Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001388.1 Hibiscus syriacus cultivar Beakdansim tig00002709_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: 74081
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6537 original size:24 final size:26
Alignment explanation
Indices: 6488--6547 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
6478 GTATTGACTT
6488 AAAAAAT-TAAACACATAAATAAAG-
1 AAAAAATATAAACACATAAATAAAGA
* * *
6512 AAAAAATATAAATACTTAAAT-GAGA
1 AAAAAATATAAACACATAAATAAAGA
6537 AAAAAATATAA
1 AAAAAATATAA
6548 TTTAGATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (26 bp):
AAAAAATATAAACACATAAATAAAGA
Found at i:7070 original size:10 final size:10
Alignment explanation
Indices: 7055--7085 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
7045 ATTTTAATAG
7055 AAAATATAAA
1 AAAATATAAA
7065 AAAATATAAA
1 AAAATATAAA
7075 AAATATATAAA
1 AAA-ATATAAA
7086 GAATTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATATAAA
Found at i:11875 original size:216 final size:213
Alignment explanation
Indices: 11482--11911 Score: 806
Period size: 216 Copynumber: 2.0 Consensus size: 213
11472 GTGATTTAGG
11482 GTTTTGGGAAATATTTTTTTGATTTAAATACAATTTTGAAATTTTAATTTAATTAATATTATTTT
1 GTTTTGGGAAATATTTTTTTGATTTAAATACAATTTTGAAATTTTAATTTAATTAATATTATTTT
11547 AATCATATATTAATAAAATAATAATAATAAATGACACATCATACATAAATATTAATAAAATAAGT
66 AATCATATATTAATAAAATAATAATAATAAATGACACATCATACATAAATATTAATAAAATAAGT
11612 CATAGTGTTTAAAATAGGAGTAATTCAAAAGTTGAATGATTAAATTGAAAACTTTTAAAGTTTAC
131 CATAGTGTTTAAAATAGGAGTAATTCAAAAGTTGAATGATTAAATTGAAAACTTTTAAAGTTTAC
11677 TGACCAAAATGGGAGAGA
196 TGACCAAAATGGGAGAGA
11695 GTTTTGGGAAATATTTTTTTGATTTAAATACAATTTTGAAATTTTAATTTAATTAATATTATTTT
1 GTTTTGGGAAATATTTTTTTGATTTAAATACAATTTTGAAATTTTAATTTAATTAATATTATTTT
*
11760 AATCATATATTAATAAAATAATAATAATAATAAATTACACATCATACATAAATATTAATAAAATA
66 AATCATATATTAAT--AA-AATAATAATAATAAATGACACATCATACATAAATATTAATAAAATA
*
11825 AGTTATAGTGTTTAAAATAGGAGTAATTCAAAAGTTGAATGATTAAATTGAAAACTTTTAAAGTT
128 AGTCATAGTGTTTAAAATAGGAGTAATTCAAAAGTTGAATGATTAAATTGAAAACTTTTAAAGTT
*
11890 TTCTGACCAAAATGGGAGAGA
193 TACTGACCAAAATGGGAGAGA
11911 G
1 G
11912 AACATAGTTG
Statistics
Matches: 211, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
213 79 0.37
215 2 0.01
216 130 0.62
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (213 bp):
GTTTTGGGAAATATTTTTTTGATTTAAATACAATTTTGAAATTTTAATTTAATTAATATTATTTT
AATCATATATTAATAAAATAATAATAATAAATGACACATCATACATAAATATTAATAAAATAAGT
CATAGTGTTTAAAATAGGAGTAATTCAAAAGTTGAATGATTAAATTGAAAACTTTTAAAGTTTAC
TGACCAAAATGGGAGAGA
Found at i:12560 original size:30 final size:31
Alignment explanation
Indices: 12526--12601 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 31
12516 ATAATAAAAT
*
12526 CTTATCATTGTAA-AGAAAAGCTTTTATAAA
1 CTTATAATTGTAAGAGAAAAGCTTTTATAAA
12556 CTTATAATTGTAATAGAGAAAAGCTTTTATAAA
1 CTTATAATTGT-A-AGAGAAAAGCTTTTATAAA
*
12589 ATTATAATTGTAA
1 CTTATAATTGTAA
12602 TAGTAAGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 10 0.24
31 2 0.05
32 2 0.05
33 27 0.66
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (31 bp):
CTTATAATTGTAAGAGAAAAGCTTTTATAAA
Found at i:12581 original size:33 final size:33
Alignment explanation
Indices: 12539--12604 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
12529 ATCATTGTAA
*
12539 AGAAAAGCTTTTATAAACTTATAATTGTAATAG
1 AGAAAAGCTTTTATAAAATTATAATTGTAATAG
12572 AGAAAAGCTTTTATAAAATTATAATTGTAATAG
1 AGAAAAGCTTTTATAAAATTATAATTGTAATAG
12605 TAAGTAAAAA
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:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (33 bp):
AGAAAAGCTTTTATAAAATTATAATTGTAATAG
Found at i:20424 original size:7 final size:7
Alignment explanation
Indices: 20412--20486 Score: 53
Period size: 7 Copynumber: 10.9 Consensus size: 7
20402 ATTTATTTAA
20412 CCTAAAC
1 CCTAAAC
20419 CCTAAAC
1 CCTAAAC
20426 CC-AAAC
1 CCTAAAC
**
20432 ATTAAAC
1 CCTAAAC
*
20439 TCTAAAC
1 CCTAAAC
* *
20446 CATATAC
1 CCTAAAC
*
20453 CCTAAAT
1 CCTAAAC
* *
20460 CATAAAT
1 CCTAAAC
*
20467 CCTAAAA
1 CCTAAAC
*
20474 CTTAAAC
1 CCTAAAC
20481 CCTAAA
1 CCTAAA
20487 TCCCAAAATC
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 4 0.08
7 47 0.92
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:20479 original size:21 final size:21
Alignment explanation
Indices: 20455--20494 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20445 CCATATACCC
* *
20455 TAAATCATAAATCCTAAAACT
1 TAAACCATAAATCCCAAAACT
*
20476 TAAACCCTAAATCCCAAAA
1 TAAACCATAAATCCCAAAA
20495 TCAAAATGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCATAAATCCCAAAACT
Found at i:22137 original size:24 final size:24
Alignment explanation
Indices: 22080--22138 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
22070 TTAAAATAAT
22080 TAAAATAACAAACAAACAAATAAAA
1 TAAAATAA-AAACAAACAAATAAAA
* *
22105 -AACAGTAAAAACAAA-ATCATAAAA
1 TAA-AATAAAAACAAACA-AATAAAA
22129 TAAAATAAAA
1 TAAAATAAAA
22139 TAAACATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.04
24 21 0.75
25 6 0.21
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.14
Consensus pattern (24 bp):
TAAAATAAAAACAAACAAATAAAA
Found at i:23341 original size:6 final size:6
Alignment explanation
Indices: 23330--23364 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
23320 AATGATATCT
23330 TTAGGG TTAGGG TTAGGG TTA-GG TTA-GG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG T
23365 ATGGATCCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:23821 original size:20 final size:20
Alignment explanation
Indices: 23796--23867 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
23786 ACATCCTGCA
*
23796 CGAAGGTCTTATAGATGGCC
1 CGAAGGACTTATAGATGGCC
* ** * *
23816 CGAAGGTCTTATCATCTTGCT
1 CGAAGGACTTAT-AGATGGCC
*
23837 CGAAAGACTTATAGATGGCC
1 CGAAGGACTTATAGATGGCC
23857 CGAAGGACTTA
1 CGAAGGACTTA
23868 CGCATCATGC
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (20 bp):
CGAAGGACTTATAGATGGCC
Found at i:23896 original size:42 final size:42
Alignment explanation
Indices: 23803--23916 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
23793 GCACGAAGGT
* *
23803 CTTATAGATGGCCCGAAGGTCTTA-TCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
*
23844 CTTATAGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
* *
23886 CTTACT-GATGGCCTGAAAGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTACTCATCA
23917 AGAAAACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 23 0.35
42 41 0.63
43 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
Found at i:24381 original size:42 final size:41
Alignment explanation
Indices: 24276--24382 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
24266 GCCCGAAGGT
* * * *
24276 CTTATGGATGGCCCGAAGGTCTTATCATCTTGCTTGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * * * *
24317 CTTATAAACGACCCAAAAGACTTATGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAT-CATCATGCTCGAAAGA
24359 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
24383 CTTATCAAGA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
41 18 0.36
42 31 0.62
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:33095 original size:6 final size:6
Alignment explanation
Indices: 33081--33116 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
33071 AATGATATCT
*
33081 TTAGAG TTAGGG TTAGGG TTAGGG TTA-GG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG T
33117 ATGGATCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:33107 original size:18 final size:17
Alignment explanation
Indices: 33081--33116 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33071 AATGATATCT
33081 TTAGAGTTAGGGTTAGGG
1 TTAGAGTTA-GGTTAGGG
*
33099 TTAGGGTTAGGTTAGGG
1 TTAGAGTTAGGTTAGGG
33116 T
1 T
33117 ATGGATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.36
Consensus pattern (17 bp):
TTAGAGTTAGGTTAGGG
Found at i:33265 original size:2 final size:2
Alignment explanation
Indices: 33260--33300 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33250 CCCTATTTTT
33260 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
33301 GGATAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33382 original size:28 final size:27
Alignment explanation
Indices: 33339--33399 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
33329 TTTAGTTTAT
33339 ATTAATTTTATTCCTTCATTTTTTATTA
1 ATTAATTTTATTCCTT-ATTTTTTATTA
*
33367 ATTATATTTTA-TCCTTATTTTTTA-TG
1 ATTA-ATTTTATTCCTTATTTTTTATTA
33393 ATTAATT
1 ATTAATT
33400 GAGTTGGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 5 0.16
27 8 0.26
28 9 0.29
29 6 0.19
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTAATTTTATTCCTTATTTTTTATTA
Found at i:33389 original size:13 final size:14
Alignment explanation
Indices: 33344--33391 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
33334 TTTATATTAA
33344 TTTTATTCCTTCATT
1 TTTTATTCCTT-ATT
** *
33359 TTTTATTAATTATA
1 TTTTATTCCTTATT
33373 TTTTA-TCCTTATT
1 TTTTATTCCTTATT
33386 TTTTAT
1 TTTTAT
33392 GATTAATTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
13 10 0.38
14 7 0.27
15 9 0.35
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTCCTTATT
Found at i:33964 original size:28 final size:27
Alignment explanation
Indices: 33921--33981 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
33911 TTTAGTTTAT
33921 ATTAATTTTATTCCTTCATTTTTTATTA
1 ATTAATTTTATTCCTT-ATTTTTTATTA
*
33949 ATTATATTTTA-TCCTTATTTTTTA-TG
1 ATTA-ATTTTATTCCTTATTTTTTATTA
33975 ATTAATT
1 ATTAATT
33982 GAGTTGGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 5 0.16
27 8 0.26
28 9 0.29
29 6 0.19
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTAATTTTATTCCTTATTTTTTATTA
Found at i:33971 original size:13 final size:14
Alignment explanation
Indices: 33926--33973 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
33916 TTTATATTAA
33926 TTTTATTCCTTCATT
1 TTTTATTCCTT-ATT
** *
33941 TTTTATTAATTATA
1 TTTTATTCCTTATT
33955 TTTTA-TCCTTATT
1 TTTTATTCCTTATT
33968 TTTTAT
1 TTTTAT
33974 GATTAATTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
13 10 0.38
14 7 0.27
15 9 0.35
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTCCTTATT
Found at i:34387 original size:582 final size:582
Alignment explanation
Indices: 33283--34447 Score: 2330
Period size: 582 Copynumber: 2.0 Consensus size: 582
33273 ATATATATAT
33283 ATATATATATATATATATGGATAAATTTTAAGTTAGAGCTTCAAATTTTAGTTTATATTAATTTT
1 ATATATATATATATATATGGATAAATTTTAAGTTAGAGCTTCAAATTTTAGTTTATATTAATTTT
33348 ATTCCTTCATTTTTTATTAATTATATTTTATCCTTATTTTTTATGATTAATTGAGTTGGAACCCT
66 ATTCCTTCATTTTTTATTAATTATATTTTATCCTTATTTTTTATGATTAATTGAGTTGGAACCCT
33413 AATTTAGTACTTGTTGACAATAACATAACAATTTTGATTTTGCTATACCTACTTCGAAAATTGTT
131 AATTTAGTACTTGTTGACAATAACATAACAATTTTGATTTTGCTATACCTACTTCGAAAATTGTT
33478 ACAAACTATTAATTTATTATAATGAAAAAAAATCATTTTTAAATATACATATTACAATATTTTTT
196 ACAAACTATTAATTTATTATAATGAAAAAAAATCATTTTTAAATATACATATTACAATATTTTTT
33543 ATCATCATCAAATATATCTTGTTGTACTTCTTCCAAATTTCATTCATGCTAGTTATAATATCCCA
261 ATCATCATCAAATATATCTTGTTGTACTTCTTCCAAATTTCATTCATGCTAGTTATAATATCCCA
33608 AATTTTGGACTGGTAATTGAAAAGTAAATTTTGAAAGTATCAAAGTGTAAATTTGTAAAAGTTTA
326 AATTTTGGACTGGTAATTGAAAAGTAAATTTTGAAAGTATCAAAGTGTAAATTTGTAAAAGTTTA
33673 GAGACTAAAAATATAAATTTTCAAAATTTATATTTTGGGTCTATAATTGAGTAGTTCAGCCCTAG
391 GAGACTAAAAATATAAATTTTCAAAATTTATATTTTGGGTCTATAATTGAGTAGTTCAGCCCTAG
33738 AATATTATTTTAGTGGGTTTTAAAATTTTGATTTAAAGTTGGTATAAAAGTTTATTAAGCGATAG
456 AATATTATTTTAGTGGGTTTTAAAATTTTGATTTAAAGTTGGTATAAAAGTTTATTAAGCGATAG
33803 AGTCTGGTAAAATATTCGGATAATCGGGTCGAATCAGAAGCTTACAAAATTTGAAGGAAGGA
521 AGTCTGGTAAAATATTCGGATAATCGGGTCGAATCAGAAGCTTACAAAATTTGAAGGAAGGA
33865 ATATATATATATATATATGGATAAATTTTAAGTTAGAGCTTCAAATTTTAGTTTATATTAATTTT
1 ATATATATATATATATATGGATAAATTTTAAGTTAGAGCTTCAAATTTTAGTTTATATTAATTTT
33930 ATTCCTTCATTTTTTATTAATTATATTTTATCCTTATTTTTTATGATTAATTGAGTTGGAACCCT
66 ATTCCTTCATTTTTTATTAATTATATTTTATCCTTATTTTTTATGATTAATTGAGTTGGAACCCT
33995 AATTTAGTACTTGTTGACAATAACATAACAATTTTGATTTTGCTATACCTACTTCGAAAATTGTT
131 AATTTAGTACTTGTTGACAATAACATAACAATTTTGATTTTGCTATACCTACTTCGAAAATTGTT
34060 ACAAACTATTAATTTATTATAATGAAAAAAAATCATTTTTAAATATACATATTACAATATTTTTT
196 ACAAACTATTAATTTATTATAATGAAAAAAAATCATTTTTAAATATACATATTACAATATTTTTT
34125 ATCATCATCAAATATATCTTGTTGTACTTCTTCCAAATTTCATTCATGCTAGTTATAATATCCCA
261 ATCATCATCAAATATATCTTGTTGTACTTCTTCCAAATTTCATTCATGCTAGTTATAATATCCCA
34190 AATTTTGGACTGGTAATTGAAAAGTAAATTTTGAAAGTATCAAAGTGTAAATTTGTAAAAGTTTA
326 AATTTTGGACTGGTAATTGAAAAGTAAATTTTGAAAGTATCAAAGTGTAAATTTGTAAAAGTTTA
34255 GAGACTAAAAATATAAATTTTCAAAATTTATATTTTGGGTCTATAATTGAGTAGTTCAGCCCTAG
391 GAGACTAAAAATATAAATTTTCAAAATTTATATTTTGGGTCTATAATTGAGTAGTTCAGCCCTAG
34320 AATATTATTTTAGTGGGTTTTAAAATTTTGATTTAAAGTTGGTATAAAAGTTTATTAAGCGATAG
456 AATATTATTTTAGTGGGTTTTAAAATTTTGATTTAAAGTTGGTATAAAAGTTTATTAAGCGATAG
34385 AGTCTGGTAAAATATTCGGATAATCGGGTCGAATCAGAAGCTTACAAAATTTGAAGGAAGGA
521 AGTCTGGTAAAATATTCGGATAATCGGGTCGAATCAGAAGCTTACAAAATTTGAAGGAAGGA
34447 A
1 A
34448 GTTTGAGGTT
Statistics
Matches: 583, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
582 583 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (582 bp):
ATATATATATATATATATGGATAAATTTTAAGTTAGAGCTTCAAATTTTAGTTTATATTAATTTT
ATTCCTTCATTTTTTATTAATTATATTTTATCCTTATTTTTTATGATTAATTGAGTTGGAACCCT
AATTTAGTACTTGTTGACAATAACATAACAATTTTGATTTTGCTATACCTACTTCGAAAATTGTT
ACAAACTATTAATTTATTATAATGAAAAAAAATCATTTTTAAATATACATATTACAATATTTTTT
ATCATCATCAAATATATCTTGTTGTACTTCTTCCAAATTTCATTCATGCTAGTTATAATATCCCA
AATTTTGGACTGGTAATTGAAAAGTAAATTTTGAAAGTATCAAAGTGTAAATTTGTAAAAGTTTA
GAGACTAAAAATATAAATTTTCAAAATTTATATTTTGGGTCTATAATTGAGTAGTTCAGCCCTAG
AATATTATTTTAGTGGGTTTTAAAATTTTGATTTAAAGTTGGTATAAAAGTTTATTAAGCGATAG
AGTCTGGTAAAATATTCGGATAATCGGGTCGAATCAGAAGCTTACAAAATTTGAAGGAAGGA
Found at i:43764 original size:15 final size:17
Alignment explanation
Indices: 43731--43774 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
43721 ATTCAATTAA
*
43731 TATATATTTATTATATT
1 TATAAATTTATTATATT
43748 TATAAATTT-TTAT-TT
1 TATAAATTTATTATATT
*
43763 TATAAATATATT
1 TATAAATTTATT
43775 CAAAACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 6 0.25
17 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATAAATTTATTATATT
Found at i:43883 original size:18 final size:18
Alignment explanation
Indices: 43862--43900 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43852 TAATTGAAAT
*
43862 TATTAAATTA-GATTTTTA
1 TATT-AATTATGATTATTA
43880 TATTAATTATGATTATTA
1 TATTAATTATGATTATTA
43898 TAT
1 TAT
43901 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTAATTATGATTATTA
Found at i:44286 original size:41 final size:40
Alignment explanation
Indices: 44204--44286 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 40
44194 ATATAGTTCA
* *
44204 AATGTAAACTATATAGTTTATATATATAGTTCATATGAAAT
1 AATGTAAACTATATAGTTTATATATATAG-TAATATCAAAT
44245 AATGTAAACTATATA-TATTATATAGTATA-TAATTATCAAAT
1 AATGTAAACTATATAGT-TTATATA-TATAGTAA-TATCAAAT
44286 A
1 A
44287 TAGTATATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
40 3 0.08
41 30 0.81
42 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (40 bp):
AATGTAAACTATATAGTTTATATATATAGTAATATCAAAT
Found at i:44414 original size:2 final size:2
Alignment explanation
Indices: 44407--44899 Score: 136
Period size: 2 Copynumber: 242.0 Consensus size: 2
44397 ACTACTAAAC
* * * *
44407 TA TA TA TA T- TA TA TA GTT TA CA TA GTT TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA
* * * *
44449 TA TA GTT TA TA CA TA TA GT- TCA TA TG TA -A TA TA TA GTT TA TA
1 TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA -TA TA TA
* * *
44491 TA TA GTT TA TA TA CTA T- TA TC TA TA TA CTA TA TA GTT TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
44534 TA AA CTA TA TA -A TT TA TA CA 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
* * *
44576 TA TA TA TA TA -A AA GT- TG TA TA GTT TA TA TA -A T- TCA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA T-A TA TA
* * *
44615 TA TT TA TA TA -A AA CTA TA TA -A TT TA TA TA TA GT- TCA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA T-A TA TA
* * * * * *
44654 GT- TCA TA TA TA AA CTA TA TA GTT TA TA CA TGG TA TA TA TT TT TA
1 -TA T-A TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA
* * *
44698 CA TA -A TA TA TA TA TA CA -A TT TA TA TA TA GTA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
44737 TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA CTT 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
* * * * *
44779 AA TA TA GTT TA TA T- TA -A TA AA CTA TA TA GTT TA TA CA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * *
44819 TA TA TA TA GT- TCA TA TA TA GTA TA TA AA AA TA -A AA TA TA TA
1 TA TA TA TA -TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
44860 GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44900 ATTGTTTCAA
Statistics
Matches: 360, Mismatches: 72, Indels: 118
0.65 0.13 0.21
Matches are distributed among these distances:
1 25 0.07
2 298 0.83
3 37 0.10
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:44421 original size:9 final size:9
Alignment explanation
Indices: 44407--44899 Score: 70
Period size: 9 Copynumber: 54.4 Consensus size: 9
44397 ACTACTAAAC
44407 TATATATAT
1 TATATATAT
44416 TATATAGT-T
1 TATATA-TAT
*
44425 TACATAGT-T
1 TATATA-TAT
44434 TATATATAT
1 TATATATAT
*
44443 AGTTTATATAGTT
1 --TATATATA--T
44456 TATACATATAGT
1 TAT--ATATA-T
* *
44468 TCATATGTAA
1 T-ATATATAT
44478 TATATAGT-T
1 TATATA-TAT
44487 TATATATAGTT
1 TATATATA--T
44498 TATATACTAT
1 TATATA-TAT
*
44508 TATCTATA-
1 TATATATAT
44516 TACTATATAGT
1 TA-TATATA-T
44527 T-TATATAT
1 TATATATAT
*
44535 AAACTATATAAT
1 -TA-TATAT-AT
*
44547 T-TATACA-
1 TATATATAT
44554 TATATATA-
1 TATATATAT
44562 TATATATA-
1 TATATATAT
44570 TATATATAT
1 TATATATAT
*
44579 ATATATAAAAGT
1 -TATAT-ATA-T
*
44591 TGTATAGT-T
1 TATATA-TAT
44600 TATATA-AT
1 TATATATAT
44608 TCATATATAT
1 T-ATATATAT
*
44618 T-TATATAA
1 TATATATAT
*
44626 AACTATATAATT
1 TA-TATAT-A-T
44638 TATATATAGT
1 TATATATA-T
44648 TCA-ATAGT-T
1 T-ATATA-TAT
*
44657 CATATATA-
1 TATATATAT
*
44665 AACTATATAGT
1 TA-TATATA-T
*
44676 T-TATACAT
1 TATATATAT
44684 GGTATATAT-T
1 --TATATATAT
* * *
44694 TTTACATAA
1 TATATATAT
44703 TATATATA-
1 TATATATAT
*
44711 TACA-AT-T
1 TATATATAT
*
44718 TATATATAG
1 TATATATAT
44727 TATATA-A-
1 TATATATAT
44734 TA-ATATA-
1 TATATATAT
* * *
44741 AATATAAAC
1 TATATATAT
44750 TATATAGT-T
1 TATATA-TAT
44759 TATATATACT
1 TATATATA-T
44769 T-TATATAT
1 TATATATAT
* * *
44777 AAAATATAG
1 TATATATAT
44786 T-T-TATAT
1 TATATATAT
* *
44793 TA-ATAAAC
1 TATATATAT
44801 TATATAGT-T
1 TATATA-TAT
* *
44810 TATACATAA
1 TATATATAT
44819 TATATATAGT
1 TATATATA-T
*
44829 TCATATATAG
1 T-ATATATAT
44839 TATATA-A-
1 TATATATAT
*
44846 -A-A-ATAA
1 TATATATAT
* *
44852 AATATATAG
1 TATATATAT
44861 TATATATA-
1 TATATATAT
44869 TATATATA-
1 TATATATAT
44877 TATATATAT
1 TATATATAT
44886 ATATATATAT
1 -TATATATAT
44896 TATA
1 TATA
44900 ATTGTTTCAA
Statistics
Matches: 356, Mismatches: 59, Indels: 138
0.64 0.11 0.25
Matches are distributed among these distances:
4 1 0.00
5 2 0.01
6 4 0.01
7 16 0.04
8 80 0.22
9 142 0.40
10 44 0.12
11 51 0.14
12 8 0.02
13 8 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (9 bp):
TATATATAT
Found at i:44535 original size:20 final size:19
Alignment explanation
Indices: 44407--44895 Score: 213
Period size: 20 Copynumber: 25.8 Consensus size: 19
44397 ACTACTAAAC
44407 TATATATAT-TATATAGTT
1 TATATATATATATATAGTT
*
44425 TACATAGTTTATATATATAGTT
1 T--ATA-TATATATATATAGTT
*
44447 TATATAGTTTATACATATAGTT
1 TATATA---TATATATATAGTT
* *
44469 CATATGTA-ATATATAGTT
1 TATATATATATATATAGTT
* *
44487 TATATATAGTTTATATACTAT
1 TATATATA-TATATATAGT-T
*
44508 TATCTATATACTATATAGTT
1 TATATATATA-TATATAGTT
* *
44528 TATATATAAACTATATAATT
1 TATATATATA-TATATAGTT
*
44548 TATACATATATATATA---
1 TATATATATATATATAGTT
*
44564 TATATATATATATATA-TA
1 TATATATATATATATAGTT
* *
44582 TATA-AAAGT-TGTATAGTT
1 TATATATA-TATATATAGTT
44600 TATATA-ATTCATATATA-TT
1 TATATATA-T-ATATATAGTT
* *
44619 TATATA-AAACTATATAATT
1 TATATATATA-TATATAGTT
44638 TATATATAGT-TCA-ATAGTT
1 TATATATA-TAT-ATATAGTT
* *
44657 CATATATAAACTATATAGTT
1 TATATATATA-TATATAGTT
* *
44677 TATACATGGTATATAT--TT
1 TATATAT-ATATATATAGTT
* *
44695 T-TACATA-ATATATA-TA
1 TATATATATATATATAGTT
* * *
44711 TACA-ATTTATATATAGTA
1 TATATATATATATATAGTT
* ***
44729 TATAATAATATAAATATAAAC
1 TAT-AT-ATATATATATAGTT
* *
44750 TATATAGTTTATATATACTT
1 TATATA-TATATATATAGTT
*
44770 TATATATA-AAATATAGTT
1 TATATATATATATATAGTT
*
44788 TATATTAATAAACTATATAGTT
1 TATA-T-ATATA-TATATAGTT
*
44810 TATACATAATATATATAGTT
1 TATATAT-ATATATATAGTT
*
44830 CATATATAGTATATA-A---
1 TATATATA-TATATATAGTT
* * *
44846 -AAATA-AAATATATAGTA
1 TATATATATATATATAGTT
*
44863 TATATATATATATATA-TA
1 TATATATATATATATAGTT
44881 TATATATATATATAT
1 TATATATATATATAT
44896 TATAATTGTT
Statistics
Matches: 364, Mismatches: 60, Indels: 94
0.70 0.12 0.18
Matches are distributed among these distances:
13 5 0.01
14 2 0.01
15 10 0.03
16 19 0.05
17 21 0.06
18 74 0.20
19 55 0.15
20 105 0.29
21 35 0.10
22 38 0.10
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (19 bp):
TATATATATATATATAGTT
Found at i:44726 original size:129 final size:121
Alignment explanation
Indices: 44522--44766 Score: 280
Period size: 129 Copynumber: 2.0 Consensus size: 121
44512 TATATACTAT
* *
44522 ATAGTTTATATATAAACTATATAATTTATACATATATATATATATATATATATATATATATATAA
1 ATAGTTCATATATAAACTATATAATTTATACATATATATATATATATACATATATATATATATAA
* *
44587 AAGTTGTATAGTTTATATAATTCATATATATTTATATAAAACTATATAATTTATATATAGTTCA
66 AAGTTATATAG--TATATAA-T-A-ATATA--AATAT-AAACTATATAATTTATATATAGTTCA
* * *
44651 ATAGTTCATATATAAACTATATAGTTTATACATGGTATATAT-T-TTTACATA-ATATATATATA
1 ATAGTTCATATATAAACTATATAATTTATACAT-ATATATATATATATACATATATATATATATA
** *
44713 CAATTTATATATAGTATATAATAATATAAATATAAACTATATAGTTTATATATA
65 -AAAGT-TATATAGTATATAATAATATAAATATAAACTATATAATTTATATATA
44767 CTTTATATAT
Statistics
Matches: 103, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
121 20 0.19
122 4 0.04
124 5 0.05
125 1 0.01
126 1 0.01
127 18 0.17
128 9 0.09
129 38 0.37
130 7 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (121 bp):
ATAGTTCATATATAAACTATATAATTTATACATATATATATATATATACATATATATATATATAA
AAGTTATATAGTATATAATAATATAAATATAAACTATATAATTTATATATAGTTCA
Found at i:44825 original size:51 final size:51
Alignment explanation
Indices: 44774--44895 Score: 120
Period size: 53 Copynumber: 2.3 Consensus size: 51
44764 ATACTTTATA
* ** *
44774 TATAAAATATAGTTTATATTAATAAACTATATAGTTTATACATAATATATA
1 TATAAAATATAGTATATAAAAATAAACTATATAGTTTATATATAATATATA
* * * *
44825 TAGTTCATATATAGTATATAAAAATAAAATATATAGTATATATATATATATATA
1 TA--TAAAATATAGTATATAAAAATAAACTATATAGTTTATATATA-ATATATA
*
44879 TATATATATATA-TATAT
1 TATA-AAATATAGTATAT
44896 TATAATTGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
51 2 0.03
52 6 0.10
53 41 0.71
54 9 0.16
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (51 bp):
TATAAAATATAGTATATAAAAATAAACTATATAGTTTATATATAATATATA
Found at i:44857 original size:33 final size:32
Alignment explanation
Indices: 44719--44876 Score: 106
Period size: 33 Copynumber: 4.8 Consensus size: 32
44709 TATACAATTT
*
44719 ATATATAGTATATA-ATA-ATATAAATATAAA
1 ATATATAGTATATATATATATATAAAAATAAA
* * *
44749 CTATATAGTTTATATATACTTTATATATAAAATATA
1 ATATATAG--TATATATA-TATATATA-AAAATAAA
* * * * * * * *
44785 GTTTATATTAATAAACTATATAGTTTATACATAAT
1 ATATATAGT-ATATA-TATATA-TATAAAAATAAA
44820 ATATATAGT-TCATATATAGTATATAAAAATAAA
1 ATATATAGTAT-ATATATA-TATATAAAAATAAA
44853 ATATATAGTATATATATATATATA
1 ATATATAGTATATATATATATATA
44877 TATATATATA
Statistics
Matches: 94, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
30 7 0.07
32 12 0.13
33 30 0.32
34 7 0.07
35 22 0.23
36 16 0.17
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (32 bp):
ATATATAGTATATATATATATATAAAAATAAA
Found at i:45928 original size:5 final size:5
Alignment explanation
Indices: 45918--45973 Score: 76
Period size: 5 Copynumber: 10.4 Consensus size: 5
45908 AGATCGAATG
45918 GACTC GACTC GAGCTC AGACTC GACTC GAGCTC GACTC GACTC GAGCTC
1 GACTC GACTC GA-CTC -GACTC GACTC GA-CTC GACTC GACTC GA-CTC
45967 GACTC GA
1 GACTC GA
45974 GTTCTTAACG
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 29 0.62
6 16 0.34
7 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (5 bp):
GACTC
Found at i:45953 original size:11 final size:11
Alignment explanation
Indices: 45920--45974 Score: 78
Period size: 11 Copynumber: 5.0 Consensus size: 11
45910 ATCGAATGGA
45920 CTCGACTCGAG
1 CTCGACTCGAG
45931 CTCAGACTCGA-
1 CTC-GACTCGAG
45942 CTCGAGCTCGA-
1 CTCGA-CTCGAG
45953 CTCGACTCGAG
1 CTCGACTCGAG
45964 CTCGACTCGAG
1 CTCGACTCGAG
45975 TTCTTAACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.17
11 27 0.66
12 7 0.17
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.18
Consensus pattern (11 bp):
CTCGACTCGAG
Found at i:45956 original size:16 final size:16
Alignment explanation
Indices: 45918--45973 Score: 103
Period size: 16 Copynumber: 3.4 Consensus size: 16
45908 AGATCGAATG
45918 GACTCGACTCGAGCTC
1 GACTCGACTCGAGCTC
45934 AGACTCGACTCGAGCTC
1 -GACTCGACTCGAGCTC
45951 GACTCGACTCGAGCTC
1 GACTCGACTCGAGCTC
45967 GACTCGA
1 GACTCGA
45974 GTTCTTAACG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
16 23 0.59
17 16 0.41
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (16 bp):
GACTCGACTCGAGCTC
Found at i:46551 original size:20 final size:21
Alignment explanation
Indices: 46526--46565 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
46516 TTTTGTAAAG
*
46526 TAGTATCGATACCAT-AGGCA
1 TAGTATCAATACCATCAGGCA
46546 TAGTATCAATACCATCAGGC
1 TAGTATCAATACCATCAGGC
46566 CCCAATGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCA
Found at i:47958 original size:15 final size:15
Alignment explanation
Indices: 47908--47960 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
47898 ATGGTGAAAG
*
47908 AAGAAGAA-GATGATA
1 AAGAAGAAGGAAGA-A
* * *
47923 AAGAAAAAGAAAGAC
1 AAGAAGAAGGAAGAA
47938 AAGAAGAAGGAAGAA
1 AAGAAGAAGGAAGAA
47953 AAGAAGAA
1 AAGAAGAA
47961 TGAGGTAGGC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (15 bp):
AAGAAGAAGGAAGAA
Found at i:48552 original size:21 final size:21
Alignment explanation
Indices: 48517--48556 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48507 TTTCAAAAGT
48517 TAAAATCAATGATTTAGAAAAA
1 TAAAATCAATGATTT-GAAAAA
*
48539 TAAAAT-ATTGATTTGAAA
1 TAAAATCAATGATTTGAAA
48557 GTTAAGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAAATCAATGATTTGAAAAA
Found at i:51403 original size:24 final size:24
Alignment explanation
Indices: 51382--51443 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
51372 TTAGGTCATA
51382 TATCATAACAGAATCCAAGTCAGG
1 TATCATAACAGAATCCAAGTCAGG
* * * *
51406 TATTAGAACATAATCCATGTCAGG
1 TATCATAACAGAATCCAAGTCAGG
51430 TATCATAACAGAAT
1 TATCATAACAGAAT
51444 TCAAATAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (24 bp):
TATCATAACAGAATCCAAGTCAGG
Found at i:53568 original size:16 final size:17
Alignment explanation
Indices: 53533--53580 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
53523 TTGTGAACAT
53533 AAAATTTGACTTTTCAA
1 AAAATTTGACTTTTCAA
53550 AAAATTTGACTTTTCAA
1 AAAATTTGACTTTTCAA
*
53567 AAATTTTGACTTTT
1 AAAATTTGACTTTT
53581 TGATTAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (17 bp):
AAAATTTGACTTTTCAA
Found at i:60409 original size:21 final size:20
Alignment explanation
Indices: 60384--60437 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
60374 TTATGACTCT
60384 TATATATTGTATTTAATGTA
1 TATATATTGTATTTAATGTA
* *
60404 TGATAT-TATGTAATTAGTGTA
1 T-ATATAT-TGTATTTAATGTA
60425 TA-ATATTG-ATTTA
1 TATATATTGTATTTA
60438 TATTATAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 4 0.14
21 16 0.57
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (20 bp):
TATATATTGTATTTAATGTA
Found at i:61162 original size:2 final size:2
Alignment explanation
Indices: 61155--61213 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
61145 TTAATCATAG
61155 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
*
61197 TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA T
61214 CAAATACAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:64873 original size:22 final size:22
Alignment explanation
Indices: 64847--64896 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
64837 AGGAAAAATA
64847 TTTTATAACTATAAATATCGTT
1 TTTTATAACTATAAATATCGTT
*
64869 TTTTATAACTATGAATATCGTT
1 TTTTATAACTATAAATATCGTT
64891 TGTTTA
1 T-TTTA
64897 AACACTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTTATAACTATAAATATCGTT
Found at i:65283 original size:60 final size:60
Alignment explanation
Indices: 65173--65285 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
65163 TATAAAGTGA
** * *
65173 TGCTTTGTTGAGTTTCTCGACTATTAAAAGTTACAAAATGGTTCATTGACTATAGGATGT
1 TGCTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGGTCCATTGACTATAGGATGT
65233 TGCTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGG-CCATCTGACTAT
1 TGCTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGGTCCAT-TGACTAT
65286 TTATATGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 3 0.06
60 45 0.94
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (60 bp):
TGCTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGGTCCATTGACTATAGGATGT
Found at i:67515 original size:23 final size:23
Alignment explanation
Indices: 67489--67558 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
67479 AGTGCCACAT
67489 ATTTGTCTCGAATGACCATATAG
1 ATTTGTCTCGAATGACCATATAG
* *
67512 ATTTATC-CAGAAGGACCACT-TAG
1 ATTTGTCTC-GAATGACCA-TATAG
*
67535 ATTTGTCTCGAATGACCACATAG
1 ATTTGTCTCGAATGACCATATAG
67558 A
1 A
67559 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 1 0.03
23 35 0.92
24 2 0.05
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (23 bp):
ATTTGTCTCGAATGACCATATAG
Found at i:67776 original size:15 final size:15
Alignment explanation
Indices: 67756--67802 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
67746 ATTATTTCAT
*
67756 TTCACATAGCATTTA
1 TTCACATAGCATATA
*
67771 TTCACATATCATATA
1 TTCACATAGCATATA
*
67786 TTCACATATCATATA
1 TTCACATAGCATATA
67801 TT
1 TT
67803 AGTGCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (15 bp):
TTCACATAGCATATA
Found at i:69852 original size:32 final size:31
Alignment explanation
Indices: 69814--69890 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
69804 CGGGGCTGTG
*
69814 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
69846 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
69877 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
69891 TTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:70784 original size:20 final size:20
Alignment explanation
Indices: 70759--70816 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
70749 GGTCAAAGAA
*
70759 AGTCAACGGTTAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
70779 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
70799 AGTCAACGGTCAACGGTC
1 AGTCAACGGTCAACGGTC
70817 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:70790 original size:7 final size:7
Alignment explanation
Indices: 70760--70816 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
70750 GTCAAAGAAA
70760 GTCAACG
1 GTCAACG
*
70767 GTTAACG
1 GTCAACG
*
70774 GTC-ACA
1 GTCAACG
70780 GTCAACG
1 GTCAACG
70787 GTCAACG
1 GTCAACG
*
70794 GTC-ACA
1 GTCAACG
70800 GTCAACG
1 GTCAACG
70807 GTCAACG
1 GTCAACG
70814 GTC
1 GTC
70817 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 10 0.24
7 32 0.76
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:70828 original size:17 final size:17
Alignment explanation
Indices: 70806--70880 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
70796 CACAGTCAAC
*
70806 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
70823 GGTCAACATTCGGGTCG
1 GGTCAACAGTCGGGTCG
70840 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
70857 GGTCAATAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
70874 GGTCAAC
1 GGTCAAC
70881 CCGGTTCAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:70898 original size:19 final size:20
Alignment explanation
Indices: 70874--70925 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
70864 AGTCGGGTCG
* *
70874 GGTCAACCCGGTTC-AGACT
1 GGTCAAACCGGTTCAAAACT
70893 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAAAACT
*
70913 GGTCAATCCGGTT
1 GGTCAAACCGGTT
70926 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (20 bp):
GGTCAAACCGGTTCAAAACT
Done.