Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004624.1 Hibiscus syriacus cultivar Beakdansim tig00010347_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: 63501
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2689 original size:21 final size:20
Alignment explanation
Indices: 2647--2690 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2637 TCAAAAGAAG
*
2647 TTTTGAGATCATCAATTTTC
1 TTTTGAGATCATCAATTATC
2667 TTTTGATGATCATC-ATTGATC
1 TTTTGA-GATCATCAATT-ATC
2688 TTT
1 TTT
2691 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (20 bp):
TTTTGAGATCATCAATTATC
Found at i:13478 original size:35 final size:35
Alignment explanation
Indices: 13386--13461 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
13376 CCAAAAAAGA
13386 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
* *
13421 AGAGTTGGATTAGGACTCAAATATTAGTTTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
13456 AGAGTT
1 AGAGTT
13462 TTTTAGTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:13858 original size:17 final size:18
Alignment explanation
Indices: 13832--13871 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13822 ATTATATGGA
13832 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
13848 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
13866 TATTAT
1 TATTAT
13872 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:14396 original size:36 final size:38
Alignment explanation
Indices: 14347--14422 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
14337 AGTGAGAGTG
*
14347 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
*
14383 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATA
14421 TA
1 TA
14423 TATATCTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
Found at i:14420 original size:2 final size:2
Alignment explanation
Indices: 14413--14451 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
14403 TACTTTGATG
* *
14413 TA TA TA TA TA TA TA TC TC 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 TA TA TA TA T
14452 TTCCTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14523 original size:9 final size:9
Alignment explanation
Indices: 14511--14535 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14501 TCTTATCTTA
14511 TTTATTTAT
1 TTTATTTAT
14520 TTTATTTAT
1 TTTATTTAT
14529 TTTATTT
1 TTTATTT
14536 TTCCCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:23367 original size:106 final size:106
Alignment explanation
Indices: 23128--23971 Score: 1086
Period size: 106 Copynumber: 8.0 Consensus size: 106
23118 ATATCGCGCC
* *
23128 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
* * * *
23192 CAGTTTCATTCAGAGCCAATTTTAATTTTACATCGAAGGATATTGG
65 CA--AT--TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * * * *
23238 ACTCGGGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAATAGTTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
23303 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * *
23344 ACTCGGGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
23409 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * *
23450 ACTCAAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATCTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
23515 AATTTCAGAG-C-----CAA--T---AGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * * *
23545 ACTCGAGACGACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAATAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * ** *
23610 ATTTTCAGGGTTAATTTCAACTTCACATAGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * *
23651 ACTCGAGAC--CACAAGTTCAACTTGACAACGAAGGGACGGCTGATTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
23714 TATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* *
23755 ACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
23820 AATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
* * ** * * * *
23861 ACTCAAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
23926 AGTTTCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
23967 ACTCG
1 ACTCG
23972 GAACAATACA
Statistics
Matches: 650, Mismatches: 70, Indels: 32
0.86 0.09 0.04
Matches are distributed among these distances:
95 80 0.12
98 1 0.00
100 3 0.00
101 3 0.00
103 1 0.00
104 93 0.14
105 1 0.00
106 406 0.62
108 1 0.00
109 4 0.01
110 57 0.09
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
Found at i:23913 original size:411 final size:414
Alignment explanation
Indices: 23128--23940 Score: 1202
Period size: 411 Copynumber: 2.0 Consensus size: 414
23118 ATATCGCGCC
* *
23128 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCAATTTCC
* * * * *
23193 AGTTTCATTCAGAGCCAATTTTAATTTTACATCGAAGGATATTGGACTCGGGACAACACAAGTTC
66 AG-TT-ATTCAGAGCCAATTTCAACTTCACATAGAAGGATATTGGACTCGAGAC-ACACAAGTTC
* * *
23258 AACTTCACAACAAAGGGACGGCTGGTTGTCAACAAATAGTTTCTCAATTTCAGAGCCAATTTCAA
128 AACTTCACAACAAAGGGACGGCTGATTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAA
* * * *
23323 CTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTG
193 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
* *
23388 GTTGTCAACAAATAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACT
258 GTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACT
* * *
23453 CAAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATCTCCCAAT
323 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATCTCCCAAT
23518 TTCAGAGCCAATAGCGAAGGATATTGG
388 TTCAGAGCCAATAGCGAAGGATATTGG
* * * *
23545 ACTCGAGACGACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAATAAA-TAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCAATTT-C
* **
23609 CA-TT-TTCAGGGTTAATTTCAACTTCACATAGAAGGATATTGGACTCGAGAC-CACAAGTTCAA
65 CAGTTATTCAGAGCCAATTTCAACTTCACATAGAAGGATATTGGACTCGAGACACACAAGTTCAA
* * *
23671 CTTGACAACGAAGGGACGGCTGATTGTCAACAAATAATTTCCCTATTTCAGAGCCAATTTCAACT
130 CTTCACAACAAAGGGACGGCTGATTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACT
*
23736 TCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGT
195 TCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGT
* * *
23801 TGTCAACAAACAATTTTCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCA
260 TGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCA
** * * * * *
23866 AGACAACACAAGCTCAACTTCACAGTGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTTT
325 AGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATCTCCCAATTT
23931 CAGAGCCAAT
390 CAGAGCCAAT
23941 TTCAACTTCA
Statistics
Matches: 355, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
411 255 0.72
413 39 0.11
415 2 0.01
416 4 0.01
417 55 0.15
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (414 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCAATTTCC
AGTTATTCAGAGCCAATTTCAACTTCACATAGAAGGATATTGGACTCGAGACACACAAGTTCAAC
TTCACAACAAAGGGACGGCTGATTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTT
CACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTT
GTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAA
GACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATCTCCCAATTTC
AGAGCCAATAGCGAAGGATATTGG
Found at i:24542 original size:35 final size:35
Alignment explanation
Indices: 24450--24521 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
24440 CCAAAAAAGA
24450 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
24485 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
24520 AG
1 AG
24522 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:25000 original size:2 final size:2
Alignment explanation
Indices: 24993--25023 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24983 TATTTTATTT
24993 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
25024 CTTTAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25403 original size:41 final size:39
Alignment explanation
Indices: 25340--25416 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 39
25330 AGGGCCCATT
* *
25340 TTTTTGTTTTATTTCTAGCTAAAGTCTCTTCCACTTTCCTC
1 TTTTTGTCTTATTTCTAGCTAAAG-C-CTCCCACTTTCCTC
25381 TTTTTGTCTTATTTCT-GACTAAAGCCTCCCACTTTC
1 TTTTTGTCTTATTTCTAG-CTAAAGCCTCCCACTTTC
25417 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 10 0.30
40 2 0.06
41 21 0.64
ACGTcount: A:0.16, C:0.26, G:0.08, T:0.51
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAGCTAAAGCCTCCCACTTTCCTC
Found at i:25483 original size:38 final size:40
Alignment explanation
Indices: 25432--25510 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
25422 AGTGAGAGGG
**
25432 TAGCTTTTCTATTTT-TAAATA-TTTTTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
25470 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
25510 T
1 T
25511 TTTTTTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 12 0.34
39 7 0.20
40 16 0.46
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.58
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:25589 original size:14 final size:15
Alignment explanation
Indices: 25570--25600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25560 TTTTCTTATC
25570 TTATTTA-TTTATTT
1 TTATTTATTTTATTT
25584 TTATTTATTTTATTT
1 TTATTTATTTTATTT
25599 TT
1 TT
25601 CCCTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:27238 original size:24 final size:23
Alignment explanation
Indices: 27221--27291 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 23
27211 CGTTCATGAA
27221 CGTTCGGTTATGTTCGTTATGTT
1 CGTTCGGTTATGTTCGTTATGTT
*
27244 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCGGTTATGTTCG-TTATGTT
27268 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCG-TTATGTT
27292 TAACCCAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 15 0.33
24 30 0.67
ACGTcount: A:0.08, C:0.11, G:0.25, T:0.55
Consensus pattern (23 bp):
CGTTCGGTTATGTTCGTTATGTT
Found at i:27253 original size:14 final size:14
Alignment explanation
Indices: 27232--27285 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
27222 GTTCGGTTAT
27232 GTTC-GTTATGTTC
1 GTTCGGTTATGTTC
27245 GTTCGGTTATG-T-
1 GTTCGGTTATGTTC
*
27257 -TT-GTTTATGTTC
1 GTTCGGTTATGTTC
27269 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
27283 GTT
1 GTT
27286 TATGTTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 7 0.21
14 18 0.53
ACGTcount: A:0.07, C:0.11, G:0.26, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:28378 original size:10 final size:10
Alignment explanation
Indices: 28363--28421 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
28353 TGGTCCCCAA
28363 CGTTTATGTT
1 CGTTTATGTT
28373 CGTTTATGTT
1 CGTTTATGTT
*
28383 CG----TGAT
1 CGTTTATGTT
28389 CGTTTATGTT
1 CGTTTATGTT
*
28399 CGTGT-T-TT
1 CGTTTATGTT
28407 -GTTTATGTT
1 CGTTTATGTT
28416 CGTTTA
1 CGTTTA
28422 CTTATTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
6 5 0.13
7 3 0.08
8 3 0.08
9 3 0.08
10 24 0.63
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:28393 original size:16 final size:17
Alignment explanation
Indices: 28372--28418 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
28362 ACGTTTATGT
28372 TCGTTTATGTTCGTG-A
1 TCGTTTATGTTCGTGTA
*
28388 TCGTTTATGTTCGTGTT
1 TCGTTTATGTTCGTGTA
*
28405 TTGTTTATGTTCGT
1 TCGTTTATGTTCGT
28419 TTACTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (17 bp):
TCGTTTATGTTCGTGTA
Found at i:28705 original size:13 final size:13
Alignment explanation
Indices: 28687--28711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28677 GTATTTTAAT
28687 ATAATATAATAAC
1 ATAATATAATAAC
28700 ATAATATAATAA
1 ATAATATAATAA
28712 TATTGATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATATAATAAC
Found at i:29296 original size:6 final size:6
Alignment explanation
Indices: 29285--29315 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29275 AATACAAGAA
29285 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
29316 TTTATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:34380 original size:17 final size:18
Alignment explanation
Indices: 34358--34405 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
34348 TGTCGAGTCT
34358 AATAATTTTTATT-TTAA
1 AATAATTTTTATTATTAA
34375 AATAATTTATATATTATTAA
1 AATAATTT-T-TATTATTAA
*
34395 AA-AATTGTTAT
1 AATAATTTTTAT
34406 ATTCAATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
19 8 0.30
20 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AATAATTTTTATTATTAA
Found at i:34408 original size:19 final size:19
Alignment explanation
Indices: 34358--34400 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
34348 TGTCGAGTCT
34358 AATAATTT-T-TATTTTAA
1 AATAATTTATATATTTTAA
34375 AATAATTTATATATTATTAA
1 AATAATTTATATATT-TTAA
34395 AA-AATT
1 AATAATT
34401 GTTATATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 1 0.04
19 8 0.35
20 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATTTATATATTTTAA
Found at i:36761 original size:20 final size:20
Alignment explanation
Indices: 36678--36754 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
36668 AATTCGATTT
* *
36678 GCGAATTTGTAAATCGAAAC
1 GCGAATCTGTAAATCGCAAC
36698 GCGAATCTGTAAATCGCAAC
1 GCGAATCTGTAAATCGCAAC
36718 GCGAATCTGTAAATCGCAAC
1 GCGAATCTGTAAATCGCAAC
36738 GCGAATCTGTAAATCGC
1 GCGAATCTGTAAATCGC
36755 GTTGCGATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
GCGAATCTGTAAATCGCAAC
Found at i:36814 original size:20 final size:19
Alignment explanation
Indices: 36783--36871 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 19
36773 GCAACAATGA
*
36783 ATTTTAAATTCGCAACTCG
1 ATTTTGAATTCGCAACTCG
36802 ATTTCTGAATTCGCAACTCG
1 ATTT-TGAATTCGCAACTCG
* *
36822 AATTTTG-TTGTAGCAACTCG
1 -ATTTTGAAT-TCGCAACTCG
*
36842 ATTTTCGAATTCGCAACACG
1 ATTTT-GAATTCGCAACTCG
36862 AATTTT-AATT
1 -ATTTTGAATT
36872 TCACAACAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
19 14 0.24
20 34 0.59
21 10 0.17
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (19 bp):
ATTTTGAATTCGCAACTCG
Found at i:36825 original size:40 final size:40
Alignment explanation
Indices: 36759--36878 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
36749 AATCGCGTTG
* *
36759 CGATTTTCAAATTCGCAACAAT-GAATTTTAAATTCGCAACT
1 CGATTTTCGAATTCGCAAC--TCGAATTTTAATTTCGCAACT
* *
36800 CGA-TTTCTGAATTCGCAACTCGAATTTT-GTTGTAGCAACT
1 CGATTTTC-GAATTCGCAACTCGAATTTTAATT-TCGCAACT
* *
36840 CGATTTTCGAATTCGCAACACGAATTTTAATTTCACAAC
1 CGATTTTCGAATTCGCAACTCGAATTTTAATTTCGCAAC
36879 AGGTTTTAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
39 2 0.03
40 45 0.68
41 19 0.29
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (40 bp):
CGATTTTCGAATTCGCAACTCGAATTTTAATTTCGCAACT
Found at i:36908 original size:69 final size:69
Alignment explanation
Indices: 36826--36963 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
36816 AACTCGAATT
* * *
36826 TTGTTGTAGCAACTCGATTTTCGAATTCGCAACACGAATTTTAATTTCACAACAGGTTTTAGTTT
1 TTGTTGTAGCAACTCGATTTTCAAATTCACAAAACGAATTTTAATTTCACAACAGGTTTTAGTTT
36891 CGCA
66 CGCA
*
36895 TTGTTGTAGCAACTCGATTTTCAAATTCACAAAACGAATTTTAATTTCGCAACAGGTTTTAGTTT
1 TTGTTGTAGCAACTCGATTTTCAAATTCACAAAACGAATTTTAATTTCACAACAGGTTTTAGTTT
36960 CGCA
66 CGCA
36964 AGACAAATGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (69 bp):
TTGTTGTAGCAACTCGATTTTCAAATTCACAAAACGAATTTTAATTTCACAACAGGTTTTAGTTT
CGCA
Found at i:37090 original size:22 final size:22
Alignment explanation
Indices: 37065--37118 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
37055 CTTTCTGGCT
37065 ACATCCGTTCCTATATCCAACG
1 ACATCCGTTCCTATATCCAACG
37087 ACATCCGTTCCTATATCCAACG
1 ACATCCGTTCCTATATCCAACG
37109 ACATCC-TTCC
1 ACATCCGTTCC
37119 CAATCTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.26, C:0.39, G:0.07, T:0.28
Consensus pattern (22 bp):
ACATCCGTTCCTATATCCAACG
Found at i:37944 original size:24 final size:24
Alignment explanation
Indices: 37917--37962 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
37907 TATTCGAAAT
37917 TTGATCTTGGTCAATACTCGGACG
1 TTGATCTTGGTCAATACTCGGACG
37941 TTGATCTTGGTCAATACTCGGA
1 TTGATCTTGGTCAATACTCGGA
37963 TTTTGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (24 bp):
TTGATCTTGGTCAATACTCGGACG
Found at i:37968 original size:24 final size:24
Alignment explanation
Indices: 37916--37969 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
37906 GTATTCGAAA
37916 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
* *
37940 GTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
37964 TTTGAT
1 TTTGAT
37970 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:40686 original size:64 final size:64
Alignment explanation
Indices: 40585--40733 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
40575 AATTTCAAAC
40585 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
40649 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
40713 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
40734 ACATCAATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:42100 original size:21 final size:21
Alignment explanation
Indices: 42074--42191 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
42064 GTGAATCGGG
*
42074 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
** *
42095 CTCTTGAACGATGACA-TGAGC
1 CTCTTGAACGATGGGAGGGA-C
* *
42116 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGAC
* ** *
42137 CTCTTGAATGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGAC
*
42158 CTCTTGAACGATAGGAGAGG-C
1 CTCTTGAACGATGGGAG-GGAC
42179 CTCTTGAACGATG
1 CTCTTGAACGATG
42192 ACAGGTGCTT
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.03
21 71 0.93
22 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGAC
Found at i:42133 original size:42 final size:41
Alignment explanation
Indices: 42074--42196 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 41
42064 GTGAATCGGG
*
42074 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACATGAGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGAGC
* * *
42116 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGAGC
* *
42158 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGACAGG
42197 TGCTTCGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGAGC
Found at i:42584 original size:21 final size:21
Alignment explanation
Indices: 42489--42584 Score: 54
Period size: 21 Copynumber: 4.6 Consensus size: 21
42479 GTAGAGCGGC
**
42489 TACCTCATCACGTAAAG-TGG
1 TACCTCATCACGTAAAGACCG
* *
42509 ATACCTCACCACGTAAAGCACCA
1 -TACCTCATCACGTAAAG-ACCG
** * *
42532 T-TGTCATCATGTAAA-ACCTC
1 TACCTCATCACGTAAAGACC-G
**
42552 TACCTCGCCACGTAAAGACCG
1 TACCTCATCACGTAAAGACCG
42573 TACCTCATCACG
1 TACCTCATCACG
42585 CCATGCACCA
Statistics
Matches: 53, Mismatches: 17, Indels: 10
0.66 0.21 0.12
Matches are distributed among these distances:
19 3 0.06
20 1 0.02
21 45 0.85
22 4 0.08
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (21 bp):
TACCTCATCACGTAAAGACCG
Found at i:42847 original size:20 final size:18
Alignment explanation
Indices: 42807--42847 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42797 CAGCTCGATC
*
42807 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGAGTG
42825 AGGTGATGGCTCTCGAAGTG
1 AGGTGATGGCTCT-G-AGTG
42845 AGG
1 AGG
42848 ACTGCTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 1 0.05
20 6 0.30
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.24
Consensus pattern (18 bp):
AGGTGATGGCTCTGAGTG
Found at i:44249 original size:20 final size:20
Alignment explanation
Indices: 44195--44239 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
44185 TCTGAAACTT
44195 AAAATCGCAATGCGAAAATG
1 AAAATCGCAATGCGAAAATG
*
44215 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCGAAAATG
44235 AAAAT
1 AAAAT
44240 GGCGTTGCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAATGCGAAAATG
Found at i:44264 original size:20 final size:20
Alignment explanation
Indices: 44241--44300 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
44231 AATGAAAATG
44241 GCGTTGCGATTTTCAGTTTC
1 GCGTTGCGATTTTCAGTTTC
** *
44261 GCGTTATGATTTTCATTTTC
1 GCGTTGCGATTTTCAGTTTC
* * *
44281 GTGTTGCGAATTTAAGTTTC
1 GCGTTGCGATTTTCAGTTTC
44301 AAATAGTCTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGTTGCGATTTTCAGTTTC
Found at i:44659 original size:22 final size:22
Alignment explanation
Indices: 44632--44674 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
44622 AGATAGATAT
44632 ATTTCGCCGGAGATGGGGACGA
1 ATTTCGCCGGAGATGGGGACGA
*
44654 ATTTCGTCGGAGATGGGGACG
1 ATTTCGCCGGAGATGGGGACG
44675 GATGTCGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (22 bp):
ATTTCGCCGGAGATGGGGACGA
Found at i:44682 original size:22 final size:22
Alignment explanation
Indices: 44639--44684 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
44629 TATATTTCGC
*
44639 CGGAGATGGGGACGAATTTCGT
1 CGGAGATGGGGACGAATGTCGT
*
44661 CGGAGATGGGGACGGATGTCGT
1 CGGAGATGGGGACGAATGTCGT
44683 CG
1 CG
44685 TAAAGAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.46, T:0.20
Consensus pattern (22 bp):
CGGAGATGGGGACGAATGTCGT
Found at i:46248 original size:34 final size:34
Alignment explanation
Indices: 46205--46271 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
46195 GTTGATTATA
46205 AATTCATCCGTGCTTCATATTATTTTCTTTTTCC
1 AATTCATCCGTGCTTCATATTATTTTCTTTTTCC
*
46239 AATTCATCCGTGCTTCATGTTATTTTCTTTTTC
1 AATTCATCCGTGCTTCATATTATTTTCTTTTTC
46272 ATATAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.07, T:0.54
Consensus pattern (34 bp):
AATTCATCCGTGCTTCATATTATTTTCTTTTTCC
Found at i:48907 original size:32 final size:34
Alignment explanation
Indices: 48863--48933 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
48853 TCTTTAAATT
48863 TGTATAATATATATTTTCCCTGTCTTACTAAGTG
1 TGTATAATATATATTTTCCCTGTCTTACTAAGTG
**
48897 TGTATAATATATATTTTCTTTGTCTTACTAAGTG
1 TGTATAATATATATTTTCCCTGTCTTACTAAGTG
48931 TGT
1 TGT
48934 CTCTTTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (34 bp):
TGTATAATATATATTTTCCCTGTCTTACTAAGTG
Found at i:53437 original size:85 final size:82
Alignment explanation
Indices: 53252--53442 Score: 240
Period size: 82 Copynumber: 2.3 Consensus size: 82
53242 GACAACCTAC
* * * *
53252 ACTATTCACGTCATTTGCTTGTCATTGACATTTCATAGCAACTCAGATAAACTGAAATATTTTAG
1 ACTATTCACGTCATTTGTTTTTCATTGACATTTCACAGCAACTCAAATAAACTGAAATATTTTAG
*
53317 AGAATCAGGGAATCTAT
66 AGAATCAGAGAATCTAT
** *
53334 ACTATTCACGTCATTTGTTTTTCATTGACATTTCACATTAACTCAAATAAACTGATATAATTTCC
1 ACTATTCACGTCATTTGTTTTTCATTGACATTTCACAGCAACTCAAATAAACTGAAAT-ATTT--
*
53399 ATTGA-AATCAGAGAATCTAT
63 -TAGAGAATCAGAGAATCTAT
* *
53419 ACTATTCACATCCTTTGTTTTTCA
1 ACTATTCACGTCATTTGTTTTTCA
53443 AAGTTAAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 51 0.54
83 4 0.04
85 36 0.38
86 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (82 bp):
ACTATTCACGTCATTTGTTTTTCATTGACATTTCACAGCAACTCAAATAAACTGAAATATTTTAG
AGAATCAGAGAATCTAT
Found at i:55590 original size:47 final size:47
Alignment explanation
Indices: 55521--55612 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
55511 ATATAATCCA
* *
55521 TATTGTTGAAGTTATATCACAATCCGCTGATGTGGCTTTTCATTCCG
1 TATTGTTGAAGATATATCACAATCCACTGATGTGGCTTTTCATTCCG
*
55568 TATTGTTGAAGATATATTACAATCCACTGATGTGGCTTTTCATTC
1 TATTGTTGAAGATATATCACAATCCACTGATGTGGCTTTTCATTC
55613 ATCATTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (47 bp):
TATTGTTGAAGATATATCACAATCCACTGATGTGGCTTTTCATTCCG
Found at i:57230 original size:15 final size:14
Alignment explanation
Indices: 57201--57240 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
57191 GCTAATAAAT
57201 TTTAAAATA-TTTC
1 TTTAAAATATTTTC
57214 TTATAAAATATTTTC
1 TT-TAAAATATTTTC
*
57229 TTTTAAATATTT
1 TTTAAAATATTT
57241 ATGTTACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 2 0.08
14 16 0.67
15 6 0.25
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAAATATTTTC
Done.