Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007359.1 Hibiscus syriacus cultivar Beakdansim tig00019744_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: 97415
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:17176 original size:90 final size:90
Alignment explanation
Indices: 17019--17237 Score: 325
Period size: 90 Copynumber: 2.4 Consensus size: 90
17009 GTCTCATCAA
* * *
17019 CATGTTTGAAC-CTTCGTTCTCTTCTTTGTTGTAGAAGTAATTGGTAAGATCTTTTTCCATCTAT
1 CATGTTTAAACTC-TCGTTCTCTTCTATGTTGTAGAAGTAATTGGTAAGATCTTTCTCCATCTAT
**
17083 AAATCGAAAGATATTGTGTGATTAAG
65 AAATCGAAAGATATTGCATGATTAAG
* *
17109 CATGTTTAAACTCTCGTTCTCTTCTATGTTGTAGAAGTAATTGGTAAGATCTTTCTCTATCTTTA
1 CATGTTTAAACTCTCGTTCTCTTCTATGTTGTAGAAGTAATTGGTAAGATCTTTCTCCATCTATA
*
17174 AATCGAAAGATATTGCATGTTTAAG
66 AATCGAAAGATATTGCATGATTAAG
*
17199 CATGTTTGAAACT-TCATTCTCTTCTATGTTGTAGAAGTA
1 CATGTTT-AAACTCTCGTTCTCTTCTATGTTGTAGAAGTA
17238 TTAGTGAACA
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
90 112 0.95
91 6 0.05
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (90 bp):
CATGTTTAAACTCTCGTTCTCTTCTATGTTGTAGAAGTAATTGGTAAGATCTTTCTCCATCTATA
AATCGAAAGATATTGCATGATTAAG
Found at i:21742 original size:16 final size:16
Alignment explanation
Indices: 21721--21753 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21711 ACAATTCATC
21721 ATTTAAAA-ATATAAAT
1 ATTTAAAAGATA-AAAT
21737 ATTTAAAAGATAAAAT
1 ATTTAAAAGATAAAAT
21753 A
1 A
21754 ATACTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATTTAAAAGATAAAAT
Found at i:24548 original size:24 final size:24
Alignment explanation
Indices: 24516--24564 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
24506 TTTGGAAAGG
24516 TAAAACAGACATGGAATTCCTCTT
1 TAAAACAGACATGGAATTCCTCTT
* *
24540 TAAAACAGACATGGAGTTCTTCTT
1 TAAAACAGACATGGAATTCCTCTT
24564 T
1 T
24565 TTATGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (24 bp):
TAAAACAGACATGGAATTCCTCTT
Found at i:31894 original size:18 final size:19
Alignment explanation
Indices: 31854--31896 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
31844 TAACCATAAT
* * *
31854 ATATATATATTATTCTTTC
1 ATATATATAATATTATTTA
31873 ATAT-TATAATATTATTTA
1 ATATATATAATATTATTTA
31891 ATATAT
1 ATATAT
31897 CAAATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATATAATATTATTTA
Found at i:31923 original size:20 final size:21
Alignment explanation
Indices: 31898--31938 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31888 TTAATATATC
31898 AAATATAATC-TAAAATTATA
1 AAATATAATCATAAAATTATA
* *
31918 AAATATATTCATAATATTATA
1 AAATATAATCATAAAATTATA
31939 TTTTAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATATAATCATAAAATTATA
Found at i:32376 original size:158 final size:155
Alignment explanation
Indices: 32104--32461 Score: 454
Period size: 158 Copynumber: 2.3 Consensus size: 155
32094 TAGTTAAAAA
* * * * ** *
32104 AATTAAAGTTACACGA-GTATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTGGTAAAAAAA
1 AATTAAAG-TACAC-ATGTATTCTACTATGGTTTAGGAGCATGTGACTAAAATTTGGTAAAAAAA
* *
32168 GTGACTTGAAATAAATCACAAATTAAAGGAATAAGGAGATTATGAAAAATTGAAGGACTAAATTG
64 GTGACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTG
32233 AAAAATAAAAAATTTGTTATCAAAAAGAGG
129 AAAAATAAAAAA-TT-TTATC-AAAAGAGG
32263 AATTGAAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTGACTAAAATTTGGTAAAAAATA
1 AATT-AAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTGACTAAAATTTGGTAAAAAA-A
* * * * *
32328 -T-ATTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTAT-AACAAATTTAAGGACTAAATT
64 GTGACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAA-AAATTGAAGGACTAAATT
*
32390 GAAAAATAAAATATTTTATCAAAAGAGG
128 GAAAAATAAAAAATTTTATCAAAAGAGG
* *
32418 AATTTAAAGTACACATGTATTATACTATGGTTTAGGAGCTTGTG
1 AA-TTAAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTG
32462 GTTCAATTTT
Statistics
Matches: 177, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
155 47 0.27
156 7 0.04
157 4 0.02
158 64 0.36
159 50 0.28
160 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (155 bp):
AATTAAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTGACTAAAATTTGGTAAAAAAAGT
GACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAA
AAATAAAAAATTTTATCAAAAGAGG
Found at i:32490 original size:155 final size:158
Alignment explanation
Indices: 32139--32513 Score: 494
Period size: 155 Copynumber: 2.4 Consensus size: 158
32129 TGTGGTATAT
* * * * * *
32139 GAGCATGTGGTTCAAATTTGGTAAAAAAAGTGACTTGAAATAAATCACAAATTAAAGGAATAAGG
1 GAGCATGTGGTTCAAATTTGGT-AAAAAATTGACTTAAAATAAATGACGAATTGAAGAAATAAGG
32204 AGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGA
65 AGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGA
*
32269 AAGTACACATGTATTCTACTATGGTTTAG
130 AAGTACACATGTATTATACTATGGTTTAG
** * *
32298 GAGCATGTGACTAAAATTTGGTAAAAAATAT-ATTTAAAATAAATGACGAATTGAAGAAATAAGG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAT-TGACTTAAAATAAATGACGAATTGAAGAAATAAGG
* * *
32362 AGATTAT-AACAAATTTAAGGACTAAATTGAAAAATAAAATA-TT-TTATC-AAAAGAGGAATTT
65 AGATTATGAA-AAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTG
32423 AAAGTACACATGTATTATACTATGGTTTAG
129 AAAGTACACATGTATTATACTATGGTTTAG
* * **
32453 GAGCTTGTGGTTCAATTTTAATAAAAAATTGACTTAAAATGAAA-GA-GTAATTGAAGAAATA
1 GAGCATGTGGTTCAAATTTGGTAAAAAATTGACTTAAAAT-AAATGACG-AATTGAAGAAATA
32514 GTTAAATCAG
Statistics
Matches: 189, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
154 2 0.01
155 86 0.46
156 8 0.04
157 4 0.02
158 69 0.37
159 20 0.11
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (158 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAATTGACTTAAAATAAATGACGAATTGAAGAAATAAGGA
GATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAA
AGTACACATGTATTATACTATGGTTTAG
Found at i:33914 original size:21 final size:21
Alignment explanation
Indices: 33877--33917 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33867 ATTATTATAT
33877 TATTATTAAAATATTAATAAA
1 TATTATTAAAATATTAATAAA
*
33898 TATT-TTAAATATGTTAATAA
1 TATTATTAAA-ATATTAATAA
33918 TTAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTATTAAAATATTAATAAA
Found at i:34244 original size:34 final size:34
Alignment explanation
Indices: 34186--34287 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
34176 TGTATATACA
34186 ATTCCATAGCCAACC-AAATTGAAAAGTTCGCAT
1 ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
34219 ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
1 ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
34253 ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
1 ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
34287 A
1 A
34288 ACTCTAGTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
33 15 0.22
34 53 0.78
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (34 bp):
ATTCCATAGCCAACCAAAATTGAAAAGTTCGCAT
Found at i:48736 original size:32 final size:32
Alignment explanation
Indices: 48700--48767 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
48690 TTTGGAAGAT
*
48700 ATTTGGTGCCGTTGACTTG-CTTGTTCCTTTCA
1 ATTTGGCGCCGTTGACTTGTC-TGTTCCTTTCA
* *
48732 ATTTGGCGCTGTTGACTTGTCTGTTCCTTTCT
1 ATTTGGCGCCGTTGACTTGTCTGTTCCTTTCA
48764 ATTT
1 ATTT
48768 TTGATCTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (32 bp):
ATTTGGCGCCGTTGACTTGTCTGTTCCTTTCA
Found at i:49472 original size:42 final size:42
Alignment explanation
Indices: 49400--49523 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
49390 GAACTCCAAA
* ** * *
49400 AAATT-ATGAAAGATACGGGTGCTCCTGAAGCAGAAATCCAG
1 AAATTCATGAAAGATATGGACGCTACGGAAGCAGAAATCCAG
* * * *
49441 AAATTTATGGAAGATAT-GATTGCTACGGAAGCTGAAATCCAG
1 AAATTCATGAAAGATATGGA-CGCTACGGAAGCAGAAATCCAG
49483 AAATTCATGAAAGATATGGACGCTACGGAAGCAGAAATCCA
1 AAATTCATGAAAGATATGGACGCTACGGAAGCAGAAATCCA
49524 AAGAATTAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 6 0.09
42 62 0.89
43 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (42 bp):
AAATTCATGAAAGATATGGACGCTACGGAAGCAGAAATCCAG
Found at i:52507 original size:28 final size:28
Alignment explanation
Indices: 52456--52557 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 28
52446 TCCGTAGAGG
* * * *
52456 ATCTCATGCAGAAACATGACGGGAATATG
1 ATCTCATGCAGAATCAGGAAGGG-ATATA
*
52485 AT-TTATGCAGAATCAGGAAGGGATATA
1 ATCTCATGCAGAATCAGGAAGGGATATA
* * *
52512 ATCTCATACAGAATCAGGACGAGGATGTA
1 ATCTCATGCAGAATCAGGAAG-GGATATA
* *
52541 ATCCCATGTAGAATCAG
1 ATCTCATGCAGAATCAG
52558 AACGAGGATA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 6 0.10
28 31 0.53
29 22 0.37
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (28 bp):
ATCTCATGCAGAATCAGGAAGGGATATA
Found at i:52553 original size:29 final size:29
Alignment explanation
Indices: 52492--52573 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
52482 ATGATTTATG
* *
52492 CAGAATCAGGAAG-GGATATAATCTCATA
1 CAGAATCAGGACGAGGATATAATCCCATA
* *
52520 CAGAATCAGGACGAGGATGTAATCCCATG
1 CAGAATCAGGACGAGGATATAATCCCATA
* * *
52549 TAGAATCAGAACGAGGATATTATCC
1 CAGAATCAGGACGAGGATATAATCC
52574 TCCGTAAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 12 0.27
29 33 0.73
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (29 bp):
CAGAATCAGGACGAGGATATAATCCCATA
Found at i:54823 original size:35 final size:35
Alignment explanation
Indices: 54777--54845 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
54767 TTATAATATA
54777 TATATATATATATATATATATATCATATTATTATT
1 TATATATATATATATATATATATCATATTATTATT
54812 TATATATATATATATATATATATCATATTATTAT
1 TATATATATATATATATATATATCATATTATTAT
54846 ATAATAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (35 bp):
TATATATATATATATATATATATCATATTATTATT
Found at i:54865 original size:2 final size:2
Alignment explanation
Indices: 54768--54848 Score: 100
Period size: 2 Copynumber: 42.0 Consensus size: 2
54758 CCGCTCAAGT
54768 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
*
54808 TA TT TA TA TA TA TA TA TA TA TA TA TA TCA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
54849 ATAAATTAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
1 5 0.07
2 61 0.87
3 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61313 original size:84 final size:84
Alignment explanation
Indices: 61107--61955 Score: 872
Period size: 84 Copynumber: 10.3 Consensus size: 84
61097 TGCAGCTTAG
* * * **
61107 CTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
* * * *
61170 CACATCATTTGCAGTATAG
66 CATATCATTTACAGCATAA
* * * * * * * * *
61189 CTTAAGTCGAGAAGAGCTATCTG---CCAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
61250 GCATAACATTTACAGCATAA
65 GCATATCATTTACAGCATAA
* * *
61270 CTCAAGGCTATAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
* * *
61334 CACATCATTTGCAGAATAA
66 CATATCATTTACAGCATAA
* * * * * * * *
61353 CTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
61415 CATATCATTTACAGCATAA
66 CATATCATTTACAGCATAA
*
61434 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
* *
61498 CATATCATTTGCAGCACAA
66 CATATCATTTACAGCATAA
* * * **
61517 CTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
61582 GCATAACATTTACAGCATAA
65 GCATATCATTTACAGCATAA
61602 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
*
61667 CATAACATTTACAGCATAA
66 CATATCATTTACAGCATAA
* *
61686 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAAACCTTCGAGTTC-AGCTACGTTCAGCTCCAA-G
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGA-CTACGCTCAGCTCCAAGG
* * *
61749 GCACATCATTTGCAGCATAG
65 GCATATCATTTACAGCATAA
* * * * * * * * * * * *
61769 CTTAAGTCGAGAAGGGCTATCTG---CCAAAGACC-CCTAATTCGATTACACTCAACTTCGAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
*
61830 CACATCATTTACAGCATAA
66 CATATCATTTACAGCATAA
* * * * * *
61849 CTCAAGGCTAGGAGGGTTATCTGTCACCAGAAGACCTTTGAGGTCGACTACACTCAGCT-CAAAG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCA-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
61913 GCACAACA-TTACAGCATAG
65 GCATATCATTTACAGCATAA
* * *
61932 CTCAAGACGAGAAGGGCTATCTGT
1 CTCAAGGCTAGAAGGGTTATCTGT
61956 CAATAAAATT
Statistics
Matches: 638, Mismatches: 108, Indels: 41
0.81 0.14 0.05
Matches are distributed among these distances:
79 17 0.03
80 100 0.16
81 74 0.12
82 18 0.03
83 148 0.23
84 228 0.36
85 53 0.08
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (84 bp):
CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
CATATCATTTACAGCATAA
Found at i:61408 original size:164 final size:165
Alignment explanation
Indices: 61107--61955 Score: 892
Period size: 164 Copynumber: 5.1 Consensus size: 165
61097 TGCAGCTTAG
* * * **
61107 CTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * ** *
61171 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTG-CCAAAGACCCTTAAGTTCGATTA
66 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCCTCGAGTTCGACTA
* *
61235 CACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 CGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
* * *
61270 CTCAAGGCTATAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
*
61335 ACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGACTA
66 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCCTCGAGTTCGACTA
* * * *
61399 CGTTCAGCTTCGAGGGCATATCATTTACAGCATAA
131 CGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
*
61434 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * * *
61499 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGA
66 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCCTCGAGTTCGA
61564 CTACGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
128 CTACGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
61602 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GG
* * * * * * * * *
61667 CATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAAACCTTCGAGTTC-A
65 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG--ACCAAAGACCCTCGAGTTCGA
* * * * *
61731 GCTACGTTCAGCTCCAA-GGCACATCATTTGCAGCATAG
128 -CTACGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
* * * * * * * * * * * *
61769 CTTAAGTCGAGAAGGGCTATCTG---CCAAAGACC-CCTAATTCGATTACACTCAACTTCGAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGG
* * * * * * * * *
61830 CACATCATTTACAGCATAACTCAAGGCTAGGAGGGTTATCTGTCACCAGAAGACCTTTGAGGTCG
65 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG--ACCA-AAGACCCTCGAGTTCG
* * * *
61895 ACTACACTCAGCT-CAAAGGCACAACA-TTACAGCATAG
127 ACTACGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
* * *
61932 CTCAAGACGAGAAGGGCTATCTGT
1 CTCAAGGCTAGAAGGGTTATCTGT
61956 CAATAAAATT
Statistics
Matches: 601, Mismatches: 73, Indels: 23
0.86 0.10 0.03
Matches are distributed among these distances:
163 116 0.19
164 262 0.44
165 1 0.00
167 37 0.06
168 147 0.24
169 38 0.06
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (165 bp):
CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCCTCGAGTTCGACTA
CGCTCAGCTCCAAGGGCATAACATTTACAGCATAA
Found at i:62574 original size:2 final size:2
Alignment explanation
Indices: 62518--62557 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
62508 CCGCTCAAGT
62518 TA TA -A TA TA TA TA TA TA TA TA TA TA TCA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
62558 ATAAATTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 29 0.85
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71708 original size:2 final size:2
Alignment explanation
Indices: 71701--71733 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71691 TTTACAACTA
71701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71734 AATACCGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73697 original size:16 final size:16
Alignment explanation
Indices: 73673--73705 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
73663 TATAAATTAA
73673 ATTAATGGTGTTCATC
1 ATTAATGGTGTTCATC
*
73689 ATTAGTGGTGTTCATC
1 ATTAATGGTGTTCATC
73705 A
1 A
73706 CCGTTCGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (16 bp):
ATTAATGGTGTTCATC
Found at i:75471 original size:19 final size:19
Alignment explanation
Indices: 75447--75486 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
75437 ATAGATACTC
75447 GAGATCGAATGAATTTAAG
1 GAGATCGAATGAATTTAAG
75466 GAGATCGAATGAATTTAAG
1 GAGATCGAATGAATTTAAG
75485 GA
1 GA
75487 AATCTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (19 bp):
GAGATCGAATGAATTTAAG
Found at i:79077 original size:12 final size:12
Alignment explanation
Indices: 79060--79094 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
79050 ATATATTAGG
79060 GTTGACAAAAAC
1 GTTGACAAAAAC
79072 GTTGAC-AAAAC
1 GTTGACAAAAAC
79083 GTTGACAAAAAC
1 GTTGACAAAAAC
79095 TAACCCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
GTTGACAAAAAC
Found at i:79422 original size:7 final size:7
Alignment explanation
Indices: 79410--79444 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
79400 AAAGTCATTT
79410 CTTCGTC
1 CTTCGTC
79417 CTTCGTC
1 CTTCGTC
79424 CTTCGTC
1 CTTCGTC
79431 CTTCGTC
1 CTTCGTC
79438 CTTCGTC
1 CTTCGTC
79445 TTCTCCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.14, T:0.43
Consensus pattern (7 bp):
CTTCGTC
Found at i:80701 original size:40 final size:40
Alignment explanation
Indices: 80657--80756 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
80647 CCTTTTTCAT
*
80657 TTTTTTACTTCGTGGTCCTTAATTTTGGTAATGATAACTA
1 TTTTTTACTTCGTGGTCCTTAATTTTGGTAATAATAACTA
* * * *
80697 TTTTTAAC-ACAGTAGTCCTTAATTTTGGTAATAATTACTA
1 TTTTTTACTTC-GTGGTCCTTAATTTTGGTAATAATAACTA
*
80737 TTTTTTACTTTGTGGTCCTT
1 TTTTTTACTTCGTGGTCCTT
80757 TAACTTTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.02
40 48 0.98
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (40 bp):
TTTTTTACTTCGTGGTCCTTAATTTTGGTAATAATAACTA
Found at i:85242 original size:27 final size:27
Alignment explanation
Indices: 85189--85245 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
85179 TATGATCAAA
* * **
85189 TTAAATTTTAAAATTAAATGTTTTTAT
1 TTAAAATTTAAAATTAAATATAATTAT
*
85216 TTAAAATTTAAATTTAAATATAATTAT
1 TTAAAATTTAAAATTAAATATAATTAT
85243 TTA
1 TTA
85246 TAATATCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTAAAATTTAAAATTAAATATAATTAT
Done.