Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008903.1 Hibiscus syriacus cultivar Beakdansim tig00112181_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: 81056
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3770 original size:23 final size:24
Alignment explanation
Indices: 3741--3790 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3731 TATGTATTTG
*
3741 ATACATATAATA-TTTTAACTCAA
1 ATACATATAATATTTTTAACTAAA
*
3764 ATACATATATTATTTTTAACTAAA
1 ATACATATAATATTTTTAACTAAA
3788 ATA
1 ATA
3791 AAATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (24 bp):
ATACATATAATATTTTTAACTAAA
Found at i:3798 original size:24 final size:24
Alignment explanation
Indices: 3745--3800 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3735 TATTTGATAC
* * *
3745 ATATAATA-TTTTAACTCAAATAC
1 ATATATTATTTTTAACTAAAATAA
3768 ATATATTATTTTTAACTAAAATAA
1 ATATATTATTTTTAACTAAAATAA
3792 A-ATTATTAT
1 ATA-TATTAT
3801 AATTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATTATTTTTAACTAAAATAA
Found at i:3863 original size:39 final size:37
Alignment explanation
Indices: 3711--3869 Score: 101
Period size: 39 Copynumber: 4.2 Consensus size: 37
3701 TTTGAATTAC
*
3711 ATATTTAGTTAAAAATAATATATGTATTTGATACATATA
1 ATATTTAGTTAAAATTAATATAT-TATTT-ATACATATA
** * * *
3750 ATATTTTAACTCAAA-TACATATATTATTTTTA-ACTAAA
1 ATA-TTTAGTTAAAATTA-ATATATTATTTATACA-TATA
* * * * * *
3788 ATAAAATTA-TTATAATT-ATAAATAACTTATATATATA
1 AT--ATTTAGTTAAAATTAATATATTATTTATACATATA
3825 ATATTTAGTTAAAATTAATATATGTATTTGATACATATA
1 ATATTTAGTTAAAATTAATATAT-TATTT-ATACATATA
3864 ATATTT
1 ATATTT
3870 TAACTAAAAT
Statistics
Matches: 89, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
35 4 0.04
36 7 0.08
37 21 0.24
38 14 0.16
39 28 0.31
40 15 0.17
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATTTAGTTAAAATTAATATATTATTTATACATATA
Found at i:3934 original size:114 final size:112
Alignment explanation
Indices: 3711--3936 Score: 287
Period size: 114 Copynumber: 2.0 Consensus size: 112
3701 TTTGAATTAC
* * *
3711 ATATTTAGTTAAAAATAATATATGTATTTGATACATATAATATTTTAACTCAAATACATATATTA
1 ATATTTAGTTAAAAATAATATATGTATTTGATACATATAATATTTTAACTAAAATAAATATATAA
* *
3776 TTTTTAACTAAAATAAAATTATTATAATTATAAATAACTTATATATATA
66 TTTTTAACTAAAATAAAATAAATATAATTATAAATAA--TATATATATA
*
3825 ATATTTAGTTAAAATTAATATATGTATTTGATACATATAATATTTTAACTAAAATGAAATAATTA
1 ATATTTAGTTAAAAATAATATATGTATTTGATACATATAATATTTTAACTAAAAT-AAAT-A-TA
*
3890 TAATTATTGTAATTATAAATATAAATAAATAT-ATT-TAAA-AATATATA
63 TAATT-TT-TAACTA-AAATA-AAATAAATATAATTATAAATAATATATA
3937 ATTATTATAA
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
114 53 0.54
115 3 0.03
116 7 0.07
117 6 0.06
118 4 0.04
119 9 0.09
120 8 0.08
121 8 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (112 bp):
ATATTTAGTTAAAAATAATATATGTATTTGATACATATAATATTTTAACTAAAATAAATATATAA
TTTTTAACTAAAATAAAATAAATATAATTATAAATAATATATATATA
Found at i:3936 original size:90 final size:91
Alignment explanation
Indices: 3764--3936 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 91
3754 TTTAACTCAA
* * *
3764 ATACATATATTATTTTTAACTAAAATAAAATTATTATAATTATAAATAACTTATATATATAATAT
1 ATACATATAATATTTTTAACTAAAATAAAATAATTATAATTATAAATAACTTATAAATATAATAT
* *
3829 TTAGTTAAAATTAATATATGTATTTG
66 ATAGTTAAAAATAATATATGTATTTG
* **
3855 ATACATATAATA-TTTTAACTAAAATGAAATAATTATAATTAT-TGTAA-TTATAAATATAAATA
1 ATACATATAATATTTTTAACTAAAATAAAATAATTATAATTATAAATAACTTATAAATAT-AAT-
*
3917 AATATATTTAAAAAT-ATATA
64 -ATATAGTTAAAAATAATATA
3937 ATTATTATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
88 9 0.13
89 6 0.09
90 33 0.47
91 22 0.31
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (91 bp):
ATACATATAATATTTTTAACTAAAATAAAATAATTATAATTATAAATAACTTATAAATATAATAT
ATAGTTAAAAATAATATATGTATTTG
Found at i:4005 original size:91 final size:91
Alignment explanation
Indices: 3918--4350 Score: 381
Period size: 93 Copynumber: 4.6 Consensus size: 91
3908 ATATAAATAA
* * *
3918 ATATATTTAAAAATATATAATTATTATAATTATCAAACTTTATTAAATATATATTTATCA-AATA
1 ATATATTTAAAAAGAGATAATTATTATAATTATCAAACTCTATTAAATATATATTTA-CATAATA
*
3982 GAATCTAATCTCAATTGAAATAAATTT
65 AAATCTAATCTCAATTGAAATAAATTT
* * *
4009 ATATAGTTT-AAAAGAGATAATTATTTTAATCATCAAACTCTATTAAAATATATATTTACATGAT
1 ATATA-TTTAAAAAGAGATAATTATTATAATTATCAAACTCTATT-AAATATATATTTACATAAT
* * *
4073 AAAATCTTATCTCAATTGAGATAGATTT
64 AAAATCTAATCTCAATTGAAATAAATTT
* *
4101 ATATATTTAAAATAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATGTATATTTATA
1 ATATATTTAAAA-AGAGATAATTATTATAATTATCAAACTCTATT--AA-ATA--TATATTTACA
* * * * *
4166 TGATAAAA-CAATATCTTAGTCGAAATAAATTT
60 TAATAAAATCTA-ATCTCAATTGAAATAAATTT
* * * *** *
4198 ATATATTCAAAAGAGAGATAATTATTGTAATTATCAAACTCTATTAATATATATAATTGTTTGAT
1 ATATATTTAAAA-AGAGATAATTATTATAATTATCAAACTCTATTAA-ATATATATTTACATAAT
* * * * **
4263 AGAA-CTTAATCTGAGTTGAGATAGGTTTTT
64 AAAATC-TAATCTCAATTGAAATA--AATTT
* * *
4293 ATATATATAAAAA-ATATAATTATTATAATTATCAAACTCTTTTAAATGATAATATTTA
1 ATATATTTAAAAAGAGATAATTATTATAATTATCAAACTCTATTAAAT-AT-ATATTTA
4351 GTTTAAGTTA
Statistics
Matches: 288, Mismatches: 39, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
91 40 0.14
92 52 0.18
93 88 0.31
94 10 0.03
95 22 0.08
96 1 0.00
97 75 0.26
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (91 bp):
ATATATTTAAAAAGAGATAATTATTATAATTATCAAACTCTATTAAATATATATTTACATAATAA
AATCTAATCTCAATTGAAATAAATTT
Found at i:4215 original size:97 final size:94
Alignment explanation
Indices: 3918--4251 Score: 346
Period size: 97 Copynumber: 3.6 Consensus size: 94
3908 ATATAAATAA
* * * *
3918 ATATATTTAAAAATATATAATTATTATAATTATCAAACTTTATT--AA-ATA-TATATTTATCA-
1 ATATA-TTAAAAAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATTATATTTA-CAT
* * *
3978 AATAGAATC-TAATCTCAATTGAAATAAATTT
64 GATAAAATCAT-ATCTCAATCGAAATAAATTT
* * *
4009 ATATAGTTTAAAAGAGATAATTATTTTAATCATCAAACTCTATT-AAA-ATA-TATATTTACATG
1 ATATA-TTAAAAAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATTATATTTACATG
* * * *
4071 ATAAAATCTTATCTCAATTGAGATAGATTT
65 ATAAAATCATATCTCAATCGAAATAAATTT
*
4101 ATATATTTAAAATAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATGTATATTTATA
1 ATATA-TTAAAA-AGAGATAATTATTGTAATTATCAAACTCTATTAAAATATAT-TATATTTACA
* *
4166 TGATAAAA-CAATATCTTAGTCGAAATAAATTT
63 TGATAAAATC-ATATCTCAATCGAAATAAATTT
*
4198 ATATATTCAAAAGAGAGATAATTATTGTAATTATCAAACTCTATTAATATATAT
1 ATATATT-AAAA-AGAGATAATTATTGTAATTATCAAACTCTATTAAAATATAT
4252 AATTGTTTGA
Statistics
Matches: 209, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
91 39 0.19
92 48 0.23
93 31 0.15
94 3 0.01
95 3 0.01
96 3 0.01
97 82 0.39
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (94 bp):
ATATATTAAAAAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATTATATTTACATGA
TAAAATCATATCTCAATCGAAATAAATTT
Found at i:4252 original size:190 final size:189
Alignment explanation
Indices: 3918--4338 Score: 468
Period size: 190 Copynumber: 2.2 Consensus size: 189
3908 ATATAAATAA
* * *
3918 ATATATTTAAAAATATATAATTATTATAATTATCAAACTTTATT--AA-ATA--TATATTTATCA
1 ATATATATAAAAA-AGATAATTATTATAATTATCAAACTCTATTAAAATATATGTATATTTAT-A
* * * * * * * *
3978 -AATAGAATCTA-ATCTCAATTGAAATAAATTTATATAGTTTAAAAGAGATAATTATTTTAATCA
64 TGATA-AAACAATATCTTAGTCGAAATAAATTTATATAGTTAAAAAGAGATAATTATTGTAATCA
*
4041 TCAAACTCTATTAAAATATATATTTACATGATAAAATCTT-ATCTCAATTGAGATA-G-ATTT
128 TCAAACTCTATTAAAATATATAATTACATGATAAAA-CTTAATCTCAATTGAGATAGGTATTT
* *
4101 ATATATTTAAAATAGAGATAATTATTGTAATTATCAAACTCTATTAAAATATATGTATATTTATA
1 ATATATATAAAA-A-AGATAATTATTATAATTATCAAACTCTATTAAAATATATGTATATTTATA
*
4166 TGATAAAACAATATCTTAGTCGAAATAAATTTATATA-TTCAAAAGAGAGATAATTATTGTAATT
64 TGATAAAACAATATCTTAGTCGAAATAAATTTATATAGTT-AAAA-AGAGATAATTATTGTAATC
* *** * * * *
4230 ATCAAACTCTATTAATATATATAATTGTTTGATAGAACTTAATCTGAGTTGAGATAGGTTTTT
127 ATCAAACTCTATTAAAATATATAATTACATGATAAAACTTAATCTCAATTGAGATAGGTATTT
* *
4293 ATATATATAAAAAATATAATTATTATAATTATCAAACTCTTTTAAA
1 ATATATATAAAAAAGATAATTATTATAATTATCAAACTCTATTAAA
4339 TGATAATATT
Statistics
Matches: 199, Mismatches: 26, Indels: 19
0.82 0.11 0.08
Matches are distributed among these distances:
183 12 0.06
184 28 0.14
186 2 0.01
187 3 0.02
188 7 0.04
189 40 0.20
190 91 0.46
191 2 0.01
192 14 0.07
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (189 bp):
ATATATATAAAAAAGATAATTATTATAATTATCAAACTCTATTAAAATATATGTATATTTATATG
ATAAAACAATATCTTAGTCGAAATAAATTTATATAGTTAAAAAGAGATAATTATTGTAATCATCA
AACTCTATTAAAATATATAATTACATGATAAAACTTAATCTCAATTGAGATAGGTATTT
Found at i:7658 original size:24 final size:25
Alignment explanation
Indices: 7630--7683 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
7620 GAATGTTTTA
*
7630 TCTGATTTTC-GATTTGAATTATGT
1 TCTGATTTTCTGATCTGAATTATGT
*
7654 TCTGA-TTTCTGATCTGGATTATGT
1 TCTGATTTTCTGATCTGAATTATGT
*
7678 TATGAT
1 TCTGAT
7684 ATATGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.20, C:0.09, G:0.19, T:0.52
Consensus pattern (25 bp):
TCTGATTTTCTGATCTGAATTATGT
Found at i:9292 original size:22 final size:22
Alignment explanation
Indices: 9267--9317 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
9257 TTCCCCCTCA
9267 ACTCACCATTAAACTCCGATCT
1 ACTCACCATTAAACTCCGATCT
9289 ACTCACCATTAAACTCCGATCT
1 ACTCACCATTAAACTCCGATCT
9311 ACTCACC
1 ACTCACC
9318 GTCCGGCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.39, G:0.04, T:0.25
Consensus pattern (22 bp):
ACTCACCATTAAACTCCGATCT
Found at i:16244 original size:394 final size:394
Alignment explanation
Indices: 15516--16303 Score: 1549
Period size: 394 Copynumber: 2.0 Consensus size: 394
15506 AGGATTACCG
15516 ACGAGAAAATGGACGACATGGAAATGAAAACGAAGCAGTTGTTGCAGAGCTCAAACAACATTCTA
1 ACGAGAAAATGGACGACATGGAAATGAAAACGAAGCAGTTGTTGCAGAGCTCAAACAACATTCTA
15581 AGTTCTCTTACAATAATCGGCCAACAATCGCAATAAATAGCGGAGACGACGAAGAATGCGTCGGA
66 AGTTCTCTTACAATAATCGGCCAACAATCGCAATAAATAGCGGAGACGACGAAGAATGCGTCGGA
15646 CCATATGGATATTGTAGTGGAACATTCGATGGCGGTTTTCAAGCAATCTCAACAAATTGCAGCTT
131 CCATATGGATATTGTAGTGGAACATTCGATGGCGGTTTTCAAGCAATCTCAACAAATTGCAGCTT
15711 TTGAATCGGAACTGAAAACAGGCCAAGAGAAAATGAAAAGCAATTTGAAAGAAAGGATGGTGATG
196 TTGAATCGGAACTGAAAACAGGCCAAGAGAAAATGAAAAGCAATTTGAAAGAAAGGATGGTGATG
* *
15776 CTTAGTGACTCGTACAGAAACTTGGGTGAAAGACTTGATGGCATTAAAGAGGAGACTGTCGAAGT
261 CCTAGTGACTCGTACAAAAACTTGGGTGAAAGACTTGATGGCATTAAAGAGGAGACTGTCGAAGT
*
15841 AGAGAAGAAGATAAGCAAAATGAGTGACGCAATGTCTGAGAAAATGAGTAATTTGCAGATCAAGG
326 AGAGAAGAAGATAAGCAAAATGAGTGACGCAATGTCTGAGAAAATGAGTAATTTGCAGATCAAAG
15906 CTGA
391 CTGA
15910 ACGAGAAAATGGACGACATGGAAATGAAAACGAAGCAGTTGTTGCAGAGCTCAAACAACATTCTA
1 ACGAGAAAATGGACGACATGGAAATGAAAACGAAGCAGTTGTTGCAGAGCTCAAACAACATTCTA
15975 AGTTCTCTTACAATAATCGGCCAACAATCGCAATAAATAGCGGAGACGACGAAGAATGCGTCGGA
66 AGTTCTCTTACAATAATCGGCCAACAATCGCAATAAATAGCGGAGACGACGAAGAATGCGTCGGA
16040 CCATATGGATATTGTAGTGGAACATTCGATGGCGGTTTTCAAGCAATCTCAACAAATTGCAGCTT
131 CCATATGGATATTGTAGTGGAACATTCGATGGCGGTTTTCAAGCAATCTCAACAAATTGCAGCTT
16105 TTGAATCGGAACTGAAAACAGGCCAAGAGAAAATGAAAAGCAATTTGAAAGAAAGGATGGTGATG
196 TTGAATCGGAACTGAAAACAGGCCAAGAGAAAATGAAAAGCAATTTGAAAGAAAGGATGGTGATG
16170 CCTAGTGACTCGTACAAAAACTTGGGTGAAAGACTTGATGGCATTAAAGAGGAGACTGTCGAAGT
261 CCTAGTGACTCGTACAAAAACTTGGGTGAAAGACTTGATGGCATTAAAGAGGAGACTGTCGAAGT
16235 AGAGAAGAAGATAAGCAAAATGAGTGACGCAATGTCTGAGAAAATGAGTAATTTGCAGATCAAAG
326 AGAGAAGAAGATAAGCAAAATGAGTGACGCAATGTCTGAGAAAATGAGTAATTTGCAGATCAAAG
16300 CTGA
391 CTGA
16304 TGATATAGGA
Statistics
Matches: 391, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
394 391 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (394 bp):
ACGAGAAAATGGACGACATGGAAATGAAAACGAAGCAGTTGTTGCAGAGCTCAAACAACATTCTA
AGTTCTCTTACAATAATCGGCCAACAATCGCAATAAATAGCGGAGACGACGAAGAATGCGTCGGA
CCATATGGATATTGTAGTGGAACATTCGATGGCGGTTTTCAAGCAATCTCAACAAATTGCAGCTT
TTGAATCGGAACTGAAAACAGGCCAAGAGAAAATGAAAAGCAATTTGAAAGAAAGGATGGTGATG
CCTAGTGACTCGTACAAAAACTTGGGTGAAAGACTTGATGGCATTAAAGAGGAGACTGTCGAAGT
AGAGAAGAAGATAAGCAAAATGAGTGACGCAATGTCTGAGAAAATGAGTAATTTGCAGATCAAAG
CTGA
Found at i:19973 original size:2 final size:2
Alignment explanation
Indices: 19966--20017 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
19956 CATACTATTA
19966 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
20008 AT AT AT AT AT
1 AT AT AT AT AT
20018 CTTTTAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20369 original size:3 final size:3
Alignment explanation
Indices: 20361--20395 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
20351 TAAATAACTT
20361 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
20396 AAGACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:20382 original size:16 final size:16
Alignment explanation
Indices: 20363--20396 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20353 AATAACTTAT
20363 AATAATAATAATAATA
1 AATAATAATAATAATA
20379 AATAATAATAATAATA
1 AATAATAATAATAATA
20395 AA
1 AA
20397 AGACAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:24188 original size:65 final size:64
Alignment explanation
Indices: 24072--24194 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 64
24062 TTGGTCTATA
* * * * *
24072 AATTTTAGTACTACTTCGAAATTTCATATGATTATTCTAATTCAAAACTAATTAAATATCTGTG
1 AATTTTAATACTACTGCAAAATTTCATATAATTATTCTAACTCAAAACTAATTAAATATCTGTG
*
24136 AATTTTAATACTACTGCAAAATTTCCATTTAATTATTCTAACTCAAAACTAATTAAATA
1 AATTTTAATACTACTGCAAAATTT-CATATAATTATTCTAACTCAAAACTAATTAAATA
24195 GTATAGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
64 21 0.40
65 31 0.60
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (64 bp):
AATTTTAATACTACTGCAAAATTTCATATAATTATTCTAACTCAAAACTAATTAAATATCTGTG
Found at i:24540 original size:24 final size:23
Alignment explanation
Indices: 24491--24541 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
24481 TTATTCGGAT
*
24491 AAAATGTTTTTGACAATGAATTA
1 AAAATGCTTTTGACAATGAATTA
24514 AAAATGCTTTTGACAATGAATTA
1 AAAATGCTTTTGACAATGAATTA
24537 AAAAT
1 AAAAT
24542 TCCTTAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (23 bp):
AAAATGCTTTTGACAATGAATTA
Found at i:25219 original size:33 final size:33
Alignment explanation
Indices: 25155--25220 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
25145 ACTCCACTAG
* * * **
25155 CAAATAATCCAAACCACGACTAATTTTGATATT
1 CAAATAATCAAAACCACAAATAATTAAGATATT
*
25188 CAAATAATTAAAACCACAAATAATTAAGATATT
1 CAAATAATCAAAACCACAAATAATTAAGATATT
25221 TTAAAATTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (33 bp):
CAAATAATCAAAACCACAAATAATTAAGATATT
Found at i:25839 original size:12 final size:12
Alignment explanation
Indices: 25814--25857 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
25804 ATCAAGAAGA
25814 AAAAATATTTTTT
1 AAAAATA-TTTTT
25827 AAAAATATTTTT
1 AAAAATATTTTT
* *
25839 AATAGTATTTTT
1 AAAAATATTTTT
*
25851 ATAAATA
1 AAAAATA
25858 AACATTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:25850 original size:13 final size:13
Alignment explanation
Indices: 25814--25838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25804 ATCAAGAAGA
25814 AAAAATATTTTTT
1 AAAAATATTTTTT
25827 AAAAATATTTTT
1 AAAAATATTTTT
25839 AATAGTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:30432 original size:21 final size:19
Alignment explanation
Indices: 30394--30439 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
30384 AATTAATCCT
30394 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
30414 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
30435 A-TAAT
1 ACTAAT
30440 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:35854 original size:23 final size:23
Alignment explanation
Indices: 35828--35896 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
35818 CACCACAGCT
*
35828 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
35851 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
35874 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
35897 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:42218 original size:21 final size:19
Alignment explanation
Indices: 42180--42225 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
42170 AATTAATCCT
42180 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
42200 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
42221 A-TAAT
1 ACTAAT
42226 TATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:47966 original size:61 final size:61
Alignment explanation
Indices: 47871--48202 Score: 601
Period size: 61 Copynumber: 5.4 Consensus size: 61
47861 AAAACTATAA
*
47871 TATTACGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
1 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
* *
47932 TATTAAGACCGAACTGGTCATTGTCAAACTATATACTTGGCTTCTAGATATTGTTGTTTTC
1 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
47993 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
1 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
48054 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
1 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
** *
48115 TATTGCGACCGAATTGGTCATTGTCAAACTATATACTTAGCCTCTAGATATTGTTGTTTTC
1 TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
*
48176 TATTACGACCGAATTGGTCATTGTCAA
1 TATTAAGACCGAATTGGTCATTGTCAA
48203 TATGTAATAT
Statistics
Matches: 262, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 262 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (61 bp):
TATTAAGACCGAATTGGTCATTGTCAAACTATATACTTGGCCTCTAGATATTGTTGTTTTC
Found at i:54700 original size:21 final size:21
Alignment explanation
Indices: 54663--54702 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54653 TCTGCTGAAA
**
54663 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
54684 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
54703 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Found at i:59224 original size:26 final size:26
Alignment explanation
Indices: 59195--59244 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
59185 GGTCTGACAT
*
59195 GGCAGCTTCTAGAAGGTCCAGTCAAC
1 GGCAGCTTCTAGAAGATCCAGTCAAC
* *
59221 GGCAGTTTCTAGAAGATCTAGTCA
1 GGCAGCTTCTAGAAGATCCAGTCA
59245 GTGCGCCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (26 bp):
GGCAGCTTCTAGAAGATCCAGTCAAC
Found at i:62488 original size:31 final size:31
Alignment explanation
Indices: 62447--62513 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
62437 TTAACGGTTG
* * *
62447 AGGGATTAAAATCGAATGGATTGATAATATT
1 AGGGAATAAAATCAAATGGATCGATAATATT
*
62478 AGGGAATAAAATCAAATTGATCGATAATATT
1 AGGGAATAAAATCAAATGGATCGATAATATT
62509 AGGGA
1 AGGGA
62514 TCATTTTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.28
Consensus pattern (31 bp):
AGGGAATAAAATCAAATGGATCGATAATATT
Found at i:79699 original size:10 final size:10
Alignment explanation
Indices: 79684--79743 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
79674 TATGCTTGAA
79684 GAAAAAAAAT
1 GAAAAAAAAT
79694 G--AAAAAAT
1 GAAAAAAAAT
*
79702 -AAAAAGAA-
1 GAAAAAAAAT
*
79710 GAAAAAAAAA
1 GAAAAAAAAT
*
79720 GAAAAAAAAA
1 GAAAAAAAAT
79730 GAAAGAAAAAT
1 GAAA-AAAAAT
79741 GAA
1 GAA
79744 GAAGGAGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
8 7 0.17
9 12 0.29
10 15 0.36
11 8 0.19
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:79705 original size:13 final size:13
Alignment explanation
Indices: 79681--79739 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 13
79671 TACTATGCTT
*
79681 GAAGAAAAAAAAT
1 GAAGAAAAAAAAA
79694 GAA-AAAATAAAAA
1 GAAGAAAA-AAAAA
79707 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
*
79720 GAA-AAAAAAAGA
1 GAAGAAAAAAAAA
79732 -AAGAAAAA
1 GAAGAAAAA
79740 TGAAGAAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.05
12 17 0.41
13 18 0.44
14 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:79716 original size:26 final size:25
Alignment explanation
Indices: 79681--79739 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
79671 TACTATGCTT
*
79681 GAAGAAAAAAAATGAAAAAATAAAAA
1 GAAGAAAAAAAAAGAAAAAA-AAAAA
*
79707 GAAGAAAAAAAAAGAAAAAAAAAGA
1 GAAGAAAAAAAAAGAAAAAAAAAAA
79732 -AAGAAAAA
1 GAAGAAAAA
79740 TGAAGAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 8 0.26
25 4 0.13
26 19 0.61
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (25 bp):
GAAGAAAAAAAAAGAAAAAAAAAAA
Found at i:80986 original size:135 final size:134
Alignment explanation
Indices: 80675--81026 Score: 480
Period size: 134 Copynumber: 2.6 Consensus size: 134
80665 AAAAAGAGGT
* * *
80675 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAAGGAGAAGAAGTT
* *
80740 CATAATGAGAAGAGCTTGTTCGACCTTCACTCGATTCATGACATTTCGAATCATTGACACCTCGC
65 CATAATGAGAAGAGCTTGTTCGACCTTCACTCGATTCAAGACATTTCGAATCATGGACACCTCGC
80805 TTGAG
130 TTGAG
* ** *
80810 GAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTC
* *
80875 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAGTCA-GGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCT-TCACTCGATTCA-AGACATTTCGAATCATGGACACCTCG
80938 CTTGAG
129 CTTGAG
* * * *
80944 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAAACTCATCC-AAAGA-GAGAAGAA-TT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAG-AAGAACTCATCCGAAAAAGGAGAAGAAGTT
* *
81006 CATAATGCGAAGAACTTGTTC
65 CATAATGAGAAGAGCTTGTTC
81027 ATCTAACAAC
Statistics
Matches: 193, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
132 21 0.11
133 8 0.04
134 86 0.45
135 77 0.40
136 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (134 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTTCACTCGATTCAAGACATTTCGAATCATGGACACCTCGCT
TGAG
Done.