Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003305.1 Hibiscus syriacus cultivar Beakdansim tig00006951_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: 100740
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:14523 original size:22 final size:22
Alignment explanation
Indices: 14497--14541 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
14487 ACTTTTTGGG
*
14497 TTTTTTTACTTTTTTATATATTA
1 TTTTTTCACTTTTTTA-ATATTA
*
14520 TTTTTTCATTTTTTTAATATTA
1 TTTTTTCACTTTTTTAATATTA
14542 GCCATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTCACTTTTTTAATATTA
Found at i:15314 original size:12 final size:12
Alignment explanation
Indices: 15297--15323 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15287 AAATGAAAAA
15297 TTTAAGTTAATT
1 TTTAAGTTAATT
15309 TTTAAGTTAATT
1 TTTAAGTTAATT
15321 TTT
1 TTT
15324 CGATCCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTAAGTTAATT
Found at i:15550 original size:2 final size:2
Alignment explanation
Indices: 15545--15572 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15535 ACACACACAC
15545 AT AT AT 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
15573 TTTCTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15973 original size:12 final size:10
Alignment explanation
Indices: 15945--15992 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
15935 ATGTTGTTCT
*
15945 AAGAAAGCAC
1 AAGAAATCAC
15955 AAGAAATCAC
1 AAGAAATCAC
15965 GAGAGAAATACAC
1 -A-AGAAAT-CAC
15978 AAGAAATCA-
1 AAGAAATCAC
15987 AAGAAA
1 AAGAAA
15993 AAAAGACACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 6 0.18
10 11 0.32
11 7 0.21
12 7 0.21
13 3 0.09
ACGTcount: A:0.62, C:0.15, G:0.17, T:0.06
Consensus pattern (10 bp):
AAGAAATCAC
Found at i:16828 original size:34 final size:32
Alignment explanation
Indices: 16790--16863 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 32
16780 CTATATATTC
16790 TTTTTTCATTTATTTT-CTTTTTTAGTATTAGCCA
1 TTTTTT-ATTTATTTTCCTTTTTTA-T-TTAGCCA
*
16824 TTTTTATATTTATTTTCCTTTTTTATTTAGCTA
1 TTTTT-TATTTATTTTCCTTTTTTATTTAGCCA
16857 TTTTTTA
1 TTTTTTA
16864 GGTTTTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 2 0.05
33 11 0.30
34 15 0.41
35 9 0.24
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (32 bp):
TTTTTTATTTATTTTCCTTTTTTATTTAGCCA
Found at i:19008 original size:76 final size:78
Alignment explanation
Indices: 18919--19068 Score: 232
Period size: 77 Copynumber: 1.9 Consensus size: 78
18909 TACATAATTC
* *
18919 ATCTATAGAAGATCCGGGTGTGCAAC-GAAAAGCACATAACATCTCAACTTTTTCACACATT-TT
1 ATCTATAGAAGATCCGGGTGTACAACAAAAAAGCACATAACATCTCAACTTTTTCACACATTCTT
18982 CCATTATTAGTTA
66 CCATTATTAGTTA
* * *
18995 ATCTATAGAAGATCCGGGTGTACGACAAAAAATCACATAACATCTCAACTTTTTCATACATTCTT
1 ATCTATAGAAGATCCGGGTGTACAACAAAAAAGCACATAACATCTCAACTTTTTCACACATTCTT
*
19060 CTATTATTA
66 CCATTATTA
19069 ATTACTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 24 0.36
77 32 0.48
78 10 0.15
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (78 bp):
ATCTATAGAAGATCCGGGTGTACAACAAAAAAGCACATAACATCTCAACTTTTTCACACATTCTT
CCATTATTAGTTA
Found at i:23016 original size:2 final size:2
Alignment explanation
Indices: 23009--23041 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22999 ATAAGTAAAA
*
23009 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23042 ATAAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:24833 original size:200 final size:201
Alignment explanation
Indices: 24484--25003 Score: 693
Period size: 200 Copynumber: 2.5 Consensus size: 201
24474 TGTATTGTTC
* * * * * * * *
24484 CGAGTCCAATATCATCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGGTTGTTGACA
1 CGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
24549 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
66 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
*
24614 AGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTAACAACCAGCCGTCC-C-TGAACTTGTG
131 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTAACAACCAGCCGTCCTCGTGAACTTGTG
24677 CTGTCT
196 CTGTCT
* *
24683 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTTGTTGAC
1 CGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-GTTTGTTGAC
* * *
24748 AACCAGTCGTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGGTGTG
65 AACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
* * *
24813 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCATTCGTTGTGAA
130 AAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTAACAACCAGCCGTCC--TC--------
*
24878 GTTGAACTTGTGTTGTCT
185 G-TGAACTTGTGCTGTCT
* * * *
24896 TGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
24961 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
25004 GGTGGCGCGA
Statistics
Matches: 278, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
199 46 0.17
200 117 0.42
203 1 0.00
212 50 0.18
213 64 0.23
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (201 bp):
CGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTAACAACCAGCCGTCCTCGTGAACTTGTG
CTGTCT
Found at i:24896 original size:106 final size:106
Alignment explanation
Indices: 24667--25001 Score: 562
Period size: 106 Copynumber: 3.2 Consensus size: 106
24657 CAGCCGTCCC
* * **
24667 TGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
1 TGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * *
24732 AAATTATTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAAT
66 AAGTT-GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGT
*
24774 TGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGGTGTGAAGTTGAAATTGGCTCTGAAATTGGG
1 TGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
24839 AAGTTGTTTGTTGACAACCAGTCGTCCATTCGTTGTGAAGT
66 AAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGT
*
24880 TGAACTTGTGTTGTCTTGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
1 TGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
24945 AAGTTGTTTGTTGACAACCAGTCATCCCTTCGTTGTGAAGT
66 AAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGT
24986 TGAACTTGTGTTGTCT
1 TGAACTTGTGTTGTCT
25002 CGGGTGGCGC
Statistics
Matches: 215, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
106 151 0.70
107 64 0.30
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (106 bp):
TGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
AAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGT
Found at i:25711 original size:37 final size:37
Alignment explanation
Indices: 25629--25713 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
25619 GTTTCATGAG
* * * * **
25629 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
25666 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
25702 GAAATTGTCTCA
1 -AAACTGTCTCA
25714 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:26374 original size:18 final size:18
Alignment explanation
Indices: 26347--26382 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
26337 TGTTGAATCC
*
26347 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
26365 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
26383 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:27506 original size:15 final size:15
Alignment explanation
Indices: 27457--27507 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
27447 TTTTGCTTCT
*
27457 TTCTTTTCTGTTCTTG
1 TTCTTTTCT-TTTTTG
27473 TT-TTTTCTTTTTTG
1 TTCTTTTCTTTTTTG
27487 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
27503 TTCTT
1 TTCTT
27508 GATTGAATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 5 0.16
15 13 0.41
16 14 0.44
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:33797 original size:43 final size:43
Alignment explanation
Indices: 33736--33880 Score: 245
Period size: 43 Copynumber: 3.4 Consensus size: 43
33726 CGTTCCTGGC
*
33736 TTCCTGCCTTGATTTTCTTGGTTCTCCTTTCCAGGTGATCAAG
1 TTCCTGCCTTGATTTTCTTGGTGCTCCTTTCCAGGTGATCAAG
33779 TTCCTGCCTTGATTTTCTTGGTGCTCCTTTCCAGGTGATCAAG
1 TTCCTGCCTTGATTTTCTTGGTGCTCCTTTCCAGGTGATCAAG
* * * *
33822 TTCCTGCCTTGATTTTCTTGGCGCTCCTTTTCAAGTGATCGAG
1 TTCCTGCCTTGATTTTCTTGGTGCTCCTTTCCAGGTGATCAAG
33865 TTCCTGCCTTGATTTT
1 TTCCTGCCTTGATTTT
33881 TTTATTTGCA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (43 bp):
TTCCTGCCTTGATTTTCTTGGTGCTCCTTTCCAGGTGATCAAG
Found at i:35769 original size:27 final size:28
Alignment explanation
Indices: 35712--35769 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
35702 ATTTAATACT
* **
35712 TATATATATAACTCCTTCCGATGTCAATA
1 TATATATATAACCCCTTCC-ACCTCAATA
*
35741 TATATATATAACCCCTTCC-CCTCATTA
1 TATATATATAACCCCTTCCACCTCAATA
35768 TA
1 TA
35770 ATTTTCTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (28 bp):
TATATATATAACCCCTTCCACCTCAATA
Found at i:36183 original size:24 final size:24
Alignment explanation
Indices: 36151--36199 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
36141 TGAATTCGGA
36151 TTCGGATAAAGATAAAATCAACAC
1 TTCGGATAAAGATAAAATCAACAC
*
36175 TTCGGATAAAGATCAAATCAACAC
1 TTCGGATAAAGATAAAATCAACAC
36199 T
1 T
36200 ATTCCAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
TTCGGATAAAGATAAAATCAACAC
Found at i:42365 original size:3 final size:3
Alignment explanation
Indices: 42351--42389 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
42341 GTGCCAGAAA
42351 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42390 ATTAGTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:43995 original size:30 final size:28
Alignment explanation
Indices: 43939--44034 Score: 95
Period size: 30 Copynumber: 3.3 Consensus size: 28
43929 TTTTATCTAT
*
43939 TTTAGTCCTTTAA-ATGTTTGTATTTGTTA
1 TTTAGTCCTTTAACAT-TCTGT-TTTGTTA
* *
43968 TTTTAGTCCTTTAACCTTCTATTTTTGTTA
1 -TTTAGTCCTTTAACATTCT-GTTTTGTTA
* *
43998 TTTAGACCCTTTAACATTCTGTTTTGGTA
1 TTTAG-TCCTTTAACATTCTGTTTTGTTA
44027 TTTAGTCC
1 TTTAGTCC
44035 CTTAGGCTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 17 0.31
30 34 0.62
31 2 0.04
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTAGTCCTTTAACATTCTGTTTTGTTA
Found at i:44022 original size:29 final size:29
Alignment explanation
Indices: 43961--44037 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
43951 AATGTTTGTA
* * *
43961 TTTGTTATTTTAGTCCTTTAACCTTCTATT
1 TTTGTTA-TTTAGCCCTTTAACATTCTAGT
43991 TTTGTTATTTAGACCCTTTAACATTCT-GT
1 TTTGTTATTTAG-CCCTTTAACATTCTAGT
*
44020 TTTGGTATTTAGTCCCTT
1 TTTGTTATTTAG-CCCTT
44038 AGGCTTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTGTTATTTAGCCCTTTAACATTCTAGT
Found at i:44766 original size:13 final size:14
Alignment explanation
Indices: 44743--44775 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44733 TAAAAATGAT
44743 TTTTATTAAAAT-TG
1 TTTT-TTAAAATATG
44757 TTTTTTAAAATATG
1 TTTTTTAAAATATG
44771 TTTTT
1 TTTTT
44776 AGGTATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTTTAAAATATG
Found at i:47461 original size:13 final size:13
Alignment explanation
Indices: 47443--47472 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47433 TACCCAACAA
*
47443 AATATATATATAT
1 AATATATATATAC
47456 AATATATATATAC
1 AATATATATATAC
47469 AATA
1 AATA
47473 AAGATGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATATATATAC
Found at i:48754 original size:13 final size:13
Alignment explanation
Indices: 48723--48782 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
48713 CAAAGCAGAG
* *
48723 AGAAAAACAAAGA
1 AGAAAAATAAAAA
*
48736 ACAAAAATAAAAA
1 AGAAAAATAAAAA
*
48749 AG-AAAATAATGAA
1 AGAAAAATAA-AAA
48762 AGAGAAAATAAACAA
1 AGA-AAAATAAA-AA
48777 AGAAAA
1 AGAAAA
48783 GGGGACAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.19
13 15 0.41
14 3 0.08
15 12 0.32
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.07
Consensus pattern (13 bp):
AGAAAAATAAAAA
Found at i:50220 original size:47 final size:46
Alignment explanation
Indices: 50136--50541 Score: 273
Period size: 47 Copynumber: 9.3 Consensus size: 46
50126 ACTGATTGCA
* *
50136 TATGAGCAGTGTCA--ACCC-T--AGATAACCAAAACTTATCACAG
1 TATGAGCAGTGTCATCACCCTTCCAGATAACCAAGACTTATCATAG
* **
50177 TATGAGCAGTGTTATCACCCTTCCGAGATGGCCAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCC-AGATAACCAAGACTTATCATAG
* * *
50224 TATGAGCAGTGTCATC-CCCTGACCAGAT--CTC----CTCATCA-CG
1 TATGAGCAGTGTCATCACCCT-TCCAGATAAC-CAAGACTTATCATAG
* *
50264 TAGGAGCCGTGTCA--ACCC-T--AGATAACCAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCCAGATAACCAAGACTTATCATAG
* * **
50305 TATGAGCAGTGTTATCACTCTTCCTAGATGGCCAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCC-AGATAACCAAGACTTATCATAG
**
50352 TATGAGCAGTGTCATC-CCC-T---G---ACCAA-ATCTCCTCATCACG
1 TATGAGCAGTGTCATCACCCTTCCAGATAACCAAGA-CTTATCAT-A-G
* *
50392 TAGGAGCCGTGTCA--ACCC-T--AGATAACCAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCCAGATAACCAAGACTTATCATAG
* *
50433 TATGAGCAGTGTTATCACCCTTCCTAGATAACAAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCC-AGATAACCAAGACTTATCATAG
* * * **
50480 TATGAGCATTGTTATCACCCTTCCTAGGTGGCCAAGACTTATCATAG
1 TATGAGCAGTGTCATCACCCTTCC-AGATAACCAAGACTTATCATAG
*
50527 TATGAGTAGTGTCAT
1 TATGAGCAGTGTCAT
50542 TAACCGACCT
Statistics
Matches: 287, Mismatches: 41, Indels: 68
0.72 0.10 0.17
Matches are distributed among these distances:
35 4 0.01
36 1 0.00
37 2 0.01
38 10 0.03
39 8 0.03
40 33 0.11
41 44 0.15
42 1 0.00
43 22 0.08
44 5 0.02
45 2 0.01
46 10 0.03
47 145 0.51
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (46 bp):
TATGAGCAGTGTCATCACCCTTCCAGATAACCAAGACTTATCATAG
Found at i:50372 original size:128 final size:128
Alignment explanation
Indices: 50139--50487 Score: 617
Period size: 128 Copynumber: 2.7 Consensus size: 128
50129 GATTGCATAT
* * * *
50139 GAGCAGTGTCAACCCTAGATAACCAAAACTTATCACAGTATGAGCAGTGTTATCACCCTTCCGAG
1 GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAG
*
50204 ATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACGTAG
66 ATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCTGACCAAATCTCCTCATCACGTAG
*
50267 GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACTCTTCCTAG
1 GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAG
50332 ATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCTGACCAAATCTCCTCATCACGTAG
66 ATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCTGACCAAATCTCCTCATCACGTAG
50395 GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAG
1 GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAG
** *
50460 ATAACAAAGACTTATCATAGTATGAGCA
66 ATGGCCAAGACTTATCATAGTATGAGCA
50488 TTGTTATCAC
Statistics
Matches: 211, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 211 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (128 bp):
GAGCCGTGTCAACCCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAG
ATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCTGACCAAATCTCCTCATCACGTAG
Found at i:50461 original size:175 final size:175
Alignment explanation
Indices: 50280--50594 Score: 481
Period size: 175 Copynumber: 1.8 Consensus size: 175
50270 CCGTGTCAAC
* *
50280 CCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACTCTTCCTAGATGGCCAAGACTT
1 CCTAGATAACAAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAGATGGCCAAGACTT
** *
50345 ATCATAGTATGAGCAGTGTCA-TCCCCTGACCAAATCTCCTCATCACGTAGGAGCCGTGTCAACC
66 ATCATAGTATGAGCAGTGTCATTAACC-GACCAAACCTCCTCATCACGTAGGAGCCGTG-CAACC
50409 CT-AGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
129 CTCAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
* *
50455 CCTAGATAACAAAGACTTATCATAGTATGAGCATTGTTATCACCCTTCCTAGGTGGCCAAGACTT
1 CCTAGATAACAAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAGATGGCCAAGACTT
* ** * * *
50520 ATCATAGTATGAGTAGTGTCATTAACCGACCTGACCTCCTCATCGCGTAGGAGTCGTGCCACCCT
66 ATCATAGTATGAGCAGTGTCATTAACCGACCAAACCTCCTCATCACGTAGGAGCCGTGCAACCCT
50585 CAGATAACCA
131 CAGATAACCA
50595 GTCATCCTCA
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
174 6 0.05
175 116 0.93
176 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (175 bp):
CCTAGATAACAAAGACTTATCATAGTATGAGCAGTGTTATCACCCTTCCTAGATGGCCAAGACTT
ATCATAGTATGAGCAGTGTCATTAACCGACCAAACCTCCTCATCACGTAGGAGCCGTGCAACCCT
CAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
Found at i:50929 original size:7 final size:7
Alignment explanation
Indices: 50917--50963 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
50907 AGCAAAAAAT
50917 ATTATTA
1 ATTATTA
50924 ATTATTA
1 ATTATTA
50931 ATTATTA
1 ATTATTA
*
50938 TTATTATTT
1 --ATTATTA
50947 ATTATTA
1 ATTATTA
50954 A-TATTA
1 ATTATTA
50960 ATTA
1 ATTA
50964 GTTGTATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 6 0.17
7 23 0.66
9 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTATTA
Found at i:50930 original size:3 final size:3
Alignment explanation
Indices: 50916--50959 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
50906 GAGCAAAAAA
*
50916 TAT TAT TAAT TAT TAAT TAT TAT TAT TATT TAT TAT TAA TAT TA
1 TAT TAT T-AT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT TA
50960 ATTAGTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:50942 original size:13 final size:13
Alignment explanation
Indices: 50916--50963 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
50906 GAGCAAAAAA
50916 TATTATTAATTAT
1 TATTATTAATTAT
50929 TA--ATT-ATTAT
1 TATTATTAATTAT
*
50939 TATTATTTATTAT
1 TATTATTAATTAT
*
50952 TAATATTAATTA
1 TATTATTAATTA
50964 GTTGTATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 3 0.10
13 17 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTAATTAT
Found at i:52578 original size:29 final size:29
Alignment explanation
Indices: 52525--52617 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
52515 TATTCGTTAT
52525 TTTAGTCCTATAACCTTCTGTTTTTGCTA
1 TTTAGTCCTATAACCTTCTGTTTTTGCTA
* * *
52554 TTTAGATCCTTTAACTTTCTG-TTTTGGTA
1 TTTAG-TCCTATAACCTTCTGTTTTTGCTA
* ** * *
52583 TTTAGTCCTCTAGGCTTCTATTTTTGCCA
1 TTTAGTCCTATAACCTTCTGTTTTTGCTA
52612 TTTAGT
1 TTTAGT
52618 TCTTTAAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 10 0.19
29 29 0.56
30 13 0.25
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (29 bp):
TTTAGTCCTATAACCTTCTGTTTTTGCTA
Found at i:52608 original size:58 final size:57
Alignment explanation
Indices: 52525--52634 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 57
52515 TATTCGTTAT
* * * *
52525 TTTAGTCCTATAACCTTCTGTTTTTGCTATTTAGATCCTTTAACTTTCTGTTTTGGTA
1 TTTAGTCCTATAACCTTCTATTTTTGCCATTTAG-TCCTTTAAATTCCTGTTTTGGTA
* ** *
52583 TTTAGTCCTCTAGGCTTCTATTTTTGCCATTTAGTTCTTTAAATTCCTGTTT
1 TTTAGTCCTATAACCTTCTATTTTTGCCATTTAGTCCTTTAAATTCCTGTTT
52635 GTACTATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 15 0.34
58 29 0.66
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (57 bp):
TTTAGTCCTATAACCTTCTATTTTTGCCATTTAGTCCTTTAAATTCCTGTTTTGGTA
Found at i:53539 original size:27 final size:27
Alignment explanation
Indices: 53509--53560 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
53499 ACATAATACT
53509 GAAGATAGAAAACAAGTAAACATTACA
1 GAAGATAGAAAACAAGTAAACATTACA
* *
53536 GAAGATATAAAACAAGTAAGCATTA
1 GAAGATAGAAAACAAGTAAACATTA
53561 TTAACATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (27 bp):
GAAGATAGAAAACAAGTAAACATTACA
Found at i:53989 original size:2 final size:2
Alignment explanation
Indices: 53982--54009 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53972 ACGGTAATCC
53982 AT AT AT 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
54010 TAAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61409 original size:40 final size:40
Alignment explanation
Indices: 61354--61434 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
61344 ATTCGGGTTC
61354 GGATAAAGAAAGATTGTGGGAGATGGTACGTTTTTATGTT
1 GGATAAAGAAAGATTGTGGGAGATGGTACGTTTTTATGTT
61394 GGATAAAGAAAGATTGTGGGAGATGGTACGTTTTTATGTT
1 GGATAAAGAAAGATTGTGGGAGATGGTACGTTTTTATGTT
61434 G
1 G
61435 CTCTCAACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (40 bp):
GGATAAAGAAAGATTGTGGGAGATGGTACGTTTTTATGTT
Found at i:66022 original size:21 final size:23
Alignment explanation
Indices: 65987--66034 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
65977 TATTATCTTG
65987 TAATTATCTTAAATTAATAAAAA
1 TAATTATCTTAAATTAATAAAAA
* *
66010 TAATTAT-TT-AATTGATTAAAA
1 TAATTATCTTAAATTAATAAAAA
66031 TAAT
1 TAAT
66035 AAGATAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATTATCTTAAATTAATAAAAA
Found at i:69665 original size:63 final size:62
Alignment explanation
Indices: 69585--69717 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 62
69575 TACGTATCAC
69585 CAGCCTGAACCTTTACCAAGGTCGAAAAACAATACTGATAACGCTGACTCTCATACTCCCCAA
1 CAGCCTGAACCTTTACCAAGGTCGAAAAACAATACTGATAACGCTGACTCTCATAC-CCCCAA
* * *
69648 CAGCCTGAACCTTTACCAAGGTCGAAAAACAATATTGATAATGCTGACTCTCATACCCCCAG
1 CAGCCTGAACCTTTACCAAGGTCGAAAAACAATACTGATAACGCTGACTCTCATACCCCCAA
69710 CAGCCTGA
1 CAGCCTGA
69718 GTCCTTGTCT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
62 13 0.19
63 54 0.81
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (62 bp):
CAGCCTGAACCTTTACCAAGGTCGAAAAACAATACTGATAACGCTGACTCTCATACCCCCAA
Found at i:80066 original size:76 final size:77
Alignment explanation
Indices: 79976--80124 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 77
79966 TACATAATTC
* * *
79976 ATCTATAGAAGATCCGGGTGTGCAACGAAAAGCACATAACATCTCAACTTTTTCACACATT-TTC
1 ATCTATAGAAGATCCGGGTGTACAACGAAAAGCACACAACATCTCAACGTTTTCACACATTCTTC
80040 CATTATTAGTTA
66 CATTATTAGTTA
* * *
80052 ATCTATATAAGATCCGGGTGTACGACGAAAATCACACAACATCTCAACGTTTTCACACATTCTTC
1 ATCTATAGAAGATCCGGGTGTACAACGAAAAGCACACAACATCTCAACGTTTTCACACATTCTTC
*
80117 TATTATTA
66 CATTATTA
80125 ATTACTAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 55 0.85
77 10 0.15
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (77 bp):
ATCTATAGAAGATCCGGGTGTACAACGAAAAGCACACAACATCTCAACGTTTTCACACATTCTTC
CATTATTAGTTA
Found at i:93620 original size:31 final size:31
Alignment explanation
Indices: 93567--93677 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 31
93557 GTTCTACGGA
*
93567 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGTA-TACCTATGTCTTTCGAG
***
93599 ACATATGGACAGTATACCTATGTTCTAAGGA-
1 ACATATGGACAGTATACCTATG-TCTTTCGAG
* * * *
93630 ACATATGGATAGTTTACCTAGGT-TCTTCGGG
1 ACATATGGACAGTATACCTATGTCT-TTCGAG
*
93661 ACCTATGGACAGT-TACC
1 ACATATGGACAGTATACC
93678 GAGGATCTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 1 0.02
30 6 0.10
31 38 0.60
32 18 0.29
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTCTTTCGAG
Found at i:93694 original size:30 final size:30
Alignment explanation
Indices: 93660--93790 Score: 244
Period size: 30 Copynumber: 4.4 Consensus size: 30
93650 GGTTCTTCGG
* *
93660 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
93690 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
93720 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
93750 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
93780 GACCTCTGGAT
1 GACCTCTGGAT
93791 TGGTCCTTCG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:98522 original size:30 final size:30
Alignment explanation
Indices: 98434--98535 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
98424 AGAGTTGAGG
* *
98434 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATG-TCTAAGGAACATATGGAAA
* ***
98465 GAATTACCTATGTCTTTCGAGACATATGGAAA
1 GTA-TACCTATGTCTAAGGA-ACATATGGAAA
*
98497 GTATACCTATGTCTAAGGAACATATGGATA
1 GTATACCTATGTCTAAGGAACATATGGAAA
*
98527 GTTTACCTA
1 GTATACCTA
98536 GGTTCTTCGG
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
30 18 0.31
31 20 0.34
32 20 0.34
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
GTATACCTATGTCTAAGGAACATATGGAAA
Found at i:98591 original size:30 final size:30
Alignment explanation
Indices: 98546--98646 Score: 175
Period size: 30 Copynumber: 3.4 Consensus size: 30
98536 GGTTCTTCGG
* * *
98546 GACCTATGGACAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
98576 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
98606 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
98636 GACCTCTGGAT
1 GACCTCTGGAT
98647 TGGTCCTTCG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Done.