Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002208.1 Hibiscus syriacus cultivar Beakdansim tig00004500_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: 43457
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4268 original size:8 final size:8
Alignment explanation
Indices: 4236--4309 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
4226 GCTTGAAGAA
*
4236 AAAAAAGG
1 AAAAAATG
*
4244 AACAAAT-
1 AAAAAATG
4251 AAAAAGATG
1 AAAAA-ATG
4260 AAAAAATG
1 AAAAAATG
4268 AAAAAATG
1 AAAAAATG
*
4276 AAAAAGA-A
1 AAAAA-ATG
4284 AAAAAATG
1 AAAAAATG
4292 -AAAAATG
1 AAAAAATG
*
4299 AAAAAAAG
1 AAAAAATG
4307 AAA
1 AAA
4310 TGAGAAAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
7 12 0.22
8 37 0.67
9 6 0.11
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:4274 original size:24 final size:24
Alignment explanation
Indices: 4231--4303 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
4221 ACTATGCTTG
* *
4231 AAGAAAAAAAAGGAACAAAT-AAA
1 AAGAAAAAAAATGAAAAAATGAAA
*
4254 AAGATGAAAAAATGAAAAAATGAAA
1 AAGA-AAAAAAATGAAAAAATGAAA
4279 AAGAAAAAAAATG-AAAAATGAAA
1 AAGAAAAAAAATGAAAAAATGAAA
4302 AA
1 AA
4304 AAGAAATGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.36
24 21 0.48
25 7 0.16
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (24 bp):
AAGAAAAAAAATGAAAAAATGAAA
Found at i:4305 original size:32 final size:32
Alignment explanation
Indices: 4251--4318 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
4241 AGGAACAAAT
*
4251 AAAAAGATGAAAAAATGAAAAAATGAAA-AAGA
1 AAAAAAATGAAAAAATGAAAAAA-GAAATAAGA
*
4283 AAAAAAATG-AAAAATGAAAAAAAGAAATGAGA
1 AAAAAAATGAAAAAATG-AAAAAAGAAATAAGA
4315 AAAA
1 AAAA
4319 GGAGGGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (32 bp):
AAAAAAATGAAAAAATGAAAAAAGAAATAAGA
Found at i:5807 original size:334 final size:334
Alignment explanation
Indices: 5193--5848 Score: 1001
Period size: 334 Copynumber: 2.0 Consensus size: 334
5183 TTGATCAACA
* * *
5193 TTTCCAATGAAGAGTTTATAATGAGAAGAACTCATCCGATATAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * *
5258 AAGAGCCTATTCGACCTATCACTCGATTCATGGCGTTTCGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
*
5323 TCAACATTTCCAGAGAATAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
131 TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
*
5388 GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATTAAAATTTCCAATGAAGAGTTC
196 GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
* * * *
5453 ATAATAAGAAGAATTCATCCAACGA-GAGAGAATAATTTCATAATGAGAAAAACTTGTCCAACTT
261 ATAATAAGAAGAACTCATCCAAAGAGGA-AGAAGAAGTTCATAATGAGAAAAACTTGTCCAACTT
5517 CGCATTAGTG
325 CGCATTAGTG
*
5527 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
** * * *
5592 AAGAGTTTGTTCGACCTATCACTTGATTCACGACATTTTGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
** * * *
5657 TTGACATTTCTA-ATTAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGGGAAAGTTCATAATG
131 TCAACATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
* * * * *
5721 AGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTGAAGAGTT
195 AGAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTT
* * *
5786 CATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
260 CATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTCCAAC
5849 CTTGGTTTGA
Statistics
Matches: 289, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
333 1 0.00
334 286 0.99
335 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (334 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCCTATTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
ATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTCCAACTTC
GCATTAGTG
Found at i:5845 original size:20 final size:20
Alignment explanation
Indices: 5782--5846 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
5772 TTCAGTGAAG
5782 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
5802 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
5821 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
5841 TGTTCA
1 AGTTCA
5847 ACCTTGGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:5909 original size:117 final size:114
Alignment explanation
Indices: 5672--5964 Score: 390
Period size: 117 Copynumber: 2.6 Consensus size: 114
5662 ATTTCTAATT
*
5672 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAG-GG--G-A-AAGTTCATAATGAGAAGAACTTG
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
5732 TT---CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 TTCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
5779 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
** * * * *
5844 TCAACCTTGGTTTGATTTCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
66 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
*
5896 AAGAGTTCATAATGAGAAGAACTCATCCAACA-A-GAGAGAAGAATTTCATAATGAGAAGAACTT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGA-AGAAGAAGTTCATAATGAGAAGAACTT
5959 GTTCAA
64 GTTCAA
5965 TCCAACGCTT
Statistics
Matches: 165, Mismatches: 8, Indels: 16
0.87 0.04 0.08
Matches are distributed among these distances:
106 4 0.02
107 29 0.18
109 1 0.01
110 1 0.01
111 25 0.15
114 2 0.01
115 1 0.01
116 2 0.01
117 99 0.60
118 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (114 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:9205 original size:55 final size:55
Alignment explanation
Indices: 9121--9229 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
9111 TAAATTACAC
9121 AAGTAATTCTTGAACTTTTAAAGTGTTATATTTTAATCACCAATATTTTTAATAA
1 AAGTAATTCTTGAACTTTTAAAGTGTTATATTTTAATCACCAATATTTTTAATAA
*
9176 AAGTAATTCTTGAACTTTTAAAGTGTTATATTTTAATCATCAATATTTTTAATA
1 AAGTAATTCTTGAACTTTTAAAGTGTTATATTTTAATCACCAATATTTTTAATA
9230 TTTTATTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (55 bp):
AAGTAATTCTTGAACTTTTAAAGTGTTATATTTTAATCACCAATATTTTTAATAA
Found at i:16503 original size:20 final size:22
Alignment explanation
Indices: 16478--16518 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
16468 TATACCTTAT
16478 CCCTAATTTA-AA-AACATAAA
1 CCCTAATTTATAACAACATAAA
16498 CCCTAATTTATAACAACATAA
1 CCCTAATTTATAACAACATAA
16519 CCTTTAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (22 bp):
CCCTAATTTATAACAACATAAA
Found at i:16976 original size:16 final size:16
Alignment explanation
Indices: 16955--16996 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
16945 AAAGTAATAC
16955 AAGTGTCACCTATCAA
1 AAGTGTCACCTATCAA
*
16971 AAGTGTCACCTCTCAA
1 AAGTGTCACCTATCAA
*
16987 AAGTGCCACC
1 AAGTGTCACC
16997 CCTGGGGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.21
Consensus pattern (16 bp):
AAGTGTCACCTATCAA
Found at i:26568 original size:37 final size:37
Alignment explanation
Indices: 26511--26615 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
26501 CATTTTCGTC
*
26511 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
26548 TTGCTAAGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
26585 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
26616 CCACAAGCAC
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:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:27011 original size:18 final size:17
Alignment explanation
Indices: 26972--27014 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
26962 ATTATATGGA
26972 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
26988 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
27006 TATTATTAT
1 TATTATTAT
27015 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:27043 original size:60 final size:60
Alignment explanation
Indices: 26971--27086 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 60
26961 TATTATATGG
*
26971 ATATTTTATTCATTTATTTTTATTA-T-TCATGTTATTATTATTATATGTATATATATATAT
1 ATATTTTATTCATTTATTTTT-TTACTAT-ATGTTATTATTATTATATATATATATATATAT
*
27031 ATATTATT-TTCATTTATTTTTTTACTATATTTTATTATTATTATATATATATATAT
1 ATATT-TTATTCATTTATTTTTTTACTATATGTTATTATTATTATATATATATATAT
27087 TTCTTTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
59 3 0.06
60 45 0.88
61 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (60 bp):
ATATTTTATTCATTTATTTTTTTACTATATGTTATTATTATTATATATATATATATATAT
Found at i:27099 original size:60 final size:60
Alignment explanation
Indices: 26979--27100 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
26969 GGATATTTTA
* *
26979 TTCATTTATTTTTATTATTCATGTTATTATTATTATATGTATATATATATATATATTATT
1 TTCATTTATTTTTATTATTCATGTTATTATTATTATATATATATATATATATATAATATT
* * * *
27039 TTCATTTATTTTT-TTACTAT-ATTTTATTATTATTATATATATATATATTTCTTTAATATT
1 TTCATTTATTTTTATTA-T-TCATGTTATTATTATTATATATATATATATATATATAATATT
27099 TT
1 TT
27101 ACTTATAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
59 3 0.06
60 50 0.93
61 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (60 bp):
TTCATTTATTTTTATTATTCATGTTATTATTATTATATATATATATATATATATAATATT
Found at i:27288 original size:22 final size:21
Alignment explanation
Indices: 27253--27307 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
27243 TTATTCGTAC
*
27253 TTTGTTATTA-TTATTTTGTTT
1 TTTGTT-TTATTTATTTTCTTT
27274 ATTTGTTTTATTTATTTTCTTT
1 -TTTGTTTTATTTATTTTCTTT
27296 TTCT-TTTTATTT
1 TT-TGTTTTATTT
27308 TTTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTGTTTTATTTATTTTCTTT
Found at i:27307 original size:30 final size:30
Alignment explanation
Indices: 27271--27327 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27261 TATTATTTTG
* *
27271 TTTATTTGTTT-TATTTATTTTCTTTTTCTT
1 TTTATTT-TTTATATATATTTTATTTTTCTT
27301 TTTATTTTTTATATATATTTTATTTTT
1 TTTATTTTTTATATATATTTTATTTTT
27328 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (30 bp):
TTTATTTTTTATATATATTTTATTTTTCTT
Found at i:31699 original size:183 final size:183
Alignment explanation
Indices: 31391--31927 Score: 968
Period size: 183 Copynumber: 2.9 Consensus size: 183
31381 ATTAAATCCG
31391 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
31456 ATAGATTATGTTCAAACTATGACACTACTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
31521 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCATTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
*
31574 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
31639 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
**
31704 TTGTCAGGCCAAAGACTTTGTGATGAGACAAACCCTTCAGTGATTTATCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
31757 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
31822 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
31886 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
31928 TAAACCTGAT
Statistics
Matches: 340, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 339 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
Found at i:33149 original size:36 final size:36
Alignment explanation
Indices: 33109--33225 Score: 99
Period size: 36 Copynumber: 3.1 Consensus size: 36
33099 ATACTTTGTC
33109 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * ** * * *
33145 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * *
33181 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
33221 TCACT
1 TCACT
33226 CAAGGCTGTT
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 40 0.70
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:33160 original size:72 final size:75
Alignment explanation
Indices: 33068--33238 Score: 208
Period size: 72 Copynumber: 2.3 Consensus size: 75
33058 ATGCAGATGA
* * * *
33068 TTATCTCACTCAA-ATTTGTTTTTATTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTATTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
33130 GAAAGAA-G-AT
64 GAAAGAAGGCAT
* *
33140 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTATTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
33205 AAGAAGGCAT
66 AAGAAGGCAT
**
33215 TTCATTTCACTCAAGGCTGTTTTT
1 TT-ATTTCACTCAAGATTGTTTTT
33239 TAAGAAGATT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 49 0.58
73 11 0.13
74 1 0.01
75 4 0.05
76 19 0.22
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTATTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:33247 original size:72 final size:72
Alignment explanation
Indices: 33103--33263 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 72
33093 TAAAACATAC
* * * *
33103 TTTGTCTCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAA
1 TTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTT-A
33168 AACAAGA-
65 AACAAGAT
*
33175 TTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCAAGGCTG-TTTT-
1 TTTGTCTCGCTTGAGACCGTTTT-ACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTGTTTTTC
*
33238 TT-AAGAAGAT
62 TTAAACAAGAT
* *
33248 TTTATCTTGCTTGAGA
1 TTTGTCTCGCTTGAGA
33264 TAGTTTCCCT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
72 27 0.36
73 24 0.32
74 3 0.04
75 8 0.11
76 14 0.18
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (72 bp):
TTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTTAA
ACAAGAT
Found at i:33263 original size:73 final size:71
Alignment explanation
Indices: 33107--33263 Score: 167
Period size: 73 Copynumber: 2.2 Consensus size: 71
33097 ACATACTTTG
* * * *
33107 TCTCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAAAACA
1 TCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTT-AAACA
*
33172 AGATTTG
65 AGATTTA
*
33179 TCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCAAGGCTG-TTTT-TT-A
1 TCTCGCTTGAGACCGTTTT-ACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTGTTTTTCTTAA
*
33241 AGAAGATTTTA
62 ACAAGA-TTTA
*
33252 TCTTGCTTGAGA
1 TCTCGCTTGAGA
33264 TAGTTTCCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
72 23 0.32
73 24 0.33
74 3 0.04
75 8 0.11
76 14 0.19
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (71 bp):
TCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTTAAACAA
GATTTA
Found at i:33300 original size:39 final size:39
Alignment explanation
Indices: 33257--33398 Score: 106
Period size: 39 Copynumber: 3.3 Consensus size: 39
33247 TTTTATCTTG
*
33257 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
33296 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
33348 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
*
33386 TTTGAGACAGTTT
1 CTTGAGACAGTTT
33399 TTCTTGAAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 28
0.68 0.09 0.24
Matches are distributed among these distances:
38 1 0.01
39 36 0.46
40 5 0.06
41 2 0.03
42 1 0.01
48 1 0.01
49 2 0.03
50 5 0.06
51 24 0.30
52 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:33482 original size:108 final size:105
Alignment explanation
Indices: 33312--33633 Score: 474
Period size: 108 Copynumber: 3.1 Consensus size: 105
33302 ACAGTTTCTC
* *
33312 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
* *
33376 TTTTGTCTCCTTTGAGACAGTTTTTCTTGAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
33416 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTCTTGAGATAGTTTCTCTCGAAACAGA
1 TTGAAAACATTTCCCTTGAAATGA--TTTTTTTCTCTC-CTTGAGATAGTTTCCCTCGAAACAGA
33481 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
63 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
33524 TTGAAAACATTTCCCTTGAAATGAATTTTATCTC-GCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
** *
33585 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
33625 TTGAAAACA
1 TTGAAAACA
33634 ATTTAACGAA
Statistics
Matches: 201, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 44 0.22
106 19 0.09
107 1 0.00
108 88 0.44
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:33580 original size:36 final size:36
Alignment explanation
Indices: 33533--33608 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
33523 ATTGAAAACA
* * *
33533 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
33569 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
33605 TTTC
1 TTTC
33609 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:34010 original size:105 final size:105
Alignment explanation
Indices: 33808--34438 Score: 918
Period size: 105 Copynumber: 6.0 Consensus size: 105
33798 ATATCGTGAC
* * * * *
33808 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
*
33872 CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
33914 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
33979 ATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
34019 ACTTCAGACAAAGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
34084 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
34124 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
34189 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
34229 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
34290 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * *
34329 ACTAAAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
** * *
34393 CGGTTCCAGAGCCAATTTCAACTTCACGAC-AGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTGG
34435 ACTC
1 ACTC
34439 GGAACAATGC
Statistics
Matches: 483, Mismatches: 33, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
99 2 0.00
100 79 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 306 0.63
106 81 0.17
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:35034 original size:37 final size:37
Alignment explanation
Indices: 34981--35085 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
34971 CATTTTCGTC
34981 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
35018 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
35055 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
35086 CCACAAGCAC
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:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:35481 original size:18 final size:17
Alignment explanation
Indices: 35442--35484 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
35432 ATTATATGGA
35442 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
35458 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
35476 TATTATTAT
1 TATTATTAT
35485 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:35707 original size:2 final size:2
Alignment explanation
Indices: 35702--35744 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35692 TTTTATTTAT
35702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35744 T
1 T
35745 CGTACTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40486 original size:44 final size:44
Alignment explanation
Indices: 40423--40542 Score: 204
Period size: 44 Copynumber: 2.7 Consensus size: 44
40413 ATAGACTTGT
* *
40423 TTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGACA
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACA
*
40467 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACA
*
40511 TTTTATTTATTTTGTTTCTTAATATTTTTATT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATT
40543 ATTTAATTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.68
Consensus pattern (44 bp):
TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACA
Found at i:43166 original size:59 final size:60
Alignment explanation
Indices: 43099--43243 Score: 204
Period size: 60 Copynumber: 2.4 Consensus size: 60
43089 TGTTAGATTT
* * *
43099 CCCTACGAAGGCGCGCTTCATGATCCGCGCC-TTCTGAC-GTGACGCCAGCTCTGACAGAA
1 CCCTACGAAGGCACGCTTCATGATCCGCGCCTTTC-CACAGTGACGCCAACTCTGACAGAA
* * *
43158 CCCTACGAAGGTACGCCTCATGATCCGCGCCTTTCCACAGTGGCGCCAACTCTGACAGAA
1 CCCTACGAAGGCACGCTTCATGATCCGCGCCTTTCCACAGTGACGCCAACTCTGACAGAA
*
43218 CCCTGCGAAGGCACGCTTCATGATCC
1 CCCTACGAAGGCACGCTTCATGATCC
43244 CGCTTTGTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
59 30 0.40
60 45 0.60
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (60 bp):
CCCTACGAAGGCACGCTTCATGATCCGCGCCTTTCCACAGTGACGCCAACTCTGACAGAA
Done.