Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002808.1 Hibiscus syriacus cultivar Beakdansim tig00005777_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: 71621
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9909 original size:32 final size:33
Alignment explanation
Indices: 9868--9949 Score: 114
Period size: 32 Copynumber: 2.5 Consensus size: 33
9858 GTGATGCTGA
9868 CTATACTATGCATTATCTGAATACAATACTGATT
1 CTAT-CTATGCATTATCTGAATACAATACTGATT
* *
9902 CT-TCTATGCATTATCTGAATGCAATATTGATT
1 CTATCTATGCATTATCTGAATACAATACTGATT
*
9934 CTAT-TGTGCATTATCT
1 CTATCTATGCATTATCT
9950 AAAAGCAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 40 0.91
33 2 0.05
34 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (33 bp):
CTATCTATGCATTATCTGAATACAATACTGATT
Found at i:9958 original size:32 final size:32
Alignment explanation
Indices: 9873--9961 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
9863 GCTGACTATA
*
9873 CTATGCATTATCTGAATA-CAATACTGATTCTT
1 CTATGCATTATCT-AAAAGCAATACTGATTCTT
* * *
9905 CTATGCATTATCTGAATGCAATATTGATTCTAT
1 CTATGCATTATCTAAAAGCAATACTGATTCT-T
*
9938 -TGTGCATTATCTAAAAGCAATACT
1 CTATGCATTATCTAAAAGCAATACT
9962 AACTTTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
CTATGCATTATCTAAAAGCAATACTGATTCTT
Found at i:14117 original size:20 final size:19
Alignment explanation
Indices: 14068--14117 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
14058 ACTTTTGAGG
*
14068 ATAAA-TTATATTTAATAT
1 ATAAATTTATAATTAATAT
14086 AT-AATTAATATAATTAATAT
1 ATAAATT--TATAATTAATAT
14106 ATTAAATTTATA
1 A-TAAATTTATA
14118 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
20 16 0.62
21 1 0.04
22 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATTTATAATTAATAT
Found at i:14854 original size:53 final size:51
Alignment explanation
Indices: 14783--14892 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 51
14773 ATTGTCCTTA
* * *
14783 TTATATATTTGTTTTTTAACAAGTTGAATTCTACTATAATTTTACTATAATTAAT
1 TTATATATTTGTTCTTTAAAAAGTTAAATTC-A-TA-AATTTTA-TATAATTAAT
* *
14838 TTATATA-TT-TTCTTTAAAAATTTAAATTCATAAATTTTATATAATTTAT
1 TTATATATTTGTTCTTTAAAAAGTTAAATTCATAAATTTTATATAATTAAT
14887 TT-TATA
1 TTATATA
14893 AAATTGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
48 4 0.08
49 11 0.22
50 7 0.14
51 2 0.04
52 1 0.02
53 16 0.32
54 2 0.04
55 7 0.14
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (51 bp):
TTATATATTTGTTCTTTAAAAAGTTAAATTCATAAATTTTATATAATTAAT
Found at i:15209 original size:24 final size:24
Alignment explanation
Indices: 15174--15230 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
15164 AAATATCAAT
15174 GTTGGGAATAACTTATTACCAAGA
1 GTTGGGAATAACTTATTACCAAGA
*
15198 GTTGGGATTAACTTATTACCAAGA
1 GTTGGGAATAACTTATTACCAAGA
*
15222 GTTGAGAAT
1 GTTGGGAAT
15231 GTTTGCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (24 bp):
GTTGGGAATAACTTATTACCAAGA
Found at i:15392 original size:17 final size:17
Alignment explanation
Indices: 15370--15417 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
15360 AAATATAAAA
15370 ATAAATATATAGGGACT
1 ATAAATATATAGGGACT
*
15387 ATAAATATA-A---AAT
1 ATAAATATATAGGGACT
15400 ATAAATATATAGGGACT
1 ATAAATATATAGGGACT
15417 A
1 A
15418 AAAAGGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
16 1 0.04
17 12 0.48
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAAATATATAGGGACT
Found at i:15406 original size:30 final size:29
Alignment explanation
Indices: 15357--15417 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
15347 AAAGACTAAA
15357 TATAAATATAAAAATAAATATATAGGGAC
1 TATAAATATAAAAATAAATATATAGGGAC
15386 TATAAATATAAAATATAAATATATAGGGAC
1 TATAAATATAAAA-ATAAATATATAGGGAC
15416 TA
1 TA
15418 AAAAGGCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (29 bp):
TATAAATATAAAAATAAATATATAGGGAC
Found at i:18462 original size:39 final size:39
Alignment explanation
Indices: 18403--18509 Score: 178
Period size: 39 Copynumber: 2.7 Consensus size: 39
18393 GCTTGATATA
* *
18403 TTTGCCAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
1 TTTGACAGGAATTGCGTAAGCTTGATCGAGAAGTGTTGC
*
18442 TTTGACAGGAATCGCGTAAGCTTGATCGAGAAGTGTTGC
1 TTTGACAGGAATTGCGTAAGCTTGATCGAGAAGTGTTGC
*
18481 TTTGACAGGAATTGCGTAAGCTTGTTCGA
1 TTTGACAGGAATTGCGTAAGCTTGATCGA
18510 AGAGTGCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (39 bp):
TTTGACAGGAATTGCGTAAGCTTGATCGAGAAGTGTTGC
Found at i:21735 original size:24 final size:24
Alignment explanation
Indices: 21690--21735 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
21680 CTTTTCAGTG
**
21690 TCTTCATCCTCGCCTTTTTCAGCA
1 TCTTCATCCTCGCCTTCCTCAGCA
* *
21714 TCTTCATCTTCTCCTTCCTCAG
1 TCTTCATCCTCGCCTTCCTCAG
21736 ATTTAGTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.07, T:0.43
Consensus pattern (24 bp):
TCTTCATCCTCGCCTTCCTCAGCA
Found at i:23087 original size:35 final size:35
Alignment explanation
Indices: 23048--23129 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
23038 AAAAGAGAGT
23048 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
1 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
* * * * * *
23083 TTTACACGCTTCAGTTCTGAAACATAATTTCTACG
1 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
23118 TTTACATGCTTC
1 TTTACATGCTTC
23130 TTGTATAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (35 bp):
TTTACATGCTTCAATACCGAAACAGAATTTCTACA
Found at i:24711 original size:3 final size:3
Alignment explanation
Indices: 24675--24731 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
24665 AGTTGACAAT
* **
24675 TTC TT- TTC TTC CTC TTC TTGC AAC TTC ATT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC -TTC TTC TTC TTC TTC TTC
24720 TTC TTC TTC TTC
1 TTC TTC TTC TTC
24732 AAAACTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.05, C:0.32, G:0.02, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:25036 original size:3 final size:3
Alignment explanation
Indices: 25023--25052 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25013 AAAATATTAC
*
25023 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25053 TATTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:26201 original size:18 final size:19
Alignment explanation
Indices: 26161--26205 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
26151 CCATTATGGG
26161 TTTTATTTTATTTTATTAC
1 TTTTATTTTATTTTATTAC
*
26180 -TTTATTTTATTTTA-TGC
1 TTTTATTTTATTTTATTAC
26197 TTTTATTTT
1 TTTTATTTT
26206 GTTTCCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTTTATTAC
Found at i:31875 original size:3 final size:3
Alignment explanation
Indices: 31867--31919 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
31857 TTTTTATCCA
*
31867 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31915 TAT TA
1 TAT TA
31920 AATATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:32432 original size:28 final size:30
Alignment explanation
Indices: 32376--32433 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
32366 AGGGACAGAG
32376 ATATAGAACGAGACAGAGAGACAAAAAAAA
1 ATATAGAACGAGACAGAGAGACAAAAAAAA
32406 ATATAG-ACAGAGACAGAGA-A-AAAAAAAA
1 ATATAGAAC-GAGACAGAGAGACAAAAAAAA
32434 CAGAGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.30
29 3 0.11
30 16 0.59
ACGTcount: A:0.66, C:0.09, G:0.19, T:0.07
Consensus pattern (30 bp):
ATATAGAACGAGACAGAGAGACAAAAAAAA
Found at i:32436 original size:21 final size:20
Alignment explanation
Indices: 32412--32451 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
32402 AAAAATATAG
*
32412 ACAGAGACAGAGAAAAAAAAA
1 ACAGAGAAAG-GAAAAAAAAA
32433 ACAGAGAAAGGAAAAAAAA
1 ACAGAGAAAGGAAAAAAAA
32452 TAAACTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.00
Consensus pattern (20 bp):
ACAGAGAAAGGAAAAAAAAA
Found at i:32749 original size:11 final size:11
Alignment explanation
Indices: 32733--32757 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32723 ACGGTGGTTG
32733 ACGGCGGATGA
1 ACGGCGGATGA
32744 ACGGCGGATGA
1 ACGGCGGATGA
32755 ACG
1 ACG
32758 CCGGCTAACG
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:0.28, C:0.20, G:0.44, T:0.08
Consensus pattern (11 bp):
ACGGCGGATGA
Found at i:33337 original size:18 final size:18
Alignment explanation
Indices: 33303--33336 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33293 AATTTAGTCA
33303 TTTATTTTATATGTTTTC
1 TTTATTTTATATGTTTTC
33321 TTTATTTTAT-TGTTTT
1 TTTATTTTATATGTTTT
33337 TAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTATTTTATATGTTTTC
Found at i:33399 original size:20 final size:21
Alignment explanation
Indices: 33370--33410 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
33360 TTTATTTTTA
33370 TTTTATTATATGAATAAATAT
1 TTTTATTATATGAATAAATAT
**
33391 TTTTA-TATATTCATAAATAT
1 TTTTATTATATGAATAAATAT
33411 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTATTATATGAATAAATAT
Found at i:34127 original size:18 final size:17
Alignment explanation
Indices: 34104--34154 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
34094 TTCTTTTCAA
34104 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
34121 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
34139 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
34155 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:34176 original size:13 final size:15
Alignment explanation
Indices: 34145--34181 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
34135 TTATATGTTT
34145 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
34160 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
34173 TA-TTTATTT
1 TATTTTATTT
34182 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:37507 original size:14 final size:15
Alignment explanation
Indices: 37478--37509 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
37468 GAATTATTTT
37478 ATTCATTAAGTTAAA
1 ATTCATTAAGTTAAA
37493 ATTCATTAA-TTAAA
1 ATTCATTAAGTTAAA
37507 ATT
1 ATT
37510 TGAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTCATTAAGTTAAA
Found at i:46413 original size:246 final size:246
Alignment explanation
Indices: 45912--46558 Score: 1197
Period size: 246 Copynumber: 2.6 Consensus size: 246
45902 ATATCTTAGT
45912 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
45976 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
46041 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
131 AAGTGTTCTTTGAG---T-T-ATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
46106 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
191 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
*
46162 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
46227 CTGATCTGATTTGGCAGAACTAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
46292 AAGTGTTCTTTGAGTTATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCA
131 AAGTGTTCTTTGAGTTATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCA
46357 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
196 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
46408 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
46473 CTGATCTGATTTGGCAGAACCAATAATTGAATTTGGAAGATGAATTTGCTCAATATCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTG
46538 GAAGTGTTCTTTGAGTTATCT
130 GAAGTGTTCTTTGAGTTATCT
46559 AATCTGGTTG
Statistics
Matches: 389, Mismatches: 6, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
246 211 0.54
247 36 0.09
248 1 0.00
250 30 0.08
251 111 0.29
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (246 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCA
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:46519 original size:330 final size:332
Alignment explanation
Indices: 45912--46590 Score: 1222
Period size: 330 Copynumber: 2.0 Consensus size: 332
45902 ATATCTTAGT
45912 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG-T-TC
45977 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGA
64 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGA
46042 AGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTG
129 AGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTG
*
46107 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTG
194 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATAATTG
* *
46172 AATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTGATCTGAT
259 AATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTAATCTG-G
46237 TTGG-CAGAA
323 TTGGACAGAA
*
46246 CTAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG-T-T-
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTG
46308 ATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAA
66 ATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAA
46373 GTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC
130 GTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC
46438 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATAATTGA
195 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATAATTGA
* *
46503 ATTTGGAAGATGAATTTGCTCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTT
260 ATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTAATCTGGTT
46568 GGACAGAA
325 GGACAGAA
*
46576 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
46591 AAAAGATGAA
Statistics
Matches: 334, Mismatches: 8, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
329 50 0.15
330 219 0.66
331 6 0.02
334 59 0.18
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (332 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTG
ATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAG
TGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCT
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATAATTGAA
TTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTATCTAATCTGGTTG
GACAGAA
Found at i:46600 original size:84 final size:84
Alignment explanation
Indices: 45912--46590 Score: 1214
Period size: 84 Copynumber: 8.2 Consensus size: 84
45902 ATATCTTAGT
45912 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
45976 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
45995 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46059 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
46078 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46143 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
46162 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGAGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46227 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
46246 CTAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAG---T
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46307 -T-ATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
46324 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46389 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
46408 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
46473 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
* *
46492 CCAATAATTGAATTTGGAAGATGAATTTGCTCAATATCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
46557 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
46576 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
46591 AAAAGATGAA
Statistics
Matches: 577, Mismatches: 10, Indels: 16
0.96 0.02 0.03
Matches are distributed among these distances:
78 45 0.08
79 31 0.05
80 1 0.00
82 1 0.00
83 147 0.25
84 347 0.60
85 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:47497 original size:113 final size:113
Alignment explanation
Indices: 47299--48078 Score: 1350
Period size: 113 Copynumber: 6.9 Consensus size: 113
47289 TCAAATCCAC
* *
47299 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
47363 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
47412 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
47477 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
47525 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
47589 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
47638 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
47703 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
47751 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
47816 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
47864 TTGATGGATCAACATTGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
47929 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *** *
47978 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
48043 AGTTCATAATGAGAAGAGCTTGTTCAAC-TTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
48079 GATACTATCA
Statistics
Matches: 638, Mismatches: 25, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
112 28 0.04
113 498 0.78
114 112 0.18
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:48400 original size:3 final size:3
Alignment explanation
Indices: 48392--48463 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
48382 TTTTTATCCA
*
48392 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
48440 TAT TAT TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TA
48464 AATAAATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:48964 original size:28 final size:30
Alignment explanation
Indices: 48908--48964 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
48898 AGGGACAGAG
48908 ATATAGAACGAGACAGAGAGACAAAAAAAA
1 ATATAGAACGAGACAGAGAGACAAAAAAAA
48938 ATATAG-ACAGAGACAGAGA-A-AAAAAAA
1 ATATAGAAC-GAGACAGAGAGACAAAAAAA
48965 CAGAGAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.27
29 3 0.12
30 16 0.62
ACGTcount: A:0.65, C:0.09, G:0.19, T:0.07
Consensus pattern (30 bp):
ATATAGAACGAGACAGAGAGACAAAAAAAA
Found at i:48969 original size:20 final size:19
Alignment explanation
Indices: 48944--48982 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
48934 AAAAATATAG
*
48944 ACAGAGACAGAGAAAAAAAA
1 ACAGAGAAAG-GAAAAAAAA
48964 ACAGAGAAAGGAAAAAAAA
1 ACAGAGAAAGGAAAAAAAA
48983 TAAACTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (19 bp):
ACAGAGAAAGGAAAAAAAA
Found at i:49921 original size:20 final size:21
Alignment explanation
Indices: 49892--49932 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49882 TTTATTTTTA
49892 TTTTATTATATGAATAAATAT
1 TTTTATTATATGAATAAATAT
**
49913 TTTTA-TATATTCATAAATAT
1 TTTTATTATATGAATAAATAT
49933 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTATTATATGAATAAATAT
Found at i:53696 original size:24 final size:24
Alignment explanation
Indices: 53667--53720 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
53657 TGTTCGATAA
* *
53667 TATGTTCGTTTATATTCGTTCATT
1 TATGTTCATTTATATGCGTTCATT
*
53691 TATGTTCATTTATGTGCGTTCATT
1 TATGTTCATTTATATGCGTTCATT
53715 TATGTT
1 TATGTT
53721 TAGCCCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTATATGCGTTCATT
Found at i:54677 original size:13 final size:13
Alignment explanation
Indices: 54658--54695 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
54648 AAAGGAGTTG
54658 CTATTTATTGTTT
1 CTATTTATTGTTT
*
54671 TTATTTATT-TATT
1 CTATTTATTGT-TT
54684 CTATTTATTGTT
1 CTATTTATTGTT
54696 GATTTAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (13 bp):
CTATTTATTGTTT
Found at i:54690 original size:17 final size:17
Alignment explanation
Indices: 54659--54692 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54649 AAGGAGTTGC
* *
54659 TATTTATTGTTTTTATT
1 TATTTATTCTATTTATT
54676 TATTTATTCTATTTATT
1 TATTTATTCTATTTATT
54693 GTTGATTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TATTTATTCTATTTATT
Found at i:56431 original size:5 final size:5
Alignment explanation
Indices: 56421--56449 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
56411 GGCGATGATG
56421 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
56450 TGGGAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:59105 original size:33 final size:33
Alignment explanation
Indices: 59063--59128 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
59053 GACTTCGCAG
59063 ATTCTCCCAGTTGGCGTAGGAGTGATACTTTCT
1 ATTCTCCCAGTTGGCGTAGGAGTGATACTTTCT
*
59096 ATTCTCCCAGTTGGCGTTGGAGTGATACTTTCT
1 ATTCTCCCAGTTGGCGTAGGAGTGATACTTTCT
59129 CTATCAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (33 bp):
ATTCTCCCAGTTGGCGTAGGAGTGATACTTTCT
Found at i:63872 original size:21 final size:21
Alignment explanation
Indices: 63848--63890 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
63838 CAGAAGAAGA
63848 AAGA-ATCAATGTCTACAATAG
1 AAGACATCAATGTCTA-AATAG
* *
63869 AAGACATTAATGTTTAAATAG
1 AAGACATCAATGTCTAAATAG
63890 A
1 A
63891 GAAAAGGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAGACATCAATGTCTAAATAG
Found at i:64017 original size:12 final size:12
Alignment explanation
Indices: 64000--64026 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
63990 CGGCGCTGTG
64000 CTTCTTAGGTTT
1 CTTCTTAGGTTT
64012 CTTCTTAGGTTT
1 CTTCTTAGGTTT
64024 CTT
1 CTT
64027 TAATTATATT
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:0.07, C:0.19, G:0.15, T:0.59
Consensus pattern (12 bp):
CTTCTTAGGTTT
Found at i:65622 original size:18 final size:18
Alignment explanation
Indices: 65599--65633 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
65589 CTCACACTAT
65599 TTTTTATTTAAAAAATAG
1 TTTTTATTTAAAAAATAG
65617 TTTTTATTTAAAAAATA
1 TTTTTATTTAAAAAATA
65634 TGTGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTTATTTAAAAAATAG
Found at i:71027 original size:30 final size:30
Alignment explanation
Indices: 70993--71050 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
70983 TGAATTTTTC
* * *
70993 AAATTGCAATTTTGGTCTCTAAACTTTTGA
1 AAATTACAATTTTAGTCCCTAAACTTTTGA
**
71023 AAATTACCCTTTTAGTCCCTAAACTTTT
1 AAATTACAATTTTAGTCCCTAAACTTTT
71051 CTAAACTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (30 bp):
AAATTACAATTTTAGTCCCTAAACTTTTGA
Found at i:71079 original size:31 final size:28
Alignment explanation
Indices: 71001--71103 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 28
70991 TCAAATTGCA
* * *
71001 ATTTTGGTCTCTAAACTTTTGAAAATTACC
1 ATTTTGGCCACTAAACTTTT-AAATTTA-C
* * *
71031 CTTTTAGTCC-CTAAACTTTTCTAAACTTTAT
1 ATTTT-GGCCACTAAAC-TTT-TAAA-TTTAC
71062 ATTTTGGCCACTAAACTTTTAAATTTAC
1 ATTTTGGCCACTAAACTTTTAAATTTAC
*
71090 ATTTTGGTCACTAA
1 ATTTTGGCCACTAA
71104 CCAAATTCGG
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 17 0.29
29 4 0.07
30 16 0.27
31 18 0.31
32 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (28 bp):
ATTTTGGCCACTAAACTTTTAAATTTAC
Done.