Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002736.1 Hibiscus syriacus cultivar Beakdansim tig00005640_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: 87377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4176 original size:28 final size:29
Alignment explanation
Indices: 4119--4180 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
4109 TGGCTAAGAT
4119 AGAACCAAAAACCTTTACAAAGGATAAAA
1 AGAACCAAAAACCTTTACAAAGGATAAAA
*
4148 AGAACCAAAACCCTTTACAAAGGATAAAA
1 AGAACCAAAAACCTTTACAAAGGATAAAA
4177 AGAA
1 AGAA
4181 GTAAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (29 bp):
AGAACCAAAAACCTTTACAAAGGATAAAA
Found at i:4588 original size:18 final size:18
Alignment explanation
Indices: 4565--4611 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
4555 ATACAAAGTA
4565 GTATCGGTACCCCTTTGG
1 GTATCGGTACCCCTTTGG
*
4583 GTATCGATACCCCTTTGG
1 GTATCGGTACCCCTTTGG
4601 GTATCGGTACC
1 GTATCGGTACC
4612 ATTTATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.32
Consensus pattern (18 bp):
GTATCGGTACCCCTTTGG
Found at i:16928 original size:60 final size:60
Alignment explanation
Indices: 16799--16928 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
16789 ACATATGAAG
* * *
16799 AATCGAGTGATCT-TTTTATAACTTTTAATAGTCAGGGGACTCAACAAAGCAACGCCCTAT
1 AATCGAGGGAT-TATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAGCAACACCCTAT
* * * * *
16859 AATCTAGGGATTATTTTGTAACTTTTAATAGTC-GAAGGACTCAACAAAGTAATACCTTAT
1 AATCGAGGGATTATTTTATAACTTTTAATAGTCAG-AGGACTCAACAAAGCAACACCCTAT
*
16919 AGTCGAGGGA
1 AATCGAGGGA
16929 CCATTTGTGT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
59 2 0.03
60 56 0.97
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (60 bp):
AATCGAGGGATTATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAGCAACACCCTAT
Found at i:16943 original size:60 final size:60
Alignment explanation
Indices: 16812--16943 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
16802 CGAGTGATCT
* * * * **
16812 TTTTATAACTTTTAATAGTCAGGGGACTCAACAAAGCAACGCCCTATAATCTAGGGATTA
1 TTTTGTAACTTTTAATAGTCAGAGGACTCAACAAAGCAACACCCTATAATCGAGGGACCA
* * * *
16872 TTTTGTAACTTTTAATAGTC-GAAGGACTCAACAAAGTAATACCTTATAGTCGAGGGACCA
1 TTTTGTAACTTTTAATAGTCAG-AGGACTCAACAAAGCAACACCCTATAATCGAGGGACCA
16932 TTTGTGT-ACTTT
1 TTT-TGTAACTTT
16944 ACCCTTTTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.02
60 56 0.93
61 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGTCAGAGGACTCAACAAAGCAACACCCTATAATCGAGGGACCA
Found at i:26848 original size:18 final size:18
Alignment explanation
Indices: 26828--26909 Score: 112
Period size: 18 Copynumber: 4.6 Consensus size: 18
26818 TGTTTATGAG
* *
26828 GGAATTAGAATCTGGGAG
1 GGAATTAGAATCTGTGAA
26846 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
26864 TGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* *
26882 CGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
26899 GGAATTAGAAT
1 GGAATTAGAAT
26910 TCAATTCCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 11 0.19
18 47 0.81
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:27647 original size:37 final size:37
Alignment explanation
Indices: 27565--27661 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
27555 TCCTACTAGA
* * **
27565 ATTCAAACTCCTAAAAACAGGATAGAATTTTGCTAGG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTAATAGG
* **
27602 ATTCAAACTCCTAAAAATAGGATAGAGTTCTAATATT
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTAATAGG
* *
27639 ATTTAAACTCCTAAAGATAGGAT
1 ATTCAAACTCCTAAAAATAGGAT
27662 CCACAAGCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
ATTCAAACTCCTAAAAATAGGATAGAATTCTAATAGG
Found at i:28108 original size:23 final size:23
Alignment explanation
Indices: 28057--28118 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
28047 TAACTCTTAT
* *
28057 TATTTATATGTATATATTTAATTA
1 TATTT-TATTTATTTATTTAATTA
28081 TATTTTATTTATTTATTT-ATTA
1 TATTTTATTTATTTATTTAATTA
*
28103 TAATTTTTTTTCATTT
1 T-ATTTTATTT-ATTT
28119 TTCTTTACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.15
23 19 0.58
24 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTTATTTATTTATTTAATTA
Found at i:28392 original size:26 final size:26
Alignment explanation
Indices: 28343--28419 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
28333 CTATTTAGTA
* * *
28343 TTTTA-TTATATTATACATACATTTT
1 TTTTATTTATACTATATATATATTTT
28368 TATATT-TTTATA-TATATATATATTTT
1 T-T-TTATTTATACTATATATATATTTT
* *
28394 TTTTATTTATACTATTTATTTATTTT
1 TTTTATTTATACTATATATATATTTT
28420 CATTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
24 2 0.05
25 8 0.19
26 26 0.60
27 7 0.16
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTATTTATACTATATATATATTTT
Found at i:28396 original size:28 final size:29
Alignment explanation
Indices: 28364--28432 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 29
28354 TATACATACA
28364 TTTTTATATTTTTATA-TATATATATATT
1 TTTTTATATTTTTATACTATATATATATT
* *
28392 TTTTT-TA--TTTATACTATTTATTTATT
1 TTTTTATATTTTTATACTATATATATATT
*
28418 TTCATTATATTTTTA
1 TT-TTTATATTTTTA
28433 GTTTCTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 6 0.18
26 12 0.36
27 4 0.12
28 7 0.21
30 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTATATTTTTATACTATATATATATT
Found at i:28540 original size:20 final size:19
Alignment explanation
Indices: 28513--28569 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
28503 TTTTATCTTC
28513 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
28532 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
28553 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
28570 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:32821 original size:16 final size:14
Alignment explanation
Indices: 32796--32850 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
32786 CAAAAAGGGC
*
32796 AAAAAGAAAAAAGA
1 AAAAACAAAAAAGA
32810 AAATAAGCAAAAAAGA
1 AAA-AA-CAAAAAAGA
32826 AGAAAACAAAAAA-A
1 A-AAAACAAAAAAGA
32840 AAAGAACAAAA
1 AAA-AACAAAA
32851 TCAAAAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 2 0.06
14 12 0.33
15 9 0.25
16 11 0.31
17 2 0.06
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAACAAAAAAGA
Found at i:32830 original size:19 final size:19
Alignment explanation
Indices: 32796--32864 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
32786 CAAAAAGGGC
*
32796 AAAAAGAAAA-AAGAAAAT
1 AAAAAAAAAAGAAGAAAAT
** *
32814 AAGCAAAAAAGAAGAAAAC
1 AAAAAAAAAAGAAGAAAAT
*
32833 AAAAAAAAAAGAACAAAAT
1 AAAAAAAAAAGAAGAAAAT
32852 CAAAAAGAAAAAG
1 -AAAAA-AAAAAG
32865 GGACAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
18 7 0.17
19 22 0.55
20 5 0.12
21 6 0.15
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAAAAT
Found at i:34588 original size:106 final size:106
Alignment explanation
Indices: 34462--34896 Score: 654
Period size: 106 Copynumber: 4.1 Consensus size: 106
34452 ATATCGTGCC
* * * *
34462 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
34527 AAATTCAGAGCCAATTTGAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
34568 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAACGCTGGTTGTCAACATACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
34633 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
34674 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
34739 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * * *
34780 ACTCAAGACAATGCAAGTTCAACTTCATGACAAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
34845 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
34886 ACTCTAGACAA
1 ACTCCAGACAA
34897 TGCAAGGACC
Statistics
Matches: 301, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 301 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:34740 original size:212 final size:212
Alignment explanation
Indices: 34462--35727 Score: 1662
Period size: 212 Copynumber: 6.0 Consensus size: 212
34452 ATATCGTGCC
* * * * *
34462 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCC
* * * * *
34527 AAATTCAGAGCCAATTTGAACTTCACAGCGAAGGATATTAGACTCCAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
34592 TCACGACGAAGGGAACGCTGGTTGTCAACATACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
34657 ACAACGAAGGATATTGG
196 ACAACGAAGGATATTGG
* * *
34674 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCC
* * *
34739 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
34804 TCATGACAAAGGGACCGCTGGTTGTCAATAAACAACTT-TCCAATTTTAGAGCCAATTTCAACTT
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTTCAGAGCCAATTTCAACTT
*
34868 CACAGCGAAGGATATTGG
195 CACAACGAAGGATATTGG
* * *
34886 ACT-----CTA-G--A---CAA--T---G-C-AA-GGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCC
* *
34932 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
34997 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTTAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
35062 A-AAGCGAAGGATATTGG
196 ACAA-CGAAGGATATTGG
*
35079 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AA-AA------
* * * * *
35144 AATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTTCAGACAACGCAA
58 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
** *
35209 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAGTTTC-CTAATTTCGGAGCCAAT
123 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCCAAT
* * *
35273 TTCAACTTCACAGCAAAAGATATTGG
187 TTCAACTTCACAACGAAGGATATTGG
* * * *
35299 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCC
35364 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
35429 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
35494 ACAACGAAGGATATTGG
196 ACAACGAAGGATATTGG
* *
35511 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAA-AAAACAATTTCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAA-AACTTCC
* * * * *
35575 CAACTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * * * * * *
35640 TTCACAACAAAGGGA-CGATTGTTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTTCAACT
130 TTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACT
* * * *
35704 TTACGATGGAGGATATTGG
194 TCACAACGAAGGATATTGG
35723 ACTCG
1 ACTCG
35728 GAACAATGCT
Statistics
Matches: 928, Mismatches: 91, Indels: 70
0.85 0.08 0.06
Matches are distributed among these distances:
192 1 0.00
193 163 0.18
194 3 0.00
195 1 0.00
196 1 0.00
198 2 0.00
199 2 0.00
201 4 0.00
204 4 0.00
206 2 0.00
207 2 0.00
209 1 0.00
210 1 0.00
211 8 0.01
212 538 0.58
213 3 0.00
214 1 0.00
218 1 0.00
219 3 0.00
220 186 0.20
221 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
ACAACGAAGGATATTGG
Found at i:34964 original size:87 final size:87
Alignment explanation
Indices: 34815--34989 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 87
34805 CATGACAAAG
* * * *
34815 GGACCGCTGGTTGTCAATAAACAACTTTCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGA
1 GGACCGCTGGTTGTCAACAAACAACTTTCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
*
34880 TATTGGACTCTAGACAATGCAA
66 TATTGGACTCCAGACAATGCAA
34902 GGACCGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGG
1 GGACCGCTGGTTGTCAACAAACAACTTTC-CAATTTCAAAGCCAATTTCAACTTCACAACGAAGG
34966 ATATTGGACTCCAGACAATGCAA
65 ATATTGGACTCCAGACAATGCAA
34989 G
1 G
34990 TTCAACTTCA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 3 0.04
87 79 0.96
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (87 bp):
GGACCGCTGGTTGTCAACAAACAACTTTCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTCCAGACAATGCAA
Found at i:35032 original size:106 final size:106
Alignment explanation
Indices: 34902--35726 Score: 1186
Period size: 106 Copynumber: 7.7 Consensus size: 106
34892 GACAATGCAA
* *
34902 GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
*
34967 TATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAG
66 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
35008 GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTTAACTTCA-AAGCGAAGG
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA-CGAAGG
*
35072 ATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAG
65 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
35114 GGACCGCTGCTTGTCAACAAACAATTTCCCAATTTCCCAATTTCGGAGCCAATTTCAACTTCACA
1 GGACCGCTGGTTGTCAACAAACAA-----C---TTCCCAATTTCAGAGCCAATTTCAACTTCACA
* * *
35179 GCGAAAGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
58 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
** * * * * *
35228 GGACCGCTGGTTGTCAACAAACAGTTTCCTAATTTCGGAGCCAATTTCAACTTCACAGCAAAAGA
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
*
35293 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
66 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
35334 GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
35399 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
66 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
35440 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
*
35505 TATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAG
66 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * * * *
35546 GGACCGCTGGTTGTTAAAAAACAATTTCCCAACTTCGGAGCCAATTTCAACTTCACAACAAAGGA
1 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
* * * *
35611 TATTGGACTCGAGACAACACAAGTTCAACTTCACAACAAAG
66 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * * * * * * *
35652 GGA-CGATTGTTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTTCAACTTTACGATGGAGG
1 GGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
35716 ATATTGGACTC
65 ATATTGGACTC
35727 GGAACAATGC
Statistics
Matches: 656, Mismatches: 52, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
105 4 0.01
106 556 0.85
111 1 0.00
114 94 0.14
115 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
Found at i:36528 original size:37 final size:37
Alignment explanation
Indices: 36475--36579 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
36465 CCTTTTCGTC
*
36475 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
36512 TTTCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
36549 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
36580 CCACCAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:37024 original size:23 final size:24
Alignment explanation
Indices: 36996--37043 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
36986 AATATGTATA
36996 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
37019 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
37043 T
1 T
37044 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:37103 original size:11 final size:11
Alignment explanation
Indices: 37056--37103 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
37046 CTTTGCGTTA
37056 TATTATATTAT
1 TATTATATTAT
* *
37067 TTTTCTATTAT
1 TATTATATTAT
37078 TATTATA-TAT
1 TATTATATTAT
37088 ATATTATATTAT
1 -TATTATATTAT
37100 TATT
1 TATT
37104 TTTTTATCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 3 0.10
11 25 0.81
12 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATATTAT
Found at i:37329 original size:42 final size:42
Alignment explanation
Indices: 37283--37371 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
37273 CTATTTAGTA
*
37283 TTTTATTATATTATACATAC-ATTT-TTATATTTTTATATATAT
1 TTTTATTATATTATACATACTATTTATT-TATTTTCAT-TATAT
* **
37325 TTTTATTATTTTATTTATACTATTTATTTATTTTCATTATAT
1 TTTTATTATATTATACATACTATTTATTTATTTTCATTATAT
37367 TTTTA
1 TTTTA
37372 GTTTCTTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 27 0.66
43 12 0.29
44 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.66
Consensus pattern (42 bp):
TTTTATTATATTATACATACTATTTATTTATTTTCATTATAT
Found at i:37355 original size:22 final size:20
Alignment explanation
Indices: 37231--37371 Score: 72
Period size: 22 Copynumber: 6.8 Consensus size: 20
37221 TTAGTTAATA
*
37231 TTATATGTATATTTATT-TT
1 TTATATATATATTTATTATT
* * *
37250 TCATTTATTTA-TTATTATT
1 TTATATATATATTTATTATT
* *
37269 ATTACTATTTAGTATTTTATTATA
1 -TTA-TATATA-TA-TTTATTATT
* * *
37293 TTATACATACATTTTTATATTT
1 TTATATATATATTTAT-TA-TT
*
37315 TTATATATATTTTTATTATT
1 TTATATATATATTTATTATT
*
37335 TTATTTATACTATTTATTTATT
1 TTATATATA-TATTTA-TTATT
*
37357 TTCAT-TATATTTTTA
1 TT-ATATATATATTTA
37372 GTTTCTTTGC
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
18 5 0.06
19 9 0.10
20 16 0.18
21 18 0.20
22 30 0.33
23 5 0.06
24 7 0.08
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
TTATATATATATTTATTATT
Found at i:37479 original size:20 final size:19
Alignment explanation
Indices: 37452--37507 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
37442 TTTTATCTTC
37452 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
37471 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
37491 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
37508 ATTATTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:43263 original size:16 final size:17
Alignment explanation
Indices: 43242--43277 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43232 ATTTATGACT
43242 ATTTTGGA-AAATTTGA
1 ATTTTGGATAAATTTGA
*
43258 ATTTTGGATTAATTTGA
1 ATTTTGGATAAATTTGA
43275 ATT
1 ATT
43278 AATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (17 bp):
ATTTTGGATAAATTTGA
Found at i:43863 original size:27 final size:25
Alignment explanation
Indices: 43824--43882 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 25
43814 TATCAACATG
*
43824 AAATAAAAATTAAACAAGGATAAAT
1 AAATAAAAATTAAACAACGATAAAT
*
43849 AAATAAGATAATTAAGCAACGATAAAT
1 AAATAA-A-AATTAAACAACGATAAAT
43876 AAATAAA
1 AAATAAA
43883 TACATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
26 2 0.07
27 22 0.73
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.20
Consensus pattern (25 bp):
AAATAAAAATTAAACAACGATAAAT
Found at i:45844 original size:3 final size:3
Alignment explanation
Indices: 45786--45835 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
45776 TGGCTTGTAA
* * * *
45786 AAT AAT AAT AGT AAT AAT AAT AGT AGT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
45834 AA
1 AA
45836 AGAATAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48334 original size:22 final size:22
Alignment explanation
Indices: 48307--48359 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
48297 AGAATTTTAA
*
48307 AAAAATGTTTAATGAAGTTTTG
1 AAAAATGGTTAATGAAGTTTTG
* *
48329 AAAAATGGTTGATGAATTTTTG
1 AAAAATGGTTAATGAAGTTTTG
48351 AAAAATGGT
1 AAAAATGGT
48360 GCCCCCTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.38
Consensus pattern (22 bp):
AAAAATGGTTAATGAAGTTTTG
Found at i:52108 original size:15 final size:16
Alignment explanation
Indices: 52077--52108 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52067 ATAACCATTT
52077 TTTTAAAAATAACTTA
1 TTTTAAAAATAACTTA
52093 TTTTAAAAATAA-TTA
1 TTTTAAAAATAACTTA
52108 T
1 T
52109 GTCTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATAACTTA
Found at i:52725 original size:27 final size:25
Alignment explanation
Indices: 52686--52744 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 25
52676 TATCAACATG
52686 AAATAAAAATTAAGCAAGGATAAAT
1 AAATAAAAATTAAGCAAGGATAAAT
*
52711 AAATAAGATAATTAAGCAATGATAAAT
1 AAATAA-A-AATTAAGCAAGGATAAAT
52738 AAATAAA
1 AAATAAA
52745 TACATGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 6 0.19
26 2 0.06
27 23 0.74
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.22
Consensus pattern (25 bp):
AAATAAAAATTAAGCAAGGATAAAT
Found at i:55342 original size:16 final size:16
Alignment explanation
Indices: 55321--55375 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
55311 GGTATTACCC
*
55321 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
55337 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
*
55353 GACCTGTTTTTAACCG
1 GACCTGTTTTTAACCT
55369 GACCTGT
1 GACCTGT
55376 AAATGATCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:55626 original size:14 final size:14
Alignment explanation
Indices: 55604--55650 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
55594 TGTGAAGGAA
*
55604 AATTAATATAGTTT
1 AATTTATATAGTTT
55618 AATTTATATA----
1 AATTTATATAGTTT
55628 AA-TTATATAGTTT
1 AATTTATATAGTTT
55641 AATTTATATA
1 AATTTATATA
55651 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:55637 original size:23 final size:24
Alignment explanation
Indices: 55603--55652 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
55593 ATGTGAAGGA
55603 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
55627 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
55650 AAA
1 AAA
55653 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:58948 original size:102 final size:99
Alignment explanation
Indices: 58772--58999 Score: 339
Period size: 102 Copynumber: 2.3 Consensus size: 99
58762 ATAAACAACG
* *
58772 AACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGACAGCTAACAACCTTATAAA
1 AACAGTAGCAACAAATTAAACAATTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
58837 AACAATCCGAATGAACAACCAACAACACAAACAAATC
66 AACAATCCGAATGAA-AA--AACAACACAAACAAATC
* * * *
58874 AACAGTAGCAACAAATTGAACAATTTATTTAAACTCTAAATAAAGGCATCTAACAACCTTATAGA
1 AACAGTAGCAACAAATTAAACAATTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
** *
58939 AGTAATCCGAATGAAAAACCAACACAAACAAATC
66 AACAATCCGAATGAAAAAACAACACAAACAAATC
*
58973 AACAGTAGCAACAAATTAAACATTTTA
1 AACAGTAGCAACAAATTAAACAATTTA
59000 GTTACCTATT
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
99 41 0.36
101 2 0.02
102 72 0.63
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (99 bp):
AACAGTAGCAACAAATTAAACAATTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
AACAATCCGAATGAAAAAACAACACAAACAAATC
Found at i:59239 original size:32 final size:33
Alignment explanation
Indices: 59171--59273 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 33
59161 TGAAACCCTT
* * *
59171 GAAAGAAAGGATTCAAATATCAACCAAAAAACAGA
1 GAAA-AAACGATTCGAATATCAACC-AAAAATAGA
59206 GAAAAAA-GATTCGAATATCAACCAAAAATAGA
1 GAAAAAACGATTCGAATATCAACCAAAAATAGA
*
59238 GAAAAAACGATTCGATTATCAACCAAAAATAGA
1 GAAAAAACGATTCGAATATCAACCAAAAATAGA
59271 GAA
1 GAA
59274 TTTGAGAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
32 15 0.23
33 42 0.66
34 3 0.05
35 4 0.06
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.15
Consensus pattern (33 bp):
GAAAAAACGATTCGAATATCAACCAAAAATAGA
Found at i:59315 original size:13 final size:13
Alignment explanation
Indices: 59297--59324 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
59287 GAGAGCTAGT
59297 GAGATCAAAATGA
1 GAGATCAAAATGA
59310 GAGATCAAAATGA
1 GAGATCAAAATGA
59323 GA
1 GA
59325 TAAATGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.25, T:0.14
Consensus pattern (13 bp):
GAGATCAAAATGA
Found at i:61039 original size:20 final size:22
Alignment explanation
Indices: 61014--61061 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
61004 TAAGGGTTAC
61014 GGTTTAGGATT-TAAAGTTTA-
1 GGTTTAGGATTATAAAGTTTAG
*
61034 GGTTTA-GATTATCAAGTTTAG
1 GGTTTAGGATTATAAAGTTTAG
61055 GGTTTAG
1 GGTTTAG
61062 AGTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (22 bp):
GGTTTAGGATTATAAAGTTTAG
Found at i:61208 original size:13 final size:13
Alignment explanation
Indices: 61192--61250 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
61182 GTACTATAAG
61192 TTACATATATAGT
1 TTACATATATAGT
*
61205 TTACAT-TACATGT
1 TTACATATATA-GT
*
61218 ATACATACTATAAG-
1 TTACATA-TAT-AGT
61232 TTACATATATAGT
1 TTACATATATAGT
61245 TTACAT
1 TTACAT
61251 TACATGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 5 0.14
13 22 0.59
14 6 0.16
15 3 0.08
16 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (13 bp):
TTACATATATAGT
Found at i:61215 original size:18 final size:18
Alignment explanation
Indices: 61192--61260 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
61182 GTACTATAAG
61192 TTACATATATAGTTTACA
1 TTACATATATAGTTTACA
* *
61210 TTACATGTATACATACTATA-A
1 TTACA--TAT--ATAGTTTACA
61231 GTTACATATATAGTTTACA
1 -TTACATATATAGTTTACA
*
61250 TTACATGTATA
1 TTACATATATA
61261 CACATACTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 21 0.52
19 1 0.03
20 6 0.15
21 1 0.03
22 11 0.28
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (18 bp):
TTACATATATAGTTTACA
Found at i:61234 original size:40 final size:41
Alignment explanation
Indices: 61183--61283 Score: 186
Period size: 40 Copynumber: 2.5 Consensus size: 41
61173 TACATACATG
61183 TACTATAAGTTACATATATAGTTTACATTACATGTAT-ACA
1 TACTATAAGTTACATATATAGTTTACATTACATGTATAACA
61223 TACTATAAGTTACATATATAGTTTACATTACATGTATACACA
1 TACTATAAGTTACATATATAGTTTACATTACATGTATA-ACA
61265 TACTATAAGTTACATATAT
1 TACTATAAGTTACATATAT
61284 TAACTATTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 37 0.63
42 22 0.37
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.40
Consensus pattern (41 bp):
TACTATAAGTTACATATATAGTTTACATTACATGTATAACA
Found at i:61629 original size:77 final size:75
Alignment explanation
Indices: 61499--61743 Score: 193
Period size: 77 Copynumber: 3.2 Consensus size: 75
61489 TTTCTTTAAT
* *
61499 ATATATATATATA-TATATATATATATATATATATATATA-TATATATTCTATATA--T-TACTT
1 ATATATATATATATTA-ATATATAT-TATA-ATATATAAACTATATATTCTATATAGTTATACAT
61559 ATATTAGTTATGCATAC
63 ATA-TAGTT-T--ATAC
* *
61576 ATATATATACTATATTAATATAAATTATAACATATAAACTATATAGTT-TATATAGTTTATACAT
1 ATATATATA-TATATTAATATATATTATAATATATAAACTATATA-TTCTATATAG-TTATACAT
*
61640 ATATAGTTTATAT
63 ATATAGTTTATAC
* * * * *
61653 ATATATATAGTATATTAATATATATAATATTTTATAAACTATATATT-TTTGTAGTTTATAC--A
1 ATATATATA-TATATTAATATATATTATAATATATAAACTATATATTCTATATAG-TTATACATA
61715 TATAGTTTATATAC
64 TATAG-TT-TATAC
*
61729 ATAGTTTATATATAT
1 ATA-TATATATATAT
61744 AGTTCACATA
Statistics
Matches: 142, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
74 6 0.04
75 2 0.01
76 33 0.23
77 72 0.51
78 13 0.09
79 3 0.02
80 6 0.04
81 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (75 bp):
ATATATATATATATTAATATATATTATAATATATAAACTATATATTCTATATAGTTATACATATA
TAGTTTATAC
Found at i:61644 original size:15 final size:15
Alignment explanation
Indices: 61624--61659 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
61614 CTATATAGTT
61624 TATATAGTTTATACA
1 TATATAGTTTATACA
*
61639 TATATAGTTTATATA
1 TATATAGTTTATACA
61654 TATATA
1 TATATA
61660 TAGTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:61654 original size:13 final size:13
Alignment explanation
Indices: 61624--61908 Score: 103
Period size: 13 Copynumber: 21.5 Consensus size: 13
61614 CTATATAGTT
61624 TATATAGTTTATACA
1 TATATAGTTTAT--A
61639 TATATAGTTTATA
1 TATATAGTTTATA
*
61652 TATATA-TATAGTA
1 TATATAGTTTA-TA
* *
61665 TAT-TAATATATA
1 TATATAGTTTATA
*
61677 TA-ATATTTTATA
1 TATATAGTTTATA
*
61689 AACTATA-TATT-T-
1 TA-TATAGT-TTATA
*
61701 T-TGTAGTTTATA
1 TATATAGTTTATA
*
61713 CATATAGTTTATA
1 TATATAGTTTATA
*
61726 TACATAGTTTATA
1 TATATAGTTTATA
*
61739 TATATAGTTCACATA
1 TATATAGTT--TATA
* * *
61754 AACATAATTTATA
1 TATATAGTTTATA
61767 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
61784 TTATATAGTTTATA
1 -TATATAGTTTATA
**
61798 -ATATA-AATATA
1 TATATAGTTTATA
* *
61809 GTTTATAATTTTATA
1 -TATAT-AGTTTATA
*
61824 TACATAGTTTATA
1 TATATAGTTTATA
**
61837 TATATAGTGCACATA
1 TATATAGT--TTATA
*
61852 AATATA-TTTATA
1 TATATAGTTTATA
*
61864 TATAGT-TTTTAATAA
1 TATA-TAGTTT-AT-A
61879 TTATATAGTTTATA
1 -TATATAGTTTATA
61893 TAT-T--TTTATA
1 TATATAGTTTATA
61903 TATATA
1 TATATA
61909 TATTATATTT
Statistics
Matches: 204, Mismatches: 35, Indels: 65
0.67 0.12 0.21
Matches are distributed among these distances:
10 14 0.07
11 7 0.03
12 29 0.14
13 78 0.38
14 16 0.08
15 40 0.20
16 10 0.05
17 3 0.01
18 7 0.03
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:61697 original size:2 final size:2
Alignment explanation
Indices: 61497--61682 Score: 117
Period size: 2 Copynumber: 95.0 Consensus size: 2
61487 TATTTCTTTA
61497 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
* ** *
61539 AT AT AT -T CT AT AT AT -T ACT -T AT AT -T AGT -T AT GC AT AC AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT
* * *
61578 AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT AT AA ACT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
61618 AT AGT TT AT AT AGT TT AT AC AT AT AT AGT TT AT AT AT AT AT AT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
61661 AGT AT AT -T A- AT AT AT AT A- AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT
61683 TTTATAAACT
Statistics
Matches: 144, Mismatches: 20, Indels: 40
0.71 0.10 0.20
Matches are distributed among these distances:
1 12 0.08
2 122 0.85
3 10 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61735 original size:26 final size:26
Alignment explanation
Indices: 61704--61780 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 26
61694 TATATTTTTG
* *
61704 TAGTTTATACATATAGTTTATATACA
1 TAGTTTATATATATAGTTTATAAACA
*
61730 TAGTTTATATATATAGTTCACATAAACA
1 TAGTTTATATATATAGTT--TATAAACA
* *
61758 TAATTTATATATATAGCTTATAA
1 TAGTTTATATATATAGTTTATAA
61781 TAATTATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 21 0.49
28 22 0.51
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (26 bp):
TAGTTTATATATATAGTTTATAAACA
Found at i:61807 original size:18 final size:18
Alignment explanation
Indices: 61763--61842 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
61753 AAACATAATT
*
61763 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
61781 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
61799 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
61817 TTTTATATACATAGTTTAT-A
1 ---TATATATATAGTTTATAA
61837 TATATA
1 TATATA
61843 GTGCACATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
17 7 0.13
18 30 0.57
19 1 0.02
20 1 0.02
21 14 0.26
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:62722 original size:64 final size:64
Alignment explanation
Indices: 62594--62733 Score: 201
Period size: 64 Copynumber: 2.2 Consensus size: 64
62584 GAACTGAAAA
*
62594 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCTGAACTGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCTGAACCGATT
* * * * *
62658 TGACCTGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTG-AATTGACCTGTATCCGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCTG-AACCGATT
*
62722 TTACCCGACCTG
1 TGACCCGACCTG
62734 CCAAGATCCG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 8 0.12
64 59 0.88
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (64 bp):
TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCTGAACCGATT
Found at i:62906 original size:11 final size:12
Alignment explanation
Indices: 62880--62920 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
62870 TTTATCCTTG
62880 TTTTATTTTTCA
1 TTTTATTTTTCA
62892 TTTTATTTTTC-
1 TTTTATTTTTCA
62903 TTTTACTTTTTCA
1 TTTTA-TTTTTCA
*
62916 ATTTA
1 TTTTA
62921 AAGAGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 17 0.65
13 4 0.15
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:67046 original size:22 final size:22
Alignment explanation
Indices: 67020--67063 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
67010 TCTACAAATA
67020 TTTACA-AAACTAACACCATAAT
1 TTTACACAAA-TAACACCATAAT
*
67042 TTTACACAAATATCACCATAAT
1 TTTACACAAATAACACCATAAT
67064 AGAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
TTTACACAAATAACACCATAAT
Found at i:69278 original size:26 final size:24
Alignment explanation
Indices: 69222--69282 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
69212 AATCATCGTT
*
69222 ATCATATGTCAGTGAAAACCAATA
1 ATCATATATCAGTGAAAACCAATA
69246 ATCATATATCAGTGAAAACCAATA
1 ATCATATATCAGTGAAAACCAATA
69270 ATCATATATCAGT
1 ATCATATATCAGT
69283 CATAGTCCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (24 bp):
ATCATATATCAGTGAAAACCAATA
Found at i:71771 original size:17 final size:17
Alignment explanation
Indices: 71748--71789 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
71738 TGATCAACAG
71748 TGGTCAACGCAAGTC-A
1 TGGTCAACGCAAGTCAA
*
71764 TCGGTCAATGCAAGTCAA
1 T-GGTCAACGCAAGTCAA
71782 TGGTCAAC
1 TGGTCAAC
71790 AGTCGACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (17 bp):
TGGTCAACGCAAGTCAA
Found at i:73356 original size:15 final size:15
Alignment explanation
Indices: 73319--73360 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
73309 TAACTTTTGA
* *
73319 AATTTATGATTATTT
1 AATTTATAATTTTTT
73334 -ATTT-TAATTTTTT
1 AATTTATAATTTTTT
73347 AATTTATAATTTTT
1 AATTTATAATTTTT
73361 AACTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
AATTTATAATTTTTT
Found at i:75509 original size:2 final size:2
Alignment explanation
Indices: 75502--75530 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
75492 CCTTCTTACT
75502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75531 GATACGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82207 original size:45 final size:44
Alignment explanation
Indices: 82088--82217 Score: 178
Period size: 45 Copynumber: 3.0 Consensus size: 44
82078 TTGGAGGAAG
*
82088 TTTCTGAAGGCTCCTCTTGCTGTGTGCAAGGGTGAGACC-TACC-A
1 TTTCTGAAGGCT-CT-ATGCTGTGTGCAAGGGTGAGACCTTACCGA
*
82132 TTTCTGAAGGCTCTA--CTGTGTGCAAGGGTGAGACCTTACCGT
1 TTTCTGAAGGCTCTATGCTGTGTGCAAGGGTGAGACCTTACCGA
*
82174 TTTCTGAAGGCTCATATGCTATGTGCAAGGGTGAGACCTTACCG
1 TTTCTGAAGGCTC-TATGCTGTGTGCAAGGGTGAGACCTTACCG
82218 CAGGCTCCTC
Statistics
Matches: 78, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
40 20 0.26
41 4 0.05
42 13 0.17
43 4 0.05
44 12 0.15
45 25 0.32
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (44 bp):
TTTCTGAAGGCTCTATGCTGTGTGCAAGGGTGAGACCTTACCGA
Found at i:82254 original size:39 final size:39
Alignment explanation
Indices: 82195--82286 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
82185 TCATATGCTA
* *
82195 TGTGCA-AGGGTGAGACCTTACCGCAGGCTCCTCGGTTT
1 TGTGCACAGGGTAAGACCTTACCGCAGGCTCCTCGGCTT
* * * * *
82233 TGTGCTCAGGGTAAGTCCTTACTGTAGGCTCCTCTGCTT
1 TGTGCACAGGGTAAGACCTTACCGCAGGCTCCTCGGCTT
*
82272 TGTGCACAGGTTAAG
1 TGTGCACAGGGTAAG
82287 CTTTATTGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 5 0.11
39 39 0.89
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.30
Consensus pattern (39 bp):
TGTGCACAGGGTAAGACCTTACCGCAGGCTCCTCGGCTT
Found at i:82747 original size:69 final size:68
Alignment explanation
Indices: 82665--82796 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 68
82655 ATATGATGAT
*
82665 TGATACTTTTAAATATTAAAAAAGTTGAAGATAAA-ATCAAAAGTTAAAAT-AGCAATATTTATG
1 TGATACTTTTAAATATTAAAAAAGTTGAAGA-AAAGATC-AAAGTTAAAATAAAC-ATATTTATG
82728 TGATAA
63 TGATAA
* * * *
82734 TGATACTTTTAAATATTGAAACAGTTGATGAAAAGATCAAATTTAAAATAAACATATTTATGT
1 TGATACTTTTAAATATTAAAAAAGTTGAAGAAAAGATCAAAGTTAAAATAAACATATTTATGT
82797 AATGAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
68 23 0.41
69 33 0.59
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.35
Consensus pattern (68 bp):
TGATACTTTTAAATATTAAAAAAGTTGAAGAAAAGATCAAAGTTAAAATAAACATATTTATGTGA
TAA
Found at i:82904 original size:14 final size:14
Alignment explanation
Indices: 82885--82911 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
82875 ATCGATACTT
82885 TGCTTTGATATTTA
1 TGCTTTGATATTTA
82899 TGCTTTGATATTT
1 TGCTTTGATATTT
82912 GTAGAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (14 bp):
TGCTTTGATATTTA
Found at i:83084 original size:15 final size:15
Alignment explanation
Indices: 83066--83095 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
83056 AATATTTTGT
*
83066 GACCTTCTCTTTTTC
1 GACCTTCTCATTTTC
83081 GACCTTCTCATTTTC
1 GACCTTCTCATTTTC
83096 TATGTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.33, G:0.07, T:0.50
Consensus pattern (15 bp):
GACCTTCTCATTTTC
Found at i:84084 original size:24 final size:23
Alignment explanation
Indices: 84034--84084 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
84024 ATTTTATGTA
* *
84034 TTAGGAGGATGAATTATAAACTT
1 TTAGGAGGATGAATTATAAAATG
84057 TTAGGA-GAGTGAACTTATAAAATG
1 TTAGGAGGA-TGAA-TTATAAAATG
84081 TTAG
1 TTAG
84085 ATGCCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 10 0.42
24 12 0.50
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (23 bp):
TTAGGAGGATGAATTATAAAATG
Found at i:84128 original size:17 final size:18
Alignment explanation
Indices: 84108--84141 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
84098 TTATCAATTA
84108 AAAAAATAT-AAAATTTT
1 AAAAAATATGAAAATTTT
*
84125 AAAATATATGAAAATTT
1 AAAAAATATGAAAATTT
84142 GAGATTTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAAAATATGAAAATTTT
Done.