Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001992.1 Hibiscus syriacus cultivar Beakdansim tig00004073_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: 59747
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Found at i:12088 original size:5 final size:5
Alignment explanation
Indices: 12078--12123 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
12068 TAAAAAAAAG
*
12078 AGAAA AGAAA AG-AA AGAAA A-AAA AGAAA GAAAAA AGAAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA -AGAAA AG-AAA AGAAA A
12124 AGAGGGGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.23
5 18 0.51
6 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:12088 original size:13 final size:13
Alignment explanation
Indices: 12072--12127 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
12062 AAATAATAAA
12072 AAAAAGAGAAAAG
1 AAAAAGAGAAAAG
12085 -AAAAGA-AAGAA-
1 AAAAAGAGAA-AAG
12096 AAAAA-AG-AAAG
1 AAAAAGAGAAAAG
12107 AAAAA-AGAAAAAG
1 AAAAAGAG-AAAAG
12120 AAAAAGAG
1 AAAAAGAG
12128 GGGTTAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
10 2 0.06
11 11 0.31
12 12 0.33
13 9 0.25
14 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAG
Found at i:12097 original size:23 final size:24
Alignment explanation
Indices: 12059--12127 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
12049 GCTTAATGAA
*
12059 AAAAAATAATAAAAAAAAGAGAAA-
1 AAAAAAGAA-AAAAAAAAGAGAAAG
*
12083 AGAAAAGAAAGAAAAAAA-AGAAAG
1 AAAAAAGAAA-AAAAAAAGAGAAAG
12107 AAAAAAGAAAAAGAAAAAGAG
1 AAAAAAGAAAAA-AAAAAGAG
12128 GGGTTAAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.21
24 28 0.74
25 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAAAGAGAAAG
Found at i:12106 original size:17 final size:17
Alignment explanation
Indices: 12071--12122 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 17
12061 AAAATAATAA
12071 AAAAAAGAGAAAAGAAAAG
1 AAAAAAGA-AAAAG-AAAG
12090 AAAGAAA-AAAAAGAAAG
1 AAA-AAAGAAAAAGAAAG
12107 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
12123 AAGAGGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.10
17 16 0.52
18 5 0.16
19 4 0.13
20 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAG
Found at i:13286 original size:83 final size:83
Alignment explanation
Indices: 13189--13745 Score: 900
Period size: 83 Copynumber: 6.7 Consensus size: 83
13179 CCTTTAGCTG
*
13189 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
13254 AAACCAATCAATGAATTT
66 AAACCAATCAATGAATTT
*
13272 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
13337 AAACCAATCAATGAATTT
66 AAACCAATCAATGAATTT
*
13355 GAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
13420 AAACCAATCAATGAATTT
66 AAACCAATCAATGAATTT
*
13438 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
13503 AAACTAATCATTGAATTT
66 AAACCAATCAATGAATTT
* * *
13521 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * *
13586 AAACTAATCATTTAATTT
66 AAACCAATCAATGAATTT
* *
13604 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
13669 AAACCAATCATTGAATTT
66 AAACCAATCAATGAATTT
* * * *
13687 GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCT
1 GAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
13746 AATTTGGTTT
Statistics
Matches: 448, Mismatches: 22, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
83 404 0.90
84 4 0.01
85 3 0.01
86 37 0.08
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCAATGAATTT
Found at i:14674 original size:113 final size:113
Alignment explanation
Indices: 14476--15707 Score: 1844
Period size: 113 Copynumber: 11.0 Consensus size: 113
14466 GCAAAGATTT
* *
14476 AAATCCATCACTTGATGGATCAGCTTTTCCAG--AGGAAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTA-G-AGTTCATAATGAGAAGAACTCATCTGA
14539 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
14589 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
14654 AAGGAAGAAGAAGATCATAATAAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
14702 AAATCTATCACTTGATGGATTATCTTTTCCATTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
14767 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
14815 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
14880 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
14928 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
14993 AAGGAAGAAGAACTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
15041 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
15106 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
15154 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATGAGAATAACTCATTTAAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGAA
15218 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *
15267 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATGAAAAGAACTTATTTAAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGAA
* *
15331 GAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * ** * *
15377 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
15442 AAGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * ** * * *
15490 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAATAACTCATATGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
15555 AAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
15603 AAATCCATCACTTGATGGGTCAAT-TTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATC---
1 AAATCCATCACTTGATGGAT-TATCTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGA
* ** *
15662 AGGA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
15708 AATGACTCTA
Statistics
Matches: 1058, Mismatches: 52, Indels: 23
0.93 0.05 0.02
Matches are distributed among these distances:
108 36 0.03
109 3 0.00
110 97 0.09
111 3 0.00
112 24 0.02
113 893 0.84
114 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATTATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:15357 original size:17 final size:17
Alignment explanation
Indices: 15297--15357 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
15287 TAGCTTTTCC
15297 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* * *
15314 AAAAGAACTT-ATTTAAAG
1 AGAAGAAGTTCA--TAATG
15332 AAGGAAGAAGTTCATAATG
1 -A-GAAGAAGTTCATAATG
15351 AGAAGAA
1 AGAAGAA
15358 TTTGTTCAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
16 1 0.03
17 14 0.42
18 5 0.15
19 5 0.15
20 7 0.21
21 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:15690 original size:17 final size:17
Alignment explanation
Indices: 15635--15690 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
15625 ATTTTTCCAG
15635 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
15652 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
15671 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
15688 AGA
1 AGA
15691 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:15945 original size:3 final size:3
Alignment explanation
Indices: 15937--16016 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
15927 ATGTTATTTA
* * * * *
15937 TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT AAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
15985 AAT AAT AAT AAT TAT TAT TAT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
16017 TAATATTACA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:15952 original size:12 final size:12
Alignment explanation
Indices: 15937--16024 Score: 90
Period size: 12 Copynumber: 7.4 Consensus size: 12
15927 ATGTTATTTA
*
15937 TATTATTATTAT
1 TATTATTATAAT
*
15949 TATTATAATAAT
1 TATTATTATAAT
15961 TATTATTATAAT
1 TATTATTATAAT
*
15973 TATAATTATAAT
1 TATTATTATAAT
* * *
15985 AATAATAATAAT
1 TATTATTATAAT
*
15997 TATTATTATTAT
1 TATTATTATAAT
16009 ATATTATT-TAA-
1 -TATTATTATAAT
16020 TATTA
1 TATTA
16025 CAAGCCCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
10 5 0.08
12 52 0.81
13 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:15962 original size:18 final size:18
Alignment explanation
Indices: 15941--16005 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
15931 TATTTATATT
*
15941 ATTATTATTATTATAATA
1 ATTATTATTATAATAATA
*
15959 ATTATTATTATAATTATA
1 ATTATTATTATAATAATA
* *
15977 ATTATAATAATAATAATA
1 ATTATTATTATAATAATA
15995 ATTATTATTAT
1 ATTATTATTAT
16006 TATATATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATTATTATAATAATA
Found at i:16527 original size:5 final size:5
Alignment explanation
Indices: 16481--16518 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
16471 ACAACGCAGC
*
16481 AAAGA AACAGA AAAGA AAAAA AAAGA AAAGA AAAGA AA
1 AAAGA AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
16519 GAAGAGAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:17430 original size:27 final size:26
Alignment explanation
Indices: 17400--17458 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
17390 TAAATATATA
*
17400 TAATAAATAATTATTTATATATATTTT
1 TAATAAATAATT-TTAATATATATTTT
* *
17427 TAATAAATTATTTTAATATTTATTTT
1 TAATAAATAATTTTAATATATATTTT
17453 TCAATA
1 T-AATA
17459 TCGAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATAAATAATTTTAATATATATTTT
Found at i:21544 original size:130 final size:130
Alignment explanation
Indices: 21382--21642 Score: 468
Period size: 130 Copynumber: 2.0 Consensus size: 130
21372 TTTACAAGCC
*
21382 TTAGAAATATTTGGGGCCATTATATAATTTTATGAAAGTTAAGGGACCTAATCAATAATTATGAA
1 TTAGAAATATTTGGGGCCATTATATAATTTTATGAAAGTTAAGAGACCTAATCAATAATTATGAA
* *
21447 AAAGTTATCGATTGTTGTGTAATTATTCAATATTTGATATACTATTCTGTAAATTAATGTTTGAG
66 AAAGTTATCGATCGTTGTGTAATTATTCAATATTTGATATACTATTATGTAAATTAATGTTTGAG
*
21512 TTAGAAATATTTGGGGCCATTATATAATTTTATGAAAGTTAAGAGACCTACTCAATAATTATGAA
1 TTAGAAATATTTGGGGCCATTATATAATTTTATGAAAGTTAAGAGACCTAATCAATAATTATGAA
* *
21577 AAAGTTATGGATCGTTGTGTAATTGTTCAATATTTGATATACTATTATGTAAATTAATGTTTGAG
66 AAAGTTATCGATCGTTGTGTAATTATTCAATATTTGATATACTATTATGTAAATTAATGTTTGAG
21642 T
1 T
21643 GTTGAAATTA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 125 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (130 bp):
TTAGAAATATTTGGGGCCATTATATAATTTTATGAAAGTTAAGAGACCTAATCAATAATTATGAA
AAAGTTATCGATCGTTGTGTAATTATTCAATATTTGATATACTATTATGTAAATTAATGTTTGAG
Found at i:23386 original size:242 final size:243
Alignment explanation
Indices: 22934--23587 Score: 955
Period size: 242 Copynumber: 2.7 Consensus size: 243
22924 TGTTTTAAAA
* *
22934 TAAAAGATTAATTACCTAGTTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTACCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* * * *
22999 GATAAATGCCTTTGAGTAAAAGATTAATTACCTAGCTGTGAATTTGGCAGAAAGGTGCCAATATT
66 GCTAAATGCCTTTGAGTAAAAGATTAATTTCCTAGCTGTGCATTTAGCAGAAAGGTGCCAATATT
* * *
23064 GCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAATGATTAATTGCCTAGCTTTGCATTTGGCT
131 GCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCA
* * *
23129 GAAAGGTTCCAATATTGCAAGTTAGATGAAATGCTAAATTCATTTGAG
196 GAAAGGTTCCAATATTGCAAGTTAGATGAAAGGATAAATACATTTGAG
* * *
23177 TAAAAGGA-TAA-TGCCTAGCTGTGCATTCGGCAGAAAGGTGTCAATATTGCAAGTTAGATGAAA
1 TAAAA-GATTAATTACCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAA
*
23240 GGCTAAATGCCTTTGAGTAAAAGATTAATTTCCTAGCTGTGCATTTAGCATAAAGGTGCCAATAT
65 GGCTAAATGCCTTTGAGTAAAAGATTAATTTCCTAGCTGTGCATTTAGCAGAAAGGTGCCAATAT
* *
23305 TGCAATTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGTCTAGCTGTGCATTTGGC
130 TGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGC
*
23370 AGAAAGGTGT-CAATATTGCAAGTTAGATGAAAGGATAAATACCTTTGAG
195 AGAAAGGT-TCCAATATTGCAAGTTAGATGAAAGGATAAATACATTTGAG
* * *
23419 TAAAATATTAATTACCTAGCTGTGAATTTGGTAGAAAGGTGCCAATATTGC-A---AGATGAAAG
1 TAAAAGATTAATTACCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* * * *
23480 GCTAAATGCCTTTGACTAAAAGATTAATTGT-CGAGCTGTGCATTTTGCAGAAAGATGCCAATAT
66 GCTAAATGCCTTTGAGTAAAAGATTAATT-TCCTAGCTGTGCATTTAGCAGAAAGGTGCCAATAT
* * **
23544 TGCAAGTTAAATGAGAGGCTAAATGCCTTTGTCTAAAAGATTAA
130 TGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAA
23588 ATGCTTAATA
Statistics
Matches: 371, Mismatches: 35, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
239 105 0.28
240 1 0.00
241 1 0.00
242 219 0.59
243 43 0.12
244 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (243 bp):
TAAAAGATTAATTACCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAGTAAAAGATTAATTTCCTAGCTGTGCATTTAGCAGAAAGGTGCCAATATT
GCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCA
GAAAGGTTCCAATATTGCAAGTTAGATGAAAGGATAAATACATTTGAG
Found at i:23607 original size:81 final size:81
Alignment explanation
Indices: 22934--23587 Score: 933
Period size: 81 Copynumber: 8.1 Consensus size: 81
22924 TGTTTTAAAA
* * *
22934 TAAAAGATTAATTACCTAGTTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
*
22999 GATAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
23015 TAAAAGATTAATTACCTAGCTGTGAATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
23080 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * *
23096 TAAATGATTAATTGCCTAGCTTTGCATTTGGCTGAAAGGTTCCAATATTGCAAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* *
23161 GCTAAATTCATTTGAG
66 GCTAAATGCCTTTGAG
* *
23177 TAAAAGGA-TAA-TGCCTAGCTGTGCATTCGGCAGAAAGGTGTCAATATTGCAAGTTAGATGAAA
1 TAAAA-GATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAA
23240 GGCTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * *
23257 TAAAAGATTAATTTCCTAGCTGTGCATTTAGCATAAAGGTGCCAATATTGCAATTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
23322 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
23338 TAAAAGATTAATTGTCTAGCTGTGCATTTGGCAGAAAGGTGTCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* *
23403 GATAAATACCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
23419 TAAAATATTAATTACCTAGCTGTGAATTTGGTAGAAAGGTGCCAATATTGC-A---AGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
*
23480 GCTAAATGCCTTTGAC
66 GCTAAATGCCTTTGAG
* * * * * *
23496 TAAAAGATTAATTGTCGAGCTGTGCATTTTGCAGAAAGATGCCAATATTGCAAGTTAAATGAGAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
**
23561 GCTAAATGCCTTTGTC
66 GCTAAATGCCTTTGAG
23577 TAAAAGATTAA
1 TAAAAGATTAA
23588 ATGCTTAATA
Statistics
Matches: 510, Mismatches: 56, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
77 65 0.13
78 1 0.00
79 2 0.00
80 70 0.14
81 370 0.73
82 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:41065 original size:22 final size:22
Alignment explanation
Indices: 41021--41065 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41011 GGTTATTATA
* * *
41021 TATATGATTTTTATCATGGATG
1 TATATGATGTTTATCACGAATG
*
41043 TATATGATGTTTATTACGAATG
1 TATATGATGTTTATCACGAATG
41065 T
1 T
41066 TTCTTCGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (22 bp):
TATATGATGTTTATCACGAATG
Found at i:46447 original size:70 final size:70
Alignment explanation
Indices: 46365--46562 Score: 281
Period size: 70 Copynumber: 2.8 Consensus size: 70
46355 TACATATCCA
* *
46365 GTTTAGCACTATAGTGCATATAAAGGACACTTAGTGCAAGTAGTGGGCACAACCTTATATGTCAT
1 GTTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACAACCTTATATGTCAT
46430 ATTCG
66 ATTCG
* * * * * *
46435 GTTTAGCACTATAATGTATATAAAGGAAACTTAGTGTAGGTGGTGGGCGCAACCTTATGTGTCAT
1 GTTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACAACCTTATATGTCAT
*
46500 ATTCT
66 ATTCG
* *
46505 ATTTAGCACTACAGTGTATATAAAGGACACTTAGTGCATA-TGGTGGGCACAACCTTAT
1 GTTTAGCACTATAGTGTATATAAAGGACACTTAGTGCA-AGTGGTGGGCACAACCTTAT
46563 GTGTATTGGT
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 111 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (70 bp):
GTTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACAACCTTATATGTCAT
ATTCG
Found at i:46845 original size:49 final size:49
Alignment explanation
Indices: 46773--46898 Score: 252
Period size: 49 Copynumber: 2.6 Consensus size: 49
46763 GTAAAGTGAA
46773 ATTGTCTCACTAAGTGTATACTTAACGTATTACATTAACTATTACTAAG
1 ATTGTCTCACTAAGTGTATACTTAACGTATTACATTAACTATTACTAAG
46822 ATTGTCTCACTAAGTGTATACTTAACGTATTACATTAACTATTACTAAG
1 ATTGTCTCACTAAGTGTATACTTAACGTATTACATTAACTATTACTAAG
46871 ATTGTCTCACTAAGTGTATACTTAACGT
1 ATTGTCTCACTAAGTGTATACTTAACGT
46899 GTGATAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (49 bp):
ATTGTCTCACTAAGTGTATACTTAACGTATTACATTAACTATTACTAAG
Found at i:47761 original size:51 final size:51
Alignment explanation
Indices: 47635--47769 Score: 128
Period size: 51 Copynumber: 2.6 Consensus size: 51
47625 TGACCTTCAT
* * * * * *
47635 AGAGACGAGGAAACAAATCAATCATGCTTTTTTTCATATTTGAACTTTACGA
1 AGAGATGAAGAAACAAATCAACCA-ACTTTTTTTCAGATTTGAACTTTACAA
* * * *
47687 ATAGATGAAGAAACAAATCAACCAAGTTTTTTTTAGATTTGAACTTTTCAA
1 AGAGATGAAGAAACAAATCAACCAACTTTTTTTCAGATTTGAACTTTACAA
* * *
47738 AGAGAT-ACGAAAGCATATGAACCAACTTTTTT
1 AGAGATGAAGAAA-CAAATCAACCAACTTTTTT
47770 AAAAAATTTG
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
50 5 0.07
51 42 0.63
52 20 0.30
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (51 bp):
AGAGATGAAGAAACAAATCAACCAACTTTTTTTCAGATTTGAACTTTACAA
Found at i:49599 original size:21 final size:23
Alignment explanation
Indices: 49534--49617 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
49524 TACATGCTTT
*
49534 TATATTATTATATT-TAT-TACA
1 TATATTAATATATTATATATACA
*
49555 TATGATATCATATCATCT-TATATAC-
1 TAT-AT-TAATAT-AT-TATATATACA
49580 TATATT-ATATATTATATATACA
1 TATATTAATATATTATATATACA
*
49602 TATTTTAATATATTAT
1 TATATTAATATATTAT
49618 TTTTTATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
20 1 0.02
21 12 0.23
22 11 0.21
23 14 0.27
24 4 0.08
25 7 0.13
26 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (23 bp):
TATATTAATATATTATATATACA
Found at i:49802 original size:12 final size:13
Alignment explanation
Indices: 49785--49828 Score: 72
Period size: 14 Copynumber: 3.4 Consensus size: 13
49775 TTTGATGTTC
49785 ATATTATATAT-T
1 ATATTATATATAT
49797 ATATTATATATAT
1 ATATTATATATAT
49810 ATATATATATATAT
1 ATAT-TATATATAT
49824 ATATT
1 ATATT
49829 TTTATGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 6 0.20
14 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTATATATAT
Found at i:49806 original size:2 final size:2
Alignment explanation
Indices: 49785--49827 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
49775 TTTGATGTTC
49785 AT AT -T AT AT AT -T AT AT -T 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 AT AT AT AT AT
49824 AT AT
1 AT AT
49828 TTTTATGTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:51926 original size:16 final size:14
Alignment explanation
Indices: 51895--51951 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 14
51885 ACTTTATTCA
51895 ATTTTTATTTATTT
1 ATTTTTATTTATTT
51909 ATTTTTCATTTGATTT
1 ATTTTT-ATTT-ATTT
* *
51925 ATTTAATATTTAATT
1 ATTT-TTATTTATTT
51940 ATTATTT-TTTAT
1 ATT-TTTATTTAT
51952 ATAACATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.29
15 11 0.31
16 13 0.37
17 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTTTATTTATTT
Found at i:54619 original size:95 final size:95
Alignment explanation
Indices: 54447--54709 Score: 350
Period size: 95 Copynumber: 2.7 Consensus size: 95
54437 AGATTATAAT
* * ** **
54447 ATTATATATATACAATAAAGCTTAAGTTGTCCCTCTAAAGCAATTACTTAAACGTCCCGTCTTTA
1 ATTATA-ATATACAATAAAGCTTAAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGTCTTTA
*
54512 TAGATAAAATTCAGCTAACCTGATAAAGGTG
65 TGGATAAAATTCAGCTAACCTGATAAAGGTG
*
54543 ATTATAATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGTCTTTAT
1 ATTATAATATACAATAAAGCTTAAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGTCTTTAT
* *
54608 GGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAAAATTCAGCTAACCTGATAAAGGTG
* *
54638 ATTATAATAT-CTATACAATGATATTAAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCAG-C
1 ATTATAATATACAATA-AA-G--CTTAAGTTATCCCTCTAGAGCAATTGGTTAAACACCCC-GTC
54701 TTTATGGAT
61 TTTATGGAT
54710 TCAGCTAGCC
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
94 4 0.03
95 91 0.61
96 7 0.05
98 46 0.31
99 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTAAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGTCTTTAT
GGATAAAATTCAGCTAACCTGATAAAGGTG
Found at i:57846 original size:53 final size:54
Alignment explanation
Indices: 57758--57864 Score: 191
Period size: 53 Copynumber: 2.0 Consensus size: 54
57748 CTTAAACGTT
57758 GTTTTAGTAATTTTAAAAATTAAATTTTATTAAATAACCAAATATATCTGGGTG
1 GTTTTAGTAATTTTAAAAATTAAATTTTATTAAATAACCAAATATATCTGGGTG
57812 GTTTTAGTAA-TTTAAAAATT-AATTTTATTAAAATAACCAAATATATCTGGGTG
1 GTTTTAGTAATTTTAAAAATTAAATTTTATT-AAATAACCAAATATATCTGGGTG
57865 ATCCAATCAC
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 9 0.17
53 33 0.63
54 10 0.19
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (54 bp):
GTTTTAGTAATTTTAAAAATTAAATTTTATTAAATAACCAAATATATCTGGGTG
Found at i:58182 original size:47 final size:48
Alignment explanation
Indices: 58117--58207 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
58107 GAGTTGGGTC
58117 ATTTCGGATTTTGATTTTATTCCAGTCTATAGTAAGTTGGGTCGCGTT
1 ATTTCGGATTTTGATTTTATTCCAGTCTATAGTAAGTTGGGTCGCGTT
* **
58165 ATTTCGG-TTTTGGTTTTATTCGGGTCTATAGTAAGTTGGGTCG
1 ATTTCGGATTTTGATTTTATTCCAGTCTATAGTAAGTTGGGTCG
58208 GTCATTCAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 33 0.82
48 7 0.17
ACGTcount: A:0.16, C:0.11, G:0.26, T:0.46
Consensus pattern (48 bp):
ATTTCGGATTTTGATTTTATTCCAGTCTATAGTAAGTTGGGTCGCGTT
Found at i:58242 original size:44 final size:45
Alignment explanation
Indices: 58113--58253 Score: 142
Period size: 47 Copynumber: 3.1 Consensus size: 45
58103 GGTAGAGTTG
* ** *
58113 GGTCATTTCGGATTTTGATTTTATTCCAGTCTATAGTAAGTTGGGTC
1 GGTCATTTCAG-TTTTG-TTTTATTCGGGTATATAGTAAGTTGGGTC
* * *
58160 GCGTTATTTCGGTTTTGGTTTTATTCGGGTCTATAGTAAGTTGGGTC
1 G-GTCATTTCAGTTTT-GTTTTATTCGGGTATATAGTAAGTTGGGTC
* *
58207 GGTCA-TTCAGTTTT-TATTTATTTGGGTATATAGTAAGTTAGGTC
1 GGTCATTTCAGTTTTGT-TTTATTCGGGTATATAGTAAGTTGGGTC
58251 GGT
1 GGT
58254 TAGGTATATG
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 28 0.34
45 8 0.10
46 3 0.04
47 33 0.40
48 10 0.12
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (45 bp):
GGTCATTTCAGTTTTGTTTTATTCGGGTATATAGTAAGTTGGGTC
Found at i:59291 original size:20 final size:20
Alignment explanation
Indices: 59265--59312 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
59255 GGACCAATTT
59265 AGGATGAAGATCATAGCTTG
1 AGGATGAAGATCATAGCTTG
*
59285 GGGATGAAGATCATAGCTTG
1 AGGATGAAGATCATAGCTTG
59305 AGGATGAA
1 AGGATGAA
59313 AATGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.33, T:0.23
Consensus pattern (20 bp):
AGGATGAAGATCATAGCTTG
Done.