Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001436.1 Hibiscus syriacus cultivar Beakdansim tig00002784_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: 149439
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8706 original size:22 final size:22
Alignment explanation
Indices: 8681--8724 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8671 TATAAAATTA
**
8681 AAAAAAAATATTTTTTAAAAAG
1 AAAAAAAATAAATTTTAAAAAG
* *
8703 AAAACACATAAATTTTAAAAAG
1 AAAAAAAATAAATTTTAAAAAG
8725 CTCATCGAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAAAAAATAAATTTTAAAAAG
Found at i:13454 original size:22 final size:22
Alignment explanation
Indices: 13416--13500 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
13406 CCAGAAACCC
* *
13416 CAGGGGGTATCGATTCCCCT-A
1 CAGGGGGAATCGGTTCCCCTCA
13437 CAGGGGAGAATCGGTTCCCCTTCA
1 CAGGGG-GAATCGGTTCCCC-TCA
* *
13461 AAGGGGGAATCAGTTCCCCTTCA
1 CAGGGGGAATCGGTTCCCC-TCA
* *
13484 -AGGGGGTATCGATTCCC
1 CAGGGGGAATCGGTTCCC
13501 TCTGCCCTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
21 6 0.11
22 25 0.46
23 17 0.31
24 6 0.11
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.22
Consensus pattern (22 bp):
CAGGGGGAATCGGTTCCCCTCA
Found at i:13476 original size:23 final size:22
Alignment explanation
Indices: 13429--13489 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
13419 GGGGTATCGA
* *
13429 TTCCCCTAC-AGGGGAGAATCGG
1 TTCCCCTTCAAGGGG-GAATCAG
13451 TTCCCCTTCAAAGGGGGAATCAG
1 TTCCCCTTC-AAGGGGGAATCAG
13474 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
13490 TATCGATTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 15 0.43
23 15 0.43
24 5 0.14
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCAG
Found at i:18932 original size:12 final size:12
Alignment explanation
Indices: 18912--18941 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18902 GCACAATTCT
18912 AGAACAAAGAAA
1 AGAACAAAGAAA
*
18924 AGAATAAAGAAA
1 AGAACAAAGAAA
18936 AGAACA
1 AGAACA
18942 CTCAAGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.07, G:0.17, T:0.03
Consensus pattern (12 bp):
AGAACAAAGAAA
Found at i:20964 original size:12 final size:13
Alignment explanation
Indices: 20937--20966 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
20927 TTAATTAGGA
20937 TTTAGAATATTAT
1 TTTAGAATATTAT
20950 TTTA-AATATTAT
1 TTTAGAATATTAT
20962 TTTAG
1 TTTAG
20967 GTATTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTAGAATATTAT
Found at i:21546 original size:17 final size:18
Alignment explanation
Indices: 21512--21553 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
21502 TTTTTAAAAA
21512 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
21530 AAATAAAA-ATAATAATT
1 AAATAAAAGATAAGAATT
21547 AAATAAA
1 AAATAAA
21554 CAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:22319 original size:20 final size:21
Alignment explanation
Indices: 22294--22335 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
22284 AATCTTGGAG
22294 AAGAAAGAT-GAAAGAG-AGAA
1 AAGAAA-ATGGAAAGAGAAGAA
22314 AAGAAAATGGAAAGAGAAGAA
1 AAGAAAATGGAAAGAGAAGAA
22335 A
1 A
22336 GTGGGGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.05
Consensus pattern (21 bp):
AAGAAAATGGAAAGAGAAGAA
Found at i:22333 original size:16 final size:18
Alignment explanation
Indices: 22291--22336 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
22281 ACGAATCTTG
22291 GAGAAGAAAGATGAAAGA
1 GAGAAGAAAGATGAAAGA
*
22309 GAGAAAAGAAA-ATGGAA-A
1 GAG--AAGAAAGATGAAAGA
22327 GAGAAGAAAG
1 GAGAAGAAAG
22337 TGGGGTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
18 7 0.29
19 5 0.21
20 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAGAAGAAAGATGAAAGA
Found at i:23866 original size:19 final size:19
Alignment explanation
Indices: 23828--23867 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23818 AAACATTGGG
* **
23828 TTTTTTTGTTTAGATCAAT
1 TTTTTTTGTTTAAAAAAAT
23847 TTTTTTTGTTTAAAAAAAT
1 TTTTTTTGTTTAAAAAAAT
23866 TT
1 TT
23868 ACGACTGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTTTTGTTTAAAAAAAT
Found at i:27414 original size:23 final size:22
Alignment explanation
Indices: 27382--27430 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
27372 CTGCATACCA
27382 ATAAATATAAATATTAATGTAT
1 ATAAATATAAATATTAATGTAT
*
27404 ATAATATATAAATATTTATGTAT
1 ATAA-ATATAAATATTAATGTAT
27427 ATAA
1 ATAA
27431 CCGTGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
ATAAATATAAATATTAATGTAT
Found at i:30385 original size:17 final size:17
Alignment explanation
Indices: 30344--30385 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30334 AACTGGTTTT
30344 TAAATTTTAATAAATTA
1 TAAATTTTAATAAATTA
*
30361 TATTATTTT-ATAAATTA
1 TA-AATTTTAATAAATTA
30378 TGAAATTT
1 T-AAATTT
30386 ATATCACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTTTAATAAATTA
Found at i:33468 original size:42 final size:42
Alignment explanation
Indices: 33402--33483 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
33392 AATGTTGATT
*
33402 TTGACCCAACTCCTTCTGTTATGGAATTGAGCA-AAATATTTG
1 TTGACCCAACTCCTTCTGTTATGGAATCGAG-AGAAATATTTG
* *
33444 TTGACCCTACTCTTTCT-TTGATGGAATCGAGAGAAATATT
1 TTGACCCAACTCCTTCTGTT-ATGGAATCGAGAGAAATATT
33484 GATGTTGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGACCCAACTCCTTCTGTTATGGAATCGAGAGAAATATTTG
Found at i:33632 original size:85 final size:84
Alignment explanation
Indices: 33452--33734 Score: 250
Period size: 85 Copynumber: 3.3 Consensus size: 84
33442 TGTTGACCCT
* * * * *
33452 ACTCTTTCTTTGATGGAATCGAGAGAAATATTGATGTTGTTCAACTC--CTGTGATGGAATCTAA
1 ACTCCTTCTGTGATGGAATCGAGCGAAATATTGATGTTTTTCAACTCTTCTGTGATGGAATCGAA
* ** *
33515 CGAAATGCTTGTTGACCTG
66 CGAAATGCTTTTTGATTTA
* * *
33534 ACTCCTTCTGTGATGGAAACGAGCGAAATGTTGATGTTTTTCAACTACTTCTGTGATGAAATCGA
1 ACTCCTTCTGTGATGGAATCGAGCGAAATATTGATGTTTTTCAACT-CTTCTGTGATGGAATCGA
33599 ACGAAATG-TTTTCTGATTTA
65 ACGAAATGCTTTT-TGATTTA
* * * * ** *
33619 ACTCCTTCAGTGATAGAATTGAGGGAAATATTGATGTTTGACCAACTCCTTCAGTGATGGAATCG
1 ACTCCTTCTGTGATGGAATCGAGCGAAATATTGATGTTT-TTCAACT-CTTCTGTGATGGAATCG
* * * *
33684 ATCAAAATGTTGTTTTTG-TTCA
64 AACGAAATG--CTTTTTGATTTA
* * *
33706 AGTCCTTCTGTGATGGAATCAACCGAAAT
1 ACTCCTTCTGTGATGGAATCGAGCGAAAT
33735 GTTGCTGAAA
Statistics
Matches: 160, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
82 40 0.25
83 1 0.01
84 3 0.02
85 58 0.36
86 27 0.17
87 25 0.16
88 2 0.01
89 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (84 bp):
ACTCCTTCTGTGATGGAATCGAGCGAAATATTGATGTTTTTCAACTCTTCTGTGATGGAATCGAA
CGAAATGCTTTTTGATTTA
Found at i:33679 original size:129 final size:128
Alignment explanation
Indices: 33534--33810 Score: 312
Period size: 129 Copynumber: 2.1 Consensus size: 128
33524 TGTTGACCTG
*
33534 ACTCCTTCTGTGATGGAAACGAGCGAAATGTTGATGTTT-TTCAACTACTTCTGTGATGAAATCG
1 ACTCCTTCTGTGATGGAAACGAGCAAAATGTTG-TGTTTGTTCAACTACTTCTGTGATGAAATC-
* * * *
33598 AA-CGAAATGTTTTCTG-ATTTAACTC-CTTC-AGTGATAGAATTGAGGGAAATATTGATGTTTG
64 AACCGAAATG-TTGCTGAAATCAAC-CACTTCTA-TGATAGAATTGAGCG-AATATTGATGTTTG
33659 ACCA
125 ACCA
* * * * * * *
33663 ACTCCTTCAGTGATGGAATCGATCAAAATGTTGTTTTTGTTCAAGTCCTTCTGTGATGGAATCAA
1 ACTCCTTCTGTGATGGAAACGAGCAAAATGTTGTGTTTGTTCAACTACTTCTGTGATGAAATCAA
* * *
33728 CCGAAATGTTGCTGAAAAATCAACCACTTCTATGATGGAATTGAGCGATTATTGATGTTTGATCA
66 CCGAAATGTTGCTG--AAATCAACCACTTCTATGATAGAATTGAGCGAATATTGATGTTTGACCA
33793 ACTCCTTCTGTGATGGAA
1 ACTCCTTCTGTGATGGAA
33811 TTAAATTTGC
Statistics
Matches: 125, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
128 11 0.09
129 57 0.46
130 34 0.27
131 22 0.18
132 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (128 bp):
ACTCCTTCTGTGATGGAAACGAGCAAAATGTTGTGTTTGTTCAACTACTTCTGTGATGAAATCAA
CCGAAATGTTGCTGAAATCAACCACTTCTATGATAGAATTGAGCGAATATTGATGTTTGACCA
Found at i:33812 original size:43 final size:44
Alignment explanation
Indices: 33389--33811 Score: 234
Period size: 43 Copynumber: 9.9 Consensus size: 44
33379 TTAAGTTGAA
* * * *
33389 CGAAATGTTGAT-TTTGACCCAACTCCTTCTGTTATGGAATTGAG
1 CGAAATATTGATGTTTGA-TCAACTCCTTCTGTGATGGAATCGAG
* * * * *
33433 CAAAATATT--TG-TTGACCCTACTCTTTCTTTGATGGAATCGAG
1 CGAAATATTGATGTTTGA-TCAACTCCTTCTGTGATGGAATCGAG
* * * *
33475 AGAAATATTGATG-TTGTTCAACT-C--CTGTGATGGAATCTAA
1 CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAATCGAG
** * * *
33515 CGAAATGCT--TG-TTGACCTGACTCCTTCTGTGATGGAAACGAG
1 CGAAATATTGATGTTTGATC-AACTCCTTCTGTGATGGAATCGAG
* * * * *
33557 CGAAATGTTGATGTTT-TTCAACTACTTCTGTGATGAAATCGAA
1 CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAATCGAG
* * * * * *
33600 CGAAATGTT--T-TCTGATTTAACTCCTTCAGTGATAGAATTGAG
1 CGAAATATTGATGTTTGA-TCAACTCCTTCTGTGATGGAATCGAG
* * * *
33642 GGAAATATTGATGTTTGACCAACTCCTTCAGTGATGGAATCGAT
1 CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAATCGAG
* * * * * * *
33686 CAAAATGTTG-TTTTTGTTCAAGTCCTTCTGTGATGGAATCAAC
1 CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAATCGAG
* * **** * *
33729 CGAAATGTTGCTGAAAAATCAAC-CACTTCTATGATGGAATTGAG
1 CGAAATATTGATGTTTGATCAACTC-CTTCTGTGATGGAATCGAG
*
33773 CG-ATTATTGATGTTTGATCAACTCCTTCTGTGATGGAAT
1 CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAAT
33812 TAAATTTGCA
Statistics
Matches: 281, Mismatches: 80, Indels: 37
0.71 0.20 0.09
Matches are distributed among these distances:
38 6 0.02
39 3 0.01
40 22 0.08
41 1 0.00
42 81 0.29
43 95 0.34
44 67 0.24
45 6 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (44 bp):
CGAAATATTGATGTTTGATCAACTCCTTCTGTGATGGAATCGAG
Found at i:36637 original size:2 final size:2
Alignment explanation
Indices: 36626--36684 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
36616 TAAAGGCAAT
36626 TA TA -A 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
36667 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
36685 CAATAAAACT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37743 original size:19 final size:20
Alignment explanation
Indices: 37707--37745 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
37697 AATAAAGACA
*
37707 TATAAAATTAATAACTAATT
1 TATAAAAATAATAACTAATT
37727 TATAAAAATAA-AACTAATT
1 TATAAAAATAATAACTAATT
37746 ACTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATAATAACTAATT
Found at i:39002 original size:3 final size:3
Alignment explanation
Indices: 38994--39150 Score: 233
Period size: 3 Copynumber: 51.7 Consensus size: 3
38984 TTATTTATTA
* *
38994 AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT
** *
39041 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
39089 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39137 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
39151 AATGGATAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
3 132 0.96
4 6 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39601 original size:113 final size:113
Alignment explanation
Indices: 39403--40175 Score: 1406
Period size: 113 Copynumber: 6.8 Consensus size: 113
39393 TCTTGATGAG
*
39403 TTCTTTTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* *** * * * *
39466 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
39516 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
39581 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
39629 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
39694 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
39742 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
39807 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
39855 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
39920 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
39968 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
40033 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
40081 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
40146 GAAAAGATGATCCACCAAATGATGGATTCA
66 GAAAAAATGATCCACCAAATGATGGATTCA
40176 TCTTTGCTAA
Statistics
Matches: 647, Mismatches: 11, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
112 1 0.00
113 645 1.00
114 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAAATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:40863 original size:52 final size:52
Alignment explanation
Indices: 40804--41256 Score: 849
Period size: 52 Copynumber: 8.8 Consensus size: 52
40794 TATGTCCAAT
*
40804 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
40856 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
40908 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
*
40960 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
41012 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-CTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
41063 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-CTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
* *
41114 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
41166 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-CTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
41217 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
41257 TGATCACATA
Statistics
Matches: 393, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
51 144 0.37
52 249 0.63
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
Found at i:41207 original size:154 final size:155
Alignment explanation
Indices: 40804--41256 Score: 881
Period size: 154 Copynumber: 2.9 Consensus size: 155
40794 TATGTCCAAT
40804 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
40869 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTT
66 TCAAAGAACACTTCCAGAAGATGCTATGTTCTG-CTAACCAGATCAGATAACTCAAAGAACACTT
40934 CCAGAAGATGCTATGTTCTGTCTAAC
130 CCAGAAGATGCTATGTTCTGTCTAAC
40960 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
41025 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGCTAACCAGATCAGATAACTCAAAGAACACTTC
66 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGCTAACCAGATCAGATAACTCAAAGAACACTTC
41090 CAGAAGATGCTATGTTCTG-CTAAC
131 CAGAAGATGCTATGTTCTGTCTAAC
*
41114 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
41179 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGCTAACCAGATCAGATAACTCAAAGAACACTTC
66 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGCTAACCAGATCAGATAACTCAAAGAACACTTC
41244 CAGAAGATGCTAT
131 CAGAAGATGCTAT
41257 TGATCACATA
Statistics
Matches: 296, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
154 147 0.50
155 51 0.17
156 98 0.33
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (155 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAAC
TCAAAGAACACTTCCAGAAGATGCTATGTTCTGCTAACCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATGTTCTGTCTAAC
Found at i:42196 original size:6 final size:6
Alignment explanation
Indices: 42185--42275 Score: 71
Period size: 6 Copynumber: 14.3 Consensus size: 6
42175 CTTGACCCCT
*
42185 TTTTTC TTTTTC TTTTTC TTCTTTTCC TTTTT- TTTTTC CTTTTC TTTCTCTTC
1 TTTTTC TTTTTC TTTTTC -T-TTTT-C TTTTTC TTTTTC TTTTTC -TT-T-TTC
*
42238 TTTTTC -TTTTC TTTTTTC TTTTTTC CTTTT- TTTTTC TT
1 TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TT
42276 CAAGCATAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
5 14 0.20
6 26 0.37
7 19 0.27
8 8 0.11
9 4 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:42228 original size:32 final size:33
Alignment explanation
Indices: 42183--42260 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
42173 ACCTTGACCC
*
42183 CTTTTTTCTTTTTCTTTTTCTTCTTTTCCTTTT
1 CTTTTTTCTTTTTCTTTCTCTTCTTTTCCTTTT
* *
42216 -TTTTTTCCTTTTCTTTCTCTTCTTTTTCTTTT
1 CTTTTTTCTTTTTCTTTCTCTTCTTTTCCTTTT
42248 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
42261 TCCTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 29 0.73
33 11 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (33 bp):
CTTTTTTCTTTTTCTTTCTCTTCTTTTCCTTTT
Found at i:53667 original size:19 final size:20
Alignment explanation
Indices: 53631--53669 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53621 AATAAAGACA
*
53631 TATAAAATTAATAACTAATT
1 TATAAAAATAATAACTAATT
53651 TATAAAAATAA-AACTAATT
1 TATAAAAATAATAACTAATT
53670 ACTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATAATAACTAATT
Found at i:54926 original size:3 final size:3
Alignment explanation
Indices: 54918--55075 Score: 246
Period size: 3 Copynumber: 52.7 Consensus size: 3
54908 TTATTTATTA
* *
54918 AAT AAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
** *
54963 AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
55011 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55059 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
55076 AATGGATAAA
Statistics
Matches: 141, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.01
3 136 0.96
4 3 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:57891 original size:128 final size:129
Alignment explanation
Indices: 57735--58008 Score: 315
Period size: 129 Copynumber: 2.1 Consensus size: 129
57725 ATTCTATCAC
* * * ** * *
57735 ATTCCATCATAGAAGGAGTCGAGTCAACAAGTATTTCGTTCAATTCCATCACA-AAAGAAGTTGG
1 ATTCTATCACAGAAGGACTCGAGTCAACAAACATTTCGCTCAATTCCATAACAGAAAG-AGTTGG
* * *
57799 G-T-CAAT-AAGCATTTTCATTCGATTCCATCACAGAAGGAGTTGAACAACATCAACATTTCTCT
65 GTTAAAATCAA-CA-TTTCATTCGATTCCATCACAGAAGGAGTTAAACAACATCAACATTTCGCT
57861 -T
128 CT
* * *
57862 GATTCTATCACAGAAGGACTCGGGTCAACAAACATTTCGCTCGATTCCATAACAGAATGAGTTGG
1 -ATTCTATCACAGAAGGACTCGAGTCAACAAACATTTCGCTCAATTCCATAACAGAAAGAGTTGG
* * ***
57927 GTTAAAATCAACATTTCGTTCGATTCCATCACAGAATGAGTTAAATTTCATCAACATTTCGCTCT
65 GTTAAAATCAACATTTCATTCGATTCCATCACAGAAGGAGTTAAACAACATCAACATTTCGCTCT
57992 ATTCTATCACAGAAGGA
1 ATTCTATCACAGAAGGA
58009 GTTGAGTGTT
Statistics
Matches: 123, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
128 51 0.41
129 64 0.52
130 6 0.05
131 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (129 bp):
ATTCTATCACAGAAGGACTCGAGTCAACAAACATTTCGCTCAATTCCATAACAGAAAGAGTTGGG
TTAAAATCAACATTTCATTCGATTCCATCACAGAAGGAGTTAAACAACATCAACATTTCGCTCT
Found at i:57950 original size:44 final size:44
Alignment explanation
Indices: 57817--58267 Score: 354
Period size: 44 Copynumber: 10.2 Consensus size: 44
57807 GCATTTTCAT
* ** *
57817 TCGATTCCATCACAGAAGGAGTT-GAACAACATCAACATTTCTC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * * * *
57860 TTGATTCTATCACAGAAGGACTCGGGTCAACA--AACATTTCGC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * * *
57902 TCGATTCCATAACAGAATGAGTTGGGTTAAAATCAACATTTCGT
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * *** **
57946 TCGATTCCATCACAGAATGAGTTAAAT-TTCATCAACATTTCGC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * * * **** *
57989 TCTATTCTATCACAGAAGGAGTTGAGTGTTTATCAATATTTCGC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * * * *
58033 TCGATTCCATCACAGAAAGAAATAAGTTGGATCAACATAAACATTTTGC
1 TCGATTCCATAACAG-AAG----GAGTTGGGTCAACATCAACATTTCGC
* * * * *
58082 TTGATTCCATAATAGAGGGAGTTGGGTCAACATCAACATTACAC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* * * *
58126 TCGATTCCATAACAG-AGGAAGTCGAGTCCACATCAACATTTTGC
1 TCGATTCCATAACAGAAGG-AGTTGGGTCAACATCAACATTTCGC
* * * * *
58170 TCAATTCCATAACAGAGGGAATTGGGTCAACCTCAACATCTCGC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
* *
58214 TTGATTCCATAACAGAAGGAGTTGGGTCAAAATCAACATTTCGC
1 TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
*
58258 TCGTTTCCAT
1 TCGATTCCAT
58268 CGCATAGAGA
Statistics
Matches: 317, Mismatches: 80, Indels: 21
0.76 0.19 0.05
Matches are distributed among these distances:
42 33 0.10
43 55 0.17
44 194 0.61
45 5 0.02
48 2 0.01
49 28 0.09
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
TCGATTCCATAACAGAAGGAGTTGGGTCAACATCAACATTTCGC
Found at i:58067 original size:87 final size:86
Alignment explanation
Indices: 57892--58230 Score: 223
Period size: 87 Copynumber: 3.8 Consensus size: 86
57882 CGGGTCAACA
* *
57892 AACATTTCGCTCGATTCCATAACAGAATGAGTTGGGTTAAAATCAACATTTCGTTCGATTCCATC
1 AACATTTCGCTCGATTCCATAACAGAAGGAGTTGGGTT-AAATCAACATTTCGCTCGATTCCATC
* ** *
57957 ACAGAATGAGTTAAATTTCATC
65 ACAGAAAGAAATAAATTGCATC
* * * * *
57979 AACATTTCGCTCTATTCTATCACAGAAGGAGTTGAGTGTT-TATCAATATTTCGCTCGATTCCAT
1 AACATTTCGCTCGATTCCATAACAGAAGGAGTTG-G-GTTAAATCAACATTTCGCTCGATTCCAT
* *
58043 CACAGAAAGAAATAAGTTGGATCAACATA
64 CACAGAAAGAAATAAATT-G-----CATC
* * * * * * * *
58072 AACATTTTGCTTGATTCCATAATAGAGGGAGTTGGGTCAACATCAACATTACACTCGATTCCATA
1 AACATTTCGCTCGATTCCATAACAGAAGGAGTTGGGTTAA-ATCAACATTTCGCTCGATTCCATC
* * * * **
58137 ACAG-AGGAAGTCGAGTCCACATC
65 ACAGAAAGAAAT-AAAT-TGCATC
* * * * * * * * *
58160 AACATTTTGCTCAATTCCATAACAGAGGGAATTGGGTCAACCTCAACATCTCGCTTGATTCCATA
1 AACATTTCGCTCGATTCCATAACAGAAGGAGTTGGGTTAA-ATCAACATTTCGCTCGATTCCATC
58225 ACAGAA
65 ACAGAA
58231 GGAGTTGGGT
Statistics
Matches: 198, Mismatches: 41, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
87 65 0.33
88 64 0.32
89 4 0.02
91 2 0.01
92 6 0.03
93 57 0.29
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (86 bp):
AACATTTCGCTCGATTCCATAACAGAAGGAGTTGGGTTAAATCAACATTTCGCTCGATTCCATCA
CAGAAAGAAATAAATTGCATC
Found at i:59755 original size:40 final size:38
Alignment explanation
Indices: 59701--59785 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 38
59691 ATAACATATC
* *
59701 AAAAGTTTAGTTTTTGTTTCATTTTAGTAGCATGCCGTTA
1 AAAATTTTAATTTTTGTTTCATTTTAGTA-CAT-CCGTTA
*
59741 AAAATTTTAATTTTTGTTTCATTTTAGTACATCCGTTC
1 AAAATTTTAATTTTTGTTTCATTTTAGTACATCCGTTA
59779 AAAATTT
1 AAAATTT
59786 AATATTTAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
38 12 0.29
39 3 0.07
40 27 0.64
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (38 bp):
AAAATTTTAATTTTTGTTTCATTTTAGTACATCCGTTA
Found at i:60175 original size:19 final size:19
Alignment explanation
Indices: 60151--60191 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
60141 AAACTAATAA
60151 AACCCTCAATTTCTGATTC
1 AACCCTCAATTTCTGATTC
*
60170 AACCCTTAATTTCTGATTC
1 AACCCTCAATTTCTGATTC
60189 AAC
1 AAC
60192 GATTTGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (19 bp):
AACCCTCAATTTCTGATTC
Found at i:60425 original size:31 final size:32
Alignment explanation
Indices: 60359--60437 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
60349 CTTAATCAAT
* *
60359 CAATCGGTTCGATTT-TAATTCTCAGATCGAT
1 CAATCGGTTCGATTTAAAATTCTCAGATCGAC
*
60390 CAATCGGTTCGATTTAAAATT-TTA-ATTCGAC
1 CAATCGGTTCGATTTAAAATTCTCAGA-TCGAC
* *
60421 CAATCGATTCGGTTTAA
1 CAATCGGTTCGATTTAA
60438 TTCGACCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 36 0.88
32 4 0.10
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
CAATCGGTTCGATTTAAAATTCTCAGATCGAC
Found at i:60438 original size:23 final size:24
Alignment explanation
Indices: 60410--60467 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
60400 GATTTAAAAT
60410 TTTAATTCGACCAA-TCGATTCGG
1 TTTAATTCGACCAATTCGATTCGG
*
60433 TTTAATTCGACCAATTCGGTTCGG
1 TTTAATTCGACCAATTCGATTCGG
*
60457 TGTAATTCGAC
1 TTTAATTCGAC
60468 GGTGGGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (24 bp):
TTTAATTCGACCAATTCGATTCGG
Found at i:63511 original size:34 final size:34
Alignment explanation
Indices: 63469--63551 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
63459 ATATGCAACA
63469 ATATATATAAATATATGAATTAAGATTCACTTAT
1 ATATATATAAATATATGAATTAAGATTCACTTAT
63503 ATATATATAAATATATGAATTAAGATTCACTTAT
1 ATATATATAAATATATGAATTAAGATTCACTTAT
*
63537 ATATATATATATATA
1 ATATATATAAATATA
63552 ACAATTGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATATATAAATATATGAATTAAGATTCACTTAT
Found at i:64632 original size:6 final size:6
Alignment explanation
Indices: 64621--64655 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
64611 AACAACTCCC
*
64621 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT TCTTC
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTC
64656 CCTCTATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CCTTCT
Found at i:66183 original size:24 final size:24
Alignment explanation
Indices: 66155--66209 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
66145 AACGGGGGAA
66155 TGAGATTCCATTCCCCCGGTAATG
1 TGAGATTCCATTCCCCCGGTAATG
66179 TGAGATTCCATTCCCCCGGTAATG
1 TGAGATTCCATTCCCCCGGTAATG
66203 TGAGATT
1 TGAGATT
66210 ACCAGTAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
TGAGATTCCATTCCCCCGGTAATG
Found at i:66799 original size:654 final size:655
Alignment explanation
Indices: 65550--66839 Score: 2248
Period size: 654 Copynumber: 2.0 Consensus size: 655
65540 ACTGAATATA
* * *
65550 AGATTACCAATGGGAATAGGATTACCGACGAGAATAAGATTACTCAGAATGTTGTATTTTGTGTT
1 AGATTACCAATAGGAATAAGATTACCGACGAGAAAAAGATTACTCAGAATGTTGTATTTTGTGTT
* * * *
65615 TGGTTTGTTTAGCATGAATGTAAGATTACAGTGTTTGGTTAAAAGAATAAAAAATTATTAGAATT
66 TGGTTCGTTTAGCAGGAATGTAAGATTACAATGTTTGGTTAAAAGAATAAAAAATTATTAGAATG
* *
65680 TATATTTTATCGAATTGTCCTTATTATATATTTATTTTTTTTAACAAGTAGAATTCTACTATAAT
131 TATATTTTACCAAATTGTCCTTATTATATATTTATTTTTTTTAACAAGTAGAATTCTACTATAAT
65745 ATTACTATAATTAATTTATATATTTTCTTTAAAAATTTTAGATTCATAAAATTTATATAACATTT
196 ATTACTATAATTAATTTATATATTTTCTTTAAAAATTTTAGATTCATAAAATTTATATAACATTT
*
65810 TTTTACAAAATTGAAAAGATAAATAGGTTTAATGAAAGGGTAAAATTTAATTTTAACCCTTGAAC
261 TTTTACAAAATTGAAAAGATAAATAGGTTTAATGAAAGGGGAAAATTTAATTTTAACCCTTGAAC
*
65875 TTAATATAAAATTCTAATTATGGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTA
326 TTAATATAAAATTCTAATTATGAATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTA
*
65940 ATTTAATATTCGTAGAATATTTTTTAATCAACGACAGAGTAAGGATACTTTTGAAAGAATTTTTT
391 ATTTAATATTCGTAGAATATTTTTTAATCAACGACAGAATAAGGATACTTTTGAAAGAATTTTTT
66005 TTTAAGAGCATTTTAGTCCAAAACGTAGGTAATCCAACAATACCTAAGAGAAGAGATGTATTAAC
456 TTTAAGAGCATTTTAGTCCAAAACGTAGGTAATCCAACAATACCTAAGAGAAGAGATGTATTAAC
66070 ATTCCCAGTCATATACCCCAAAATACCACTGTTAGGAAAAAAATATTACCGGAGGTTGGGAATGT
521 ATTCCCAGTCATATACCCCAAAATACCACTGTTAGGAAAAAAATATTACCGGAGGTTGGGAATGT
**
66135 TGGCCAACCAAACGGGGGAATGAGATTCCATTCCCCCGG-TAATGTGAGATTCCATTCCCCCGGT
586 TGGCCAACCAAACGGAAGAATGAGATTCCATT-CCCCGGATAATGTGAGATTCCATTCCCCCGGT
66199 AATGTG
650 AATGTG
* * **
66205 AGATTACCAGTAGGAATAAGATTATCGACGAGAAAAAGATTACTGGGAATGTTGTATTTTGTGTT
1 AGATTACCAATAGGAATAAGATTACCGACGAGAAAAAGATTACTCAGAATGTTGTATTTTGTGTT
* * *
66270 TGGTTCGTTTAGTAGGAATGTAAGATTACAATGTTTGGTTAAAGGAATAAAAGATTATTAGAATG
66 TGGTTCGTTTAGCAGGAATGTAAGATTACAATGTTTGGTTAAAAGAATAAAAAATTATTAGAATG
66335 TATATTTTACCAAATTGTCCTTATTATATATTTA-TTTTTTTAACAAGTAGAATTCTACTATAAT
131 TATATTTTACCAAATTGTCCTTATTATATATTTATTTTTTTTAACAAGTAGAATTCTACTATAAT
* *
66399 ATTATTATAATTAATTTATATATTTTCTTTAAAAATTTTAGATTCATAAAATTTATATAA-TTTT
196 ATTACTATAATTAATTTATATATTTTCTTTAAAAATTTTAGATTCATAAAATTTATATAACATTT
* *
66463 TTTTACAAAATTGAAAAGATAAATAGGTTTAATGAACGGGGAAAATTTTATTTTAAACCC-TGAA
261 TTTTACAAAATTGAAAAGATAAATAGGTTTAATGAAAGGGGAAAATTTAATTTT-AACCCTTGAA
66527 CTTAATATAAAATTCTAATTATGAACTTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTG
325 CTTAATATAAAATTCTAATTATGAA-TTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTG
* *
66592 TAATTTAATATTCGTAGAATATTTTTTATTCAACGACAGAATAAGGATATTTTTGAAAGAA-TTT
389 TAATTTAATATTCGTAGAATATTTTTTAATCAACGACAGAATAAGGATACTTTTGAAAGAATTTT
*
66656 TTTTTAAGAGCATTTTAGTCCAAAACGTAGGTAATCCAACAATACCTAAGAGAATAGATGTATTA
454 TTTTTAAGAGCATTTTAGTCCAAAACGTAGGTAATCCAACAATACCTAAGAGAAGAGATGTATTA
66721 ACATTCCCAGTCATATACCCTCAAAATACCACTGTTAGGAAAAAAATATTACCGGAGGTTGGGAA
519 ACATTCCCAGTCATATACCC-CAAAATACCACTGTTAGGAAAAAAATATTACCGGAGGTTGGGAA
*
66786 TGTTGGCCAACCAAACGGAAGAATGAGATTCCATTCCCGGGATAATGTGAGATT
583 TGTTGGCCAACCAAACGGAAGAATGAGATTCCATTCCCCGGATAATGTGAGATT
66840 ACTCCAACCA
Statistics
Matches: 602, Mismatches: 29, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
653 174 0.29
654 280 0.47
655 148 0.25
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (655 bp):
AGATTACCAATAGGAATAAGATTACCGACGAGAAAAAGATTACTCAGAATGTTGTATTTTGTGTT
TGGTTCGTTTAGCAGGAATGTAAGATTACAATGTTTGGTTAAAAGAATAAAAAATTATTAGAATG
TATATTTTACCAAATTGTCCTTATTATATATTTATTTTTTTTAACAAGTAGAATTCTACTATAAT
ATTACTATAATTAATTTATATATTTTCTTTAAAAATTTTAGATTCATAAAATTTATATAACATTT
TTTTACAAAATTGAAAAGATAAATAGGTTTAATGAAAGGGGAAAATTTAATTTTAACCCTTGAAC
TTAATATAAAATTCTAATTATGAATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTA
ATTTAATATTCGTAGAATATTTTTTAATCAACGACAGAATAAGGATACTTTTGAAAGAATTTTTT
TTTAAGAGCATTTTAGTCCAAAACGTAGGTAATCCAACAATACCTAAGAGAAGAGATGTATTAAC
ATTCCCAGTCATATACCCCAAAATACCACTGTTAGGAAAAAAATATTACCGGAGGTTGGGAATGT
TGGCCAACCAAACGGAAGAATGAGATTCCATTCCCCGGATAATGTGAGATTCCATTCCCCCGGTA
ATGTG
Found at i:70524 original size:21 final size:20
Alignment explanation
Indices: 70490--70528 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
70480 AGGGGCCTCG
*
70490 GTATCAATATTGCCACCCTAA
1 GTATCAATACTGCC-CCCTAA
*
70511 GTATCGATACTGCCCCCT
1 GTATCAATACTGCCCCCT
70529 CCATGACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCAATACTGCCCCCTAA
Found at i:70697 original size:21 final size:20
Alignment explanation
Indices: 70671--70709 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
70661 CAACCATTTT
70671 AATAAAACAAATACAAAATAA
1 AATAAAACAAATA-AAAATAA
*
70692 AATAAAATAAATAAAAAT
1 AATAAAACAAATAAAAAT
70710 GCTACACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AATAAAACAAATAAAAATAA
Found at i:75470 original size:21 final size:21
Alignment explanation
Indices: 75430--75471 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
75420 TAGCATTCTG
**
75430 GAGCCCCTTGGTCTTGATACC
1 GAGCCCCTTGGTCTCAATACC
75451 GAGCCCCTTGGTCTCAATACC
1 GAGCCCCTTGGTCTCAATACC
75472 AGACCCTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.36, G:0.21, T:0.26
Consensus pattern (21 bp):
GAGCCCCTTGGTCTCAATACC
Found at i:82599 original size:17 final size:17
Alignment explanation
Indices: 82555--82609 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
82545 GAATGGACTC
* *
82555 GACTTGAGCTAAAGCTC
1 GACTTGAGCTCAAGCTT
82572 GACTTGAGCTCAAGCTT
1 GACTTGAGCTCAAGCTT
*
82589 GACTTGAGCTCGAGCTT
1 GACTTGAGCTCAAGCTT
82606 GACT
1 GACT
82610 CAAGTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (17 bp):
GACTTGAGCTCAAGCTT
Found at i:92749 original size:2 final size:2
Alignment explanation
Indices: 92742--92768 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92732 TTATTATACC
92742 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
92769 CCTAAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:95585 original size:37 final size:36
Alignment explanation
Indices: 95507--95581 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 36
95497 GTTTAGGGTT
95507 TATAATTAATATAAAATATATAAAATATTATATATA
1 TATAATTAATATAAAATATATAAAATATTATATATA
*
95543 TATAATTAATATAAAA-ATATATAATATTATATATA
1 TATAATTAATATAAAATATATAAAATATTATATATA
95578 TATA
1 TATA
95582 TAATCAGGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
TATAATTAATATAAAATATATAAAATATTATATATA
Found at i:99028 original size:15 final size:15
Alignment explanation
Indices: 99010--99039 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
99000 TTTATTTTTC
*
99010 ATATTTTTTGAATTA
1 ATATTTTTTAAATTA
99025 ATATTTTTTAAATTA
1 ATATTTTTTAAATTA
99040 TTTATTAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATATTTTTTAAATTA
Found at i:102643 original size:87 final size:87
Alignment explanation
Indices: 102547--102722 Score: 318
Period size: 87 Copynumber: 2.0 Consensus size: 87
102537 ATAGTTTTTA
102547 GTGTTTTAATTAAGATTTAAGATGTTAATTTAGGAATTATCTTTAGCTTGTTTTTAGGAATTTAA
1 GTGTTTTAATTAAGATTTAAGATGTTAATTTAGGAATTATCTTTAGCTTGTTTTTAGGAATTTAA
102612 GGGCTATAAATACCCTT-TCAGG
66 GGGCTATAAATA-CCTTCTCAGG
* *
102634 GTGTTTTAATTAGGATTTAAGATGTTATTTTAGGAATTATCTTTAGCTTGTTTTTAGGAATTTAA
1 GTGTTTTAATTAAGATTTAAGATGTTAATTTAGGAATTATCTTTAGCTTGTTTTTAGGAATTTAA
102699 GGGCTATAAATACCTTCTCAGG
66 GGGCTATAAATACCTTCTCAGG
102721 GT
1 GT
102723 AAGCCTATAA
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
86 4 0.05
87 82 0.95
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (87 bp):
GTGTTTTAATTAAGATTTAAGATGTTAATTTAGGAATTATCTTTAGCTTGTTTTTAGGAATTTAA
GGGCTATAAATACCTTCTCAGG
Found at i:103032 original size:21 final size:21
Alignment explanation
Indices: 103003--103055 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
102993 ATTCTGACTA
103003 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
103024 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
103045 TCGCAATGCGA
1 TCGCATTGCGA
103056 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:103087 original size:20 final size:20
Alignment explanation
Indices: 103072--103131 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
103062 AAATCGAAAT
103072 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
103092 GAGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
103112 GCGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAC
103132 ACTGAATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:103991 original size:24 final size:24
Alignment explanation
Indices: 103959--104012 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
103949 GTATTTGAAA
103959 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
103983 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
104007 TTTGAT
1 TTTGAT
104013 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:106274 original size:12 final size:12
Alignment explanation
Indices: 106259--106289 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
106249 CAAGAAAAAG
106259 GCAATCAAAATC
1 GCAATCAAAATC
106271 GCAATCAAAATC
1 GCAATCAAAATC
*
106283 CCAATCA
1 GCAATCA
106290 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:106601 original size:140 final size:140
Alignment explanation
Indices: 106349--106618 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
106339 AAACGTTGTA
*
106349 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
* *
106414 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
106479 TATTTGTATT
131 TATTTGTATT
106489 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
106554 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
106619 CACAACGCGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATTTGTATT
Found at i:106614 original size:20 final size:20
Alignment explanation
Indices: 106589--106827 Score: 145
Period size: 20 Copynumber: 12.8 Consensus size: 20
106579 TTACACATTC
*
106589 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
106609 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
106629 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
106648 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
106663 ATTTGACTATCTCAACACGA
1 ATTTGACTATCGCAACGCGA
*
106683 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
106702 A----A-AACCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
106717 ATTTGTCTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
106737 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGA
*
106757 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* * *
106777 A----A--ATCACAACACAA
1 ATTTGACTATCGCAACGCGA
* * *
106791 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
106811 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
106828 AGAAAATCGC
Statistics
Matches: 162, Mismatches: 39, Indels: 36
0.68 0.16 0.15
Matches are distributed among these distances:
14 27 0.17
15 6 0.04
16 1 0.01
18 1 0.01
19 5 0.03
20 122 0.75
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:106684 original size:54 final size:54
Alignment explanation
Indices: 106597--106751 Score: 231
Period size: 54 Copynumber: 2.9 Consensus size: 54
106587 TCATTTGAAT
* *
106597 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCTCAACGCGAATTTGATTATCGCAACGCAAAA
* * *
106651 ATCGCAACGCGAATTTGACTATCTCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCTCAACGCGAATTTGATTATCGCAACGCAAAA
* *
106705 ACCGCAACGCGAATTTGTCTATCGT-AACGCGAATTTGATTATCGCAA
1 ATCGCAACGCGAATTTGACTATC-TCAACGCGAATTTGATTATCGCAA
106752 TGGGTATTTG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 89 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCTCAACGCGAATTTGATTATCGCAACGCAAAA
Found at i:106734 original size:74 final size:74
Alignment explanation
Indices: 106651--106826 Score: 194
Period size: 74 Copynumber: 2.4 Consensus size: 74
106641 CAACTCAAAA
* * *
106651 ATCGCAACGCGAATTTGACTATCTCAACACGAATATGACTATCGCAACGCA-AAAACCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACG-AGAAAACCACAACAC
*
106715 GAATTTG-TCT
65 AAATTTGAT-T
* * *** * * *
106725 ATCGTAACGCGAATTTGATTATCGCAATGGGTATTTGACTATCGCAACGAGAAAATCACAACACA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGAGAAAACCACAACACA
106790 AATTTGATT
66 AATTTGATT
* *
106799 ATCGCAACGGGTATTTGACTATCGCAAC
1 ATCGCAACGCGAATTTGACTATCGCAAC
106827 GAGAAAATCG
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
73 1 0.01
74 81 0.98
75 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGAGAAAACCACAACACA
AATTTGATT
Found at i:106856 original size:54 final size:54
Alignment explanation
Indices: 106744--106876 Score: 171
Period size: 54 Copynumber: 2.5 Consensus size: 54
106734 CGAATTTGAT
* * *
106744 TATCGCAATGGGTATTTGACTATCGCAACGAGAAAATCACAACACAAATTTGAT
1 TATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCACAACACAAATTAGAC
* **
106798 TATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAA-AGCGTATTAGAC
1 TATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCACAACA-CAAATTAGAC
* *
106852 TATCGCAACGGG-AATTGACTTTCGC
1 TATCGCAACGGGTATTTGACTATCGC
106877 GTTGCGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
53 12 0.17
54 58 0.83
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (54 bp):
TATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCACAACACAAATTAGAC
Found at i:107082 original size:14 final size:14
Alignment explanation
Indices: 107022--107083 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
107012 CACAAATAAG
*
107022 AATTATTTACACATC
1 AATT-TTTACAAATC
**
107037 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
107052 AACTTTTACAAATC
1 AATTTTTACAAATC
*
107066 AATTTTTATAAATC
1 AATTTTTACAAATC
107080 AATT
1 AATT
107084 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:107938 original size:20 final size:20
Alignment explanation
Indices: 107913--107990 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
107903 TCGCTTTGAA
107913 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
* *
107933 AATCGCGTTGCGACAGTCAT
1 AATCGCATTGCGATAGTCAT
* *
107953 AATCGTATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAT
*
107973 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
107991 GAAAAATCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:108752 original size:15 final size:16
Alignment explanation
Indices: 108722--108755 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
108712 CCATTTTGTC
108722 TTTATTACTGTTATTA
1 TTTATTACTGTTATTA
*
108738 TTTATTA-TTTTATTA
1 TTTATTACTGTTATTA
108753 TTT
1 TTT
108756 TTCTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTATTACTGTTATTA
Found at i:108764 original size:20 final size:21
Alignment explanation
Indices: 108739--108792 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
108729 CTGTTATTAT
*
108739 TTATTATTTTATTATT-TTTC
1 TTATTATTTTATTATTATTTA
** *
108759 TTATTAAATTATAATTATTTA
1 TTATTATTTTATTATTATTTA
108780 TT-TTATTTTATTA
1 TTATTATTTTATTA
108793 CATCTTTTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTATTTTATTATTATTTA
Found at i:110265 original size:21 final size:21
Alignment explanation
Indices: 110241--110297 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
110231 AAAAGTTTAC
*
110241 TACGTCCCAAGAAAAGCTGGT
1 TACGTCCCAAGAAAAGCTAGT
110262 TACGT-CCAAGGAAAAGCTAGT
1 TACGTCCCAA-GAAAAGCTAGT
* * *
110283 TGCATCCCAGGAAAA
1 TACGTCCCAAGAAAA
110298 ATTCTAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (21 bp):
TACGTCCCAAGAAAAGCTAGT
Found at i:112059 original size:27 final size:28
Alignment explanation
Indices: 112000--112063 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
111990 GTTAGGACAC
* *
112000 TGCAGAAAAACTGATTTGGTTCGAACAG
1 TGCAGAAAAACAGACTTGGTTCGAACAG
*
112028 AGCAGAAAAA-AGACTTGGTTCGAACTA-
1 TGCAGAAAAACAGACTTGGTTCGAAC-AG
112055 TGCAGAAAA
1 TGCAGAAAA
112064 GTTAGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (28 bp):
TGCAGAAAAACAGACTTGGTTCGAACAG
Found at i:114277 original size:86 final size:86
Alignment explanation
Indices: 114135--114295 Score: 202
Period size: 86 Copynumber: 1.9 Consensus size: 86
114125 TTAAACATTA
*
114135 TATTTTATCTTTGTTTTATATATTTTAGTTTAAATATATGTTAGAATTTCAATTAGGATTT-AGT
1 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATATATGTTAGAATTTCAATTAGGATTTAAG-
114199 ATATTATTTTAAATAGTATTTT
65 ATATTATTTTAAATAGTATTTT
* * ** * *
114221 TATTTTATCTTTGTTTTAGGTATTTTAGTTTGAATAGT-T-TTAAGTGTTTTATTTAGGATTTAA
1 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATA-TATGTT-AGAATTTCAATTAGGATTTAA
*
114284 GATGTTATTTTA
64 GATATTATTTTA
114296 GGAATGATCT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 2 0.03
86 59 0.92
87 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (86 bp):
TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATATATGTTAGAATTTCAATTAGGATTTAAGA
TATTATTTTAAATAGTATTTT
Found at i:114284 original size:20 final size:20
Alignment explanation
Indices: 114259--114298 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
114249 TTTGAATAGT
*
114259 TTTAAG-TGTTTTATTTAGGA
1 TTTAAGATGTTAT-TTTAGGA
114279 TTTAAGATGTTATTTTAGGA
1 TTTAAGATGTTATTTTAGGA
114299 ATGATCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTAAGATGTTATTTTAGGA
Found at i:115789 original size:18 final size:18
Alignment explanation
Indices: 115766--115803 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
115756 AATTATTACT
115766 CTGATTTTAAATTGGTTC
1 CTGATTTTAAATTGGTTC
115784 CTGATTTTAAATTGGTTC
1 CTGATTTTAAATTGGTTC
115802 CT
1 CT
115804 AAACTTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (18 bp):
CTGATTTTAAATTGGTTC
Found at i:118057 original size:110 final size:110
Alignment explanation
Indices: 117890--118094 Score: 261
Period size: 110 Copynumber: 1.9 Consensus size: 110
117880 AAATTGAATC
* * * * * * *
117890 TCTATTAATTGTTGACCTAGAAGTTATAAAAAGATAAAATAATTTTTTAGTCCTCTATGTTTATA
1 TCTATTAATTATTGACATAGAAGTTATAAAAAGATAAAATAACTTTTTAATCATCTATATTTACA
* *
117955 ATTTTATCAATTTGATCACTAAAA-GTTATTAATTTAATCTAGAG
66 ATTTTATCAATATGACCACTAAAATGTTATTAATTTAATCTAGAG
*
117999 TCTATTAATTATTGATATAGAAGTTAT-AAAAGAATTAAAATAACTTTTTAATCATCTATATTTA
1 TCTATTAATTATTGACATAGAAGTTATAAAAAG-A-TAAAATAACTTTTTAATCATCTATATTTA
* * *
118063 CATTTTTATTAATATGACCATTAAAATGTTAT
64 CAATTTTATCAATATGACCACTAAAATGTTAT
118095 CAATGTAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
108 5 0.06
109 25 0.31
110 45 0.56
111 5 0.06
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (110 bp):
TCTATTAATTATTGACATAGAAGTTATAAAAAGATAAAATAACTTTTTAATCATCTATATTTACA
ATTTTATCAATATGACCACTAAAATGTTATTAATTTAATCTAGAG
Found at i:122030 original size:30 final size:31
Alignment explanation
Indices: 121988--122083 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
121978 ATTTTTAATG
* * *
121988 TAACCTTTGAACTTTAGATATAATATTATTT
1 TAACCATTGAACTTTAGATAAAATATCATTT
**
122019 TAACC-TTGAACTTTAGATGCAATATCATTT
1 TAACCATTGAACTTTAGATAAAATATCATTT
* * *
122049 TAACCATTAAACTTGAGATAAAATATCAATT
1 TAACCATTGAACTTTAGATAAAATATCATTT
122080 TAAC
1 TAAC
122084 ACTAGAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 27 0.48
31 29 0.52
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (31 bp):
TAACCATTGAACTTTAGATAAAATATCATTT
Found at i:123275 original size:2 final size:2
Alignment explanation
Indices: 123268--123320 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
123258 GGTTAAAAGA
123268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123310 AT AT AT AT AT A
1 AT AT AT AT AT A
123321 GAATCTATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:130175 original size:2 final size:2
Alignment explanation
Indices: 130168--130242 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
130158 ACATACATAC
130168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
130210 AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
130243 GCATGTATAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131048 original size:19 final size:19
Alignment explanation
Indices: 131024--131075 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
131014 AGCATATGAT
131024 TAACAGCTCAACAAACGAC
1 TAACAGCTCAACAAACGAC
131043 TAACAGCTCAACAAACGAC
1 TAACAGCTCAACAAACGAC
131062 TAACAGCTCAACAA
1 TAACAGCTCAACAA
131076 CTTAACTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.48, C:0.31, G:0.10, T:0.12
Consensus pattern (19 bp):
TAACAGCTCAACAAACGAC
Found at i:136239 original size:29 final size:30
Alignment explanation
Indices: 136206--136266 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
136196 AATGGAGCAT
136206 CACGT-GGAGCATCACGCATGGATGAAGAG
1 CACGTGGGAGCATCACGCATGGATGAAGAG
* * * *
136235 CACGTGGGAGCATTACGCGTTGATGGAGAG
1 CACGTGGGAGCATCACGCATGGATGAAGAG
136265 CA
1 CA
136267 GATAGGACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.28, C:0.20, G:0.36, T:0.16
Consensus pattern (30 bp):
CACGTGGGAGCATCACGCATGGATGAAGAG
Found at i:139664 original size:16 final size:16
Alignment explanation
Indices: 139643--139673 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
139633 ACAAGCTAAC
139643 AAACTATTCTAGAACA
1 AAACTATTCTAGAACA
139659 AAACTATTCTAGAAC
1 AAACTATTCTAGAAC
139674 TCACAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (16 bp):
AAACTATTCTAGAACA
Done.