Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006861.1 Hibiscus syriacus cultivar Beakdansim tig00017452_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: 89695
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2393 original size:12 final size:12
Alignment explanation
Indices: 2364--2404 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2354 TCCATTACAT
2364 TTTTTACTTTTA
1 TTTTTACTTTTA
*
2376 TCTTTACTTTT-
1 TTTTTACTTTTA
2387 TGTTTTA-TTTTA
1 T-TTTTACTTTTA
2399 TTTTTA
1 TTTTTA
2405 TTCATTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTACTTTTA
Found at i:3852 original size:18 final size:18
Alignment explanation
Indices: 3812--3854 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3802 CTTGTTAAAT
*
3812 ATTGTTTGGAATGCTATG
1 ATTGTTTGGAATACTATG
*
3830 CTTGTTTGGGAATAC-ATG
1 ATTGTTT-GGAATACTATG
3848 ATTGTTT
1 ATTGTTT
3855 AGGTTAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.47
Consensus pattern (18 bp):
ATTGTTTGGAATACTATG
Found at i:4313 original size:17 final size:17
Alignment explanation
Indices: 4290--4334 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4280 TATACTCCAT
4290 AAAAAAAACAGCAGTTCG
1 AAAAAAAA-AGCAGTTCG
**
4308 AAAAAAAAAGTTGTTCG
1 AAAAAAAAAGCAGTTCG
4325 AAAAAAAAAG
1 AAAAAAAAAG
4335 AAAAAAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAAAAAAGCAGTTCG
Found at i:6276 original size:23 final size:23
Alignment explanation
Indices: 6250--6316 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
6240 ATTTTATATA
*
6250 GCACTTTGGTACATTTCTACGCG
1 GCACTTCGGTACATTTCTACGCG
* *
6273 GCACTTCGGTGA-AATTCTACGTG
1 GCACTTCGGT-ACATTTCTACGCG
* *
6296 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTACATTTCTACG
6317 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
GCACTTCGGTACATTTCTACGCG
Found at i:12117 original size:21 final size:19
Alignment explanation
Indices: 12093--12144 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 19
12083 ACATATGTAA
12093 TCCTTTGGAACAT-TTATGCGG
1 TCCTTTGGAACATATT-T--GG
12114 TCCTTTGAGACACATATTTGG
1 TCCTTTG-GA-ACATATTTGG
12135 TCCTTTGGAA
1 TCCTTTGGAA
12145 AATGTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 16 0.57
22 2 0.07
23 5 0.18
24 2 0.07
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (19 bp):
TCCTTTGGAACATATTTGG
Found at i:13983 original size:26 final size:25
Alignment explanation
Indices: 13947--14001 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
13937 GATAAGCTTA
*
13947 TGTATGGAATGCATATATTATGCAGT
1 TGTATGGAATGCATATATAATGCA-T
* * *
13973 TGTATTGAATGGATGTATAATGCAT
1 TGTATGGAATGCATATATAATGCAT
13998 TGTA
1 TGTA
14002 CTCTATTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (25 bp):
TGTATGGAATGCATATATAATGCAT
Found at i:15607 original size:28 final size:29
Alignment explanation
Indices: 15571--15631 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
15561 GTCAAAACGG
15571 GCCATTAATAATGCACCATGTC-AAAAAT
1 GCCATTAATAATGCACCATGTCAAAAAAT
15599 GCCATTAATAATGCACCATGTCAAAAAAT
1 GCCATTAATAATGCACCATGTCAAAAAAT
15628 GCCA
1 GCCA
15632 ACAACTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (29 bp):
GCCATTAATAATGCACCATGTCAAAAAAT
Found at i:16459 original size:23 final size:23
Alignment explanation
Indices: 16433--16479 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16423 GTAATGTTTG
16433 TCCTATTTACCTCCTTAAGGTAA
1 TCCTATTTACCTCCTTAAGGTAA
*
16456 TCCTATTTACGTCCTTAAGGTAA
1 TCCTATTTACCTCCTTAAGGTAA
16479 T
1 T
16480 GAATTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (23 bp):
TCCTATTTACCTCCTTAAGGTAA
Found at i:20177 original size:13 final size:13
Alignment explanation
Indices: 20124--20188 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
20114 TAAAGAAAAC
* *
20124 AAATAAGATAAAG
1 AAATAAAATAAAT
20137 AGAATAAAATAAA-
1 A-AATAAAATAAAT
20150 AGAGA-AAAATAAAAT
1 A-A-ATAAAAT-AAAT
20165 AAATAAAATAAAT
1 AAATAAAATAAAT
*
20178 AAATAAGATAA
1 AAATAAAATAA
20189 GGAAAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 24 0.53
14 20 0.44
15 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:20188 original size:9 final size:9
Alignment explanation
Indices: 20139--20180 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
20129 AGATAAAGAG
20139 AATAAAATA
1 AATAAAATA
20148 AA-AGAGAA-A
1 AATA-A-AATA
20157 AATAAAATA
1 AATAAAATA
20166 AATAAAATA
1 AATAAAATA
20175 AATAAA
1 AATAAA
20181 TAAGATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.10
9 23 0.79
10 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (9 bp):
AATAAAATA
Found at i:20248 original size:2 final size:2
Alignment explanation
Indices: 20241--20265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20231 AAAAGGAAAA
20241 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20266 CATCAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20323 original size:38 final size:40
Alignment explanation
Indices: 20254--20333 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
20244 TATATATATA
* *
20254 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACATAAAAATATTAATAAAATAGAA-AAGC
*
20294 TATATATATATACA-AAAAATATTTA-AAAATAGAAAAGC
1 TATATATATATACATAAAAATATTAATAAAATAGAAAAGC
20332 TA
1 TA
20334 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
39 10 0.28
40 14 0.39
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACATAAAAATATTAATAAAATAGAAAAGC
Found at i:20545 original size:25 final size:27
Alignment explanation
Indices: 20496--20546 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
20486 ACAAGATTTT
**
20496 AAAAACAATAATATAATAATGAATAAC
1 AAAAACAATAATATAATAAAAAATAAC
20523 AAAAACAA-AA-ATAATAAAAAATAA
1 AAAAACAATAATATAATAAAAAATAA
20547 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 2 0.09
27 8 0.36
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.18
Consensus pattern (27 bp):
AAAAACAATAATATAATAAAAAATAAC
Found at i:20592 original size:2 final size:2
Alignment explanation
Indices: 20546--20576 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20536 ATAAAAAATA
20546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20577 AAGTTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20709 original size:29 final size:32
Alignment explanation
Indices: 20654--20728 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
20644 TAATAATACG
*
20654 TATATAAATAATCTATTAAAAGTATAA-AAAA
1 TATATATATAATCTATTAAAAGTATAATAAAA
*
20685 TATATATATAA-CTA-TATAAAG-ATAATTACAA
1 TATATATATAATCTATTA-AAAGTATAA-TAAAA
20716 TATATATAGTAAT
1 TATATATA-TAAT
20729 AATAGACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 6 0.16
30 7 0.19
31 21 0.57
32 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (32 bp):
TATATATATAATCTATTAAAAGTATAATAAAA
Found at i:20771 original size:21 final size:19
Alignment explanation
Indices: 20757--20827 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 19
20747 ATATTAAATA
20757 AATAAATATATATATATAAT
1 AATAAA-ATATATATATAAT
20777 AATAAAATATAGTA-A-AAT
1 AATAAAATATA-TATATAAT
*
20795 AATCAAATGA-A-A-ATAAT
1 AATAAAAT-ATATATATAAT
*
20812 -TTAAAATATATATATA
1 AATAAAATATATATATA
20828 TATACGTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
15 1 0.02
16 8 0.19
17 4 0.10
18 14 0.33
19 7 0.17
20 8 0.19
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
AATAAAATATATATATAAT
Found at i:21288 original size:35 final size:35
Alignment explanation
Indices: 21249--21320 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
21239 CTAAAAAACC
*
21249 CTATTTTAGACTAGTATTTGAGTCTTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
21284 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
21319 CT
1 CT
21321 TCTTTTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:21990 original size:106 final size:105
Alignment explanation
Indices: 21804--22537 Score: 979
Period size: 106 Copynumber: 7.0 Consensus size: 105
21794 TGTATTGTTC
* ** * * * *
21804 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * * *
21869 GCCAACCGCCCCTTCGCTATGAAGTTGAGCTTGTGCAATCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGC-GTCT
* * * * *
21910 TGAGTCTAATATCCTTCGATGCGAAGTTGAAATTGACCCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
21975 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
* *
22016 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
22081 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCGTCT
* * *
22120 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
22185 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
* * * *
22226 CGAGTCCAATAT-C--C----T-ACGCT---ATTGGCTCTGAAATTGGGAGATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
22280 ACCAGCTGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
* * *
22321 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
22386 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
*
22427 CGAGTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
22492 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-CGTCT
22533 CGAGT
1 CGAGT
22538 GGCGCGATAT
Statistics
Matches: 561, Mismatches: 53, Indels: 28
0.87 0.08 0.04
Matches are distributed among these distances:
95 79 0.14
96 1 0.00
98 4 0.01
99 1 0.00
102 1 0.00
103 4 0.01
104 100 0.18
105 1 0.00
106 369 0.66
107 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCGTCT
Found at i:22366 original size:305 final size:306
Alignment explanation
Indices: 21948--22537 Score: 1029
Period size: 305 Copynumber: 1.9 Consensus size: 306
21938 GAAATTGACC
* *
21948 CTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
1 CTGAAATTGGGAAATTGTTTATTGACAACCAGCCGCCCCTTCGTTGTGAAGTTGAACTTGTGTCG
*
22013 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTG
* *
22078 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCTCGAGTCCAATATCCTTCGATGT
131 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATGT
*
22142 GAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAGCTGTCCCTTCGTTGTGA
196 GAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGA
22207 AGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTACGCTATTGGCT
261 AGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTACGCTATTGGCT
* * *
22253 CTGAAATTGGGAGATTGTTTATTGACAACCAGCTGCCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 CTGAAATTGGGAAATTGTTTATTGACAACCAGCCGCCCCTTCGTTGTGAAGTTGAACTTGTGTCG
* *
22318 TCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTG
22383 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAACATCCTTCGATG
131 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCCCGAGTCCAACATCCTTCGATG
* * *
22448 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTG
195 TGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTG
*
22513 AAGTTGAACTTGTGTTGTCTCGAGT
260 AAGTTGAACTTGTGTCGTCTCGAGT
22538 GGCGCGATAT
Statistics
Matches: 268, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
305 160 0.60
307 108 0.40
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (306 bp):
CTGAAATTGGGAAATTGTTTATTGACAACCAGCCGCCCCTTCGTTGTGAAGTTGAACTTGTGTCG
TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTG
ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATGT
GAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGA
AGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTACGCTATTGGCT
Found at i:23563 original size:23 final size:22
Alignment explanation
Indices: 23520--23576 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
23510 TGAACCCATC
*
23520 TTATTTTTTGTTCTTTCTCTTT
1 TTATTTTTTCTTCTTTCTCTTT
*
23542 TTATTTTGTTCTTTTTTCTCTTT
1 TTATTTT-TTCTTCTTTCTCTTT
23565 TTCAATTTTTTC
1 TT--ATTTTTTC
23577 AATTTAGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 7 0.23
23 15 0.50
24 3 0.10
25 5 0.17
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (22 bp):
TTATTTTTTCTTCTTTCTCTTT
Found at i:30637 original size:23 final size:23
Alignment explanation
Indices: 30611--30655 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
30601 CACCACAGCT
*
30611 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
30634 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
30656 ATATAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:30873 original size:149 final size:149
Alignment explanation
Indices: 30623--30937 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
30613 TATAATTGCA
30623 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
30687 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATT
* *
30752 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
30772 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
*
30837 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTC
*
30902 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
30921 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
30938 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTC
CAAAGAATATACATATATC
Found at i:32422 original size:21 final size:21
Alignment explanation
Indices: 32398--32442 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32388 TTTTGTTCGT
* *
32398 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32419 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32440 TTG
1 TTG
32443 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:34066 original size:9 final size:9
Alignment explanation
Indices: 34034--34058 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34024 TAAAAGGGAA
34034 AAATAAAAT
1 AAATAAAAT
34043 AAATAAAAT
1 AAATAAAAT
34052 AAATAAA
1 AAATAAA
34059 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:34124 original size:2 final size:2
Alignment explanation
Indices: 34117--34157 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34107 TGAAAAATGA
34117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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 A
34158 CATCAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34633 original size:2 final size:2
Alignment explanation
Indices: 34626--34656 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34616 TATTAAAGAA
34626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34657 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34678 original size:16 final size:16
Alignment explanation
Indices: 34657--34706 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
34647 TATATATATA
34657 ATAATAATAATAAAAT
1 ATAATAATAATAAAAT
*
34673 ATAATAA-AAAAAAAT
1 ATAATAATAATAAAAT
* *
34688 GAAAATAAT-TTAAAAT
1 -ATAATAATAATAAAAT
34704 ATA
1 ATA
34707 TATATATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAATAATAATAAAAT
Found at i:34774 original size:66 final size:63
Alignment explanation
Indices: 34636--34767 Score: 162
Period size: 66 Copynumber: 2.1 Consensus size: 63
34626 ATATATATAT
34636 ATATATATATATATATATATAATAATAATAATAAAATATAATAAAAAAAAATGAAAATAATTTAA
1 ATATATATATATATATATATAATAATAATAATAAAATATAATAAAAAAAAATG-AAATAA--TAA
34701 A
63 A
* * * *
34702 ATATATATATATATATATATACGT-ATAATAATAACAT-GAATAATAAAAAAT-AAATGAATAAA
1 ATATATATATATATATATATA-ATAATAATAATAAAATATAATAAAAAAAAATGAAAT-AATAAA
34764 ATAT
1 ATAT
34768 CCATATAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
62 8 0.13
63 4 0.07
64 2 0.03
65 12 0.20
66 33 0.55
67 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (63 bp):
ATATATATATATATATATATAATAATAATAATAAAATATAATAAAAAAAAATGAAATAATAAA
Found at i:35180 original size:35 final size:35
Alignment explanation
Indices: 35141--35212 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
35131 CAAAAAAACC
35141 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
35176 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
35211 CT
1 CT
35213 TCTTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:36867 original size:24 final size:22
Alignment explanation
Indices: 36823--36867 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
36813 AAACTATATT
*
36823 AAAAATATATAAAATACAAATA
1 AAAAATATATAAAATAAAAATA
*
36845 AAAAATATAATTATAATAAAAAT
1 AAAAATAT-A-TAAAATAAAAAT
36868 TTATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATATATAAAATAAAAATA
Found at i:50294 original size:24 final size:24
Alignment explanation
Indices: 50267--50324 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
50257 AAATACCCTG
*
50267 AAACCACCCATCAATTTCCAAGAA
1 AAACTACCCATCAATTTCCAAGAA
*
50291 AAACTACCCATCACTTTCCAAGAA
1 AAACTACCCATCAATTTCCAAGAA
*
50315 ACACTACCCA
1 AAACTACCCA
50325 CCCACCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.43, C:0.36, G:0.03, T:0.17
Consensus pattern (24 bp):
AAACTACCCATCAATTTCCAAGAA
Found at i:54872 original size:19 final size:19
Alignment explanation
Indices: 54845--54896 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
54835 TTGGACTCTT
*
54845 AGTGTATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
54864 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
54883 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
54897 TAAAATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:54967 original size:64 final size:63
Alignment explanation
Indices: 54863--55091 Score: 211
Period size: 65 Copynumber: 3.6 Consensus size: 63
54853 GGTGCACTAA
*
54863 GAGTGCATCGGTGCACTA-A-GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCC
1 GAGTGCATCGATGCA-TAGATG-GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CC
54926 T
63 T
* *
54927 GAGTGCATCGATGCAT-GACTGGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ACT
1 GAGTGCATCGATGCATAGA-TGGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAC-
54990 CT
62 CT
* * * * *
54992 GAGTGCATCGATGTATAGTAT-GTGCATCGATGCATGAAATGCATTTGATGTTT-AATTTATTCC
1 GAGTGCATCGATGCATAG-ATGGTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACC
55055 AT
63 -T
* *
55057 G-GTGCATCGATGCATGGATTGGTGCATCGGTGCAT
1 GAGTGCATCGATGCATAGA-TGGTGCATCGATGCAT
55092 CACTTTGAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 27
0.78 0.07 0.15
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 62 0.45
65 66 0.47
66 5 0.04
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (63 bp):
GAGTGCATCGATGCATAGATGGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCT
Found at i:56201 original size:22 final size:22
Alignment explanation
Indices: 56174--56216 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
56164 GAAGGAGCAC
56174 GAGAGGAGCTAGGAGCAACTCA
1 GAGAGGAGCTAGGAGCAACTCA
56196 GAGAGGAGCTAGGAGCAACTC
1 GAGAGGAGCTAGGAGCAACTC
56217 GTGAAGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.37, T:0.09
Consensus pattern (22 bp):
GAGAGGAGCTAGGAGCAACTCA
Found at i:57828 original size:21 final size:22
Alignment explanation
Indices: 57773--57853 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
57763 CATGGCCTTG
57773 TGCATCGATGCACATTCAAGGC
1 TGCATCGATGCACATTCAAGGC
* * *
57795 TTGCATCGGTGCACCTTCATGG-
1 -TGCATCGATGCACATTCAAGGC
* *
57817 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGC
57841 TGCATCGATGCAC
1 TGCATCGATGCAC
57854 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 14 0.30
22 1 0.02
23 20 0.43
24 12 0.26
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGC
Found at i:57864 original size:44 final size:44
Alignment explanation
Indices: 57776--57869 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
57766 GGCCTTGTGC
* * *
57776 ATCGATGCACATTCAAGGCTTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
* *
57820 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCATGCATCGATGCACCT-TCATAGTGT
57864 ATCGAT
1 ATCGAT
57870 TCATGAAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 26 0.60
45 17 0.40
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATAGTGT
Found at i:63580 original size:21 final size:21
Alignment explanation
Indices: 63554--63602 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
63544 GGGAGCGTCA
63554 GTGCATCGATGCATACCCAAG
1 GTGCATCGATGCATACCCAAG
* *
63575 GTGCATTGATGCATACTCAAG
1 GTGCATCGATGCATACCCAAG
63596 GTGCATC
1 GTGCATC
63603 AAGTGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCATACCCAAG
Found at i:63708 original size:64 final size:63
Alignment explanation
Indices: 63640--63819 Score: 213
Period size: 65 Copynumber: 2.8 Consensus size: 63
63630 TTAGACCCTT
* * *
63640 AGTGCATCGGTGCACTAAG-AGTGCACCGATGCATAAAATGCATTCAATGTTTCA-AAATAGC-C
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-A-CTC
63702 TG
62 TG
* *
63704 AGTGCATCGATGCATGGTTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACTCTG
* *
63769 AGTGCATCGATGCATAGTATGTGCATCAATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
63820 CAATTTATTC
Statistics
Matches: 101, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 44 0.44
65 52 0.51
66 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACTCTG
Found at i:63793 original size:65 final size:65
Alignment explanation
Indices: 63660--63867 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 65
63650 TGCACTAAGA
* * *
63660 GTGCACCGATGCATAAAATGCATTCAATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
63724 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATCGATGCATAGT
63787 AT-
64 -TG
* * ** * *
63789 GTGCATCAATGCATGAAATGCATTCGATG--TTCAATTTATTCCATG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATA-GCC-TGAGTGCATCGATGCATAG-
63851 TTG
63 TTG
*
63854 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
63868 CACTTTGAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 45 0.36
65 69 0.56
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
Found at i:73624 original size:46 final size:46
Alignment explanation
Indices: 73516--74003 Score: 771
Period size: 46 Copynumber: 10.6 Consensus size: 46
73506 TTAATTTCAA
* * * *
73516 TTATGGCCT-CTTGTCATGCCTTAATACACCCGTTCATACATTTTTAG
1 TTATGGCATCCTT-TCATGCCTTAATGCATCCGTTCATGCA-TTTTAG
73563 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* * *
73609 TTATGACATCCTTTCATGCCTTAAAAGCACCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTT-AATGCATCCGTTCATGCATTTTAG
* * *
73656 TTATGACATCCTTTCATGCCTTAATTCATCCGTTCATGCATTTTAT
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
73702 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGTATTCTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
73748 GTATGACATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
*
73794 TTATGGCATCCTTTCATGCCCTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
73840 TTATGGCATCCTTTCATGCCTTAACGCATTCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
*
73886 TTATGGCATCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
73932 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
*
73978 TTATGTCATCCTTTCATGCCTTAATG
1 TTATGGCATCCTTTCATGCCTTAATG
74004 ACAACATAGT
Statistics
Matches: 409, Mismatches: 30, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
46 330 0.81
47 76 0.19
48 3 0.01
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
Done.