Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006836.1 Hibiscus syriacus cultivar Beakdansim tig00017375_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: 72028
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2144 original size:114 final size:113
Alignment explanation
Indices: 1854--2184 Score: 394
Period size: 114 Copynumber: 2.9 Consensus size: 113
1844 GGATAAACCA
* * * *
1854 ATCAACATTTCCAATGGATGGGTTC-TAATGAGAAGAACTCGTTCGACGAGGGAGAATAAGTTCA
1 ATCAACATTTCC-ATGGA-GAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
* * *
1918 TAATTAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCACAGAAAGAGGTGT
64 TAA-T-G-AGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
* * *
1971 ATCAACATTTCCATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGACAAGAAGTTTATA
1 ATCAACATTTCCATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATA
* * *
2036 ATGAGAACTTGTTCAACCTTGGTTTGATTTCAACACAGAAGGAGGTGG
66 ATGAGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
* * * * *
2084 ATTAATATTTCCAGTGGAGAGTTTATAATGAGAAAAACTCATCCGACGAGGTAGAAGAAGTTCAT
1 ATCAACATTTCCA-TGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
* *
2149 AATGAGAATAACTTGTTCAAACTTAGTTCGATTCCA
65 AATGAG---AACTTGTTCAACCTTGGTTCGATTCCA
2185 TCATATAAGG
Statistics
Matches: 184, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
113 50 0.27
114 52 0.28
115 6 0.03
116 41 0.22
117 35 0.19
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (113 bp):
ATCAACATTTCCATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATA
ATGAGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
Found at i:2510 original size:3 final size:3
Alignment explanation
Indices: 2502--2551 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
2492 TCAACTCTTA
* *
2502 TAT TAT TAT TAT TAT TAT TAT TAT AAAA TAT TAT TATT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA-T TA-T TAT TAT
2550 TA
1 TA
2552 CAAAATACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 33 0.80
4 8 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2556 original size:27 final size:25
Alignment explanation
Indices: 2505--2558 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
2495 ACTCTTATAT
*
2505 TATTATTATTATTATTATTATAAAA
1 TATTATTATTATTATTATTACAAAA
2530 TATTATTATTTATTTATTATTACAAAA
1 TATTATTA-TTA-TTATTATTACAAAA
2557 TA
1 TA
2559 CCCAAACTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
26 3 0.12
27 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATTATTATTATTATTACAAAA
Found at i:3738 original size:22 final size:22
Alignment explanation
Indices: 3713--3755 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3703 TCCTGGCATA
3713 TTTATTTTCTT-ATTTTAATTTT
1 TTTA-TTTCTTAATTTTAATTTT
3735 TTTATTTCTTAATTTTAATTT
1 TTTATTTCTTAATTTTAATTT
3756 AATTTGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTCTTAATTTTAATTTT
Found at i:4618 original size:2 final size:2
Alignment explanation
Indices: 4611--4671 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
4601 TATGTTCTTT
4611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4652 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
4672 GGGGGTATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4946 original size:13 final size:13
Alignment explanation
Indices: 4928--4953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4918 GGATTTTTTT
4928 AAAATATTGTTTC
1 AAAATATTGTTTC
4941 AAAATATTGTTTC
1 AAAATATTGTTTC
4954 GATTTTTTTA
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:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AAAATATTGTTTC
Found at i:5827 original size:23 final size:23
Alignment explanation
Indices: 5761--5831 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
5751 ACCAAAATAT
* * **
5761 GTGCCA-AAAGGTAGAAGAAAAT
1 GTGCCATAAAGGCAGAGGAAAGC
*
5783 GTGTCATAAAGGCAGAGGAAAGC
1 GTGCCATAAAGGCAGAGGAAAGC
*
5806 GTGCCATACAGGCAGAGGAAAGC
1 GTGCCATAAAGGCAGAGGAAAGC
5829 GTG
1 GTG
5832 TCATGCATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.39, C:0.14, G:0.34, T:0.13
Consensus pattern (23 bp):
GTGCCATAAAGGCAGAGGAAAGC
Found at i:6403 original size:26 final size:26
Alignment explanation
Indices: 6353--6404 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
6343 TTTAAATTTT
*
6353 AAAATTTTAGATAAAATAAACATAAA
1 AAAATTTTAGATAAAAGAAACATAAA
6379 AAAATTTTATAGA-AAAAGAAA-ATAAA
1 AAAA-TTT-TAGATAAAAGAAACATAAA
6405 TTATCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (26 bp):
AAAATTTTAGATAAAAGAAACATAAA
Found at i:6992 original size:2 final size:2
Alignment explanation
Indices: 6985--7009 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6975 TTTAAGTAAT
6985 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
7010 TAATGATTAA
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
Found at i:10253 original size:3 final size:3
Alignment explanation
Indices: 10245--10279 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
10235 CTGAAAACAA
10245 AAT AAT AAT AAT AA- AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
10280 CCCAGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:10770 original size:42 final size:41
Alignment explanation
Indices: 10672--10778 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
10662 GGTCGAAGGT
* * *
10672 CTTACGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGG
1 CTTACTGATAGCCCGAAGGACTTATCATCATGATCGAAAGA
* *
10713 CTTA-TAGAT-GACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACT-GATAG-CCCGAAGGACTT-ATCATCATGATCGAAAGA
*
10755 CTTACTGATAGCCCGAATGACTTA
1 CTTACTGATAGCCCGAAGGACTTA
10779 CCAATTTGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
40 1 0.02
41 19 0.35
42 32 0.59
43 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTACTGATAGCCCGAAGGACTTATCATCATGATCGAAAGA
Found at i:11169 original size:41 final size:42
Alignment explanation
Indices: 11124--11226 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
11114 GTCCGAAATT
* ** *
11124 CTTATGGATGGCCCGAAGGATTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
** *
11165 CTTATAGATGAACCGAAGAATTTAATCATCAAGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
* *
11207 CTTATTGATGGCACGAAGGA
1 CTTATAGATGGCCCGAAGGA
11227 CTTACCAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
Found at i:11208 original size:196 final size:197
Alignment explanation
Indices: 10865--11293 Score: 614
Period size: 196 Copynumber: 2.2 Consensus size: 197
10855 AATTTAAATG
* * * * * *
10865 AGAAACTTTGGGAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCT
1 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
* * * *
10930 TATGGATGACCTGAAGGACTTATCATCTTGCTCGAAAGGCTTGTAGATGACCCAAATGATTTAAT
66 TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATGATTTAAT
** *
10995 CATAATGCTTGAAAGACTTACTGATGGCCCGAAGGA-TTACCAATTTTGGAAATAGTTTACTAGG
131 CATAATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
11059 TA
196 TA
* *
11061 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGTCCGAAATTCT
1 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
* * *
11126 TATGGATGGCCCGAAGGATTTATCATCTTGCTCGAAAGACTTATAGATGAACCGAA-GAATTTAA
66 TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATG-ATTTAA
*
11190 TCATCAA-GCTCAAAAGACTTATTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTA
130 TCAT-AATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTA
11254 GGTA
194 GGTA
* *
11258 AGAAACTTTGGAAGTCATTTTCTT-ACTTTTCAAAAA
1 AGAAACTTTGGAAATCATTTT-TTCATTTTTCAAAAA
11294 TTTCAATTTT
Statistics
Matches: 208, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
195 1 0.00
196 142 0.68
197 63 0.30
198 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (197 bp):
AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATGATTTAAT
CATAATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
TA
Found at i:11474 original size:451 final size:450
Alignment explanation
Indices: 10611--11486 Score: 1337
Period size: 451 Copynumber: 1.9 Consensus size: 450
10601 TATTTAAATG
* * *
10611 AGAAACTTTGGAAATCATTCTCATTTTTTAAAAAACACGTGAAAACATCCTGGTCGAAGGTCTTA
1 AGAAACTTTGGAAATCATTCTCATTTTTCAAAAAACACGTGAAAACATCATGGTCGAAAGTCTTA
* * *
10676 CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGGCTTATAGATGACCCGAAGGATTTAATCA
66 CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAATCA
* * * *
10741 TCATGCTCGAAAGACTTACTGATAGCCCGAATGACTTACCAATTTGGGAAATAGTTTACTAGGTA
131 TCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTA
*
10806 AGAAACTTTGGAAATAGTTTTTATTACTTTTCAAAAATTTCAATTTTTAAATTTAAATGAGAAAC
196 AGAAACTTTGGAAATAG-TTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAAC
*
10871 TTTGGGAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGA
260 TTTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGA
* *
10936 TGACCTGAAGGACTTATCATCTTGCTCGAAAGGCTTGTAGATGACCCAAATGATTTAATCATAAT
325 TGACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATGATTTAATCATAAT
* *
11001 GCTTGAAAGACTTACTGATGGCCCGAAGGA-TTACCAATTTTGGAAATAGTTTACTAGGTA
390 GCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
* * *
11061 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCAT-GTCCGAAATTC
1 AGAAACTTTGGAAATCA--TTCTCATTTTTCAAAAAACACGTGAAAACATCATGGT-CGAAAGTC
* * * *
11125 TTATGGATGGCCCGAAGGATTTATCATCTTGCTCGAAAGACTTATAGATGAACCGAAGAATTTAA
63 TTACGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAA
* * *
11190 TCATCAAGCTCAAAAGACTTATTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAG
128 TCATCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAG
* * *
11255 GTAAGAAACTTTGGAAGTCA-TTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGA
193 GTAAGAAACTTTGGAAAT-AGTTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGA
* * * *
11319 AACTTTGGAAATTGTTTTCTTATTTTTTGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTAT
257 AACTTTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTAT
* * *
11384 GGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGGCCTAAA-GTATTTAATCA
322 GGATGACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATG-ATTTAATCA
*
11448 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
386 TAATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
11487 TAATGGCCCG
Statistics
Matches: 383, Mismatches: 37, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
450 18 0.05
451 191 0.50
452 173 0.45
453 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (450 bp):
AGAAACTTTGGAAATCATTCTCATTTTTCAAAAAACACGTGAAAACATCATGGTCGAAAGTCTTA
CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAATCA
TCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTA
AGAAACTTTGGAAATAGTTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACT
TTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGAT
GACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATGATTTAATCATAATG
CTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
Found at i:11504 original size:19 final size:19
Alignment explanation
Indices: 11457--11508 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
11447 ATCATGCTCG
*
11457 AAAGACTTACTGATGGCCC
1 AAAGACTTACTAATGGCCC
11476 AAAGGACTTACTAATGGCCC
1 AAA-GACTTACTAATGGCCC
*
11496 GAAGACTTACTAA
1 AAAGACTTACTAA
11509 GTAAGAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (19 bp):
AAAGACTTACTAATGGCCC
Found at i:12679 original size:12 final size:12
Alignment explanation
Indices: 12662--12689 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12652 GAATGACAGA
12662 ATTTTGTAAAGT
1 ATTTTGTAAAGT
12674 ATTTTGTAAAGT
1 ATTTTGTAAAGT
12686 ATTT
1 ATTT
12690 CCCCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (12 bp):
ATTTTGTAAAGT
Found at i:13217 original size:2 final size:2
Alignment explanation
Indices: 13210--13272 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
13200 AGTTTTATTG
13210 TA TA TA TA 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
*
13252 TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
13273 TCTACCGCCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23320 original size:21 final size:19
Alignment explanation
Indices: 23282--23327 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
23272 AATTAATCCT
23282 ACTAACTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
23302 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
23323 A-TAAT
1 ACTAAT
23328 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:25091 original size:16 final size:16
Alignment explanation
Indices: 25070--25108 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
25060 AAGGGTTCTT
25070 GTTTTATACAGTTTCA
1 GTTTTATACAGTTTCA
25086 GTTTTATACAGTTTCA
1 GTTTTATACAGTTTCA
*
25102 GTCTTAT
1 GTTTTAT
25109 CACTTTGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (16 bp):
GTTTTATACAGTTTCA
Found at i:38747 original size:17 final size:18
Alignment explanation
Indices: 38725--38765 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38715 GAATTCCAGA
38725 ATACCAAAAT-GGTATCG
1 ATACCAAAATGGGTATCG
38742 ATACCAAAATGGGTATCG
1 ATACCAAAATGGGTATCG
*
38760 GTACCA
1 ATACCA
38766 TAGAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (18 bp):
ATACCAAAATGGGTATCG
Found at i:39364 original size:419 final size:419
Alignment explanation
Indices: 38586--39424 Score: 1273
Period size: 419 Copynumber: 2.0 Consensus size: 419
38576 CAGTAGTGAT
* *
38586 ACTATAAAGTTAAATTGAAGGATAGTATATGAACCAGATGAACAATATCAATACTTATTAAAGAA
1 ACTATAAAGTTAAACTGAAGGATAATATATGAACCAGATGAACAATATCAATACTTATTAAAGAA
* * * *
38651 GTATCGATACTGATGTGGAGGTATCAATACTAAGAGGAAGATATCGATACCATAATCGAAAATGG
66 GTATCGATACTGATATAGAGGTATCAATACCAAGAGAAAGATATCGATACCATAATCGAAAATGG
38716 AATTCCAGAATACCAAAATGGTATCGATACCAAAATGGGTATCGGTACCATAGAAGAGAAGTATA
131 AATTCCAGAATACCAAAATGGTATCGATACCAAAATGGGTATCGGTACCATAGAAGAGAAGTATA
* * ** *
38781 AGTATTGTATGAGGGGTACCGATACTATTCAGGTTGAAATGTTGAATTAGATATTTCATTTTGTT
196 AGTACTGTAGGAGGGGTACCGATACTATTCAGCCTGAAATGTTGAATTAGATATTTCATTTCGTT
* *
38846 TATATAAGTTCAAATTGATTATTCATTAATGGAAAGTTGGTATTGATCTTAGATATATTGATGTG
261 TATATAAGTGCAAATTGATTATTCATTAATGGAAAGTTGGTATTGATCTTAGATATATTGATGTA
* * *
38911 TAGATTGGTAACGACAGTGTATTGATCGAAGCGATTTAACAAAGAGACTGAACAAAAGTTAAAAA
326 TAGATTGGGAACGACAGTGTACTGATCAAAGCGATTTAACAAAGAGACTGAACAAAAGTTAAAAA
38976 AGATTTCGTTTAGAACTTACGTGAGGCAA
391 AGATTTCGTTTAGAACTTACGTGAGGCAA
* * *
39005 ACTATAAGGTTAAACTGGAGGATAATATATGAACCAGATGAACAATATCGATACTTATTAAAGAA
1 ACTATAAAGTTAAACTGAAGGATAATATATGAACCAGATGAACAATATCAATACTTATTAAAGAA
* * * * **
39070 GTATCGATATTGATATAGAGGTATCGATACCAAGAGAAAGGTATTGATACTGTAATCGAAAATGG
66 GTATCGATACTGATATAGAGGTATCAATACCAAGAGAAAGATATCGATACCATAATCGAAAATGG
* * * * * * *
39135 AATTTCGGAATGCTAAAATGGTATCGATACCAAAGTGGGTATTGGTACCATAGAAGAGAAGTATT
131 AATTCCAGAATACCAAAATGGTATCGATACCAAAATGGGTATCGGTACCATAGAAGAGAAGTATA
* * *
39200 GGTACTGTAGGAGGGGTACCGATACTTTTCAGCCTGAAATTTTGAATTAGATATTTCATTTCGTT
196 AGTACTGTAGGAGGGGTACCGATACTATTCAGCCTGAAATGTTGAATTAGATATTTCATTTCGTT
* * * **
39265 TATGTAAGTGCAAATTGGTTATTCATTAATGGAGAGTTGGTATTTTTCTTAGATATATTGATGTA
261 TATATAAGTGCAAATTGATTATTCATTAATGGAAAGTTGGTATTGATCTTAGATATATTGATGTA
* * * *
39330 TAGATTGGGAATGACAGTGTACTGATCAAAGCGATTTAGCAAATAGACTGAACGAAAGTTAAAAA
326 TAGATTGGGAACGACAGTGTACTGATCAAAGCGATTTAACAAAGAGACTGAACAAAAGTTAAAAA
*
39395 GGATTTCGTTTAGAACTTACGTGAGGCAA
391 AGATTTCGTTTAGAACTTACGTGAGGCAA
39424 A
1 A
39425 TATGAGTACA
Statistics
Matches: 375, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
419 375 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (419 bp):
ACTATAAAGTTAAACTGAAGGATAATATATGAACCAGATGAACAATATCAATACTTATTAAAGAA
GTATCGATACTGATATAGAGGTATCAATACCAAGAGAAAGATATCGATACCATAATCGAAAATGG
AATTCCAGAATACCAAAATGGTATCGATACCAAAATGGGTATCGGTACCATAGAAGAGAAGTATA
AGTACTGTAGGAGGGGTACCGATACTATTCAGCCTGAAATGTTGAATTAGATATTTCATTTCGTT
TATATAAGTGCAAATTGATTATTCATTAATGGAAAGTTGGTATTGATCTTAGATATATTGATGTA
TAGATTGGGAACGACAGTGTACTGATCAAAGCGATTTAACAAAGAGACTGAACAAAAGTTAAAAA
AGATTTCGTTTAGAACTTACGTGAGGCAA
Found at i:43293 original size:16 final size:17
Alignment explanation
Indices: 43252--43286 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43242 ATATGATTTA
43252 TAAC-TTAAAAGCTTTG
1 TAACTTTAAAAGCTTTG
43268 TAACTTTAAAAGC-TTG
1 TAACTTTAAAAGCTTTG
43284 TAA
1 TAA
43287 TATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TAACTTTAAAAGCTTTG
Found at i:45540 original size:2 final size:2
Alignment explanation
Indices: 45533--45557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45523 CCGCCCCGAT
45533 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
45558 TTTTATTTTT
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
Found at i:45586 original size:32 final size:33
Alignment explanation
Indices: 45543--45628 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 33
45533 TATATATATA
45543 TATATATATATATATTTTTATTTTTTATATTAAT
1 TATATATATA-ATATTTTTATTTTTTATATTAAT
45577 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTT-TATTTTTTATATTAAT
45611 TATATATATAATATTTTT
1 TATATATATAATATTTTT
45629 GGGTTCGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
33 8 0.16
34 43 0.84
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (33 bp):
TATATATATAATATTTTTATTTTTTATATTAAT
Found at i:45615 original size:25 final size:25
Alignment explanation
Indices: 45551--45615 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
45541 TATATATATA
* *
45551 TATATATTTTTATTTTTTATATTAAT
1 TATATA-TATTATATTTTATATTAAT
* **
45577 TATATATATAATATTTTATATTTTT
1 TATATATATTATATTTTATATTAAT
45602 TATAT-TAATTATAT
1 TATATAT-ATTATAT
45616 ATATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 1 0.03
25 25 0.78
26 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATATATTATATTTTATATTAAT
Found at i:57834 original size:16 final size:19
Alignment explanation
Indices: 57796--57834 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57786 ACGAGAGAAA
57796 AAGATATTCCTTTAGGATT
1 AAGATATTCCTTTAGGATT
57815 AAGATATT-CTTT-GG-TT
1 AAGATATTCCTTTAGGATT
57831 AAGA
1 AAGA
57835 GTAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 4 0.20
19 8 0.40
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (19 bp):
AAGATATTCCTTTAGGATT
Found at i:62842 original size:23 final size:23
Alignment explanation
Indices: 62782--62861 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
62772 ATGATAAACA
* *
62782 AACACTAAATGAACACGTTCATG
1 AACATTAAATGAACACGTTCGTG
*
62805 AATATATAAATGAACACGTTCGTG
1 AACAT-TAAATGAACACGTTCGTG
* **
62829 AACATTAAACGAACATATTCGTG
1 AACATTAAATGAACACGTTCGTG
*
62852 AACAATAAAT
1 AACATTAAAT
62862 AAACGAATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (23 bp):
AACATTAAATGAACACGTTCGTG
Found at i:66995 original size:3 final size:3
Alignment explanation
Indices: 66987--67041 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
66977 TCATTTCATT
**
66987 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
67032 TT- TT- TTA TTA
1 TTA TTA TTA TTA
67042 ATAAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:68558 original size:17 final size:17
Alignment explanation
Indices: 68538--68601 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
68528 TTTTAAATGA
68538 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
68555 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
68577 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
68596 ATAAAT
1 ATAAAT
68602 TATATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:68569 original size:24 final size:24
Alignment explanation
Indices: 68542--68611 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 24
68532 AAATGAATAA
68542 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
68566 ATA--TTA-TTTT-TAAA-TA-A-
1 ATATTTTACTTTTATAAATTATAT
68583 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
68607 ATATT
1 ATATT
68612 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 5 0.13
20 8 0.21
21 8 0.21
22 5 0.13
23 1 0.03
24 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTTACTTTTATAAATTATAT
Found at i:68576 original size:22 final size:21
Alignment explanation
Indices: 68542--68622 Score: 94
Period size: 22 Copynumber: 3.9 Consensus size: 21
68532 AAATGAATAA
*
68542 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
68564 ATATATTA-TTTTTAAA-TAA
1 ATATATTACTTTTTAAATTAT
*
68583 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
68605 ATATATTATTTTTTAAAT
1 ATATATTACTTTTTAAAT
68623 GTTATATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 9 0.18
20 8 0.16
21 13 0.26
22 20 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTACTTTTTAAATTAT
Found at i:68588 original size:41 final size:42
Alignment explanation
Indices: 68537--68622 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 42
68527 TTTTTAAATG
68537 AATAAATATTTTACTTTTATAAATTATATATATTA-TTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
68578 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
68620 AAT
1 AAT
68623 GTTATATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
Found at i:68628 original size:21 final size:20
Alignment explanation
Indices: 68551--68629 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
68541 AATATTTTAC
*
68551 TTTTATAAATTATATATATTA
1 TTTTTTAAATT-TATATATTA
** *
68572 -TTTTTAAATAAATATTTTA
1 TTTTTTAAATTTATATATTA
*
68591 CTTTTATAAATTATATATATTA
1 -TTTTTTAAATT-TATATATTA
68613 TTTTTTAAATGTTATAT
1 TTTTTTAAAT-TTATAT
68630 TAATATTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 22 0.49
22 8 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTTAAATTTATATATTA
Found at i:69295 original size:25 final size:26
Alignment explanation
Indices: 69267--69323 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
69257 ATTACTTATG
69267 ATTTTCATAATATTTATT-ATATTTT
1 ATTTTCATAATATTTATTAATATTTT
** * *
69292 ATTTT-ATTTTTTTTATTAATGTTTT
1 ATTTTCATAATATTTATTAATATTTT
69317 ATTTTCA
1 ATTTTCA
69324 GGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.35
25 16 0.62
26 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (26 bp):
ATTTTCATAATATTTATTAATATTTT
Found at i:70714 original size:17 final size:17
Alignment explanation
Indices: 70694--70757 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
70684 TTTTAAATGA
70694 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
70711 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
70733 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
70752 ATAAAT
1 ATAAAT
70758 TATATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:70725 original size:24 final size:24
Alignment explanation
Indices: 70698--70767 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 24
70688 AAATGAATAA
70698 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
70722 ATA--TTA-TTTT-TAAA-TA-A-
1 ATATTTTACTTTTATAAATTATAT
70739 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
70763 ATATT
1 ATATT
70768 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 5 0.13
20 8 0.21
21 8 0.21
22 5 0.13
23 1 0.03
24 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTTACTTTTATAAATTATAT
Found at i:70732 original size:22 final size:21
Alignment explanation
Indices: 70698--70778 Score: 94
Period size: 22 Copynumber: 3.9 Consensus size: 21
70688 AAATGAATAA
*
70698 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
70720 ATATATTA-TTTTTAAA-TAA
1 ATATATTACTTTTTAAATTAT
*
70739 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
70761 ATATATTATTTTTTAAAT
1 ATATATTACTTTTTAAAT
70779 GTTATATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 9 0.18
20 8 0.16
21 13 0.26
22 20 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTACTTTTTAAATTAT
Found at i:70744 original size:41 final size:42
Alignment explanation
Indices: 70693--70778 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 42
70683 TTTTTAAATG
70693 AATAAATATTTTACTTTTATAAATTATATATATTA-TTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
70734 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
70776 AAT
1 AAT
70779 GTTATATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
Found at i:70784 original size:21 final size:20
Alignment explanation
Indices: 70707--70785 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
70697 AATATTTTAC
*
70707 TTTTATAAATTATATATATTA
1 TTTTTTAAATT-TATATATTA
** *
70728 -TTTTTAAATAAATATTTTA
1 TTTTTTAAATTTATATATTA
*
70747 CTTTTATAAATTATATATATTA
1 -TTTTTTAAATT-TATATATTA
70769 TTTTTTAAATGTTATAT
1 TTTTTTAAAT-TTATAT
70786 TAATATTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 22 0.49
22 8 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTTAAATTTATATATTA
Found at i:70895 original size:22 final size:23
Alignment explanation
Indices: 70853--70895 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
70843 CTTTTTCTGA
*
70853 TATTTCTAAATAAATAAATATCT
1 TATTTATAAATAAATAAATATCT
*
70876 TATTTATAAA-AAATATATAT
1 TATTTATAAATAAATAAATAT
70896 ATATTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATCT
Done.