Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007937.1 Hibiscus syriacus cultivar Beakdansim tig00110347_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: 820613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:767879 original size:30 final size:29
Alignment explanation
Indices: 767814--767889 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
767804 ATTCGGTTTT
*****
767814 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
767843 GGTGCTATTCTGGTAAATAATTCGAAAAAG
1 GGTGCTATTCTGGTAAATAATTC-AAAAAG
767873 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
767890 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:771150 original size:91 final size:91
Alignment explanation
Indices: 770995--771162 Score: 336
Period size: 91 Copynumber: 1.8 Consensus size: 91
770985 TCAACGGGGA
770995 GATTTTTCTGGCTAACCTGATGGAGTTACCCTTTGAAGAGTTCGATTTGATTCTCGGCGTAGATT
1 GATTTTTCTGGCTAACCTGATGGAGTTACCCTTTGAAGAGTTCGATTTGATTCTCGGCGTAGATT
771060 GGTTGAACAAACATCGAGTAAATATT
66 GGTTGAACAAACATCGAGTAAATATT
771086 GATTTTTCTGGCTAACCTGATGGAGTTACCCTTTGAAGAGTTCGATTTGATTCTCGGCGTAGATT
1 GATTTTTCTGGCTAACCTGATGGAGTTACCCTTTGAAGAGTTCGATTTGATTCTCGGCGTAGATT
771151 GGTTGAACAAAC
66 GGTTGAACAAAC
771163 CTGATGGAGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (91 bp):
GATTTTTCTGGCTAACCTGATGGAGTTACCCTTTGAAGAGTTCGATTTGATTCTCGGCGTAGATT
GGTTGAACAAACATCGAGTAAATATT
Found at i:775021 original size:17 final size:17
Alignment explanation
Indices: 774999--775080 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 17
774989 TGACCGGTCA
*
774999 TGACCCGACCCGATAGT
1 TGACCCGACCCGACAGT
*
775016 TGACCCGACCCGACCGT
1 TGACCCGACCCGACAGT
775033 TGACCCGA-CC--C-GT
1 TGACCCGACCCGACAGT
775046 TGACCCGA-CC--CA-T
1 TGACCCGACCCGACAGT
*
775059 TGACCCGACCCGACCGT
1 TGACCCGACCCGACAGT
775076 TGACC
1 TGACC
775081 GTTGACCGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
13 22 0.39
14 3 0.05
16 3 0.05
17 29 0.51
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACAGT
Found at i:775047 original size:13 final size:13
Alignment explanation
Indices: 775022--775070 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
775012 TAGTTGACCC
775022 GACCCGA-CCGTT
1 GACCCGACCCGTT
775034 GACCCGACCCGTT
1 GACCCGACCCGTT
*
775047 GACCCGACCCATT
1 GACCCGACCCGTT
775060 GACCCGACCCG
1 GACCCGACCCG
775071 ACCGTTGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 7 0.21
13 27 0.79
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:775130 original size:29 final size:29
Alignment explanation
Indices: 775088--775169 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
775078 ACCGTTGACC
*
775088 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
775117 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
775146 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
775170 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:775182 original size:30 final size:29
Alignment explanation
Indices: 775117--775192 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
775107 ATTCGGTTTT
*****
775117 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
775146 GGTGCTATTCTGGTAAATAATTCGAAAAAG
1 GGTGCTATTCTGGTAAATAATTC-AAAAAG
775176 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
775193 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:782283 original size:17 final size:17
Alignment explanation
Indices: 782261--782328 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
782251 GACCGGTCAC
*
782261 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
782278 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
782295 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
782308 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
782325 GACC
1 GACC
782329 GTTGACTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 10 0.22
14 3 0.07
16 3 0.07
17 29 0.64
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:782308 original size:13 final size:13
Alignment explanation
Indices: 782283--782318 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
782273 TAGTTGACCC
782283 GACCCGA-CCGTT
1 GACCCGACCCGTT
782295 GACCCGACCCGTT
1 GACCCGACCCGTT
782308 GACCCGACCCG
1 GACCCGACCCG
782319 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:782378 original size:29 final size:29
Alignment explanation
Indices: 782335--782417 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
782325 GACCGTTGAC
*
782335 TGGTGCTATTTTGGTAAATAATTCGGTTT
1 TGGTGCTATTCTGGTAAATAATTCGGTTT
*
782364 TGGTGCTATTCTGGTAAATAATTCAGTTT
1 TGGTGCTATTCTGGTAAATAATTCGGTTT
*
782393 TGGTGATATTCTGGTAAATAATTCG
1 TGGTGCTATTCTGGTAAATAATTCG
782418 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (29 bp):
TGGTGCTATTCTGGTAAATAATTCGGTTT
Found at i:784612 original size:12 final size:12
Alignment explanation
Indices: 784595--784620 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
784585 TAAAAAGTTT
784595 TTGGATAAATAC
1 TTGGATAAATAC
784607 TTGGATAAATAC
1 TTGGATAAATAC
784619 TT
1 TT
784621 AATTTATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTGGATAAATAC
Found at i:794259 original size:34 final size:34
Alignment explanation
Indices: 794211--794287 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
794201 AAGTTTAGGC
*
794211 AGAGTTTCAGCATAAAATGGGCGGAATTTTGGGT
1 AGAGTTTCAGCATAAAATGGGCAGAATTTTGGGT
*
794245 AGAGTTTC-GACATAAAATGGGCATAATTTTGGGT
1 AGAGTTTCAG-CATAAAATGGGCAGAATTTTGGGT
794279 AGAGTTTCA
1 AGAGTTTCA
794288 ACGAAAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (34 bp):
AGAGTTTCAGCATAAAATGGGCAGAATTTTGGGT
Found at i:796798 original size:8 final size:9
Alignment explanation
Indices: 796787--796825 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
796777 CATTTTCTTG
796787 TTTTTATTT
1 TTTTTATTT
796796 TTTTTATTT
1 TTTTTATTT
796805 GTTGTTTA-TT
1 -TT-TTTATTT
796815 TTTTTATTT
1 TTTTTATTT
796824 TT
1 TT
796826 ATCTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.15
9 15 0.56
10 4 0.15
11 4 0.15
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (9 bp):
TTTTTATTT
Found at i:796816 original size:19 final size:19
Alignment explanation
Indices: 796784--796823 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
796774 AGTCATTTTC
796784 TTGTTTTTATTTTTTTTAT
1 TTGTTTTTATTTTTTTTAT
796803 TTGTTGTTTA-TTTTTTTAT
1 TTGTT-TTTATTTTTTTTAT
796822 TT
1 TT
796824 TTATCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.82
Consensus pattern (19 bp):
TTGTTTTTATTTTTTTTAT
Found at i:796893 original size:10 final size:10
Alignment explanation
Indices: 796875--797241 Score: 54
Period size: 11 Copynumber: 35.1 Consensus size: 10
796865 TACTTTATTT
796875 TTTTATTTTA
1 TTTTATTTTA
* *
796885 TTTTGTTTTCC
1 TTTTATTTT-A
**
796896 TAATATTTTA
1 TTTTATTTTA
796906 TTATTATTATTA
1 TT-TTATT-TTA
796918 TTATTATTATTA
1 TT-TTATT-TTA
**
796930 TTATATATATACA
1 TT-T-TAT-TTTA
796943 TATTT-TTTTA
1 T-TTTATTTTA
* *
796953 CTATTATTTTC
1 -TTTTATTTTA
796964 TTTCT-TTTTA
1 TTT-TATTTTA
796974 -TTT-TTTTA
1 TTTTATTTTA
*
796982 TTCTA-TTTA
1 TTTTATTTTA
796991 -TTT-TTTTA
1 TTTTATTTTA
796999 TTTTTATTTTCA
1 -TTTTATTTT-A
797011 CTTTGT-TTTTA
1 -TTT-TATTTTA
**
797022 -TTTCCTTTA
1 TTTTATTTTA
*
797031 TATTAATTTTA
1 T-TTTATTTTA
797042 TTTCTTCATTTTA
1 -TT-TT-ATTTTA
797055 TTTTATTCCTGT-
1 TTTTATT--T-TA
797067 TTTTA-TTTA
1 TTTTATTTTA
797076 -TTTATTGTATA
1 TTTTATT-T-TA
* *
797087 TGTTGTTATTA
1 TTTTATT-TTA
*
797098 TTTTATTTATT
1 TTTTATTT-TA
797109 TTTTATCTTTA
1 TTTTAT-TTTA
797120 TTTTTATTTT-
1 -TTTTATTTTA
797130 TTTT-TTTTA
1 TTTTATTTTA
*
797139 TTTT-CTTTA
1 TTTTATTTTA
797148 TCTCATT-TTTTA
1 T-T--TTATTTTA
* *
797160 TTTCATTTGTT
1 TTTTATTT-TA
*
797171 TTCTTATCTT-
1 TT-TTATTTTA
* *
797181 CTTTACTTTA
1 TTTTATTTTA
*
797191 TTTTA-TTTG
1 TTTTATTTTA
*
797200 CTTTATTTTA
1 TTTTATTTTA
797210 -TTTATTTTCA
1 TTTTATTTT-A
797220 TTATT-TTTTA
1 TT-TTATTTTA
*
797230 TTCTTTTTTTA
1 TT-TTATTTTA
797241 T
1 T
797242 AACGCTTTTC
Statistics
Matches: 265, Mismatches: 45, Indels: 93
0.66 0.11 0.23
Matches are distributed among these distances:
8 22 0.08
9 50 0.19
10 45 0.17
11 68 0.26
12 64 0.24
13 14 0.05
14 2 0.01
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:796911 original size:3 final size:3
Alignment explanation
Indices: 796899--796933 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
796889 GTTTTCCTAA
796899 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
796934 ATATATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:796980 original size:9 final size:9
Alignment explanation
Indices: 796945--797239 Score: 53
Period size: 9 Copynumber: 30.7 Consensus size: 9
796935 TATATACATA
796945 TTTTTTTACT
1 TTTTTTTA-T
* *
796955 ATTATTTTCT
1 -TTTTTTTAT
796965 TTCTTTTTA-
1 TT-TTTTTAT
796974 TTTTTTTAT
1 TTTTTTTAT
* *
796983 TCTATTTA-
1 TTTTTTTAT
796991 TTTTTTTATT
1 TTTTTTTA-T
797001 TTTATTTTCACT
1 TTT-TTTT-A-T
797013 TTGTTTTTAT
1 TT-TTTTTAT
*
797023 TTCCTTTATAT
1 TT--TTTTTAT
**
797034 TAATTTTA-
1 TTTTTTTAT
* *
797042 TTTCTTCAT
1 TTTTTTTAT
797051 TTTATTTTAT
1 TTT-TTTTAT
797061 TCCTGTTTTTATT
1 T--T-TTTTTA-T
797074 TATTTATTGTAT
1 T-TTT-TT-TAT
* *
797086 ATGTTGTTAT
1 -TTTTTTTAT
*
797096 TAT-TTTAT
1 TTTTTTTAT
*
797104 TTATTTT-T
1 TTTTTTTAT
* *
797112 TATCTTTAT
1 TTTTTTTAT
*
797121 TTTTATTTTT
1 TTTT-TTTAT
797131 TTTTTTTAT
1 TTTTTTTAT
*
797140 TTTCTTTAT
1 TTTTTTTAT
797149 CTCATTTTTTAT
1 -T--TTTTTTAT
** *
797161 TTCATTT-G
1 TTTTTTTAT
*
797169 TTTTCTTAT
1 TTTTTTTAT
* *
797178 CTTCTTTACT
1 TTTTTTTA-T
*
797188 TTATTTTAT
1 TTTTTTTAT
**
797197 TTGCTTTAT
1 TTTTTTTAT
*
797206 TTTATTTAT
1 TTTTTTTAT
**
797215 TTTCATTAT
1 TTTTTTTAT
*
797224 TTTTTATTCT
1 TTTTT-TTAT
797234 TTTTTT
1 TTTTTT
797240 ATAACGCTTT
Statistics
Matches: 200, Mismatches: 58, Indels: 54
0.64 0.19 0.17
Matches are distributed among these distances:
8 30 0.15
9 72 0.36
10 42 0.21
11 22 0.11
12 27 0.14
13 7 0.04
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:796981 original size:8 final size:8
Alignment explanation
Indices: 796968--797003 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
796958 ATTTTCTTTC
796968 TTTTTATT
1 TTTTTATT
796976 TTTTTATT
1 TTTTTATT
*
796984 CTATTTATT
1 -TTTTTATT
796993 TTTTTATT
1 TTTTTATT
797001 TTT
1 TTT
797004 ATTTTCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTATT
Found at i:796982 original size:23 final size:23
Alignment explanation
Indices: 796956--797024 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
796946 TTTTTTACTA
*
796956 TTATTTTCTTTCTTTTTATTTTT
1 TTATTTTCTTTATTTTTATTTTT
* *
796979 TTATTCTATTTATTTTT-TTATTT
1 TTATTTTCTTTATTTTTATT-TTT
*
797002 TTATTTTCACTTTGTTTTTATTT
1 TTATTTT--CTTTATTTTTATTT
797025 CCTTTATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 2 0.06
23 23 0.64
25 9 0.25
26 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (23 bp):
TTATTTTCTTTATTTTTATTTTT
Found at i:796985 original size:17 final size:17
Alignment explanation
Indices: 796965--797000 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
796955 ATTATTTTCT
*
796965 TTCTTTTTATTTTTTTA
1 TTCTATTTATTTTTTTA
796982 TTCTATTTATTTTTTTA
1 TTCTATTTATTTTTTTA
796999 TT
1 TT
797001 TTTATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTATTTATTTTTTTA
Found at i:796988 original size:31 final size:29
Alignment explanation
Indices: 796943--797008 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
796933 TATATATACA
*
796943 TATTTTTTTACTA-TTATTTTCTTTCTTTT
1 TATTTTTTTACTATTTATTTT-TTTATTTT
796972 TATTTTTTTATTCTATTTATTTTTTTATTTT
1 TATTTTTTTA--CTATTTATTTTTTTATTTT
797003 TATTTT
1 TATTTT
797009 CACTTTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 10 0.30
31 16 0.48
32 7 0.21
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (29 bp):
TATTTTTTTACTATTTATTTTTTTATTTT
Found at i:797145 original size:28 final size:28
Alignment explanation
Indices: 796956--797239 Score: 94
Period size: 28 Copynumber: 9.7 Consensus size: 28
796946 TTTTTTACTA
796956 TTATTTTCTT-TCTTT-TTATTT-TTTTAT
1 TTATTTT-TTATCTTTATT-TTTATTTTAT
796983 TCTATTTATTT-T-TTTATTTTTATTTTCACT
1 T-TATTT-TTTATCTTTATTTTTATTTT-A-T
* * * *
797013 TTGTTTTTATTTCCTTTATATTAATTTTAT
1 TTATTTTT-TAT-CTTTATTTTTATTTTAT
* *
797043 TTCTTCATTTTAT-TTTATTCCTGT-TTTTAT
1 TTATT--TTTTATCTTTATT--TTTATTTTAT
* * *
797073 TTATTTATTGTATATGTTGTTATTATTTTAT
1 TTATTT-TT-TATCT-TTATTTTTATTTTAT
797104 TTATTTTTTATCTTTATTTTTATTTT-T
1 TTATTTTTTATCTTTATTTTTATTTTAT
* * *
797131 TTTTTTTATTTTCTTTATCTCATT-TTTTAT
1 TTATTTT-TTATCTTTAT-T-TTTATTTTAT
* *
797161 TTCATTTGTTT-TCTTATCTTCTTTACTTTATT
1 TT-ATTT-TTTATCTT-TATT-TTTATTTTA-T
797193 TTATTTGCTTTAT-TTTA--TTTATTTTCA-
1 TTATTT--TTTATCTTTATTTTTATTTT-AT
797220 TTATTTTTTATTCTTT-TTTT
1 TTATTTTTTA-TCTTTATTTT
797240 ATAACGCTTT
Statistics
Matches: 197, Mismatches: 25, Indels: 69
0.68 0.09 0.24
Matches are distributed among these distances:
25 4 0.02
26 1 0.01
27 23 0.12
28 46 0.23
29 24 0.12
30 37 0.19
31 33 0.17
32 28 0.14
33 1 0.01
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.74
Consensus pattern (28 bp):
TTATTTTTTATCTTTATTTTTATTTTAT
Found at i:797194 original size:38 final size:34
Alignment explanation
Indices: 797115--797239 Score: 73
Period size: 33 Copynumber: 3.6 Consensus size: 34
797105 TATTTTTTAT
*
797115 CTTTATTTTTAT-TTTTT-TTTTTTATTTTCTTTA
1 CTTTATTTTT-TATTTTTTTTTTTTATCTTCTTTA
*
797148 -TCTCATTTTTTATTTCATTTGTTTTCTTATCTTCTTTA
1 CT-TTATTTTTTATTT--TTT-TTTT-TTATCTTCTTTA
* * * *
797186 CTTTA--TTTTATTTGCTTTATTTTAT-TTATTTT
1 CTTTATTTTTTATTT-TTTTTTTTTATCTTCTTTA
* *
797218 CATTATTTTTTATTCTTTTTTT
1 CTTTATTTTTTATTTTTTTTTT
797240 ATAACGCTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
32 11 0.16
33 19 0.27
34 10 0.14
35 4 0.06
36 8 0.11
37 4 0.06
38 13 0.19
39 1 0.01
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (34 bp):
CTTTATTTTTTATTTTTTTTTTTTATCTTCTTTA
Found at i:800523 original size:14 final size:14
Alignment explanation
Indices: 800506--800537 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
800496 ATTTAACTGG
800506 AAATATTTTTTAAA
1 AAATATTTTTTAAA
*
800520 AAATATTTTTTGAA
1 AAATATTTTTTAAA
800534 AAAT
1 AAAT
800538 GAATTATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAATATTTTTTAAA
Found at i:800569 original size:14 final size:14
Alignment explanation
Indices: 800506--800594 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
800496 ATTTAACTGG
*
800506 AAATATTTTTTAAA
1 AAATATTTTTTAGA
800520 AAATATTTTTT-GAA
1 AAATATTTTTTAG-A
800534 AAATGAATTATATCTTATGA
1 AAAT--ATT-T-T-TTA-GA
800554 AAATATTTTTTAGA
1 AAATATTTTTTAGA
*
800568 AAGTGTAATATTTTTAGA
1 AA--AT-AT-TTTTTAGA
800586 AAATATTTT
1 AAATATTTT
800595 ACGATATTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 24
0.69 0.03 0.28
Matches are distributed among these distances:
14 23 0.38
15 5 0.08
16 6 0.10
17 4 0.07
18 14 0.23
19 2 0.03
20 5 0.08
21 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (14 bp):
AAATATTTTTTAGA
Found at i:800757 original size:20 final size:20
Alignment explanation
Indices: 800705--800758 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
800695 AATTTAATAT
*
800705 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
800727 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
800747 TATTATTTTTAT
1 TATTATTTTTAT
800759 ATTTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:800809 original size:32 final size:30
Alignment explanation
Indices: 800734--800814 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 30
800724 AAATAATTTA
* *
800734 TTTATT-ATTAAAATATTAT-TTTTATATT
1 TTTATTAATAAAAATATTATATTGTATATT
800762 TTTATTAATAAAAATATTATATTGGTATA-T
1 TTTATTAATAAAAATATTATATT-GTATATT
800792 TTTATTGAAATAAAAATATTATA
1 TTTATT--AATAAAAATATTATA
800815 AATTATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 6 0.13
29 12 0.26
30 9 0.20
31 4 0.09
32 15 0.33
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTATTAATAAAAATATTATATTGTATATT
Found at i:800822 original size:31 final size:28
Alignment explanation
Indices: 800715--800823 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 28
800705 TATTATTTTT
* * * *
800715 AAAATATTAAAATAATTTATTTATT-ATT
1 AAAATATTATAATTATAT-TTTATTAATA
**
800743 AAAATATTATTTTTATATTTTTATTAATA
1 AAAATATTATAATTATA-TTTTATTAATA
*
800772 AAAATATTATATTGGTATATTTTATTGAAATA
1 AAAATATTATAAT--TATATTTTATT--AATA
800804 AAAATATTATAAATTATATT
1 AAAATATTAT-AATTATATT
800824 AATTATTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
28 18 0.27
29 15 0.23
30 7 0.11
31 10 0.15
32 14 0.21
33 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
AAAATATTATAATTATATTTTATTAATA
Found at i:800878 original size:22 final size:23
Alignment explanation
Indices: 800853--800896 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
800843 AGTGTTATAT
800853 TATATTTTAAA-ATATTAATTAG
1 TATATTTTAAATATATTAATTAG
*
800875 TATATTTTAAATATATTTATTA
1 TATATTTTAAATATATTAATTA
800897 AAATATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATTTTAAATATATTAATTAG
Found at i:800902 original size:23 final size:23
Alignment explanation
Indices: 800854--800918 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
800844 GTGTTATATT
* **
800854 ATATTTTAAA-ATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
800876 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
* *
800899 ATATATTAGAT-TA-TTATTAA
1 ATATTTTAAATATATTTATTAA
800919 TATTAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.19
22 12 0.32
23 18 0.49
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:801119 original size:51 final size:50
Alignment explanation
Indices: 801023--801120 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
801013 ATATTATTAA
* ** *
801023 AATAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTTTAT
1 AATAAAAATATAATA-CTTATATTATTAAAATATAATAAAATATTTTTTAT
801074 AATAAAAATATAATA-TTATATTATTAGAAATATTAATAAAATATTTT
1 AATAAAAATATAATACTTATATTATTA-AAATA-TAATAAAATATTTT
801121 AAATATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 11 0.27
50 4 0.10
51 26 0.63
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (50 bp):
AATAAAAATATAATACTTATATTATTAAAATATAATAAAATATTTTTTAT
Found at i:806629 original size:16 final size:16
Alignment explanation
Indices: 806608--806646 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
806598 GATATTACCC
806608 GACCTGTTTTAAACCT
1 GACCTGTTTTAAACCT
*
806624 GACCTGTTTTTAACCT
1 GACCTGTTTTAAACCT
806640 GACCTGT
1 GACCTGT
806647 AAATGATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTAAACCT
Found at i:806687 original size:16 final size:16
Alignment explanation
Indices: 806657--806718 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
806647 AAATGATCCA
* *
806657 ACTTGTTATTGACCTG
1 ACTTGATATTTACCTG
806673 A-TCTGATATTTACCTG
1 ACT-TGATATTTACCTG
* *
806689 ACTTGACATTTACCTA
1 ACTTGATATTTACCTG
806705 ACTT-ATATATTACC
1 ACTTGATAT-TTACC
806719 ATGGACGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.11
16 33 0.87
17 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (16 bp):
ACTTGATATTTACCTG
Found at i:806862 original size:13 final size:13
Alignment explanation
Indices: 806846--806872 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
806836 TACCTATTAT
806846 ATAAAATTATTTA
1 ATAAAATTATTTA
806859 ATAAAATTATTTA
1 ATAAAATTATTTA
806872 A
1 A
806873 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:806882 original size:15 final size:14
Alignment explanation
Indices: 806846--806888 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
806836 TACCTATTAT
806846 ATAAAATTATTT-A
1 ATAAAATTATTTAA
806859 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
806873 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
806888 A
1 A
806889 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:806971 original size:23 final size:24
Alignment explanation
Indices: 806928--806981 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
806918 CAATGATTAA
*
806928 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGCTTAATTT
806952 ATGTAAATT-ATATAGCTTAATTT
1 ATGTAAATTAATATAGCTTAATTT
806975 ATGTAAA
1 ATGTAAA
806982 GAAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
ATGTAAATTAATATAGCTTAATTT
Found at i:807251 original size:12 final size:11
Alignment explanation
Indices: 807225--807266 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
807215 GATAATGATA
*
807225 ATTTAAATAAC
1 ATTTGAATAAC
*
807236 ATTTGATATAAA
1 ATTTGA-ATAAC
807248 ATTTGAATAAC
1 ATTTGAATAAC
807259 ATTTGAAT
1 ATTTGAAT
807267 TAATTCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:807855 original size:13 final size:14
Alignment explanation
Indices: 807806--807881 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
807796 TATTAAATAA
807806 TAATTGCATGTTAT
1 TAATTGCATGTTAT
**
807820 TAATT-CATG-TGG
1 TAATTGCATGTTAT
807832 T-ATTGCATGTTAT
1 TAATTGCATGTTAT
807845 TAATT-CATG-T-T
1 TAATTGCATGTTAT
**
807856 GCATTGCATGTTAT
1 TAATTGCATGTTAT
807870 TAATTG-ATGTTA
1 TAATTGCATGTTA
807882 CATTAGGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
11 7 0.15
12 11 0.23
13 17 0.35
14 13 0.27
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:807880 original size:25 final size:25
Alignment explanation
Indices: 807808--807885 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
807798 TTAAATAATA
* *
807808 ATTGCATGTTATTAATTCATGTGGT
1 ATTGCATGTTATTAATTCATGTTGC
807833 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTGC
* *
807858 ATTGCATGTTATTAATTGATGTTAC
1 ATTGCATGTTATTAATTCATGTTGC
807883 ATT
1 ATT
807886 AGGTGTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTGC
Found at i:808588 original size:24 final size:24
Alignment explanation
Indices: 808535--808588 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
808525 ATTTCATCCC
* *
808535 TATATAATTTATATTAATAAACTAT
1 TATATAATTAATAATAATAAAC-AT
808560 T-TATAATTAATAATAATATAA-AT
1 TATATAATTAATAATAATA-AACAT
808583 TATATA
1 TATATA
808589 TTAGAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 19 0.76
25 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATAATTAATAATAATAAACAT
Found at i:808611 original size:44 final size:44
Alignment explanation
Indices: 808561--808703 Score: 119
Period size: 44 Copynumber: 3.1 Consensus size: 44
808551 ATAAACTATT
808561 TATAATTAATAATAATATAAATTATA-TATTAGAATTAATATTAA
1 TATAATTAAT-ATAATATAAATTATAGTATTAGAATTAATATTAA
* * * * *
808605 TATAATTAAT-TAATATTAACTTATATTAATAGAATATAGTTTATAA
1 TATAATTAATATAATA-TAAATTATAGTATTAGAAT-TAATAT-TAA
* * * *
808651 TTTGTAATTAATATCAATATAAAATATAGTCTGTAAAATTAATATTAA
1 --TATAATTAATAT-AATATAAATTATAGTAT-TAGAATTAATATTAA
808699 TATAA
1 TATAA
808704 ACTATATTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
42 5 0.07
43 8 0.11
44 18 0.24
45 4 0.05
46 7 0.09
48 12 0.16
49 13 0.17
50 9 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (44 bp):
TATAATTAATATAATATAAATTATAGTATTAGAATTAATATTAA
Found at i:808615 original size:19 final size:20
Alignment explanation
Indices: 808560--808634 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 20
808550 AATAAACTAT
*
808560 TTATAATTAATAATAATATAAA
1 TTATAATTAAT--TAATATTAA
808582 TTATATATTAGAATTAATATTAA
1 TTATA-ATT--AATTAATATTAA
808605 -TATAATTAATTAATATTAA
1 TTATAATTAATTAATATTAA
808624 CTTAT-ATTAAT
1 -TTATAATTAAT
808635 AGAATATAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
19 12 0.26
20 6 0.13
21 6 0.13
22 9 0.19
23 11 0.23
25 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (20 bp):
TTATAATTAATTAATATTAA
Found at i:808616 original size:13 final size:16
Alignment explanation
Indices: 808598--808635 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
808588 ATTAGAATTA
808598 ATATTAATA-TAA-TT
1 ATATTAATATTAACTT
808612 A-ATTAATATTAACTT
1 ATATTAATATTAACTT
808627 ATATTAATA
1 ATATTAATA
808636 GAATATAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 4 0.19
15 3 0.14
16 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTAATATTAACTT
Found at i:808650 original size:41 final size:41
Alignment explanation
Indices: 808536--808652 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 41
808526 TTTCATCCCT
* *
808536 ATATAATTTATATTAATA-AA-CTATTTATAATTAATAATA
1 ATATAAATTATATTAATAGAATATATTTATAATTAATAATA
*
808575 ATATAAATTATA-TATTAGAATTAATATTAATATAATTAAT--TA
1 ATATAAATTATATTAATAGAA-T-ATATT--TATAATTAATAATA
*
808617 ATATTAACTTATATTAATAGAATATAGTTTATAATT
1 ATA-TAAATTATATTAATAGAATATA-TTTATAATT
808653 TGTAATTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
38 4 0.06
39 13 0.20
41 7 0.11
42 12 0.19
43 11 0.17
44 17 0.27
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (41 bp):
ATATAAATTATATTAATAGAATATATTTATAATTAATAATA
Found at i:808678 original size:29 final size:30
Alignment explanation
Indices: 808646--808709 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
808636 GAATATAGTT
*
808646 TATAATTTGT-AATTAATATCAATATAAAA
1 TATAATCTGTAAATTAATATCAATATAAAA
* * *
808675 TATAGTCTGTAAAATTAATATTAATATAAAC
1 TATAATCTGT-AAATTAATATCAATATAAAA
808706 TATA
1 TATA
808710 TTTTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.28
31 21 0.72
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (30 bp):
TATAATCTGTAAATTAATATCAATATAAAA
Found at i:808745 original size:66 final size:64
Alignment explanation
Indices: 808667--808840 Score: 165
Period size: 64 Copynumber: 2.7 Consensus size: 64
808657 ATTAATATCA
* *
808667 ATATAAAATATAGTCTGTAAAATTAATATTAATATAAACTATATTTTATAAATTATATAGTATAA
1 ATATAAAATATAGT-T-TAAAATTAATATTAATATAAACTATATTTTATAAACTATATACTAT-A
808732 TT
63 TT
* * * * *
808734 -TATAAACTATAGTTAATATAATTAATATT-A-ATAGAGTATAGTTTATAAACTATATACTATAT
1 ATATAAAATATAGTT--TAAAATTAATATTAATATAAACTATATTTTATAAACTATATACTATAT
808796 T
64 T
* * * *
808797 AATATAAATTATAGTTAAGAAATTAACATTAATGTAAACTATAT
1 -ATATAAAATATAGTTTA-AAATTAATATTAATATAAACTATAT
808841 AGTCATTAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
63 4 0.05
64 34 0.40
65 16 0.19
66 31 0.36
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (64 bp):
ATATAAAATATAGTTTAAAATTAATATTAATATAAACTATATTTTATAAACTATATACTATATT
Found at i:808874 original size:21 final size:21
Alignment explanation
Indices: 808850--808961 Score: 110
Period size: 21 Copynumber: 5.5 Consensus size: 21
808840 TAGTCATTAA
*
808850 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGTTTATAAAG
**
808871 TATATTCTATAGTTTATAAAG
1 TATAAACTATAGTTTATAAAG
**
808892 TATAAA-TATAGTACACT-AA-
1 TATAAACTATAGTTTA-TAAAG
808911 TATAAACTATAGTTTATAAA-
1 TATAAACTATAGTTTATAAAG
*
808931 TGATATACTATAGTTT-TAAAG
1 T-ATAAACTATAGTTTATAAAG
808952 TAT-AACTATA
1 TATAAACTATA
808962 TAGTACACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
19 13 0.17
20 25 0.33
21 37 0.49
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (21 bp):
TATAAACTATAGTTTATAAAG
Found at i:808992 original size:62 final size:62
Alignment explanation
Indices: 808825--808992 Score: 245
Period size: 61 Copynumber: 2.8 Consensus size: 62
808815 GAAATTAACA
* * * *
808825 TTAATGTA-AACTATATAGT-CATTAATATAAACTATAGTTTATAAATTATATTCTATAGTT
1 TTAAAGTATAACTATATAGTACACTAATATAAACTATAGTTTATAAATGATATACTATAGTT
808885 TATAAAGTATAA--ATATAGTACACTAATATAAACTATAGTTTATAAATGATATACTATAGTT
1 T-TAAAGTATAACTATATAGTACACTAATATAAACTATAGTTTATAAATGATATACTATAGTT
**
808946 TTAAAGTATAACTATATAGTACACTAATATAAACTATTTTTTATAAA
1 TTAAAGTATAACTATATAGTACACTAATATAAACTATAGTTTATAAA
808993 CTATAGGTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
60 18 0.19
61 45 0.46
62 34 0.35
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (62 bp):
TTAAAGTATAACTATATAGTACACTAATATAAACTATAGTTTATAAATGATATACTATAGTT
Found at i:809066 original size:57 final size:55
Alignment explanation
Indices: 808992--809129 Score: 161
Period size: 57 Copynumber: 2.4 Consensus size: 55
808982 TTTTTTATAA
* * * *
808992 ACTATAGGTTACATATATAATTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTATATATATAATTTATATATAC-TATAAATAG-TT-TATACACACATAT
* *
809049 ACTATAAGTTATATATATATAGTTTATATATACTATACATAGTTTATACACACATGT
1 ACTATAAGTTATATATATA-A-TTTATATATACTATAAATAGTTTATACACACATAT
*
809106 ACTATAAGTTATATATATAGTTTA
1 ACTATAAGTTATATATATAATTTA
809130 CATGTATACA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
55 4 0.06
57 46 0.65
58 3 0.04
59 16 0.23
60 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (55 bp):
ACTATAAGTTATATATATAATTTATATATACTATAAATAGTTTATACACACATAT
Found at i:809085 original size:20 final size:20
Alignment explanation
Indices: 809004--809096 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 20
808994 TATAGGTTAC
*
809004 ATATATAATTTATATA-ACAT
1 ATATATAGTTTATATATAC-T
*
809024 ATAAATAGATTGTATATATAC-
1 ATATATAG-TT-TATATATACT
*
809045 ATATACTA--TAAGT-TATA-T
1 ATATA-TAGTTTA-TATATACT
809063 ATATATAGTTTATATATACT
1 ATATATAGTTTATATATACT
*
809083 ATACATAGTTTATA
1 ATATATAGTTTATA
809097 CACACATGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
17 2 0.04
18 11 0.19
19 8 0.14
20 20 0.35
21 6 0.11
22 8 0.14
23 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATATAGTTTATATATACT
Found at i:809431 original size:7 final size:7
Alignment explanation
Indices: 809417--809454 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
809407 TACATATATA
809417 GTTTAGG
1 GTTTAGG
*
809424 GGTTAGG
1 GTTTAGG
809431 GTTTAGG
1 GTTTAGG
*
809438 ATTTAGG
1 GTTTAGG
809445 GTTTAGG
1 GTTTAGG
809452 GTT
1 GTT
809455 AAGGATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:809444 original size:21 final size:21
Alignment explanation
Indices: 809418--809463 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
809408 ACATATATAG
*
809418 TTTAGGGGTTAGGGTTTAGGA
1 TTTAGGGGTTAGGGTTAAGGA
*
809439 TTTAGGGTTTAGGGTTAAGGA
1 TTTAGGGGTTAGGGTTAAGGA
809460 TTTA
1 TTTA
809464 ATGTTCATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
TTTAGGGGTTAGGGTTAAGGA
Found at i:809553 original size:2 final size:2
Alignment explanation
Indices: 809546--809689 Score: 81
Period size: 2 Copynumber: 75.5 Consensus size: 2
809536 TTCTATAAAC
809546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A 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
* * * * * *
809586 TA TA TA GA TT TC T- TA TA T- TA -A T- TA TA CA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
809624 CA TA TA TA TA TA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
809664 TT TA TA GTT TA TA CA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA T
809690 TAATATAAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
1 9 0.08
2 96 0.90
3 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:809710 original size:14 final size:14
Alignment explanation
Indices: 809637--809717 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
809627 ATATATATAA
809637 TATAAATTATAATT
1 TATAAATTATAATT
* *
809651 TATAAACTATATTTT
1 TATAAATTATA-ATT
** *
809666 TATAGTTTATACATA
1 TATAAATTATA-ATT
*
809681 TATATA-TATTAA--
1 TATAAATTA-TAATT
809693 TATAAATTATAATT
1 TATAAATTATAATT
*
809707 TATAAACTATA
1 TATAAATTATA
809718 TACTTTATAG
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
12 8 0.16
13 2 0.04
14 23 0.46
15 17 0.34
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (14 bp):
TATAAATTATAATT
Found at i:809725 original size:23 final size:22
Alignment explanation
Indices: 809699--809741 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
809689 TTAATATAAA
809699 TTATAATTTATAAACTATATACT
1 TTATAATTTATAAA-TATATACT
* *
809722 TTATAGTTTATACATATATA
1 TTATAATTTATAAATATATA
809742 GTTACGTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATAATTTATAAATATATACT
Found at i:809738 original size:57 final size:57
Alignment explanation
Indices: 809617--809741 Score: 216
Period size: 57 Copynumber: 2.2 Consensus size: 57
809607 TTATACATAC
* *
809617 ATACATACATATATATATAATATAAATTATAATTTATAAACTATATTTTTATAGTTT
1 ATACATATATATATATATAATATAAATTATAATTTATAAACTATATCTTTATAGTTT
809674 ATACATATATATATAT-TAATATAAATTATAATTTATAAACTATATACTTTATAGTTT
1 ATACATATATATATATATAATATAAATTATAATTTATAAACTATAT-CTTTATAGTTT
809731 ATACATATATA
1 ATACATATATA
809742 GTTACGTACA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
56 29 0.45
57 36 0.55
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (57 bp):
ATACATATATATATATATAATATAAATTATAATTTATAAACTATATCTTTATAGTTT
Found at i:809760 original size:57 final size:56
Alignment explanation
Indices: 809625--809741 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 56
809615 ACATACATAC
* *
809625 ATATATATA-TAATATAAATTATAATTTATAAACTATATTTTTATAGTTTATACAT
1 ATATATATAGTAACATAAATTATAATTTATAAACTATATCTTTATAGTTTATACAT
* *
809680 ATATATATATTAATATAAATTATAATTTATAAACTATATACTTTATAGTTTATACAT
1 ATATATATAGTAACATAAATTATAATTTATAAACTATAT-CTTTATAGTTTATACAT
809737 ATATA
1 ATATA
809742 GTTACGTACA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 9 0.15
56 29 0.49
57 21 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (56 bp):
ATATATATAGTAACATAAATTATAATTTATAAACTATATCTTTATAGTTTATACAT
Found at i:809769 original size:13 final size:13
Alignment explanation
Indices: 809723--809801 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
809713 CTATATACTT
809723 TATAGTTTATACATA
1 TATAGTTTAT--ATA
**
809738 TATAG-TTACGTA
1 TATAGTTTATATA
*
809750 CATAGTTTATATA
1 TATAGTTTATATA
*
809763 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
809778 CATAATTTATATA
1 TATAGTTTATATA
*
809791 TATAGCTTATA
1 TATAGTTTATA
809802 ATAATTATAT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
12 6 0.12
13 24 0.50
14 3 0.06
15 15 0.31
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:812297 original size:27 final size:22
Alignment explanation
Indices: 812232--812288 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
812222 TTGTTTAAGG
812232 TGTTTTAAAAATATTAATTTAA
1 TGTTTTAAAAATATTAATTTAA
812254 TGTTTTAAAAATATTAATTTAA
1 TGTTTTAAAAATATTAATTTAA
812276 TGTTTTAAAAATA
1 TGTTTTAAAAATA
812289 AATTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TGTTTTAAAAATATTAATTTAA
Found at i:813498 original size:20 final size:18
Alignment explanation
Indices: 813454--813499 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
813444 CTTAGCAAAG
* *
813454 AATCGATCCCTTTGACCA
1 AATCGATCCCCTTGAACA
813472 AATCGATCCCCTTGAAACA
1 AATCGATCCCCTTG-AACA
813491 AGATCGATC
1 A-ATCGATC
813500 TCAGTCCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 4 0.17
20 7 0.29
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (18 bp):
AATCGATCCCCTTGAACA
Found at i:816392 original size:18 final size:17
Alignment explanation
Indices: 816360--816393 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
816350 AATTTTTAAA
816360 TTTTAATATTTTTATTC
1 TTTTAATATTTTTATTC
*
816377 TTTTTATATTTATTATT
1 TTTTAATATTT-TTATT
816394 AATTAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATATTTTTATTC
Found at i:819408 original size:44 final size:45
Alignment explanation
Indices: 819354--819443 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 45
819344 GGAAGGCACA
819354 ATTTGCCATCCAAATAGATTTTACAC-TT-TCAA-AGAAAGAGAAGC
1 ATTTGCCATCC-AATAGATTTT-CACTTTCTCAATAGAAAGAGAAGC
*
819398 ATTTGTCATCCAATAGATTTTCACTTTTCTCAATAGAAAGAGAAGC
1 ATTTGCCATCCAATAGATTTTCAC-TTTCTCAATAGAAAGAGAAGC
819444 CTAGGCATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
42 3 0.07
43 10 0.24
44 12 0.29
45 4 0.10
46 12 0.29
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (45 bp):
ATTTGCCATCCAATAGATTTTCACTTTCTCAATAGAAAGAGAAGC
Done.