Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000107.1 Hibiscus syriacus cultivar Beakdansim tig00000191_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: 91607
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1880 original size:21 final size:21
Alignment explanation
Indices: 1854--1893 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1844 TCCCCTTTGA
*
1854 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1875 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1894 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3842 original size:15 final size:15
Alignment explanation
Indices: 3805--3843 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3795 ATTTTGAATA
* *
3805 TTTGGAATGTTTGAT
1 TTTGGATTGTTGGAT
3820 TTTGGGATTGTTGGAT
1 TTT-GGATTGTTGGAT
3836 TTTGGATT
1 TTTGGATT
3844 TATGGATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (15 bp):
TTTGGATTGTTGGAT
Found at i:8818 original size:47 final size:49
Alignment explanation
Indices: 8718--8827 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 49
8708 GATAATCACC
*
8718 GCAATTATTCGTATGTGTATGTTCTTGTTTTTTTTTTCTTTTTCTAAGTAT
1 GCAATTATTCGTATGTGTATATTCTTG--TTTTTTTTCTTTTTCTAAGTAT
*
8769 GCAATTATTCGTATGTGTCTATTCTTG-TTTTTTTC-TTTTCTAAGTAT
1 GCAATTATTCGTATGTGTATATTCTTGTTTTTTTTCTTTTTCTAAGTAT
*
8816 GCATTTATTCGT
1 GCAATTATTCGT
8828 GCGTATTGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 23 0.41
48 8 0.14
51 25 0.45
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (49 bp):
GCAATTATTCGTATGTGTATATTCTTGTTTTTTTTCTTTTTCTAAGTAT
Found at i:14901 original size:67 final size:69
Alignment explanation
Indices: 14793--14922 Score: 228
Period size: 67 Copynumber: 1.9 Consensus size: 69
14783 CTTATTGTAT
14793 ACTAAATAATTTTTATTTATGAAATTTCTTATCAATTTTATTATTTTATA-TTATATAACTCAGA
1 ACTAAATAATTTTTATTTATGAAATTTCTTATCAATTTTATTATTTTATATTTATATAACTCAGA
14857 GTAA
66 GTAA
* *
14861 ACTATATAA-TTTTATTTATGAAATTTCTTATCAATTTTATTATTTTATATTTGTATAACTCA
1 ACTAAATAATTTTTATTTATGAAATTTCTTATCAATTTTATTATTTTATATTTATATAACTCA
14923 CATTTCAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 40 0.68
68 19 0.32
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (69 bp):
ACTAAATAATTTTTATTTATGAAATTTCTTATCAATTTTATTATTTTATATTTATATAACTCAGA
GTAA
Found at i:14908 original size:33 final size:33
Alignment explanation
Indices: 14803--14908 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
14793 ACTAAATAAT
14803 TTTTATTTATGAAATTTCTTATCAATTTTATTA
1 TTTTATTTATGAAATTTCTTATCAATTTTATTA
* ** * * * *
14836 TTTTATATTAT-ATAA-CTCAGAGTAAACTATATAA
1 TTTTAT-TTATGA-AATTTCTTA-TCAATTTTATTA
14870 TTTTATTTATGAAATTTCTTATCAATTTTATTA
1 TTTTATTTATGAAATTTCTTATCAATTTTATTA
14903 TTTTAT
1 TTTTAT
14909 ATTTGTATAA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (33 bp):
TTTTATTTATGAAATTTCTTATCAATTTTATTA
Found at i:14978 original size:19 final size:17
Alignment explanation
Indices: 14937--14979 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
14927 TCAATTTATG
14937 TAATATTTTTTTAATAA
1 TAATATTTTTTTAATAA
* *
14954 TTATATTTTAATTTAATTA
1 TAATATTTT--TTTAATAA
14973 TAATATT
1 TAATATT
14980 ATTTGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATATTTTTTTAATAA
Found at i:24466 original size:13 final size:13
Alignment explanation
Indices: 24448--24481 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
24438 AATTATAGTA
*
24448 TAATTAATTAACT
1 TAATTAATTAAAT
*
24461 TAATTATTTAAAT
1 TAATTAATTAAAT
24474 TAATTAAT
1 TAATTAAT
24482 GATGAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTAATTAAAT
Found at i:24493 original size:17 final size:15
Alignment explanation
Indices: 24460--24505 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
24450 ATTAATTAAC
*
24460 TTAATTAT-TTAAA-
1 TTAATTATGTGAAAT
24473 TTAATTAATGATGAAAT
1 TTAATT-ATG-TGAAAT
24490 TTAATTATGTGAAAT
1 TTAATTATGTGAAAT
24505 T
1 T
24506 AAGGTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 7 0.25
16 7 0.25
17 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (15 bp):
TTAATTATGTGAAAT
Found at i:25580 original size:54 final size:54
Alignment explanation
Indices: 25516--25637 Score: 183
Period size: 54 Copynumber: 2.3 Consensus size: 54
25506 TGGGGCTTTG
* *
25516 GTTGGGGGCTTATACGGGGGAGTTGGAGCTTTGGTTGGTGGTGCTGGTGCA-GTA
1 GTTGGGGGCTTATACGGGGGAGTTGGAGCTTTGGTTGGGGGTGCTGGTG-ATGGA
* *
25570 GTTGGGGGCTTATACGGGGGGGTTGGGGCTTTGGTTGGGGGTGCTGGTGATGGA
1 GTTGGGGGCTTATACGGGGGAGTTGGAGCTTTGGTTGGGGGTGCTGGTGATGGA
*
25624 GGTGGGGGCTTATA
1 GTTGGGGGCTTATA
25638 TTGTGGAGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 1 0.02
54 61 0.98
ACGTcount: A:0.10, C:0.08, G:0.52, T:0.30
Consensus pattern (54 bp):
GTTGGGGGCTTATACGGGGGAGTTGGAGCTTTGGTTGGGGGTGCTGGTGATGGA
Found at i:25649 original size:54 final size:54
Alignment explanation
Indices: 25518--25651 Score: 180
Period size: 54 Copynumber: 2.5 Consensus size: 54
25508 GGGCTTTGGT
* * * *
25518 TGGGGGCTTATACGGGGGAGTTGGAGCTTTGGTTGGTGGTGCTGGTGCAGTAGT
1 TGGGGGCTTATACGGGGGAGTTGGGGCTTTGGTTGGGGGTGCTGGTGCAGGAGG
*
25572 TGGGGGCTTATACGGGGGGGTTGGGGCTTTGGTTGGGGGTGCTGGTG-ATGGAGG
1 TGGGGGCTTATACGGGGGAGTTGGGGCTTTGGTTGGGGGTGCTGGTGCA-GGAGG
** *
25626 TGGGGGCTTATATTGTGGAGTTGGGG
1 TGGGGGCTTATACGGGGGAGTTGGGG
25652 GTGCTGGTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 69 0.99
ACGTcount: A:0.10, C:0.07, G:0.52, T:0.31
Consensus pattern (54 bp):
TGGGGGCTTATACGGGGGAGTTGGGGCTTTGGTTGGGGGTGCTGGTGCAGGAGG
Found at i:25688 original size:42 final size:42
Alignment explanation
Indices: 25603--25688 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
25593 TGGGGCTTTG
* * *
25603 GTTGGGGGTGCTGGTGATGGAGGTGGGGGCTTATATTGTGGA
1 GTTGGGGGTGCTGGTGATGGAGATGGGGGCTTATATGGGGGA
25645 GTTGGGGGTGCTGGTGGA-GGAGATGGGGGCTTATATGGGGGA
1 GTTGGGGGTGCTGGT-GATGGAGATGGGGGCTTATATGGGGGA
25687 GT
1 GT
25689 AGTAGCCTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.13, C:0.05, G:0.55, T:0.28
Consensus pattern (42 bp):
GTTGGGGGTGCTGGTGATGGAGATGGGGGCTTATATGGGGGA
Found at i:31902 original size:161 final size:161
Alignment explanation
Indices: 31637--31958 Score: 635
Period size: 161 Copynumber: 2.0 Consensus size: 161
31627 TCTCAGTTTA
31637 GTGGGTCTCATGTGGGCCATTTATTTCAATGTATTTAATGACACTCGTTATGTCGAGGAGGTGAG
1 GTGGGTCTCATGTGGGCCATTTATTTCAATGTATTTAATGACACTCGTTATGTCGAGGAGGTGAG
31702 TCCCTTAAAAAATTATTATTTTTAAATAATTTGTAAAATTAATAAAATAATAAAAATAAAACGCG
66 TCCCTTAAAAAATTATTATTTTTAAATAATTTGTAAAATTAATAAAATAATAAAAATAAAACGCG
31767 AAAGAACTCGTCACCTCGAGGTGACTAGTCT
131 AAAGAACTCGTCACCTCGAGGTGACTAGTCT
*
31798 GTGGGTCTCATGTGGGCCATTTATTTCAATGTATTTAATGACACTCGTTATGTCGAGGAGGTGGG
1 GTGGGTCTCATGTGGGCCATTTATTTCAATGTATTTAATGACACTCGTTATGTCGAGGAGGTGAG
31863 TCCCTTAAAAAATTATTATTTTTAAATAATTTGTAAAATTAATAAAATAATAAAAATAAAACGCG
66 TCCCTTAAAAAATTATTATTTTTAAATAATTTGTAAAATTAATAAAATAATAAAAATAAAACGCG
31928 AAAGAACTCGTCACCTCGAGGTGACTAGTCT
131 AAAGAACTCGTCACCTCGAGGTGACTAGTCT
31959 CCCTTGAATT
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (161 bp):
GTGGGTCTCATGTGGGCCATTTATTTCAATGTATTTAATGACACTCGTTATGTCGAGGAGGTGAG
TCCCTTAAAAAATTATTATTTTTAAATAATTTGTAAAATTAATAAAATAATAAAAATAAAACGCG
AAAGAACTCGTCACCTCGAGGTGACTAGTCT
Found at i:32531 original size:3 final size:3
Alignment explanation
Indices: 32523--32564 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
32513 GTTCACATAC
* * *
32523 GTT GTT GTT GTT GTT GTT ATT ATT ATT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
32565 TATTTCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:35504 original size:15 final size:15
Alignment explanation
Indices: 35469--35506 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
35459 TCAGAATATT
* *
35469 TTATCATATTTTTTA
1 TTATAATATTTTTAA
35484 TT-TAATATTTTTAA
1 TTATAATATTTTTAA
35498 TTATAATAT
1 TTATAATAT
35507 CATTTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATAATATTTTTAA
Found at i:38502 original size:3 final size:3
Alignment explanation
Indices: 38479--38535 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
38469 TTGGGCTTTG
*
38479 TAA TAT TAA TAAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38524 TAA TAA TAA TAA
1 TAA TAA TAA TAA
38536 AATGGGTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:38945 original size:113 final size:113
Alignment explanation
Indices: 38761--39913 Score: 1331
Period size: 113 Copynumber: 10.0 Consensus size: 113
38751 TAGAGTCATT
* ** * *
38761 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACCTT-TTCTTTCTTTTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**** * *
38825 ATTATGAACTTTCTCTGGAAAGGTTGATCCATCAAGTGATGGATTTGAG
65 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
38874 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
38939 TTATGAACTCGAACGGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
38987 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
39052 TTATGAACTCGAACGGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
39100 CAAAAGGTTGAACAAATTCTTCTCATTA-GAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
39163 TTATGAACTCGAACGGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
39211 CAAAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
39276 TTATGAACTCGAACTGCAAAAGCTGATCCATTAAGTGATGGATTTAAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
39324 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
39389 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
39437 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * *** ** *
39502 TTATGAACTTTCTCTGAAAATTGATGCTGATCTATCTCCTTCTGGCAATGTTGAT
66 TTATGAACTCGAACTGGAAA---A-GCTGATCCATCAAGTGATGG--AT-TTGAG
* ** ** ** *** ** *** *
39557 CCATCGAATG-ATGAATTC-AAGCAAAAGGTTGAACAAATTCTT-C-TCATT-ATGAACTTA-TT
1 CAAAAGGTTGAACAAATTCTTCTCATTA---TGAACTTCTTCTTCCTTC-TTCA-G-A-TGAGTT
* ** * * * *
39616 CTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTCGAA-CTGGAAAAGCTGATCCATCAAGT
59 CTT-C-TCATT---ATGA--AC-TCGAACT-GGAA----AAGCT-G---ATC-CA----TCAAGT
39679 GATGGATTTGAG
102 GATGGATTTGAG
39691 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
39756 TTATAAACTCGAACTGCAAAAGCTGATCCATTAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
39804 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
39869 TTGTGAACTCGAACTGGAAATGCTGATCCATTGAA-TGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTGATCCA-TCAAGTGATGGATTT
39914 AAATCTTTGC
Statistics
Matches: 894, Mismatches: 98, Indels: 96
0.82 0.09 0.09
Matches are distributed among these distances:
111 98 0.11
112 27 0.03
113 608 0.68
114 3 0.00
116 1 0.00
117 15 0.02
118 5 0.01
119 11 0.01
120 13 0.01
121 19 0.02
122 7 0.01
123 2 0.00
125 6 0.01
126 4 0.00
127 2 0.00
128 6 0.01
129 6 0.01
130 1 0.00
131 2 0.00
132 7 0.01
133 18 0.02
134 13 0.01
135 11 0.01
136 3 0.00
137 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:39629 original size:367 final size:367
Alignment explanation
Indices: 39186--39877 Score: 1260
Period size: 367 Copynumber: 1.9 Consensus size: 367
39176 CGGGAAAAGC
* ** *
39186 TGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTATTCTCATTATGAACTTATTCT
*
39251 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGCAAAAGCTGATCCATTAAGTGATG
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGCAAAAGCTGATCCATCAAGTGATG
39316 GATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
131 GATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* *
39381 TCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
196 TCTTCTCATTATAAACTCGAACTGCAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
39446 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
261 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
39511 TTCTCTGAAAATTGATGCTGATCTATCTCCTTCTGGCAATGT
326 TTCTCTGAAAATTGATGCTGATCTATCTCCTTCTGGCAATGT
*
39553 TGATCCATCGAA-TGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTC
1 TGATCCATC-AAGTGATGAATTCAAGCAAAAGGTTGAACAAATTATTCTCATTATGAACTTATTC
*
39617 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGAT
65 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGCAAAAGCTGATCCATCAAGTGAT
*
39682 GGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
130 GGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
39747 TTCTTCTCATTATAAACTCGAACTGCAAAAGCTGATCCATTAAGTGATGGATTTGAGCAAAAGGT
195 TTCTTCTCATTATAAACTCGAACTGCAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGT
*
39812 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAAC
260 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
39877 T
325 T
39878 CGAACTGGAA
Statistics
Matches: 312, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
367 310 0.99
368 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (367 bp):
TGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTATTCTCATTATGAACTTATTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGCAAAAGCTGATCCATCAAGTGATG
GATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
TCTTCTCATTATAAACTCGAACTGCAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
TTCTCTGAAAATTGATGCTGATCTATCTCCTTCTGGCAATGT
Found at i:40996 original size:95 final size:94
Alignment explanation
Indices: 40704--40996 Score: 491
Period size: 94 Copynumber: 3.1 Consensus size: 94
40694 CTTATTTCTA
* * * * * *
40704 CTATGAGCAAATTCATCTTTCAATATCCAATGATTGGTTCTGT-GGTTTC-TACCAAACCAGACC
1 CTATGAGCACATTCATCTTCCAA-ATTCAATGATTGGTTTTTTGGGTTTCATACCAAACCAGATC
40767 AGATAACTCAAAGAACACTTCCAGAAGATG
65 AGATAACTCAAAGAACACTTCCAGAAGATG
40797 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTTCATACCAAACCAGATCA
40862 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
40891 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTT-GGGTTTCATACCAAACCAGATC
40956 AGATAACTCAAAGAACACTTCCAGAAGATG
65 AGATAACTCAAAGAACACTTCCAGAAGATG
40986 CTATGAGCACA
1 CTATGAGCACA
40997 CGACACTTGT
Statistics
Matches: 190, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
92 16 0.08
93 27 0.14
94 85 0.45
95 62 0.33
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (94 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTTCATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATG
Found at i:41795 original size:9 final size:9
Alignment explanation
Indices: 41781--41855 Score: 69
Period size: 10 Copynumber: 7.3 Consensus size: 9
41771 TTGACCCCCC
41781 TTTTTCTTT
1 TTTTTCTTT
41790 TTTTTCTTTTTT
1 TTTTTC---TTT
41802 TTTTTCTCTT
1 TTTTTCT-TT
41812 TTTCTTCTTT
1 TTT-TTCTTT
41822 TTTTATCTCTT
1 TTTT-TCT-TT
41833 TTTCTTCTTTT
1 TTT-TTC-TTT
41844 TTTTTCTTT
1 TTTTTCTTT
41853 TTT
1 TTT
41856 CTTCAAGCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
9 14 0.25
10 16 0.28
11 16 0.28
12 11 0.19
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:41813 original size:20 final size:21
Alignment explanation
Indices: 41781--41859 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
41771 TTGACCCCCC
*
41781 TTTTTCTTTTTTTTCTT-TTTT
1 TTTTTC-TCTTTTTCTTCTTTT
41802 TTTTTCTCTTTTTCTTCTTTT
1 TTTTTCTCTTTTTCTTCTTTT
*
41823 TTTATCTCTTTTTCTTCTTTT
1 TTTTTCTCTTTTTCTTCTTTT
41844 TTTTTCT-TTTTTCTTC
1 TTTTTCTCTTTTTCTTC
41860 AAGCATAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTCTTTTTCTTCTTTT
Found at i:41825 original size:32 final size:31
Alignment explanation
Indices: 41784--41855 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
41774 ACCCCCCTTT
* *
41784 TTCTTTTTTT-TCTTTTTTTTTTTCTCTTTTTC
1 TTCTTTTTTTATC-TCTTTTTCTTCT-TTTTTC
*
41816 TTCTTTTTTTATCTCTTTTTCTTCTTTTTTT
1 TTCTTTTTTTATCTCTTTTTCTTCTTTTTTC
41847 TTCTTTTTT
1 TTCTTTTTT
41856 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.39
32 20 0.56
33 2 0.06
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (31 bp):
TTCTTTTTTTATCTCTTTTTCTTCTTTTTTC
Found at i:54656 original size:17 final size:16
Alignment explanation
Indices: 54634--54665 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54624 GGGATTTGTA
54634 ATATTAATAAATAATAT
1 ATATTAAT-AATAATAT
54651 ATATTAATAATAATA
1 ATATTAATAATAATA
54666 ATAATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAATAATAATAT
Found at i:54661 original size:3 final size:3
Alignment explanation
Indices: 54632--54693 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
54622 TTGGGATTTG
* * * * *
54632 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
54679 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
54694 AAATGGGTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:59857 original size:2 final size:2
Alignment explanation
Indices: 59850--59883 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59840 AGCGAAAATG
59850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59884 GTTTAACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63927 original size:29 final size:29
Alignment explanation
Indices: 63895--63951 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
63885 GTTTCAAAAT
63895 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
63924 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
63952 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:64113 original size:111 final size:108
Alignment explanation
Indices: 63916--64133 Score: 251
Period size: 111 Copynumber: 2.0 Consensus size: 108
63906 AAAAAATATT
* * *
63916 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTTCCAGGT
* *
63981 GACTTAAGACAACTCTTTTCTTCGATATTAAAAAATAAATAAAC
66 GACTTAAGACAACTCCTTTCTT-AATATTAAAAAATAAATAAAC
** *
64025 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGA-TATCC
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACT-TCC
* ** ** *
64089 AGTTGTTTTAAGAC-TGTCCTTTCTTAATATTTAAAAATAAATAAA
62 AGGTGACTTAAGACAACTCCTTTCTTAATATTAAAAAATAAATAAA
64134 TATATATTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
109 10 0.11
110 24 0.26
111 42 0.46
112 15 0.16
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (108 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTTCCAGGT
GACTTAAGACAACTCCTTTCTTAATATTAAAAAATAAATAAAC
Found at i:64212 original size:2 final size:2
Alignment explanation
Indices: 64207--64246 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
64197 TATTATTTAT
* * *
64207 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64247 AATAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:64262 original size:3 final size:3
Alignment explanation
Indices: 64247--64302 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
64237 TATTTATATA
* * *
64247 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAA AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
64294 AA- AAT AAT A
1 AAT AAT AAT A
64303 TTTCAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:64275 original size:20 final size:21
Alignment explanation
Indices: 64247--64302 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
64237 TATTTATATA
64247 AATAATAAAAATAATAATAAT
1 AATAATAAAAATAATAATAAT
*
64268 GA-AATAAAAATAATAATAAT
1 AATAATAAAAATAATAATAAT
64288 AATAAT-AAAATAATA
1 AATAATAAAAATAATA
64303 TTTCAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAATAAAAATAATAATAAT
Found at i:64313 original size:26 final size:25
Alignment explanation
Indices: 64244--64300 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
64234 ATTTATTTAT
*
64244 ATAAATAATAAAAATAATAATAATGAA
1 ATAAA-AAT-AAAATAATAATAATAAA
64271 ATAAAAATAATAATAATAATAATAAA
1 ATAAAAATAA-AATAATAATAATAAA
64297 ATAA
1 ATAA
64301 TATTTCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.75
27 5 0.18
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
ATAAAAATAAAATAATAATAATAAA
Found at i:65589 original size:3 final size:3
Alignment explanation
Indices: 65583--65644 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
65573 AATAATTATT
*
65583 TAA TAA TAA T-A TAA T-A TAA T-A TAA T-A TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
65627 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
65645 AAACAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 8 0.16
3 41 0.84
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:65598 original size:5 final size:5
Alignment explanation
Indices: 65583--65625 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
65573 AATAATTATT
65583 TAATAA TAATA TAATA TAATA TAATA TAATA TTAATAA TAATA
1 TAAT-A TAATA TAATA TAATA TAATA TAATA -TAAT-A TAATA
65626 ATTTTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.63
6 12 0.34
7 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:65603 original size:10 final size:11
Alignment explanation
Indices: 65572--65644 Score: 69
Period size: 12 Copynumber: 6.5 Consensus size: 11
65562 TTGGACTTTG
* *
65572 TAATAATTATT
1 TAATAATAATA
65583 TAATAATAATA
1 TAATAATAATA
65594 TAAT-ATAATA
1 TAATAATAATA
65604 TAAT-ATAATA
1 TAATAATAATA
65614 TTAATAATAATAA
1 -TAATAATAAT-A
**
65627 TTTTAATAATAA
1 TAATAATAAT-A
65639 TAATAA
1 TAATAA
65645 AAACAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
10 16 0.30
11 17 0.32
12 19 0.36
13 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATA
Found at i:65608 original size:32 final size:33
Alignment explanation
Indices: 65572--65644 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
65562 TTGGACTTTG
*
65572 TAATAATTAT-TTAATAATAATATAATATAAT-A
1 TAATAATAATATTAATAATAATA-AATATAATAA
* *
65604 TAAT-ATAATATTAATAATAATAATTTTAATAA
1 TAATAATAATATTAATAATAATAAATATAATAA
65636 TAATAATAA
1 TAATAATAA
65645 AAACAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 10 0.29
32 21 0.60
33 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAATAATAATATTAATAATAATAAATATAATAA
Found at i:65626 original size:15 final size:15
Alignment explanation
Indices: 65572--65643 Score: 76
Period size: 15 Copynumber: 4.7 Consensus size: 15
65562 TTGGACTTTG
*
65572 TAATAATTAT-TTAA
1 TAATAATAATATTAA
*
65586 TAATAATATAATATAATA
1 TAAT-A-ATAATATTA-A
65604 TAAT-ATAATATTAA
1 TAATAATAATATTAA
*
65618 TAATAATAATTTTAA
1 TAATAATAATATTAA
65633 TAATAATAATA
1 TAATAATAATA
65644 AAAACAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.19
15 28 0.58
16 4 0.08
17 2 0.04
18 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATAATATTAA
Found at i:65902 original size:76 final size:76
Alignment explanation
Indices: 65800--66284 Score: 898
Period size: 76 Copynumber: 6.4 Consensus size: 76
65790 AAGGTCCTAA
* * *
65800 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65865 AGGCTTTTTGG
66 AGGCTTTTTGG
*
65876 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65941 AGGCTTTTTGG
66 AGGCTTTTTGG
*
65952 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGACAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
66017 AGACTTTTTGG
66 AGGCTTTTTGG
66028 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
66093 AGGCTTTTTGG
66 AGGCTTTTTGG
66104 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
66169 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
66180 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
66245 AGGCTTTTTGG
66 AGGCTTTTTGG
66256 AAACATCATGCACTGTAGGACTTACAGAT
1 AAACATCATGCACTGTAGGACTTACAGAT
66285 ATGGGAAATA
Statistics
Matches: 399, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 399 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:66575 original size:73 final size:73
Alignment explanation
Indices: 66455--66883 Score: 734
Period size: 73 Copynumber: 5.9 Consensus size: 73
66445 AACTCAAAAT
* * * *
66455 AACTGTCTTAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
66520 TTCAAGTGA
65 TTCGAGTGA
*
66529 AACTGTCTTAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
66594 TCGAGTGA
66 TCGAGTGA
* *
66602 AACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
66667 TCGAGTGA
66 TCGAGTGA
*
66675 AACTGTCTCAAGTGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
66739 TCGAGTGA
66 TCGAGTGA
* *
66747 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
66812 TCGAGTGA
66 TCGAGTGA
*
66820 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
66884 GAAAACATCC
Statistics
Matches: 342, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
72 70 0.20
73 251 0.73
74 21 0.06
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGA
Found at i:66753 original size:145 final size:145
Alignment explanation
Indices: 66455--66883 Score: 741
Period size: 145 Copynumber: 2.9 Consensus size: 145
66445 AACTCAAAAT
* * *
66455 AACTGTCTTAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGT
* *
66520 TTCAAGTGAAACTGTCTTAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCGAGTGAAACTGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
66585 AGTTCTGTTTCGAGTGA
129 AGTTCTGTTTCGAGTGA
* * *
66602 AACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
*
66667 TCGAGTGAAACTGTCTCAAGTGAGACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAG
66 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAG
66732 TTCTGTTTCGAGTGA
131 TTCTGTTTCGAGTGA
*
66747 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
66812 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66 TCGAGTGAAACTGTCTCAAGCGAGACAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66877 GTTCTGT
130 GTTCTGT
66884 GAAAACATCC
Statistics
Matches: 267, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
145 143 0.54
146 105 0.39
147 19 0.07
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (145 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTTTGTT
TCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAG
TTCTGTTTCGAGTGA
Found at i:66856 original size:218 final size:219
Alignment explanation
Indices: 66455--66883 Score: 743
Period size: 218 Copynumber: 2.0 Consensus size: 219
66445 AACTCAAAAT
* * *
66455 AACTGTCTTAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-CTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
66520 TTCAAGTGAAACTGTCTTAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
*
66585 AGTTCTGTTTCGAGTGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAG
130 AGTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAG
66650 TGAGATAAAGTTCTGTTTCGAGTGA
195 TGAGATAAAGTTCTGTTTCGAGTGA
*
66675 AACTGTCTCAAGTGAGACAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAACTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
* *
66739 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66 TCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
* * *
66804 GTTTTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGT
131 GTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAGT
66869 GAGATAAAGTTCTGT
196 GAGATAAAGTTCTGT
66884 GAAAACATCC
Statistics
Matches: 198, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
218 179 0.90
220 19 0.10
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (219 bp):
AACTGTCTCAAGCGAGACAAACTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
GTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTAAAGT
GAGATAAAGTTCTGTTTCGAGTGA
Found at i:67167 original size:165 final size:165
Alignment explanation
Indices: 66918--67244 Score: 503
Period size: 165 Copynumber: 2.0 Consensus size: 165
66908 TATGGATGTG
* * * *
66918 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCATTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTC
* **
66983 AGAATAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
* **
67048 TGGGTAACATTCCCCAATCTCAAGATAATGCTGTT
131 TAGGTAACATGACCCAATCTCAAGATAATGCTGTT
*
67083 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
* *
67148 C-GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATATCATGTTGA
65 CAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
**
67212 TTAGGTAGGATGACCCAATCTCAAGATAATGCT
130 TTAGGTAACATGACCCAATCTCAAGATAATGCT
67245 CATTCTTGTG
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
165 104 0.71
166 42 0.29
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGAT
TAGGTAACATGACCCAATCTCAAGATAATGCTGTT
Found at i:67782 original size:22 final size:22
Alignment explanation
Indices: 67757--67811 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
67747 AATAAAGCTT
67757 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
67779 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
67801 TCATCTTTGAA
1 TCATCTTTGAA
67812 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:74505 original size:6 final size:6
Alignment explanation
Indices: 74490--74523 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
74480 ACAAACGTAA
* *
74490 AAATGC AAATGT AAATGT AAATGC AAATGT AAAT
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAAT
74524 ATGTGAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (6 bp):
AAATGT
Found at i:76108 original size:26 final size:27
Alignment explanation
Indices: 76057--76124 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
76047 AAATAAAATG
76057 AAATATTAAT-AAAATAATA-TACATAT
1 AAATATT-ATGAAAATAATATTACATAT
*
76083 AAATATTATGAAAATAATAATTATATAT
1 AAATATTATGAAAATAAT-ATTACATAT
*
76111 AAAAATTATGAAAA
1 AAATATTATGAAAA
76125 GAAAGAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 2 0.05
26 15 0.41
27 1 0.03
28 19 0.51
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATATTATGAAAATAATATTACATAT
Found at i:76119 original size:28 final size:29
Alignment explanation
Indices: 76069--76124 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
76059 ATATTAATAA
*
76069 AATAATATACATATAAATATTATGAAAAT
1 AATAATATACATATAAAAATTATGAAAAT
*
76098 AATAAT-TATATATAAAAATTATGAAAA
1 AATAATATACATATAAAAATTATGAAAA
76125 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (29 bp):
AATAATATACATATAAAAATTATGAAAAT
Found at i:76144 original size:28 final size:28
Alignment explanation
Indices: 76081--76153 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
76071 TAATATACAT
* * * *
76081 ATAAATATTATGAAAATAATAATTATAT
1 ATAAAAATTATGAAAAAAAGAATTATAA
76109 ATAAAAATTATGAAAAGAAAGAATTATAA
1 ATAAAAATTATGAAAA-AAAGAATTATAA
*
76138 ATTAAATAAATATGAA
1 A-TAAA-AATTATGAA
76154 TTTTTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.41
29 10 0.27
30 4 0.11
31 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (28 bp):
ATAAAAATTATGAAAAAAAGAATTATAA
Found at i:76813 original size:108 final size:105
Alignment explanation
Indices: 76616--76827 Score: 239
Period size: 108 Copynumber: 2.0 Consensus size: 105
76606 AAAATATATT
* * * * *
76616 AATTTATATATTTATAAATAAATATTTATTTATTTAGAAATATCAGTAAAGGACTTCTAGGTGCC
1 AATTAATATATTTATAAATAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCC
* * *
76681 TTAAGACATCTCTTTCTTCGATATTAAAAAACAAATAAAC
66 TTAAGACATCCCTTTATTCAATATTAAAAAACAAATAAAC
* *
76721 AATTAATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGT
1 AATTAATAT-ATTTAT-AAATA-AATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGG
** * *
76786 TGTTTTAAGAC-TGCCCTTTATT-AATATTGAAAAATAAATAAA
62 TGCCTTAAGACAT-CCCTTTATTCAATATTAAAAAACAAATAAA
76828 TATATATAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
105 8 0.09
106 6 0.07
107 5 0.06
108 45 0.51
109 24 0.27
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (105 bp):
AATTAATATATTTATAAATAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCC
TTAAGACATCCCTTTATTCAATATTAAAAAACAAATAAAC
Found at i:76928 original size:3 final size:3
Alignment explanation
Indices: 76913--76961 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
76903 TATTTATATA
* *
76913 AAT AAT AAA AAT AAT AAT GA- AAT AA- AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
76958 AAT A
1 AAT A
76962 TTGCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 5 0.13
3 34 0.87
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:76941 original size:25 final size:25
Alignment explanation
Indices: 76912--76961 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
76902 TTATTTATAT
*
76912 AAATAATAAAAATAATAATGAAATA
1 AAATAATAAAAATAATAATAAAATA
*
76937 AAATAATAATAATAATAATAAAATA
1 AAATAATAAAAATAATAATAAAATA
76962 TTGCAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAATAATAAAAATAATAATAAAATA
Found at i:78239 original size:3 final size:3
Alignment explanation
Indices: 78233--78297 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
78223 AATAATTATT
*
78233 TAA TAA TAA T-A TAA T-A TAA T-A TAA TATA TATA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA
**
78277 TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
78298 AAATGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 39 0.75
4 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:78248 original size:5 final size:5
Alignment explanation
Indices: 78233--78281 Score: 62
Period size: 5 Copynumber: 9.0 Consensus size: 5
78223 AATAATTATT
78233 TAATAA TAATA TAATA TAATA TAATA TATATA TAATA TTAATAA TAATA
1 TAAT-A TAATA TAATA TAATA TAATA TA-ATA TAATA -TAAT-A TAATA
78282 ATTTTAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 22 0.55
6 17 0.43
7 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:78288 original size:15 final size:15
Alignment explanation
Indices: 78233--78297 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
78223 AATAATTATT
*
78233 TAATAATAAT-ATAA
1 TAATAATATTAATAA
78247 T-ATAATA-TAATATA
1 TAATAATATTAATA-A
78261 TATATAATATTAATAA
1 TA-ATAATATTAATAA
*
78277 TAATAATTTTAATAA
1 TAATAATATTAATAA
78292 TAATAA
1 TAATAA
78298 AAATGAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
12 1 0.02
13 9 0.20
14 3 0.07
15 18 0.40
16 9 0.20
17 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATATTAATAA
Found at i:78289 original size:21 final size:20
Alignment explanation
Indices: 78233--78297 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
78223 AATAATTATT
78233 TAATAATAA-TATAATATAA
1 TAATAATAATTATAATATAA
78252 T-ATAATATATATATAATATTAA
1 TAATAATA-AT-TATAATA-TAA
*
78274 TAATAATAATTTTAATAATAA
1 TAATAATAATTATAAT-ATAA
78295 TAA
1 TAA
78298 AAATGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
21 18 0.46
22 7 0.18
23 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATAATAATTATAATATAA
Found at i:87372 original size:37 final size:37
Alignment explanation
Indices: 87297--87370 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
87287 AGTTGGAAAT
* *
87297 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
87334 ATTTATATACTTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATTGAAAATCATAAA
87370 A
1 A
87371 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 6 0.18
37 23 0.70
38 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:89199 original size:21 final size:22
Alignment explanation
Indices: 89164--89211 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
89154 CAATACATAT
89164 TAGGTAGCGTTATATAATGTAA
1 TAGGTAGCGTTATATAATGTAA
89186 TAGGTAGC-TTATATAATGTAA
1 TAGGTAGCGTTATATAATGTAA
89207 TAGGT
1 TAGGT
89212 TAATTACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (22 bp):
TAGGTAGCGTTATATAATGTAA
Found at i:89245 original size:83 final size:86
Alignment explanation
Indices: 89077--89263 Score: 251
Period size: 83 Copynumber: 2.2 Consensus size: 86
89067 AAAATAATAA
* *
89077 ATTAGGTA-CGTTATATAATGTAATAGGTAACGTTTATATAATAAAAATAGGTTAATTACTGGAA
1 ATTAGGTAGCGTTATATAATGTAATAGGTAACGCTTATATAATAAAAATAGGTTAATTACTAGAA
*
89141 ACATTATCAATCACAATACAT
66 ACATTATCAATCACAAAACAT
**
89162 ATTAGGTAGCGTTATATAATGTAATAGGT-A-GCTTATATAAT-GTAATAGGTTAATTACTAGAA
1 ATTAGGTAGCGTTATATAATGTAATAGGTAACGCTTATATAATAAAAATAGGTTAATTACTAGAA
*
89224 ATATTATCAAAT-ACAAAACAT
66 ACATTATC-AATCACAAAACAT
*
89245 ATTA-GTAGCACTTATATAA
1 ATTAGGTAGC-GTTATATAA
89264 ATAATAGATA
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
82 5 0.05
83 45 0.49
84 13 0.14
85 9 0.10
86 20 0.22
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (86 bp):
ATTAGGTAGCGTTATATAATGTAATAGGTAACGCTTATATAATAAAAATAGGTTAATTACTAGAA
ACATTATCAATCACAAAACAT
Done.