Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003918.1 Hibiscus syriacus cultivar Beakdansim tig00008470_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: 76217
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2594 original size:22 final size:22
Alignment explanation
Indices: 2567--2640 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
2557 ATTAATATTT
2567 TAATATTTTAAAATATTATATA
1 TAATATTTTAAAATATTATATA
* * *
2589 TAATA-TTTATAATTATTATTTT
1 TAATATTTTA-AAATATTATATA
*
2611 TAA-ATTATTAAAATAATATATA
1 TAATATT-TTAAAATATTATATA
2633 T-ATATTTT
1 TAATATTTT
2641 TATATTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 8 0.20
22 30 0.73
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTTTAAAATATTATATA
Found at i:2610 original size:35 final size:35
Alignment explanation
Indices: 2561--2643 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
2551 CGATATATTA
* * * *
2561 ATATTTTAATATTTTAAAATATTATATATAATATTT
1 ATATATTATTATTTTAAAATATTA-AAATAATATAT
*
2597 ATA-ATTATTATTTTTAAATTATTAAAATAATATAT
1 ATATATTATTA-TTTTAAAATATTAAAATAATATAT
*
2632 ATATATTTTTAT
1 ATATATTATTAT
2644 ATTTTTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 18 0.46
36 21 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
ATATATTATTATTTTAAAATATTAAAATAATATAT
Found at i:4919 original size:89 final size:89
Alignment explanation
Indices: 4766--4944 Score: 286
Period size: 89 Copynumber: 2.0 Consensus size: 89
4756 ATAACCCACA
* * *
4766 AGGTTGCCATTGAACGTAATTGAATAATGAGGCGTAGTTAAGCAAATTCTGATCCACTCTCAGAA
1 AGGTTGCCATTGAACGTAATTGAATAATGAGGCGTAGTAAAGCAAATTCTAATCCACTCCCAGAA
* *
4831 TACCACTAGTAATCTCATAGCTTC
66 CACCACTAGTAATCTCACAGCTTC
*
4855 AGGTTTCCATTGAACGTAATTGAATAATGAGGCGTAGTAAAGCAAATTCTAATCCACTCCCAGAA
1 AGGTTGCCATTGAACGTAATTGAATAATGAGGCGTAGTAAAGCAAATTCTAATCCACTCCCAGAA
* *
4920 CACCACTGGTAATTTCACAGCTTC
66 CACCACTAGTAATCTCACAGCTTC
4944 A
1 A
4945 AGGACAGTCT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (89 bp):
AGGTTGCCATTGAACGTAATTGAATAATGAGGCGTAGTAAAGCAAATTCTAATCCACTCCCAGAA
CACCACTAGTAATCTCACAGCTTC
Found at i:6067 original size:19 final size:20
Alignment explanation
Indices: 6039--6090 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6029 TGCAAAAATG
*
6039 GTATCAATACCATA-TAAGA
1 GTATCGATACCATAGTAAGA
** *
6058 GTATCGATACCATAGTGGGG
1 GTATCGATACCATAGTAAGA
6078 GTATCGATACCAT
1 GTATCGATACCAT
6091 TGAGCTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:6478 original size:54 final size:54
Alignment explanation
Indices: 6412--6687 Score: 389
Period size: 54 Copynumber: 5.1 Consensus size: 54
6402 TTACCAAATA
*
6412 GGCACTATGTGTGCAAATCACGTAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
6466 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATTTATTGATGAATAACCATTTC
1 GGCACTATGTGTGCAAA-TCACGAAATTCATCATATGTTGATGAATAACCGTTTC
6520 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
6574 GGCACTATGCGTGTAAATCAC-AGAATTCATCATATGTTGAT-AGTAACCATTTC
1 GGCACTATGTGTGCAAATCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
* * *
6627 GGCACTAAGTGTGCAAAGT-ACGTAATTCATCATATGTTGATGAATAACCGTTTT
1 GGCACTATGTGTGCAAA-TCACGAAATTCATCATATGTTGATGAATAACCGTTTC
6681 GGCACTA
1 GGCACTA
6688 CGAGTGCATT
Statistics
Matches: 196, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
53 46 0.23
54 149 0.76
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:13596 original size:17 final size:18
Alignment explanation
Indices: 13571--13610 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
13561 CCGCCTGAAA
*
13571 ATTTAAAATTATT-ATAT
1 ATTTTAAATTATTAATAT
*
13588 ATTTTAAATTTTTAATAT
1 ATTTTAAATTATTAATAT
13606 ATTTT
1 ATTTT
13611 TTATTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAAATTATTAATAT
Found at i:14182 original size:27 final size:28
Alignment explanation
Indices: 14132--14186 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
14122 ACAACGTTGC
*
14132 TTTCAAGCATTGGCTCGACGACATAATA
1 TTTCAAGCATTGGCTCAACGACATAATA
* *
14160 TTTCAAGTATT-GCTCAAGGACATAATA
1 TTTCAAGCATTGGCTCAACGACATAATA
14187 GAAACGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (28 bp):
TTTCAAGCATTGGCTCAACGACATAATA
Found at i:16059 original size:14 final size:14
Alignment explanation
Indices: 16040--16071 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16030 CATAATCCCT
*
16040 CTAAATTCTAAACC
1 CTAAATCCTAAACC
16054 CTAAATCCTAAACC
1 CTAAATCCTAAACC
16068 CTAA
1 CTAA
16072 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAATCCTAAACC
Found at i:16306 original size:23 final size:23
Alignment explanation
Indices: 16280--16324 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16270 TCCGAGGCTT
*
16280 AGCTCGATTGAAGCTCAAACTCG
1 AGCTCGATTCAAGCTCAAACTCG
* *
16303 AGCTCGGTTCAAGCTCGAACTC
1 AGCTCGATTCAAGCTCAAACTC
16325 AAATTCGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCAAACTCG
Found at i:20830 original size:4 final size:4
Alignment explanation
Indices: 20821--20854 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
20811 TGTGCACATA
20821 TATG TATG TATG TATG TATG TTAATG TATG TATG
1 TATG TATG TATG TATG TATG -T-ATG TATG TATG
20855 GTGATGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 23 0.82
5 2 0.07
6 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:22431 original size:30 final size:32
Alignment explanation
Indices: 22396--22457 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
22386 GTTTTGAAGC
22396 TATATAAT-T-TTATTGGAGTATCTGTAATTA
1 TATATAATATCTTATTGGAGTATCTGTAATTA
22426 TATATAATATCTTATTGGAGTATCTGTAATTA
1 TATATAATATCTTATTGGAGTATCTGTAATTA
22458 GGGTATTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 8 0.27
31 1 0.03
32 21 0.70
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (32 bp):
TATATAATATCTTATTGGAGTATCTGTAATTA
Found at i:27401 original size:20 final size:21
Alignment explanation
Indices: 27376--27426 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
27366 CCCTCTATAT
27376 ATTATTTTTTCAAT-AAAATA
1 ATTATTTTTTCAATAAAAATA
*
27396 ATTATTTTTATTGAATAAAAATA
1 ATTA-TTTT-TTCAATAAAAATA
27419 A-TATTTTT
1 ATTATTTTT
27427 ATTATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 7 0.26
23 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTATTTTTTCAATAAAAATA
Found at i:27401 original size:23 final size:23
Alignment explanation
Indices: 27376--27429 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
27366 CCCTCTATAT
27376 ATTA-TTTT-TTCAAT-AAAATA
1 ATTATTTTTATTCAATAAAAATA
*
27396 ATTATTTTTATTGAATAAAAATA
1 ATTATTTTTATTCAATAAAAATA
27419 A-TATTTTTATT
1 ATTATTTTTATT
27430 ATTATTTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 15 0.50
23 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTTTTATTCAATAAAAATA
Found at i:27639 original size:3 final size:3
Alignment explanation
Indices: 27631--27663 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
27621 AGTTTTTTCC
27631 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27664 TAGTAGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38994 original size:10 final size:10
Alignment explanation
Indices: 38971--39005 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
38961 AGATTCAATC
38971 AAGAACAAAA
1 AAGAACAAAA
38981 AAGAA-AAAA
1 AAGAACAAAA
38990 CAAGAACAAAA
1 -AAGAACAAAA
39001 AAGAA
1 AAGAA
39006 AAGAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (10 bp):
AAGAACAAAA
Found at i:38995 original size:20 final size:20
Alignment explanation
Indices: 38970--39007 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38960 AAGATTCAAT
38970 CAAGAACAAAAAAGAAAAAA
1 CAAGAACAAAAAAGAAAAAA
38990 CAAGAACAAAAAAGAAAA
1 CAAGAACAAAAAAGAAAA
39008 GAAGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
CAAGAACAAAAAAGAAAAAA
Found at i:39023 original size:22 final size:20
Alignment explanation
Indices: 38974--39023 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
38964 TTCAATCAAG
*
38974 AACAAAAAAGAAAAAACAAG
1 AACAAAAAAGAAAAAACAAA
38994 AACAAAAAAGAAAAGAAGCAAA
1 AACAAAAAAGAAAA-AA-CAAA
39016 AATCAAAA
1 AA-CAAAA
39024 GGAAAATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 5 0.19
23 5 0.19
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (20 bp):
AACAAAAAAGAAAAAACAAA
Found at i:40112 original size:18 final size:18
Alignment explanation
Indices: 40078--40113 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40068 TCAACATCAA
* *
40078 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
40096 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
40114 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:40656 original size:36 final size:37
Alignment explanation
Indices: 40600--40675 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
40590 GTGCTCACCA
*
40600 TTGTCTCTCTTAAGACAGTTTCCCTT-GAAACAAA-CT
1 TTGTCTCTCTTAAGACAGTTTCACTTGGAAA-AAACCT
* *
40636 TTGTCTCTCTTGAGATAGTTTCACTTGGAAAAAACCT
1 TTGTCTCTCTTAAGACAGTTTCACTTGGAAAAAACCT
40673 TTG
1 TTG
40676 AAATTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTAAGACAGTTTCACTTGGAAAAAACCT
Found at i:41777 original size:84 final size:84
Alignment explanation
Indices: 41636--41796 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 84
41626 AGCGAAGGAT
41636 ATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTCTCAACAAACAAT
1 ATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTCTCAACAAACAAT
*
41701 TTCCCATTTTCAAAAGGGC
66 TTCCCAATTTCAAAAGGGC
** * * *
41720 ATTGGACTTGAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTCTCAACAAACAAT
41785 TTCCCAATTTCA
66 TTCCCAATTTCA
41797 TAACCAATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
ATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTCTCAACAAACAAT
TTCCCAATTTCAAAAGGGC
Found at i:41867 original size:190 final size:190
Alignment explanation
Indices: 41539--41896 Score: 626
Period size: 190 Copynumber: 1.9 Consensus size: 190
41529 CGCGCCACCC
* *
41539 GAGACAACACAAGTTCAACTTCACAACGAATGGACGACTGGTTGTCAACAAATAACTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATT
*
41604 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
66 TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
41669 AACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
131 AACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
* * * *
41729 GAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATT
* *
41794 TCATAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC
66 TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
*
41859 AACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCA
131 AACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCA
41897 GTTCCAGAAC
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
190 158 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (190 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATT
TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
AACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
Found at i:41908 original size:106 final size:106
Alignment explanation
Indices: 41720--41941 Score: 363
Period size: 106 Copynumber: 2.1 Consensus size: 106
41710 TCAAAAGGGC
* * *
41720 ATTGGACTTGAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* *
41785 TTCCCAATTTCATAACCAATTTCAACTTCACAGCGAAGGAT
66 TTCCCAATTCCAGAACCAATTTCAACTTCACAGCGAAGGAT
41826 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* * * *
41891 TTCCCAGTTCCAGAACCAATTTCAACTTCACGGTGGAGGAT
66 TTCCCAATTCCAGAACCAATTTCAACTTCACAGCGAAGGAT
41932 ATTGGACTCG
1 ATTGGACTCG
41942 GAACAATACA
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (106 bp):
ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
TTCCCAATTCCAGAACCAATTTCAACTTCACAGCGAAGGAT
Found at i:43395 original size:16 final size:16
Alignment explanation
Indices: 43376--43424 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
43366 TATTATTTAC
* *
43376 TTATTTTATTTATATG
1 TTATATTATATATATG
*
43392 TTATATTATATATATA
1 TTATATTATATATATG
43408 TATATATATATATATAT
1 T-TATAT-TATATATAT
43425 ATATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 5 0.18
18 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATATTATATATATG
Found at i:43405 original size:2 final size:2
Alignment explanation
Indices: 43393--43432 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
43383 ATTTATATGT
43393 TA TA T- TA TA 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 TA TA TA TA TA T
43433 TTACGTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:51247 original size:21 final size:22
Alignment explanation
Indices: 51206--51259 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
51196 GATTTAAAAT
* *
51206 ATAAA-TAATTAAATATCGATA
1 ATAAATTAATTTAATATAGATA
51227 ATAAATTAATTTAATA-AGATA
1 ATAAATTAATTTAATATAGATA
* *
51248 AGACATTAATTT
1 ATAAATTAATTT
51260 TTTAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAAATTAATTTAATATAGATA
Found at i:51629 original size:21 final size:22
Alignment explanation
Indices: 51603--51643 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
51593 AAAAAATTAT
*
51603 CTAAAACATTAGT-TTTTTTAC
1 CTAAAACATTAATGTTTTTTAC
51624 CTAAAACATTAATGTTTTTT
1 CTAAAACATTAATGTTTTTT
51644 CAACATTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
CTAAAACATTAATGTTTTTTAC
Found at i:62048 original size:17 final size:19
Alignment explanation
Indices: 62007--62049 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
61997 GCTGAGAGAG
62007 GAGTATCAATACTCTAATTA
1 GAGTATCAATACTCTAA-TA
*
62027 GAGTATCGATACTC-AA-A
1 GAGTATCAATACTCTAATA
62044 GAGTAT
1 GAGTAT
62050 TGGCACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
GAGTATCAATACTCTAATA
Found at i:62750 original size:24 final size:22
Alignment explanation
Indices: 62710--62767 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
62700 GCACCGAAAT
*
62710 ATCCATAAAACATAAATAT-TAA
1 ATCCA-AAGACATAAATATCTAA
62732 TCATCCAAAGACATAAAATATCTAA
1 --ATCCAAAGACAT-AAATATCTAA
62757 ATCCAAAGACA
1 ATCCAAAGACA
62768 ACCAAATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 17 0.55
24 11 0.35
25 3 0.10
ACGTcount: A:0.55, C:0.19, G:0.03, T:0.22
Consensus pattern (22 bp):
ATCCAAAGACATAAATATCTAA
Found at i:64289 original size:2 final size:2
Alignment explanation
Indices: 64284--64407 Score: 64
Period size: 2 Copynumber: 65.0 Consensus size: 2
64274 GTGTGTGTGC
*
64284 AT AT AT AT AT AT AT AT AT A- AT AT -T GT AT AT GA- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* * * * *
64323 AG A- AT GT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AA AG GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
64362 AT GT AA AT AA AA AC AT AC AT AT AT AT AT AT AT AT AT GT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64404 AT AT
1 AT AT
64408 GTATGTATAA
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
1 7 0.07
2 86 0.91
3 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (2 bp):
AT
Found at i:64412 original size:14 final size:14
Alignment explanation
Indices: 64380--64418 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
64370 AAAAACATAC
* *
64380 ATATATATATATAT
1 ATATGTATAAATAT
64394 ATATGTATAAATAT
1 ATATGTATAAATAT
*
64408 GTATGTATAAA
1 ATATGTATAAA
64419 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (14 bp):
ATATGTATAAATAT
Found at i:64874 original size:20 final size:20
Alignment explanation
Indices: 64804--64872 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
64794 AATGCCACAA
64804 GAACAATATCGGTATTATAT
1 GAACAATATCGGTATTATAT
64824 GAACAATATCGGTATTATAT
1 GAACAATATCGGTATTATAT
** * *
64844 GAATGATATTGGTATTGTAT
1 GAACAATATCGGTATTATAT
64864 GAACAATAT
1 GAACAATAT
64873 TGATACCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (20 bp):
GAACAATATCGGTATTATAT
Found at i:70485 original size:26 final size:26
Alignment explanation
Indices: 70455--70508 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
70445 CTTTAAAATC
70455 TTCTTCATTTGTTGAACTTCATGAAT
1 TTCTTCATTTGTTGAACTTCATGAAT
* *
70481 TTCTTCCTTTGTTGGACTTCATGAAT
1 TTCTTCATTTGTTGAACTTCATGAAT
70507 TT
1 TT
70509 TCTAAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.52
Consensus pattern (26 bp):
TTCTTCATTTGTTGAACTTCATGAAT
Done.