCCGTCCCCATATC
34502 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
34524 CGGCGAC
1 CGGCGAC
34531 CCCCCTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:34945 original size:20 final size:20
Alignment explanation
Indices: 34874--34948 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
34864 CGAAATAAAA
*
34874 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTCATTT
* *
34894 TCGCGTTGTGAATTTTATTT
1 TCGCGTTGCGAATTTCATTT
*
34914 TTGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
*
34934 TCGTGTTGCGAATTT
1 TCGCGTTGCGAATTT
34949 AAGTTTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCATTT
Found at i:34955 original size:20 final size:20
Alignment explanation
Indices: 34918--34955 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34908 TTATTTTTGC
* *
34918 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTAAGTTTCGT
34938 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
34956 AAAAACTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCGT
Found at i:36501 original size:42 final size:42
Alignment explanation
Indices: 36442--36582 Score: 201
Period size: 42 Copynumber: 3.4 Consensus size: 42
36432 CCCCCCACTT
*
36442 CGAGAGCCATCACCTGATTGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
* *
36484 CGAGAGTCATCACCTGATCGAGCCGATTCTACAGCTTGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
* * * * * *
36526 TGAGAGTCATCACCTGATCGAGTCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
36568 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
36583 ATTCCATCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.21
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
Found at i:36846 original size:21 final size:21
Alignment explanation
Indices: 36832--36880 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
36822 CTTTACGTGG
36832 TGAGGTATCTACTTTACATAA
1 TGAGGTATCTACTTTACATAA
*
36853 TGAGGTATCTACTTTACATTA
1 TGAGGTATCTACTTTACATAA
36874 TGAGGTA
1 TGAGGTA
36881 GCCGCTCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
TGAGGTATCTACTTTACATAA
Found at i:37200 original size:21 final size:21
Alignment explanation
Indices: 37172--37269 Score: 162
Period size: 21 Copynumber: 4.7 Consensus size: 21
37162 GATTCACCTG
37172 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
37193 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
37214 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
37235 TCATCGTTCAAGAGCCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
37256 CCATCGTTCAAGAG
1 TCATCGTTCAAGAG
37270 CCCAATTCAC
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:38456 original size:31 final size:31
Alignment explanation
Indices: 38420--38483 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
38410 GCAAGTGTTG
38420 TTAACATATATACTTGTTGGTTTGAAAATGT
1 TTAACATATATACTTGTTGGTTTGAAAATGT
38451 TTAACATATATACTTGTTGGTTTGAAAATGT
1 TTAACATATATACTTGTTGGTTTGAAAATGT
38482 TT
1 TT
38484 GGTTAAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (31 bp):
TTAACATATATACTTGTTGGTTTGAAAATGT
Found at i:38821 original size:20 final size:20
Alignment explanation
Indices: 38793--38853 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
38783 GTCAAATTCA
* *
38793 CGTTGCGAATTTGATTTTCG
1 CGTTACGAATTTGACTTTCG
*
38813 CGTTACGAATTTTACTTTCG
1 CGTTACGAATTTGACTTTCG
**
38833 CGTTTTGAATTTGACTTTCG
1 CGTTACGAATTTGACTTTCG
38853 C
1 C
38854 AACAATCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (20 bp):
CGTTACGAATTTGACTTTCG
Found at i:42080 original size:22 final size:22
Alignment explanation
Indices: 42036--42097 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
42026 ATTGAATATT
42036 TGTCCCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGTATA
42054 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
42076 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
42098 ACCCTCGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.40
22 24 0.60
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:43103 original size:28 final size:28
Alignment explanation
Indices: 43059--43117 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
43049 GCCATATAAG
*
43059 CTTTCCTTTAGCTTATATAACATCCAAA
1 CTTTCCTTTAGCATATATAACATCCAAA
43087 CTTTCCTTTAGCATATATAACATCCAAA
1 CTTTCCTTTAGCATATATAACATCCAAA
43115 CTT
1 CTT
43118 CCATTTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (28 bp):
CTTTCCTTTAGCATATATAACATCCAAA
Found at i:48065 original size:22 final size:22
Alignment explanation
Indices: 48040--48084 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48030 GATTACAAAT
*
48040 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTACTAC
48062 AGGGAACCGATTCCCCTACTAC
1 AGGGAACCGATTCCCCTACTAC
48084 A
1 A
48085 ATACTGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.18
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTACTAC
Found at i:48687 original size:22 final size:21
Alignment explanation
Indices: 48662--48723 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 21
48652 ATTGAATATT
48662 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACT-TATA
*
48684 TGTCCCAAAGGACCAC---TA
1 TGTCCCGAAGGACCACTTATA
48702 TGTCCCGAAGGACCACTATATA
1 TGTCCCGAAGGACCACT-TATA
48724 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 17 0.50
22 17 0.50
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTTATA
Found at i:53303 original size:84 final size:85
Alignment explanation
Indices: 53203--53369 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 85
53193 AAATACAATC
* * ** * * *
53203 ATGACACACGAATGTGTGTCATCTT-TTTTAATGGCGTGTGCTTCAATGACACGCAATTAA-GTC
1 ATGACACACAAATGTGTGTCATCTTAATTT-ATAACGAGGGCTTCAATGACACGCAATGAATGTC
* *
53266 ATACATGTGTGTCATAAATTT
65 ATAAATGTGCGTCATAAATTT
* *
53287 ATGACACACAAATGTGTGTCATCTTAATTTATAACGAGGGCTTCAATGACGCTCAATGAATGTCA
1 ATGACACACAAATGTGTGTCATCTTAATTTATAACGAGGGCTTCAATGACACGCAATGAATGTCA
53352 TAAATGTGCGTCATAAAT
66 TAAATGTGCGTCATAAAT
53370 GTGTGTCATA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
84 47 0.67
85 23 0.33
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTAATTTATAACGAGGGCTTCAATGACACGCAATGAATGTCA
TAAATGTGCGTCATAAATTT
Found at i:53364 original size:13 final size:13
Alignment explanation
Indices: 53348--53395 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
53338 CTCAATGAAT
53348 GTCATAAATGTGC
1 GTCATAAATGTGC
*
53361 GTCATAAATGTGT
1 GTCATAAATGTGC
*
53374 GTCATAAATGCGC
1 GTCATAAATGTGC
53387 GTCATAAAT
1 GTCATAAAT
53396 TTATGACGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
GTCATAAATGTGC
Found at i:53370 original size:26 final size:26
Alignment explanation
Indices: 53341--53395 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
53331 AATGACGCTC
*
53341 AATGAATGTCATAAATGTGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
**
53367 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
53393 AAT
1 AAT
53396 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (26 bp):
AATGAATGTCATAAATGCGCGTCATA
Found at i:54855 original size:24 final size:24
Alignment explanation
Indices: 54817--54870 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
54807 CTCAAACATC
*
54817 ATCAAAATCCAAGTATTGACCAAT
1 ATCAAAATCCAAGTATTGACCAAG
* *
54841 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
54865 ATCAAA
1 ATCAAA
54871 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:54884 original size:24 final size:24
Alignment explanation
Indices: 54833--54884 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
54823 ATCCAAGTAT
* * *
54833 TGACCAATATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
54857 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
54881 TGAC
1 TGAC
54885 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:55017 original size:12 final size:12
Alignment explanation
Indices: 54996--55029 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54986 GGTTGTGAGT
*
54996 TTTGAGATTGTG
1 TTTGATATTGTG
55008 TTTGATATTGTG
1 TTTGATATTGTG
*
55020 TTTGGTATTG
1 TTTGATATTG
55030 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:55695 original size:20 final size:20
Alignment explanation
Indices: 55672--55713 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55662 TGTGATTGTA
* *
55672 GAAACTGAGTTGTGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
55692 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
55712 GA
1 GA
55714 GTTTGCATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:62247 original size:23 final size:22
Alignment explanation
Indices: 62216--62260 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
62206 AGTTCTTTGT
*
62216 ATTTATGATATGTTTATCTCTGC
1 ATTTATGATACGTTT-TCTCTGC
* *
62239 ATTTGTGATGCGTTTTCTCTGC
1 ATTTATGATACGTTTTCTCTGC
62261 CTTTTGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (22 bp):
ATTTATGATACGTTTTCTCTGC
Found at i:69344 original size:33 final size:33
Alignment explanation
Indices: 69307--69371 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
69297 TTATGAAATA
*
69307 TAAAGCATATATTGTAATATATA-GT-ATAATGTT
1 TAAAGCATAGA-T-TAATATATATGTAATAATGTT
*
69340 TAAAGTATAGATTAATATATATGTAATAATGT
1 TAAAGCATAGATTAATATATATGTAATAATGT
69372 AGCTTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 9 0.32
32 3 0.11
33 16 0.57
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.42
Consensus pattern (33 bp):
TAAAGCATAGATTAATATATATGTAATAATGTT
Found at i:74114 original size:21 final size:21
Alignment explanation
Indices: 74090--74135 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
74080 TTTCAAAGAC
*
74090 ACTTACCAAGGTACTTCATCT
1 ACTTACCAAGGTAATTCATCT
74111 ACTTACCAAGGTAATTCATCT
1 ACTTACCAAGGTAATTCATCT
74132 ACTT
1 ACTT
74136 CCACTTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (21 bp):
ACTTACCAAGGTAATTCATCT
Done.