Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007973.1 Hibiscus syriacus cultivar Beakdansim tig00110410_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: 1299094
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1245680 original size:28 final size:28
Alignment explanation
Indices: 1245594--1245682 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
1245584 TCACCAAAAA
1245594 TTAGGGGTTTGTTTTGTTTTATAGTGAT
1 TTAGGGGTTTGTTTTGTTTTATAGTGAT
* * *
1245622 TTAGGGTTCTTGATTATTGCTTTCT--T-A-
1 TTAGGGGT-TTG-TT-TTGTTTTATAGTGAT
1245649 TTAGGGGTTTGTTTTGTTTTATAGTGAT
1 TTAGGGGTTTGTTTTGTTTTATAGTGAT
1245677 TTAGGG
1 TTAGGG
1245683 TTTTTGATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
24 7 0.15
25 2 0.04
26 4 0.08
27 8 0.17
28 14 0.29
29 4 0.08
30 2 0.04
31 7 0.15
ACGTcount: A:0.15, C:0.03, G:0.27, T:0.55
Consensus pattern (28 bp):
TTAGGGGTTTGTTTTGTTTTATAGTGAT
Found at i:1245706 original size:28 final size:28
Alignment explanation
Indices: 1245620--1245706 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
1245610 TTTTATAGTG
*
1245620 ATTTAGGGTTCTTGATTATTGCTTTCTT
1 ATTTAGGGTTTTTGATTATTGCTTTCTT
* * *
1245648 A-TTAGGG-GTTTG-TT-TTGTTTTATAGT
1 ATTTAGGGTTTTTGATTATTGCTTTCT--T
1245674 GATTTAGGGTTTTTGATTATTGCTTTCTT
1 -ATTTAGGGTTTTTGATTATTGCTTTCTT
1245703 ATTT
1 ATTT
1245707 TATGTTTAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
24 7 0.16
25 2 0.04
26 4 0.09
27 7 0.16
28 11 0.24
29 5 0.11
30 2 0.04
31 7 0.16
ACGTcount: A:0.15, C:0.06, G:0.21, T:0.59
Consensus pattern (28 bp):
ATTTAGGGTTTTTGATTATTGCTTTCTT
Found at i:1250935 original size:16 final size:16
Alignment explanation
Indices: 1250916--1250947 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1250906 GTTTTTTTAT
1250916 AACCGATTTTTTAAAA
1 AACCGATTTTTTAAAA
*
1250932 AACCGGTTTTTTAAAA
1 AACCGATTTTTTAAAA
1250948 CCAAAACCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (16 bp):
AACCGATTTTTTAAAA
Found at i:1251094 original size:25 final size:20
Alignment explanation
Indices: 1251045--1251095 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1251035 TGGGAAAAAA
1251045 CCGGATCGGATAAAACCGAT
1 CCGGATCGGATAAAACCGAT
1251065 CCGGATCGGATAAAACCGAT
1 CCGGATCGGATAAAACCGAT
*
1251085 CCAGATCGGAT
1 CCGGATCGGAT
1251096 TGAAATCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (20 bp):
CCGGATCGGATAAAACCGAT
Found at i:1254206 original size:17 final size:18
Alignment explanation
Indices: 1254174--1254209 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1254164 AAGCTGCTTA
1254174 CTTTACGCTATATTTCAT
1 CTTTACGCTATATTTCAT
*
1254192 CTTTTCGCT-TATTTCAT
1 CTTTACGCTATATTTCAT
1254209 C
1 C
1254210 CGCTGCCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.53
Consensus pattern (18 bp):
CTTTACGCTATATTTCAT
Found at i:1255726 original size:11 final size:10
Alignment explanation
Indices: 1255682--1255726 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
1255672 CAAAATCTCG
*
1255682 TTTTTTCAGA
1 TTTTTTCCGA
*
1255692 TTTTTCCCGA
1 TTTTTTCCGA
1255702 TTTTTTCCGA
1 TTTTTTCCGA
*
1255712 TTTTTTCCGG
1 TTTTTTCCGA
1255722 TTTTT
1 TTTTT
1255727 AGTCGATCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.09, C:0.18, G:0.11, T:0.62
Consensus pattern (10 bp):
TTTTTTCCGA
Found at i:1256672 original size:230 final size:227
Alignment explanation
Indices: 1256315--1256768 Score: 724
Period size: 230 Copynumber: 2.0 Consensus size: 227
1256305 GGTCGGTCGG
*
1256315 TTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACTCGACCCGAA
1 TTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAA
*
1256380 AATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTT
66 AATAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTT
1256445 TT-CAATTAAGTCACTG-TTTATTGAATAAAAATA-ATTTTTTATTATTTTGGGTCGGGTCGGGT
131 TTCCAATTAAG-CACTGTTTTATTGAATAAAAATACATTTTTTATTATTTTGGGTCGGGTC--G-
1256507 TGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTAA
192 -GG-TTTCTAATTCATATATTCGGGTCGGGTCGGGTAA
1256545 TTTTTTAAGTGTGATATTCGGGTCGGGTC-AGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAC
1 TTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGA-
1256609 CCAAA-AAATA-AATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCA-ATATA
65 --AAATAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT-ATATATA
* *
1256671 TTTTTTCCAATTGAGCACTGTTTTTATTGAATAAAAATACTTTTTTTATTATTTTGGGTCGGGTC
127 TTTTTTCCAATTAAGCACTG-TTTTATTGAATAAAAATACATTTTTTATTATTTTGGGTCGGGTC
1256736 GGGTTTCTAATTCATATATTCGGGTCGGGTCGG
191 GGGTTTCTAATTCATATATTCGGGTCGGGTCGG
1256769 TTGAAACTTT
Statistics
Matches: 212, Mismatches: 4, Indels: 18
0.91 0.02 0.08
Matches are distributed among these distances:
228 30 0.14
229 35 0.17
230 90 0.42
231 13 0.06
232 20 0.09
233 24 0.11
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (227 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAA
AATAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTT
TTCCAATTAAGCACTGTTTTATTGAATAAAAATACATTTTTTATTATTTTGGGTCGGGTCGGGTT
TCTAATTCATATATTCGGGTCGGGTCGGGTAA
Found at i:1257179 original size:17 final size:18
Alignment explanation
Indices: 1257157--1257196 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1257147 TATGGAATTG
*
1257157 GATTCTAATTCC-TGACA
1 GATTCTAATTCCTTCACA
1257174 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
1257192 GATTC
1 GATTC
1257197 AACTCCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:1257298 original size:3 final size:3
Alignment explanation
Indices: 1257285--1257380 Score: 143
Period size: 3 Copynumber: 34.3 Consensus size: 3
1257275 CTTTTCGTCC
1257285 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1257331 -TA TTA TTA TTA TTA -TA TT- TTA TTA -TA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1257374 TTA TTA T
1 TTA TTA T
1257381 AAGAGAGATA
Statistics
Matches: 86, Mismatches: 0, Indels: 14
0.86 0.00 0.14
Matches are distributed among these distances:
2 14 0.16
3 72 0.84
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1257325 original size:14 final size:14
Alignment explanation
Indices: 1257285--1257380 Score: 126
Period size: 14 Copynumber: 6.9 Consensus size: 14
1257275 CTTTTCGTCC
*
1257285 TTATTTTATTATTA
1 TTATATTATTATTA
1257299 TTATTATTATTATTA
1 TTA-TATTATTATTA
1257314 TTAT-TATATTATTA
1 TTATAT-TATTATTA
1257328 TTATATTATTATTA
1 TTATATTATTATTA
1257342 TTATATT-TTATTA
1 TTATATTATTATTA
1257355 -TATTATTATTATTA
1 TTA-TATTATTATTA
*
1257369 TTATTTTATTAT
1 TTATATTATTAT
1257381 AAGAGAGATA
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
12 2 0.03
13 11 0.15
14 45 0.61
15 16 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:1257549 original size:25 final size:25
Alignment explanation
Indices: 1257521--1257572 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
1257511 TTGTACATGA
1257521 TGGTTGCGCATACAACTGATAACAC
1 TGGTTGCGCATACAACTGATAACAC
*
1257546 TGGTTGCGCATACAGCTGATAACAC
1 TGGTTGCGCATACAACTGATAACAC
1257571 TG
1 TG
1257573 CAGTTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
TGGTTGCGCATACAACTGATAACAC
Found at i:1260659 original size:45 final size:45
Alignment explanation
Indices: 1260595--1260731 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 45
1260585 TGAGATTTCA
* * *
1260595 ACAAACGTTCAAGAATTAAACAATGTTGCGCATGGAATGGTGCCC
1 ACAAACGTTCAAGAATTAAACAATGATGTGCATGGCATGGTGCCC
*
1260640 ACAAACGTTCAAGAATTAAACAATGATGTGCATGGCATGGTGTCC
1 ACAAACGTTCAAGAATTAAACAATGATGTGCATGGCATGGTGCCC
** * * *
1260685 ACTCATGTTGAAGAATTAAATAATGATGTGCATGGCATGGTGCCC
1 ACAAACGTTCAAGAATTAAACAATGATGTGCATGGCATGGTGCCC
1260730 AC
1 AC
1260732 CCATGTTGAT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
ACAAACGTTCAAGAATTAAACAATGATGTGCATGGCATGGTGCCC
Found at i:1260950 original size:99 final size:99
Alignment explanation
Indices: 1260779--1261130 Score: 458
Period size: 99 Copynumber: 3.6 Consensus size: 99
1260769 TTAAATAATG
* * *
1260779 GTAGTGCACATGGCGTGGTCCAAGGAGAAGATAATGGTACGGAAAATAATAGTGGAAATGGGACC
1 GTAGTGCACATGGCGTGGTCCAAGAAGAAGATAGTGGTGCGGAAAATAATAGTGGAAATGGGACC
** *
1260844 GACCATTATACACGTGAATCTAATACACATGGGA
66 GGTCATTATACACGTGAATCTAATGCACATGGGA
* * * *
1260878 GTAGTGCACATGGTGTGGTCCAAGAAGAAGGTAGTGGTGTGGCAAATAATAGTGGAAATGGGACC
1 GTAGTGCACATGGCGTGGTCCAAGAAGAAGATAGTGGTGCGGAAAATAATAGTGGAAATGGGACC
**
1260943 GGTCATTATACGTGTGAAT-TCAATGCACATGGGA
66 GGTCATTATACACGTGAATCT-AATGCACATGGGA
* * **
1260977 GTAGTACACATGACGTGGTCCAAGAAGAAGATAGTGGTGC-GACAAATAATCA-TGGAAATAAGA
1 GTAGTGCACATGGCGTGGTCCAAGAAGAAGATAGTGGTGCGGA-AAATAAT-AGTGGAAATGGGA
*
1261040 CCGGTCATTATACACGTGAATCCAATGCACATGGGA
64 CCGGTCATTATACACGTGAATCTAATGCACATGGGA
* * * * *
1261076 GTAATCCACATGGCGTGATCCAAGAAGAAGATAGTGGTGTGGAAAATAATCGTGG
1 GTAGTGCACATGGCGTGGTCCAAGAAGAAGATAGTGGTGCGGAAAATAATAGTGG
1261131 TGACAGCTTA
Statistics
Matches: 218, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.01
99 213 0.98
100 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (99 bp):
GTAGTGCACATGGCGTGGTCCAAGAAGAAGATAGTGGTGCGGAAAATAATAGTGGAAATGGGACC
GGTCATTATACACGTGAATCTAATGCACATGGGA
Found at i:1263025 original size:25 final size:25
Alignment explanation
Indices: 1262996--1263047 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1262986 TTGTGCATGA
1262996 TGGTTGCACATACAACTGATAACAC
1 TGGTTGCACATACAACTGATAACAC
* **
1263021 TGGTTGCGCATACATTTGATAACAC
1 TGGTTGCACATACAACTGATAACAC
1263046 TG
1 TG
1263048 CAGCTAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (25 bp):
TGGTTGCACATACAACTGATAACAC
Found at i:1263589 original size:29 final size:29
Alignment explanation
Indices: 1263554--1263635 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1263544 AAACTAAATT
*
1263554 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1263583 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1263612 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1263636 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1264948 original size:15 final size:15
Alignment explanation
Indices: 1264925--1264954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1264915 ACGAGGCTGG
1264925 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1264940 AATTCCAACAATAAC
1 AATTACAACAATAAC
1264955 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1268341 original size:29 final size:29
Alignment explanation
Indices: 1268306--1268380 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
1268296 AAACTAAATT
*
1268306 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1268335 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1268364 GATGTCATTGCTTACAT
1 GATGTCATTGCTTACAT
1268381 AAATTTAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1277849 original size:4 final size:4
Alignment explanation
Indices: 1277840--1277865 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1277830 AAAGATAAAA
1277840 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1277866 GCATGCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1278922 original size:18 final size:18
Alignment explanation
Indices: 1278899--1278933 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1278889 ACACTTTATA
1278899 TTTTTATATTTTTAATTT
1 TTTTTATATTTTTAATTT
1278917 TTTTTATATTTTTAATT
1 TTTTTATATTTTTAATT
1278934 CAATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATATTTTTAATTT
Found at i:1278922 original size:26 final size:26
Alignment explanation
Indices: 1278893--1278966 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
1278883 GTTTTGACAC
1278893 TTTATATTTTTATATTTTTAATTTTT-
1 TTTATATTTTTA-ATTTTTAATTTTTA
**
1278919 TTTATATTTTTAATTCAATAATTTTTA
1 TTTATATTTTTAATT-TTTAATTTTTA
1278946 TTTAT-TCTTTTAATTTTTAAT
1 TTTATAT-TTTTAATTTTTAAT
1278967 AATACCGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.07
26 25 0.61
27 13 0.32
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATATTTTTAATTTTTAATTTTTA
Found at i:1279057 original size:15 final size:16
Alignment explanation
Indices: 1279037--1279066 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1279027 AATAATTTCT
1279037 TAATTTTAG-TTTTTG
1 TAATTTTAGATTTTTG
1279052 TAATTTTAGATTTTT
1 TAATTTTAGATTTTT
1279067 AATATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (16 bp):
TAATTTTAGATTTTTG
Found at i:1280636 original size:36 final size:36
Alignment explanation
Indices: 1280552--1280639 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
1280542 TTACATACAA
* *
1280552 TTAATGTTCACACAGAAAGGATCATGTTCCTCGCAC
1 TTAATATTCACAGAGAAAGGATCATGTTCCTCGCAC
*
1280588 TTAATATTCACAGAGAAGGGATCATGTTCCTCGCAC
1 TTAATATTCACAGAGAAAGGATCATGTTCCTCGCAC
*
1280624 TTGATATTCACAGAGA
1 TTAATATTCACAGAGA
1280640 TACCAAAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (36 bp):
TTAATATTCACAGAGAAAGGATCATGTTCCTCGCAC
Found at i:1284828 original size:3 final size:3
Alignment explanation
Indices: 1284820--1284915 Score: 147
Period size: 3 Copynumber: 31.7 Consensus size: 3
1284810 TTTTTATCCA
* *
1284820 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1284868 TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
1284914 TA
1 TA
1284916 ACATATATAT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1294348 original size:20 final size:20
Alignment explanation
Indices: 1294323--1294363 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1294313 AAGATATCTT
*
1294323 TGCCTGGTCTTATCA-AGATA
1 TGCCTGGT-TTAGCACAGATA
1294343 TGCCTGGTTTAGCACAGATA
1 TGCCTGGTTTAGCACAGATA
1294363 T
1 T
1294364 AGTGATACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
TGCCTGGTTTAGCACAGATA
Found at i:1298820 original size:80 final size:82
Alignment explanation
Indices: 1298573--1299011 Score: 597
Period size: 80 Copynumber: 5.5 Consensus size: 82
1298563 GATGAATTCA
* *
1298573 ATAGCATCTTCTGGAAGTGTTCTTTGAGTT-TCTGATCTGGTTGGACAGAA-CAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGG-CAGAACCAATCATTGAATT
*
1298636 TAGAAGATGAATTTG-TC
65 TAGAAGATGAATGTGTTC
*
1298653 AATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGCAGAACCAATCATTGAAT
1298718 TT-GAAAGATGAATGTGTTC
64 TTAG-AAGATGAATGTGTTC
* *
1298737 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTATTTGG-A-AAACAATCATTGAATTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAACCAATCATTGAATTT
*
1298800 GGAAGATGAATGTGTTC
66 AGAAGATGAATGTGTTC
*
1298817 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGAACCAATCA--G-ATTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAACCAATCATTGAATTT
* *
1298879 AGAAGATGAATTTG-CC
66 AGAAGATGAATGTGTTC
1298895 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA-
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGCAGAACCAATCATTGAAT
* *
1298959 TTCGTA-A-GAATGTGTTC
64 TTAGAAGATGAATGTGTTC
1298976 ATAGCATCTTCT-GAAGTG---TTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1299012 ATTCAGTAGA
Statistics
Matches: 326, Mismatches: 18, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
75 1 0.00
76 17 0.05
78 1 0.00
79 61 0.19
80 110 0.34
81 34 0.10
82 32 0.10
83 68 0.21
84 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (82 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAACCAATCATTGAATTT
AGAAGATGAATGTGTTC
Found at i:1298970 original size:159 final size:161
Alignment explanation
Indices: 1298559--1299011 Score: 607
Period size: 159 Copynumber: 2.9 Consensus size: 161
1298549 AAACATTAAA
1298559 TGAAGATGAA-TT-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTT-TCTGATCTGG-TTGGACA
1 TGAAGATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
* * *
1298620 GAACAATCATTGAGTTTAGAAGATGAATTTG-TCAATAGTATCTTCTGGAAGTGTTCTTTGAGTT
65 GAACAATCATTGA-ATTAGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTT
1298684 ATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
128 ATCTGATCTGGTTTGGCAGAACCAATCA-TGAATT
* *
1298719 TGAAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-ATTTGG
1 TG-AAGATGAAT-T-TGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
* *
1298782 -AAAACAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
63 CAGAACAATCATTGAA-TTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1298846 TATCTGATCTGG-TTGGCAGAACCAATCA-G-ATT
127 TATCTGATCTGGTTTGGCAGAACCAATCATGAATT
1298878 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 T-GAAGATGAATTTG-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
* *
1298943 AGAACCAATCATTGAATTCGTA-A-GAATGTGTTCATAGCATCTTCT-GAAGTG---TTTGAGTT
64 AGAA-CAATCATTGAATTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
1299002 ATCTGATCTG
128 ATCTGATCTG
1299012 ATTCAGTAGA
Statistics
Matches: 267, Mismatches: 11, Indels: 35
0.85 0.04 0.11
Matches are distributed among these distances:
155 18 0.07
157 1 0.00
158 8 0.03
159 74 0.28
160 10 0.04
161 15 0.06
162 27 0.10
163 68 0.25
164 33 0.12
165 13 0.05
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (161 bp):
TGAAGATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACAATCATTGAATTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAACCAATCATGAATT
Done.