Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000278.1 Hibiscus syriacus cultivar Beakdansim tig00000514_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: 50081
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:87 original size:18 final size:18
Alignment explanation
Indices: 74--110 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
64 AATTATTTTC
74 TTTCA-AATTTTTATGAT
1 TTTCATAATTTTTATGAT
91 TTTCATAATTTTTAT-AT
1 TTTCATAATTTTTATGAT
108 TTT
1 TTT
111 TTATTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCATAATTTTTATGAT
Found at i:2466 original size:21 final size:22
Alignment explanation
Indices: 2421--2493 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
2411 CATACATGCA
*
2421 TTTACATTTTGTATCTGTTCAT
1 TTTACATTTTGTATCTGTACAT
*
2443 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
* *
2464 TTTACATCTTTGAAT-TGCACAT
1 TTTACAT-TTTGTATCTGTACAT
*
2486 TTTGCATT
1 TTTACATT
2494 CTTATTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.41
22 19 0.46
23 5 0.12
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:5049 original size:15 final size:15
Alignment explanation
Indices: 5029--5085 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
5019 AAGAAAGAAG
5029 AAGGAAAAAAACAAA
1 AAGGAAAAAAACAAA
5044 AAGG----AAA-AAA
1 AAGGAAAAAAACAAA
5054 AAGGAAAAAAAACAAA
1 AAGG-AAAAAAACAAA
*
5070 AA-GAAAAAAAGAAA
1 AAGGAAAAAAACAAA
5084 AA
1 AA
5086 AAGGGGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
10 7 0.20
11 3 0.09
14 12 0.34
15 8 0.23
16 5 0.14
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAACAAA
Found at i:5050 original size:26 final size:23
Alignment explanation
Indices: 5018--5087 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 23
5008 CTCATCCAGC
5018 AAAGAAAGAAGAAGGAAAAAAACAA
1 AAAGAAA-AA-AAGGAAAAAAACAA
5043 AAAGGAAAAAAAAGGAAAAAAAACAA
1 AAA-G-AAAAAAAGG-AAAAAAACAA
5069 AAAGAAAAAAA-GAAAAAAA
1 AAAGAAAAAAAGGAAAAAAA
5088 GGGGAAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.17
23 1 0.02
24 7 0.17
25 8 0.19
26 16 0.38
27 3 0.07
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAAGGAAAAAAACAA
Found at i:5054 original size:16 final size:17
Alignment explanation
Indices: 5049--5089 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
5039 ACAAAAAGGA
5049 AAAAAAAGGAAAAAAA-
1 AAAAAAAGGAAAAAAAG
*
5065 ACAAAAA-GAAAAAAAG
1 AAAAAAAGGAAAAAAAG
5081 AAAAAAAGG
1 AAAAAAAGG
5090 GGAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 12 0.57
17 1 0.05
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGGAAAAAAAG
Found at i:5056 original size:10 final size:10
Alignment explanation
Indices: 5041--5065 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5031 GGAAAAAAAC
5041 AAAAAGGAAA
1 AAAAAGGAAA
5051 AAAAAGGAAA
1 AAAAAGGAAA
5061 AAAAA
1 AAAAA
5066 CAAAAAGAAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGGAAA
Found at i:5086 original size:15 final size:15
Alignment explanation
Indices: 5022--5088 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
5012 TCCAGCAAAG
* *
5022 AAAGAAGAAGGAAAA
1 AAAGAAAAAAGAAAA
* *
5037 AAACAAAAAGGAAAAA
1 AAAGAAAAAAG-AAAA
5053 AAAGGAAAAAA-AACAA
1 AAA-GAAAAAAGAA-AA
5069 AAAGAAAAAAAGAAAA
1 AAAG-AAAAAAGAAAA
5085 AAAG
1 AAAG
5089 GGGAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 12 0.28
16 24 0.56
17 7 0.16
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:9843 original size:22 final size:22
Alignment explanation
Indices: 9791--9865 Score: 118
Period size: 21 Copynumber: 3.5 Consensus size: 22
9781 ATCTACACTC
9791 TTCAAAGATGATAGATTCTC-T
1 TTCAAAGATGATAGATTCTCTT
9812 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
9834 TTTAAAGATGATATA-TCTCTT
1 TTCAAAGATGATAGATTCTCTT
9855 TTCAAAGATGA
1 TTCAAAGATGA
9866 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 36 0.72
22 14 0.28
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:10668 original size:76 final size:76
Alignment explanation
Indices: 10542--11485 Score: 1717
Period size: 76 Copynumber: 12.4 Consensus size: 76
10532 CTATTTCCCA
10542 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
10607 AGGCTTAGGGT
66 AGCCTTAGGGT
**
10618 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
10683 AGCCTTAGGGT
66 AGCCTTAGGGT
10694 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
10759 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* * *
10771 CATCTGTATGTCCTACAGTGCATGATGTTTCCAAAAAACTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
10836 AGCCTTAGGGT
66 AGCCTTAGGGT
10847 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
10912 AGCCTTAGGGT
66 AGCCTTAGGGT
*
10923 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
10988 AGCCTTAGGGT
66 AGCCTTAGGGT
10999 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
11064 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
11076 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
11141 AGCCATAGGGT
66 AGCCTTAGGGT
11152 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11217 AGCCTTAGGGT
66 AGCCTTAGGGT
*
11228 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11293 AGCCTTAGGGT
66 AGCCTTAGGGT
*
11304 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11369 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
11380 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
11445 AACCTTAGGGT
66 AGCCTTAGGGT
**
11456 CATCTGTAAGTCCTTTAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
11486 TCAACATTTC
Statistics
Matches: 843, Mismatches: 23, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
76 694 0.82
77 149 0.18
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:11093 original size:305 final size:305
Alignment explanation
Indices: 10542--11485 Score: 1746
Period size: 305 Copynumber: 3.1 Consensus size: 305
10532 CTATTTCCCA
10542 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
10607 AGGCTTAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
10672 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
*
10737 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTATGTCCTACAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
*
10802 CAAAAAACTTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
10847 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
10912 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
10977 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
11042 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
* * *
11107 TAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCATAGGGT
261 CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
11152 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11217 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
11282 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
*
11346 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
* *
11411 CAAAAAACCTTCGGGAGATTTTTGATGTTTTCAAAACCTTAGGGT
261 CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
**
11456 CATCTGTAAGTCCTTTAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
11486 TCAACATTTC
Statistics
Matches: 619, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
304 142 0.23
305 477 0.77
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (305 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:11632 original size:3 final size:3
Alignment explanation
Indices: 11624--11673 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
11614 TAAAATTAAA
* *
11624 ATT ATT ATT TTT ATT ATT ATT ATT AAT A-T ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
11669 ATT AT
1 ATT AT
11674 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11674 original size:21 final size:21
Alignment explanation
Indices: 11624--11676 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11614 TAAAATTAAA
* *
11624 ATTATTATTTTTATTATTATT
1 ATTATTATATATATTATTATT
*
11645 ATTAATATATATATTATTATT
1 ATTATTATATATATTATTATT
11666 ATTATTATATA
1 ATTATTATATA
11677 AATAAATTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTATATATATTATTATT
Found at i:17123 original size:25 final size:25
Alignment explanation
Indices: 17095--17145 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
17085 TAATAAATAG
17095 TGATAATACAAAACATATCATATAA
1 TGATAATACAAAACATATCATATAA
** *
17120 TGATAATATGAAAGATATCATATAA
1 TGATAATACAAAACATATCATATAA
17145 T
1 T
17146 AATATATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (25 bp):
TGATAATACAAAACATATCATATAA
Found at i:21609 original size:31 final size:31
Alignment explanation
Indices: 21571--21631 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
21561 CTTATTAGGG
*
21571 AGAGATACTAGAGTCTCTTTGAATTCAATTA
1 AGAGATACTAGAGTCTCTTTGAATCCAATTA
21602 AGAGATACTAGAGTCTCTTTGAATCCAATT
1 AGAGATACTAGAGTCTCTTTGAATCCAATT
21632 GAATTGGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (31 bp):
AGAGATACTAGAGTCTCTTTGAATCCAATTA
Found at i:23027 original size:17 final size:17
Alignment explanation
Indices: 22994--23076 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 17
22984 AATCTACGTT
*
22994 TGATAATTGTAAAACATC
1 TGATAACTGT-AAACATC
23012 TGATAACTGTAAACATC
1 TGATAACTGTAAACATC
* * * *
23029 TTATAATTGAAAATCATA
1 TGATAACTGTAAA-CATC
* * *
23047 TAATAACTTTAAATATC
1 TGATAACTGTAAACATC
*
23064 TGATAAATGTAAA
1 TGATAACTGTAAA
23077 TATTTAGAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
17 29 0.58
18 21 0.42
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (17 bp):
TGATAACTGTAAACATC
Found at i:23035 original size:35 final size:36
Alignment explanation
Indices: 22994--23076 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 36
22984 AATCTACGTT
* *
22994 TGATAATTGTAAAA-CATCTGATAACTGTAAACATC
1 TGATAATTGTAAAATCATATAATAACTGTAAACATC
* * *
23029 TTATAATTG-AAAATCATATAATAACTTTAAATATC
1 TGATAATTGTAAAATCATATAATAACTGTAAACATC
*
23064 TGATAAATGTAAA
1 TGATAATTGTAAA
23077 TATTTAGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 4 0.10
35 32 0.82
36 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (36 bp):
TGATAATTGTAAAATCATATAATAACTGTAAACATC
Found at i:26035 original size:14 final size:15
Alignment explanation
Indices: 26016--26044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26006 ACTAAATCAT
26016 TATTTT-TTTAAAAA
1 TATTTTATTTAAAAA
26030 TATTTTATTTAAAAA
1 TATTTTATTTAAAAA
26045 GATTCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTATTTAAAAA
Found at i:31488 original size:11 final size:11
Alignment explanation
Indices: 31472--31496 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31462 TAGGAAAACG
31472 GATTAATATAC
1 GATTAATATAC
31483 GATTAATATAC
1 GATTAATATAC
31494 GAT
1 GAT
31497 ATTATCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (11 bp):
GATTAATATAC
Found at i:31785 original size:112 final size:112
Alignment explanation
Indices: 31634--32317 Score: 1022
Period size: 112 Copynumber: 6.1 Consensus size: 112
31624 TTGTCGGTTT
* * * * * *
31634 GTGTCGATATTTTATAAAAATATATTGATCCATAACAATATAACATGTAAGAAAATAATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACC
* * *
31699 GGTTTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAA
66 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
31746 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACACGTAAAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGT--AAAAAAATGACAAAA
* *
31811 TCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
64 CCGGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
31860 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACC
* *
31925 GGTCTATAAATGACAAAACAGCTAAAGCGCTACCGGATATATTGAAA
66 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
31972 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACC
32036 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
32083 GTGTCGATACTTTATAAAAATATATCGATCAATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACC
*
32148 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* ** * *
32195 GTGTCGATACTTTATAAAAATGTATTAAGT-CATAACAATGTAACA-GATAAAAAAATGCCAAAA
1 GTGTCGATACTTTATAAAAATATATCGA-TCCATAACAATATAACACG-TAAAAAAATGACAAAA
* *
32258 CCGGTATATAAATGACAAAACAGGT----CGCTACCGGATATGTTGATA
64 CCGGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
32303 GCGTCGATATTTTAT
1 GTGTCGATACTTTAT
32318 TATAAGTATC
Statistics
Matches: 534, Mismatches: 33, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
108 31 0.06
111 107 0.20
112 292 0.55
113 1 0.00
114 103 0.19
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACC
GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:32135 original size:223 final size:223
Alignment explanation
Indices: 31634--32317 Score: 1047
Period size: 223 Copynumber: 3.1 Consensus size: 223
31624 TTGTCGGTTT
* * * * * *
31634 GTGTCGATATTTTATAAAAATATATTGATCCATAACAATATAACATGTAAGAAAATAATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
31699 GGTTTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
31764 AATATATTGATCCATAACAATATAACACGTAAAAAAAAATGACAAAATCGGTCTATAAATGACAA
131 AATATATTGATCCATAACAATATAACA-GT--AAAAAAATGACAAAACCGGTATATAAATGACAA
31829 AACAGGTAAAGCGCTACCGGATATATTGAAA
193 AACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
31860 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACACGTAAAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
31925 GGTCTATAAATGACAAAACAGCTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
31990 AATATATCGATCCATAACAATATAACATGT-AAAAAATGACAAAACCGGTATATAAATGACAAAA
131 AATATATTGATCCATAACAATATAACA-GTAAAAAAATGACAAAACCGGTATATAAATGACAAAA
32054 CAGGTAAAGCGCTACCGGATATATTGAAA
195 CAGGTAAAGCGCTACCGGATATATTGAAA
*
32083 GTGTCGATACTTTATAAAAATATATCGATCAATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
32148 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * * *
32213 AATGTATTAAGT-CATAACAATGTAACAGATAAAAAAATGCCAAAACCGGTATATAAATGACAAA
131 AATATATTGA-TCCATAACAATATAACAG-TAAAAAAATGACAAAACCGGTATATAAATGACAAA
* *
32277 ACAGGT----CGCTACCGGATATGTTGATA
194 ACAGGTAAAGCGCTACCGGATATATTGAAA
* *
32303 GCGTCGATATTTTAT
1 GTGTCGATACTTTAT
32318 TATAAGTATC
Statistics
Matches: 424, Mismatches: 31, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
220 31 0.07
222 1 0.00
223 207 0.49
224 39 0.09
226 146 0.34
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (223 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATATATTGATCCATAACAATATAACAGTAAAAAAATGACAAAACCGGTATATAAATGACAAAAC
AGGTAAAGCGCTACCGGATATATTGAAA
Found at i:32559 original size:181 final size:177
Alignment explanation
Indices: 32192--32639 Score: 594
Period size: 181 Copynumber: 2.5 Consensus size: 177
32182 GGATATATTG
* * * *
32192 AAAGTGTCGATACTTTATAAAAATGTATTAAGT-CATAACAATGTAACAGATAAAAAAATGCCAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGA-TCCATAACAATATAACAG-TAAAAATATGACAA
** * * * * *
32256 AACCGGTATATAAATGACAAAACAGGTCGCTACCGGATATGTTGATAGCGTCGATATTTTATTAT
64 AACCGGTATCGAAATGACAAAACCGGTAGCTACCAGATATGTTGAAAGCGTCGATACTTTATTAT
* * *
32321 AAGTATCGACGCTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
129 AAGTATCGACGATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
* * *
32370 AAAGTGTCGATATTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACA-GTAAAAATATGACAAA
* *
32435 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
65 ACCGGTATCGAAATGACAAAACCGGT----AGCTACCAGATATGTTGAAAGCGTCGATACTTTAT
*
32500 TATAATTATCGAC-ATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
126 TATAAGTATCGACGATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
* * *
32551 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAATAATATAGCAGGAAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACA-GTAAAAATATGACAAA
*
32616 ATCGGTATCGAAATGACAAAACCG
65 ACCGGTATCGAAATGACAAAACCG
32640 ATAATAAAAA
Statistics
Matches: 235, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
177 1 0.00
178 76 0.32
179 1 0.00
181 115 0.49
182 42 0.18
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (177 bp):
AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGTAAAAATATGACAAAA
CCGGTATCGAAATGACAAAACCGGTAGCTACCAGATATGTTGAAAGCGTCGATACTTTATTATAA
GTATCGACGATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:33509 original size:2 final size:2
Alignment explanation
Indices: 33502--33534 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33492 AAGATAGAAA
33502 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 A
33535 AGTTAGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36734 original size:16 final size:16
Alignment explanation
Indices: 36713--36780 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
36703 AATTGATTGG
36713 GTTATTTTCGGTTCGA
1 GTTATTTTCGGTTCGA
* *
36729 GTTATTTTCGATTCGG
1 GTTATTTTCGGTTCGA
* **
36745 GTTAATTTCACTTC-A
1 GTTATTTTCGGTTCGA
* *
36760 TGTTACTTTCGGTTCGG
1 -GTTATTTTCGGTTCGA
36777 GTTA
1 GTTA
36781 AATTGGATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (16 bp):
GTTATTTTCGGTTCGA
Found at i:47494 original size:18 final size:18
Alignment explanation
Indices: 47471--47506 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47461 GTAGAACACA
47471 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
47489 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
47507 GTAGAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Done.