Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001580.1 Hibiscus syriacus cultivar Beakdansim tig00003145_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: 72857
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3124 original size:26 final size:26
Alignment explanation
Indices: 3085--3138 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
3075 ATTTTTGCTT
* *
3085 TGATAAATATTTCTTTCGTTTAGTTA
1 TGATAAATAATTCTTTCGTTTAATTA
3111 TGATAAATAATTCTTTCGTTTAATTA
1 TGATAAATAATTCTTTCGTTTAATTA
3137 TG
1 TG
3139 CATGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (26 bp):
TGATAAATAATTCTTTCGTTTAATTA
Found at i:5832 original size:23 final size:22
Alignment explanation
Indices: 5793--5837 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5783 AAAAATACCA
5793 AAATAAAAATGAGTAAAATAATG
1 AAATAAAAATGAGTAAAA-AATG
*
5816 AAATAAATATGCA-TAAAAAATG
1 AAATAAAAATG-AGTAAAAAATG
5838 TCAAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 15 0.75
24 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.22
Consensus pattern (22 bp):
AAATAAAAATGAGTAAAAAATG
Found at i:7770 original size:67 final size:66
Alignment explanation
Indices: 7587--8161 Score: 347
Period size: 67 Copynumber: 8.4 Consensus size: 66
7577 TGTCTTGAAA
* * * * * * *
7587 GAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATATATGTTGTTTCATGAGAAAC-AGCCT
1 GAGACAAAATTTGTTTTAAGGGAAACAAT-TCAAAGGT-TTTG-TGTTTCAAGAGAAACTA-TCT
7651 CAAGG
62 CAAGG
* * *
7656 GAGACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTATTTCA
1 GAGACAAAA-TTTGTTTTAAGGGAAA-CAATTCAAAGGTTTTGTGTTTCAAGAGAAACTATCTCA
7721 AGG
64 AGG
*
7724 GAGACAAAATTTGTTTTAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC-ATTTTCA
1 GAGACAAAATTTGTTTTAAGGGAAACAAT-TCAAAGGTTTTGTGTTTCAAGAGAAACTA-TCTCA
*
7788 A-A
64 AGG
****** *
7790 G-GTTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTGTGTTTCAAGAGAAACT
1 GAGACAAAATTTGT-TTT-AAGGGAAACAA-TTCAAAGG-----TTTTGTGTTTCAAGAGAAACT
*
7854 GTCTCAAGG
58 ATCTCAAGG
* * ** * * *
7863 GTGACAAATTTTTGTTTTAAGAAAAACATATTCAAA-GATTGGTGTTTCAAGAGAAACTGTCTCA
1 GAGACAAA-ATTTGTTTTAAGGGAAACA-ATTCAAAGGTTTTGTGTTTCAAGAGAAACTATCTCA
7927 AGG
64 AGG
** * * *
7930 GAGACAAAATTTTGTTTTAAGAAAAACATATTCAAA-GATTGGTGTTTCAAGAGAAACTGTCTCA
1 GAGACAAAA-TTTGTTTTAAGGGAAACA-ATTCAAAGGTTTTGTGTTTCAAGAGAAACTATCTCA
*
7994 AGA
64 AGG
* ** *** * *
7997 GAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGAGAAACTG
1 GAGACAAAA-TTTGTTTTAAGGGAAACAAT-TCAA-AG-G---TTTTGTGTTTCAAGAGAAACTA
*
8062 TCTCAAGA
59 TCTCAAGG
* * * * * * * * **
8070 GAGACAAAACTTATTTCCAAAGAAAACAGATTCAAA-GATTT-TGCTTCAAGGGAAACCGTCTCA
1 GAGACAAAATTTGTTT-TAAGGGAAACA-ATTCAAAGGTTTTGTGTTTCAAGAGAAACTATCTCA
*
8133 AGA
64 AGG
*
8136 GAGACAAAATTTGTTTCAAGGGAAAC
1 GAGACAAAATTTGTTTTAAGGGAAAC
8162 TGTCTCAAGA
Statistics
Matches: 421, Mismatches: 57, Indels: 60
0.78 0.11 0.11
Matches are distributed among these distances:
65 14 0.03
66 45 0.11
67 185 0.44
68 31 0.07
69 13 0.03
70 24 0.06
71 2 0.00
72 32 0.08
73 63 0.15
74 6 0.01
75 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
GAGACAAAATTTGTTTTAAGGGAAACAATTCAAAGGTTTTGTGTTTCAAGAGAAACTATCTCAAG
G
Found at i:7808 original size:36 final size:36
Alignment explanation
Indices: 7761--7852 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
7751 ATCTCAAAGG
* *
7761 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
7797 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
7833 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
7853 TGTCTCAAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (36 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
Found at i:7909 original size:30 final size:30
Alignment explanation
Indices: 7875--7986 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 30
7865 GACAAATTTT
*
7875 TGTTTTAAGAAAAACATATTCAAAGATTGG
1 TGTTTCAAGAAAAACATATTCAAAGATTGG
* * *
7905 TGTTTCAAGAGAAAC-TGTCTCAAGGGAGACAAAATT-T
1 TGTTTCAAGAAAAACATAT-TCAA---AG-----ATTGG
*
7942 TGTTTTAAGAAAAACATATTCAAAGATTGG
1 TGTTTCAAGAAAAACATATTCAAAGATTGG
*
7972 TGTTTCAAGAGAAAC
1 TGTTTCAAGAAAAAC
7987 TGTCTCAAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 22
0.66 0.11 0.24
Matches are distributed among these distances:
29 5 0.08
30 30 0.49
33 2 0.03
34 2 0.03
37 17 0.28
38 5 0.08
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAAAAACATATTCAAAGATTGG
Found at i:8015 original size:207 final size:207
Alignment explanation
Indices: 7631--8023 Score: 481
Period size: 207 Copynumber: 1.9 Consensus size: 207
7621 AGATATATGT
* ** *
7631 TGTTTCATGAGAAACAGCCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATT
1 TGTTTCAAGAGAAACAGCCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACAAATTCAAAGATT
* * **
7696 TTGTGTTTCAAGAGAAACTATTTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAATCTCAAAGG
66 TGGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAAGG
* * * *******
7761 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAA
131 ATTGGTGTTTCAAGAGAAACATTCTCAAAGGACAAAACTTGTGTTTCAAGAGAAACAATTTCAAA
7826 GGTTTCTTTTTG
196 GGTTTCTTTTTG
* * * * *
7838 TGTTTCAAGAGAAACTGTCTCAAGGGTGACAAATTTTTGTTTTAAGAAAAACATATTCAAAGA-T
1 TGTTTCAAGAGAAACAGCCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACAAATTCAAAGATT
*
7902 TGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACATAT-TCAAA
66 TGGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTTGTTTTAAGAAAAACA-ATCTCAAA
*
7966 -GATTGGTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAACTT-TGTTTCAAGGGAAAC
129 GGATTGGTGTTTCAAGAGAAACAT-TCTCAA-AG-GACAAAACTTGTGTTTCAAGAGAAAC
8024 TGTCTCAAGA
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
205 1 0.01
206 59 0.38
207 91 0.58
208 5 0.03
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (207 bp):
TGTTTCAAGAGAAACAGCCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACAAATTCAAAGATT
TGGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAAGG
ATTGGTGTTTCAAGAGAAACATTCTCAAAGGACAAAACTTGTGTTTCAAGAGAAACAATTTCAAA
GGTTTCTTTTTG
Found at i:8059 original size:36 final size:36
Alignment explanation
Indices: 7972--8252 Score: 289
Period size: 36 Copynumber: 7.9 Consensus size: 36
7962 CAAAGATTGG
*
7972 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TA
*
8009 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
8045 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--TA
* * * *
8083 T-TTCCAA-AGAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATA
* * * *
8111 TGCTTCAAGGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
*
8147 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
8183 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT-
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TA
* *
8219 TAGTTCCAA-AGAAAACTGTCTCAAGGGAGACAAA
1 T-GTTTCAAGAG-AAACTGTCTCAAGAGAGACAAA
8253 TTTTTTTACA
Statistics
Matches: 209, Mismatches: 18, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
28 3 0.01
29 11 0.05
30 3 0.01
31 1 0.00
32 2 0.01
34 2 0.01
35 1 0.00
36 109 0.52
37 73 0.35
38 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
Found at i:8192 original size:21 final size:21
Alignment explanation
Indices: 8130--8194 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
8120 GGAAACCGTC
*
8130 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATATGTT
* *
8151 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATATGTT
8166 TCAAGAGAGACAAAATATGTT
1 TCAAGAGAGACAAAATATGTT
8187 TCAAGAGA
1 TCAAGAGA
8195 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATATGTT
Found at i:8199 original size:138 final size:140
Alignment explanation
Indices: 7905--8234 Score: 524
Period size: 138 Copynumber: 2.4 Consensus size: 140
7895 CAAAGATTGG
* *** *
7905 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT-TTGTTTTAAGAAAAACATATTCAAAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATT-TCCAAAG-AAAACAGATTCAAAGA
* *
7968 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
64 TTGGTGCTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
8033 AGAGACAAAATA
129 AGAGACAAAATA
8045 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAACAGATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAACAGATTCAAAGATT
* *
8110 -TTGCTTCAAGGGAAACCGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG
66 GGTGCTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
8173 AGACAAAATA
131 AGACAAAATA
*
8183 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAAC
8235 TGTCTCAAGG
Statistics
Matches: 178, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
138 89 0.50
139 31 0.17
140 50 0.28
141 6 0.03
142 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (140 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAACAGATTCAAAGATT
GGTGCTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
AGACAAAATA
Found at i:8205 original size:72 final size:73
Alignment explanation
Indices: 8114--8252 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
8104 AAGATTTTGC
* * * * *
8114 TTCAAGGGAAACCGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTGTCTCAAGAGAGACA
8178 AAATATGT
66 AAATATGT
* *
8186 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTGTCTCAAGGGAGACA
1 TTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTGTCTCAAGAGAGACA
8251 AA
66 AA
8253 TTTTTTTACA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 29 0.49
73 30 0.51
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (73 bp):
TTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTGTCTCAAGAGAGACA
AAATATGT
Found at i:8364 original size:36 final size:36
Alignment explanation
Indices: 8314--8384 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
8304 TCAAGGTTTA
*
8314 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* *
8350 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
8385 CTTCTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
Found at i:8494 original size:36 final size:36
Alignment explanation
Indices: 8441--8566 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
8431 GTGAAAACTG
* *
8441 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAA
* * * * ** * *
8477 TCTTAAGGGAAATAAATCTTCTTTCCAGTAAAACAG
1 TCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAA
* *
8513 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAATAACAA
1 TCTCAAGTGAGATAAA-TCTTGTTTTAAGAAAAACAA
8549 TCTCAAGTGAGATAAATC
1 TCTCAAGTGAGATAAATC
8567 ATCAGCATTA
Statistics
Matches: 69, Mismatches: 20, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
35 2 0.03
36 65 0.94
37 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAA
Found at i:9986 original size:95 final size:95
Alignment explanation
Indices: 9818--9999 Score: 283
Period size: 95 Copynumber: 1.9 Consensus size: 95
9808 ATATGTAAAT
* * * * *
9818 ACCTTTATCAGGTTAGCTGAATCTTATCCATTAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAAAGGG
* * *
9883 ATAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAACTTTATTGTATAGTATAATC
*
9913 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAAAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAAAGGG
9978 ACAACTCAAACTTTATTGTATA
66 ACAACTCAAACTTTATTGTATA
10000 TAAATAATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 78 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAAAGGG
ACAACTCAAACTTTATTGTATAGTATAATC
Found at i:13929 original size:19 final size:17
Alignment explanation
Indices: 13905--13941 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
13895 AAAAAGATAG
13905 ATAAATAAATTAAAATGAA
1 ATAAATAAA-T-AAATGAA
13924 ATAAATAAATAAATGAA
1 ATAAATAAATAAATGAA
13941 A
1 A
13942 GATATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAAATAAATAAATGAA
Found at i:14102 original size:18 final size:18
Alignment explanation
Indices: 14054--14118 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
14044 ATATACACAT
* * *
14054 AATAATAATACTATATAA
1 AATAAAAATAATATATTA
14072 TAATAAAACATAATATATTA
1 -AATAAAA-ATAATATATTA
* *
14092 AATAAAAATAAAAAATTA
1 AATAAAAATAATATATTA
14110 AACTAAAAA
1 AA-TAAAAA
14119 AATTAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 11 0.28
19 19 0.49
20 9 0.23
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAAATAATATATTA
Found at i:15890 original size:67 final size:67
Alignment explanation
Indices: 15748--16109 Score: 294
Period size: 67 Copynumber: 5.3 Consensus size: 67
15738 AGATATATGT
* * * * * *
15748 TGTTTCATGAGAAACGGCCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAGAAA-CAATTCAAAGGTT
15813 TTG
65 TTG
* * *
15816 TGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAATTTT-TTTCAAGGGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAGAAACAAT-TCAAAGGTT
15880 TTG
65 TTG
* **** *
15883 TGTTTCAAGAGAAACAT-TTTCAA---AG--GTTTTTTTGTGTTTCAAGAGAAACACTTTCAAAG
1 TGTTTCAAGAGAAAC-TGTCTCAAGGGAGACAAAATTTTGT-TTT-AAGAGAAACA-ATTCAAAG
15942 GTTTCTTTTTG
62 G-----TTTTG
* * *
15953 TGTTTCAAGAGAAATTGTCTCAAGGGTA-ACAAAATTTTGTTTTAAGAAAAACATATTCAAA-GA
1 TGTTTCAAGAGAAACTGTCTCAAGGG-AGACAAAATTTTGTTTTAAGAGAAACA-ATTCAAAGGT
*
16016 TTGG
64 TTTG
* * * *
16020 TGTTTCAAGAGAAATTGTCTCAAAGGAGACAAAATTTTGTTTTAAGAAAAACATATTCAAA-GAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAGAAACA-ATTCAAAGGTT
*
16084 TGG
65 TTG
* *
16087 TGTTTCTAGAGAAATTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
16110 TAGATATTTG
Statistics
Matches: 248, Mismatches: 27, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
62 4 0.02
63 1 0.00
64 4 0.02
65 16 0.06
66 5 0.02
67 132 0.53
68 35 0.14
69 1 0.00
70 24 0.10
72 1 0.00
73 15 0.06
74 4 0.02
75 6 0.02
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAGAAACAATTCAAAGGTTT
TG
Found at i:15958 original size:36 final size:34
Alignment explanation
Indices: 15854--15966 Score: 151
Period size: 34 Copynumber: 3.4 Consensus size: 34
15844 ACAAAATTTT
* * *
15854 TTTCAAGGGAAACAATCTCAAAGG---TTTTGTG
1 TTTCAAGAGAAACACTTTCAAAGGTTTTTTTGTG
*
15885 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTG
1 TTTCAAGAGAAACACTTTCAAAGGTTTTTTTGTG
15919 TTTCAAGAGAAACACTTTCAAAGGTTTCTTTTTGTG
1 TTTCAAGAGAAACACTTTCAAAGG-TT-TTTTTGTG
15955 TTTCAAGAGAAA
1 TTTCAAGAGAAA
15967 TTGTCTCAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 21 0.29
34 30 0.41
35 2 0.03
36 20 0.27
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (34 bp):
TTTCAAGAGAAACACTTTCAAAGGTTTTTTTGTG
Found at i:16162 original size:36 final size:36
Alignment explanation
Indices: 16115--16260 Score: 202
Period size: 36 Copynumber: 4.0 Consensus size: 36
16105 CTCAATAGAT
*
16115 ATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
1 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
16151 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
*
16187 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
** * * * * *
16223 ACTCAGCTCCAAAGAAAACTGTCTCAAGGGAGACAAA
1 A-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
16260 A
1 A
16261 AATTTTTACA
Statistics
Matches: 99, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 71 0.72
37 28 0.28
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (36 bp):
ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
Found at i:16199 original size:21 final size:21
Alignment explanation
Indices: 16137--16201 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
16127 GGAAACTATC
16137 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
16158 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
16173 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
16194 TCAAGAGA
1 TCAAGAGA
16202 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:17981 original size:95 final size:95
Alignment explanation
Indices: 17825--18006 Score: 258
Period size: 95 Copynumber: 1.9 Consensus size: 95
17815 ATATATAAAT
* * * * * *
17825 ACCTTTATCAGGTTAGCTTAATCTTATCCATAAAGCTAGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTACCAGGCTAACTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTGCCTTAGAGGG
* *
17890 ACAGCTCAATCTTTATTGTATAGTATAATC
66 ACAACTCAAACTTTATTGTATAGTATAATC
* *
17920 ACCTTTACCAGGCTAACTGAATATTATCCATAAAG-TCGGGGCATTTAACCAATTGCTTTAGAGG
1 ACCTTTACCAGGCTAACTGAATATTATCCATAAAGCT-AGGGCATTTAACCAATTGCCTTAGAGG
17984 GACAACTCAAACTTTATTGTATA
65 GACAACTCAAACTTTATTGTATA
18007 TAAATAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 75 0.99
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (95 bp):
ACCTTTACCAGGCTAACTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAACTTTATTGTATAGTATAATC
Found at i:20797 original size:17 final size:16
Alignment explanation
Indices: 20766--20799 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20756 CATGTGAGGA
20766 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
20782 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
20799 T
1 T
20800 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:31027 original size:17 final size:16
Alignment explanation
Indices: 30996--31029 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
30986 CACGTGAGGA
30996 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
31012 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
31029 T
1 T
31030 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:33584 original size:21 final size:21
Alignment explanation
Indices: 33558--33607 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
33548 CATAACATGA
33558 TGCATCGATGCATGATCAAGG
1 TGCATCGATGCATGATCAAGG
33579 TGCATCGATGCATGATCAAGG
1 TGCATCGATGCATGATCAAGG
33600 TGCATCGA
1 TGCATCGA
33608 CACCCCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCATGATCAAGG
Found at i:33685 original size:20 final size:21
Alignment explanation
Indices: 33660--33714 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
33650 TTGCAGCCTT
*
33660 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
*
33680 GATGCATCGATTCATGGCAAG
1 GATGCATCGATGCATGGCAAG
33701 GATGCATCGATGCA
1 GATGCATCGATGCA
33715 CTAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:33947 original size:30 final size:29
Alignment explanation
Indices: 33894--33952 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33884 AACTTTGAAT
33894 AAATTCAATTCAAATCCAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAACATTTTGC
*
33923 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCC-AAAACATTTTGC
33953 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATTCAATTCAAATCCAAAACATTTTGC
Found at i:34534 original size:20 final size:20
Alignment explanation
Indices: 34498--34535 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34488 AAAGTTTTCC
*
34498 AAAAATTTTTATGCAATTTA
1 AAAAATTTATATGCAATTTA
34518 AAAAATTTGATAT-CAATT
1 AAAAATTT-ATATGCAATT
34536 GCTAAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAAATTTATATGCAATTTA
Found at i:35290 original size:19 final size:20
Alignment explanation
Indices: 35247--35294 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
35237 TCTAAATCCT
*
35247 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
35267 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
35286 TTTTCAAAA
1 TTTTCAAAA
35295 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:36614 original size:20 final size:21
Alignment explanation
Indices: 36589--36643 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
36579 TTGCAGCCTT
36589 GATGCATGGATGCATGGC-AG
1 GATGCATGGATGCATGGCAAG
*
36609 GATGCATCGATGCATGGCAAG
1 GATGCATGGATGCATGGCAAG
36630 GATGCATGGATGCA
1 GATGCATGGATGCA
36644 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.20
Consensus pattern (21 bp):
GATGCATGGATGCATGGCAAG
Found at i:36689 original size:20 final size:22
Alignment explanation
Indices: 36664--36719 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
36654 TCGATGTTTG
*
36664 GATGCATGGATGCATT-G-CCT
1 GATGCATGGATGCATTAGTCCA
* *
36684 GATGCATCGATGCATTAGTGCA
1 GATGCATGGATGCATTAGTCCA
36706 GATGCATGGATGCA
1 GATGCATGGATGCA
36720 CTTTGACACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (22 bp):
GATGCATGGATGCATTAGTCCA
Found at i:36836 original size:30 final size:30
Alignment explanation
Indices: 36802--36861 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
36792 AACTTTGAAT
36802 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
36832 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
36862 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:37970 original size:18 final size:18
Alignment explanation
Indices: 37922--37986 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
37912 ATATACACAT
* * *
37922 AATAATAATACTATATAA
1 AATAAAAATAATATATTA
37940 TAATAAAACATAATATATTA
1 -AATAAAA-ATAATATATTA
* *
37960 AATAAAAATAAAAAATTA
1 AATAAAAATAATATATTA
37978 AACTAAAAA
1 AA-TAAAAA
37987 ATTAAAATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 11 0.28
19 19 0.49
20 9 0.23
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAAATAATATATTA
Found at i:37984 original size:13 final size:13
Alignment explanation
Indices: 37968--37992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37958 TAAATAAAAA
37968 TAAAAAATTAAAC
1 TAAAAAATTAAAC
37981 TAAAAAATTAAA
1 TAAAAAATTAAA
37993 ATACAAATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAATTAAAC
Found at i:39266 original size:4 final size:4
Alignment explanation
Indices: 39257--39377 Score: 110
Period size: 4 Copynumber: 30.8 Consensus size: 4
39247 CTAATTTCCT
*
39257 CTCC CTCC CTCC CTCC CTCTC C-CT CTCC CTCC CTCC CTCC CT-- CTCC
1 CTCC CTCC CTCC CTCC CTC-C CTCC CTCC CTCC CTCC CTCC CTCC CTCC
*
39303 CTCC CTCC CTCC CTCC CT-C CT-C CTCC CTCTC C-CC CTCCC CTCC TCTCT
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC-C CTCC CT-CC CTCC -CTCC
* * * *
39351 CTCT CTCC CTCT CTCT CTCT CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTC
39378 TCTCTCTCTC
Statistics
Matches: 102, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.02
3 9 0.09
4 80 0.78
5 11 0.11
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (4 bp):
CTCC
Found at i:39277 original size:18 final size:18
Alignment explanation
Indices: 39261--39388 Score: 117
Period size: 18 Copynumber: 7.2 Consensus size: 18
39251 TTTCCTCTCC
39261 CTCCCTCCCTCCCTCTCCCT
1 CTCCCTCCCT-CC-CTCCCT
39281 CTCCCTCCCTCCCTCCCT
1 CTCCCTCCCTCCCTCCCT
39299 CTCCCTCCCTCCCT-CC-
1 CTCCCTCCCTCCCTCCCT
39315 CTCCCT-CCT-CCTCCCT
1 CTCCCTCCCTCCCTCCCT
39331 CT-CC-CCCTCCC-CTCCT
1 CTCCCTCCCTCCCTC-CCT
* *
39347 CTCTCTCTCTCCCTCTCTCT
1 CTCCCTCCCTCCCTC-C-CT
* * *
39367 CTCTCTCCCTCTCTCTCT
1 CTCCCTCCCTCCCTCCCT
39385 CTCC
1 CTCC
39389 ATCTCTCTCT
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
14 3 0.03
15 11 0.12
16 15 0.16
17 3 0.03
18 31 0.33
19 5 0.05
20 25 0.27
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCCCTCCCTCCCTCCCT
Found at i:39352 original size:2 final size:2
Alignment explanation
Indices: 39345--39406 Score: 90
Period size: 2 Copynumber: 31.0 Consensus size: 2
39335 CCCTCCCCTC
* *
39345 CT CT CT CT CT CT CC CT CT CT CT CT CT CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39387 C- CAT CT CT CT CT CT CT CT CT
1 CT C-T CT CT CT CT CT CT CT CT
39407 AGTTTTTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.02, C:0.53, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:39378 original size:8 final size:8
Alignment explanation
Indices: 39255--39403 Score: 121
Period size: 8 Copynumber: 18.6 Consensus size: 8
39245 AACTAATTTC
39255 CTCTCCCT
1 CTCTCCCT
*
39263 CCCTCCCT
1 CTCTCCCT
*
39271 CCCTCTCC-
1 CTCTC-CCT
39279 CTCTCCCT
1 CTCTCCCT
*
39287 CCCTCCCT
1 CTCTCCCT
39295 CCCTCTCCCT
1 --CTCTCCCT
*
39305 CCCTCCCT
1 CTCTCCCT
*
39313 CCCTCCCT
1 CTCTCCCT
39321 CCTCCTCCCT
1 -CT-CTCCCT
39331 CTC-CCC-
1 CTCTCCCT
39337 CTC-CCCT
1 CTCTCCCT
*
39344 CCTCTCTCT
1 -CTCTCCCT
39353 CTCTCCCT
1 CTCTCCCT
*
39361 CTCTCTCT
1 CTCTCCCT
39369 CTCTCCCT
1 CTCTCCCT
39377 CTCT--CT
1 CTCTCCCT
*
39383 CTCTCCAT
1 CTCTCCCT
*
39391 CTCTCTCT
1 CTCTCCCT
39399 CTCTC
1 CTCTC
39404 TCTAGTTTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
6 12 0.10
7 5 0.04
8 79 0.68
9 8 0.07
10 13 0.11
ACGTcount: A:0.01, C:0.65, G:0.00, T:0.34
Consensus pattern (8 bp):
CTCTCCCT
Found at i:39393 original size:14 final size:14
Alignment explanation
Indices: 39255--39406 Score: 118
Period size: 14 Copynumber: 11.0 Consensus size: 14
39245 AACTAATTTC
* *
39255 CTCTCCCTCCCTCC
1 CTCTCTCTCCCTCT
*
39269 CTCCCTCTCCCTCT
1 CTCTCTCTCCCTCT
* * *
39283 CCCTCCCTCCCTCC
1 CTCTCTCTCCCTCT
*
39297 CTCTCCCTCCCTC-
1 CTCTCTCTCCCTCT
*
39310 C-CTCCCTCCCTCCT
1 CTCTCTCTCCCT-CT
*
39324 CCTCCCTCTCCC-C-
1 -CTCTCTCTCCCTCT
*
39337 CTC-CCCT-CCTCT
1 CTCTCTCTCCCTCT
39349 CTCTCTCTCCCTCTCT
1 CTCTCTCT-CC-CTCT
39365 CTCTCTCTCCCTCT
1 CTCTCTCTCCCTCT
*
39379 CTCTCTCTCCATCT
1 CTCTCTCTCCCTCT
*
39393 CTCTCTCTCTCTCT
1 CTCTCTCTCCCTCT
39407 AGTTTTTGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.02
11 4 0.04
12 16 0.14
13 5 0.04
14 63 0.56
15 4 0.04
16 19 0.17
ACGTcount: A:0.01, C:0.64, G:0.00, T:0.35
Consensus pattern (14 bp):
CTCTCTCTCCCTCT
Found at i:42514 original size:2 final size:2
Alignment explanation
Indices: 42507--42574 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
42497 TCTAACAATA
42507 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
42549 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
42575 TTGTTTGTAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47932 original size:34 final size:34
Alignment explanation
Indices: 47873--47939 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
47863 TTCTTGAGAG
*
47873 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
47907 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
47940 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:49538 original size:23 final size:23
Alignment explanation
Indices: 49512--49566 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
49502 GGATTTACAA
49512 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
49535 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
49558 GAACCAATT
1 GAACCAATT
49567 GCAACCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
GAACCAATTCAAGCGAATGGCTT
Found at i:49606 original size:54 final size:55
Alignment explanation
Indices: 49535--49655 Score: 165
Period size: 54 Copynumber: 2.2 Consensus size: 55
49525 CGAATGGCTT
* * ** *
49535 GAACCAA-TTCAAGCGAATGGCTTGAACCAATTGCAACCATTTATTTATTTGCAA
1 GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
* *
49589 GAACCAACTCCAA-CGAATGACTTGGACCAGTTGCAACCATTTATGGATTCGCAA
1 GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
49643 GAACCAACTCCAA
1 GAACCAACTCCAA
49656 TGATTGATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 55 0.93
55 4 0.07
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (55 bp):
GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
Found at i:50043 original size:136 final size:131
Alignment explanation
Indices: 49866--50139 Score: 433
Period size: 136 Copynumber: 2.1 Consensus size: 131
49856 CTTCAACGAC
49866 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACC-AAAAGCAT
1 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
** *
49930 AAAAGAAAGAAAAGAAAAAAAGAATGTAAATTCCATGAAATCTGGGCATCCCATGCTGGTGCCCA
66 ---A-AAAG-AAAGAAAAAAA-AATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCCA
49995 TGTCTGG
125 TGTCTGG
* *
50002 TCACTGTAATCACCATTTTTTATCCCAAAATTATTTATTATTCTATTATTATTACCAAAAAGCAT
1 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
*
50067 AAAAGAAAGAAAAAAAAATGTAAATTCCATGAAATCAAGGCATTCCATGCTGGAGCCCATGTCTG
66 AAAAGAAAGAAAAAAAAATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCCATGTCTG
50132 G
131 G
50133 TCACTGT
1 TCACTGT
50140 TGTTGCACCC
Statistics
Matches: 131, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
131 53 0.40
132 11 0.08
133 4 0.03
134 1 0.01
136 54 0.41
137 8 0.06
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (131 bp):
TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
AAAAGAAAGAAAAAAAAATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCCATGTCTG
G
Found at i:53949 original size:2 final size:2
Alignment explanation
Indices: 53942--53994 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
53932 AACCCACATA
53942 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
53984 AT AT AT AT AT A
1 AT AT AT AT AT A
53995 ATAAAATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54131 original size:17 final size:18
Alignment explanation
Indices: 54096--54131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54086 CAACTTAAAA
*
54096 AAGATGAACAATTCAAAG
1 AAGATGAACAATCCAAAG
54114 AAGATGAACAA-CCAAAG
1 AAGATGAACAATCCAAAG
54131 A
1 A
54132 TGAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.11
Consensus pattern (18 bp):
AAGATGAACAATCCAAAG
Found at i:55923 original size:15 final size:15
Alignment explanation
Indices: 55903--55931 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55893 CTCTGACGGT
55903 GCTGACGACGACAAG
1 GCTGACGACGACAAG
55918 GCTGACGACGACAA
1 GCTGACGACGACAA
55932 ACAAGGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.28, G:0.31, T:0.07
Consensus pattern (15 bp):
GCTGACGACGACAAG
Found at i:68318 original size:20 final size:20
Alignment explanation
Indices: 68289--68327 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68279 ATTCTACCAC
*
68289 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
68309 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
68328 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Done.