Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003367.1 Hibiscus syriacus cultivar Beakdansim tig00007079_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: 105903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:753 original size:17 final size:15
Alignment explanation
Indices: 731--770 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
721 TTTAAGAAAA
731 AATATTATATTCTTATT
1 AATATTATA-T-TTATT
748 AATATT-TATTTATT
1 AATATTATATTTATT
762 AATATTATA
1 AATATTATA
771 GAAAGTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.50
15 3 0.14
16 2 0.09
17 6 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATTATATTTATT
Found at i:2238 original size:35 final size:36
Alignment explanation
Indices: 2189--2259 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
2179 AGTTATGCAT
* *
2189 ACAAAGATCATGTTATA-TAATACCAAAAGTATTAC
1 ACAAAGATCATGTTAGATTAATACCAAAAGCATTAC
*
2224 ACAAAGATCCTGTTAGATTAATACCAAAAGCATTAC
1 ACAAAGATCATGTTAGATTAATACCAAAAGCATTAC
2260 GGTAAGAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (36 bp):
ACAAAGATCATGTTAGATTAATACCAAAAGCATTAC
Found at i:2969 original size:33 final size:33
Alignment explanation
Indices: 2932--3033 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
2922 GCATTGCACA
*
2932 ATTTGAATTTTTATTTTTGCATTTCTACTTTGT
1 ATTTGAATTTTCATTTTTGCATTTCTACTTTGT
* * *
2965 ATTTGCATTTGCATTTTTGCATTTTTACGTTTGT
1 ATTTGAATTTTCATTTTTGCATTTCTAC-TTTGT
*
2999 ATTT-ACATTTTCA-TTTTGCATTTGTATCTTTGT
1 ATTTGA-ATTTTCATTTTTGCATTTCTA-CTTTGT
3032 AT
1 AT
3034 AATTACATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 43 0.73
34 16 0.27
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (33 bp):
ATTTGAATTTTCATTTTTGCATTTCTACTTTGT
Found at i:7321 original size:72 final size:73
Alignment explanation
Indices: 7204--7351 Score: 217
Period size: 72 Copynumber: 2.0 Consensus size: 73
7194 GGGGCATGCT
* * * *
7204 GAAGGCCCACAACATCATGTGTTAAAGATCATTGACTTGAGCAAATATTTCCAATGAGACAGAAA
1 GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
*
7269 GGTATGAA
66 GGAATGAA
* * *
7277 GAAGGCCTACATCATCATATGTT-AAGATCATTGACTTGACCAAATATTTTCAATAAGACAAAAA
1 GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
7341 GGAATGAA
66 GGAATGAA
7349 GAA
1 GAA
7352 TGAAAATGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 47 0.70
73 20 0.30
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (73 bp):
GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
GGAATGAA
Found at i:8165 original size:54 final size:54
Alignment explanation
Indices: 8100--8203 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
8090 CTGACCAGAA
* *
8100 ATCTGGGCAGAAACCACATGAAATGATGAATGTATTGTCAAATATTTTACGAAT
1 ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTACGAAT
* *
8154 ATCTGTGCAGAAACCACAGGAAATGATGAATGTATTATCAAATGTTTTAC
1 ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTAC
8204 AAACCAGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (54 bp):
ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTACGAAT
Found at i:9433 original size:36 final size:36
Alignment explanation
Indices: 9336--9440 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 36
9326 ACTACATTTT
* *
9336 GCTTGAGACATTTTCACTCGAAACAATAATTTATCTC
1 GCTTGAGACAGTTTCACTAGAAACAA-AATTTATCTC
* ** ** *
9373 ACTTGAGATTGTTTTTCTTA-AAACAAAATTTGTCTC
1 GCTTGAGACAGTTTCAC-TAGAAACAAAATTTATCTC
9409 GCTTGAGACAGTTTCACTAGAAACAGAAATTT
1 GCTTGAGACAGTTTCACTAGAAACA-AAATTT
9441 CCATCACTCG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
35 2 0.04
36 26 0.50
37 23 0.44
38 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (36 bp):
GCTTGAGACAGTTTCACTAGAAACAAAATTTATCTC
Found at i:9440 original size:73 final size:73
Alignment explanation
Indices: 9288--9433 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
9278 GTTTTCAAAT
* * * *
9288 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACATTTTGCTTGAGACATTTTCAC
1 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
*
9353 TCGAAACA
66 TAGAAACA
***
9361 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCAC
1 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
9426 TAGAAACA
66 TAGAAACA
9434 GAAATTTCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (73 bp):
ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
TAGAAACA
Found at i:9732 original size:15 final size:15
Alignment explanation
Indices: 9712--9750 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
9702 TTGGGCCAGG
9712 TATATATATTTAAAT
1 TATATATATTTAAAT
*
9727 TATATATA--TATAT
1 TATATATATTTAAAT
9740 TATATATATTT
1 TATATATATTT
9751 TTTAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 12 0.57
15 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATATATTTAAAT
Found at i:10507 original size:134 final size:134
Alignment explanation
Indices: 10172--10531 Score: 429
Period size: 139 Copynumber: 2.6 Consensus size: 134
10162 ATAGATCAAC
*
10172 ATCAACATTTCCAGAAGG-GTTCATAATGAGAAAAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * ** *
10236 ATGAGAATAACTTGTTCGACCTTAGCTTGATTCATCATTTATGGAGTTGAATGAAAGAAAAACCT
65 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAAT---A-AAAAACCT
10301 CACTTGAGG
126 CACTTGAGG
* * *
10310 ATCAATATTTTCAAAGGAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAAAGG-AGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * **
10375 ATGAGAAGAACTTATTCAATCTT-GCCTTAATTCATCACATATGAAGTTGAAT-CAACACCTCTT
65 ATGAGAAGAACTTGTTCAACCTTAG-CTTAATTCATCACATATGAAGTTGAATAAAAAACCTCAC
10438 TTGAGG
129 TTGAGG
* * * * *
10444 ATCAGCATTTCCACAAGGAGTTCATAATGAGAAGAACTCATCTGAGGAAGAAGAAGAAATTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
10509 CTGAGAAGAACTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
10532 TTGCTATATT
Statistics
Matches: 191, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
134 85 0.45
135 4 0.02
137 4 0.02
138 12 0.06
139 86 0.45
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (134 bp):
ATCAACATTTCCAAAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAATAAAAAACCTCACTT
GAGG
Found at i:10516 original size:23 final size:22
Alignment explanation
Indices: 10473--10518 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
10463 GTTCATAATG
10473 AGAAGAACTCATCTGAGGAAGA
1 AGAAGAACTCATCTGAGGAAGA
*
10495 AGAAGAAATTCATACTGA-GAAGA
1 AGAAG-AACTCAT-CTGAGGAAGA
10518 A
1 A
10519 CTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.15
Consensus pattern (22 bp):
AGAAGAACTCATCTGAGGAAGA
Found at i:10549 original size:134 final size:132
Alignment explanation
Indices: 10172--10549 Score: 388
Period size: 134 Copynumber: 2.8 Consensus size: 132
10162 ATAGATCAAC
*
10172 ATCAACATTTCCAGAAGG-GTTCATAATGAGAAAAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
10236 ATGAGAATAACTTGTTCGACC-TTAGCTTGATTCATCATTTATGGAGTTGAATGAAAGAAAAACC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTT-ATTCAACA--TATGAAGTTGAAT---A-AAAAACC
10300 TCACTTGAGG
123 TCACTTGAGG
* * *
10310 ATCAATATTTTCAAAGGAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAAAGG-AGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
10375 ATGAGAAGAACTTATTCAA--TCTTGCCTTAATTCATCACATATGAAGTTGAAT-CAACACCTCT
65 ATGAGAAGAACTTGTTCAACCTTTTG-CTT-ATTCA--ACATATGAAGTTGAATAAAAAACCTCA
*
10437 TTTGAGG
126 CTTGAGG
* * * * *
10444 ATCAGCATTTCCACAAGGAGTTCATAATGAGAAGAACTCATCTGAGGAAGAAGAAGAAATTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
10509 CTGAGAAGAACTTGTTCAACCTTTTGCTATATTTCAACATA
65 ATGAGAAGAACTTGTTCAACCTTTTGCT-TA-TTCAACATA
10550 GAATGAGATA
Statistics
Matches: 202, Mismatches: 27, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
134 87 0.43
135 7 0.03
136 9 0.04
137 4 0.02
138 13 0.06
139 80 0.40
141 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (132 bp):
ATCAACATTTCCAAAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTTATTCAACATATGAAGTTGAATAAAAAACCTCACTTGA
GG
Found at i:11976 original size:23 final size:23
Alignment explanation
Indices: 11950--11993 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11940 TCTATTCCGA
*
11950 TATTTTTAAATAAATAAATATTG
1 TATTTATAAATAAATAAATATTG
* *
11973 TATTTATAAATATATATATAT
1 TATTTATAAATAAATAAATAT
11994 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTG
Found at i:11989 original size:2 final size:2
Alignment explanation
Indices: 11977--12016 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
11967 ATATTGTATT
*
11977 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12017 GTTATTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12258 original size:2 final size:2
Alignment explanation
Indices: 12251--12306 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
12241 CTGCTCATAA
*
12251 AT AT AT AT GT AT AT 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 AT AT AT AT AT AT AT
12293 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12307 TTACTTCGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14628 original size:2 final size:2
Alignment explanation
Indices: 14617--14658 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
14607 CATTTACCAT
14617 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14658 T
1 T
14659 GCCAAACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15839 original size:14 final size:14
Alignment explanation
Indices: 15804--15839 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15794 ACACACATAT
15804 ATATATATATATAC
1 ATATATATATATAC
*
15818 ATACATATATATAC
1 ATATATATATATAC
*
15832 ATGTATAT
1 ATATATAT
15840 GTAATTATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:15873 original size:25 final size:26
Alignment explanation
Indices: 15827--15887 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
15817 CATACATATA
15827 TATACATGTATATGTAATTATGTATG
1 TATACATGTATATGTAATTATGTATG
*
15853 TATACATGTGT-TGT-ATGTATGTATG
1 TATACATGTATATGTAAT-TATGTATG
*
15878 TATGCATGTA
1 TATACATGTA
15888 AATGAGAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 19 0.61
26 10 0.32
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.46
Consensus pattern (26 bp):
TATACATGTATATGTAATTATGTATG
Found at i:18342 original size:21 final size:23
Alignment explanation
Indices: 18313--18368 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
18303 AATTTTCATG
* *
18313 ATAATATTAATT-A-TATTTTTT
1 ATAAAATTAATTAATTATTTTTA
18334 ATAAAATTAATTTAATTATTTTTA
1 ATAAAATTAA-TTAATTATTTTTA
*
18358 ATTAAATTAAT
1 ATAAAATTAAT
18369 ACTTGATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 2 0.07
24 16 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATAAAATTAATTAATTATTTTTA
Found at i:24305 original size:23 final size:23
Alignment explanation
Indices: 24261--24309 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
24251 ATAAAGAACC
*
24261 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
24284 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
24307 AAA
1 AAA
24310 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:28158 original size:22 final size:22
Alignment explanation
Indices: 28133--28176 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28123 GCTGTTCTTT
28133 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
28155 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
28177 GCCGATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAGAATGATTCCCATTTCA
Found at i:29468 original size:20 final size:20
Alignment explanation
Indices: 29443--29482 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29433 AAGAGAAACC
29443 TTTTTTATTATTTATGTTTA
1 TTTTTTATTATTTATGTTTA
29463 TTTTTTATTATTTATGTTTA
1 TTTTTTATTATTTATGTTTA
29483 AAGGAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTATTATTTATGTTTA
Found at i:29634 original size:7 final size:7
Alignment explanation
Indices: 29622--29671 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
29612 TGAAAATTGA
29622 TAATAAT
1 TAATAAT
29629 TAATAATT
1 TAATAA-T
29637 TAATAAT
1 TAATAAT
*
29644 AAAT-AT
1 TAATAAT
29650 TAATAAT
1 TAATAAT
*
29657 AAAT-AT
1 TAATAAT
29663 TAAATAAT
1 T-AATAAT
29671 T
1 T
29672 GATTATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
6 7 0.20
7 18 0.51
8 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATAAT
Found at i:29654 original size:13 final size:13
Alignment explanation
Indices: 29622--29670 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
29612 TGAAAATTGA
*
29622 TAATAATTAATAATT
1 TAATAATAAAT-A-T
29637 TAATAATAAATAT
1 TAATAATAAATAT
29650 TAATAATAAATAT
1 TAATAATAAATAT
29663 TAAATAAT
1 T-AATAAT
29671 TGATTATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 15 0.47
14 7 0.22
15 10 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:29817 original size:23 final size:23
Alignment explanation
Indices: 29787--29832 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29777 AGTTCTTTTT
29787 TTTAGTCTATCTAAAATAAAATA
1 TTTAGTCTATCTAAAATAAAATA
29810 TTTAGTCTATCTAAAATAAAATA
1 TTTAGTCTATCTAAAATAAAATA
29833 GGAGATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (23 bp):
TTTAGTCTATCTAAAATAAAATA
Found at i:31457 original size:69 final size:69
Alignment explanation
Indices: 31328--31463 Score: 173
Period size: 69 Copynumber: 2.0 Consensus size: 69
31318 CTAATATATA
** * * *
31328 TTCTAAATAATATCAACCATTTGACAACGAACGTTCAATCACCTTGCTGTAGCCGCTGGTGCTCA
1 TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
31393 AATG
66 AATG
* * * * * *
31397 TTCTAAATACTCTCAACTATTTGACAACGAACACTCAATTACCCTACTGCATCCGTTGGTGCTCA
1 TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
31462 AA
66 AA
31464 CCCGTGACCT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (69 bp):
TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
AATG
Found at i:32909 original size:13 final size:13
Alignment explanation
Indices: 32893--32918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32883 AAATATTAAT
32893 TATATTATTATTA
1 TATATTATTATTA
32906 TATATTATTATTA
1 TATATTATTATTA
32919 ATACAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATTATTATTA
Found at i:45011 original size:25 final size:25
Alignment explanation
Indices: 44976--45040 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
44966 CTTTTCAAAT
44976 CACC-TTTCGGTGGATTTGTTTTTC
1 CACCTTTTCGGTGGATTTGTTTTTC
45000 CACCTTTTCGGTGGATTTGTTTTTC
1 CACCTTTTCGGTGGATTTGTTTTTC
45025 CACCTTTTCGGTGGAT
1 CACCTTTTCGGTGGAT
45041 AGTCAACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.48
Consensus pattern (25 bp):
CACCTTTTCGGTGGATTTGTTTTTC
Found at i:55166 original size:38 final size:36
Alignment explanation
Indices: 55085--55166 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 36
55075 GTAAAAAAAT
* *
55085 AATATATATAAATATTATGAATTTAAATTTTTAAAG
1 AATATATATAAATATTATGAACTTAAATTTATAAAG
* * *
55121 AAAATATATAAATATTTTCTAACTTATAATATTATAAA-
1 AATATATATAAATATTAT-GAACTTA-AAT-TTATAAAG
55159 AATATATA
1 AATATATA
55167 ATAAGGACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
36 16 0.43
37 5 0.14
38 10 0.27
39 6 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (36 bp):
AATATATATAAATATTATGAACTTAAATTTATAAAG
Found at i:55311 original size:18 final size:19
Alignment explanation
Indices: 55288--55330 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
55278 CAGTAATCCT
55288 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
*
55306 ATTCCCACTGGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
55326 ATTCC
1 ATTCC
55331 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:55318 original size:20 final size:20
Alignment explanation
Indices: 55293--55330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55283 ATCCTATTCC
55293 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
55313 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
55331 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:56890 original size:24 final size:23
Alignment explanation
Indices: 56843--56892 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
56833 GATTCTCTTC
56843 TTTTTTTTAAATTCTGCACTAAT
1 TTTTTTTTAAATTCTGCACTAAT
* * *
56866 TTTTTTTTACATTTTGCACTAAA
1 TTTTTTTTAAATTCTGCACTAAT
56889 TTTT
1 TTTT
56893 CCAAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTTTTAAATTCTGCACTAAT
Found at i:59587 original size:20 final size:20
Alignment explanation
Indices: 59556--59787 Score: 279
Period size: 20 Copynumber: 11.7 Consensus size: 20
59546 ATAACACATA
59556 ACCCGGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
* * *
59576 ACCCAGACGCTTTAAAAATG
1 ACCCGGAGGCTTTACAAATG
* *
59596 ACCCGGAGGCCTTACAAATA
1 ACCCGGAGGCTTTACAAATG
* *
59616 ACCCAGAGGCTTTTCAAATG
1 ACCCGGAGGCTTTACAAATG
**
59636 ACCCAAAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
*
59656 ACCCTGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
*
59676 ACTCGGAGGCTTTACAAA--
1 ACCCGGAGGCTTTACAAATG
* *
59694 ACCTGGAGGCTTTACAAATT
1 ACCCGGAGGCTTTACAAATG
* **
59714 ATCTAGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
*
59734 ACCCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
*
59754 ACCCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
*
59774 ACCTGGAGGCTTTA
1 ACCCGGAGGCTTTA
59788 ATTTTCTAGA
Statistics
Matches: 182, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
18 16 0.09
20 166 0.91
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (20 bp):
ACCCGGAGGCTTTACAAATG
Found at i:68157 original size:16 final size:16
Alignment explanation
Indices: 68136--68168 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
68126 TAATAAATAG
68136 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68152 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68168 A
1 A
68169 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:68248 original size:10 final size:10
Alignment explanation
Indices: 68233--68307 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
68223 CATTTAATAA
68233 ATAAACGAAC
1 ATAAACGAAC
68243 ATAAACGAAC
1 ATAAACGAAC
68253 ----ACGAAC
1 ATAAACGAAC
68259 ATAAACGAAC
1 ATAAACGAAC
** *
68269 ACGAAC-ATAA
1 ATAAACGA-AC
68279 ATGAACACGAAC
1 AT-AA-ACGAAC
68291 ATAAACGAAC
1 ATAAACGAAC
68301 ATAAACG
1 ATAAACG
68308 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:68258 original size:16 final size:16
Alignment explanation
Indices: 68237--68301 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
68227 TAATAAATAA
68237 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68253 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
68269 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
68285 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
68301 A
1 A
68302 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:69067 original size:14 final size:14
Alignment explanation
Indices: 69050--69105 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
69040 AATGAACATA
69050 AACGAACATAATCG
1 AACGAACATAATCG
69064 AACGAACAT-A---
1 AACGAACATAATCG
* *
69074 AACAAACATAACCG
1 AACGAACATAATCG
69088 AACGAACATAATCG
1 AACGAACATAATCG
69102 AACG
1 AACG
69106 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:69070 original size:24 final size:24
Alignment explanation
Indices: 69043--69104 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
69033 ATAAATAAAT
*
69043 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
69067 GAACATAAACAAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
69091 GAACATAATCGAAC
1 GAACATAAACGAAC
69105 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:74018 original size:59 final size:60
Alignment explanation
Indices: 73944--74057 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
73934 TTGCTGTCAT
* *
73944 AAACAATTAACACATTCCATGTAAGCAAA-TCAACCACAAATTCGAAACAAGATATAAAC
1 AAACAATTAACACATTCCATGCAAGCAAACACAACCACAAATTCGAAACAAGATATAAAC
* * *
74003 AAACAATTAATACATTCCATGCAAGTAAACACAACCAGAAATTCGAAACAAGATA
1 AAACAATTAACACATTCCATGCAAGCAAACACAACCACAAATTCGAAACAAGATA
74058 CAAATAACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 26 0.53
60 23 0.47
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (60 bp):
AAACAATTAACACATTCCATGCAAGCAAACACAACCACAAATTCGAAACAAGATATAAAC
Found at i:90800 original size:3 final size:3
Alignment explanation
Indices: 90792--90818 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
90782 AAGACGTAAG
90792 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
90819 AAACAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.