Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000150.1 Hibiscus syriacus cultivar Beakdansim tig00000267_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: 68344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1366 original size:14 final size:14
Alignment explanation
Indices: 1347--1374 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1337 GTCTTTTCTT
1347 GAGTACTTCATTTG
1 GAGTACTTCATTTG
1361 GAGTACTTCATTTG
1 GAGTACTTCATTTG
1375 AAGTCCCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
GAGTACTTCATTTG
Found at i:5553 original size:30 final size:30
Alignment explanation
Indices: 5519--5614 Score: 192
Period size: 30 Copynumber: 3.2 Consensus size: 30
5509 AATATGAAAT
5519 ATTTTAGTTTATTTGTACATATAAATTTTA
1 ATTTTAGTTTATTTGTACATATAAATTTTA
5549 ATTTTAGTTTATTTGTACATATAAATTTTA
1 ATTTTAGTTTATTTGTACATATAAATTTTA
5579 ATTTTAGTTTATTTGTACATATAAATTTTA
1 ATTTTAGTTTATTTGTACATATAAATTTTA
5609 ATTTTA
1 ATTTTA
5615 ATACAATTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
ATTTTAGTTTATTTGTACATATAAATTTTA
Found at i:14034 original size:20 final size:20
Alignment explanation
Indices: 14009--14050 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13999 CTGGGCTGAC
14009 CCGAAAGGGTTTTAGACAAA
1 CCGAAAGGGTTTTAGACAAA
14029 CCGAAAGGGTTTTAGACAAA
1 CCGAAAGGGTTTTAGACAAA
14049 CC
1 CC
14051 TAATAGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (20 bp):
CCGAAAGGGTTTTAGACAAA
Found at i:16445 original size:20 final size:20
Alignment explanation
Indices: 16407--16451 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16397 TTTTCAAGTT
*
16407 GAGTTGAGTTTATAGAATTG
1 GAGTTGAGTTGATAGAATTG
*
16427 GAGTTGAGTTGAGTA-AATTT
1 GAGTTGAGTTGA-TAGAATTG
16447 GAGTT
1 GAGTT
16452 ATTCAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (20 bp):
GAGTTGAGTTGATAGAATTG
Found at i:16551 original size:2 final size:2
Alignment explanation
Indices: 16544--16573 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16534 TCCATAAACA
16544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16574 CATGCATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21496 original size:20 final size:20
Alignment explanation
Indices: 21458--21502 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
21448 TTTTCAAGTT
*
21458 GAGTTGAGTTTATAGAATTG
1 GAGTTGAGTTGATAGAATTG
*
21478 GAGTTGAGTTGAGTA-AATTT
1 GAGTTGAGTTGA-TAGAATTG
21498 GAGTT
1 GAGTT
21503 ATTCAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (20 bp):
GAGTTGAGTTGATAGAATTG
Found at i:23007 original size:32 final size:31
Alignment explanation
Indices: 22971--23047 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
22961 CGGGGCCGTG
*
22971 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
23003 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
23034 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
23048 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:23030 original size:63 final size:63
Alignment explanation
Indices: 22924--23047 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
22914 CCCTAAGGGA
* * ** *
22924 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
22987 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
23048 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:23942 original size:17 final size:16
Alignment explanation
Indices: 23922--23976 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
23912 GGAAGTCAAC
23922 GGTCAACGGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
23939 GGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
23956 GGTC-A-GTCGGGTCG
1 GGTCAACGTCGGGTCG
23970 GGTCAAC
1 GGTCAAC
23977 CCGGTTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
16 1 0.03
17 20 0.57
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:23964 original size:14 final size:14
Alignment explanation
Indices: 23930--23974 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 14
23920 ACGGTCAACG
23930 GTCGGGTCGGGTCAACA
1 GTCGGGTCGGGT---CA
23947 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
23961 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
23975 ACCCGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.57
17 12 0.43
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:24004 original size:10 final size:10
Alignment explanation
Indices: 23972--24021 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
23962 TCGGGTCGGG
*
23972 TCAACCCGGT
1 TCAAACCGGT
*
23982 TCAGACCGG-
1 TCAAACCGGT
23991 TCAAACCGGT
1 TCAAACCGGT
*
24001 TCAAAACTGG-
1 TC-AAACCGGT
24011 TCAAACCGGT
1 TCAAACCGGT
24021 T
1 T
24022 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:24012 original size:20 final size:19
Alignment explanation
Indices: 23970--24021 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
23960 AGTCGGGTCG
* *
23970 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
23989 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
24009 GGTCAAACCGGTT
1 GGTCAAACCGGTT
24022 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:24061 original size:9 final size:9
Alignment explanation
Indices: 24047--24073 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
24037 CTCCCTGCGA
24047 CGGCGCGTG
1 CGGCGCGTG
24056 CGGCGCGTG
1 CGGCGCGTG
24065 CGGCGCGTG
1 CGGCGCGTG
24074 AACAGTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.56, T:0.11
Consensus pattern (9 bp):
CGGCGCGTG
Found at i:30296 original size:32 final size:31
Alignment explanation
Indices: 30260--30336 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
30250 CGGGGCCGTG
*
30260 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** * *
30292 GGGCCTACCCGAGAATAATCTCAGGGCTGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
30323 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
30337 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:31241 original size:17 final size:16
Alignment explanation
Indices: 31219--31273 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
31209 AACGGTCAAC
31219 GGTCAACGGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
31236 GGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
31253 GGTC-A-GTCGGGTCG
1 GGTCAACGTCGGGTCG
31267 GGTCAAC
1 GGTCAAC
31274 CCGGTTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
16 1 0.03
17 20 0.57
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:31261 original size:14 final size:14
Alignment explanation
Indices: 31227--31271 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 14
31217 ACGGTCAACG
31227 GTCGGGTCGGGTCAACA
1 GTCGGGTCGGGT---CA
31244 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
31258 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
31272 ACCCGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.57
17 12 0.43
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:31301 original size:10 final size:10
Alignment explanation
Indices: 31269--31318 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
31259 TCGGGTCGGG
*
31269 TCAACCCGGT
1 TCAAACCGGT
*
31279 TCAGACCGG-
1 TCAAACCGGT
31288 TCAAACCGGT
1 TCAAACCGGT
*
31298 TCAAAACTGG-
1 TC-AAACCGGT
31308 TCAAACCGGT
1 TCAAACCGGT
31318 T
1 T
31319 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:31309 original size:20 final size:19
Alignment explanation
Indices: 31267--31318 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
31257 AGTCGGGTCG
* *
31267 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
31286 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
31306 GGTCAAACCGGTT
1 GGTCAAACCGGTT
31319 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:36630 original size:13 final size:13
Alignment explanation
Indices: 36612--36648 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
36602 ATGTTGATAA
*
36612 GTTCATTGTTTTC
1 GTTCATTGTCTTC
36625 GTTCATTGTCTTC
1 GTTCATTGTCTTC
*
36638 ATTCATTGTCT
1 GTTCATTGTCT
36649 AAGATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.19, G:0.14, T:0.57
Consensus pattern (13 bp):
GTTCATTGTCTTC
Found at i:37686 original size:32 final size:31
Alignment explanation
Indices: 37627--37686 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
37617 ATAATATTAT
* * *
37627 AATAATCTTTTATATATGTAAAGATATTTAC
1 AATAATCTATTATATATATAAACATATTTAC
*
37658 AATAATACTATTATATATATATACATATT
1 AATAAT-CTATTATATATATAAACATATT
37687 CAATTAGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 6 0.25
32 18 0.75
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
AATAATCTATTATATATATAAACATATTTAC
Found at i:41164 original size:14 final size:14
Alignment explanation
Indices: 41145--41173 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41135 AAATGTGGGG
41145 TTGAAGATTGCTAT
1 TTGAAGATTGCTAT
41159 TTGAAGATTGCTAT
1 TTGAAGATTGCTAT
41173 T
1 T
41174 AAATACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGAAGATTGCTAT
Found at i:43743 original size:31 final size:31
Alignment explanation
Indices: 43708--43790 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
43698 AAGGCGACCT
*
43708 TTGGGTAGGCTCTGCGGCCCCGAGATCTTTC
1 TTGGGTAGGCCCTGCGGCCCCGAGATCTTTC
43739 TTGGGTAGGCCCTGCGGCCCCGAGATCTTTC
1 TTGGGTAGGCCCTGCGGCCCCGAGATCTTTC
* *
43770 TTGGGTAGGCCCCGTGGCCCC
1 TTGGGTAGGCCCTGCGGCCCC
43791 AATAACTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.08, C:0.33, G:0.34, T:0.25
Consensus pattern (31 bp):
TTGGGTAGGCCCTGCGGCCCCGAGATCTTTC
Found at i:43804 original size:31 final size:31
Alignment explanation
Indices: 43708--43807 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
43698 AAGGCGACCT
* * * * *
43708 TTGGGTAGGCTCTGCGGCCCCGAGATCTTTC
1 TTGGGTAGGCCCCGCGGCCCCAAGAACTTAC
* * * *
43739 TTGGGTAGGCCCTGCGGCCCCGAGATCTTTC
1 TTGGGTAGGCCCCGCGGCCCCAAGAACTTAC
* *
43770 TTGGGTAGGCCCCGTGGCCCCAATAACTTAC
1 TTGGGTAGGCCCCGCGGCCCCAAGAACTTAC
43801 TTGGGTA
1 TTGGGTA
43808 AGCTCTCAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.27
Consensus pattern (31 bp):
TTGGGTAGGCCCCGCGGCCCCAAGAACTTAC
Found at i:50037 original size:20 final size:20
Alignment explanation
Indices: 49992--50037 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
49982 TAGGTATAAT
* * *
49992 CAAACTGAGTTGACCTGACG
1 CAAACCGAGTTGACCCGACC
50012 CAAACCGAGTTGACCCGACC
1 CAAACCGAGTTGACCCGACC
*
50032 CGAACC
1 CAAACC
50038 ATTGACCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (20 bp):
CAAACCGAGTTGACCCGACC
Found at i:50807 original size:31 final size:31
Alignment explanation
Indices: 50772--50891 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 31
50762 TAATGCGACC
** *
50772 CTTGGGTAGGCTCTACGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCTGTGGCCCCAAGATCTTT
*
50803 CTTGGGTAGGC-CTGTTGCCCCAAGATCTTTT
1 CTTGGGTAGGCTCTGTGGCCCCAAGATC-TTT
* * * * *
50834 ATTGGGTAGCCCCCGTGGCCCCAAGAACTTT
1 CTTGGGTAGGCTCTGTGGCCCCAAGATCTTT
* **
50865 CTTGGGTAGGCTTTCAGGCCCCAAGAT
1 CTTGGGTAGGCTCTGTGGCCCCAAGAT
50892 GTTCCCTTAG
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
30 12 0.17
31 45 0.64
32 13 0.19
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGTGGCCCCAAGATCTTT
Found at i:52209 original size:37 final size:37
Alignment explanation
Indices: 52168--52240 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
52158 GCTAAGTAAA
52168 CCTATTCTATGACTCAATTAAAAAGCATACAAAATTG
1 CCTATTCTATGACTCAATTAAAAAGCATACAAAATTG
52205 CCTATTCTATGACTCAATTAAAAAGCATACAAAATT
1 CCTATTCTATGACTCAATTAAAAAGCATACAAAATT
52241 ACAAGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (37 bp):
CCTATTCTATGACTCAATTAAAAAGCATACAAAATTG
Found at i:52485 original size:22 final size:22
Alignment explanation
Indices: 52457--52498 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52447 CCTATTTACA
52457 AACCGGACCCAAACCAAACCCG
1 AACCGGACCCAAACCAAACCCG
* *
52479 AACCGGATCCAAACTAAACC
1 AACCGGACCCAAACCAAACC
52499 TAATTGTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.40, G:0.12, T:0.05
Consensus pattern (22 bp):
AACCGGACCCAAACCAAACCCG
Found at i:53259 original size:14 final size:14
Alignment explanation
Indices: 53235--53286 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
53225 TATATCATCA
*
53235 TAAACCCTAAATCT
1 TAAAGCCTAAATCT
* *
53249 TAAAGCTTAAATCC
1 TAAAGCCTAAATCT
*
53263 TAAATCCTAAATC-
1 TAAAGCCTAAATCT
53276 T-AAGCCTAAAT
1 TAAAGCCTAAAT
53287 TCTAAACCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 9 0.28
13 1 0.03
14 22 0.69
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (14 bp):
TAAAGCCTAAATCT
Found at i:53291 original size:26 final size:28
Alignment explanation
Indices: 53235--53298 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 28
53225 TATATCATCA
*
53235 TAAACCCTAAATCTTAAAGCTTAAATCC
1 TAAACCCTAAATCTTAAAGCCTAAATCC
* *
53263 TAAATCCTAAATC-T-AAGCCTAAATTC
1 TAAACCCTAAATCTTAAAGCCTAAATCC
53289 TAAACCCTAA
1 TAAACCCTAA
53299 TTTAAAACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 19 0.59
27 1 0.03
28 12 0.38
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.28
Consensus pattern (28 bp):
TAAACCCTAAATCTTAAAGCCTAAATCC
Found at i:54220 original size:23 final size:24
Alignment explanation
Indices: 54194--54243 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
54184 TTATTTATTA
54194 TTCGCAAATATGTTCGTTTA-ATG
1 TTCGCAAATATGTTCGTTTATATG
** *
54217 TTCGTGAATGTGTTCGTTTATATG
1 TTCGCAAATATGTTCGTTTATATG
54241 TTC
1 TTC
54244 ATGAACGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (24 bp):
TTCGCAAATATGTTCGTTTATATG
Found at i:54242 original size:12 final size:12
Alignment explanation
Indices: 54201--54243 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
54191 TTATTCGCAA
54201 ATATGTTCGTTT
1 ATATGTTCGTTT
**
54213 A-ATGTTCGTGA
1 ATATGTTCGTTT
*
54224 ATGTGTTCGTTT
1 ATATGTTCGTTT
54236 ATATGTTC
1 ATATGTTC
54244 ATGAACGTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (12 bp):
ATATGTTCGTTT
Found at i:54248 original size:24 final size:23
Alignment explanation
Indices: 54204--54255 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
54194 TTCGCAAATA
* *
54204 TGTTCGTTTAATGTTCGTGAATG
1 TGTTCGTTTAATGTTCATGAACG
54227 TGTTCGTTTATATGTTCATGAACG
1 TGTTCGTTTA-ATGTTCATGAACG
54251 TGTTC
1 TGTTC
54256 ATGAACATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCATGAACG
Found at i:54291 original size:22 final size:22
Alignment explanation
Indices: 54266--54310 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54256 ATGAACATGC
*
54266 TCATTTTGCGTT-ATTTTAGTGT
1 TCATTTAGCGTTCA-TTTAGTGT
*
54288 TCATTTAGTGTTCATTTAGTGT
1 TCATTTAGCGTTCATTTAGTGT
54310 T
1 T
54311 GTTTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (22 bp):
TCATTTAGCGTTCATTTAGTGT
Found at i:54296 original size:11 final size:11
Alignment explanation
Indices: 54280--54310 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
54270 TTTGCGTTAT
54280 TTTAGTGTTCA
1 TTTAGTGTTCA
54291 TTTAGTGTTCA
1 TTTAGTGTTCA
54302 TTTAGTGTT
1 TTTAGTGTT
54311 GTTTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.19, T:0.58
Consensus pattern (11 bp):
TTTAGTGTTCA
Found at i:60921 original size:22 final size:22
Alignment explanation
Indices: 60896--60949 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
60886 AAGAAGTTGG
60896 ACAAGATAATTAAACAAAAGTA
1 ACAAGATAATTAAACAAAAGTA
*
60918 ACAAGATAATTAAACAAAAGTG
1 ACAAGATAATTAAACAAAAGTA
60940 ACAAGATAAT
1 ACAAGATAAT
60950 CCAATAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
ACAAGATAATTAAACAAAAGTA
Found at i:65170 original size:26 final size:26
Alignment explanation
Indices: 65132--65191 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
65122 GAAATTCTAG
*
65132 AACT-ACTGTATCGGAATGTACACCC
1 AACTAACTTTATCGGAATGTACACCC
65157 AACTAACTTTATCGGAATGTACACCC
1 AACTAACTTTATCGGAATGTACACCC
65183 AACTAACTT
1 AACTAACTT
65192 ACTCCTCACG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (26 bp):
AACTAACTTTATCGGAATGTACACCC
Found at i:66923 original size:13 final size:13
Alignment explanation
Indices: 66892--66922 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
66882 TTATTACTCA
66892 TTTTTTAATTTTT
1 TTTTTTAATTTTT
66905 TTTTTT-ATTTTT
1 TTTTTTAATTTTT
66917 TTTTTT
1 TTTTTT
66923 TCATGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTAATTTTT
Found at i:67038 original size:37 final size:37
Alignment explanation
Indices: 66991--67089 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 37
66981 TTAGATTACA
* *
66991 TATATATATATATGTTATTTTTTAT-TATCTGTTTAT
1 TATATATATATATATTATTTTTTATGTATCTATTTAT
* * *
67027 TAATTTATATATATATTTACTTTTTTATGTTTTTATTTAT
1 T-ATATATATATATA-TTA-TTTTTTATGTATCTATTTAT
67067 TATATATATATATATTATTTTTT
1 TATATATATATATATTATTTTTT
67090 CTTTTTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 1 0.02
37 17 0.32
38 6 0.11
39 20 0.38
40 9 0.17
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (37 bp):
TATATATATATATATTATTTTTTATGTATCTATTTAT
Found at i:67038 original size:39 final size:36
Alignment explanation
Indices: 66991--67089 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 36
66981 TTAGATTACA
66991 TATATATATATATGTTATTTTTTATTATCTGTTTATTAAT
1 TATATATATATAT-TTATTTTTTA-TAT-T-TTTATTAAT
* *
67031 T-TATATATATATTTACTTTTTTATGTTTTTATTTAT
1 TATATATATATATTTA-TTTTTTATATTTTTATTAAT
67067 TATATATATATATATTATTTTTT
1 TATATATATATAT-TTATTTTTT
67090 CTTTTTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
36 9 0.17
37 18 0.33
38 8 0.15
39 18 0.33
40 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (36 bp):
TATATATATATATTTATTTTTTATATTTTTATTAAT
Found at i:67067 original size:4 final size:4
Alignment explanation
Indices: 67005--67246 Score: 71
Period size: 4 Copynumber: 60.5 Consensus size: 4
66995 TATATATATG
* * * * *
67005 TTAT TT-T TTA- TTAT CTGT TTAT TAAT TTAT ATAT ATAT TTACT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT
* * * *
67051 TTAT GTT-T TTAT TTAT TATAT ATAT ATAT ATTAT TT-T TTCTT TTTT
1 TTAT -TTAT TTAT TTAT T-TAT TTAT TTAT -TTAT TTAT TT-AT TTAT
* * * * *
67097 TTAT TTAT TTAT TTGT TTAT TTAT AT-T TTCT TCTTT TTCT TTA- TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT
* * * **
67143 TTAT ATT-T TTAC ATAT TT-T TTAT TTAT TGT-T TTAT CT-T TGCT TTAT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT
* *
67189 TTAT CTTATCT TTAT TTAAT TT-T TT-T TTCT TCAT TTAAT TTAAT TTAT
1 TTAT -TTA--T TTAT TT-AT TTAT TTAT TTAT TTAT TT-AT TT-AT TTAT
67237 TTAT TTAT TT
1 TTAT TTAT TT
67247 CTTACCTTTT
Statistics
Matches: 182, Mismatches: 30, Indels: 52
0.69 0.11 0.20
Matches are distributed among these distances:
3 33 0.18
4 109 0.60
5 36 0.20
6 3 0.02
7 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:67126 original size:36 final size:37
Alignment explanation
Indices: 66993--67148 Score: 122
Period size: 36 Copynumber: 4.2 Consensus size: 37
66983 AGATTACATA
* * * * *
66993 TATATATATATGTTATTTTTTATTATCTGTTTATTAATT
1 TATATATATATATTATATTTT-CT-TCTTTTTATTTATT
*
67032 TATATATATAT-TTACT-TTTT-TATGTTTTTATTTATT
1 TATATATATATATTA-TATTTTCT-TCTTTTTATTTATT
* *
67068 ATATATATATATATTATTTTTTCTTTTTTTTATTTATT
1 -TATATATATATATTATATTTTCTTCTTTTTATTTATT
* * * *
67106 TATTTGTTTAT-TTATATTTTCTTCTTTTTCTTTATT
1 TATATATATATATTATATTTTCTTCTTTTTATTTATT
*
67142 TTTATAT
1 TATATAT
67149 TTTTACATAT
Statistics
Matches: 99, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
36 39 0.39
37 20 0.20
38 27 0.27
39 13 0.13
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (37 bp):
TATATATATATATTATATTTTCTTCTTTTTATTTATT
Found at i:67193 original size:15 final size:15
Alignment explanation
Indices: 67173--67206 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
67163 TATTTATTGT
67173 TTTATCTT-TGCTTTA
1 TTTATCTTAT-CTTTA
67188 TTTATCTTATCTTTA
1 TTTATCTTATCTTTA
67203 TTTA
1 TTTA
67207 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATCTTATCTTTA
Done.