Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000648.1 Hibiscus syriacus cultivar Beakdansim tig00001254_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: 53905
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:640 original size:27 final size:27
Alignment explanation
Indices: 602--659 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
592 CAACTCTTGA
*
602 TTCACTGCTTCCAGAAGAGTTTGTAGG
1 TTCACTGCTTCCAGAAGAGTTTGCAGG
629 TTCACTGCTTCCAGAAGAGTTTGCAGG
1 TTCACTGCTTCCAGAAGAGTTTGCAGG
656 TTCA
1 TTCA
660 GCTGGGTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (27 bp):
TTCACTGCTTCCAGAAGAGTTTGCAGG
Found at i:8442 original size:54 final size:53
Alignment explanation
Indices: 8383--8484 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 53
8373 GGCACCCTTA
* *
8383 AAACTTTGAATGTAAATTAGGTATCGGTACCT-TGAGGAGGTATCGATACTCTTG
1 AAACTTCGAATGTAAATTAGGTATCAGTA--TATGAGGAGGTATCGATACTCTTG
* * *
8437 AAACTTCGAATGTAATTTTGGTATCAGTATATGTGGAGGTATCGATAC
1 AAACTTCGAATGTAAATTAGGTATCAGTATATGAGGAGGTATCGATAC
8485 CCCTGAAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
52 1 0.02
53 16 0.38
54 25 0.60
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (53 bp):
AAACTTCGAATGTAAATTAGGTATCAGTATATGAGGAGGTATCGATACTCTTG
Found at i:12450 original size:45 final size:45
Alignment explanation
Indices: 12396--12685 Score: 492
Period size: 45 Copynumber: 6.5 Consensus size: 45
12386 CATTTATCAT
*
12396 ATAAGCTCGTAAGCTTATTCTACCAATATACTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
12441 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
* *
12486 ATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATTCT
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
*
12531 ATAAGCTCCTAAGCTTATTTTACCAATATACTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
* *
12576 ATAAGCTCCTAAGCTTATTTTACCAATATACTTACCATTTACTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
* **
12621 ATAAGCTCGTAAACTTATTTTACCAATATACTTGTCA-TTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
12665 ATAAGCTCGTAAGCTTATTTT
1 ATAAGCTCGTAAGCTTATTTT
12686 CATGTTTACC
Statistics
Matches: 233, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
44 26 0.11
45 207 0.89
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
Found at i:12808 original size:40 final size:40
Alignment explanation
Indices: 12759--12838 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
12749 ATAGGAGTCA
* * * *
12759 AATATTGCACCGAAGTGTTGAGGTCGAGCTTTACTCACCT
1 AATAATGCACCGAAGTGCTAAGGTCGAGCTTTACCCACCT
* *
12799 AATAATGCACCGTAGTGCTAAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAAGTGCTAAGGTCGAGCTTTACCCACCT
12839 GGTACACCGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTAAGGTCGAGCTTTACCCACCT
Found at i:12922 original size:33 final size:33
Alignment explanation
Indices: 12866--12931 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12856 TGTATCGTGT
*
12866 CTTCACTAGAAACTTTAGGCCTACACT-ATATGC
1 CTTCACTAGAAACTCTAGGCCTAC-CTAATATGC
* * *
12899 CTTCTCTAGACACTCTAGTCCTACCTAATATGC
1 CTTCACTAGAAACTCTAGGCCTACCTAATATGC
12932 AGCTGCTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (33 bp):
CTTCACTAGAAACTCTAGGCCTACCTAATATGC
Found at i:16929 original size:31 final size:31
Alignment explanation
Indices: 16891--17046 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
16881 CCCGAAGGAC
* * *
16891 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
16922 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
16953 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
16984 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17015 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17046 C
1 C
17047 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:17754 original size:23 final size:22
Alignment explanation
Indices: 17728--17785 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
17718 TTCGCTTGAG
*
17728 GGGTATCGATTCCCCCATTGAAT
1 GGGTACCGATTCCCCC-TTGAAT
*
17751 GGGTACCAATT--CCCTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
17771 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
17786 TTGCCCAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 16 0.53
21 3 0.10
22 2 0.07
23 9 0.30
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (22 bp):
GGGTACCGATTCCCCCTTGAAT
Found at i:21454 original size:31 final size:31
Alignment explanation
Indices: 21416--21538 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
21406 CCCGAAAGAC
* *
21416 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAT
*
21447 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
21478 CAGTCCATATGTCCCAAAGAACATAGGTAAAT
1 CAGTCCATATGTCCCGAAGAACATAGGT-AAT
21510 -AGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
21539 ACCCTCGACC
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
30 2 0.02
31 79 0.94
32 3 0.04
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:21539 original size:31 final size:31
Alignment explanation
Indices: 21429--21539 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
21419 TCCATAGATT
*
21429 CCGAAGAACCTAGGT-AATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAAT-AGTCCATATGTC
*
21460 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
*
21491 CCAAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
21522 CCGAAGAACATAGGTAAA
1 CCGAAGAACATAGGTAAA
21540 CCCTCGACCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 72 0.97
32 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAATAGTCCATATGTC
Found at i:22225 original size:22 final size:21
Alignment explanation
Indices: 22200--22259 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
22190 TTTGCTTGAG
*
22200 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
22222 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
22242 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
22260 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:23216 original size:15 final size:14
Alignment explanation
Indices: 23198--23272 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 14
23188 TCTCATCTCA
23198 TTTTTTTCTCTTTTC
1 TTTTTTTCT-TTTTC
23213 TTTTCTTT-TTTTTC
1 TTTT-TTTCTTTTTC
*
23227 TATTTGTTTTTTTCTTC
1 T-TTT-TTTCTTT-TTC
*
23244 TTCGTTTTCTTTTTC
1 TT-TTTTTCTTTTTC
23259 TTTTTATTCTTTTT
1 TTTTT-TTCTTTTT
23273 TGTAATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.16
15 24 0.48
16 13 0.26
17 5 0.10
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:23263 original size:12 final size:12
Alignment explanation
Indices: 23200--23263 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
23190 TCATCTCATT
23200 TTTTTCTCTTTTC
1 TTTTTCT-TTTTC
23213 -TTTTCTTTTT-
1 TTTTTCTTTTTC
* *
23223 TTTCTATTTGTT-
1 TTTTTCTTT-TTC
*
23235 TTTTTCTTCTTC
1 TTTTTCTTTTTC
*
23247 GTTTTCTTTTTC
1 TTTTTCTTTTTC
23259 TTTTT
1 TTTTT
23264 ATTCTTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
11 12 0.30
12 28 0.70
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:23272 original size:35 final size:35
Alignment explanation
Indices: 23183--23273 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 35
23173 TGAAATATTA
* *
23183 TTTTTTCTCATCTCATTTTTTTCTCTTTTCTTTTCTT
1 TTTTTTCT-ATTTC-TTTTTTTCTCTCTTCTTTTCTT
*
23220 TTTTTTCTATTTGTTTTTTTCT-TCTTCGTTTTCTT
1 TTTTTTCTATTTCTTTTTTTCTCTCTTC-TTTTCTT
*
23255 TTTCTTTTTA-TTCTTTTTT
1 TTT-TTTCTATTTCTTTTTT
23274 GTAATATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
34 4 0.09
35 27 0.57
36 8 0.17
37 8 0.17
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.77
Consensus pattern (35 bp):
TTTTTTCTATTTCTTTTTTTCTCTCTTCTTTTCTT
Found at i:26042 original size:45 final size:45
Alignment explanation
Indices: 25991--26385 Score: 614
Period size: 45 Copynumber: 8.8 Consensus size: 45
25981 TATAAAATTT
* * *
25991 CTTATCATTTA-TCCTATAAGCTCATAAGCTTATTCTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
26036 CTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
** *
26081 CTTACCATTTATTCCATAAGCTTATAAGTTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
26126 CTTACTATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
26171 CTTACCATTTATTCCATAATCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
26216 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
26261 CTTATCATTTATTCTATAAGCTCGTAAACTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
26306 CTTATCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
26351 TTTGCCA-TTATTCCATAAGCTAGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
26386 CATGTTTACC
Statistics
Matches: 325, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
44 26 0.08
45 296 0.91
46 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.42
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:26092 original size:24 final size:24
Alignment explanation
Indices: 26065--26138 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
26055 GCTCGTAAGC
*
26065 TTATTTTACCAATATACTTACCAT
1 TTATTTTACCAATATACTTACAAT
*
26089 TTA--TT-CC-ATA-AGCTTATAAGT
1 TTATTTTACCAATATA-CTTACAA-T
*
26110 TTATTTTACCAATATACTTACTAT
1 TTATTTTACCAATATACTTACAAT
26134 TTATT
1 TTATT
26139 CCATAAGCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 1 0.03
20 8 0.21
21 6 0.15
22 2 0.05
23 2 0.05
24 11 0.28
25 8 0.21
26 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (24 bp):
TTATTTTACCAATATACTTACAAT
Found at i:27519 original size:30 final size:29
Alignment explanation
Indices: 27477--27542 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
27467 ATAACCCATC
* * *
27477 AATTTTCCAAAATTTATAAATTGATCCCCA
1 AATTTT-CAAAAATTACAAAATGATCCCCA
* *
27507 AGTTTTCAAAAATTACAAAATGGTCCCCA
1 AATTTTCAAAAATTACAAAATGATCCCCA
27536 AATTTTC
1 AATTTTC
27543 TAAGGCCTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTTTCAAAAATTACAAAATGATCCCCA
Found at i:29444 original size:21 final size:21
Alignment explanation
Indices: 29406--29452 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29396 GTCAAGGATC
* *
29406 TATGTGGTCATTCAGGATAAT
1 TATGTGGTCATCCAGGATAAA
* *
29427 TATGTGGTCCTCCGGGATAAA
1 TATGTGGTCATCCAGGATAAA
29448 TATGT
1 TATGT
29453 TACACTTCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (21 bp):
TATGTGGTCATCCAGGATAAA
Found at i:29481 original size:23 final size:22
Alignment explanation
Indices: 29455--29534 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
29445 AAATATGTTA
*
29455 CACTTCGGTGCAACCCTATGTGG
1 CACTTCGGTGCAA-ACTATGTGG
29478 CACTTCGGTGCAAACTATGTGG
1 CACTTCGGTGCAAACTATGTGG
* * *
29500 TC-CTCCAG-G-ACAATTATGTGG
1 -CACTTCGGTGCA-AACTATGTGG
29521 CACTTCGGTGCAAA
1 CACTTCGGTGCAAA
29535 TTACGAGCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 15 0.33
23 15 0.33
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
CACTTCGGTGCAAACTATGTGG
Found at i:29706 original size:21 final size:21
Alignment explanation
Indices: 29669--29716 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29659 GTCAAGGATC
* * *
29669 TATGTGGTCATTCGGGATAAT
1 TATGTGGTCACTCGGGACAAA
29690 TATGTGGTC-CTCGGGGACAAA
1 TATGTGGTCACTC-GGGACAAA
29711 TATGTG
1 TATGTG
29717 ACACTTCGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.33
Consensus pattern (21 bp):
TATGTGGTCACTCGGGACAAA
Found at i:29783 original size:263 final size:263
Alignment explanation
Indices: 29316--29843 Score: 993
Period size: 263 Copynumber: 2.0 Consensus size: 263
29306 AAATGATGTA
29316 CATTTTGAATGAACTTAATTATGTGATTAAAAGCCCAATGTATATATATGAGGATTAGAGGTATA
1 CATTTTGAATGAACTTAATTATGTGATTAAAAGCCCAATGTATATATATGAGGATTAGAGGTATA
*
29381 ATTGGCATGCCAAGAGTCAAGGATCTATGTGGTCATTCAGGATAATTATGTGGTCCTCCGGGATA
66 ATTGGCATGCCAAGAGTCAAGGATCTATGTGGTCATTCAGGATAATTATGTGGTCCTCCGGGACA
* *
29446 AATATGTTACACTTCGGTGCAACCCTATGTGGCACTTCGGTGCAAACTATGTGGTCCTCCAGGAC
131 AATATGTGACACTTCGGTGCAACCCTATGTGGCACTTCGGTGCAAACTATATGGTCCTCCAGGAC
29511 AATTATGTGGCACTTCGGTGCAAATTACGAGCTGTGGTGACAACATTAGTGCACAACCTTATAGT
196 AATTATGTGGCACTTCGGTGCAAATTACGAGCTGTGGTGACAACATTAGTGCACAACCTTATAGT
29576 ACT
261 ACT
29579 CATTTTGAATGAACTTAATTATGTGATTAAAAGCCCAATGTATATATATGAGGATTAGAGGTATA
1 CATTTTGAATGAACTTAATTATGTGATTAAAAGCCCAATGTATATATATGAGGATTAGAGGTATA
* * *
29644 GTTGGCATGCCAAGAGTCAAGGATCTATGTGGTCATTCGGGATAATTATGTGGTCCTCGGGGACA
66 ATTGGCATGCCAAGAGTCAAGGATCTATGTGGTCATTCAGGATAATTATGTGGTCCTCCGGGACA
*
29709 AATATGTGACACTTCGGTGCAACCCTATTTGGCACTTCGGTGCAAACTATATGGTCCTCCAGGAC
131 AATATGTGACACTTCGGTGCAACCCTATGTGGCACTTCGGTGCAAACTATATGGTCCTCCAGGAC
29774 AATTATGTGGCACTTCGGTGCAAATTACGAGCTGTGGTGACAACATTAGTGCACAACCTTATAGT
196 AATTATGTGGCACTTCGGTGCAAATTACGAGCTGTGGTGACAACATTAGTGCACAACCTTATAGT
29839 ACT
261 ACT
29842 CA
1 CA
29844 AATACCTAGA
Statistics
Matches: 258, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
263 258 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (263 bp):
CATTTTGAATGAACTTAATTATGTGATTAAAAGCCCAATGTATATATATGAGGATTAGAGGTATA
ATTGGCATGCCAAGAGTCAAGGATCTATGTGGTCATTCAGGATAATTATGTGGTCCTCCGGGACA
AATATGTGACACTTCGGTGCAACCCTATGTGGCACTTCGGTGCAAACTATATGGTCCTCCAGGAC
AATTATGTGGCACTTCGGTGCAAATTACGAGCTGTGGTGACAACATTAGTGCACAACCTTATAGT
ACT
Found at i:31063 original size:73 final size:73
Alignment explanation
Indices: 30944--31196 Score: 362
Period size: 73 Copynumber: 3.5 Consensus size: 73
30934 ATCCTAGTTA
* * * * *
30944 GATTTCAACTTCACAACAAATGATATCGAGCCCAAAAGATTCGACTTAAATTTACGACAAATGAG
1 GATTTCAACTTCACAACGAAGGATATCGAGCCCAAAAGTTTCGACTTAACTTCACGACAAATGAG
*
31009 TCACCTAC
66 TCACCCAC
* * ** * *
31017 GATTTTAACTTCACAACGAAGGATATCGTGGTCAAAAGTTTCGACTTAACTTCACAACGAATGAG
1 GATTTCAACTTCACAACGAAGGATATCGAGCCCAAAAGTTTCGACTTAACTTCACGACAAATGAG
31082 TCACCCAC
66 TCACCCAC
* *
31090 GATTTCAACTTCACAACGAAGGATATCGAGCCCAAAAGTTTCGTCTTAACTTCACGACAAATTAG
1 GATTTCAACTTCACAACGAAGGATATCGAGCCCAAAAGTTTCGACTTAACTTCACGACAAATGAG
31155 TCACCCAC
66 TCACCCAC
* *
31163 GATTTCAACTTCACGACGAAGGATATCGTGCCCA
1 GATTTCAACTTCACAACGAAGGATATCGAGCCCA
31197 GGAGATTGGC
Statistics
Matches: 158, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 158 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (73 bp):
GATTTCAACTTCACAACGAAGGATATCGAGCCCAAAAGTTTCGACTTAACTTCACGACAAATGAG
TCACCCAC
Found at i:31787 original size:37 final size:37
Alignment explanation
Indices: 31741--31939 Score: 159
Period size: 37 Copynumber: 5.4 Consensus size: 37
31731 ATATAATATA
*
31741 ATATAGTTTTTGAAAATATTTTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAATACTTTTTGAAAACATATAAT
*
31778 ATATAGTTTTT-AAAAT-CGATTTTTGAAAATATATACA-
1 ATATAGTTTTTGAAAATAC--TTTTTGAAAACATATA-AT
* *
31815 GTAT-GGTTTTGAAAATACGTTTTTGAAAA-AGTATAAT
1 ATATAGTTTTTGAAAATAC-TTTTTGAAAACA-TATAAT
* *
31852 ATATAG-TTTTGAAAACACATTTTTGAAAACGTATAAT
1 ATATAGTTTTTGAAAATAC-TTTTTGAAAACATATAAT
* * *
31889 ATATA-ATTTT-AAAA-ACGGTGTTTGAAAACGTAT-AT
1 ATATAGTTTTTGAAAATAC--TTTTTGAAAACATATAAT
31924 AATATAG-TTTTGAAAA
1 -ATATAGTTTTTGAAAA
31940 CATATATATA
Statistics
Matches: 137, Mismatches: 11, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
35 4 0.03
36 39 0.28
37 91 0.66
38 3 0.02
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.41
Consensus pattern (37 bp):
ATATAGTTTTTGAAAATACTTTTTGAAAACATATAAT
Found at i:31937 original size:23 final size:20
Alignment explanation
Indices: 31909--31954 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 20
31899 AAAAACGGTG
31909 TTTGAAAACGTATATAATATAGT
1 TTTGAAAAC--ATAT-ATATAGT
31932 TTTGAAAACATATATATAGT
1 TTTGAAAACATATATATAGT
31952 TTT
1 TTT
31955 TTAAAACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
21 4 0.17
23 9 0.39
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (20 bp):
TTTGAAAACATATATATAGT
Found at i:31955 original size:21 final size:22
Alignment explanation
Indices: 31909--31964 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
31899 AAAAACGGTG
31909 TTTGAAAACGTATATAATATAGT
1 TTTGAAAACG-ATATAATATAGT
31932 TTTGAAAAC-ATAT-ATATAGTT
1 TTTGAAAACGATATAATATAG-T
*
31953 TTTTAAAACGAT
1 TTTGAAAACGAT
31965 TTTTGGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 2 0.07
23 9 0.30
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (22 bp):
TTTGAAAACGATATAATATAGT
Found at i:32060 original size:5 final size:5
Alignment explanation
Indices: 32043--32980 Score: 1556
Period size: 5 Copynumber: 189.8 Consensus size: 5
32033 TAGTTTTTAT
* *
32043 TATTA TATT- TATTA TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32092 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32142 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32192 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32242 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32292 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32342 TA-T- TATTG TATTG TA-TG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32389 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32438 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32487 TATTG TATTG TA-TG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32536 TATTG TATTG TATTG TATTG TATTG TA-TG TA-TG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32584 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32634 TATTG TATTG TATTG TATTG TA-TG TATTG TATTG TATTG TA-TG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
32682 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTC TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
* * * * * * * * * *
32732 TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
* * * *
32782 TATTC TATTC TATTC TATTC TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
32832 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
32882 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTC
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
* * * * * * * * *
32932 TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATT
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATT
32981 ATTTATTTAT
Statistics
Matches: 917, Mismatches: 6, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
3 2 0.00
4 38 0.04
5 877 0.96
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (5 bp):
TATTG
Found at i:36400 original size:21 final size:20
Alignment explanation
Indices: 36374--36431 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
36364 AGTCGAGGGT
36374 TTATGTGGTCATTCGGGACAA
1 TTATGTGG-CATTCGGGACAA
* *
36395 TTATGTGGCCTTTCAGGACAA
1 TTATGTGG-CATTCGGGACAA
36416 TTATGTGGCACTTCGG
1 TTATGTGGCA-TTCGG
36432 TGCAAATTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (20 bp):
TTATGTGGCATTCGGGACAA
Found at i:39795 original size:22 final size:22
Alignment explanation
Indices: 39763--39804 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39753 TGTTTACTGT
*
39763 TGAATGGTGAACCGTTCAGCGC
1 TGAATGCTGAACCGTTCAGCGC
39785 TGAATGCTGAACCGTTCAGC
1 TGAATGCTGAACCGTTCAGC
39805 ATTCAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (22 bp):
TGAATGCTGAACCGTTCAGCGC
Found at i:40933 original size:24 final size:22
Alignment explanation
Indices: 40888--40952 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 22
40878 CAAAATATTA
* *
40888 ATTATTAAAATATTTAAAAATAT
1 ATTATTAATAT-TTTAATAATAT
40911 ATTTATTAATATTTCTAATAATAT
1 A-TTATTAATATTT-TAATAATAT
*
40935 AATATT-ATATTTTTAATA
1 ATTATTAATA-TTTTAATA
40953 TTACTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 8 0.22
23 10 0.28
24 18 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTAATATTTTAATAATAT
Done.