Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003643.1 Hibiscus syriacus cultivar Beakdansim tig00007736_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: 56573
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1718 original size:23 final size:25
Alignment explanation
Indices: 1687--1744 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
1677 AAAATTGTTG
*
1687 ATTTAAAA-TGTTGTGACTTGTTTC
1 ATTTAAAATTGTTCTGACTTGTTTC
*
1711 ATTTAAATATTGTTCTGACTTGTTTG
1 ATTTAAA-ATTGTTCTGACTTGTTTC
1737 ATTTAAAA
1 ATTTAAAA
1745 AAAAATTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 7 0.23
25 2 0.07
26 21 0.70
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (25 bp):
ATTTAAAATTGTTCTGACTTGTTTC
Found at i:2108 original size:18 final size:19
Alignment explanation
Indices: 2074--2109 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2064 ACATTATTCA
2074 TTTTCAAATTGTGTTTATG
1 TTTTCAAATTGTGTTTATG
*
2093 TTTTCAATTTGT-TTTAT
1 TTTTCAAATTGTGTTTAT
2110 AATTTGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (19 bp):
TTTTCAAATTGTGTTTATG
Found at i:4519 original size:144 final size:143
Alignment explanation
Indices: 4256--4535 Score: 322
Period size: 143 Copynumber: 1.9 Consensus size: 143
4246 TTGAGTAGAC
* * *
4256 AAGAATAAAGGTAACGTGTAAAATTAAAATTAAAAAGAATATAAATCTTCTTTTGAGTATTAAAA
1 AAGAATAAAGGTAACATGCAAAATTAAAATTAAAAAGAAAATAAATCTTCTTTTGAGTATTAAAA
* *
4321 ATATTTTTAATCAGAAAATGATAAAGATTAAGGGTCAGTTTGACATGTATTGAAAAAGTGACTAG
66 ATATTTTTAATCA-AAAAGGATAAAGATTAAGGGTCAATTTGACATGTATTG-AAAAGTGACTAG
4386 TAAAAGTAAGCAGAT
129 TAAAAGTAAGCAGAT
*
4401 AAGAAT-AAGGTAACATGCAAAATT-AAATTAAAAA-ATAAATAACTC-T-TTTTG-GTATTAAA
1 AAGAATAAAGGTAACATGCAAAATTAAAATTAAAAAGA-AAATAAATCTTCTTTTGAGTATTAAA
* ** *
4460 AATATTCTTTTTTTAATC-AAAGGGATAAAGATTAAGGGTCAATTTGGTATGTTTTTGAAAAGTG
65 AATA-----TTTTTAATCAAAAAGGATAAAGATTAAGGGTCAATTTGACATG-TATTGAAAAGTG
**
4524 ACTTTTAAAAGT
124 ACTAGTAAAAGT
4536 GTTATAGAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
140 12 0.10
141 5 0.04
142 2 0.02
143 62 0.53
144 20 0.17
145 15 0.13
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (143 bp):
AAGAATAAAGGTAACATGCAAAATTAAAATTAAAAAGAAAATAAATCTTCTTTTGAGTATTAAAA
ATATTTTTAATCAAAAAGGATAAAGATTAAGGGTCAATTTGACATGTATTGAAAAGTGACTAGTA
AAAGTAAGCAGAT
Found at i:4672 original size:25 final size:24
Alignment explanation
Indices: 4625--4672 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
4615 TAATACTATG
** *
4625 ATATATAAAATATATCAACTTAAA
1 ATATATAAAATATAAAAAATTAAA
4649 ATATAATAAAATATAAAAAATTAA
1 ATAT-ATAAAATATAAAAAATTAA
4673 GATAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATATAAAATATAAAAAATTAAA
Found at i:14719 original size:24 final size:24
Alignment explanation
Indices: 14679--14724 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
14669 TTGGTGTAAT
14679 TTAGAGGCTAACCAGTTGGTACAA
1 TTAGAGGCTAACCAGTTGGTACAA
*
14703 TTAGAGG-TCAACTAGTTGGTAC
1 TTAGAGGCT-AACCAGTTGGTAC
14725 CATTGTCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (24 bp):
TTAGAGGCTAACCAGTTGGTACAA
Found at i:21301 original size:27 final size:27
Alignment explanation
Indices: 21263--21334 Score: 144
Period size: 27 Copynumber: 2.7 Consensus size: 27
21253 AAAACTTTAC
21263 ATAAATTAAAATTAAGGACAATTTTTT
1 ATAAATTAAAATTAAGGACAATTTTTT
21290 ATAAATTAAAATTAAGGACAATTTTTT
1 ATAAATTAAAATTAAGGACAATTTTTT
21317 ATAAATTAAAATTAAGGA
1 ATAAATTAAAATTAAGGA
21335 TAAAACCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (27 bp):
ATAAATTAAAATTAAGGACAATTTTTT
Found at i:24929 original size:12 final size:12
Alignment explanation
Indices: 24908--24953 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
24898 TATAGTATAT
*
24908 TTTGTGACGTTA
1 TTTGTAACGTTA
24920 TTTGTAACGTTA
1 TTTGTAACGTTA
24932 TTTGTAACGTTA
1 TTTGTAACGTTA
24944 TTTGTAACGT
1 TTTGTAACGT
24954 CGTATAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.50
Consensus pattern (12 bp):
TTTGTAACGTTA
Found at i:27211 original size:16 final size:16
Alignment explanation
Indices: 27190--27220 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27180 ATGCTCCATC
27190 AGCGTTAAGCTTCATT
1 AGCGTTAAGCTTCATT
27206 AGCGTTAAGCTTCAT
1 AGCGTTAAGCTTCAT
27221 CCAACCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (16 bp):
AGCGTTAAGCTTCATT
Found at i:33868 original size:2 final size:2
Alignment explanation
Indices: 33861--33898 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
33851 GTTTCAACGT
33861 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
33899 AAATTAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34334 original size:60 final size:60
Alignment explanation
Indices: 34237--34397 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
34227 ATAATAAGAT
* * * *
34237 ATTGTTTTATTGAGTCA-TCGAATATTAAAAGTTATAAAATGGTCTCCTGATAATAGAAA
1 ATTGATTTGTTGAGTCATTCGACTATTAAAAGTTATAAAATGGTCTCCTGACAATAGAAA
* *
34296 GTTGATTTGTTGAGTCATTCGACTATTAAAAGTTATAAAATGGTCTCCTGACAATATAAA
1 ATTGATTTGTTGAGTCATTCGACTATTAAAAGTTATAAAATGGTCTCCTGACAATAGAAA
*
34356 ATTGATTTGTTGAGTCATTCGACTATTAAAAGTTACAAAATG
1 ATTGATTTGTTGAGTCATTCGACTATTAAAAGTTATAAAATG
34398 ATCATCCGAC
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 14 0.15
60 79 0.85
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (60 bp):
ATTGATTTGTTGAGTCATTCGACTATTAAAAGTTATAAAATGGTCTCCTGACAATAGAAA
Found at i:36068 original size:21 final size:19
Alignment explanation
Indices: 36034--36162 Score: 107
Period size: 21 Copynumber: 6.3 Consensus size: 19
36024 TTGCATTTAT
*
36034 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
36053 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
36076 TCCAAGTTCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGA--TAG
*
36097 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
36116 TCCAAGTTCGCATTGCGATTTAT
1 TCCAAGTTCG--TTGCGA--TAG
36139 TCC-AGATTCGTTGCGATAG
1 TCCAAG-TTCGTTGCGATAG
36158 TCCAA
1 TCCAA
36163 AATCGCAACG
Statistics
Matches: 93, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
19 23 0.25
20 1 0.01
21 48 0.52
22 2 0.02
23 19 0.20
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:36109 original size:42 final size:42
Alignment explanation
Indices: 36024--36155 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 42
36014 ATTTACATAT
* * *
36024 TTGC-ATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCGCG
1 TTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATT--CG
36065 TTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCG
* *
36107 TTGCGA--TAGTCCAAGTTCGCATTGCGATTTATTCCAGATTCG
1 TTGCGATTTATTCCAAGTTCG--TTGCGATTTATTCCAAATTCG
36149 TTGCGAT
1 TTGCGAT
36156 AGTCCAAAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
40 12 0.15
41 4 0.05
42 55 0.69
44 9 0.11
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (42 bp):
TTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCG
Found at i:36132 original size:63 final size:63
Alignment explanation
Indices: 36024--36155 Score: 232
Period size: 63 Copynumber: 2.1 Consensus size: 63
36014 ATTTACATAT
*
36024 TTGC-ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCA-AGTTCG
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAGA-TTCG
36086 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAGATTCG
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAGATTCG
36149 TTGCGAT
1 TTGCGAT
36156 AGTCCAAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
62 4 0.06
63 62 0.93
64 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (63 bp):
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAGATTCG
Found at i:36169 original size:42 final size:42
Alignment explanation
Indices: 36086--36169 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
36076 TCCAAGTTCG
**
36086 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCA
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
*
36128 TTGCGATTTATTCCAGATTCGTTGCGATAGTCCAAAATCGCA
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
36170 ACGACAGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (42 bp):
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAATCGCA
Found at i:36259 original size:6 final size:6
Alignment explanation
Indices: 36248--36292 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
36238 GACACGTATT
36248 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
36293 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:36969 original size:21 final size:21
Alignment explanation
Indices: 36917--37081 Score: 169
Period size: 21 Copynumber: 7.9 Consensus size: 21
36907 CGTTGCGATT
*
36917 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
36936 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
36959 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
* *
36979 TATGTA-AATCGCAATGCGATA-
1 T-TGGACTATCGCAATGCGA-AC
* *
37000 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
37021 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
37042 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
37063 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
37082 TAGTCCAAGT
Statistics
Matches: 124, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.05
20 16 0.13
21 92 0.74
23 10 0.08
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:37095 original size:21 final size:21
Alignment explanation
Indices: 37071--37123 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
37061 ACTTCGACTA
37071 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
37092 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
37113 TCGCGTTGCGA
1 TCGCATTGCGA
37124 ATCTGGAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:38373 original size:18 final size:18
Alignment explanation
Indices: 38339--38373 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38329 AAAATTGTTT
*
38339 TAAAATAAAAGATAAGAA
1 TAAAATAAAAGAAAAGAA
*
38357 TAAAATAAAATAAAAGA
1 TAAAATAAAAGAAAAGA
38374 GAATGATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (18 bp):
TAAAATAAAAGAAAAGAA
Found at i:38382 original size:23 final size:23
Alignment explanation
Indices: 38339--38389 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
38329 AAAATTGTTT
*
38339 TAAAATAAAAGATAAGAATAAAA
1 TAAAATAAAAGAGAAGAATAAAA
38362 TAAAATAAAAGAGAATG-ATAAAA
1 TAAAATAAAAGAGAA-GAATAAAA
*
38385 AAAAA
1 TAAAA
38390 ATTTAAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.16
Consensus pattern (23 bp):
TAAAATAAAAGAGAAGAATAAAA
Found at i:39009 original size:25 final size:25
Alignment explanation
Indices: 38976--39024 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
38966 TTTAAAAATA
*
38976 AAAATAAAACAAAGAAAAAATTTTG
1 AAAAGAAAACAAAGAAAAAATTTTG
** *
39001 AAAAGAAAAGGAAGAAAAACTTTT
1 AAAAGAAAACAAAGAAAAAATTTT
39025 ATAAAACCAG
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:0.65, C:0.04, G:0.12, T:0.18
Consensus pattern (25 bp):
AAAAGAAAACAAAGAAAAAATTTTG
Found at i:46336 original size:81 final size:81
Alignment explanation
Indices: 46232--47283 Score: 1494
Period size: 81 Copynumber: 13.0 Consensus size: 81
46222 TTTTTCATCC
* * * **
46232 CAAAGGTATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCGAATGCACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
46297 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * * * *
46313 TAAAGGTATTTAACCTTTCATCTAACTAGCATGACTAACACCTTTCTGTCAAATGCTCAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
46378 CATTTAATATTTTACT
66 CATTTAATCTTTTACT
* * * *
46394 CAAATGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTTTCAAATGCACAGCTGGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
* *
46459 CATTTAATCGTTTACC
66 CATTTAATCTTTTACT
* * * *
46475 CAAAGGTATATTTAACCTTTCATCTAACTGACATGATAGACACATTTCTATCAAATGCACAACTA
1 CAAAGG--TATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTA
46540 GGCATTTAATCTTTTACT
64 GGCATTTAATCTTTTACT
* * *
46558 CAAATGTATTTAACCTTTCATTTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
46623 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * *
46639 CAAATGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATTCTCAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
46704 CATTTAATTTTTTACT
66 CATTTAATCTTTTACT
* * * *
46720 CAAAGGTATTTAACCTTTCATTTAACTGGCGTGATTGACACCTTTTTGTCAAATGAACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
46785 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
46801 CAAAGGTATTTAACCTTTCATCTAACTGGAATGATTGACACATTTCTGTCAAATGCACATCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
46866 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * ** ** * **
46882 CAAAGGTATTTAACCTTACGTCTAGCTAACATGATTGACATATTTCTGTCAAATACACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
46947 CATTTAATATTTTACT
66 CATTTAATCTTTTACT
* * *
46963 CAAAGGTTTTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGTCAAATGCATAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
47028 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *** *
47044 CAAAGGTATTTAACCTTTCATCTAACTGGCATTATTGATGGCTTTCTGTCAAATGAACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
47109 C-TTTAATGTTTTACT
66 CATTTAATCTTTTACT
* *
47124 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACATCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
47189 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * * * *
47205 CTAACGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAAAGCACAACTATG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
47270 CATTTAATCTTTTA
66 CATTTAATCTTTTA
47284 ATTTAAAGCA
Statistics
Matches: 862, Mismatches: 106, Indels: 6
0.89 0.11 0.01
Matches are distributed among these distances:
80 72 0.08
81 718 0.83
83 72 0.08
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
CATTTAATCTTTTACT
Found at i:47230 original size:21 final size:22
Alignment explanation
Indices: 47190--47230 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47180 ACATCTAGGC
* *
47190 ATTTAATCTTTTACTCTAACGT
1 ATTTAACCTTTCACTCTAACGT
47212 ATTTAACCTTTCA-TCTAAC
1 ATTTAACCTTTCACTCTAAC
47231 TGGCATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTAACCTTTCACTCTAACGT
Done.