Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006299.1 Hibiscus syriacus cultivar Beakdansim tig00015057_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: 114754
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:13176 original size:19 final size:19
Alignment explanation
Indices: 13152--13190 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13142 TCTCTGTTGG
13152 TTGGTTGTTGTTCTCTTGC
1 TTGGTTGTTGTTCTCTTGC
*
13171 TTGGTTGTTTTTCTCTTGC
1 TTGGTTGTTGTTCTCTTGC
13190 T
1 T
13191 CATTGTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.23, T:0.62
Consensus pattern (19 bp):
TTGGTTGTTGTTCTCTTGC
Found at i:16345 original size:10 final size:11
Alignment explanation
Indices: 16330--16358 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16320 TTTTTCTTTC
16330 ATTTTTTTCAA
1 ATTTTTTTCAA
16341 ATTTTTTTCAA
1 ATTTTTTTCAA
16352 ATTTTTT
1 ATTTTTT
16359 ACTAACCCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTTTCAA
Found at i:17700 original size:17 final size:17
Alignment explanation
Indices: 17678--17800 Score: 93
Period size: 17 Copynumber: 7.1 Consensus size: 17
17668 AATTAAGAGT
*
17678 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
17695 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
17712 TAGTTTAATTAATTAAC
1 TAGTTTAATGAATGAAC
* * *
17729 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* * ** *
17747 TTGTAATCTTGAATAAAC
1 TAGT-TTAATGAATGAAC
* *
17765 TAATTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
17782 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
17799 TA
1 TA
17801 CTTTGTTAAA
Statistics
Matches: 80, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
17 56 0.70
18 24 0.30
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:21685 original size:17 final size:17
Alignment explanation
Indices: 21564--21686 Score: 79
Period size: 17 Copynumber: 7.1 Consensus size: 17
21554 AATTAAGAGT
*
21564 TAGTTTAATAAATGAAC
1 TAGTTTAATCAATGAAC
* *
21581 TAGTTTGATGAATGAAC
1 TAGTTTAATCAATGAAC
* *
21598 TAGTTTAATTAATTAAC
1 TAGTTTAATCAATGAAC
** *
21615 TAACATTATTCAATGAAC
1 T-AGTTTAATCAATGAAC
* *
21633 T--TGTAATCTTGAATAAAC
1 TAGTTTAATC---AATGAAC
* *
21651 TAGTTTGATGAATGAAC
1 TAGTTTAATCAATGAAC
*
21668 TAGTTTAATCAATAAAC
1 TAGTTTAATCAATGAAC
21685 TA
1 TA
21687 CTTTGTTAAA
Statistics
Matches: 79, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
15 4 0.05
17 52 0.66
18 19 0.24
20 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Found at i:25408 original size:17 final size:17
Alignment explanation
Indices: 25360--25409 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
25350 TAAGAGTTAT
*
25360 TTTAATAAATGAACTAG
1 TTTAATAAATAAACTAG
* *
25377 TTTGATGAATAAACTAG
1 TTTAATAAATAAACTAG
* *
25394 TTTAATTAATTAACTA
1 TTTAATAAATAAACTA
25410 ACTTTATTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTAATAAATAAACTAG
Found at i:29264 original size:17 final size:17
Alignment explanation
Indices: 29242--29284 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29232 AATTAAGAGT
29242 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
29259 TAGTTTCATGAATGAAT
1 TAGTTTAATAAATGAAC
29276 TAGTTTAAT
1 TAGTTTAAT
29285 TAATTAACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:29338 original size:17 final size:17
Alignment explanation
Indices: 29316--29348 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29306 CTTGTAATAT
*
29316 TGAATGAACTAGTTTGA
1 TGAATGAACTACTTTGA
29333 TGAATGAACTACTTTG
1 TGAATGAACTACTTTG
29349 TTAAATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (17 bp):
TGAATGAACTACTTTGA
Found at i:33439 original size:2 final size:2
Alignment explanation
Indices: 33432--33467 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33422 TATCTTTCAA
33432 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
33468 CAAATGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34279 original size:19 final size:20
Alignment explanation
Indices: 34257--34296 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
34247 TTAGGTTCTA
34257 TTTGA-TATTTTAAAAAAGT
1 TTTGAGTATTTTAAAAAAGT
*
34276 TTTGAGTTTTTTTAAAAAAGT
1 TTTGAG-TATTTTAAAAAAGT
34297 ATACTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTGAGTATTTTAAAAAAGT
Found at i:36749 original size:20 final size:20
Alignment explanation
Indices: 36724--36761 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36714 TTTGGTTCAC
36724 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
36744 GGAATGTAATATTACCAG
1 GGAATGTAAGATTACCAG
36762 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:44463 original size:26 final size:26
Alignment explanation
Indices: 44427--44480 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
44417 TTGACTCCTT
44427 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTTTTCAGTGAATATCTTCTC
44453 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTTTTCAGTGAATATCTTCTC
44479 GT
1 GT
44481 GTTTTACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.54
Consensus pattern (26 bp):
GTTTCTTTTTCAGTGAATATCTTCTC
Found at i:44823 original size:2 final size:2
Alignment explanation
Indices: 44816--44856 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
44806 ATCATATCCC
44816 AT AT AT AT 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 AT AT AT AT A
44857 ATCTCACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55089 original size:21 final size:19
Alignment explanation
Indices: 55022--55090 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 19
55012 ATTATAGTGG
*
55022 TTGTAGGATTTTCAGAAATT
1 TTGTAGGATTTTCAG-AGTT
*
55042 GTTGTAGGATTTTCAGTAGTGA
1 -TTGTAGGATTTTCAG-AGT-T
*
55064 CTGTAGGATTTTCAGCAGGTT
1 TTGTAGGATTTTCAG-A-GTT
55085 TTGTAG
1 TTGTAG
55091 TGTTGGTAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (19 bp):
TTGTAGGATTTTCAGAGTT
Found at i:57016 original size:106 final size:105
Alignment explanation
Indices: 56830--57262 Score: 564
Period size: 106 Copynumber: 4.0 Consensus size: 105
56820 AGTATTGTTC
* * * * * *
56830 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCCGGAACTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGACTCTGAAACT-GAAAATGGTTTGTTGAC
** * * * * *
56894 AGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGTTGTCT
64 AACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
56936 TGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAAAAGTGGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGAAAA-TGGTTTGTTGACA
57001 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * **
57042 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTTGGTAATGGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAA-CTGAAAATGGTTTGTTGACA
57107 ACCAG-CTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
57148 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTTAATGAAATTGAAAAGTGGTTTGTT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAACTGAAAA-TGGTTTGTT
57213 GACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
57258 CGAGT
1 CGAGT
57263 GGTGCGATAT
Statistics
Matches: 294, Mismatches: 23, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
105 5 0.02
106 216 0.73
107 5 0.02
109 5 0.02
110 62 0.21
111 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGAAAATGGTTTGTTGACAA
CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:74027 original size:981 final size:980
Alignment explanation
Indices: 72127--74087 Score: 3913
Period size: 981 Copynumber: 2.0 Consensus size: 980
72117 CTATACTTGA
72127 GTCGAATTTGCTCTTGACTATCAGGTTCATTGCAATACACCACTCTTTTCGCCCGATTTGGGTGT
1 GTCGAATTTGCTCTTGACTATCAGGTTCATTGCAATACACCACTCTTTTCGCCCGATTTGGGTGT
72192 GTTCATCAAGAGAATCCGACCGACAACACACAAATGAGCAAAGTTTGCTTAATTGTATGCTACGT
66 GTTCATCAAGAGAATCCGACCGACAACACACAAATGAGCAAAGTTTGCTTAATTGTATGCTACGT
72257 CTCCTAACTCTAGCCATTGCAGAAGCTTAAATCCAGAAAGGGTTTCCTCTTCTGGAAAATAATCA
131 CTCCTAACTCTAGCCATTGCAGAAGCTTAAATCCAGAAAGGGTTTCCTCTTCTGGAAAATAATCA
72322 CTAAAAACCTCAGATTTCCCTCATATTAATCTTCCAAATAAACCACTAATTCACCACAAACAAAA
196 CTAAAAACCTCAGATTTCCCTCATATTAATCTTCCAAATAAACCACTAATTCACCACAAACAAAA
72387 GAATAATCTTCAAAATTCCCCTTTATAAACACAGTATGAAAAGTAATCCCCTTCCAATTCAATCA
261 GAATAATCTTCAAAATTCCCCTTTATAAACACAGTATGAAAAGTAATCCCCTTCCAATTCAATCA
72452 AATTCACCAAAACATAAACAACCTCAATGACTAAATATTATTATCTTTGCACCCACATGAGCTTT
326 AATTCACCAAAACATAAACAACCTCAATGACTAAATATTATTATCTTTGCACCCACATGAGCTTT
72517 GAATGCCTTGGATATCTGAGCTAAAATCCCAACAAAGAAAACACATGAAATAGCTTTAAAAAACT
391 GAATGCCTTGGATATCTGAGCTAAAATCCCAACAAAGAAAACACATGAAATAGCTTTAAAAAACT
72582 CAACTTTTCATTTCAAAAAAGCATGACCAATACTTGAAAGGAACCTCATATTTGTGACCTTAACT
456 CAACTTTTCATTTCAAAAAAGCATGACCAATACTTGAAAGGAACCTCATATTTGTGACCTTAACT
72647 TCAACAATTTAAGACAACCCCACAAATTAAATTGTCTTGAAAAGACGTAATCCTTAATACGACCA
521 TCAACAATTTAAGACAACCCCACAAATTAAATTGTCTTGAAAAGACGTAATCCTTAATACGACCA
72712 TTATCGAAAGTAAATTCCCTACTTTCAGTTGAAGTTCCAGAGATCTCTTCCTTGTTGTCTGAAAG
586 TTATCGAAAGTAAATTCCCTACTTTCAGTTGAAGTTCCAGAGATCTCTTCCTTGTTGTCTGAAAG
72777 TTTCTAGGTTTAAAATTGAGTGTTAGAAAGGCAACATAATTTTCTTTTAAATATAAGAAGAAGAA
651 TTTCTAGGTTTAAAATTGAGTGTTAGAAAGGCAACATAATTTTCTTTTAAATATAAGAAGAAGAA
72842 GAAGAAGGTGAGTGCTTTACAGCTTTGCACTAGTCTCAGAAAGAGTAGTTAGCTTTGCCGCTGTT
716 GAAGAAGGTGAGTGCTTTACAGCTTTGCACTAGTCTCAGAAAGAGTAGTTAGCTTTGCCGCTGTT
72907 ATAAGCAAGAACTAACCCATGAAAACTTAACATAGATGGCACATCACTGGATAATTGCCTAAACA
781 ATAAGCAAGAACTAACCCATGAAAACTTAACATAGATGGCACATCACTGGATAATTGCCTAAACA
72972 CAGAACGGGTAAATTACAATTAAGCCATCTGAAGTTCAACATTTTCTTATTTTTTGGGTAAAATA
846 CAGAACGGGTAAATTACAATTAAGCCATCTGAAGTTCAACATTTTCTTATTTTTTGGGTAAAATA
73037 CACAAATGGTTCACCGACTATAGTGTGTTACTTTATTGAGTCTCATAACTATTAAAATTTACAAA
911 CACAAATGGTTCACCGACTATAGTGTGTTACTTTATTGAGTCTCATAACTATTAAAATTTACAAA
73102 ATGAT
976 ATGAT
73107 GTCGAATTTGCTCTTGACTATCAGGTTCATTGCAATACACCACTCTTTTCGCCCGATTTGGGTGT
1 GTCGAATTTGCTCTTGACTATCAGGTTCATTGCAATACACCACTCTTTTCGCCCGATTTGGGTGT
73172 GTTCATCAAGAGAATCCGACCGACAACACACAAATGAGCAAAGTTTGCTTAATTGTATGCTACGT
66 GTTCATCAAGAGAATCCGACCGACAACACACAAATGAGCAAAGTTTGCTTAATTGTATGCTACGT
73237 CTCCTAACTCTAGCCATTGCAGAAGCTTAAATCCAGAAAGGGTTTTCCTCTTCTGGAAAATAATC
131 CTCCTAACTCTAGCCATTGCAGAAGCTTAAATCCAGAAAGGG-TTTCCTCTTCTGGAAAATAATC
73302 ACTAAAAACCTCAGATTTCCCTCATATTAATCTTCCAAATAAACCACTAATTCACCACAAACAAA
195 ACTAAAAACCTCAGATTTCCCTCATATTAATCTTCCAAATAAACCACTAATTCACCACAAACAAA
73367 AGAATAATCTTCAAAATTCCCCTTTATAAACACAGTATGAAAAGTAATCCCCTTCCAATTCAATC
260 AGAATAATCTTCAAAATTCCCCTTTATAAACACAGTATGAAAAGTAATCCCCTTCCAATTCAATC
73432 AAATTCACCAAAACATAAACAACCTCAATGACTAAATATTATTATCTTTGCACCCACATGAGCTT
325 AAATTCACCAAAACATAAACAACCTCAATGACTAAATATTATTATCTTTGCACCCACATGAGCTT
73497 TGAATGCCTTGGATATCTGAGCTAAAATCCCAACAAAGAAAACACATGAAATAGCTTTAAAAAAC
390 TGAATGCCTTGGATATCTGAGCTAAAATCCCAACAAAGAAAACACATGAAATAGCTTTAAAAAAC
73562 TCAACTTTTCATTTCAAAAAAGCATGACCAATACTTGAAAGGAACCTCATATTTGTGACCTTAAC
455 TCAACTTTTCATTTCAAAAAAGCATGACCAATACTTGAAAGGAACCTCATATTTGTGACCTTAAC
73627 TTCAACAATTTAAGACAACCCCACAAATTAAATTGTCTTGAAAAGACGTAATCCTTAATACGACC
520 TTCAACAATTTAAGACAACCCCACAAATTAAATTGTCTTGAAAAGACGTAATCCTTAATACGACC
73692 ATTATCGAAAGTAAATTCCCTACTTTCAGTTGAAGTTCCAGAGATCTCTTCCTTGTTGTCTGAAA
585 ATTATCGAAAGTAAATTCCCTACTTTCAGTTGAAGTTCCAGAGATCTCTTCCTTGTTGTCTGAAA
73757 GTTTCTAGGTTTAAAATTGAGTGTTAGAAAGGCAACATAATTTTCTTTTAAATATAAGAAGAAGA
650 GTTTCTAGGTTTAAAATTGAGTGTTAGAAAGGCAACATAATTTTCTTTTAAATATAAGAAGAAGA
73822 AGAAGAAGGTGAGTGCTTTACAGCTTTGCACTAGTCTCAGAAAGAGTAGTTAGCTTTGCCGCTGT
715 AGAAGAAGGTGAGTGCTTTACAGCTTTGCACTAGTCTCAGAAAGAGTAGTTAGCTTTGCCGCTGT
73887 TATAAGCAAGAACTAACCCATGAAAACTTAACATAGATGGCACATCACTGGATAATTGCCTAAAC
780 TATAAGCAAGAACTAACCCATGAAAACTTAACATAGATGGCACATCACTGGATAATTGCCTAAAC
73952 ACAGAACGGGTAAATTACAATTAAGCCATCTGAAGTTCAACATTTTCTTATTTTTTGGGTAAAAT
845 ACAGAACGGGTAAATTACAATTAAGCCATCTGAAGTTCAACATTTTCTTATTTTTTGGGTAAAAT
74017 ACACAAATGGTTCACCGACTATAGTGTGTTACTTTATTGAGTCTCATAACTATTAAAATTTACAA
910 ACACAAATGGTTCACCGACTATAGTGTGTTACTTTATTGAGTCTCATAACTATTAAAATTTACAA
74082 AATGAT
975 AATGAT
74088 ATTAACTATA
Statistics
Matches: 980, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
980 172 0.18
981 808 0.82
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (980 bp):
GTCGAATTTGCTCTTGACTATCAGGTTCATTGCAATACACCACTCTTTTCGCCCGATTTGGGTGT
GTTCATCAAGAGAATCCGACCGACAACACACAAATGAGCAAAGTTTGCTTAATTGTATGCTACGT
CTCCTAACTCTAGCCATTGCAGAAGCTTAAATCCAGAAAGGGTTTCCTCTTCTGGAAAATAATCA
CTAAAAACCTCAGATTTCCCTCATATTAATCTTCCAAATAAACCACTAATTCACCACAAACAAAA
GAATAATCTTCAAAATTCCCCTTTATAAACACAGTATGAAAAGTAATCCCCTTCCAATTCAATCA
AATTCACCAAAACATAAACAACCTCAATGACTAAATATTATTATCTTTGCACCCACATGAGCTTT
GAATGCCTTGGATATCTGAGCTAAAATCCCAACAAAGAAAACACATGAAATAGCTTTAAAAAACT
CAACTTTTCATTTCAAAAAAGCATGACCAATACTTGAAAGGAACCTCATATTTGTGACCTTAACT
TCAACAATTTAAGACAACCCCACAAATTAAATTGTCTTGAAAAGACGTAATCCTTAATACGACCA
TTATCGAAAGTAAATTCCCTACTTTCAGTTGAAGTTCCAGAGATCTCTTCCTTGTTGTCTGAAAG
TTTCTAGGTTTAAAATTGAGTGTTAGAAAGGCAACATAATTTTCTTTTAAATATAAGAAGAAGAA
GAAGAAGGTGAGTGCTTTACAGCTTTGCACTAGTCTCAGAAAGAGTAGTTAGCTTTGCCGCTGTT
ATAAGCAAGAACTAACCCATGAAAACTTAACATAGATGGCACATCACTGGATAATTGCCTAAACA
CAGAACGGGTAAATTACAATTAAGCCATCTGAAGTTCAACATTTTCTTATTTTTTGGGTAAAATA
CACAAATGGTTCACCGACTATAGTGTGTTACTTTATTGAGTCTCATAACTATTAAAATTTACAAA
ATGAT
Found at i:76181 original size:18 final size:18
Alignment explanation
Indices: 76155--76189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76145 TTTCTCCATC
*
76155 ATGAATCCATTTGTTTCT
1 ATGAATCCATATGTTTCT
*
76173 ATGATTCCATATGTTTC
1 ATGAATCCATATGTTTC
76190 ATAGTAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (18 bp):
ATGAATCCATATGTTTCT
Found at i:82153 original size:87 final size:87
Alignment explanation
Indices: 82006--82167 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
81996 ATGTTATATT
* *
82006 ATTTATCTAGAAATATTATCAAGTAGAATAACATATTAAGTAACGCTTATATAATATAATAGATA
1 ATTTAACTAGAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAATATAATAGATA
*
82071 GCGTTTATATAATAAAATAGGC
66 GCGCTTATATAATAAAATAGGC
* * * * *
82093 ATTTAACTGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACTAGAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAATATAATAGATA
82158 GCGCTTATAT
66 GCGCTTATAT
82168 TGACCTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (87 bp):
ATTTAACTAGAAATATTATCAAGTACAATAACATATTAAGTAACGCTTATATAATATAATAGATA
GCGCTTATATAATAAAATAGGC
Found at i:83051 original size:23 final size:23
Alignment explanation
Indices: 83021--83093 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
83011 ATACTTTACA
83021 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
83044 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* * *
83067 ATATAACCGCTACTTATTACATC
1 ATATAAGCGCTACCTATTACATT
83090 ATAT
1 ATAT
83094 TTTTATCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:85750 original size:12 final size:12
Alignment explanation
Indices: 85701--85758 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
85691 ATTTGGATCA
* *
85701 TCATCATCATCA
1 TCATCGTCATCT
*
85713 TCATCGTCATTT
1 TCATCGTCATCT
85725 TCATCGTCATCT
1 TCATCGTCATCT
*
85737 TCATCGTCAGCT
1 TCATCGTCATCT
*
85749 TCATCTTCAT
1 TCATCGTCAT
85759 TGACCGCTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.41
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:85756 original size:6 final size:6
Alignment explanation
Indices: 85701--85758 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
85691 ATTTGGATCA
* * * * * * *
85701 TCATCA TCATCA TCATCG TCATTT TCATCG TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
85749 TCATCT TCAT
1 TCATCT TCAT
85759 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:87295 original size:20 final size:19
Alignment explanation
Indices: 87249--87295 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
87239 TCTGGTAGCG
87249 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
87268 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
87289 TTTTACC
1 TTTTACC
87296 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:90305 original size:72 final size:73
Alignment explanation
Indices: 90185--90348 Score: 204
Period size: 72 Copynumber: 2.3 Consensus size: 73
90175 TACCTAAGTC
* * * * *
90185 ATAGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAACAGAATGTCAAATGGGTACCAA
1 ATAGGTAACGATACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACCAA
90250 GACCCC-T
66 GACCCCTT
* * * * * *
90257 ATAGGTATCGACACCCTTGTGTTAATTTTGGCTACAAGAAAAATAGAATGCCTAATGGGTACCGA
1 ATAGGTAACGATACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACCAA
*
90322 TACCCCTT
66 GACCCCTT
*
90330 AGAGGTAACGATACCCTTA
1 ATAGGTAACGATACCCTTA
90349 GTCGTTTAAC
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
72 60 0.79
73 16 0.21
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (73 bp):
ATAGGTAACGATACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACCAA
GACCCCTT
Found at i:90348 original size:18 final size:19
Alignment explanation
Indices: 90314--90349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
90304 ATGCCTAATG
*
90314 GGTACCGATACCCCTTAGA
1 GGTAACGATACCCCTTAGA
90333 GGTAACGATA-CCCTTAG
1 GGTAACGATACCCCTTAG
90350 TCGTTTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTAACGATACCCCTTAGA
Found at i:92276 original size:21 final size:21
Alignment explanation
Indices: 92252--92291 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
92242 AGAAATTATT
*
92252 TTTTGAAATACAAAAATGATA
1 TTTTAAAATACAAAAATGATA
**
92273 TTTTAAAATTGAAAAATGA
1 TTTTAAAATACAAAAATGA
92292 AAATGATCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTAAAATACAAAAATGATA
Found at i:96133 original size:21 final size:21
Alignment explanation
Indices: 96107--96160 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
96097 TTTGTGCAAC
*
96107 AGGTATCGATACCCCCTTTAT
1 AGGTATCGATACCCCCTTGAT
*
96128 AGGTATCGATACCCCCTTGCT
1 AGGTATCGATACCCCCTTGAT
96149 AGGTATCGATAC
1 AGGTATCGATAC
96161 TCCTTCAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (21 bp):
AGGTATCGATACCCCCTTGAT
Found at i:96713 original size:12 final size:13
Alignment explanation
Indices: 96684--96716 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
96674 ATATTATGAT
*
96684 TTTTCAAACATTG
1 TTTTCAAACATAG
96697 TTTTCAAA-ATAG
1 TTTTCAAACATAG
96709 TTTTCAAA
1 TTTTCAAA
96717 GTTTGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:98936 original size:72 final size:72
Alignment explanation
Indices: 98793--98928 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
98783 ATACCTAAGT
* * * * *
98793 CATAGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAACAGAATGTCAAATGGGTACCA
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACCA
98858 AGACCCC
66 AGACCCC
* * * *
98865 CATAGGTATCGACACCCTTGTGTTAATTTTGGCTACAAGAAAAATAGAATGCCTAATGGGTACC
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACC
98929 GATACCCCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (72 bp):
CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAGAATGCCAAATGGGTACCA
AGACCCC
Found at i:108096 original size:17 final size:17
Alignment explanation
Indices: 108074--108106 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
108064 CATGTTCCTG
108074 AAAATGAAAAAAAATGT
1 AAAATGAAAAAAAATGT
*
108091 AAAATGATAAAAAATG
1 AAAATGAAAAAAAATG
108107 AAATTGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGAAAAAAAATGT
Found at i:110705 original size:20 final size:20
Alignment explanation
Indices: 110668--110705 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
110658 TTTATATAAC
110668 ATATTAGGGTATCTCGATTT
1 ATATTAGGGTATCTCGATTT
*
110688 ATATTTGGG-ATCTACGAT
1 ATATTAGGGTATCT-CGAT
110706 ATTTTCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
ATATTAGGGTATCTCGATTT
Found at i:111895 original size:14 final size:14
Alignment explanation
Indices: 111876--111924 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
111866 TTGATTTTAA
111876 TTTTAATATTAATT
1 TTTTAATATTAATT
111890 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
111900 ATTAAATATTAATT
1 TTTTAATATTAATT
111914 TTTTAATATTA
1 TTTTAATATTA
111925 TATTATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:111939 original size:21 final size:20
Alignment explanation
Indices: 111915--112000 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
111905 ATATTAATTT
111915 TTTAATATTATATTATAGATA
1 TTTAATATTATATTATA-ATA
*
111936 TTTAATTTTATATTAT-ATA
1 TTTAATATTATATTATAATA
* *
111955 TATTAATTTATATATTATTAAAA
1 T-TTAATAT-TATATTA-TAATA
*
111978 TTTAATATT-TATTTTAATTA
1 TTTAATATTATATTATAA-TA
111998 TTT
1 TTT
112001 TGATTTAAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
19 7 0.13
20 15 0.27
21 23 0.42
22 7 0.13
23 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTAATATTATATTATAATA
Found at i:111966 original size:12 final size:12
Alignment explanation
Indices: 111842--111971 Score: 55
Period size: 12 Copynumber: 10.9 Consensus size: 12
111832 TCAAAGAGGT
111842 TTTATAT-TTAA
1 TTTATATATTAA
111853 TTT-TATATTATA
1 TTTATATATTA-A
111865 TTTGAT-T-TTAA
1 TTT-ATATATTAA
111876 TTT-TAATATTAA
1 TTTAT-ATATTAA
* *
111888 TTT-TTTAAATAA
1 TTTATAT-ATTAA
* *
111900 ATTAAATATTAA
1 TTTATATATTAA
*
111912 TTTTTTAATATTATA
1 -TTTAT-ATATTA-A
*
111927 TTATAGATATTTAA
1 TT-TATATA-TTAA
111941 TTT-TATATT-A
1 TTTATATATTAA
111951 --TATATATTAA
1 TTTATATATTAA
111961 TTTATATATTA
1 TTTATATATTA
111972 TTAAAATTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 35
0.65 0.09 0.26
Matches are distributed among these distances:
8 1 0.01
9 7 0.08
10 5 0.06
11 14 0.16
12 37 0.42
13 5 0.06
14 15 0.17
15 5 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTATATATTAA
Found at i:111996 original size:17 final size:16
Alignment explanation
Indices: 111936--111996 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 16
111926 ATTATAGATA
111936 TTTAATTTTATATTATAT
1 TTTAA-TTTATATT-TAT
111954 ATATTAATTTATATATTAT
1 -T-TTAATTTATAT-TTAT
**
111973 TAAAATTTAATATTTAT
1 TTTAATTT-ATATTTAT
111990 TTTAATT
1 TTTAATT
111997 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 14 0.40
18 5 0.14
19 11 0.31
20 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTATATTTAT
Done.