Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005389.1 Hibiscus syriacus cultivar Beakdansim tig00012355_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: 77511
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3315 original size:23 final size:22
Alignment explanation
Indices: 3249--3315 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
3239 TGCCACATAA
* *
3249 TTGTCCCAAAGGACCATATAAGT
1 TTGTCCC-AAGGACCACATAGGT
*
3272 TTGTCCTGAAGGACCACATAGGTT
1 TTGTCC-CAAGGACCACATAGG-T
3296 TTGTCCCAAGGACCACATAG
1 TTGTCCCAAGGACCACATAG
3316 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 31 0.82
24 7 0.18
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (22 bp):
TTGTCCCAAGGACCACATAGGT
Found at i:4817 original size:3 final size:3
Alignment explanation
Indices: 4805--4841 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
4795 TAGTAAAAAT
4805 TAA T-A TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4842 AAACGGGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5277 original size:42 final size:41
Alignment explanation
Indices: 5180--5280 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
5170 AAGGTCTTAT
*
5180 AGATGGCCCGAAGGACTTTTCACCTTACTCGAAAGACTAAC
1 AGATGGCCCGAAGGACTTTTCACCATACTCGAAAGACTAAC
* ** * * *
5221 AGATGACCTAAAGGA-TTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTTT--TCACCATACTCGAAAGACTAAC
*
5263 TGATGGCCCGAAGGACTT
1 AGATGGCCCGAAGGACTT
5281 ACAAATTTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
40 3 0.07
41 12 0.26
42 29 0.63
43 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTTTCACCATACTCGAAAGACTAAC
Found at i:5471 original size:21 final size:21
Alignment explanation
Indices: 5447--5494 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5437 AAATGGCCCG
5447 AAGACTTATCATCTTGCTCGA
1 AAGACTTATCATCTTGCTCGA
5468 AAGACTTATCATCTTGCTCGA
1 AAGACTTATCATCTTGCTCGA
5489 AAGACT
1 AAGACT
5495 AACTGATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (21 bp):
AAGACTTATCATCTTGCTCGA
Found at i:5538 original size:256 final size:253
Alignment explanation
Indices: 4990--5473 Score: 634
Period size: 256 Copynumber: 1.9 Consensus size: 253
4980 GAAGGGTTTT
* * * * *
4990 ATCATGCTCGAAAGATTTACTGAT-ATCCCGAAGGACTTACCAATTTTGGAAATAATTTACTAGG
1 ATCATGCCCGAAAGACTTACTCATGA-CCCAAAGGACTTACAAATTTTGGAAATAATTTACTAGG
* *
5054 TAAGAAACTTTGGAAATCACTTTTCTTTCAAAAATTTCATTTTCTGAAAACACTAAATGAGAAAC
65 TAAGAAAATTTGGAAATCACTTTTCTTTCAAAAATTTCATCTTCTGAAAACACTAAATGAGAAAC
* * *
5119 TTTGGAAATCGCTTTCTCATGTTTGAAAATCATGTGAAACATCCTTGCCCAAAGGTCTTATAGAT
130 TTTGGAAATCACTTTCTCATGTTTGAAAATCATGTGAAACATCCTTGCCCAAAGGTCTTACAAAT
* * * *
5184 GGCCCGAAGGACTTTTCACCTTACTCGAAAGACTAACAGATGACCTAAAGGATTTAATC
195 GGCCCGAAGGACTTATCACCTTACTCGAAAGACTAACACATGACCGAAAGGATCTAATC
* * * *
5243 ATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAATTTACTAGGT
1 ATCATGCCCGAAAGACTTACTCATGACCCAAAGGACTTACAAATTTTGGAAATAATTTACTAGGT
* ** * *
5308 AATAAAATTTGGAAATTGCTTTCTTACATTTC-AAAATTTCATCTTCTGAAAATATTAAATGAGA
66 AAGAAAATTTGGAAATCAC-TT-TT-C-TTTCAAAAATTTCATCTTCTGAAAACACTAAATGAGA
* *
5372 AACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC-TGCCCGAAGGTCTTA
127 AACTTTGGAAATCACTTTCTCATGTTT-GAAAATCATGTG-AAACATCCTTGCCCAAAGGTCTTA
* *
5436 CAAATGGCCCGAA-GACTTATCATCTTGCTCGAAAGACT
190 CAAATGGCCCGAAGGACTTATCACCTTACTCGAAAGACT
5474 TATCATCTTG
Statistics
Matches: 206, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
253 76 0.37
254 2 0.01
255 2 0.01
256 77 0.37
257 41 0.20
258 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (253 bp):
ATCATGCCCGAAAGACTTACTCATGACCCAAAGGACTTACAAATTTTGGAAATAATTTACTAGGT
AAGAAAATTTGGAAATCACTTTTCTTTCAAAAATTTCATCTTCTGAAAACACTAAATGAGAAACT
TTGGAAATCACTTTCTCATGTTTGAAAATCATGTGAAACATCCTTGCCCAAAGGTCTTACAAATG
GCCCGAAGGACTTATCACCTTACTCGAAAGACTAACACATGACCGAAAGGATCTAATC
Found at i:14076 original size:23 final size:22
Alignment explanation
Indices: 14030--14081 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
14020 TCCCGAAGGA
*
14030 CCACATAGGTTACACTGAAGTG
1 CCACATAGGTTACACAGAAGTG
*
14052 CCACATAGGTTTGCACAGAAGTG
1 CCACATAGG-TTACACAGAAGTG
14075 CCACATA
1 CCACATA
14082 TTTGTCCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (22 bp):
CCACATAGGTTACACAGAAGTG
Found at i:14099 original size:21 final size:21
Alignment explanation
Indices: 14075--14187 Score: 190
Period size: 21 Copynumber: 5.4 Consensus size: 21
14065 CACAGAAGTG
* *
14075 CCACATATTTGTCCCGAATGA
1 CCACATAATTATCCCGAATGA
14096 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGA
14117 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGA
14138 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGA
* *
14159 CCACATAATTATCCTGAAGGA
1 CCACATAATTATCCCGAATGA
14180 CCACATAA
1 CCACATAA
14188 AACCCTCGAC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (21 bp):
CCACATAATTATCCCGAATGA
Found at i:20996 original size:22 final size:22
Alignment explanation
Indices: 20971--21082 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 22
20961 CCACATCTCG
*
20971 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTACCACA
*
20993 TAA-TTGTC-CCGAAGTACCATA
1 TAATTTG-CACCGAAGTACCACA
** * * *
21014 TAGGTTGTACCAAAGTGCCACA
1 TAATTTGCACCGAAGTACCACA
*
21036 TAGGTTTGCACCGAAGTACCACA
1 TA-ATTTGCACCGAAGTACCACA
* *
21059 T-ATTTGTC-TCGAAGGACCACA
1 TAATTTG-CACCGAAGTACCACA
21080 TAA
1 TAA
21083 AACCCTCGAC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
21 32 0.46
22 21 0.30
23 17 0.24
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (22 bp):
TAATTTGCACCGAAGTACCACA
Found at i:25727 original size:26 final size:26
Alignment explanation
Indices: 25688--25738 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
25678 GGTACATTTT
**
25688 GGGGAATTGGGGTTGATTCCCAAACG
1 GGGGAATTAAGGTTGATTCCCAAACG
*
25714 GGGGAATTAAGGTTGATTCCTAAAC
1 GGGGAATTAAGGTTGATTCCCAAAC
25739 AGGGAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.25
Consensus pattern (26 bp):
GGGGAATTAAGGTTGATTCCCAAACG
Found at i:25752 original size:25 final size:26
Alignment explanation
Indices: 25697--25752 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
25687 TGGGGAATTG
* *
25697 GGGTTGATTCCCAAACGGGGGAATTA
1 GGGTTGATTCCCAAACGAGGGAAATA
* *
25723 AGGTTGATTCCTAAAC-AGGGAAATA
1 GGGTTGATTCCCAAACGAGGGAAATA
25748 GGGTT
1 GGGTT
25753 CTTGTTATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.25
Consensus pattern (26 bp):
GGGTTGATTCCCAAACGAGGGAAATA
Found at i:28406 original size:18 final size:17
Alignment explanation
Indices: 28379--28471 Score: 78
Period size: 18 Copynumber: 5.1 Consensus size: 17
28369 TACTTTTTGA
28379 AATTTAATTTTTATATT
1 AATTTAATTTTTATATT
*
28396 AATTATAATTTGTATATTATA
1 AATT-TAATTT-T-TA-TATT
**
28417 AATTTGGTTTTTATATT
1 AATTTAATTTTTATATT
28434 AATTCTAATTCTTTATATT
1 AATT-TAATT-TTTATATT
* *
28453 ATTTATAATTCTTATATT
1 AATT-TAATTTTTATATT
28471 A
1 A
28472 TAAATTTTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
17 11 0.18
18 19 0.31
19 18 0.30
20 6 0.10
21 7 0.11
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
AATTTAATTTTTATATT
Found at i:28421 original size:38 final size:39
Alignment explanation
Indices: 28378--28454 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
28368 TTACTTTTTG
28378 AAATTTAATTTTTATATTAATTATAATT-TGTATATTAT
1 AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
** * *
28416 AAATTTGGTTTTTATATTAATTCTAATTCTTTATATTAT
1 AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
28455 TTATAATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (39 bp):
AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
Found at i:28472 original size:18 final size:19
Alignment explanation
Indices: 28426--28472 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
28416 AAATTTGGTT
* *
28426 TTTATATTAATTCTAATTC
1 TTTATATTATTTATAATTC
28445 TTTATATTATTTATAATTC
1 TTTATATTATTTATAATTC
28464 -TTATATTAT
1 TTTATATTAT
28473 AAATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATTTATAATTC
Found at i:29079 original size:23 final size:23
Alignment explanation
Indices: 29049--29106 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
29039 CAACAGCAAC
*
29049 CAGCAAGCATCACTATATCAATT
1 CAGCAAGCATCACTACATCAATT
* * *
29072 CAGCAAGCATTATTGCATCAATT
1 CAGCAAGCATCACTACATCAATT
*
29095 CAGCAATCATCA
1 CAGCAAGCATCA
29107 TGCATTCAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (23 bp):
CAGCAAGCATCACTACATCAATT
Found at i:31821 original size:12 final size:12
Alignment explanation
Indices: 31804--31874 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
31794 TTTCGAATAT
*
31804 TTTGGATTCAGG
1 TTTGGATTCGGG
31816 TTTGGATTCGGG
1 TTTGGATTCGGG
31828 --T---T-CGGG
1 TTTGGATTCGGG
* *
31834 TTTGGATTCAGA
1 TTTGGATTCGGG
31846 TTTGGATTCGGG
1 TTTGGATTCGGG
31858 TTTGGATTCGGG
1 TTTGGATTCGGG
31870 TTTGG
1 TTTGG
31875 GTTTGGATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 4 0.08
7 1 0.02
8 1 0.02
10 1 0.02
11 1 0.02
12 40 0.83
ACGTcount: A:0.11, C:0.08, G:0.38, T:0.42
Consensus pattern (12 bp):
TTTGGATTCGGG
Found at i:31837 original size:18 final size:18
Alignment explanation
Indices: 31814--31891 Score: 84
Period size: 18 Copynumber: 4.0 Consensus size: 18
31804 TTTGGATTCA
31814 GGTTTGGATTCGGGTTCG
1 GGTTTGGATTCGGGTTCG
31832 GGTTTGGATTCAGATTTGGATTCG
1 GGTTTGGATTC-G----GG-TTCG
*
31856 GGTTTGGATTCGGGTTTG
1 GGTTTGGATTCGGGTTCG
*
31874 GGTTTGGATTCGGATTCG
1 GGTTTGGATTCGGGTTCG
31892 AGTTCGTGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 30 0.59
19 3 0.06
23 3 0.06
24 15 0.29
ACGTcount: A:0.10, C:0.09, G:0.40, T:0.41
Consensus pattern (18 bp):
GGTTTGGATTCGGGTTCG
Found at i:31838 original size:30 final size:30
Alignment explanation
Indices: 31804--31891 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
31794 TTTCGAATAT
*
31804 TTTGGATTCAGGTTTGGATTCGGGTTCGGG
1 TTTGGATTCAGGTTTGGATTCGGGTTCGGA
* *
31834 TTTGGATTCAGATTTGGATTCGGGTTTGGA
1 TTTGGATTCAGGTTTGGATTCGGGTTCGGA
* * ** *
31864 TTCGGGTTTGGGTTTGGATTCGGATTCG
1 TTTGGATTCAGGTTTGGATTCGGGTTCG
31892 AGTTCGTGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.11, C:0.09, G:0.38, T:0.42
Consensus pattern (30 bp):
TTTGGATTCAGGTTTGGATTCGGGTTCGGA
Found at i:31863 original size:42 final size:42
Alignment explanation
Indices: 31804--31920 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
31794 TTTCGAATAT
* *
31804 TTTGGATTCAGGTTTGGATTCGGGTTCGGGTTTGGATTCAGA
1 TTTGGATTCGGGTTTGGATTCGGGTTTGGGTTTGGATTCAGA
*
31846 TTTGGATTCGGGTTTGGATTCGGGTTTGGGTTTGGATTCGGA
1 TTTGGATTCGGGTTTGGATTCGGGTTTGGGTTTGGATTCAGA
* * * *
31888 -TTCGAGTTCGTGTTTGGGTTCAGGTTTGGGTTT
1 TTTGGA-TTCGGGTTTGGATTCGGGTTTGGGTTT
31921 TGTTTCAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 4 0.06
42 63 0.94
ACGTcount: A:0.10, C:0.09, G:0.38, T:0.44
Consensus pattern (42 bp):
TTTGGATTCGGGTTTGGATTCGGGTTTGGGTTTGGATTCAGA
Found at i:31903 original size:30 final size:30
Alignment explanation
Indices: 31814--31907 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
31804 TTTGGATTCA
* * * * **
31814 GGTTTGGATTCGGGTTCGGGTTTGGATTCA
1 GGTTTGGATTCGGATTCGGATTCGGGTTTG
* * *
31844 GATTTGGATTCGGGTTTGGATTCGGGTTTG
1 GGTTTGGATTCGGATTCGGATTCGGGTTTG
*
31874 GGTTTGGATTCGGATTC-GAGTTCGTGTTTG
1 GGTTTGGATTCGGATTCGGA-TTCGGGTTTG
31904 GGTT
1 GGTT
31908 CAGGTTTGGG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 2 0.04
30 50 0.96
ACGTcount: A:0.10, C:0.09, G:0.39, T:0.43
Consensus pattern (30 bp):
GGTTTGGATTCGGATTCGGATTCGGGTTTG
Found at i:32370 original size:113 final size:113
Alignment explanation
Indices: 32155--32372 Score: 241
Period size: 113 Copynumber: 1.9 Consensus size: 113
32145 AAAAGGGTTT
* ** *
32155 AATTTTTGGGTGTTTGATCAAAAAAATAGGAATGGGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
1 AATTTTTGGGTGTTTAATCAAAAAAATAAAAATGGGTTTAGGTTTTGGTGTTTATGAAGATCAAA
* * * *
32220 TAATGGTTTGGGGAAGAACTGGGATGAACACATATGAACAATGGTTGA
66 TAAAGGTTTGGGGAAGAACTGGGATGAAAAAAGATGAACAATGGTTGA
*
32268 AATTTTT-GGTGTTTAATCGAAAAAAATATAAAAT-GGTTTGGGTTTTGGTGTTTATGAAGAT-A
1 AATTTTTGGGTGTTTAATC-AAAAAAATA-AAAATGGGTTTAGGTTTTGGTGTTTATGAAGATCA
* *
32330 AA-AAGAGGATTTTTGGGATGAACAT-GGAT-AAAAAAGATGAACA
64 AATAA-AGG--TTTGGGGAAGAAC-TGGGATGAAAAAAGATGAACA
32373 CGAATGAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
111 2 0.02
112 15 0.17
113 52 0.59
114 18 0.20
115 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (113 bp):
AATTTTTGGGTGTTTAATCAAAAAAATAAAAATGGGTTTAGGTTTTGGTGTTTATGAAGATCAAA
TAAAGGTTTGGGGAAGAACTGGGATGAAAAAAGATGAACAATGGTTGA
Found at i:32777 original size:25 final size:24
Alignment explanation
Indices: 32735--32792 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 24
32725 TTCAATTAAT
32735 ATATATATGTTTATTTAATAAATTA
1 ATATATA-GTTTATTTAATAAATTA
32760 ATATATAGTTTATATTAATAAATTA
1 ATATATAGTTTAT-TTAATAAATTA
32785 ATATATAG
1 ATATATAG
32793 GTCATGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
ATATATAGTTTATTTAATAAATTA
Found at i:32807 original size:29 final size:25
Alignment explanation
Indices: 32735--32831 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 25
32725 TTCAATTAAT
*
32735 ATATATATGTTTAT-TTAATAAATTA
1 ATATATA-GTTTATACTAATAAATTA
*
32760 ATATATAGTTTATATTAATAAATTA
1 ATATATAGTTTATACTAATAAATTA
32785 ATATATAGGTCATGTATACTAATGAATTATATA
1 ATATATA-GT--T-TATACTAAT-AA--AT-TA
32818 ATATATAGTTTATA
1 ATATATAGTTTATA
32832 TATACCATAT
Statistics
Matches: 62, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
24 6 0.10
25 25 0.40
26 2 0.03
28 1 0.02
29 12 0.19
30 3 0.05
32 4 0.06
33 9 0.15
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (25 bp):
ATATATAGTTTATACTAATAAATTA
Found at i:32835 original size:18 final size:18
Alignment explanation
Indices: 32812--32853 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32802 ACTAATGAAT
* *
32812 TATATAATATATAGTTTA
1 TATATAACATATACTTTA
*
32830 TATATACCATATACTTTA
1 TATATAACATATACTTTA
32848 TATATA
1 TATATA
32854 TAGTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (18 bp):
TATATAACATATACTTTA
Found at i:32835 original size:20 final size:20
Alignment explanation
Indices: 32812--33300 Score: 94
Period size: 20 Copynumber: 23.6 Consensus size: 20
32802 ACTAATGAAT
32812 TATATAATATATAGTTTATA
1 TATATAATATATAGTTTATA
**
32832 TATACCATATACT--TTATATA
1 TATATAATATA-TAGTT-TATA
*
32852 TATAGTTTTTATATATAGTTTATA
1 TATA----TAATATATAGTTTATA
*
32876 TTGTAATCAAATATATAGTATTCATA
1 -TAT-AT--AATATATAGT-TT-ATA
* * *
32902 CATATAATATATACTTTAAA
1 TATATAATATATAGTTTATA
* **
32922 TTTAT-ATAGTATAAATTATA
1 TATATAATA-TATAGTTTATA
32942 TAAGTATAA-AT-TA-TATTATA
1 T-A-TATAATATATAGT-TTATA
* **
32962 TTATATAGTATATA-AATATCA
1 -TATATAATATATAGTTTAT-A
*
32983 -ACTATAGTATATAGTTTATA
1 TA-TATAATATATAGTTTATA
*
33003 TATA-AA-CTATAGTTTATA
1 TATATAATATATAGTTTATA
*
33021 TAT-TATATATATAGTATATA
1 TATATA-ATATATAGTTTATA
* * *
33041 CTATATAA-ACTAAACTATATA
1 -TATATAATA-TATAGTTTATA
* *
33062 T-TGTAGT-TGATA-TTTATA
1 TATATAATAT-ATAGTTTATA
33080 TACTAT-ATACTATAGTTTATA
1 TA-TATAATA-TATAGTTTATA
33101 TAGT-T--TAT-T--TTTATA
1 TA-TATAATATATAGTTTATA
* * ***
33116 TATAGTTCATATGTAAACTATA
1 TATA--TAATATATAGTTTATA
*
33138 CTATATAGTATATATAGTTTTTA
1 -TATATA--ATATATAGTTTATA
*
33161 TATATAATATATAGTATATA
1 TATATAATATATAGTTTATA
* *
33181 AATATCAACTATAGTAAATAATATATA
1 TATAT-AA-TATA-T-AGT--T-TATA
*
33208 AATATAA-ACTATAGTTTATA
1 TATATAATA-TATAGTTTATA
*
33228 TATATAGTATATA--TTATA
1 TATATAATATATAGTTTATA
* *
33246 TAAATAGTTTATATAGTTTATA
1 TATATA--ATATATAGTTTATA
*
33268 TGTA-AACTATATAGTTTATA
1 TATATAA-TATATAGTTTATA
*
33288 TATATAGTATATA
1 TATATAATATATA
33301 CTATATAAAT
Statistics
Matches: 346, Mismatches: 58, Indels: 130
0.65 0.11 0.24
Matches are distributed among these distances:
14 1 0.00
15 8 0.02
17 2 0.01
18 33 0.10
19 23 0.07
20 134 0.39
21 42 0.12
22 37 0.11
23 18 0.05
24 24 0.07
25 9 0.03
26 6 0.02
27 9 0.03
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATAATATATAGTTTATA
Found at i:32836 original size:33 final size:32
Alignment explanation
Indices: 32783--32866 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 32
32773 ATTAATAAAT
* * * *
32783 TAATATATAGGTCATGTATACTA-ATGAATTATA
1 TAATATATAGTTTATATATACCATAT-AATT-TA
*
32816 TAATATATAGTTTATATATACCATATACTTTA
1 TAATATATAGTTTATATATACCATATAATTTA
*
32848 T-ATATATAGTTTTTATATA
1 TAATATATAGTTTATATATA
32867 TAGTTTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 17 0.39
32 3 0.07
33 22 0.50
34 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (32 bp):
TAATATATAGTTTATATATACCATATAATTTA
Found at i:32854 original size:13 final size:13
Alignment explanation
Indices: 32838--32876 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
32828 TATATATACC
*
32838 ATATACTTTATAT
1 ATATAGTTTATAT
*
32851 ATATAGTTTTTAT
1 ATATAGTTTATAT
32864 ATATAGTTTATAT
1 ATATAGTTTATAT
32877 TGTAATCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:32929 original size:15 final size:14
Alignment explanation
Indices: 32909--32957 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
32899 ATACATATAA
*
32909 TATATACTTTAAATT
1 TATATACTATAAA-T
*
32924 TATATAGTATAAAT
1 TATATACTATAAAT
*
32938 TATATAAGTATAAAT
1 TATAT-ACTATAAAT
32953 TATAT
1 TATAT
32958 TATATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (14 bp):
TATATACTATAAAT
Found at i:33005 original size:25 final size:26
Alignment explanation
Indices: 32958--33031 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
32948 TAAATTATAT
* * *
32958 TATATTATATAGTATATAAATATCAAC
1 TATAGTATATAGTAT-TATATATAAAC
32985 TATAGTATATAGT-TTATATATAAAC
1 TATAGTATATAGTATTATATATAAAC
*
33010 TATAGTTTATA-TATTATATATA
1 TATAGTATATAGTATTATATATA
33032 TAGTATATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 28 0.67
26 1 0.02
27 12 0.29
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (26 bp):
TATAGTATATAGTATTATATATAAAC
Found at i:33030 original size:27 final size:27
Alignment explanation
Indices: 32958--33033 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
32948 TAAATTATAT
* *
32958 TATA-TTATATAGTATATAAATATCAAC
1 TATAGTTATATAGT-TATATATATAAAC
32985 TATAG-TATATAGTT-TATATATAAAC
1 TATAGTTATATAGTTATATATATAAAC
33010 TATAGTTTATATA-TTATATATATA
1 TATAG-TTATATAGTTATATATATA
33034 GTATATACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 14 0.33
26 3 0.07
27 26 0.60
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (27 bp):
TATAGTTATATAGTTATATATATAAAC
Found at i:33038 original size:9 final size:8
Alignment explanation
Indices: 32924--33307 Score: 67
Period size: 9 Copynumber: 45.0 Consensus size: 8
32914 ACTTTAAATT
32924 TATATAGTA
1 TATATA-TA
*
32933 TAAAT-TA
1 TATATATA
32940 TATA-AGTA
1 TATATA-TA
*
32948 TAAAT-TA
1 TATATATA
32955 TAT-TATA
1 TATATATA
32962 T-TATATA
1 TATATATA
*
32969 GTATATAAA
1 -TATATATA
32978 TATCA-ACTA
1 TAT-ATA-TA
32987 TAGTATATA
1 TA-TATATA
*
32996 GTTTATATA
1 -TATATATA
*
33005 TAAACTATA
1 TATA-TATA
*
33014 GTTTATATA
1 -TATATATA
33023 T-TATATA
1 TATATATA
33030 TATAGTATA
1 TATA-TATA
33039 TACTATATA
1 TA-TATATA
* *
33048 AACTAAACTA
1 TA-TATA-TA
*
33058 TATAT-TG
1 TATATATA
33065 TAGT-TGATA
1 TA-TAT-ATA
*
33074 TTTATATA
1 TATATATA
33082 CTATATACTA
1 -TATATA-TA
*
33092 TAGTTTATA
1 TA-TATATA
* *
33101 TAGTTTATT
1 TA-TATATA
*
33110 TTTATATA
1 TATATATA
33118 TAGT-TCATA
1 TA-TAT-ATA
* *
33127 TGTAAACTA
1 TATATA-TA
33136 TACTATATA
1 TA-TATATA
33145 GTATATATA
1 -TATATATA
* *
33154 GTTTTTATA
1 -TATATATA
33163 TATA-ATA
1 TATATATA
33170 TATAGTATA
1 TATA-TATA
*
33179 TAAATATCA
1 TATATAT-A
33188 -ACTATAGTA
1 TA-TATA-TA
*
33197 AATA-ATA
1 TATATATA
*
33204 TATAAATA
1 TATATATA
*
33212 TAAACTATA
1 TATA-TATA
*
33221 GTTTATATA
1 -TATATATA
33230 TATAGTATA
1 TATA-TATA
33239 TAT-TATA
1 TATATATA
* *
33246 TAAATAGTT
1 TATATA-TA
*
33255 TATATAGTT
1 TATATA-TA
*
33264 TATATGTA
1 TATATATA
*
33272 AACTATATA
1 TA-TATATA
*
33281 GTTTATATA
1 -TATATATA
33290 TATAGTATA
1 TATA-TATA
33299 TACTATATA
1 TA-TATATA
33308 AATAGTTTAT
Statistics
Matches: 277, Mismatches: 51, Indels: 94
0.66 0.12 0.22
Matches are distributed among these distances:
6 2 0.01
7 45 0.16
8 51 0.18
9 153 0.55
10 26 0.09
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (8 bp):
TATATATA
Found at i:33038 original size:25 final size:25
Alignment explanation
Indices: 32958--33153 Score: 84
Period size: 25 Copynumber: 7.8 Consensus size: 25
32948 TAAATTATAT
* * *
32958 TATATTATATAGTATATAAATATCAAC
1 TATAGTATATAGT-T-TATATATAAAC
32985 TATAGTATATAGTTTATATATAAAC
1 TATAGTATATAGTTTATATATAAAC
* *
33010 TATAGT-T-TA-TATAT-TATATA-
1 TATAGTATATAGTTTATATATAAAC
* * *
33030 TATAGTATATACTATATAAACTAAAC
1 TATAGTATATAGTTTATATA-TAAAC
* * *
33056 TATA-TATTGTAGTTGATATTTATATAC
1 TATAGTA-TATAGTT--TATATATAAAC
* **
33083 TATA-TACTATAGTTTATATAGTTTATT
1 TATAGTA-TATAGTTTATATA--TAAAC
* * *
33110 TTTA-TATATAGTTCATATGTAAAC
1 TATAGTATATAGTTTATATATAAAC
* *
33134 TATACTATATAGTATATATA
1 TATAGTATATAGTTTATATA
33154 GTTTTTATAT
Statistics
Matches: 127, Mismatches: 30, Indels: 26
0.69 0.16 0.14
Matches are distributed among these distances:
20 6 0.05
21 6 0.05
22 6 0.05
23 7 0.06
24 7 0.06
25 37 0.29
26 20 0.16
27 34 0.27
28 4 0.03
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (25 bp):
TATAGTATATAGTTTATATATAAAC
Found at i:33101 original size:41 final size:39
Alignment explanation
Indices: 32985--33102 Score: 100
Period size: 39 Copynumber: 3.0 Consensus size: 39
32975 AAATATCAAC
* *
32985 TATAGTATATAGTTTATA-TATAAACTATAGTTTATATAT
1 TATA-TATATAGTATATACTATATACTATAGTTTATATAT
**
33024 TATATATATAGTATATACTATATAAACTA-A-ACTATATAT
1 TATATATATAGTATATACTATAT--ACTATAGTTTATATAT
* *
33063 TGTAGT-TGATATTTATATACTATATACTATAGTTTATATA
1 TATA-TAT-ATA-GTATATACTATATACTATAGTTTATATA
33103 GTTTATTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
38 12 0.19
39 23 0.37
40 6 0.10
41 22 0.35
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (39 bp):
TATATATATAGTATATACTATATACTATAGTTTATATAT
Found at i:33234 original size:40 final size:40
Alignment explanation
Indices: 33190--33268 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
33180 AAATATCAAC
33190 TATAGTAAATAATATATAAATA-TAAACTATAGTTTATATA
1 TATAGTAAATAATATATAAATAGTAAA-TATAGTTTATATA
* * **
33230 TATAGTATATATTATATAAATAGTTTATATAGTTTATAT
1 TATAGTAAATAATATATAAATAGTAAATATAGTTTATAT
33269 GTAAACTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (40 bp):
TATAGTAAATAATATATAAATAGTAAATATAGTTTATATA
Found at i:33245 original size:7 final size:6
Alignment explanation
Indices: 32924--33307 Score: 67
Period size: 7 Copynumber: 60.0 Consensus size: 6
32914 ACTTTAAATT
* *
32924 TATATA GTATAAA T-TATA TA-AGTA TAAAT- TATAT- TATAT- TATATA
1 TATATA -TATATA TATATA TATA-TA TATATA TATATA TATATA TATATA
* * * *
32969 GTATATA AATATCA -ACTATA GTATATA GTTTATA TATAAA CTATAGTT
1 -TATATA TATAT-A TA-TATA -TATATA -TATATA TATATA -TATA-TA
* * *
33017 TATATA T-TATA TATATA GTATATA CTATATA AACTAAA CTATATA T-TGTA
1 TATATA TATATA TATATA -TATATA -TATATA TA-TATA -TATATA TATATA
* * * * *
33067 GT-TGATA TTTATA TACTATA TACTATA GTTTATA TAGTTTA TTTTTA
1 -TAT-ATA TATATA TA-TATA TA-TATA -TATATA TA-TATA TATATA
* * * *
33114 TATATA GT-TCATA TGTAAA CTATACTA TATAGTA TATATA GTTTTTA
1 TATATA -TAT-ATA TATATA -TATA-TA TATA-TA TATATA -TATATA
* * *
33161 TATATA -ATATA TAGTATA TAAATA TCA-ACTA TAGTAAA TA-ATA TATAAA
1 TATATA TATATA TA-TATA TATATA T-ATA-TA TA-TATA TATATA TATATA
* * * *
33210 TATAAA CTATAGTT TATATA TATAGTA TATAT- TATATA AATAGTT TATATA
1 TATATA -TATA-TA TATATA TATA-TA TATATA TATATA TATA-TA TATATA
* * * *
33261 GTTTATA TGTAAA CTATATA GTTTATA TATATA GTATATA CTATATA
1 -TATATA TATATA -TATATA -TATATA TATATA -TATATA -TATATA
33308 AATAGTTTAT
Statistics
Matches: 283, Mismatches: 52, Indels: 84
0.68 0.12 0.20
Matches are distributed among these distances:
5 41 0.14
6 84 0.30
7 153 0.54
8 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:33279 original size:40 final size:41
Alignment explanation
Indices: 33202--33300 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
33192 TAGTAAATAA
* * *
33202 TATATAAATA-TAAACTATAGTTTATATATATAGTATATA-T
1 TATATAAATAGTATA-TATAGTTTATATATAAACTATATAGT
* *
33242 TATATAAATAGTTTATATAGTTTATATGTAAACTATATAGTT
1 TATATAAATAGTATATATAGTTTATATATAAACTATATAG-T
*
33284 TATATATATAGTATATA
1 TATATAAATAGTATATA
33301 CTATATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 31 0.63
41 2 0.04
42 16 0.33
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (41 bp):
TATATAAATAGTATATATAGTTTATATATAAACTATATAGT
Found at i:33340 original size:60 final size:60
Alignment explanation
Indices: 33147--33338 Score: 176
Period size: 60 Copynumber: 3.1 Consensus size: 60
33137 ACTATATAGT
* * * ** *
33147 ATATATAGTTTTTATATATAATATATAGTATATAAATA-TCAACTATAGTAAATAATATATAAA
1 ATATATAGTTTATATATATAGTATATACTATATAAATAGTTTA-TATAGT---TCATATATAAA
* * *
33210 TATAAACTATAGTTTATATATATAGTATATATTATATAAATAGTTTATATAGTTTATATGTAAA
1 -AT--A-TATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCATATATAAA
*
33274 CTATATAGTTTATATATATAGTATATACTATATAAATAGTTTATA-A-TTCAT-TAATAAA
1 ATATATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCATAT-ATAAA
*
33332 TTATATA
1 ATATATA
33339 TATTGTTCAT
Statistics
Matches: 111, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
57 1 0.01
58 14 0.13
59 1 0.01
60 41 0.37
61 1 0.01
63 1 0.01
64 11 0.10
66 1 0.01
67 38 0.34
68 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (60 bp):
ATATATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCATATATAAA
Found at i:33405 original size:20 final size:20
Alignment explanation
Indices: 33337--33412 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
33327 ATAAATTATA
* *
33337 TATATTGTTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
* *
33357 TATATAGTTTATAGAGTTTATAC
1 TATATAGTTTAT--A-TGTAAAC
33380 -ATATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
*
33399 TATATAGTATATAT
1 TATATAGTTTATAT
33413 AGTTCATATG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 5 0.11
20 23 0.51
22 12 0.27
23 5 0.11
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (20 bp):
TATATAGTTTATATGTAAAC
Found at i:33412 original size:29 final size:29
Alignment explanation
Indices: 33380--33447 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
33370 GAGTTTATAC
33380 ATATAGTTTATATGTAAACTATATAGTAT
1 ATATAGTTTATATGTAAACTATATAGTAT
*
33409 ATATAGTTCATATGTAAACTATATAGTAT
1 ATATAGTTTATATGTAAACTATATAGTAT
33438 ATATAGTTTA
1 ATATAGTTTA
33448 CATATAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (29 bp):
ATATAGTTTATATGTAAACTATATAGTAT
Found at i:43655 original size:74 final size:74
Alignment explanation
Indices: 43496--43643 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
43486 GAGTGGCCAA
43496 GGCATATGAGTGAATGAAAGTAGTCACAGGATGACTCTGACCGACTAGCTTGGGGGTGAAAGGTA
1 GGCATATGAGTGAATGAAAGTAGTCACAGGATGACTCTGACCGACTAGCTTGGGGGTGAAAGGTA
43561 TGCTCCCTT
66 TGCTCCCTT
43570 GGCATATGAGTGAATGAAAGTAGTCACAGGATGACTCTGACCGACTAGCTTGGGGGTGAAAGGTA
1 GGCATATGAGTGAATGAAAGTAGTCACAGGATGACTCTGACCGACTAGCTTGGGGGTGAAAGGTA
43635 TGCTCCCTT
66 TGCTCCCTT
43644 TCACCTAGAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (74 bp):
GGCATATGAGTGAATGAAAGTAGTCACAGGATGACTCTGACCGACTAGCTTGGGGGTGAAAGGTA
TGCTCCCTT
Found at i:45733 original size:22 final size:22
Alignment explanation
Indices: 45705--45768 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
45695 ACTACTATCT
*
45705 ATAAACTATATAGTTTATATTA
1 ATAAACTATATAATTTATATTA
45727 ATAAACTATATAATTTATATTA
1 ATAAACTATATAATTTATATTA
45749 ATAAACTATATAATTTATAT
1 ATAAACTATATAATTTATAT
45769 ATAGTGTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAACTATATAATTTATATTA
Found at i:45862 original size:2 final size:2
Alignment explanation
Indices: 45857--45957 Score: 86
Period size: 2 Copynumber: 51.5 Consensus size: 2
45847 TTATACATGG
* *
45857 TA TA TA TA GTT TA TA -A TA TA TA TA GT- TA TA TA TA TA TA TA AA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
45899 TG TA AA CTA TA TA -A TT TA TA TA TA T- TT 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 TA
45939 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
45958 TGTTTGAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
1 5 0.06
2 72 0.90
3 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45878 original size:18 final size:18
Alignment explanation
Indices: 45798--45896 Score: 55
Period size: 20 Copynumber: 5.5 Consensus size: 18
45788 ATTATTCATA
*
45798 ATATATA-AGTTGTATAGT
1 ATATATATAGTT-TATAAT
* * *
45816 TTATATATAATTCATATAT
1 ATATATATAGTTTATA-AT
* *
45835 AAACTATATAATTTATACAT
1 ATA-TATATAGTTTATA-AT
*
45855 GGTATATATAGTTTAT-A-
1 -ATATATATAGTTTATAAT
45872 ATATATATAG-TTAT-AT
1 ATATATATAGTTTATAAT
45888 ATATATATA
1 ATATATATA
45897 AATGTAAACT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.08
16 18 0.28
18 10 0.16
19 5 0.08
20 25 0.39
21 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (18 bp):
ATATATATAGTTTATAAT
Found at i:46542 original size:48 final size:48
Alignment explanation
Indices: 46490--46589 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
46480 TATATGATAG
* *
46490 AGATCCGACTTGAATTTTATCTGTCAATGATGTGACCCGATATGAACA
1 AGATCCAACTTGAATTTTATCTATCAATGATGTGACCCGATATGAACA
* *
46538 AGATCCAACTTGAATTTTATCTATCAATGATGTGACCCGATCTGAACG
1 AGATCCAACTTGAATTTTATCTATCAATGATGTGACCCGATATGAACA
46586 AGAT
1 AGAT
46590 ACATCTGAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (48 bp):
AGATCCAACTTGAATTTTATCTATCAATGATGTGACCCGATATGAACA
Found at i:50055 original size:13 final size:13
Alignment explanation
Indices: 50015--50063 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
50005 TTTTTATTTT
50015 TATTTTTAAAAAGA
1 TATTTTTAAAAA-A
50029 TACTTTTT--AAAA
1 TA-TTTTTAAAAAA
50041 TATTTTTAAAAAA
1 TATTTTTAAAAAA
*
50054 TATTATTAAA
1 TATTTTTAAA
50064 GTTTCCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.16
12 3 0.10
13 16 0.52
14 2 0.06
15 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTTTTAAAAAA
Found at i:52666 original size:19 final size:19
Alignment explanation
Indices: 52651--52690 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
52641 TTGTAAATGT
*
52651 TATTTTTAATTATAAAAAAA
1 TATTTTTAATTAT-AAATAA
52671 TATTTTTAATTATAAATAA
1 TATTTTTAATTATAAATAA
52690 T
1 T
52691 TAAAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTTTAATTATAAATAA
Found at i:54103 original size:60 final size:59
Alignment explanation
Indices: 54036--54160 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
54026 AAACATATGA
* * * *
54036 ATAGTCAGACGACCATTTTGTAACTTTTAATAGTCGGGAA-ACTCAACAAAGCAATGTCTT
1 ATAGTCAGACGACCATTTTGAAACTTTT-ATAGTC-AGAAGACTCAACAAAACAATATCTT
** * *
54096 ATAGTCAGGGGATCATTTTGAAACTTTTATAGTCAGAAGACTCAACAAAACAATATTTT
1 ATAGTCAGACGACCATTTTGAAACTTTTATAGTCAGAAGACTCAACAAAACAATATCTT
54155 ATAGTC
1 ATAGTC
54161 TTGTGTACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 3 0.05
59 29 0.52
60 24 0.43
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (59 bp):
ATAGTCAGACGACCATTTTGAAACTTTTATAGTCAGAAGACTCAACAAAACAATATCTT
Found at i:58553 original size:59 final size:57
Alignment explanation
Indices: 58510--58675 Score: 185
Period size: 56 Copynumber: 2.9 Consensus size: 57
58500 CGTCTGGGTT
*
58510 CTTAGATATTTCTTTAGAAATTTCGAGTTCATCTTC-AAAGGTAAGATCGTTTCTTA
1 CTTAGATATTTCTTTAGAAATTTCGAGTTCATCTTCAAAAGGTAAGATCGTTGCTTA
* *
58566 CTTAGATATTTCTTTAGAGATTTCGAGTTCCTCTTCAAAAGGTAAGATC-TT-CATTCA
1 CTTAGATATTTCTTTAGAAATTTCGAGTTCATCTTCAAAAGGTAAGATCGTTGC-TT-A
* * * * *
58623 ATACAATTATATTTCTTTAGAGATTTCAAGTTCATCTTCAAAAGGTAAAGATC
1 CT--TA-GATATTTCTTTAGAAATTTCGAGTTCATCTTCAAAAGGT-AAGATC
58676 ATTCTATACG
Statistics
Matches: 96, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
55 1 0.01
56 38 0.40
57 14 0.15
59 1 0.01
60 36 0.38
61 6 0.06
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (57 bp):
CTTAGATATTTCTTTAGAAATTTCGAGTTCATCTTCAAAAGGTAAGATCGTTGCTTA
Found at i:58574 original size:56 final size:59
Alignment explanation
Indices: 58510--58675 Score: 216
Period size: 60 Copynumber: 2.8 Consensus size: 59
58500 CGTCTGGGTT
* *
58510 CTTAGATATTTCTTTAGAAATTTCGAGTTCATCTTC-AAAGGTAAGATCGT-TTC-TTA
1 CTTAGATATTTCTTTAGAGATTTCGAGTTCATCTTCAAAAGGTAAGATCGTATTCAATA
* *
58566 CTTAGATATTTCTTTAGAGATTTCGAGTTCCTCTTCAAAAGGTAAGATCTTCATTCAATA
1 CTTAGATATTTCTTTAGAGATTTCGAGTTCATCTTCAAAAGGTAAGATCGT-ATTCAATA
*
58626 CAATT--ATATTTCTTTAGAGATTTCAAGTTCATCTTCAAAAGGTAAAGATC
1 C--TTAGATATTTCTTTAGAGATTTCGAGTTCATCTTCAAAAGGT-AAGATC
58676 ATTCTATACG
Statistics
Matches: 97, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
56 34 0.35
57 13 0.13
59 3 0.03
60 39 0.40
61 6 0.06
62 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (59 bp):
CTTAGATATTTCTTTAGAGATTTCGAGTTCATCTTCAAAAGGTAAGATCGTATTCAATA
Found at i:59966 original size:30 final size:30
Alignment explanation
Indices: 59930--59989 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
59920 AACAGAAAAC
59930 AAAGAATACTTCGTGGAATAAAATCCGCTG
1 AAAGAATACTTCGTGGAATAAAATCCGCTG
* *
59960 AAAGAATAGTTTGTGGAATAAAATCCGCTG
1 AAAGAATACTTCGTGGAATAAAATCCGCTG
59990 TAGTCATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (30 bp):
AAAGAATACTTCGTGGAATAAAATCCGCTG
Found at i:62215 original size:31 final size:31
Alignment explanation
Indices: 62169--62238 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
62159 TAAGGGGAAA
* * *
62169 TAGTCCCTAACATTATTGATCTATTCAATTT
1 TAGTCTCTAACATTATAGATCCATTCAATTT
* *
62200 TAGTCTCTAATATTATAGATCCGTTCAATTT
1 TAGTCTCTAACATTATAGATCCATTCAATTT
62231 TAGTCTCT
1 TAGTCTCT
62239 TAGACGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (31 bp):
TAGTCTCTAACATTATAGATCCATTCAATTT
Found at i:63168 original size:88 final size:88
Alignment explanation
Indices: 63019--63194 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
63009 GTTAAAACTC
63019 ATTTCAGTTTGCTACAGTTGCTGAACAAGTAAAGATAACAACGAGAAGAACCTAGTTAAATGCAA
1 ATTTCAGTTTGCTACAGTTGCTGAACAAGTAAAGATAACAACGAGAAGAACCTAGTTAAATGCAA
63084 TATCAAGGTCATTATTGACGTTG
66 TATCAAGGTCATTATTGACGTTG
63107 ATTTCAGTTTGCTACAGTTGCTGAACAAGTAAAGATAACAACGAGAAGAACCTAGTTAAATGCAA
1 ATTTCAGTTTGCTACAGTTGCTGAACAAGTAAAGATAACAACGAGAAGAACCTAGTTAAATGCAA
63172 TATCAAGGTCATTATTGACGTTG
66 TATCAAGGTCATTATTGACGTTG
63195 CAAGGCGTAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (88 bp):
ATTTCAGTTTGCTACAGTTGCTGAACAAGTAAAGATAACAACGAGAAGAACCTAGTTAAATGCAA
TATCAAGGTCATTATTGACGTTG
Found at i:63460 original size:37 final size:37
Alignment explanation
Indices: 63228--63733 Score: 429
Period size: 37 Copynumber: 14.2 Consensus size: 37
63218 TCCCATATAT
* *
63228 ATATATATATATATATAG-TTTAAAAACACTTTT--AA
1 ATATATATAT-TATATAGTTTTTAAAACATTTTTGAAA
* * *
63263 ACATATATA-TA-ATAG-TTTTGAAACATGTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTG-AAA
*
63298 CATTTATATATTATATAGTTTTTAAAACA-TTTT-AAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
63334 ATAT-TATATATATATAATTTTTAAAAACATTTTTG--A
1 ATATATATAT-TATATAGTTTTT-AAAACATTTTTGAAA
*
63370 A-A-ATATATTATATAGTTTTTAAAACA-TTTTAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * * *
63404 ATAAATATAATATAAAGTTTTCAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
63441 ATATATATATTATATAGTTTTGAAATCA-TTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
63477 ATAAATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
63514 ATATATATATTATATAGTTTTGAAATCA-TTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
63550 ATAAATATAATATATAATTTTTAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * * *
63587 ATATATATATTATATAGTTCTGAAATCATTTTTGAAG
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
**
63624 ACCTATA-A-TATATAG-TTTT-AAACATTTTT--AA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
** * *
63655 A-A-A-CCA-TATA-A-TTTTGAAAACATTTTTCAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTT-GAAA
* * * *
63687 AAATATATATAATATAGAATTTTAAAATACTTTTTGAAA
1 ATATATATATTATATAG-TTTTTAAAACA-TTTTTGAAA
63726 ATATATAT
1 ATATATAT
63734 TATATAAAGG
Statistics
Matches: 379, Mismatches: 59, Indels: 62
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.01
29 16 0.04
31 2 0.01
32 22 0.06
33 18 0.05
34 21 0.06
35 39 0.10
36 106 0.28
37 112 0.30
38 7 0.02
39 27 0.07
40 5 0.01
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:63478 original size:73 final size:73
Alignment explanation
Indices: 63265--63618 Score: 467
Period size: 73 Copynumber: 4.9 Consensus size: 73
63255 ACTTTTAAAC
* * * * *
63265 ATAT-ATATAATAG-TTTTGAAACATGTTTGAAAACATTTATATATTATATAGTTTTTAAAACAT
1 ATATAATATAA-AGTTTTTAAAACATTTTTG-AAA-ATATATATATTATATAGTTTTGAAATCAT
63328 TTT-AAAAT-A
63 TTTGAAAATAA
* * *
63337 TTATATATATATAA-TTTTTAAAAACATTTTTG--AA-A-ATATATTATATAGTTTTTAAAACAT
1 ATATA-ATATA-AAGTTTTT-AAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCAT
*
63397 TTTAAAAATAA
63 TTTGAAAATAA
*
63408 ATATAATATAAAGTTTTCAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTTT
1 ATATAATATAAAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTTT
63473 GAAAATAA
66 GAAAATAA
*
63481 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTTT
1 ATATAATATAAAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTTT
63546 GAAAATAA
66 GAAAATAA
*
63554 ATATAATATATAA-TTTTTAAAACATTTTTGAAAATATATATATTATATAGTTCTGAAATCATTT
1 ATATAATATA-AAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTT
63618 T
65 T
63619 TGAAGACCTA
Statistics
Matches: 256, Mismatches: 13, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
69 42 0.16
70 14 0.05
71 8 0.03
72 5 0.02
73 165 0.64
74 11 0.04
75 11 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (73 bp):
ATATAATATAAAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTGAAATCATTTT
GAAAATAA
Found at i:63663 original size:27 final size:29
Alignment explanation
Indices: 63633--63687 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
63623 GACCTATAAT
*
63633 ATATAGTTTT-AAACATTTTT-AAAAACC
1 ATATAATTTTAAAACATTTTTCAAAAACC
63660 ATATAATTTTGAAAACATTTTTCAAAAA
1 ATATAATTTT-AAAACATTTTTCAAAAA
63688 AATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
29 10 0.42
30 5 0.21
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (29 bp):
ATATAATTTTAAAACATTTTTCAAAAACC
Found at i:63664 original size:73 final size:71
Alignment explanation
Indices: 63228--63657 Score: 459
Period size: 73 Copynumber: 6.0 Consensus size: 71
63218 TCCCATATAT
* * * * *
63228 ATATATATATATATATAG-TTTAAAAACACTTTT-AAACATATAT-ATA-ATAGTTTTGAAACAT
1 ATATATATAT-TATATAGTTTTGAAATCA-TTTTGAAATAAATATAATATATAGTTTTAAAACAT
*
63289 GTTTGAAAA
64 TTTTG-AAA
* * * * * *
63298 CATTTATATATTATATAGTTTTTAAAACATTTTAAAAT-ATTATATATATATAATTTTTAAAAAC
1 -ATATATATATTATATAGTTTTGAAATCATTTTGAAATAAATATA-ATATAT-AGTTTT-AAAAC
63362 ATTTTTG--A
62 ATTTTTGAAA
* * * *
63370 A-A-ATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATAAAGTTTTCAAAACAT
1 ATATATATATTATATAGTTTTGAAATCATTTT-GAAATAAATATAATATATAGTTTT-AAAACAT
63433 TTTTGAAA
64 TTTTGAAA
63441 ATATATATATTATATAGTTTTGAAATCATTTTGAAAATAAATATAATATATAGTTTTTAAAACAT
1 ATATATATATTATATAGTTTTGAAATCATTTTG-AAATAAATATAATATATAG-TTTTAAAACAT
63506 TTTTGAAA
64 TTTTGAAA
*
63514 ATATATATATTATATAGTTTTGAAATCATTTTGAAAATAAATATAATATATAATTTTTAAAACAT
1 ATATATATATTATATAGTTTTGAAATCATTTTG-AAATAAATATAATATAT-AGTTTTAAAACAT
63579 TTTTGAAA
64 TTTTGAAA
* * **
63587 ATATATATATTATATAGTTCTGAAATCATTTTTG-AAGACCTATAATATATAGTTTT-AAACATT
1 ATATATATATTATATAGTTTTGAAATCA-TTTTGAAATAAATATAATATATAGTTTTAAAACATT
*
63650 TTTAAAA
65 TTTGAAA
63657 A
1 A
63658 CCATATAATT
Statistics
Matches: 318, Mismatches: 24, Indels: 35
0.84 0.06 0.09
Matches are distributed among these distances:
69 45 0.14
70 38 0.12
71 34 0.11
72 18 0.06
73 158 0.50
74 15 0.05
75 10 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (71 bp):
ATATATATATTATATAGTTTTGAAATCATTTTGAAATAAATATAATATATAGTTTTAAAACATTT
TTGAAA
Found at i:63773 original size:11 final size:10
Alignment explanation
Indices: 63757--63834 Score: 52
Period size: 11 Copynumber: 7.4 Consensus size: 10
63747 TTGGAAAATA
63757 TTTTATTCTAT
1 TTTTATT-TAT
63768 TTTTA-TTAT
1 TTTTATTTAT
*
63777 TATTATTTATT
1 TTTTATTTA-T
63788 TATTTATTTAT
1 T-TTTATTTAT
63799 ATTTTATTT-T
1 -TTTTATTTAT
* *
63809 ATTAATTTCAT
1 TTTTATTT-AT
*
63820 TTTTTTATTAT
1 TTTTAT-TTAT
63831 TTTT
1 TTTT
63835 TCCATGTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
9 13 0.25
10 5 0.09
11 25 0.47
12 10 0.19
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:63795 original size:32 final size:33
Alignment explanation
Indices: 63758--63828 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
63748 TGGAAAATAT
63758 TTTATTCTAT-TTTTATTATTATT-ATTT-ATTTA
1 TTTATT-TATATTTTATT-TTATTAATTTCATTTA
*
63790 TTTATTTATATTTTATTTTATTAATTTCATTTT
1 TTTATTTATATTTTATTTTATTAATTTCATTTA
63823 TTTATT
1 TTTATT
63829 ATTTTTTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 8 0.23
32 17 0.49
33 10 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (33 bp):
TTTATTTATATTTTATTTTATTAATTTCATTTA
Found at i:63823 original size:20 final size:19
Alignment explanation
Indices: 63782--63829 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
63772 ATTATTATTA
*
63782 TTTATTTATTTATTTATAT
1 TTTATTTATTAATTTATAT
*
63801 TTTATTTTATTAATTT-CAT
1 TTTA-TTTATTAATTTATAT
63820 TTT-TTTATTA
1 TTTATTTATTA
63830 TTTTTTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
19 9 0.35
20 10 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTATTAATTTATAT
Found at i:63827 original size:37 final size:36
Alignment explanation
Indices: 63755--63833 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
63745 TTTTGGAAAA
*
63755 TATTTTATTCTATTTTTATTATTATTATTTATTTATT
1 TATTTTATTCTATTTTTATTATTATCATTTATTTA-T
* *
63792 TATTTATATTTTA-TTTTATTAATT-TCATTTTTTTAT
1 TATTT-TATTCTATTTTTATT-ATTATCATTTATTTAT
63828 TATTTT
1 TATTTT
63834 TTCCATGTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 1 0.03
36 6 0.16
37 21 0.57
38 9 0.24
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (36 bp):
TATTTTATTCTATTTTTATTATTATCATTTATTTAT
Found at i:65066 original size:5 final size:5
Alignment explanation
Indices: 65056--65082 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
65046 TCTTTTATTA
65056 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
65083 CTTTGGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:70545 original size:84 final size:84
Alignment explanation
Indices: 70281--71152 Score: 814
Period size: 84 Copynumber: 10.5 Consensus size: 84
70271 GGGCTATCTG
* * *
70281 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAACG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
70346 CTAGAAGGGTTATCTGCCAA
66 CTAGAAGGGTTATCTG-CAA
* * * * ** * * * *
70366 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGTAGTATAGCTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
* * **
70430 CGAGAAGGG--CTCT-CTT
66 CTAGAAGGGTTATCTGCAA
* *
70446 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACTCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
*
70511 CTAGAAAGGTTATCTGCAA
66 CTAGAAGGGTTATCTGCAA
* * * * * * * *
70530 CCAAAGACCTTCGAGTTCGACTACTCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
* * *
70594 CGAGAAGGGCTATATG---
66 CTAGAAGGGTTATCTGCAA
* *
70610 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACGGCATAACTCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
**
70675 CTAGAACAGTTATCTGTCAA
66 CTAGAAGGGTTATCTG-CAA
* * * *
70695 -CAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAAGGAATATCATTTACAACATAACTCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
**
70759 CTAGAAGGGTTATCTGTGA
66 CTAGAAGGGTTATCTGCAA
* * * * * * * *
70778 CCAAAAGACCCTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCATTTGCATCATAACTTAAG
1 CC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAG
* * *
70842 TCGAGTAGGGTTATCTGCCAA
65 GCTAGAAGGGTTATCTG-CAA
* * * * * * * * *
70863 CCAAAGACCTTCGAGTTCGACTACGCTCTG-TTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
*
70927 CGAGAAGGGTTATCTG---
66 CTAGAAGGGTTATCTGCAA
* * * * *
70943 CTAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACGGCATAAATCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
71008 CTAGAAGGGTTATCTGTCAA
66 CTAGAAGGGTTATCTG-CAA
* * * * * * * *
71028 -CAAAGACCTTCGAGTTCGACTCCACTCAGC-TCAAAGGAACCATCATTTGCAGTATAGCTCAAG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCA-CATCATTTACAGCATAACTCAAG
71091 G-TAAGAAGGGTTATCTG---
65 GCT-AGAAGGGTTATCTGCAA
* * * * *
71108 CCAAAGACCTTCGAGTTCGATTCCATTCAGC-TCGAGGGCATATCA
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCA
71153 ACCACGTTGC
Statistics
Matches: 642, Mismatches: 124, Indels: 47
0.79 0.15 0.06
Matches are distributed among these distances:
80 88 0.14
81 142 0.22
82 3 0.00
83 49 0.08
84 301 0.47
85 59 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGG
CTAGAAGGGTTATCTGCAA
Found at i:70616 original size:164 final size:165
Alignment explanation
Indices: 70245--71152 Score: 1153
Period size: 165 Copynumber: 5.5 Consensus size: 165
70235 TAAAGAAACT
70245 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* *
70310 GCTTTGAGGGCACATCATTTACAGCATAACTCAACGCTAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC
* * *
70375 TTTGAGTTCGACTACGCTCAGCTTCAAGGCACATC
131 TTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * * *
70410 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTCTCTTCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* *
70475 GCTTCGAGGGCACATCATTTATAGCATAACTCAAGGCTAGAAAGGTTATCTG-CAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC
*
70539 TTCGAGTTCGACTACTCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
*
70574 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* ** *
70639 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAACAGTTATCTGTCAA-CAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC
* * * * * *
70703 CTCGAGTTTGATTACACTCAGCTTCGAAGGAATATC
131 TTCGAGTTCGACTACACTCAGC-TCCAAGGCACATC
* * * * * * * * * *
70739 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCTCGAGTTTGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTCGAGTTCGATTACA
* * * * * * * * *
70804 CTCAGC-TCCAAGGCATATCATTTGCATCATAACTTAAGTCGAGTAGGGTTATCTGCCAACCAAA
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAA
* * *
70868 GACCTTCGAGTTCGACTACGCTCTGTTCCAAGGCACATC
127 GACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* *
70907 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * * *
70972 GCTTCGAGGGCACATAATTTACGGCATAAATCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC
* * *
71036 TTCGAGTTCGACTCCACTCAGCTCAAAGGAACCATC
131 TTCGAGTTCGACTACACTCAGCTCCAAGGCA-CATC
* * * * * * *
71072 ATTTGCAGTATAGCTCAAGGT-AAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTCCATTC
1 ATTTGCAGCATAGCTTAA-GTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
*
71136 AGC-TCGAGGGCATATCA
65 AGCTTCGAGGGCACATCA
71153 ACCACGTTGC
Statistics
Matches: 635, Mismatches: 98, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
164 249 0.39
165 250 0.39
166 4 0.01
167 2 0.00
168 80 0.13
169 50 0.08
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC
TTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
Found at i:70951 original size:333 final size:329
Alignment explanation
Indices: 70245--71127 Score: 1227
Period size: 333 Copynumber: 2.7 Consensus size: 329
70235 TAAAGAAACT
70245 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * * *
70310 GCTTTGAGGGCACATCATTTACAGCATAACTCAACGCTAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACC
* * * * * * * *
70375 TTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGC
130 TTCGAGTTCGACTACACTCAGCTTCAAGGAACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGT
* * * * *
70440 TCTCT-TCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAA
195 TATCTGTCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATAA
* *
70504 CTCAAGGCTAGAAAGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACTCTCAGCTCCAAGGC
260 CTCAAGGCGAGAAAGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
70569 ACATC
325 ACATC
*
70574 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
** *
70639 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAACAGTTATCTGTCAACAAAGACCC
66 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCT
* * * * ** *
70704 TCGAGTTTGATTACACTCAGCTTCGAAGGAATATCATTTACAACATAACTCAAGGCTAGAAGGGT
131 TCGAGTTCGACTACACTCAGCTTC-AAGGAACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGT
* * * * *
70769 TATCTGTGACCAAAAGACCCTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCATTTGCATCA
195 TATCTGT--CC-AAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCA
* * * * * *
70833 TAACTTAAGTCGAGTAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCTGTTCCA
257 TAACTCAAGGCGAGAAAGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
70898 AGGCACATC
321 AGGCACATC
* *
70907 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* *
70972 GCTTCGAGGGCACATAATTTACGGCATAAATCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCT
66 GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCT
*
71037 TCGAGTTCGACTCCACTCAGC-TCAAAGGAACCATCATTTGCAGTATAGCTCAAGG-TAAGAAGG
131 TCGAGTTCGACTACACTCAGCTTC-AAGGAA-CATCATTTGCAGTATAGCTCAAGGCT-AGAAGG
*
71100 GTTATCTG-CCAAAGACCTTCGAGTTCGA
193 GTTATCTGTCCAAAGACCCTCGAGTTCGA
71128 TTCCATTCAG
Statistics
Matches: 486, Mismatches: 60, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
328 28 0.06
329 163 0.34
330 3 0.01
332 49 0.10
333 243 0.50
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (329 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCT
TCGAGTTCGACTACACTCAGCTTCAAGGAACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGTT
ATCTGTCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATAAC
TCAAGGCGAGAAAGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATC
Found at i:71517 original size:16 final size:16
Alignment explanation
Indices: 71456--71519 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
71446 CTACAAAAAC
* *
71456 ATTTTACTATATTATAT
1 ATTTTA-TATATTTTTT
* *
71473 A-TTTATTTATTTATT
1 ATTTTATATATTTTTT
71488 ATTATTAT-TATTTTTT
1 ATT-TTATATATTTTTT
71504 ATTTTATATATTTTTT
1 ATTTTATATATTTTTT
71520 TACAGGCCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 11 0.28
16 23 0.59
17 5 0.13
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTATATATTTTTT
Found at i:71520 original size:17 final size:17
Alignment explanation
Indices: 71465--71521 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
71455 CATTTTACTA
*
71465 TATTATATATTTATTTATT
1 TATTAT-TA-TTATTTTTT
71484 TATTATTATTATTATTTTT
1 TATTATTATTA-T-TTTTT
71503 TATT-TTATATATTTTTT
1 TATTATTAT-TATTTTTT
71520 TA
1 TA
71522 CAGGCCTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 16 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTATTATTTTTT
Found at i:71609 original size:33 final size:33
Alignment explanation
Indices: 71567--71639 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
71557 TTCAGAAAAT
* * *
71567 AAACCAACGTATTTGAGTCTTACTGAATCACTA
1 AAACCAACGTATTTGAGTCATACTAAAACACTA
*
71600 AAACCAACGTATTTGAGTCATATTAAAACACTA
1 AAACCAACGTATTTGAGTCATACTAAAACACTA
71633 AAACCAA
1 AAACCAA
71640 AGCATTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCATACTAAAACACTA
Found at i:72024 original size:4 final size:4
Alignment explanation
Indices: 72015--72039 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
72005 TACATTGTTA
72015 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
72040 CGTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:74547 original size:21 final size:21
Alignment explanation
Indices: 74511--74576 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
74501 CGATCCATTA
*
74511 ATCCGATCT-GAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
74531 ATCCGATCTAAAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
*
74552 ATCCAATCTAAAAAATCGGAT
1 ATCCGATCTAAAAAATCGGAT
74573 ATCC
1 ATCC
74577 AATCCGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
20 9 0.21
21 34 0.79
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (21 bp):
ATCCGATCTAAAAAATCGGAT
Found at i:74577 original size:21 final size:21
Alignment explanation
Indices: 74521--74580 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
74511 ATCCGATCTG
*
74521 AAAATCGGATATCCGATCTAA
1 AAAATCGGATATCCAATCTAA
74542 AAAATCGGATATCCAATCTAA
1 AAAATCGGATATCCAATCTAA
74563 AAAATCGGATATCCAATC
1 AAAATCGGATATCCAATC
74581 CGTTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAATCGGATATCCAATCTAA
Found at i:75504 original size:15 final size:16
Alignment explanation
Indices: 75462--75495 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
75452 CGGATATCCG
*
75462 ATCCGAAATTTTGGAT
1 ATCCGAATTTTTGGAT
75478 ATCCGAATTTTTGGAT
1 ATCCGAATTTTTGGAT
75494 AT
1 AT
75496 TGATTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (16 bp):
ATCCGAATTTTTGGAT
Done.