Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007119.1 Hibiscus syriacus cultivar Beakdansim tig00018604_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: 58467
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6390 original size:10 final size:10
Alignment explanation
Indices: 6375--6399 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6365 TGCACATCAT
6375 TTTAGTTGCA
1 TTTAGTTGCA
6385 TTTAGTTGCA
1 TTTAGTTGCA
6395 TTTAG
1 TTTAG
6400 GTTATATTGT
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:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:22771 original size:18 final size:17
Alignment explanation
Indices: 22750--22810 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
22740 TTTCCCTGAG
22750 GAAAAAAAGAAAAAAAA
1 GAAAAAAAGAAAAAAAA
*
22767 GGAAAAAGAGAAAAAGAGAA
1 -GAAAAAAAGAAAAA-A-AA
22787 -AAAAAAAGGAAAATAAAA
1 GAAAAAAA-GAAAA-AAAA
22805 GAAAAA
1 GAAAAA
22811 TAAAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 21 0.58
19 12 0.33
20 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
GAAAAAAAGAAAAAAAA
Found at i:24505 original size:135 final size:135
Alignment explanation
Indices: 24047--24553 Score: 635
Period size: 136 Copynumber: 3.7 Consensus size: 135
24037 AAGAGTGGTG
* *
24047 GAGTGAATCAAATTTTCTCGAGTCTTACCTCCCCTAAAGAGTAGCAGAACAGATTCTTCTTCTTC
1 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTC
** * *
24112 TTCATTCAGATTTGATCTTTATGAAGAGTAGTGAAACAAATCACATTCGATTCAATCTTCCCTGA
66 -T--TTCAGATTTGATCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGA
* *
24177 ATAGTAGT
128 AGAGCAGT
* * * *
24185 GGAGTGAATCAAATTTTTCTCGAGTTTGGCCTCCCCTAAAGAGTAGCGGAGCATA-T-TT-TTCT
1 -GAGTGAATCAAA-TTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCT
* * * * * *
24247 TTTTTCAAATTT-AGTATTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGT
64 TCTTTCAGATTTGA-TCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGA
*
24311 AGAGCAGCA
128 AGAGCAG-T
*
24320 GAGTGAATCAAACTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTC
1 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTC
* * *
24385 TTTCAGATTTGATCTTCCTGAAGAGTAGTGAAGCAAATCACATTTGATTTAATCTTCCCTGAAGA
66 TTTCAGATTTGATCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGA
*
24450 ACAGT
131 GCAGT
* * * *
24455 GAGTGAATCAAATTTTATTGAGTCTGACCTCCGCTAAAGAGTAGCAGAGCAAATTCTTCTTCTTC
1 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTC
** *
24520 TTTCAGATTCAATCTCCCTTGAAGAGCAGTGAAG
66 TTTCAGATTTGATCTTCC-TGAAGAGCAGTGAAG
24554 TGAATCAAAT
Statistics
Matches: 316, Mismatches: 44, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
133 37 0.12
134 68 0.22
135 77 0.24
136 78 0.25
137 6 0.02
138 2 0.01
139 13 0.04
140 35 0.11
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (135 bp):
GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTC
TTTCAGATTTGATCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGA
GCAGT
Found at i:24616 original size:95 final size:95
Alignment explanation
Indices: 24430--24654 Score: 274
Period size: 95 Copynumber: 2.4 Consensus size: 95
24420 AATCACATTT
* * * *
24430 GATTTAATCTTCCCTGAAGAACAGTG-AGTGAATCAAATTTTATTGAGTCTGACCTCCGCTAAAG
1 GATTTAATC-TCCCTGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAG
* * *
24494 AGTAGCAGAGCAAATTCTTCTTCTTCTTTCA
65 AATAGCAGAGAAAATTCTTCTTATTCTTTCA
* * *
24525 GATTCAATCTCCCTTGAAGAGCAGTGAAGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAAT
1 GATTTAATCTCCC-TGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAG
**
24590 AATAGTGGA-AAAATTCTTCTTATTCTTTCA
65 AATAGCAGAGAAAATTCTTCTTATTCTTTCA
* * * *
24620 GATTTGATCTTCCTGAAGAGTAGTGAAGTAAATCA
1 GATTTAATCTCCCTGAAGAGCAGTGAAGTGAATCA
24655 CATTGGATGT
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
94 24 0.22
95 48 0.43
96 39 0.35
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (95 bp):
GATTTAATCTCCCTGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAGA
ATAGCAGAGAAAATTCTTCTTATTCTTTCA
Found at i:25074 original size:25 final size:25
Alignment explanation
Indices: 25027--25073 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25017 GGATTTTGTT
*
25027 TTATTTTATTGTAGTTTTATTTTGG
1 TTATTTTATTGTACTTTTATTTTGG
*
25052 TTATTTTATTTTAC-TTTATTTT
1 TTATTTTATTGTACTTTTATTTT
25074 TATAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (25 bp):
TTATTTTATTGTACTTTTATTTTGG
Found at i:25184 original size:21 final size:23
Alignment explanation
Indices: 25155--25210 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
25145 TTTTTAGGAA
*
25155 AAAATATATATAATACATAGTTT
1 AAAATATATATAGTACATAGTTT
*
25178 AAAATATATATAGTATATAGTTT
1 AAAATATATATAGTACATAGTTT
25201 AAAATATATA
1 AAAATATATA
25211 GTTTTAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AAAATATATATAGTACATAGTTT
Found at i:25209 original size:67 final size:68
Alignment explanation
Indices: 25085--25267 Score: 196
Period size: 67 Copynumber: 2.6 Consensus size: 68
25075 ATAATAATTG
* *
25085 TATATAATATATAGTATAATTTAAAATAAGTATATATATATA-TATATATATAGTATATAGTTTT
1 TATAT-ATATATAGCATAATTTAAAAT-A-TATATATATATAGT-T-TA-A-AATATATAG-TTT
25149 TAG-GAAAAAA
58 TAGAGAAAAAA
*
25159 TATATATA-ATA-CATAGTTTAAAATATATATAGTATATAGTTTAAAATATATAGTTTTAGAGAA
1 TATATATATATAGCATAATTTAAAATATATATA-TATATAGTTTAAAATATATAGTTTTAGAGAA
*
25222 ATAA
65 AAAA
* *
25226 TATATATATGTAGTATAATTTAAAATATATATA-ATATAGTTT
1 TATATATATATAGCATAATTTAAAATATATATATATATAGTTT
25268 TTTAAACATA
Statistics
Matches: 97, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
66 6 0.06
67 31 0.32
68 3 0.03
69 26 0.27
70 8 0.08
71 12 0.12
72 3 0.03
73 3 0.03
74 5 0.05
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.43
Consensus pattern (68 bp):
TATATATATATAGCATAATTTAAAATATATATATATATAGTTTAAAATATATAGTTTTAGAGAAA
AAA
Found at i:25211 original size:21 final size:21
Alignment explanation
Indices: 25160--25267 Score: 74
Period size: 23 Copynumber: 4.9 Consensus size: 21
25150 AGGAAAAAAT
* *
25160 ATATATAATACATAGTTTAAAA
1 ATATATAGTATATAGTTT-AAA
25182 TATATATAGTATATAGTTTAAA
1 -ATATATAGTATATAGTTTAAA
* * ** *
25204 ATATATAGTTTTAGAGAAATAAT
1 ATATATAG-TATATAG-TTTAAA
*
25227 ATATATATGTAGTATAATTTAAA
1 ATATATA-GTA-TATAGTTTAAA
25250 ATATATA-TAATATAGTTT
1 ATATATAGT-ATATAGTTT
25268 TTTAAACATA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
21 16 0.24
22 9 0.14
23 37 0.56
24 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (21 bp):
ATATATAGTATATAGTTTAAA
Found at i:25283 original size:67 final size:63
Alignment explanation
Indices: 25145--25283 Score: 145
Period size: 69 Copynumber: 2.1 Consensus size: 63
25135 TAGTATATAG
* *
25145 TTTTTAGGAAAAAATATATATAATACATAGTTTAAAATATATATAGTATATAGTTTAAAATATA
1 TTTTTAGGAAAAAATATATATAATACATAATTTAAAATATATATAG-ATATAGTTTAAAACATA
* * * *
25209 TAGTTTTAGAGAAATAATATATATATGTAGTATAATTTAAAATATATATA-ATATAGTTTTTTAA
1 T--TTTTAG-GAAAAAATATATATA-ATA-CATAATTTAAAATATATATAGATATAG--TTTAAA
25273 ACATA
59 ACATA
25278 TTTTTA
1 TTTTTA
25284 AAATATAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
64 1 0.02
66 6 0.10
67 25 0.40
68 2 0.03
69 28 0.45
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (63 bp):
TTTTTAGGAAAAAATATATATAATACATAATTTAAAATATATATAGATATAGTTTAAAACATA
Found at i:34456 original size:20 final size:20
Alignment explanation
Indices: 34431--34484 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
34421 AGGGTGTCAA
34431 AGTGCATCCATGCACCCTGC
1 AGTGCATCCATGCACCCTGC
*
34451 AGTGCATCTATGCA-CCTGC
1 AGTGCATCCATGCACCCTGC
*
34470 AGTGTATCCATGCAC
1 AGTGCATCCATGCAC
34485 TAGTGCATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:34657 original size:21 final size:20
Alignment explanation
Indices: 34620--34658 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
34610 GAATTTAATG
* *
34620 AATGGGTACCGATGCACCTT
1 AATGGGTACCAAAGCACCTT
34640 AATGGTGTACCAAAGCACC
1 AATGG-GTACCAAAGCACC
34659 CTGTTATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (20 bp):
AATGGGTACCAAAGCACCTT
Found at i:34982 original size:34 final size:33
Alignment explanation
Indices: 34943--35011 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 33
34933 TTGTAAAGGA
*
34943 GAAATGTTCTAGCTTAGCCCGTGTAAAAGCTAGG
1 GAAATGTTCTAGCTTAGCCCGTG-AAAAACTAGG
* *
34977 GAAATGTTCTAGTTTATCCCGTGAAAAACTAGG
1 GAAATGTTCTAGCTTAGCCCGTGAAAAACTAGG
35010 GA
1 GA
35012 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (33 bp):
GAAATGTTCTAGCTTAGCCCGTGAAAAACTAGG
Found at i:37692 original size:18 final size:18
Alignment explanation
Indices: 37669--37726 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
37659 CAACAATTGA
*
37669 TAACAATTGTTATATTTT
1 TAACAATTGATATATTTT
37687 TAACAATTGATATCATTTTGT
1 TAACAATTGATAT-A-TTT-T
* *
37708 TAACAATTGGTATCTTTT
1 TAACAATTGATATATTTT
37726 T
1 T
37727 CATTAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.41
19 4 0.12
20 3 0.09
21 13 0.38
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (18 bp):
TAACAATTGATATATTTT
Found at i:37712 original size:21 final size:20
Alignment explanation
Indices: 37669--37726 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
37659 CAACAATTGA
*
37669 TAACAATTGTTAT-A-TTTT
1 TAACAATTGATATCATTTTT
37687 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTT-T
*
37708 TAACAATTGGTATC-TTTTT
1 TAACAATTGATATCATTTTT
37727 CATTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 2 0.06
20 7 0.20
21 14 0.40
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
TAACAATTGATATCATTTTT
Found at i:37996 original size:19 final size:19
Alignment explanation
Indices: 37947--38001 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
37937 AGGGTGTCAA
*
37947 AGTGCATCCATGCACCCTGC
1 AGTGCATCCATGCA-CTTGC
* * *
37967 AATGAATCCATGCACTTGT
1 AGTGCATCCATGCACTTGC
37986 AGTGCATCCATGCACT
1 AGTGCATCCATGCACT
38002 CAAACACCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (19 bp):
AGTGCATCCATGCACTTGC
Found at i:38045 original size:20 final size:20
Alignment explanation
Indices: 38020--38057 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38010 GAATGCAATT
*
38020 AGTGCATCGATGCACCCTGC
1 AGTGCATCCATGCACCCTGC
38040 AGTGCATCCATGCACCCT
1 AGTGCATCCATGCACCCT
38058 AGCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:38203 original size:20 final size:22
Alignment explanation
Indices: 38165--38204 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
38155 TTTTGAGCAA
38165 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
38187 AAAAT-ATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
38205 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:38459 original size:34 final size:33
Alignment explanation
Indices: 38420--38490 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
38410 TTTTGTAAAG
* *
38420 GGGAAAGGTTCTAGCTTAGCCTGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
38454 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
38487 GGGA
1 GGGA
38491 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:41762 original size:23 final size:23
Alignment explanation
Indices: 41702--41762 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
41692 TATGGAACTA
*
41702 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTC
* * *
41725 TGGTGCAATTCTACGTGGCACTC
1 CGGTGCATTTCTACGCGGCACTC
*
41748 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
41763 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTC
Found at i:42557 original size:21 final size:23
Alignment explanation
Indices: 42515--42557 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
42505 AATAATAATA
*
42515 ATAATAATTAAATATATGAACAT
1 ATAATAATTAAATATATAAACAT
42538 ATAA-AATTAAA-ATATAAACA
1 ATAATAATTAAATATATAAACA
42558 AACAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAATAATTAAATATATAAACAT
Found at i:43211 original size:43 final size:43
Alignment explanation
Indices: 43150--43245 Score: 174
Period size: 43 Copynumber: 2.2 Consensus size: 43
43140 CCGGAGGGAA
* *
43150 GCCGGTCACCGGCCGGCAGCCATCTGTCGCCGCCAATCCCGCC
1 GCCGGCCACCAGCCGGCAGCCATCTGTCGCCGCCAATCCCGCC
43193 GCCGGCCACCAGCCGGCAGCCATCTGTCGCCGCCAATCCCGCC
1 GCCGGCCACCAGCCGGCAGCCATCTGTCGCCGCCAATCCCGCC
43236 GCCGGCCACC
1 GCCGGCCACC
43246 GTATCCAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.12, C:0.51, G:0.27, T:0.09
Consensus pattern (43 bp):
GCCGGCCACCAGCCGGCAGCCATCTGTCGCCGCCAATCCCGCC
Found at i:44040 original size:3 final size:3
Alignment explanation
Indices: 44034--44091 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
44024 TAATATTTTT
*
44034 TAA TAA TAA TAA TAA TAA T-A TAA -AA TAA TAA TAG TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
44078 -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
44092 CAAATGGATG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:44096 original size:16 final size:15
Alignment explanation
Indices: 44034--44091 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 15
44024 TAATATTTTT
*
44034 TAATAATAATAATAA
1 TAATAAAAATAATAA
44049 TAATATAAAATAATAA
1 TAATA-AAAATAATAA
*
44065 TAGTAATAAATAA-AA
1 TAATAA-AAATAATAA
*
44080 TAATAATAATAA
1 TAATAAAAATAA
44092 CAAATGGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 19 0.51
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
TAATAAAAATAATAA
Found at i:44548 original size:122 final size:123
Alignment explanation
Indices: 44382--44857 Score: 685
Period size: 122 Copynumber: 4.0 Consensus size: 123
44372 TACCTACTTC
* * *
44382 ATCTATATCCTTCTGTGATAGAATCAAT-CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTATGATAGAGTC-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
44446 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
65 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
44505 ATCTATCTCCTTCTATGATAGAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
44569 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
66 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
*
44627 ATCTATCTCCTTCTGTGATAGAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
44691 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C--
66 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
*** * * * * *
44746 --C-ATC-AAGT-GATG--A-ATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* * *
44803 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTTCTAGAACAGTTGAT
66 TCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGAT
44858 CCATTGAATG
Statistics
Matches: 333, Mismatches: 16, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
111 6 0.02
112 43 0.13
113 41 0.12
114 2 0.01
115 1 0.00
116 3 0.01
117 1 0.00
121 1 0.00
122 212 0.64
123 23 0.07
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (123 bp):
ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTG
Found at i:44787 original size:112 final size:113
Alignment explanation
Indices: 44656--44861 Score: 344
Period size: 113 Copynumber: 1.8 Consensus size: 113
44646 AGAGTCATGC
*
44656 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
*
44720 ATGAACTT-TCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTCT-TCTAGAAAAGTTGATCCATCAAGTGATGAATTCAAGCA
* *
44768 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
*
44833 ATGAACTTCTTCTAGAACAGTTGATCCAT
66 ATGAACTTCTTCTAGAAAAGTTGATCCAT
44862 TGAATGATGG
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 39 0.45
113 47 0.54
114 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTTCTTCTAGAAAAGTTGATCCATCAAGTGATGAATTCAAGCA
Found at i:46045 original size:21 final size:21
Alignment explanation
Indices: 46016--46056 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
46006 GTTTATGTGA
*
46016 AAAATAAATTGAATTTCAAAC
1 AAAAGAAATTGAATTTCAAAC
46037 AAAAGAAATTGAATTTCAAA
1 AAAAGAAATTGAATTTCAAA
46057 AAGATAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAGAAATTGAATTTCAAAC
Found at i:53783 original size:15 final size:15
Alignment explanation
Indices: 53763--53794 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53753 TGCAATGAAT
*
53763 AATGAATGTGTGCAA
1 AATGAATGTATGCAA
53778 AATGAATGTATGCAA
1 AATGAATGTATGCAA
53793 AA
1 AA
53795 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:57716 original size:24 final size:24
Alignment explanation
Indices: 57675--57734 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
57665 TTAATATAAA
*
57675 AAAAAATAAATATTAATAAACATTT
1 AAAAAATAAATATAAATAAA-ATTT
* *
57700 AAAAAATAATTA-AAATATAATTT
1 AAAAAATAAATATAAATAAAATTT
* *
57723 ATAAAATTAATA
1 AAAAAATAAATA
57735 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 13 0.45
24 5 0.17
25 11 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAAATAAATATAAATAAAATTT
Done.