Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004895.1 Hibiscus syriacus cultivar Beakdansim tig00011018_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: 56479
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4365 original size:3 final size:3
Alignment explanation
Indices: 4347--4417 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
4337 TTTGGGCCTG
* *
4347 TAA TAA TAT TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4395 TAA TAA TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
4418 TTTAAATGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:10770 original size:182 final size:181
Alignment explanation
Indices: 10464--10942 Score: 733
Period size: 182 Copynumber: 2.6 Consensus size: 181
10454 GTATGTATCA
* * *
10464 ATACAAATAAAAAGGTATCAATCCATAACAATATAACAAGTAAAAATATGACAAACCAGTTTCAT
1 ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACAGTTTCAT
* *
10529 TATGACAAAATCGGTAAAGCGCTATCGGATATGTTGAATGTGTCGATACCATTGAAATAAGTATC
66 TATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
10594 AACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
131 AACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
* * * *
10645 ATACAAATAAAAATGTATCGATCTATAATAATAAAACAAGTAAAAATATGACAAAACATGTATCA
1 ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACA-GTTTCA
* *
10710 TTATGACAAAATCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGAAATAAGTAT
65 TTATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTAT
* * *
10775 CGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCG
130 CAACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
** * *
10827 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGATTTA
1 ATAC-AAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACAG-TTTC
* * * *
10892 ATTATGAAAAAACCGGTAAAGCACTACTGGATATGTTGAAAGTGTCGATAC
64 ATTATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAC
10943 TTTAATACGC
Statistics
Matches: 267, Mismatches: 28, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
181 52 0.19
182 120 0.45
183 95 0.36
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (181 bp):
ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACAGTTTCAT
TATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
AACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
Found at i:13029 original size:21 final size:21
Alignment explanation
Indices: 13003--13044 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12993 TTACGAAAGT
*
13003 CACTGTAGCA-GTGCATCGATG
1 CACTGTAG-AGGTACATCGATG
13024 CACTGTAGAGGTACATCGATG
1 CACTGTAGAGGTACATCGATG
13045 TACAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
CACTGTAGAGGTACATCGATG
Found at i:15298 original size:22 final size:24
Alignment explanation
Indices: 15248--15299 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
15238 GTTTTTTCTT
15248 TTTATATAAAATGATAGTATAATTA
1 TTTATATAAAATGATAG-ATAATTA
*
15273 -TTATATAAAATGATA-A-ATTTA
1 TTTATATAAAATGATAGATAATTA
15294 TTTATA
1 TTTATA
15300 AATTCATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
24 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
TTTATATAAAATGATAGATAATTA
Found at i:16072 original size:21 final size:22
Alignment explanation
Indices: 16041--16081 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16031 ACACCCAAGC
16041 AAAAGCAAAACGTAAGTTGAAT
1 AAAAGCAAAACGTAAGTTGAAT
* *
16063 AAAAG-AAAACTTAATTTGA
1 AAAAGCAAAACGTAAGTTGA
16082 TTTTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (22 bp):
AAAAGCAAAACGTAAGTTGAAT
Found at i:20399 original size:128 final size:127
Alignment explanation
Indices: 20047--20399 Score: 365
Period size: 128 Copynumber: 2.8 Consensus size: 127
20037 TTACTTTAAA
* ** * * *** * * *
20047 GTAATAGGTAAATTTGCAATGTAAGTGGTAAAAATACACATTTTTCATGACAAAATTA-GTAAAC
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAA-TAGGTCAAC
* * * * ** *
20111 ACAATGTATTGATA-ATTTTTAAAATTGTATCAATCCCAAAAAATTGAAATCGATAATTATAAT
65 ATAAAGTATCGATACATTTTT-AAATTGTATCGATCCCAAAAAATCAAAACCGATAATTATAAT
* *
20174 GTAATAGGTAAATTTACAATTTAACCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACA
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
* *
20239 TAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCAAAACCGATAATTATAAT
66 TAAAGTATCGATACATTT-TTAAATTGTATCGATCCCAAAAA-ATCAAAACCGATAATTATAAT
* * * *
20302 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAGAATAGGTCCACA
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
* *
20367 TAATGTATC-A-ACACTTTTTAAATTTGTGTCGAT
66 TAAAGTATCGATACA-TTTTTAAA-TTGTATCGAT
20400 ACTTTTGGTC
Statistics
Matches: 187, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
126 10 0.05
127 77 0.41
128 98 0.52
129 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (127 bp):
GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
TAAAGTATCGATACATTTTTAAATTGTATCGATCCCAAAAAATCAAAACCGATAATTATAAT
Found at i:20497 original size:199 final size:198
Alignment explanation
Indices: 20237--21400 Score: 1536
Period size: 199 Copynumber: 5.8 Consensus size: 198
20227 AATAGGTCAA
* * *
20237 CATAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCAAAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAAT-CCAAAAACATCGAAACCGATAATTATAA
* * * * *
20301 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAGAATAGGTCCAC
63 TATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAAC
* *
20366 ATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAACGAGG
128 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGG
20431 TGCACG
193 TGCACG
* * * * *
20437 CATAAAATGTCCATACATTTAAAATTGCATCGATCACAAAAACATCGAAACCAATAATTATAATA
1 CATAAAGTGTCGATACATTTAAAATTGTATCAATC-CAAAAACATCGAAACCGATAATTATAATA
* * * * *
20502 TAATAGGTAAATTTACAATTTAACCGGTAGAAATATATCGGTTTAATTAGAGAATA-GTCCACAA
65 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACAT
* *
20566 AATATATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCCAACGAGGTG
130 AATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
*
20631 CATG
195 CACG
* *
20635 CATAAAGTGTCGATACATTTATTAAA-AGTATCAATCCTAAAAACATCAAAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAATCC-AAAAACATCGAAACCGATAATTATAA
* *
20699 TATAATAGGTAAATTGACAATGTAACCGGTAGAAAT-TAACCGG-TTAATTAGAAAATAGATCAA
63 TATAATAGGTAAATTTACAATGTAACCGGTAGAAATAT-ACCGGTTTAATTAGAAAATAGGTCAA
* * ** * * * * *
20762 CATAATGTATCGATACATTTTAAAAATGTGTCGATACTTTTTGTCCATAATGAATGTCAAATGAG
127 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAG
*
20827 GTGCACA
192 GTGCACG
* * *
20834 CATAAAGTGTCGATACATTTATTAAA-AGTATCAATCACAAAAATATCGAAACTGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAATC-CAAAAACATCGAAACCGATAATTATAA
* * * * *
20898 TATAATATGTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAAAATAGGTTAAC
63 TATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAAC
* *
20963 ATAATGTATTGACACTTTTTAAATTTGTGTCCATACATTTT-GTCCAGAATGAATGCCCAACGAG
128 ATAATGTATCGACACTTTTTAAATTTGTGTCGATAC-TTTTGGTCCAGAATGAATGCCCAACGAG
21027 GTGCACG
192 GTGCACG
*
21034 CATAAAGTGTCGATACATTTAAAATTGTAT-ATATCCTAAAAGCATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTAAAATTGTATCA-ATCC-AAAAACATCGAAACCGATAATTATAAT
* * * *
21098 GTAATAGGTAAATTTAAAATGTAACCGGTAGAAATATACCAGTTTAATTAGAAAATAGGTTAACA
64 ATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACA
*
21163 TAATGTATCGACACTTTTTAAATTTGTGTCGATA-TTGTTTGTCCAGAATGAATGCCCAACGAGG
129 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTT-TTGGTCCAGAATGAATGCCCAACGAGG
*
21227 TACACG
193 TGCACG
* *
21233 CATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATTGAAACCGATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCAAT-CCAAAAACATCGAAACCGATAATTATAATA
* * * ** *
21298 TAATAGTTAAATTTACAATGTAACCAGTAAAAATATACATGTTTAATTAGAGAATAGGTCAACAT
65 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACAT
* * *
21363 AATGTATCGACACTTTTTAAATTTATATCGATATTTTT
130 AATGTATCGACACTTTTTAAATTTGTGTCGATACTTTT
21401 TAAAATTACG
Statistics
Matches: 856, Mismatches: 89, Indels: 39
0.87 0.09 0.04
Matches are distributed among these distances:
197 2 0.00
198 116 0.14
199 610 0.71
200 124 0.14
201 4 0.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTAAAATTGTATCAATCCAAAAACATCGAAACCGATAATTATAATAT
AATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATA
ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGC
ACG
Found at i:21738 original size:18 final size:16
Alignment explanation
Indices: 21695--21753 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
21685 CCTTCTCAAA
*
21695 CTTCTTCTCAACCAAG
1 CTTCTTCTCAACCAAC
*
21711 C-TCTTTTCAACGACAAC
1 CTTCTTCTCAAC--CAAC
21728 CTTCTTCTCAACCAATC
1 CTTCTTCTCAACCAA-C
21745 GCTTCTTCT
1 -CTTCTTCT
21754 GAACAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.26
16 4 0.11
17 5 0.14
18 17 0.49
ACGTcount: A:0.22, C:0.37, G:0.05, T:0.36
Consensus pattern (16 bp):
CTTCTTCTCAACCAAC
Found at i:21762 original size:18 final size:18
Alignment explanation
Indices: 21728--21762 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21718 CAACGACAAC
*
21728 CTTCTTCTCAACCAATCG
1 CTTCTTCTCAACAAATCG
*
21746 CTTCTTCTGAACAAATC
1 CTTCTTCTCAACAAATC
21763 AGGTCGTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (18 bp):
CTTCTTCTCAACAAATCG
Found at i:24358 original size:24 final size:23
Alignment explanation
Indices: 24327--24371 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
24317 TTCATTTCAT
24327 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGGAGTTTGAATTTAA
*
24350 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTGAATTT
24372 CGATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTGAATTTAA
Found at i:24382 original size:24 final size:24
Alignment explanation
Indices: 24331--24383 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
24321 TTTCATATTT
* * *
24331 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
**
24355 AATTTGAGTTTGAATTTCGATATA
1 AATTTGAGTTTGAATTTAAATATA
24379 AATTT
1 AATTT
24384 CGGCTCCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:26204 original size:199 final size:198
Alignment explanation
Indices: 25823--26787 Score: 1291
Period size: 198 Copynumber: 4.8 Consensus size: 198
25813 AATAGGTAAA
* * * * *
25823 CATAATGTATCGATA-ATTT-TTAAAATTGTATCAATCCTAAAAACATCGAAATCGATAATTATA
1 CATAAAGTGTCGATACATTTATTAAAA--GTATCGATCCCAAAAACATCGAAACCGATAATTATA
* *
25886 ATGTAATAGGTAAATTTACAATGTAATCGGTAGAGATATACCAGTTTAATTAGAAAATAGGTCAA
64 ATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATA-CAG-TTAATTAGAAAATAGGTCAA
* * *
25951 CATAATGTATCGACAC-TTTTTAAATTTGTGTCGATACTTTTTGT-CAATAATGAATGCCCAACG
127 CATAATGTATCGATACATTTTT-AATTTGTGTCGATACTTTTTGTCCAA-AATGAATACCAAACG
26014 AGGTGCACG
190 AGGTGCACG
* ** **
26023 CATAAAGTGTCGATATATTTATTGTAAGTATCGATCCCAAAAACATTAAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
26088 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACTAGTTAATTAGAAAATAGGTCAACAT
66 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATAC-AGTTAATTAGAAAATAGGTCAACAT
* * *
26153 AATGTATCGATACATTTTTAATTTGTGTCGATATTTTTTCTCCAAAATGAATGCCCAAA-GAGGT
130 AATGTATCGATACATTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAAT-ACCAAACGAGGT
*
26217 GCACA
194 GCACG
* * * * *
26222 CATTAAGTGTCGATGCATTTA--AAATTGTATCGATCTCAAAAACATCGAAATCGATAATTATAA
1 CATAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* *
26285 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGTTTAATTAGAAAATAGGTCAACA
65 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACAG-TTAATTAGAAAATAGGTCAACA
* *
26350 TAATGTATCGATACATTTTTAAATTGTGTCGATAC-TTTTGTCCATAATGAATACCAAACGAGGT
129 TAATGTATCGATACATTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATACCAAACGAGGT
26414 GCACG
194 GCACG
* * *
26419 CATAAAGTGCCGATTCATTTATTAAAATTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
*
26484 GTAATAGGTAAATTGACAATGTAACCGGTAGAAAT-TAACATGTTAATTAGAAAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT-ACA-GTTAATTAGAAAATAGGTCAACA
* ** * * *
26548 TAATGTATCAATACATTTTTAAAATGTGTCGATACTTTTTGTCTAGAATGAATACCAAACTAGGT
129 TAATGTATCGATACATTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATACCAAACGAGGT
*
26613 GCATG
194 GCACG
*
26618 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * *
26683 GTAATAGATAAATTTACAATGTAATCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATA-C-AGTTAATTAGAAAATAGGTCAACA
* * * * *
26748 TAATGTATTGACACATTTTAAATTTGTATCGATATTTTTT
129 TAATGTATCGATACATTTTTAATTTGTGTCGATACTTTTT
26788 AAAAATTACG
Statistics
Matches: 679, Mismatches: 69, Indels: 34
0.87 0.09 0.04
Matches are distributed among these distances:
196 5 0.01
197 45 0.07
198 252 0.37
199 218 0.32
200 150 0.22
201 5 0.01
202 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACAGTTAATTAGAAAATAGGTCAACATA
ATGTATCGATACATTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATACCAAACGAGGTGC
ACG
Found at i:26573 original size:21 final size:20
Alignment explanation
Indices: 26549--26587 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
26539 AGGTCAACAT
26549 AATGTATCAATACATTTTTAA
1 AATGTATCAATAC-TTTTTAA
* *
26570 AATGTGTCGATACTTTTT
1 AATGTATCAATACTTTTT
26588 GTCTAGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
AATGTATCAATACTTTTTAA
Found at i:30738 original size:16 final size:16
Alignment explanation
Indices: 30719--30753 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30709 AAATAATTTA
*
30719 AAAATCAAATAATAAT
1 AAAATAAAATAATAAT
*
30735 AAAATAAAATATTAAT
1 AAAATAAAATAATAAT
30751 AAA
1 AAA
30754 TATTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATAATAAT
Found at i:35452 original size:2 final size:2
Alignment explanation
Indices: 35445--35486 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35435 TCTTGACGGT
*
35445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35487 AGAAAACTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:36853 original size:12 final size:12
Alignment explanation
Indices: 36836--36860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36826 AACTAGATTG
36836 AGAAATAAATAA
1 AGAAATAAATAA
36848 AGAAATAAATAA
1 AGAAATAAATAA
36860 A
1 A
36861 TAAAACGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AGAAATAAATAA
Found at i:39425 original size:2 final size:2
Alignment explanation
Indices: 39418--39444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39408 AAACCTAAGG
39418 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39445 TTCCCCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40900 original size:134 final size:134
Alignment explanation
Indices: 40657--40920 Score: 341
Period size: 134 Copynumber: 2.0 Consensus size: 134
40647 GGAAGATGGG
* *
40657 TCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAACATTGACTCATTCCTCTGTTCTCCA
1 TCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAACATTGACTCATTCCACTGCTCTCCA
* ** * * *
40722 GGAAAAATTGAATCGAACTTGATTTGTTTCACAGCTCTTCAGGAAGACTAAATTTGAAAGATTGA
66 GGAAAAATTGAACCGAACTTGATTTACTTCACAGCCCTTCAGGAAGACCAAATCTGAAAGATTGA
40787 AAAA
131 AAAA
** * * *
40791 TCTGCTCTGCTACTCTTTAGGGGAGATCAGACTTGAGAAACATTGACTCATTTCACTGCTCTTCA
1 TCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAACATTGACTCATTCCACTGCTCTCCA
* * * * * *
40856 GGGAAGATTTAACCGAATTTGATTTACTTCACTA-CCCTTTAGGAAGACCAAATCTGAAATATTG
66 GGAAAAATTGAACCGAACTTGATTTACTTCAC-AGCCCTTCAGGAAGACCAAATCTGAAAGATTG
40920 A
130 A
40921 CTCCTCTTCG
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
134 109 0.99
135 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (134 bp):
TCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAACATTGACTCATTCCACTGCTCTCCA
GGAAAAATTGAACCGAACTTGATTTACTTCACAGCCCTTCAGGAAGACCAAATCTGAAAGATTGA
AAAA
Found at i:40980 original size:45 final size:45
Alignment explanation
Indices: 40909--41739 Score: 312
Period size: 38 Copynumber: 21.0 Consensus size: 45
40899 AAGACCAAAT
* * * **
40909 CTGAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACA
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * *
40954 CTAAAAGATTGACTTCTCTGCACGAGAAATTCAAGAA-AGACAACA
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATA-ACAACA
* * *
40999 CTGAAATATTGACTTCTCTGT-ACGAGAAAATCAAGAATAACAATA
1 CTGAAAGATTGACTTCTCT-TCACGAGAAAGTCAAGAATAACAACA
* * * *
41044 CTGAGAGATTGACTTATCTTCACGATAAAGTCAAGAATAACAATA
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41089 CTGAGAGATTGACTTCTCTTCACGAGAAAGTTAAGAAT---AA-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41130 ---AAAGATTGAATTCTCTTCACGAGGAAGTCAAGAATAAC-A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41170 --G---GATTGACTCCTCTTCACGAGGGAA-T-AAGGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGA-GAAAGTCAA-GAATAACAACA
* *
41205 C--AAAGATTGACTTCTCTTCACGAGAGAGTCACGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
41243 C--AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41281 C--AAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAACGA
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAAC-A
* *
41325 CT----GA-T---TTCTCTTTACGAGGAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
*
41357 C--AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT---AA-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * *
41396 ---AAAGATTGAATTCTCTTCATGAGGAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * * *
41433 CT--AAGATAGACTTCTCTTAATGAGTAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41471 C--AAAGACTGACTTCTCTTCACGAGGAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * * *
41509 C--AAAGATTAACTTATCTTCACGAGGAAGTAAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41547 C--AAAGACTGACTTCTCTTCACGAGTAAGTCAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* *
41585 C--AAAGACTGACTTCTCTTCACGAGTAAGTCAAGAATAACAA-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * *
41627 --G--A-CTT-ACTTCTCTTAACGAGGAAGTCAAGAATAACAA-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * *
41665 -T-----ATTGATTTCTCTTCACGAGGAAGTTAAGAAT----A-A
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
* * *
41699 C--AAAGACTGACTTCTCTTCACGAGGAAGTTAAGAATAACAA
1 CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAA
41740 AGATTGACTC
Statistics
Matches: 669, Mismatches: 67, Indels: 103
0.80 0.08 0.12
Matches are distributed among these distances:
32 2 0.00
34 5 0.01
35 3 0.00
37 8 0.01
38 479 0.72
39 8 0.01
40 3 0.00
41 2 0.00
42 8 0.01
44 3 0.00
45 147 0.22
46 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (45 bp):
CTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACA
Found at i:41068 original size:90 final size:90
Alignment explanation
Indices: 40909--41128 Score: 264
Period size: 90 Copynumber: 2.4 Consensus size: 90
40899 AAGACCAAAT
* * ** *
40909 CTGAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTG
1 CTGAAATATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTATCTG
*
40974 CACGAGAAATTCAAGAA-AGACAACA
66 CACGAGAAAGTCAAGAATA-ACAACA
* * * *
40999 CTGAAATATTGACTTCTCTGT-ACGAGAAAATCAAGAATAACAATACTGAGAGATTGACTTATCT
1 CTGAAATATTGACTTCTCT-TCACGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTATCT
* * *
41063 TCACGATAAAGTCAAGAATAACAATA
65 GCACGAGAAAGTCAAGAATAACAACA
* * *
41089 CTGAGAGATTGACTTCTCTTCACGAGAAAGTTAAGAATAA
1 CTGAAATATTGACTTCTCTTCACGAGAAAGTCAAGAATAA
41129 AAAAGATTGA
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
89 1 0.01
90 107 0.97
91 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (90 bp):
CTGAAATATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAACACTAAAAGATTGACTTATCTG
CACGAGAAAGTCAAGAATAACAACA
Found at i:41145 original size:38 final size:38
Alignment explanation
Indices: 41094--41769 Score: 955
Period size: 38 Copynumber: 17.8 Consensus size: 38
41084 CAATACTGAG
* * *
41094 AGATTGACTTCTCTTCACGAGAAAGTTAAGAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
41132 AGATTGAATTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
41170 GGATTGACTCCTCTTCACGAGGGAA-T-AAGGAATAACAA
1 AGATTGACTTCTCTTCACGA-GGAAGTCAA-GAATAACAA
*
41208 AGATTGACTTCTCTTCACGA-GAGAGTCACGAATAACAA
1 AGATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAA
*
41246 AGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
41284 AGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * * *
41322 CGACTGATTTCTCTTTACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
41360 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
41398 AGATTGAATTCTCTTCATGAGGAAGTCAAGAATAACTA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * * *
41436 AGATAGACTTCTCTTAATGAGTAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
41474 AGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
41512 AGATTAACTTATCTTCACGAGGAAGTAAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
41550 AGACTGACTTCTCTTCACGAGTAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
41588 AGACTGACTTCTCTTCACGAGTAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
41626 AGACTT-ACTTCTCTTAACGAGGAAGTCAAGAATAACAA
1 AGA-TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
41664 ATATTGATTTCTCTTCACGAGGAAGTTAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
41702 AGACTGACTTCTCTTCACGAGGAAGTTAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
41740 AGATTGACTCCTCTTCGCGAGGAAGTCAAG
1 AGATTGACTTCTCTTCACGAGGAAGTCAAG
41770 TAGAAACTTC
Statistics
Matches: 569, Mismatches: 61, Indels: 16
0.88 0.09 0.02
Matches are distributed among these distances:
36 2 0.00
37 5 0.01
38 555 0.98
39 7 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (38 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
Found at i:42650 original size:244 final size:252
Alignment explanation
Indices: 42200--42724 Score: 735
Period size: 244 Copynumber: 2.1 Consensus size: 252
42190 AGAAATAGTT
*
42200 TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAA
1 TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACATTAAA
* * *
42265 TGAGAAACTTTTGAAATCACTTTCTTATTTTTTCGAAATTAATGTGAAAACATCCTATCCGAAGG
66 AGAGAAACTTTGGAAATCACTTTCTCA---TTTC--AATTAA-GTGAAAACATCCTATCCGAAGG
*
42330 TCTTACGAATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACATATGACCCAAAGAATTT
125 TCTTACGAATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTT
*
42395 AATCATCATGCTCAAAAGAC-T-T-ATGGCCCAAATGACTTACCAATTTGGAAAATAGTTTAC
190 AATCATCATGCTCAAAAGACTTATGATGGCCCAAAGGACTTACCAATTTGGAAAATAGTTTAC
42455 TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACATTAAA
1 TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACATTAAA
* *
42520 AGAGAAACTTTGGAAATCGCTTTCTCA-TTC-A-T-A-TGAAAACATCCTA-CTTGAAGGTCTTA
66 AGAGAAACTTTGGAAATCACTTTCTCATTTCAATTAAGTGAAAACATCCTATC-CGAAGGTCTTA
* * * * * * * * *
42579 TGGATGGCCCGAAGGACTTGTCATCTTGCTGGAAAGACTTACAGATGACCCGAAGGATTTAATTA
130 CGAATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTTAATCA
* * *
42644 TCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTAC
195 TCATGCTCAAAAGACTTA-TGATGGCCCAAAGGACTTACCAATTTGGAAAATAGTTTAC
42703 TAGGTAAGAAACTTTGGAAATC
1 TAGGTAAGAAACTTTGGAAATC
42725 GATTGTGTTA
Statistics
Matches: 245, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
243 1 0.00
244 92 0.38
245 1 0.00
246 1 0.00
247 2 0.01
248 58 0.24
251 3 0.01
255 87 0.36
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (252 bp):
TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACATTAAA
AGAGAAACTTTGGAAATCACTTTCTCATTTCAATTAAGTGAAAACATCCTATCCGAAGGTCTTAC
GAATGGCCCAAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTTAATCAT
CATGCTCAAAAGACTTATGATGGCCCAAAGGACTTACCAATTTGGAAAATAGTTTAC
Found at i:44552 original size:275 final size:276
Alignment explanation
Indices: 44050--44597 Score: 839
Period size: 275 Copynumber: 2.0 Consensus size: 276
44040 CTTAGCTTTC
* *
44050 TTGTATAATCTATAATAAATCTATCAACCTTTTGAGTATTTATATTATGTTCTTAAGTTCATCAA
1 TTGTATAATCTATAATAAATCTATCAACCTTTTGAGTATTCAGATTATGTTCTTAAGTTCATCAA
44115 GAAGAACATGTTATAGTCTATATGTTTTTGATGGTCAAACAATCCCATATTTAGAATTCAGTCCT
66 GAAGAACATGTTATAG-CTATATGTTTTTGATGGTCAAACAATCCCATATTTAGAATTCAGTCCT
* * * * * *
44180 CAAATAACTGACCTATACTAAATCTATCTACTCCACTATTCCATTTGTGAAGATTATAATTATCA
130 CAAATAACTGACCCATACTAAATCCATCTACTCCACCATTCCATTTGTGAAGATTAGAATCATAA
* **
44245 CTGAACGTCTTCAAAATAAGTGTAGTCTAGTTAGTTTTGCAATATCATACACAAGAGATGTCCCA
195 CTGAACGTCTTCAAAATAAGTGTAGGCTAGTTAGTTTTGCAATATCATACACAAGAGATACCCCA
44310 TGTTGTCCGCTCCCATA
260 TGTTGTCCGCTCCCATA
*
44327 TTGTATAATCTATAATAAATTTATCAACCTTTTGAGTATTCAGATTATGTTCTTAAGTTCATCAA
1 TTGTATAATCTATAATAAATCTATCAACCTTTTGAGTATTCAGATTATGTTCTTAAGTTCATCAA
* * *
44392 GAAGAACCTGTTATAG-TATGTGTTTTTGATGGTCAGACAATCCCATATTTAGAATTCAGTCCTC
66 GAAGAACATGTTATAGCTATATGTTTTTGATGGTCAAACAATCCCATATTTAGAATTCAGTCCTC
* * *
44456 AAATAACTGACCCATACTAAATCCGTCTACTCTACCATTCCATTTGTGAAGATTAGGATCATAAC
131 AAATAACTGACCCATACTAAATCCATCTACTCCACCATTCCATTTGTGAAGATTAGAATCATAAC
* * * * * *
44521 TGAACTTCTTCTACAA-AATTTTAGGCTAGTTAGTTTTGTAATGTCATACACAAGAGATACCCCA
196 TGAACGTCTTC-AAAATAAGTGTAGGCTAGTTAGTTTTGCAATATCATACACAAGAGATACCCCA
*
44585 TGTTGTCTGCTCC
260 TGTTGTCCGCTCC
44598 TATGCGTATC
Statistics
Matches: 245, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
275 165 0.67
276 3 0.01
277 77 0.31
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (276 bp):
TTGTATAATCTATAATAAATCTATCAACCTTTTGAGTATTCAGATTATGTTCTTAAGTTCATCAA
GAAGAACATGTTATAGCTATATGTTTTTGATGGTCAAACAATCCCATATTTAGAATTCAGTCCTC
AAATAACTGACCCATACTAAATCCATCTACTCCACCATTCCATTTGTGAAGATTAGAATCATAAC
TGAACGTCTTCAAAATAAGTGTAGGCTAGTTAGTTTTGCAATATCATACACAAGAGATACCCCAT
GTTGTCCGCTCCCATA
Found at i:50540 original size:2 final size:2
Alignment explanation
Indices: 50533--50557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50523 AAATCTAAGG
50533 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50558 TCCCCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.