Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001448.1 Hibiscus syriacus cultivar Beakdansim tig00002799_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: 1849635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1814120 original size:21 final size:19
Alignment explanation
Indices: 1814094--1814141 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1814084 AAATAAGAAA
1814094 AATAATAATTAAAAGAATAAT
1 AATAATAA-TAAAA-AATAAT
*
1814115 AATAATAATAAAATATAAT
1 AATAATAATAAAAAATAAT
1814134 ATATAATA
1 A-ATAATA
1814142 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 11 0.44
21 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAATAATAAAAAATAAT
Found at i:1814160 original size:15 final size:15
Alignment explanation
Indices: 1814140--1814174 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1814130 TAATATATAA
1814140 TATATTTTTAAAAAC
1 TATATTTTTAAAAAC
1814155 TATATTTTTAAAAAC
1 TATATTTTTAAAAAC
1814170 TATAT
1 TATAT
1814175 ATATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATTTTTAAAAAC
Found at i:1814286 original size:2 final size:2
Alignment explanation
Indices: 1814281--1814306 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1814271 TATTTCAAAT
1814281 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
1814307 AAATGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1814289 original size:18 final size:20
Alignment explanation
Indices: 1814252--1814293 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1814242 TTTAAAAATG
1814252 ATTTCAAAACTATAATATAT
1 ATTTCAAAACTATAATATAT
*
1814272 ATTTC-AAATTATATATATAT
1 ATTTCAAAACTATA-ATATAT
1814292 AT
1 AT
1814294 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTCAAAACTATAATATAT
Found at i:1814326 original size:23 final size:23
Alignment explanation
Indices: 1814300--1814343 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1814290 ATATATATAT
*
1814300 ATATATAAAATGTTTTCAAAATC
1 ATATATAAAATGTTTCCAAAATC
* *
1814323 ATATATTATATGTTTCCAAAA
1 ATATATAAAATGTTTCCAAAA
1814344 AAGTTTTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (23 bp):
ATATATAAAATGTTTCCAAAATC
Found at i:1814350 original size:35 final size:34
Alignment explanation
Indices: 1814287--1814405 Score: 112
Period size: 37 Copynumber: 3.3 Consensus size: 34
1814277 AAATTATATA
* ** *
1814287 TATATATATATATATATATAAAATGTTTTCAAAAT
1 TATATATATATATTTCCA-AAAAAGTTTTCAAAAT
* *
1814322 CATATATTATATGTTTCCAAAAAAGTTTTCCAAAAAT
1 TATATA-TATATATTTCCAAAAAAGTTTT-C-AAAAT
* *
1814359 TATATAATATATATTTTCAAAAACCGTTTTCAAAAT
1 TATAT-ATATATATTTCCAAAAA-AGTTTTCAAAAT
1814395 TATATATATAT
1 TATATATATAT
1814406 TATATGTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
35 20 0.29
36 19 0.28
37 24 0.35
38 6 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (34 bp):
TATATATATATATTTCCAAAAAAGTTTTCAAAAT
Found at i:1814358 original size:37 final size:37
Alignment explanation
Indices: 1814311--1814424 Score: 124
Period size: 37 Copynumber: 3.0 Consensus size: 37
1814301 TATATAAAAT
* *
1814311 GTTTTC-AAAATCATATATTATATGTTTCCAAAAA-A
1 GTTTTCAAAAATTATATATTATATGTTTTCAAAAACA
* * *
1814346 GTTTTCCAAAAATTATATAATATATATTTTCAAAAACC
1 GTTTT-CAAAAATTATATATTATATGTTTTCAAAAACA
1814384 GTTTTCAAAATTATATATATATTATATGTATTTCAAAAACA
1 GTTTTCAAAA--AT-TATATATTATATGT-TTTCAAAAACA
1814425 TTCGCAAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
35 5 0.08
36 1 0.02
37 29 0.45
38 5 0.08
39 2 0.03
40 12 0.19
41 10 0.16
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (37 bp):
GTTTTCAAAAATTATATATTATATGTTTTCAAAAACA
Found at i:1815198 original size:84 final size:84
Alignment explanation
Indices: 1815079--1815775 Score: 777
Period size: 84 Copynumber: 8.5 Consensus size: 84
1815069 AAGGTCTTTA
* *
1815079 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCGA
1815144 ACTCGAAGGTCTTTTGTTG
66 ACTCGAAGGTCTTTTGTTG
* * * * * *
1815163 GCAGATAACCCTT-TATGACTTAAGTTATACTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATC
1 GCAGATAACCCTTCT-CGACTTAAGCTATGCTGCAAATGATG-TGCCTCGGAGCTGAGCGTAATC
*
1815227 GAACTCG-GGGTCTTTTGTTG
64 GAACTCGAAGGTCTTTTGTTG
* * * * *
1815247 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGAGCTGAGCGTAATCG
*
1815312 AACTCG-GGGTC---T-TTG
65 AACTCGAAGGTCTTTTGTTG
* ** *
1815327 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCGA
1815392 ACTCGAAGGTCTTTTGTTG
66 ACTCGAAGGTCTTTTGTTG
* * * * * *
1815411 GCAGATAACCTTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGGAGCTGAGCGTAATCG
*
1815476 AACTCG-GGGTC---T-TTG
65 AACTCGAAGGTCTTTTGTTG
* ** *
1815491 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCGA
1815556 ACTCGAAGGTCTTTTGTTG
66 ACTCGAAGGTCTTTTGTTG
* * * * *
1815575 GCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTCAGAGCTGAG-GTAATCG
1 GCAGAT-AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCG
1815638 AACTCGAAGGTC---T-TTG
65 AACTCGAAGGTCTTTTGTTG
* * * *
1815654 GCAGATAGCCCTCCTCGACTTAAGCTATGCTGCAAATGAT-TGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCGA
* * *
1815718 ACTCAAAGGTCTTTTGGTC
66 ACTCGAAGGTCTTTTGTTG
* * * * * *
1815737 ACAGAT-ACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
1815776 TTGTTTTAAA
Statistics
Matches: 523, Mismatches: 68, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
78 13 0.02
79 97 0.19
80 93 0.18
81 2 0.00
82 27 0.05
83 29 0.06
84 215 0.41
85 47 0.09
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATCGA
ACTCGAAGGTCTTTTGTTG
Found at i:1815241 original size:164 final size:162
Alignment explanation
Indices: 1815061--1815775 Score: 869
Period size: 164 Copynumber: 4.4 Consensus size: 162
1815051 GTTGAATATA
* * * * *
1815061 CGAACTCAAAGGTC-T-TTAGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-C
1 CGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCC
* * * * * *
1815123 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT-TATGACTTAAG
66 CTCGAAGCTGAGTGTAATCGAACTCG-AGGTC---T-TTGGCAGATAGCCCTTCT-CGACTTAAG
* * * * * * *
1815187 TTATACTGCAAATGATGTTCCCTCGAAGCTGAGTGTAAT
125 CTATGCTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGT
*
1815226 CGAACTCG-GGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG
1 CGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG
*
1815290 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
64 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1815355 GCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
129 GCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
*
1815389 CGAACTCGAAGGTCTTTTGTTGGCAGATAACCTTTCTTGACTTAAGTTATACTGCAAATGATGTG
1 CGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG
*
1815454 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
64 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1815519 GCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
129 GCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
* * * *
1815553 CGAACTCGAAGGTCTTTTGTTGGCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 CGAACTCGAAGGTC--TTGTTGGCAGAT-AACCCTTCTTGACTTAAGTTATACTGCAAATGATGT
*
1815617 G-CCTC-AGAGCTGAG-GTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTCCTCGACTTAAGC
63 GCCCTCGA-AGCTGAGTGTAATCGAACTCG-AGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
*
1815679 TATGCTGCAAATGAT-TGCCTTGGAGCTGAGCGTAGT
126 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
* * * * * *
1815715 CGAACTCAAAGGTCTT-TTGGTCACAGAT-ACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 CGAACTCGAAGGTCTTGTTGG---CAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGAT
1815776 TTGTTTTAAA
Statistics
Matches: 501, Mismatches: 35, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
159 4 0.01
160 2 0.00
161 29 0.06
162 50 0.10
163 79 0.16
164 258 0.51
165 9 0.02
167 1 0.00
168 46 0.09
169 23 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (162 bp):
CGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCC
CTCGAAGCTGAGTGTAATCGAACTCGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
Found at i:1815434 original size:248 final size:244
Alignment explanation
Indices: 1815061--1815721 Score: 874
Period size: 248 Copynumber: 2.7 Consensus size: 244
1815051 GTTGAATATA
* *
1815061 CGAACTCAAAGGTCTTTAGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
1 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
1815126 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTT-ATGACTTAAGTTA
66 AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAA-CCTTTCTTGACTTAAGTTA
*
1815190 TACTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTTGTTGGCAGATAA
130 TACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTC---T-TTGGCAGATAA
* * * *
1815255 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
191 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCCTAG-AGCTGAGCGTAAT
* *
1815310 CGAACTCG-GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
1 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
1815374 AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCTTTCTTGACTTAAGTTAT
66 AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCTTTCTTGACTTAAGTTAT
*
1815439 ACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTT
131 ACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAACCCTT
* * *
1815504 CTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
196 CTCGACTTAAGCTATACTGCAAATGATGTGCCCTAGAGCTGAGCGTAAT
* * * *
1815553 CGAACTCGAAGGTCTTTTGTTGGCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 CGAACTCGAAGGTC---T-TTGGCAGAT-AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * * * *
1815617 GCCTCAGAGCTGAG-GTAATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTCCTCGACTTAA
61 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCTTTCTTGACTTAA
* * * * * *
1815677 GCTATGCTGCAAATGAT-TG-CCTTGGAGCTGAGCGTAGTCGAACTC
126 GTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
1815722 AAAGGTCTTT
Statistics
Matches: 372, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
241 22 0.06
242 2 0.01
243 56 0.15
244 51 0.14
245 1 0.00
247 25 0.07
248 208 0.56
249 7 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (244 bp):
CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCTTTCTTGACTTAAGTTAT
ACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAACCCTT
CTCGACTTAAGCTATACTGCAAATGATGTGCCCTAGAGCTGAGCGTAAT
Found at i:1819114 original size:18 final size:19
Alignment explanation
Indices: 1819073--1819117 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1819063 AGTTAATGTG
1819073 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1819092 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1819110 AATGCAAA
1 AATGCAAA
1819118 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1821357 original size:10 final size:10
Alignment explanation
Indices: 1821344--1821378 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
1821334 GCCGGCTATC
1821344 GCCGACGGTG
1 GCCGACGGTG
1821354 GCCGACGGTG
1 GCCGACGGTG
1821364 GCCGACGGTG
1 GCCGACGGTG
1821374 GCCGA
1 GCCGA
1821379 GCAAACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.11, C:0.31, G:0.49, T:0.09
Consensus pattern (10 bp):
GCCGACGGTG
Found at i:1822141 original size:21 final size:20
Alignment explanation
Indices: 1822098--1822169 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1822088 AACAAAAAGA
* * *
1822098 AATAAATAAAAAAGAAAAAT
1 AATAATTAAAAAATAATAAT
1822118 AATAATTAAAAGAATAATAAT
1 AATAATTAAAA-AATAATAAT
1822139 AATAA-TAAAAAA-AATAAT
1 AATAATTAAAAAATAATAAT
1822157 AAT-A-TAAAAAATA
1 AATAATTAAAAAATA
1822170 TTTTTAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.17
18 10 0.21
19 2 0.04
20 15 0.32
21 12 0.26
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (20 bp):
AATAATTAAAAAATAATAAT
Found at i:1822154 original size:15 final size:15
Alignment explanation
Indices: 1822136--1822169 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1822126 AAAGAATAAT
1822136 AATAATAATAAAAAA
1 AATAATAATAAAAAA
*
1822151 AATAATAATATAAAA
1 AATAATAATAAAAAA
1822166 AATA
1 AATA
1822170 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAATAAAAAA
Found at i:1822167 original size:18 final size:19
Alignment explanation
Indices: 1822102--1822165 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
1822092 AAAAGAAATA
*
1822102 AATAAAAAAGAAAAATAAT
1 AATATAAAAGAAAAATAAT
*
1822121 AAT-TAAAAGAATAATAAT
1 AATATAAAAGAAAAATAAT
1822139 AATA-ATAAA-AAAAATAAT
1 AATATA-AAAGAAAAATAAT
1822157 AATATAAAA
1 AATATAAAA
1822166 AATATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 32 0.82
19 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (19 bp):
AATATAAAAGAAAAATAAT
Found at i:1822201 original size:31 final size:30
Alignment explanation
Indices: 1822163--1822220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1822153 TAATAATATA
*
1822163 AAAAATATTTTTAAAAACTATATTATATTTT
1 AAAAATA-TTTCAAAAACTATATTATATTTT
* *
1822194 AAAAATATTTCCAAAATTATATTATAT
1 AAAAATATTTCAAAAACTATATTATAT
1822221 AATTTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAAATATTTCAAAAACTATATTATATTTT
Found at i:1822250 original size:35 final size:35
Alignment explanation
Indices: 1822186--1822498 Score: 201
Period size: 34 Copynumber: 9.1 Consensus size: 35
1822176 AAAACTATAT
* *
1822186 TATATTTT-AAAAATATTTCCAAAA-T-TATATTA
1 TATATTTTCAAAAATGTTTTCAAAATTATATATTA
1822218 TATAATTTTCAAAAATGTTTT-AAAATTATATATTA
1 TAT-ATTTTCAAAAATGTTTTCAAAATTATATATTA
* * ***
1822253 CATGTTTTCAAAAATGTTTTTTTTAA-TATATA-T-
1 TATATTTTCAAAAATG-TTTTCAAAATTATATATTA
* * *
1822286 TATA-TTT-AAAAATGATTTCAAAACTATATAATA
1 TATATTTTCAAAAATGTTTTCAAAATTATATATTA
*
1822319 TATATTTTC-AAAATGTTTTCAAAAATTATATAATA
1 TATATTTTCAAAAATGTTTTC-AAAATTATATATTA
* * * * * *
1822354 TATA-TAT-ATATAT-ATAT-ATATATATATATATATA
1 TATATTTTCAAAAATGTTTTCA-AAAT-TATATAT-TA
* *
1822388 TATATATT--AAAATGTTTTCAAAAATCATATATTA
1 TATATTTTCAAAAATGTTTTC-AAAATTATATATTA
* *
1822422 TATATGTTTCCAAAAAAGTTTTCCAAAAATTATATAATA
1 TATAT-TTT-CAAAAATGTTTT-C-AAAATTATATATTA
*
1822461 TATATTTTCAAAAACCGTTTTCAAAATTATATA-TA
1 TATATTTTCAAAAA-TGTTTTCAAAATTATATATTA
1822496 TAT
1 TAT
1822499 TATATGTATT
Statistics
Matches: 221, Mismatches: 34, Indels: 49
0.73 0.11 0.16
Matches are distributed among these distances:
30 5 0.02
31 14 0.06
32 10 0.05
33 23 0.10
34 57 0.26
35 52 0.24
36 16 0.07
37 8 0.04
38 17 0.08
39 19 0.09
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
TATATTTTCAAAAATGTTTTCAAAATTATATATTA
Found at i:1822273 original size:99 final size:99
Alignment explanation
Indices: 1822163--1822350 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 99
1822153 TAATAATATA
* *
1822163 AAAAATA-TTTTTAAAAACTATATTATATTTTAAAAAT-ATTTCCAAAATTATATTATATA-ATT
1 AAAAATATTTTTTAAAAA-TATATTATA-TTTAAAAATGATTT-CAAAACTATATAATATATATT
1822225 TTCAAAAATGTTTT-AAAATTATATATTACATGTTTTC
63 TTC-AAAATGTTTTAAAAATTATATATTACATGTTTTC
* * *
1822262 AAAAATGTTTTTTTTAATATATATTATATTTAAAAATGATTTCAAAACTATATAATATATATTTT
1 AAAAAT-ATTTTTTAAAAATATATTATATTTAAAAATGATTTCAAAACTATATAATATATATTTT
1822327 CAAAATGTTTTCAAAAATTATATA
65 CAAAATGTTTT-AAAAATTATATA
1822351 ATATATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
99 40 0.51
100 19 0.24
101 19 0.24
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (99 bp):
AAAAATATTTTTTAAAAATATATTATATTTAAAAATGATTTCAAAACTATATAATATATATTTTC
AAAATGTTTTAAAAATTATATATTACATGTTTTC
Found at i:1822356 original size:2 final size:2
Alignment explanation
Indices: 1822345--1822394 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1822335 TTTCAAAAAT
1822345 TA TA TA -A 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
1822386 TA TA TA TA T
1 TA TA TA TA T
1822395 TAAAATGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1822431 original size:25 final size:26
Alignment explanation
Indices: 1822389--1822437 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1822379 ATATATATAT
1822389 ATATATTAAAATGTTTT-CAAAAATC
1 ATATATTAAAATGTTTTCCAAAAATC
*
1822414 ATATATTATATATG-TTTCCAAAAA
1 ATATATTA-AAATGTTTTCCAAAAA
1822438 AGTTTTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATATTAAAATGTTTTCCAAAAATC
Found at i:1822435 original size:26 final size:25
Alignment explanation
Indices: 1822389--1822437 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1822379 ATATATATAT
*
1822389 ATATATTAAAATGTTTTCAAAAATC
1 ATATATTAAAATGTTTCCAAAAATC
*
1822414 ATATATTATATATGTTTCCAAAAA
1 ATATATTA-AAATGTTTCCAAAAA
1822438 AGTTTTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATATTAAAATGTTTCCAAAAATC
Found at i:1822443 original size:38 final size:37
Alignment explanation
Indices: 1822396--1822515 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 37
1822386 TATATATATT
* *
1822396 AAAATGTTTTCAAAAATCATATATTATATATGTTTCCA
1 AAAAAGTTTTCAAAAATTATATATTATATATGTTT-CA
*
1822434 AAAAAGTTTTCCAAAAATTATATAATATATAT-TTTCA
1 AAAAAGTTTT-CAAAAATTATATATTATATATGTTTCA
*
1822471 AAAACCGTTTTC-AAAATTATATATATATTATATGTATTTCA
1 AAAA-AGTTTTCAAAAATTATATAT-TA-TATATG--TTTCA
1822512 AAAA
1 AAAA
1822516 CATTCGCAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
36 11 0.16
37 9 0.13
38 22 0.31
39 19 0.27
41 9 0.13
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAAAGTTTTCAAAAATTATATATTATATATGTTTCA
Found at i:1829621 original size:2 final size:2
Alignment explanation
Indices: 1829614--1829686 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1829604 TATGAATGAG
1829614 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
1829656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1829687 TATGTTTTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1836571 original size:20 final size:20
Alignment explanation
Indices: 1836533--1836571 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1836523 ACCTCATATT
*
1836533 ATTTTTAAGTATGGTTTATG
1 ATTTTTAAGTATGGATTATG
* *
1836553 ATTTTTAATTGTGGATTAT
1 ATTTTTAAGTATGGATTAT
1836572 TTCCATAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (20 bp):
ATTTTTAAGTATGGATTATG
Found at i:1837435 original size:2 final size:2
Alignment explanation
Indices: 1837428--1837495 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1837418 AATGAGTAGA
1837428 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
1837470 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
1837496 GTTTTAAATG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1842575 original size:20 final size:20
Alignment explanation
Indices: 1842550--1842592 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1842540 TTTCACCACA
*
1842550 TCAAATCCTCTCCAATTCTC
1 TCAAATCCTCTCAAATTCTC
*
1842570 TCAAATCCTCTTAAATTCTC
1 TCAAATCCTCTCAAATTCTC
1842590 TCA
1 TCA
1842593 CAGCTCGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (20 bp):
TCAAATCCTCTCAAATTCTC
Found at i:1842580 original size:10 final size:10
Alignment explanation
Indices: 1842550--1842592 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1842540 TTTCACCACA
1842550 TCAAATCCTC
1 TCAAATCCTC
* *
1842560 TCCAATTCTC
1 TCAAATCCTC
1842570 TCAAATCCTC
1 TCAAATCCTC
* *
1842580 TTAAATTCTC
1 TCAAATCCTC
1842590 TCA
1 TCA
1842593 CAGCTCGTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (10 bp):
TCAAATCCTC
Found at i:1842706 original size:16 final size:16
Alignment explanation
Indices: 1842632--1842706 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
1842622 TTTTATTTTA
*
1842632 TTTTATATTTAATTAT
1 TTTTTTATTTAATTAT
*
1842648 TATTTTATTTAATTAT
1 TTTTTTATTTAATTAT
*** *
1842664 TTAACTATTTAAATTTTT
1 TTTTTTATTT-AA-TTAT
1842682 TAGTATTTTATTTAATTAT
1 T--T-TTTTATTTAATTAT
1842701 TTTTTT
1 TTTTTT
1842707 GCAGTTATAA
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
16 24 0.56
17 3 0.07
18 4 0.09
19 4 0.09
20 3 0.07
21 5 0.12
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (16 bp):
TTTTTTATTTAATTAT
Found at i:1842864 original size:27 final size:28
Alignment explanation
Indices: 1842820--1842876 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
1842810 TGATTAATAA
** * *
1842820 TAGTTTATTTATTTAATTTT-TTATTAT
1 TAGTTTATAAATTAAATTTTGTAATTAT
1842847 TAGTTTATAAATTAAATTTTGTAATTAT
1 TAGTTTATAAATTAAATTTTGTAATTAT
1842875 TA
1 TA
1842877 ATATTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TAGTTTATAAATTAAATTTTGTAATTAT
Found at i:1844754 original size:3 final size:3
Alignment explanation
Indices: 1844748--1844796 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1844738 GACGACGACA
*
1844748 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1844796 A
1 A
1844797 CAGTGAGGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1848650 original size:30 final size:30
Alignment explanation
Indices: 1848616--1848677 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1848606 GGATTGACGG
1848616 GTGATATTTACGCA-TTGAGAGGATCGTTGT
1 GTGATATTTACG-AGTTGAGAGGATCGTTGT
* * *
1848646 GTGATGTTTTCGAGTTGAGAGGATTGTTGT
1 GTGATATTTACGAGTTGAGAGGATCGTTGT
1848676 GT
1 GT
1848678 AAATGTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.19, C:0.06, G:0.34, T:0.40
Consensus pattern (30 bp):
GTGATATTTACGAGTTGAGAGGATCGTTGT
Found at i:1848696 original size:31 final size:30
Alignment explanation
Indices: 1848631--1848697 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1848621 ATTTACGCAT
* * *
1848631 TGAGAGGATCGTTGTGTGATGTTTTCGAGT
1 TGAGAGGATCGTTGTGTAATGTTTACGAGG
* *
1848661 TGAGAGGATTGTTGTGTAAATGTTTACGGGG
1 TGAGAGGATCGTTGTGT-AATGTTTACGAGG
1848692 TGAGAG
1 TGAGAG
1848698 CGTTTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.21, C:0.04, G:0.39, T:0.36
Consensus pattern (30 bp):
TGAGAGGATCGTTGTGTAATGTTTACGAGG
Found at i:1849606 original size:2 final size:2
Alignment explanation
Indices: 1849599--1849635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1849589 TTTTCACAAT
1849599 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.