Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003475.1 Hibiscus syriacus cultivar Beakdansim tig00007348_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: 74149
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7550 original size:16 final size:16
Alignment explanation
Indices: 7517--7550 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7507 TTACTATTCA
* *
7517 CGTGAATAGTGCATTT
1 CGTGAATAGTGAAATT
7533 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
7549 CG
1 CG
7551 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:13410 original size:6 final size:6
Alignment explanation
Indices: 13399--13427 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13389 GTATCACTCA
13399 CTTCAG CTTCAG CTTCAG CTTCAG CTTCA
1 CTTCAG CTTCAG CTTCAG CTTCAG CTTCA
13428 TTTCCTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.34
Consensus pattern (6 bp):
CTTCAG
Found at i:18386 original size:7 final size:7
Alignment explanation
Indices: 18374--18537 Score: 134
Period size: 7 Copynumber: 23.4 Consensus size: 7
18364 TATGATAAGA
18374 TTTAGGG
1 TTTAGGG
18381 TTTAGGG
1 TTTAGGG
18388 TTTAGGG
1 TTTAGGG
*
18395 TCTAGGG
1 TTTAGGG
*
18402 TCTAGGG
1 TTTAGGG
18409 TTTAGGG
1 TTTAGGG
* *
18416 TTTATGA
1 TTTAGGG
*
18423 TTTAAGG
1 TTTAGGG
*
18430 TTTAGAG
1 TTTAGGG
*
18437 TTTAGAG
1 TTTAGGG
*
18444 TTTAGAG
1 TTTAGGG
*
18451 TTTATGG
1 TTTAGGG
*
18458 TTTA-TG
1 TTTAGGG
* *
18464 TAATAGGA
1 T-TTAGGG
*
18472 TTTAAGG
1 TTTAGGG
*
18479 TTTAGAG
1 TTTAGGG
*
18486 TTTAGTG
1 TTTAGGG
*
18493 TTTATGG
1 TTTAGGG
* *
18500 TTTAAGA
1 TTTAGGG
18507 TTTA-GG
1 TTTAGGG
18513 TGTTAGGG
1 T-TTAGGG
18521 TTTAGGG
1 TTTAGGG
18528 TTTAGGG
1 TTTAGGG
18535 TTT
1 TTT
18538 TAGAGTTTAT
Statistics
Matches: 128, Mismatches: 25, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
6 4 0.03
7 120 0.94
8 4 0.03
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:18588 original size:14 final size:14
Alignment explanation
Indices: 18571--18617 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18561 AAGTTTATAA
18571 TTTAATGTTTAGGG
1 TTTAATGTTTAGGG
18585 TTTATATG-TTAGGG
1 TTTA-ATGTTTAGGG
* **
18599 GTTAGGGTTTAGGG
1 TTTAATGTTTAGGG
18613 TTTAA
1 TTTAA
18618 GTTGTAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 22 0.85
15 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
TTTAATGTTTAGGG
Found at i:20552 original size:12 final size:12
Alignment explanation
Indices: 20532--20656 Score: 114
Period size: 12 Copynumber: 10.8 Consensus size: 12
20522 GTCAAGCTTG
20532 AATCGAGCTCAC
1 AATCGAGCTCAC
*
20544 AATCAAGCTCAC
1 AATCGAGCTCAC
**
20556 AATCGAGCTTGC
1 AATCGAGCTCAC
*
20568 -ATTGAGCTCAC
1 AATCGAGCTCAC
*
20579 AATTGAGCTCAC
1 AATCGAGCTCAC
**
20591 AATCGAGCT-TG
1 AATCGAGCTCAC
*
20602 AATTGAGCTCAC
1 AATCGAGCTCAC
**
20614 AATCGAGCT-TG
1 AATCGAGCTCAC
*
20625 AATCGAGCTCAA
1 AATCGAGCTCAC
*
20637 AATCGAGCT-TC
1 AATCGAGCTCAC
20648 AATCGAGCT
1 AATCGAGCT
20657 TGAGTCTTGA
Statistics
Matches: 90, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
11 34 0.38
12 56 0.62
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (12 bp):
AATCGAGCTCAC
Found at i:20552 original size:23 final size:23
Alignment explanation
Indices: 20526--20656 Score: 129
Period size: 23 Copynumber: 5.7 Consensus size: 23
20516 GCTTAAGTCA
* *
20526 AGCTTGAATCGAGCTCACAATCA
1 AGCTTCAATCGAGCTCACAATCG
* ** *
20549 AGCTCACAATCGAGCTTGC-ATTG
1 AGCT-TCAATCGAGCTCACAATCG
* *
20572 AGCTCACAATTGAGCTCACAATCG
1 AGCT-TCAATCGAGCTCACAATCG
* *
20596 AGCTTGAATTGAGCTCACAATCG
1 AGCTTCAATCGAGCTCACAATCG
* *
20619 AGCTTGAATCGAGCTCAAAATCG
1 AGCTTCAATCGAGCTCACAATCG
20642 AGCTTCAATCGAGCT
1 AGCTTCAATCGAGCT
20657 TGAGTCTTGA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
23 74 0.81
24 17 0.19
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
AGCTTCAATCGAGCTCACAATCG
Found at i:20575 original size:35 final size:35
Alignment explanation
Indices: 20526--20622 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
20516 GCTTAAGTCA
* *
20526 AGCTTGAATCGAGCTCACAATCAAGCTCACAATCG
1 AGCTTGAATTGAGCTCACAATCGAGCTCACAATCG
* *
20561 AGCTTGCATTGAGCTCACAATTGAGCTCACAATCG
1 AGCTTGAATTGAGCTCACAATCGAGCTCACAATCG
20596 AGCTTGAATTGAGCTCACAATCGAGCT
1 AGCTTGAATTGAGCTCACAATCGAGCT
20623 TGAATCGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (35 bp):
AGCTTGAATTGAGCTCACAATCGAGCTCACAATCG
Found at i:20628 original size:11 final size:11
Alignment explanation
Indices: 20591--20659 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
20581 TTGAGCTCAC
20591 AATCGAGCTTG
1 AATCGAGCTTG
* **
20602 AATTGAGCTCAC
1 AATCGAGCT-TG
20614 AATCGAGCTTG
1 AATCGAGCTTG
**
20625 AATCGAGCTCAA
1 AATCGAGCT-TG
*
20637 AATCGAGCTTC
1 AATCGAGCTTG
20648 AATCGAGCTTG
1 AATCGAGCTTG
20659 A
1 A
20660 GTCTTGAGCT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 28 0.62
12 17 0.38
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (11 bp):
AATCGAGCTTG
Found at i:20677 original size:58 final size:58
Alignment explanation
Indices: 20549--20659 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
20539 CTCACAATCA
* * * *
20549 AGCTCACAATCGAGCTTGCATTGAGCTCACAATTGAGCTCACAATCGAGCTTGAATTG
1 AGCTCACAATCGAGCTTGAATCGAGCTCAAAATCGAGCTCACAATCGAGCTTGAATTG
*
20607 AGCTCACAATCGAGCTTGAATCGAGCTCAAAATCGAGCT-TCAATCGAGCTTGA
1 AGCTCACAATCGAGCTTGAATCGAGCTCAAAATCGAGCTCACAATCGAGCTTGA
20660 GTCTTGAGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 13 0.27
58 35 0.73
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (58 bp):
AGCTCACAATCGAGCTTGAATCGAGCTCAAAATCGAGCTCACAATCGAGCTTGAATTG
Found at i:25908 original size:3 final size:3
Alignment explanation
Indices: 25896--25925 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
25886 AATCGGCCCT
25896 ACA A-A ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
25926 AACCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:26461 original size:37 final size:37
Alignment explanation
Indices: 26371--26475 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
26361 CATTTTCGTC
*
26371 CTACTACGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* ** *
26408 TTGTTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
26445 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
26476 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:27107 original size:78 final size:78
Alignment explanation
Indices: 27025--27181 Score: 187
Period size: 78 Copynumber: 2.0 Consensus size: 78
27015 TCTATTTACG
* *
27025 TATATTACCTTTTATCATTATTATATATATTA-TATT-TATTGCT-TCATTTTCTTTATG-TGTA
1 TATATTACCTTTT-TCATT-TTATATATA-TACTATTAT-TTACTATCATTTT-TCTATGCTGTA
27086 TTTTATTTATTTATTTATA
61 -TTTATTTATTTATTTATA
* * *
27105 TATATTACCTTTTTTATTTTATATTTATACTATTATTTACTATCATTTTTCTATGCTTTATTTAT
1 TATATTACCTTTTTCATTTTATATATATACTATTATTTACTATCATTTTTCTATGCTGTATTTAT
27170 TTATTTATTTAT
66 TTATTTATTTAT
27182 TATTTTATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
77 2 0.03
78 38 0.56
79 15 0.22
80 13 0.19
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (78 bp):
TATATTACCTTTTTCATTTTATATATATACTATTATTTACTATCATTTTTCTATGCTGTATTTAT
TTATTTATTTATA
Found at i:27143 original size:23 final size:23
Alignment explanation
Indices: 27091--27143 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
27081 GTGTATTTTA
*
27091 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
27114 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
27135 TATTATTTA
1 T-TTATTTA
27144 CTATCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:27170 original size:4 final size:4
Alignment explanation
Indices: 27161--27257 Score: 67
Period size: 4 Copynumber: 22.8 Consensus size: 4
27151 TTTTCTATGC
*
27161 TTTA TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTT- CTT- TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA
27207 TGGTTGAA TTTA TTTA TTTA TTTA TTTTA TTTA TTTTA TTTTA TTTTA TTT
1 T--TT--A TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA -TTTA TTT
27258 TTTTTATATC
Statistics
Matches: 81, Mismatches: 2, Indels: 20
0.79 0.02 0.19
Matches are distributed among these distances:
3 8 0.10
4 42 0.52
5 28 0.35
6 2 0.02
8 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:27178 original size:37 final size:36
Alignment explanation
Indices: 27087--27181 Score: 88
Period size: 37 Copynumber: 2.6 Consensus size: 36
27077 TTATGTGTAT
* * *
27087 TTTATTTATTTATTTATATATATTACCTTTTTTATT
1 TTTATTTATTTATTTATTTATATTACATTTTTTATC
*
27123 TTATATTTATACTA-TTATTTACTA-T-CATTTTTCTATGC
1 TT-TATTTAT-TTATTTATTTA-TATTACATTTTT-TAT-C
27161 TTTATTTATTTATTTATTTAT
1 TTTATTTATTTATTTATTTAT
27182 TATTTTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
36 11 0.23
37 31 0.65
38 6 0.12
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.66
Consensus pattern (36 bp):
TTTATTTATTTATTTATTTATATTACATTTTTTATC
Found at i:27191 original size:5 final size:5
Alignment explanation
Indices: 27161--27264 Score: 82
Period size: 5 Copynumber: 22.0 Consensus size: 5
27151 TTTTCTATGC
27161 TTTA- TTTA- TTTA- TTTATT TATTAT TTTAT TTTAT TTCT-T TTTAT
1 TTTAT TTTAT TTTAT TTTA-T T-TTAT TTTAT TTTAT TT-TAT TTTAT
** * *
27205 TTTGG TTGAA TTTA- TTTA- TTTA- TTTAT TTTA- TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
27251 TTTAT TTT-T TTTAT
1 TTTAT TTTAT TTTAT
27265 ATCTAACATG
Statistics
Matches: 86, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
4 33 0.38
5 46 0.53
6 4 0.05
7 3 0.03
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:28351 original size:5 final size:5
Alignment explanation
Indices: 28341--28368 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28331 TCTTTTCATC
28341 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28369 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:29774 original size:7 final size:8
Alignment explanation
Indices: 29752--29790 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
29742 GAACATTTCA
*
29752 TGCATTCT
1 TGCATTTT
29760 TGCATTTT
1 TGCATTTT
29768 T-CATTTT
1 TGCATTTT
*
29775 TGCCTTTT
1 TGCATTTT
29783 TGCATTTT
1 TGCATTTT
29791 CATATACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.62
Consensus pattern (8 bp):
TGCATTTT
Found at i:29777 original size:15 final size:16
Alignment explanation
Indices: 29752--29790 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
29742 GAACATTTCA
*
29752 TGCATTCTTGCATTTT
1 TGCATTTTTGCATTTT
*
29768 T-CATTTTTGCCTTTT
1 TGCATTTTTGCATTTT
29783 TGCATTTT
1 TGCATTTT
29791 CATATACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.62
Consensus pattern (16 bp):
TGCATTTTTGCATTTT
Found at i:30938 original size:10 final size:9
Alignment explanation
Indices: 30918--30981 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 9
30908 AGATTCAATC
30918 AGAACAAAAA
1 AGAA-AAAAA
*
30928 GGAAAAAAA
1 AGAAAAAAA
30937 AG--AAAAA
1 AGAAAAAAA
30944 AGAAAAGAAGCA
1 AGAAAA-AA--A
30956 A-AAAAAAA
1 AGAAAAAAA
30964 AGAAAACAAA
1 AGAAAA-AAA
30974 AGAAAAAA
1 AGAAAAAA
30982 GAAAGAACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
7 7 0.16
8 2 0.04
9 14 0.31
10 16 0.36
11 4 0.09
12 2 0.04
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:30942 original size:7 final size:7
Alignment explanation
Indices: 30932--31009 Score: 63
Period size: 7 Copynumber: 11.0 Consensus size: 7
30922 CAAAAAGGAA
30932 AAAAAAG
1 AAAAAAG
30939 AAAAAAG
1 AAAAAAG
30946 AAAAGAAG
1 AAAA-AAG
30954 CAAAAAA-
1 -AAAAAAG
30961 AAAAGAA-
1 AAAA-AAG
30968 AACAAAAG
1 AA-AAAAG
30976 AAAAAAG
1 AAAAAAG
*
30983 AAAGAA-
1 AAAAAAG
* *
30989 CAAAAAT
1 AAAAAAG
*
30996 CAAAAAG
1 AAAAAAG
31003 AAAAAAG
1 AAAAAAG
31010 GACAAAAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
6 8 0.13
7 39 0.65
8 9 0.15
9 4 0.07
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:30948 original size:16 final size:16
Alignment explanation
Indices: 30923--31008 Score: 64
Period size: 20 Copynumber: 4.8 Consensus size: 16
30913 CAATCAGAAC
* *
30923 AAAAAGGAAAAAAAAG
1 AAAAAAGAAAAAAAAA
30939 AAAAAAGAAAAGAAGCAAAA
1 AAAAAAG-AAA-AA--AAAA
*
30959 AAAAAAGAAAACAAAAG
1 AAAAAAGAAAA-AAAAA
30976 AAAAAAGAAAGAACAAAA
1 AAAAAAGAAA-AA-AAAA
30994 ATCAAAAAGAAAAAA
1 A--AAAAAGAAAAAA
31009 GGACAAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
16 6 0.11
17 17 0.30
18 9 0.16
19 6 0.11
20 19 0.33
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.01
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:30969 original size:25 final size:25
Alignment explanation
Indices: 30930--30993 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
30920 AACAAAAAGG
*
30930 AAAAAAAAGAAAAAAGAAAAGAAGC
1 AAAAAAAAGAAAAAACAAAAGAAGC
30955 AAAAAAAA-AAGAAAACAAAAGAA--
1 AAAAAAAAGAA-AAAACAAAAGAAGC
*
30978 AAAAGAAAGAACAAAA
1 AAAAAAAAGAA-AAAA
30994 ATCAAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 19 0.56
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAAAACAAAAGAAGC
Found at i:30983 original size:17 final size:17
Alignment explanation
Indices: 30923--30985 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
30913 CAATCAGAAC
*
30923 AAAAAGGAAAA-AAAAG
1 AAAAAAGAAAACAAAAG
30939 AAAAAAGAAAAGAAGCAAAA-
1 AAAAAAG--AA-AA-CAAAAG
30959 AAAAAAGAAAACAAAAG
1 AAAAAAGAAAACAAAAG
30976 AAAAAAGAAA
1 AAAAAAGAAA
30986 GAACAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
16 11 0.28
17 12 0.30
18 4 0.10
19 2 0.05
20 7 0.17
21 4 0.10
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAACAAAAG
Found at i:30994 original size:20 final size:19
Alignment explanation
Indices: 30934--30993 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 19
30924 AAAAGGAAAA
30934 AAAAGAAAAAAGAAAAGAAGC
1 AAAAGAAAAAAG-AAAGAA-C
30955 AAAA-AAAAAAG-AA-AAC
1 AAAAGAAAAAAGAAAGAAC
30971 AAAAGAAAAAAGAAAGAAC
1 AAAAGAAAAAAGAAAGAAC
30990 AAAA
1 AAAA
30994 ATCAAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.14
17 9 0.25
18 4 0.11
19 7 0.19
20 7 0.19
21 4 0.11
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAGAAAGAAC
Found at i:31000 original size:20 final size:18
Alignment explanation
Indices: 30934--31005 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 18
30924 AAAAGGAAAA
30934 AAAAGAAAAAAGAAAAGAAGC
1 AAAA-AAAAAAG-AAAGAA-C
30955 AAAAAAAAAAG-AA-AAC
1 AAAAAAAAAAGAAAGAAC
30971 AAAAGAAAAAAGAAAGAAC
1 AAAA-AAAAAAGAAAGAAC
30990 AAAAATCAAAAAGAAA
1 AAAAA--AAAAAGAAA
31006 AAAGGACAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.11
17 9 0.20
18 5 0.11
19 7 0.15
20 16 0.35
21 4 0.09
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (18 bp):
AAAAAAAAAAGAAAGAAC
Found at i:31019 original size:37 final size:37
Alignment explanation
Indices: 30920--31008 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 37
30910 ATTCAATCAG
30920 AACAAAAAGGAAAAAAAAGAAAAAAGAAAAGAAGCAAA
1 AACAAAAA-GAAAAAAAAGAAAAAAGAAAAGAAGCAAA
30958 AA-AAAAAGAAAACAAAAGAAAAAAG-AAAGAA-CAAA
1 AACAAAAAGAAAA-AAAAGAAAAAAGAAAAGAAGCAAA
30993 AATCAAAAAGAAAAAA
1 AA-CAAAAAGAAAAAA
31009 GGACAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
35 6 0.12
36 13 0.27
37 27 0.56
38 2 0.04
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (37 bp):
AACAAAAAGAAAAAAAAGAAAAAAGAAAAGAAGCAAA
Found at i:31667 original size:22 final size:22
Alignment explanation
Indices: 31639--31693 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
31629 GCTACCCCAT
31639 CAAACCTTTGAGCACCAAATGC
1 CAAACCTTTGAGCACCAAATGC
*
31661 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCACCAAATGC
31683 CAAACCTTTGA
1 CAAACCTTTGA
31694 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCACCAAATGC
Found at i:33557 original size:106 final size:106
Alignment explanation
Indices: 32604--33556 Score: 1476
Period size: 106 Copynumber: 9.0 Consensus size: 106
32594 GTGCCACTAG
* * * * * * * *
32604 AGACAACACAAGCTCAACTTCACAATGAAGGGACGGATGGTTGTCAACAAATAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
32669 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
32710 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
32775 CAGAGCCAATTTCAGCTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
32816 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
32881 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
32922 AGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
32987 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
33028 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
33093 CAGAGCCAATTTCAACTTCACATCGAAAGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
33134 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
33199 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAATCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
33240 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
33305 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * *
33346 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
33411 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * * * * * * *
33452 AGATAACACAAGCTCAACTTCAC-AGCAAAGGGGCGGCTGATTGTCAACAAACAATTTCTCAGTT
1 AGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATT
* * * *
33516 CCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
33557 GGAACAATAC
Statistics
Matches: 791, Mismatches: 55, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
105 1 0.00
106 790 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:33866 original size:83 final size:83
Alignment explanation
Indices: 33754--33916 Score: 245
Period size: 83 Copynumber: 2.0 Consensus size: 83
33744 TATCTATCAA
* * * * *
33754 CAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCGCATCATTTACAGCATAGCTCAAGGCT
1 CAAAGACCGTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCT
*
33819 AGAAGGGCTATCTGTTAG
66 AGAAGAGCTATCTGTTAG
* *
33837 CAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCGTTTACAACATAACTCAAGGCT
1 CAAAGACCGTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCT
*
33902 AGAAGAGTTATCTGT
66 AGAAGAGCTATCTGT
33917 CATCAAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (83 bp):
CAAAGACCGTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCT
AGAAGAGCTATCTGTTAG
Found at i:34479 original size:37 final size:37
Alignment explanation
Indices: 34389--34493 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
34379 CATTTTCGTC
* *
34389 CTACTAGGATTCAAACTCCTAAAAATATGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
34426 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
34463 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
34494 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:35183 original size:4 final size:4
Alignment explanation
Indices: 35174--35266 Score: 59
Period size: 4 Copynumber: 21.8 Consensus size: 4
35164 TTTTCTATGC
*
35174 TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTT- CTT- TTTA TTT- TGGTTGAA
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA T--TT--A
35224 TTTA TTTA TTTA TTTA TTTTA TTTA TTTTA TTTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA -TTTA TTT
35267 TTTTTATATC
Statistics
Matches: 77, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
3 8 0.10
4 38 0.49
5 28 0.36
6 2 0.03
8 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:35191 original size:37 final size:36
Alignment explanation
Indices: 35100--35191 Score: 82
Period size: 37 Copynumber: 2.5 Consensus size: 36
35090 TTATGTGTAT
* * *
35100 TTTATTTATTTATTTATATATATTACCTTTTTTATT
1 TTTATTTATTTATTTATTTATATTACATTTTTTATC
*
35136 TTATATTTATACTA-TTATTTACTA-T-CATTTTTCTATGC
1 TT-TATTTAT-TTATTTATTTA-TATTACATTTTT-TAT-C
35174 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
35192 ATTTTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
36 10 0.22
37 29 0.64
38 6 0.13
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.66
Consensus pattern (36 bp):
TTTATTTATTTATTTATTTATATTACATTTTTTATC
Found at i:35200 original size:5 final size:5
Alignment explanation
Indices: 35190--35273 Score: 81
Period size: 5 Copynumber: 17.8 Consensus size: 5
35180 TATTTATTTA
** * *
35190 TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T TTA-T TTA-T
1 TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT TTATT TTATT
35237 TTATT TTA-T TTATT TTATT TTATT TTATT TT-TT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT
35274 ATCTAACATG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
4 21 0.31
5 46 0.68
6 1 0.01
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:39638 original size:147 final size:147
Alignment explanation
Indices: 39371--39668 Score: 524
Period size: 147 Copynumber: 2.0 Consensus size: 147
39361 CATTTTAATC
*
39371 ATTTTTGTTAAAATTCTTGAGAATTGAGGTATATGATCCATGAATTGAGATTTTCTTTGTATAAA
1 ATTTTTGTTAAAATTCTTGAGAATTGAAGTATATGATCCATGAATTGAGATTTTCTTTGTATAAA
* * * *
39436 ATGGTTTTATCATCAATATAAACATTAGCAATCGCTTTGTCCATTGTGAAGTTTCTGTTTTCTGA
66 ATGGTTTTATCATCAATATAAACAATAACAATCGCTTTGTCCATTATGAAGTTTCTGTTTTATGA
39501 ACATTTCCTGCTCAACT
131 ACATTTCCTGCTCAACT
*
39518 ATTTTTGTTAAATTTCTTGAGAATTGAAGTATATGATCCATGAATTGAGATTTTCTTTGTATAAA
1 ATTTTTGTTAAAATTCTTGAGAATTGAAGTATATGATCCATGAATTGAGATTTTCTTTGTATAAA
*
39583 ATGGTTTTATCATCAATATAAACAATAATAATCGCTTTGTCCATTATGAAGTTTCTGTTTTATGA
66 ATGGTTTTATCATCAATATAAACAATAACAATCGCTTTGTCCATTATGAAGTTTCTGTTTTATGA
*
39648 ACATTTCCTGCTCTACT
131 ACATTTCCTGCTCAACT
39665 ATTT
1 ATTT
39669 ATGTCTCTGG
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 143 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (147 bp):
ATTTTTGTTAAAATTCTTGAGAATTGAAGTATATGATCCATGAATTGAGATTTTCTTTGTATAAA
ATGGTTTTATCATCAATATAAACAATAACAATCGCTTTGTCCATTATGAAGTTTCTGTTTTATGA
ACATTTCCTGCTCAACT
Found at i:47218 original size:56 final size:56
Alignment explanation
Indices: 47096--47240 Score: 177
Period size: 56 Copynumber: 2.6 Consensus size: 56
47086 TTCGGACCTC
* * * * *
47096 TTATTTTTATAATTCTTAATAATAAAAACTGATAGATATACTCGATTTTGAAATCT
1 TTATTTTTATGATTCTTAATGATAACAACTGATAAATATACTCGATTTAGAAATCT
* *
47152 TTATTTTTATGTTTCTTAATGATAACAACTGATAAATATACTCGATTTCAG-AGTCT
1 TTATTTTTATGATTCTTAATGATAACAACTGATAAATATACTCGATTT-AGAAATCT
* * *
47208 TTATTTTTATGCTTATTAATG-TAACAACCGATA
1 TTATTTTTATGATTCTTAATGATAACAACTGATA
47241 GACGAAGCAC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
55 11 0.14
56 66 0.85
57 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (56 bp):
TTATTTTTATGATTCTTAATGATAACAACTGATAAATATACTCGATTTAGAAATCT
Found at i:48431 original size:13 final size:14
Alignment explanation
Indices: 48401--48433 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
48391 GAGTTTAAGA
48401 TTTAGGATATATGG
1 TTTAGGATATATGG
48415 TTTAGGATATA-GG
1 TTTAGGATATATGG
48428 TTTAGG
1 TTTAGG
48434 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.42
Consensus pattern (14 bp):
TTTAGGATATATGG
Found at i:54223 original size:20 final size:20
Alignment explanation
Indices: 54195--54236 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54185 GTGAAACTCC
* * *
54195 AAAAGAAGAAGAAGAAGAAG
1 AAAAAAAGAACAAGAAAAAG
54215 AAAAAAAGAACAAGAAAAAG
1 AAAAAAAGAACAAGAAAAAG
54235 AA
1 AA
54237 GGATGTAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAACAAGAAAAAG
Found at i:63239 original size:17 final size:17
Alignment explanation
Indices: 63213--63254 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
63203 CATAATCTTT
63213 TTATAA-TTATAATAATA
1 TTATAATTTAT-ATAATA
*
63230 TT-TAATTTATATTATA
1 TTATAATTTATATAATA
63246 TTATAATTT
1 TTATAATTT
63255 TTATTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATAATTTATATAATA
Found at i:63259 original size:17 final size:17
Alignment explanation
Indices: 63213--63266 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
63203 CATAATCTTT
* * *
63213 TTATAATTATAATAATA
1 TTATAATTTTTATTATA
*
63230 TT-TAATTTATATTATA
1 TTATAATTTTTATTATA
63246 TTATAATTTTTATTA-A
1 TTATAATTTTTATTATA
63262 TTATA
1 TTATA
63267 TCTAATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATAATTTTTATTATA
Found at i:69986 original size:21 final size:21
Alignment explanation
Indices: 69939--69998 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
69929 CCATGGTCCT
*
69939 ATTTAGGGTTTCTGAGTTTATG
1 ATTTAGGGTTT-AGAGTTTATG
* *
69961 -GTTAGGGTTTAGAGTTTGTG
1 ATTTAGGGTTTAGAGTTTATG
*
69981 ATTTAGGGGTTAGAGTTT
1 ATTTAGGGTTTAGAGTTT
69999 TAAATTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (21 bp):
ATTTAGGGTTTAGAGTTTATG
Found at i:71686 original size:25 final size:25
Alignment explanation
Indices: 71652--71702 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
71642 TGCTTTAGAA
71652 CCTTGATTCCTGACCAGACTCGACT
1 CCTTGATTCCTGACCAGACTCGACT
*
71677 CCTTGATTCCTGATCAGACTCGACT
1 CCTTGATTCCTGACCAGACTCGACT
71702 C
1 C
71703 GACCAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (25 bp):
CCTTGATTCCTGACCAGACTCGACT
Done.