Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004079.1 Hibiscus syriacus cultivar Beakdansim tig00008926_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: 117853
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:689 original size:86 final size:89
Alignment explanation
Indices: 529--912 Score: 543
Period size: 86 Copynumber: 4.4 Consensus size: 89
519 GGATTGAACA
*
529 AGTTCTTCTCATTATGAACTCTTCACTGGAAACACTGATGCAAGGTTG-A-AAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTCTTCTCATT
* *
592 ATGACTTCTTCTTCCTCGTTGGATG
66 ATGA-ATCTTCTTCCTCATTGGATG
* *
617 AGTT-TTCTCATTATG-ACTCTCCACTAGAAACACTGATGCAAGGTTGAACAAGTTCTTCTAATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTCTTCTCATT
*
680 ATGAACTTCTTCTTCCACATTGGATG
66 ATGAA--TCTTCTTCCTCATTGGATG
*
706 AGTTCTTCTCATTATGAACTCTCCACTGG-AACACTGATGCAAGGTTGAACAAGTTATTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTCTTCTCATT
** * *
770 ATGCTTC-TATTCCTCA-TGAATG
66 ATGAATCTTCTTCCTCATTGGATG
792 AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTC-T-TCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTCTTCTCATT
855 ATGAACTTCTTCTTCCTCATTGGATG
66 ATGAA--TCTTCTTCCTCATTGGATG
* *
881 AGTTCTTCTCATTATAAACTCTCAACTGGAAA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAA
913 TGTTGATCCA
Statistics
Matches: 264, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
85 8 0.03
86 64 0.24
87 47 0.18
88 31 0.12
89 56 0.21
90 47 0.18
91 11 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (89 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGCAAGGTTGAACAAGTTCTTCTCATT
ATGAATCTTCTTCCTCATTGGATG
Found at i:826 original size:177 final size:174
Alignment explanation
Indices: 529--911 Score: 601
Period size: 177 Copynumber: 2.2 Consensus size: 174
519 GGATTGAACA
* *
529 AGTTCTTCTCATTATGAACTCTTCACTGGAAACACTGATGCAAGGTTGAAAGTTCTTCTCATTAT
1 AGTTCTTCTCATTATGAACTCTCCACTGG-AACACTGATGCAAGGTTGAAAGTTATTCTCATTAT
* * *
594 GACTTCTTCTTCCTCGTTGGATGAGTTTTCTCATTATGACTCTCCACTAGAAACACTGATGCAAG
65 GACTTCTTATTCCTCGATGAATGAGTTTTCTCATTATGACTCTCCACTAGAAACACTGATGCAAG
659 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTTCCACATTGGATG
130 GTTGAACAAGTTCTTC--ATTATGAACTTCTTCTTCCACATTGGATG
706 AGTTCTTCTCATTATGAACTCTCCACTGGAACACTGATGCAAGGTTGAACAAGTTATTCTCATTA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAACACTGATGCAAGGTTG-A-AAGTTATTCTCATTA
*
771 TG-CTTC-TATTCCTC-ATGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACACTGATGC
64 TGACTTCTTATTCCTCGATGAATGAGTT-TTCTCATTATG-ACTCTCCACTAGAAACACTGATGC
*
833 AAGGTTGAACAAGTTCTTCATTATGAACTTCTTCTTCCTCATTGGATG
127 AAGGTTGAACAAGTTCTTCATTATGAACTTCTTCTTCCACATTGGATG
* *
881 AGTTCTTCTCATTATAAACTCTCAACTGGAA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAA
912 ATGTTGATCC
Statistics
Matches: 193, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
175 66 0.34
176 36 0.19
177 75 0.39
178 16 0.08
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (174 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAACACTGATGCAAGGTTGAAAGTTATTCTCATTATG
ACTTCTTATTCCTCGATGAATGAGTTTTCTCATTATGACTCTCCACTAGAAACACTGATGCAAGG
TTGAACAAGTTCTTCATTATGAACTTCTTCTTCCACATTGGATG
Found at i:1036 original size:104 final size:105
Alignment explanation
Indices: 839--1327 Score: 653
Period size: 102 Copynumber: 4.7 Consensus size: 105
829 ATGCAAGGTT
* *
839 GAACAAGTTC-T-TCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTATAAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTCATTATGAACT
* *
901 CTCAACTGGAAATGTTGATCCACCTCATTCTGTGGTGAATTTGAAAG
61 CT--TCTGGAAATGTTGATTCACCTCATTCTGTGGTGAATTTGAAAG
*
948 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGG-GGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * * * *
1012 GGAAATGTTGATTCATCTCCTTCTGCGGTGGACTTGAAAG
66 GGAAATGTTGATTCACCTCATTCTGTGGTGAATTTGAAAG
* * *
1052 GGACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAG-T-TT-TCATTATAAACTCCTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* *
1114 GGAAAT-ATGGTTCA-CTCATTCTGTGGTGAATTTGAAAG
66 GGAAATGTTGATTCACCTCATTCTGTGGTGAATTTGAAAG
* *
1152 GGACAAGTTCTTCTCATTATGAACTTTCTTCTTTAGGACGAGTTCTTCTCATTATGAAC-C-TCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* *
1215 GGAAATGTTGGTTCACCTCATTCTGTGGTGAATTTTAAAG
66 GGAAATGTTGATTCACCTCATTCTGTGGTGAATTTGAAAG
1255 GAA-AAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTT-TCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1318 GGAAATGTTG
66 GGAAATGTTG
1328 GTTTCCTTTT
Statistics
Matches: 344, Mismatches: 25, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
100 61 0.18
101 27 0.08
102 74 0.22
103 50 0.15
104 73 0.21
105 3 0.01
106 24 0.07
107 2 0.01
108 4 0.01
109 13 0.04
110 2 0.01
111 11 0.03
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATTCACCTCATTCTGTGGTGAATTTGAAAG
Found at i:1890 original size:54 final size:54
Alignment explanation
Indices: 1739--1909 Score: 197
Period size: 54 Copynumber: 3.2 Consensus size: 54
1729 ACCCCGAAAG
** * * * *
1739 CTTAGTTTCTTTGAATGTTCATTTGATAAA-AATCATGAAACTTTTAAAAATTGGA
1 CTTAGTTTCTTTGAA-AATCATTTGA-AAATAATCAAGAAACTTCTGAAAATCGGA
** *
1794 CTTAGTTTCTTT-AAAA-CATTTGAAAATCTTCAAGAAACTTCTGAAAATCAGA
1 CTTAGTTTCTTTGAAAATCATTTGAAAATAATCAAGAAACTTCTGAAAATCGGA
*
1846 CTTAGTTTCTTTGAAAACTCATTT-AAAATGATCAAGAAACTTCTGAAAATCGGA
1 CTTAGTTTCTTTGAAAA-TCATTTGAAAATAATCAAGAAACTTCTGAAAATCGGA
1900 CTTAGTTTCT
1 CTTAGTTTCT
1910 AAAAAACACA
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
51 3 0.03
52 37 0.37
53 4 0.04
54 39 0.39
55 17 0.17
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (54 bp):
CTTAGTTTCTTTGAAAATCATTTGAAAATAATCAAGAAACTTCTGAAAATCGGA
Found at i:2319 original size:25 final size:25
Alignment explanation
Indices: 2285--2343 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
2275 TATGTTTTCT
2285 TGTTTCATTAAAGCCTCAAAAGAAA
1 TGTTTCATTAAAGCCTCAAAAGAAA
2310 TGTTTCATTAAAGCCTCAAAAGAAA
1 TGTTTCATTAAAGCCTCAAAAGAAA
2335 TGTTTCATT
1 TGTTTCATT
2344 TGTGGAACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (25 bp):
TGTTTCATTAAAGCCTCAAAAGAAA
Found at i:2933 original size:54 final size:54
Alignment explanation
Indices: 2849--2953 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
2839 CATTGGTTCA
* *
2849 TAAAACATTTGACAACACATGCATCATTTCCTGTGGTTTCTACCCAGATTTTCG
1 TAAAACATTTGACAACACATGCATCATTTCCTATGGCTTCTACCCAGATTTTCG
* * *
2903 TAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGATTT
1 TAAAACATTTGACAACACATGCATCATTTCCTATGGCTTCTACCCAGATTT
2954 CTTGTCAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (54 bp):
TAAAACATTTGACAACACATGCATCATTTCCTATGGCTTCTACCCAGATTTTCG
Found at i:5199 original size:20 final size:20
Alignment explanation
Indices: 5174--5211 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5164 TTTGGTTCAC
5174 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
*
5194 GGAATGTAAGATTACCAG
1 GGAATGGAAGATTACCAG
5212 GAAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:16261 original size:89 final size:89
Alignment explanation
Indices: 16110--16312 Score: 302
Period size: 89 Copynumber: 2.3 Consensus size: 89
16100 CCTTGGGTAA
* * *
16110 GCCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTCAGGTAACCCTACGGATCTAA
1 GCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTCTAGTGTGCTTCAGGTAACCCTACGGATCTAA
* *
16175 GGATGCCCTTTAGTAGGCCCATAG
66 GGATACCCTTGAGTAGGCCCATAG
16199 GCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTACTAG-GTGCTT-AGGGTAACCCTACGGATCT
1 GCCCCAAGGCATATCCTTAGGTTGGTTCCCTTT-CTAGTGTGCTTCA-GGTAACCCTACGGATCT
* *
16262 AATGATACCCTTGGGTAGGCCCATAG
64 AAGGATACCCTTGAGTAGGCCCATAG
*
16288 GCCCCAAGGAATATCCTTAGGTTGG
1 GCCCCAAGGCATATCCTTAGGTTGG
16313 CTATATTTTT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
88 1 0.01
89 101 0.97
90 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (89 bp):
GCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTCTAGTGTGCTTCAGGTAACCCTACGGATCTAA
GGATACCCTTGAGTAGGCCCATAG
Found at i:20884 original size:4 final size:4
Alignment explanation
Indices: 20875--20905 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20865 TTCAACTATG
*
20875 TATT TATT TATT CATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
20906 ACATGCATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:22462 original size:3 final size:3
Alignment explanation
Indices: 22454--22493 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
22444 AATTTAATTT
22454 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22494 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23493 original size:25 final size:26
Alignment explanation
Indices: 23436--23503 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
23426 TATTAATTTT
23436 AATGCTATGTAATAAATGTAACAAAA
1 AATGCTATGTAATAAATGTAACAAAA
*
23462 AATGCTATATAATAAATGTAAC-AAA
1 AATGCTATGTAATAAATGTAACAAAA
*
23487 AATGCTATGTATTAAAT
1 AATGCTATGTAATAAAT
23504 ATTTAATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 18 0.46
26 21 0.54
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (26 bp):
AATGCTATGTAATAAATGTAACAAAA
Found at i:25491 original size:2 final size:2
Alignment explanation
Indices: 25484--25526 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
25474 AGTCCTTTTC
25484 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
25526 A
1 A
25527 AGTAAGTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25727 original size:15 final size:16
Alignment explanation
Indices: 25700--25729 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25690 ATAAATAAAT
25700 GAACATAAACGAACAC
1 GAACATAAACGAACAC
25716 GAACAT-AACGAACA
1 GAACATAAACGAACA
25730 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.23, G:0.13, T:0.07
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:25811 original size:10 final size:10
Alignment explanation
Indices: 25796--25865 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
25786 CATTTAATAA
25796 ATAAACGAAC
1 ATAAACGAAC
25806 ATAAACGAAC
1 ATAAACGAAC
25816 ----ACGAAC
1 ATAAACGAAC
25822 ATAAACGAAC
1 ATAAACGAAC
* *
25832 ATGAAC-ATAA
1 ATAAACGA-AC
25842 ATGAACACGAAC
1 AT-AA-ACGAAC
25854 ATAAACGAAC
1 ATAAACGAAC
25864 AT
1 AT
25866 CAACACTGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 32 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:25870 original size:16 final size:16
Alignment explanation
Indices: 25800--25864 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
25790 TAATAAATAA
25800 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
25816 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
25832 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
25848 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
25864 A
1 A
25865 TCAACACTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:26881 original size:10 final size:10
Alignment explanation
Indices: 26866--26913 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
26856 ATAAATGAAA
26866 GAACATAAAC
1 GAACATAAAC
26876 GAACATAATCGAAC
1 GAACAT-A---AAC
26890 GAACATAAAC
1 GAACATAAAC
*
26900 GAACATAACC
1 GAACATAAAC
26910 GAAC
1 GAAC
26914 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:26881 original size:24 final size:25
Alignment explanation
Indices: 26853--26907 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
26843 GATTGGGTTA
26853 AACATAAAT-GAAAGAACATAAACG
1 AACATAAATCGAAAGAACATAAACG
*
26877 AACAT-AATCGAACGAACATAAACG
1 AACATAAATCGAAAGAACATAAACG
26901 AACATAA
1 AACATAA
26908 CCGAACGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.86
25 1 0.04
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (25 bp):
AACATAAATCGAAAGAACATAAACG
Found at i:26890 original size:14 final size:14
Alignment explanation
Indices: 26873--26903 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26863 AAAGAACATA
*
26873 AACGAACATAATCG
1 AACGAACATAAACG
26887 AACGAACATAAACG
1 AACGAACATAAACG
26901 AAC
1 AAC
26904 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:26912 original size:24 final size:24
Alignment explanation
Indices: 26866--26914 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
26856 ATAAATGAAA
*
26866 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
26890 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
26914 G
1 G
26915 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:27148 original size:30 final size:29
Alignment explanation
Indices: 27106--27162 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
27096 AAAGGAAGTT
*
27106 GATAAATCAGTGATCAAAATATAATAATC
1 GATAAATAAGTGATCAAAATATAATAATC
*
27135 GATAACATAAGTGATCAAAATTTAATAA
1 GATAA-ATAAGTGATCAAAATATAATAA
27163 ATTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (29 bp):
GATAAATAAGTGATCAAAATATAATAATC
Found at i:27345 original size:19 final size:17
Alignment explanation
Indices: 27302--27349 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
27292 GTATTTTGGC
*
27302 TTATTATTATT-ATTATT
1 TTATT-TTATTAAATATT
27319 TTATTTTATTAAATATT
1 TTATTTTATTAAATATT
27336 TTACTATTTATTAA
1 TTA-T-TTTATTAA
27350 TAAATATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 5 0.19
17 13 0.48
18 1 0.04
19 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATTAAATATT
Found at i:29154 original size:15 final size:15
Alignment explanation
Indices: 29134--29196 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
29124 TGAGACATTA
**
29134 CCCGCCCCGCATCCG
1 CCCGCCCCAAATCCG
29149 CCCGCCCCAAATCCG
1 CCCGCCCCAAATCCG
*
29164 -CC-CCGC--ATCCG
1 CCCGCCCCAAATCCG
*
29175 CCCGCCCCAAATTCG
1 CCCGCCCCAAATCCG
29190 CCCGCCC
1 CCCGCCC
29197 AGCTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 5 0.13
12 2 0.05
13 6 0.15
14 2 0.05
15 24 0.62
ACGTcount: A:0.13, C:0.63, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCAAATCCG
Found at i:29171 original size:26 final size:26
Alignment explanation
Indices: 29135--29192 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
29125 GAGACATTAC
29135 CCGCCCCGCATCCGCCCGCCCCAAAT
1 CCGCCCCGCATCCGCCCGCCCCAAAT
29161 CCGCCCCGCATCCGCCCGCCCCAAAT
1 CCGCCCCGCATCCGCCCGCCCCAAAT
*
29187 TCGCCC
1 CCGCCC
29193 GCCCAGCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.62, G:0.16, T:0.09
Consensus pattern (26 bp):
CCGCCCCGCATCCGCCCGCCCCAAAT
Found at i:31824 original size:21 final size:23
Alignment explanation
Indices: 31790--31840 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
31780 GGAGCAATAC
31790 TAGATGATTTTAG-TTTCAAATG
1 TAGATGATTTTAGTTTTCAAATG
31812 TAGATGA-TTTAGTTTTCAAATG
1 TAGATGATTTTAGTTTTCAAATG
*
31834 CAGATGA
1 TAGATGA
31841 GGAGAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (23 bp):
TAGATGATTTTAGTTTTCAAATG
Found at i:37223 original size:24 final size:24
Alignment explanation
Indices: 37196--37243 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
37186 AATAACCAAG
*
37196 ATAAA-TATAAATATACCATTAAAA
1 ATAAAGTATAAACA-ACCATTAAAA
*
37220 ATAAAGTTTAAACAACCATTAAAA
1 ATAAAGTATAAACAACCATTAAAA
37244 CAACCCCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (24 bp):
ATAAAGTATAAACAACCATTAAAA
Found at i:52019 original size:14 final size:15
Alignment explanation
Indices: 52000--52033 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
51990 TTTTGTCCGG
52000 TTATAAATATT-ATA
1 TTATAAATATTAATA
*
52014 TTATAATTATTAATA
1 TTATAAATATTAATA
52029 TTATA
1 TTATA
52034 TTATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAAATATTAATA
Found at i:52024 original size:9 final size:9
Alignment explanation
Indices: 52012--52080 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
52002 ATAAATATTA
52012 TATTATAAT
1 TATTATAAT
*
52021 TATTAATATT
1 TATT-ATAAT
*
52031 ATATTATAAC
1 -TATTATAAT
*
52041 TATTATTAT
1 TATTATAAT
*
52050 TATTATAAC
1 TATTATAAT
*
52059 AATTA-AA-
1 TATTATAAT
*
52066 AATTATAAT
1 TATTATAAT
52075 TATTAT
1 TATTAT
52081 TAATATTGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
7 5 0.11
8 4 0.09
9 27 0.57
10 7 0.15
11 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (9 bp):
TATTATAAT
Found at i:52056 original size:23 final size:20
Alignment explanation
Indices: 52000--52052 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
51990 TTTTGTCCGG
*
52000 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
52020 TTATTAATATTATATTATAA
1 TTATTAATATTATATTATAA
* *
52040 CTATTATTATTAT
1 TTATTAATATTAT
52053 TATAACAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:53216 original size:18 final size:18
Alignment explanation
Indices: 53193--53235 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
53183 ACCGGTATTC
53193 TTCTTCGGTGACTTTCGT
1 TTCTTCGGTGACTTTCGT
53211 TTCTTCGGTGACTTTCGT
1 TTCTTCGGTGACTTTCGT
*
53229 CTCTTCG
1 TTCTTCG
53236 TCGGAGCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.05, C:0.26, G:0.21, T:0.49
Consensus pattern (18 bp):
TTCTTCGGTGACTTTCGT
Found at i:53716 original size:3 final size:3
Alignment explanation
Indices: 53708--53754 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
53698 TGTTTATCTT
53708 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53755 TTAAACGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54065 original size:14 final size:14
Alignment explanation
Indices: 54046--54073 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54036 TTCGCCCTGT
54046 TTATATATTTTGTG
1 TTATATATTTTGTG
54060 TTATATATTTTGTG
1 TTATATATTTTGTG
54074 CATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (14 bp):
TTATATATTTTGTG
Found at i:54887 original size:16 final size:16
Alignment explanation
Indices: 54862--54908 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
54852 CATAACACCA
54862 AAAT-AATAAATCAAAG
1 AAATGAATAAAT-AAAG
*
54878 AAA-GAATAAATAAAT
1 AAATGAATAAATAAAG
*
54893 AAATGAATAAAAAAAG
1 AAATGAATAAATAAAG
54909 TCAAAAAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (16 bp):
AAATGAATAAATAAAG
Found at i:56203 original size:6 final size:5
Alignment explanation
Indices: 56127--56207 Score: 76
Period size: 5 Copynumber: 16.2 Consensus size: 5
56117 CTGGAAAAGA
* * * * * *
56127 AAAAT AAAAT GAAAT AAATT AAAAT -AAAT TAAAT TAAAT TAAAT -GAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
56175 AAAAT AAAAT AAAAT AAAAT AATAAT AATAAT A
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT A
56208 TACTAAATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
4 7 0.10
5 50 0.75
6 10 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (5 bp):
AAAAT
Found at i:56349 original size:33 final size:31
Alignment explanation
Indices: 56229--56400 Score: 84
Period size: 32 Copynumber: 5.2 Consensus size: 31
56219 ATTTATATAA
* *
56229 TATATATATTTCAAAATACGTTTTT-AAACTA-
1 TATATAGATTTCAAAAT--GTTTTTAAAAATAT
* * * *
56260 TATATTGTATTTTAAAAAGTTTTCAAAACTATATGT
1 TATATAG-ATTTCAAAATGTTTTTAAAA--ATA--T
*
56296 TATATAGTTTTCAAAATG-TTTTAAAAATAT
1 TATATAGATTTCAAAATGTTTTTAAAAATAT
56326 TATATAAGATTTCAAACAATGTTTTTAAAACTATATAT
1 TATAT-AGATTTC-AA-AATGTTTTT-AAA--A-ATAT
*
56364 TATATA-ATTTTCAAAAATATTTTTAAAAACTA-
1 TATATAGA-TTTC-AAAATGTTTTTAAAAA-TAT
56396 TATAT
1 TATAT
56401 TATATAATCT
Statistics
Matches: 111, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
30 11 0.10
31 14 0.13
32 19 0.17
33 9 0.08
34 11 0.10
35 14 0.13
36 15 0.14
37 9 0.08
38 9 0.08
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (31 bp):
TATATAGATTTCAAAATGTTTTTAAAAATAT
Found at i:56419 original size:39 final size:36
Alignment explanation
Indices: 56279--56551 Score: 257
Period size: 36 Copynumber: 7.7 Consensus size: 36
56269 TTTTAAAAAG
* * * *
56279 TTTTCAAAACTATATGTTATATAGTTTTC-AAAATG
1 TTTTAAAAACTATATATTATATAATTTTCAAAAATT
56314 TTTTAAAAA-TAT-TA-TATA-AGA-TTTCAAACAATGT
1 TTTTAAAAACTATATATTATATA-ATTTTCAAA-AAT-T
56348 TTTT-AAAACTATATATTATATAATTTTCAAAAATAT
1 TTTTAAAAACTATATATTATATAATTTTCAAAAAT-T
56384 TTTTAAAAACTATATATTATATAATCTTTCAAAAAATAT
1 TTTTAAAAACTATATATTATATAAT-TTTC-AAAAAT-T
**
56423 TTTTTTAAACTATATATTATATAATTTTTCAAAAATGT
1 TTTTAAAAACTATATATTATATAA-TTTTCAAAAAT-T
* *
56461 TTTT-AAAACCATATA-T-TAT-ATTTT-AAAAATG
1 TTTTAAAAACTATATATTATATAATTTTCAAAAATT
* *
56492 TTTTAAAAACTATATACTATATAAGTTTTC-AAAATG
1 TTTTAAAAACTATATATTATATAA-TTTTCAAAAATT
* *
56528 TTTTAAAAACTATACAATATATAA
1 TTTTAAAAACTATATATTATATAA
56552 ATGTTCTCAA
Statistics
Matches: 205, Mismatches: 14, Indels: 37
0.80 0.05 0.14
Matches are distributed among these distances:
31 9 0.04
32 22 0.11
33 13 0.06
34 14 0.07
35 14 0.07
36 46 0.22
37 37 0.18
38 15 0.07
39 34 0.17
40 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATAATTTTCAAAAATT
Found at i:56436 original size:144 final size:144
Alignment explanation
Indices: 56285--56551 Score: 362
Period size: 144 Copynumber: 1.9 Consensus size: 144
56275 AAAGTTTTCA
* *
56285 AAACTATATGTTATAT-AGTTTTC-AAAATG-TTTTAAAAATATTATATAAGATTTCAAACAATG
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACA-TATATAAGATTTCAAA-AATG
* * * * *
56347 TTTTTAAAACTATATATTATATAA-TTTTCAAAAATATTTTTAAAAACTATATATTATATAATCT
64 TTTTAAAAACTATATACTATATAAGTTTTC-AAAAT-GTTTTAAAAACTATACAATATATAATCT
56411 TTCAAAAAATATTTTTTT
127 TTCAAAAAATATTTTTTT
* * * * *
56429 AAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACCATATATTATATTTTAAAAATGTT
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACATATATAAGATTTCAAAAATGTT
56494 TTAAAAACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATACAATATATAA
66 TTAAAAACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATACAATATATAA
56552 ATGTTCTCAA
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
144 37 0.35
145 37 0.35
146 24 0.22
147 9 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (144 bp):
AAACTATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACATATATAAGATTTCAAAAATGTT
TTAAAAACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATACAATATATAATCTTTCA
AAAAATATTTTTTT
Found at i:56489 original size:32 final size:32
Alignment explanation
Indices: 56440--56609 Score: 109
Period size: 32 Copynumber: 5.3 Consensus size: 32
56430 AACTATATAT
* *
56440 TATATAAT-TTTTCAAAAATGTTTTTAAAACCA
1 TATATTATATTTT-AAAAATGTTTTAAAAACCA
*
56472 TATATTATATTTTAAAAATGTTTTAAAAACTA
1 TATATTATATTTTAAAAATGTTTTAAAAACCA
*
56504 TATACTATATAAGTTTTCAAAATGTTTTAAAAA-C-
1 TATA-T-TAT-A-TTTTAAAAATGTTTTAAAAACCA
* * * * * **
56538 TATA-CA-A-TATATAAATGTTCTCAAAATTA
1 TATATTATATTTTAAAAATGTTTTAAAAACCA
* * *
56567 TACATTATATTTTAAAAATATTTTCAAAAACTA
1 TATATTATATTTTAAAAATGTTTT-AAAAACCA
*
56600 TATAATATAT
1 TATATTATAT
56610 AAATTTTCGA
Statistics
Matches: 105, Mismatches: 22, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
27 14 0.13
29 4 0.04
30 1 0.01
31 2 0.02
32 38 0.36
33 19 0.18
34 7 0.07
35 1 0.01
36 19 0.18
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (32 bp):
TATATTATATTTTAAAAATGTTTTAAAAACCA
Found at i:56553 original size:27 final size:27
Alignment explanation
Indices: 56523--56613 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 27
56513 TAAGTTTTCA
56523 AAATGTTTTAAAAACTATACAATATAT
1 AAATGTTTTAAAAACTATACAATATAT
* * * *
56550 AAATGTTCTCAAAATTATACATTATATTTTAA
1 AAATGTTTTAAAAACTATACA--ATA---TAT
* *
56582 AAATATTTTCAAAAACTATATAATATAT
1 AAATGTTTT-AAAAACTATACAATATAT
56610 AAAT
1 AAAT
56614 TTTCGAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
27 18 0.38
28 6 0.12
29 3 0.06
31 3 0.06
32 9 0.19
33 9 0.19
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATACAATATAT
Found at i:56616 original size:37 final size:37
Alignment explanation
Indices: 56575--56687 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 37
56565 TATACATTAT
56575 ATTTTAAAAATATTTTCAAAAACTATATAATATATAA
1 ATTTTAAAAATATTTTCAAAAACTATATAATATATAA
* * * * *
56612 ATTTTCGAAAATCGTTTTCTAAAAATTATATATTATAT-T
1 ATTTT-AAAAAT-ATTTTC-AAAAACTATATAATATATAA
* * * *
56651 TTTTTAAAAACATTTTCACAAACTATATTACTATATA
1 ATTTTAAAAATATTTTCAAAAACTATA-TAATATATA
56688 CATATATATA
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
36 8 0.14
37 17 0.29
38 9 0.15
39 9 0.15
40 16 0.27
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (37 bp):
ATTTTAAAAATATTTTCAAAAACTATATAATATATAA
Found at i:56694 original size:2 final size:2
Alignment explanation
Indices: 56682--56711 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56672 ACTATATTAC
*
56682 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56712 ACAAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:61182 original size:44 final size:44
Alignment explanation
Indices: 61117--61213 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
61107 TTCTACTAAT
* *
61117 AAACTCCGCTAAAAGTCAGGTTATGTAGCGGCGTTTGTATACTA
1 AAACGCCGCTAAAAGTCAGGTTATATAGCGGCGTTTGTATACTA
* * * *
61161 AAACGCCGCTAAAGGTTAGGTTATATAGCGGCTTTTGTATTCTA
1 AAACGCCGCTAAAAGTCAGGTTATATAGCGGCGTTTGTATACTA
*
61205 AAATGCCGC
1 AAACGCCGC
61214 AACATGTTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (44 bp):
AAACGCCGCTAAAAGTCAGGTTATATAGCGGCGTTTGTATACTA
Found at i:64125 original size:65 final size:62
Alignment explanation
Indices: 64056--64215 Score: 173
Period size: 65 Copynumber: 2.5 Consensus size: 62
64046 AATTAAATTG
*
64056 AACATCGAATGCATTTCATGCATCAATGCACA-TACCATGCACCGATGCA-CTGAG-TATGTTAT
1 AACATCGAATGCATTTGATGCATCAATGCACAGT--CATGCACCGATGCACCTG-GCTAT-TT-T
64118 GAA
61 G-A
* * * *
64121 AACATTGAATGCATTTGATGCATCGATACACCAGTCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCAATGCA-CAGTCATGCACCGATGCAC-CTGGCTATTTTGA
*
64185 AACATCGAATGCACTTGATGCATCAATGCAC
1 AACATCGAATGCATTTGATGCATCAATGCAC
64216 TCTTAGTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
63 1 0.01
64 27 0.33
65 41 0.51
66 5 0.06
67 7 0.09
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTGATGCATCAATGCACAGTCATGCACCGATGCACCTGGCTATTTTGA
Found at i:70045 original size:24 final size:24
Alignment explanation
Indices: 70017--70096 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
70007 CACTTAACAA
70017 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
70041 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
70062 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
70085 TGCATCGATGCA
1 TGCATCGATGCA
70097 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:72407 original size:22 final size:22
Alignment explanation
Indices: 72381--72425 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
72371 AGTAAGGGGG
72381 AGTAATTTGGA-GTAATTTTCAA
1 AGTAATTT-GATGTAATTTTCAA
*
72403 AGTAATTTGATTTAATTTTCAA
1 AGTAATTTGATGTAATTTTCAA
72425 A
1 A
72426 ATTGATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (22 bp):
AGTAATTTGATGTAATTTTCAA
Found at i:72898 original size:65 final size:64
Alignment explanation
Indices: 72744--72953 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
72734 TCTTTCAGAG
* * * *
72744 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCACC-ATACATGCACCGATGCACTCAGGATATT--A-TGAAACATCGAATGC
72806 ATT
62 ATT
* * * *
72809 TCATGCATCGATGCA-CATACCATGCACCGATGCATTGAGGATGTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCATA-CATGCACCGATGCACTCAGGATATTATG-AAACATCGAATGCAT
72873 T
64 T
** * * * *
72874 TGATGCATCGATGCACCAGT-CATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCA-TACATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCATT
72938 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
72954 TCTTAGTGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 4 0.03
64 46 0.38
65 65 0.54
66 4 0.03
67 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCATACATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCATT
Found at i:74484 original size:22 final size:22
Alignment explanation
Indices: 74446--74510 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
74436 AGGTAAAAAT
*
74446 AAAATGAA-AATAAAATATATAA
1 AAAATGAATAA-ATAATATATAA
74468 AAAATGAATAAATAATATGA-AA
1 AAAATGAATAAATAATAT-ATAA
* *
74490 ATAATAAAT-AATAATAGTATA
1 AAAATGAATAAATAATA-TATA
74511 GGGATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.22
22 25 0.69
23 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (22 bp):
AAAATGAATAAATAATATATAA
Found at i:76217 original size:28 final size:28
Alignment explanation
Indices: 76157--76216 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
76147 GAAGATTCGA
*
76157 TTTTTCAAGAGAAACATTTTCAACGGTT
1 TTTTTCAAGAGAAACAATTTCAACGGTT
*
76185 TTTTTCAAGAGAAACAATTTCAA-GATT
1 TTTTTCAAGAGAAACAATTTCAACGGTT
76212 TTTTT
1 TTTTT
76217 TTATGTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (28 bp):
TTTTTCAAGAGAAACAATTTCAACGGTT
Found at i:76262 original size:33 final size:31
Alignment explanation
Indices: 76159--76298 Score: 128
Period size: 35 Copynumber: 4.4 Consensus size: 31
76149 AGATTCGATT
*
76159 TTTCAAGAGAAAC-ATTTTCAACGG--TTTT-
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTTTTG
* **
76187 TTTCAAGAGAAACAATTTCAAGATTTTTTTTTATG
1 TTTCAAGAGAAACGATTTCAA-A--GGTTTTT-TG
76222 TTTCAAGAGAAACGATTTCAAAGGTTTTCTGTG
1 TTTCAAGAGAAACGATTTCAAAGGTTTT-T-TG
*
76255 TTTCAAGAGAAAACGATTTCAAAGG-TATTTG
1 TTTCAAGAG-AAACGATTTCAAAGGTTTTTTG
76286 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
76299 TGTCTCAAGA
Statistics
Matches: 94, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
28 19 0.20
29 1 0.01
30 4 0.04
31 11 0.12
32 5 0.05
33 17 0.18
34 17 0.18
35 20 0.21
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTTTTG
Found at i:76291 original size:31 final size:34
Alignment explanation
Indices: 76220--76297 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
76210 TTTTTTTTTA
*
76220 TGTTTCAAGAG-AAACGATTTCAAAGGTTTTCTG
1 TGTTTCAAGAGAAAACGATTTCAAAGGTTATCTG
76253 TGTTTCAAGAGAAAACGATTTCAAAGG-TAT-T-
1 TGTTTCAAGAGAAAACGATTTCAAAGGTTATCTG
76284 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
76298 CTGTCTCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 14 0.33
32 1 0.02
33 13 0.30
34 15 0.35
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (34 bp):
TGTTTCAAGAGAAAACGATTTCAAAGGTTATCTG
Found at i:76405 original size:30 final size:30
Alignment explanation
Indices: 76371--76427 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
76361 GTAAAACATA
*
76371 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
76401 TTCAAAGTTTATGTTTCAAGAGAAACT
1 TTCAAAGTTTATGTTTCAAGAGAAACT
76428 CTCTCAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:76563 original size:36 final size:36
Alignment explanation
Indices: 76513--76598 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
76503 TCAACGTTTA
* * *
76513 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAATT
*
76549 TGTTTCAAGGGAAACTATCTCAAGAGAAACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAATT
** *
76585 CATTTCAAGTGAAA
1 TGTTTCAAGAGAAA
76599 TATTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAATT
Found at i:76709 original size:104 final size:102
Alignment explanation
Indices: 76384--76869 Score: 639
Period size: 101 Copynumber: 4.9 Consensus size: 102
76374 AAAGATTTTG
* *
76384 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTCTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
76448 TGTTTCAAGGGAAACTATCTCAAG--AGATTAAATATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAAAGA-CAAA-ATTCA
* *
76486 TTTCAAGGGATATGTTTTCAACGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
76550 GTTTCAAGGGAAACTATCTCAAGAGAA-ACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGA-AAGACAAAATTCA
* * *
76587 TTTCAAGTGAAATATTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTC
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-
* *
76652 CTGCTTCGAGGGAAACTATCTCAAGAAAGACAAAATTCA
65 -TGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTCA
*
76691 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* *
76756 GTTTCAAGGGAAACTATCTCAAGAGAGA-TAAA---A
66 GTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTCA
76789 TTTCAAGGG--A-------AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* *
76845 CTGCTTCGAGGGAAACTATCTCAAG
65 -TGTTTCAAGGGAAACTATCTCAAG
76870 CGAGATAAAC
Statistics
Matches: 353, Mismatches: 22, Indels: 29
0.87 0.05 0.07
Matches are distributed among these distances:
89 41 0.12
90 3 0.01
91 22 0.06
96 1 0.00
98 10 0.03
101 137 0.39
102 42 0.12
103 3 0.01
104 94 0.27
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTCA
Found at i:76776 original size:37 final size:37
Alignment explanation
Indices: 76718--76791 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
76708 TCAATGTTTA
* * *
76718 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
76755 TGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
76792 CAAGGGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:76805 original size:89 final size:91
Alignment explanation
Indices: 76710--76878 Score: 288
Period size: 89 Copynumber: 1.9 Consensus size: 91
76700 AAATGTTTTC
* *
76710 AATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TTT-TGTTTCAAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGCTTCAAGGGAAACTAT
76773 CTCAAGAGAGATAAAATTTCAAGGGA
66 CTCAAGAGAGATAAAATTTCAAGGGA
*
76799 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGCTTCGAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGCTTCAAGGGAAACTAT
*
76864 CTCAAGCGAGATAAA
66 CTCAAGAGAGATAAA
76879 CTCTTGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
89 41 0.55
90 3 0.04
91 30 0.41
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (91 bp):
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGCTTCAAGGGAAACTAT
CTCAAGAGAGATAAAATTTCAAGGGA
Found at i:76933 original size:36 final size:36
Alignment explanation
Indices: 76874--77006 Score: 108
Period size: 36 Copynumber: 3.7 Consensus size: 36
76864 CTCAAGCGAG
* * * *
76874 ATAAACTCTTGTTTTAAGAAAAACAATATTGAGGGAA
1 ATAAA-TCTTCTTTCAAGTAAAACAATCTTGAGGGAA
* * ** * *
76911 ATAAATCTTCTTTCGAGTAAAACAGTCTCAAGTGAG
1 ATAAATCTTCTTTCAAGTAAAACAATCTTGAGGGAA
* * *
76947 ACAAAGTATGT-TTT-AAGAAAAACAATCTTGAGGGAA
1 ATAAA-TCT-TCTTTCAAGTAAAACAATCTTGAGGGAA
76983 ATAAATCTTCTTTCAAGTAAAACA
1 ATAAATCTTCTTTCAAGTAAAACA
77007 GTCTCAAGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
34 1 0.01
35 5 0.07
36 53 0.76
37 10 0.14
38 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (36 bp):
ATAAATCTTCTTTCAAGTAAAACAATCTTGAGGGAA
Found at i:76940 original size:73 final size:72
Alignment explanation
Indices: 76863--77096 Score: 342
Period size: 72 Copynumber: 3.2 Consensus size: 72
76853 AGGGAAACTA
* * * * *
76863 TCTCAAGCGAGATAAACTCTTGTTTTAAGAAAAACAATATTGAGGGAAATAAATCTTCTTTCGAG
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAG
76928 TAAAACAG
65 TAAAACAG
*
76936 TCTCAAGTGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGT
77001 AAAACAG
66 AAAACAG
* ** ** *
77008 TCTCAAGTGAGACAATGTCTGTTTTAAGAATGACAATCTCAAGGGGAAATAAATATTCTTTCAAG
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGA-GGGAAATAAATCTTCTTTCAAG
77073 TAAAACAG
65 TAAAACAG
77081 TCTCAAGTGAGACAAA
1 TCTCAAGTGAGACAAA
77097 TCATCTGTAT
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 87 0.60
73 59 0.40
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (72 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGT
AAAACAG
Found at i:78248 original size:83 final size:87
Alignment explanation
Indices: 78151--78377 Score: 248
Period size: 95 Copynumber: 2.6 Consensus size: 87
78141 GGCTAGGTGA
*
78151 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-TAT-GTA-AAT-ACC
1 ATCCATAAAGCTGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAATTATAGTATAATCACC
* *
78212 TTTATCAGGTTAGCTGAATCTT
66 TTTATCAGGCTAGCTGAATATT
* * * *
78234 ATCCATAAATCTGGGGCATTTAACCAATTTC-CTTAGAGGAACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTACTC-TAGAGGGACAGCTC-A-----A-T-TATAGT
78298 ATAATCACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
78329 ATCCATAAAGCCGGGGCGTTTAACCAATTACTTTAGAGGGACAACTCAA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAA
78378 GATTTATTGT
Statistics
Matches: 117, Mismatches: 13, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
82 1 0.01
83 41 0.35
84 1 0.01
89 2 0.02
92 3 0.03
93 3 0.03
94 4 0.03
95 62 0.53
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (87 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAATTATAGTATAATCACC
TTTATCAGGCTAGCTGAATATT
Found at i:78377 original size:95 final size:95
Alignment explanation
Indices: 78209--78390 Score: 274
Period size: 95 Copynumber: 1.9 Consensus size: 95
78199 ATATGTAAAT
* * * * *
78209 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAATCTGGGGCATTTAACCAATTTCCTTAGAGGA
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTACCTTAGAGGA
* *
78274 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGATTTATTGTATAGTATAATC
* * *
78304 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTACTTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTACCTTAGAGGA
78369 ACAACTCAAGATTTATTGTATA
66 ACAACTCAAGATTTATTGTATA
78391 TAAATAATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTACCTTAGAGGA
ACAACTCAAGATTTATTGTATAGTATAATC
Found at i:82567 original size:2 final size:2
Alignment explanation
Indices: 82562--82611 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
82552 AAAAAACTTT
82562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82604 TA TA TA TA
1 TA TA TA TA
82612 AAGTAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82680 original size:21 final size:23
Alignment explanation
Indices: 82647--82700 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
82637 AATAAAATGA
82647 AAATAAAAT-ATAT-AAAA-AAT
1 AAATAAAATAATATGAAAATAAT
*
82667 GAATAAAATAATATGAAAATAAT
1 AAATAAAATAATATGAAAATAAT
82690 AAATAATAATA
1 AAATAA-AATA
82701 GTATCGGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 4 0.14
23 8 0.29
24 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATAAAATAATATGAAAATAAT
Found at i:85429 original size:83 final size:82
Alignment explanation
Indices: 85325--85484 Score: 230
Period size: 83 Copynumber: 1.9 Consensus size: 82
85315 AACAAACGCA
** * * *
85325 ACTATGATGAACTCTATTACGGCATTTGTATAAAAACGCCGTTATCGTACTACTATGTTGCGGCG
1 ACTATGATGAACTCTATTACGGCATTTGTATAAAAACGCCGCCAACGTACTAATATGTTGAGGCG
85390 TTTGTTGAAAAAATATC
66 TTTGTTGAAAAAATATC
* * * *
85407 ACTATAGATGAACTTTATTACGGCGTTTGTATAAAAACGCCGCCAACGTATTAATCTGTTGAGGC
1 ACTAT-GATGAACTCTATTACGGCATTTGTATAAAAACGCCGCCAACGTACTAATATGTTGAGGC
85472 GTTTGTTGAAAAA
65 GTTTGTTGAAAAA
85485 CGCCACTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
82 5 0.07
83 63 0.93
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (82 bp):
ACTATGATGAACTCTATTACGGCATTTGTATAAAAACGCCGCCAACGTACTAATATGTTGAGGCG
TTTGTTGAAAAAATATC
Found at i:89730 original size:2 final size:2
Alignment explanation
Indices: 89717--89780 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
89707 CATCTTTTTC
*
89717 AT AT AT AC 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
89759 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
89781 GAAGTTTACA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97968 original size:22 final size:22
Alignment explanation
Indices: 97941--97996 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
97931 ATCTCATATG
97941 TGTAGATGATTTTAGTTTCAAA
1 TGTAGATGATTTTAGTTTCAAA
97963 TGTAGATGATTTTAGTTTCAAA
1 TGTAGATGATTTTAGTTTCAAA
*
97985 TGTGGATGATTT
1 TGTAGATGATTT
97997 ACTTTTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (22 bp):
TGTAGATGATTTTAGTTTCAAA
Found at i:104836 original size:42 final size:42
Alignment explanation
Indices: 104765--104850 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
104755 ACATGTCATT
*
104765 ATCTTATGGTGATGCATTAAAATCATTGTTAAATTTTTAACA
1 ATCTTATGGTGATGCATCAAAATCATTGTTAAATTTTTAACA
* *
104807 ATCTTATGGTGATGCATCAATATCGTTGTTAAATTTTTAACA
1 ATCTTATGGTGATGCATCAAAATCATTGTTAAATTTTTAACA
104849 AT
1 AT
104851 GGATTATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (42 bp):
ATCTTATGGTGATGCATCAAAATCATTGTTAAATTTTTAACA
Found at i:108200 original size:15 final size:15
Alignment explanation
Indices: 108180--108229 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
108170 CGTATTGGTG
108180 CGCATGAATCCAATA
1 CGCATGAATCCAATA
*
108195 CGCATGAATCCAATG
1 CGCATGAATCCAATA
*
108210 CACATGAATCCAATA
1 CGCATGAATCCAATA
*
108225 TGCAT
1 CGCAT
108230 TGGTCCAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (15 bp):
CGCATGAATCCAATA
Found at i:108509 original size:39 final size:39
Alignment explanation
Indices: 108465--108573 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
108455 TGGCATCTCG
*
108465 CGTGGGGTCCAAGAAGGAAATTGTCATGGTGCACATTCA
1 CGTGGGGTCCAAGAAGGAAATTGTCATGGTGCACACTCA
* * * *
108504 CGTGGGATCCAAGAAGAAAATTGGCATGGTGTACACTCA
1 CGTGGGGTCCAAGAAGGAAATTGTCATGGTGCACACTCA
*
108543 CGTGGGGTCCAAGAAAGAAATTGTCATGGTG
1 CGTGGGGTCCAAGAAGGAAATTGTCATGGTG
108574 TGGCAAATAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (39 bp):
CGTGGGGTCCAAGAAGGAAATTGTCATGGTGCACACTCA
Found at i:111887 original size:17 final size:17
Alignment explanation
Indices: 111865--111899 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
111855 GTTTTATGGC
111865 TAAACTCATAACAAACT
1 TAAACTCATAACAAACT
111882 TAAACTCATAACAAACT
1 TAAACTCATAACAAACT
111899 T
1 T
111900 TACTCTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAACTCATAACAAACT
Found at i:116663 original size:9 final size:8
Alignment explanation
Indices: 116644--116679 Score: 54
Period size: 9 Copynumber: 4.2 Consensus size: 8
116634 ACCCACCTTA
116644 TTTTTCTT
1 TTTTTCTT
116652 TTTTTCTCT
1 TTTTTCT-T
116661 TTTTTCTT
1 TTTTTCTT
116669 TTTGTTCTT
1 TTT-TTCTT
116678 TT
1 TT
116680 CTCTTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 11 0.42
9 15 0.58
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:116670 original size:16 final size:16
Alignment explanation
Indices: 116644--116686 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
116634 ACCCACCTTA
*
116644 TTTTTCTTTTTTTCTCT
1 TTTTTCTTTTTGT-TCT
116661 TTTTTCTTTTTGTTCT
1 TTTTTCTTTTTGTTCT
*
116677 TTTCTCTTTT
1 TTTTTCTTTT
116687 CTCTAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTGTTCT
Done.