Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005980.1 Hibiscus syriacus cultivar Beakdansim tig00014057_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: 64291
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7995 original size:18 final size:19
Alignment explanation
Indices: 7974--8014 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
7964 ATCTATGAAC
*
7974 ATAAAAGA-TTTAAGAAGA
1 ATAAAAGAGTTGAAGAAGA
*
7992 ATAAAAGAGTTGAAGAATA
1 ATAAAAGAGTTGAAGAAGA
8011 ATAA
1 ATAA
8015 CAAGGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (19 bp):
ATAAAAGAGTTGAAGAAGA
Found at i:12018 original size:18 final size:18
Alignment explanation
Indices: 11995--12029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11985 ATGTATTCAT
11995 CTAAAAAAGATAATGGAA
1 CTAAAAAAGATAATGGAA
* *
12013 CTAAAAATGATGATGGA
1 CTAAAAAAGATAATGGA
12030 TAGAAGACCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (18 bp):
CTAAAAAAGATAATGGAA
Found at i:14413 original size:16 final size:17
Alignment explanation
Indices: 14392--14427 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
14382 ATCAGAGATC
*
14392 TTATTT-TTCTTTAAAT
1 TTATTTCTTCGTTAAAT
14408 TTATTTCTTCGTTAAAT
1 TTATTTCTTCGTTAAAT
14425 TTA
1 TTA
14428 ATTATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTTCTTCGTTAAAT
Found at i:18199 original size:20 final size:20
Alignment explanation
Indices: 18176--18225 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
18166 TTGTTCATGG
* *
18176 GTATCAATACTGACCCTTTA
1 GTATCAATACTAAACCTTTA
* *
18196 GTATCGATACTAAACCTTTG
1 GTATCAATACTAAACCTTTA
18216 GTATCAATAC
1 GTATCAATAC
18226 CCACATGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCAATACTAAACCTTTA
Found at i:26958 original size:15 final size:16
Alignment explanation
Indices: 26920--26959 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
26910 ATAGAACCTC
*
26920 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
26936 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
26952 T-AATCATT
1 TGAATCATT
26960 TTGAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:29781 original size:20 final size:22
Alignment explanation
Indices: 29758--29811 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
29748 TATATTATAG
29758 AAAATATTAATATTTTTGA-T-
1 AAAATATTAATATTTTTGATTA
*
29778 AAAATATT-AT-TTTTTTATTA
1 AAAATATTAATATTTTTGATTA
29798 AAAATATTAATATT
1 AAAATATTAATATT
29812 AGACGCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 3 0.10
20 16 0.55
21 2 0.07
22 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAAATATTAATATTTTTGATTA
Found at i:30212 original size:48 final size:48
Alignment explanation
Indices: 30157--30259 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 48
30147 GGATCTTTAA
30157 GCGTCTTCAATGTAATTTTTCCTATGCAAAATGATTTTGAAAATCTTG
1 GCGTCTTCAATGTAATTTTTCCTATGCAAAATGATTTTGAAAATCTTG
30205 GCGTCTTCAATGTAATTTTTCCTATGCAAAATGATTTTGAAAATCTTG
1 GCGTCTTCAATGTAATTTTTCCTATGCAAAATGATTTTGAAAATCTTG
*
30253 ACGTCTT
1 GCGTCTT
30260 TAGGTTTAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (48 bp):
GCGTCTTCAATGTAATTTTTCCTATGCAAAATGATTTTGAAAATCTTG
Found at i:30412 original size:11 final size:11
Alignment explanation
Indices: 30371--30449 Score: 70
Period size: 11 Copynumber: 6.7 Consensus size: 11
30361 GTTTTTATTT
*
30371 TAATATTTAAA
1 TAATATTTTAA
*
30382 TAAAATCTTTAA
1 TAATAT-TTTAA
30394 TTTAATATTTTAA
1 --TAATATTTTAA
30407 TAATA-TTTAA
1 TAATATTTTAA
30417 TAATGATTTGATAA
1 TAAT-ATTT--TAA
*
30431 TAATAATTTAA
1 TAATATTTTAA
30442 TAATATTT
1 TAATATTT
30450 AATGATTTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
10 9 0.16
11 21 0.38
12 6 0.11
13 8 0.14
14 12 0.21
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:30433 original size:14 final size:14
Alignment explanation
Indices: 30414--30487 Score: 73
Period size: 14 Copynumber: 5.2 Consensus size: 14
30404 TAATAATATT
30414 TAATAATGATTTGA
1 TAATAATGATTTGA
* *
30428 TAATAATAATTTAA
1 TAATAATGATTTGA
30442 TAATATTTAATGATTTGA
1 T-A-A--TAATGATTTGA
30460 TAATAATGA-TT--
1 TAATAATGATTTGA
30471 TAATAATGATTTGA
1 TAATAATGATTTGA
30485 TAA
1 TAA
30488 CATTTTTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 9 0.18
12 2 0.04
13 2 0.04
14 22 0.45
15 1 0.02
16 2 0.04
17 1 0.02
18 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATAATGATTTGA
Found at i:30463 original size:11 final size:11
Alignment explanation
Indices: 30402--30487 Score: 72
Period size: 11 Copynumber: 7.7 Consensus size: 11
30392 AATTTAATAT
30402 TTTAATAAT-A
1 TTTAATAATGA
30412 TTTAATAATGA
1 TTTAATAATGA
*
30423 TTTGATAATAATAA
1 -TT--TAATAATGA
30437 TTTAATAAT-A
1 TTTAATAATGA
*
30447 TTTAATGAT--
1 TTTAATAATGA
30456 TTGATAATAATGA
1 TT--TAATAATGA
30469 TTTAATAATGA
1 TTTAATAATGA
*
30480 TTTGATAA
1 TTTAATAA
30488 CATTTTTGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
9 2 0.03
10 18 0.28
11 30 0.47
12 2 0.03
13 4 0.06
14 8 0.12
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (11 bp):
TTTAATAATGA
Found at i:30476 original size:32 final size:32
Alignment explanation
Indices: 30396--30482 Score: 120
Period size: 32 Copynumber: 2.6 Consensus size: 32
30386 ATCTTTAATT
*
30396 TAATATTTTAATAATATTTAATAATGATTTGATAA
1 TAATAATTTAATAATA-TT--TAATGATTTGATAA
30431 TAATAATTTAATAATATTTAATGATTTGATAA
1 TAATAATTTAATAATATTTAATGATTTGATAA
*
30463 TAATGATTTAATAATGATTT
1 TAATAATTTAATAAT-ATTT
30483 GATAACATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 28 0.57
33 4 0.08
34 2 0.04
35 15 0.31
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (32 bp):
TAATAATTTAATAATATTTAATGATTTGATAA
Found at i:32215 original size:24 final size:24
Alignment explanation
Indices: 32188--32294 Score: 83
Period size: 24 Copynumber: 4.4 Consensus size: 24
32178 GACCACATTG
*
32188 AAATCATTATTAGTAATCATTACT
1 AAATCATTATTAATAATCATTACT
* *
32212 AAATCATTAGT-ATCAAATCATTTCT
1 AAATCATTATTAAT--AATCATTACT
* ** * *
32237 -TATTTTTAAATTAATAATAATTATT
1 AAATCATT--ATTAATAATCATTACT
*
32262 AAATCATTATTAATAATCATTATT
1 AAATCATTATTAATAATCATTACT
32286 AAATCATTA
1 AAATCATTA
32295 GTTTGAAATC
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
23 1 0.02
24 38 0.60
25 16 0.25
26 6 0.10
27 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATCATTATTAATAATCATTACT
Found at i:32272 original size:11 final size:12
Alignment explanation
Indices: 32246--32308 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 12
32236 TTATTTTTAA
*
32246 ATTAATAATAATT
1 ATTAA-AATCATT
32259 ATT-AAATCATT
1 ATTAAAATCATT
32270 ATTAATAATCATT
1 ATTAA-AATCATT
32283 ATT-AAATCATT
1 ATTAAAATCATT
*
32294 AGTTTGAAATCATT
1 A--TTAAAATCATT
32308 A
1 A
32309 AATATTTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 17 0.39
12 3 0.07
13 15 0.34
14 9 0.20
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (12 bp):
ATTAAAATCATT
Found at i:32279 original size:13 final size:13
Alignment explanation
Indices: 32246--32287 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
32236 TTATTTTTAA
*
32246 ATTAATAATAATT
1 ATTAATAATCATT
32259 ATT-A-AATCATT
1 ATTAATAATCATT
32270 ATTAATAATCATT
1 ATTAATAATCATT
32283 ATTAA
1 ATTAA
32288 ATCATTAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 15 0.58
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTAATAATCATT
Found at i:32564 original size:20 final size:20
Alignment explanation
Indices: 32536--32575 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
32526 ATCAAAAATG
32536 TTATCAAATCATTATTATCA
1 TTATCAAATCATTATTATCA
*
32556 TTATTAAATCATTATTATCA
1 TTATCAAATCATTATTATCA
32576 AATCATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATCAAATCATTATTATCA
Found at i:32566 original size:11 final size:11
Alignment explanation
Indices: 32536--32634 Score: 75
Period size: 11 Copynumber: 9.3 Consensus size: 11
32526 ATCAAAAATG
*
32536 TTATCAAATCA
1 TTATTAAATCA
32547 TTATT--ATCA
1 TTATTAAATCA
32556 TTATTAAATCA
1 TTATTAAATCA
32567 TTATT--ATCAAA
1 TTATTAAATC--A
*
32578 TCATTAAAT-A
1 TTATTAAATCA
*
32588 TTATCAAATCA
1 TTATTAAATCA
*
32599 TTTATCAAATCA
1 -TTATTAAATCA
*
32611 TTACTAAAT-A
1 TTATTAAATCA
*
32621 TTATTAAAACA
1 TTATTAAATCA
32632 TTA
1 TTA
32635 AATTAAAGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
9 12 0.17
10 16 0.23
11 30 0.42
12 11 0.15
13 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATTAAATCA
Found at i:32599 original size:52 final size:52
Alignment explanation
Indices: 32517--32637 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 52
32507 AATAATTGAG
* * * *
32517 TATTATTAAATCA-AAAATGTTATCAAATCA-TTAT-TATCATTATTAAATCAT
1 TATTA-TAAATCATTAAATATTATCAAATCATTTATAAATCATTACTAAAT-AT
32568 TATTATCAAATCATTAAATATTATCAAATCATTTATCAAATCATTACTAAATAT
1 TATTAT-AAATCATTAAATATTATCAAATCATTTAT-AAATCATTACTAAATAT
32622 TATTA-AAA-CATTAAAT
1 TATTATAAATCATTAAAT
32638 TAAAGATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
50 1 0.02
51 19 0.31
52 18 0.30
53 4 0.07
54 7 0.11
55 12 0.20
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (52 bp):
TATTATAAATCATTAAATATTATCAAATCATTTATAAATCATTACTAAATAT
Found at i:32605 original size:12 final size:12
Alignment explanation
Indices: 32588--32612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32578 TCATTAAATA
32588 TTATCAAATCAT
1 TTATCAAATCAT
32600 TTATCAAATCAT
1 TTATCAAATCAT
32612 T
1 T
32613 ACTAAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATCAAATCAT
Found at i:32624 original size:33 final size:32
Alignment explanation
Indices: 32536--32633 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 32
32526 ATCAAAAATG
*
32536 TTATCAAATCATTAT-TATCATTATTAAATCATT
1 TTATCAAATCATTATAAAT-ATTATTAAATCA-T
*
32569 ATTATCAAATCA-T-TAAATATTATCAAATCAT
1 -TTATCAAATCATTATAAATATTATTAAATCAT
*
32600 TTATCAAATCATTACTAAATATTATTAAAACAT
1 TTATCAAATCATTA-TAAATATTATTAAATCAT
32633 T
1 T
32634 AAATTAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 11 0.20
31 2 0.04
32 12 0.21
33 20 0.36
34 11 0.20
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (32 bp):
TTATCAAATCATTATAAATATTATTAAATCAT
Found at i:38096 original size:40 final size:40
Alignment explanation
Indices: 38036--38116 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
38026 AGGTAGCAAA
*
38036 CGGGTCATTCGGATCAAGTTTGGACCTGGTCGTTTCGGGT
1 CGGGTCATTCGGATCAAGTTTGGACCGGGTCGTTTCGGGT
* *
38076 CGGGTCATTCGGATCGAGTTTGGATCGGGTCGTTTCGGGT
1 CGGGTCATTCGGATCAAGTTTGGACCGGGTCGTTTCGGGT
38116 C
1 C
38117 AGGTAATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.11, C:0.20, G:0.37, T:0.32
Consensus pattern (40 bp):
CGGGTCATTCGGATCAAGTTTGGACCGGGTCGTTTCGGGT
Found at i:38262 original size:32 final size:32
Alignment explanation
Indices: 38188--38263 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
38178 AATTTTCAGG
* * * *
38188 TCGGGTGATTATTGGATCGGTTGTTTTTTGGT
1 TCGGGTCAATATTGGATCGGTTGATTTTTGGA
* ** *
38220 TTGGACCAATATTGGATTGGTTGATTTTTGGA
1 TCGGGTCAATATTGGATCGGTTGATTTTTGGA
38252 TCGGGTCAATAT
1 TCGGGTCAATAT
38264 CGGGTCCGAT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.45
Consensus pattern (32 bp):
TCGGGTCAATATTGGATCGGTTGATTTTTGGA
Found at i:38996 original size:18 final size:18
Alignment explanation
Indices: 38973--39015 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
38963 TTATTTTATT
38973 ATAAATT-TAATATTTTTA
1 ATAAATTATAA-ATTTTTA
*
38991 ATAAATTATCAATTTTTA
1 ATAAATTATAAATTTTTA
39009 A-AAATTA
1 ATAAATTA
39016 ATTTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATTATAAATTTTTA
Found at i:39775 original size:2 final size:2
Alignment explanation
Indices: 39768--39804 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39758 TTTTGGTAGG
39768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39805 AAAGGTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41030 original size:17 final size:17
Alignment explanation
Indices: 41008--41043 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40998 TATTTACATT
41008 TTATTTAAAATAATTTA
1 TTATTTAAAATAATTTA
**
41025 TTATTTTTAATAATTTA
1 TTATTTAAAATAATTTA
41042 TT
1 TT
41044 TTAATCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTAAAATAATTTA
Found at i:44959 original size:14 final size:15
Alignment explanation
Indices: 44940--44968 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44930 AATGCAAATT
44940 TAGGAAAAG-ACAAA
1 TAGGAAAAGAACAAA
44954 TAGGAAAAGAACAAA
1 TAGGAAAAGAACAAA
44969 CAACAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
TAGGAAAAGAACAAA
Found at i:47262 original size:42 final size:42
Alignment explanation
Indices: 47213--47449 Score: 154
Period size: 42 Copynumber: 5.7 Consensus size: 42
47203 AAAATGATAC
*
47213 TTTAGCGGTGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * *
47255 TTTAGCGGCG-TTTATAGCAA-AAATGCCGTAATAGA-TACGT--
1 TTTAGCGGCGTTTTTTA--AACAAACGCCGCAATAGAGT-GGTAA
*
47295 TTATAGTGGCGTTTTTT-AACAAACGCCGCAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * ** * *
47337 TTTAGCGGC-ATTTTTACACAAACGCCGTGAT--AGTGTTAT
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * **
47376 TTATAGTGGCATTTGTTT-AACAAACGCCGCTATAGAG-AATAAA
1 TT-TAGCGGCGTTT-TTTAAACAAACGCCGCAATAGAGTGGT-AA
* * *
47419 TTTAGCGGCATTTATAAAACAAACGCCGCAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAA
47450 ATAGTATTGT
Statistics
Matches: 149, Mismatches: 29, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
39 10 0.07
40 28 0.19
41 47 0.32
42 57 0.38
43 7 0.05
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:47318 original size:82 final size:79
Alignment explanation
Indices: 47222--47473 Score: 274
Period size: 82 Copynumber: 3.1 Consensus size: 79
47212 CTTTAGCGGT
* *
47222 GTTTTTTAAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATAGCAAAAATGCCGTAAT
1 GTTTTTT-AACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATA-CAAAAACGCCGTAAT
47287 AGATACGTTTATAGTGGC
64 AG-TA-GTTTATAGTGGC
* * *
47305 GTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTTTACACAAACGCCGTGATAG
1 GTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATACAAAAACGCCGTAATAG
47370 T-GTTATTTATAGTGGC
66 TAG---TTTATAGTGGC
* * ** * *
47386 ATTTGTTTAACAAACGCCGCTATAGAG-AATAAATTTAGCGGCATTTATAAAACAAACGCCGCAA
1 GTTT-TTTAACAAACGCCGCAATAGAGTGGT-AATTTAGCGGCATTTATACAA-AAACGCCG-TA
47450 ATAGTATTGTTTATAGTGGC
62 ATAGTA--GTTTATAGTGGC
47470 GTTT
1 GTTT
47474 ATGCAAAAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
78 1 0.01
80 1 0.01
81 29 0.20
82 78 0.54
83 15 0.10
84 19 0.13
87 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (79 bp):
GTTTTTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCATTTATACAAAAACGCCGTAATAG
TAGTTTATAGTGGC
Found at i:47489 original size:84 final size:82
Alignment explanation
Indices: 47315--47495 Score: 193
Period size: 84 Copynumber: 2.2 Consensus size: 82
47305 GTTTTTTAAC
** * * ** *
47315 AAACGCCGCAATAGAGTGGT-AATTTAGCGGCATTTTTACACAAACGCCGTGATAGTGTTATTTA
1 AAACGCCGCAATAGAG-AATAAATTTAGCGGCATTTTAAAACAAACGCCGAAATAGTATTATTTA
* ** *
47379 TAGTGGCATTTGTTTAAC
65 TAGTGGCATTTATGCAAA
* *
47397 AAACGCCGCTATAGAGAATAAATTTAGCGGCATTTATAAAACAAACGCCGCAAATAGTATTGTTT
1 AAACGCCGCAATAGAGAATAAATTTAGCGGCATTT-TAAAACAAACGCCG-AAATAGTATTATTT
*
47462 ATAGTGGCGTTTATGCAAA
64 ATAGTGGCATTTATGCAAA
*
47481 AAATGCCGCAATAGA
1 AAACGCCGCAATAGA
47496 TTAATAATAA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
81 1 0.01
82 30 0.38
83 12 0.15
84 37 0.46
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (82 bp):
AAACGCCGCAATAGAGAATAAATTTAGCGGCATTTTAAAACAAACGCCGAAATAGTATTATTTAT
AGTGGCATTTATGCAAA
Found at i:48987 original size:42 final size:42
Alignment explanation
Indices: 48925--49062 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 42
48915 ATTTTTATCG
* * *
48925 AAAAACGCCGCTATAGACCACACTTTTGTGGCATTTGTATAA
1 AAAAACGCCGCCATAAACCACACTTTTGCGGCATTTGTATAA
* * **
48967 AAAAACGCCGCCATAAACCACATTTTTTTGCGGCGTTTACATAA
1 AAAAACGCCGCCATAAACCACA--CTTTTGCGGCATTTGTATAA
* * **
49011 AAAAATGCCGCCATAAACCACACTTTTGCGACATTTGT-TTC
1 AAAAACGCCGCCATAAACCACACTTTTGCGGCATTTGTATAA
49052 AAAAACGCCGC
1 AAAAACGCCGC
49063 AATATGTTCA
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
41 11 0.14
42 31 0.40
44 36 0.46
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCCATAAACCACACTTTTGCGGCATTTGTATAA
Found at i:51834 original size:16 final size:17
Alignment explanation
Indices: 51810--51842 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51800 GATATCGTTA
51810 TCAT-TTTTTTTATTAC
1 TCATGTTTTTTTATTAC
51826 TCATGTTTTTTTATTAC
1 TCATGTTTTTTTATTAC
51843 AGATATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
TCATGTTTTTTTATTAC
Found at i:53352 original size:21 final size:21
Alignment explanation
Indices: 53328--53380 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
53318 GGAAGCAGAA
* *
53328 AGAGAAGCAGTGGCAGCACAG
1 AGAGAAGCAGCGGCAACACAG
53349 AGAG-AGACAGCGGCAACACAG
1 AGAGAAG-CAGCGGCAACACAG
53370 AGAGAAGCAGC
1 AGAGAAGCAGC
53381 ATATCAGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.42, C:0.21, G:0.36, T:0.02
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAACACAG
Found at i:53795 original size:43 final size:43
Alignment explanation
Indices: 53744--54053 Score: 214
Period size: 43 Copynumber: 7.2 Consensus size: 43
53734 CATATATTTA
* * *
53744 GCGGCGTTTGCGCTAAAAACGCCGCTAAATCTCAATACCTATT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATCTCAATACCTACT
* * * * *
53787 GCAGCGTTTGTGATAAAAACGCCGTTAAATATCAACATCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATCTCAATACCTACT
* ** *
53830 GCGGCATTTGTGGGAAAAACGCCACTAAA-CATCAATACCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATC-TCAATACCTACT
** * * ** *
53873 GCGGCGTTTGTGGGAAAAATGTCGCTAAAAATCAACACCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATCTCAATACCTACT
* *** ** * *
53916 GCGGCATTAACGGGAAAAACGCCGC-AAAACATCAACACCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATC-TCAATACCTACT
* * ** * * *
53959 GCGGCGTTAGCGGGAAAAATGCCGC-AAAACATCAACACCTACT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATC-TCAATACCTACT
* * * *
54002 GCGGCGTTTGTGAAAAAAATGCCGCTAAA-CATCAACACCTATT
1 GCGGCGTTTGTGATAAAAACGCCGCTAAATC-TCAATACCTACT
54045 GCGGCGTTT
1 GCGGCGTTT
54054 TTTGTTGAAA
Statistics
Matches: 225, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 4 0.02
43 218 0.97
44 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (43 bp):
GCGGCGTTTGTGATAAAAACGCCGCTAAATCTCAATACCTACT
Found at i:53858 original size:86 final size:86
Alignment explanation
Indices: 53758--54053 Score: 353
Period size: 86 Copynumber: 3.4 Consensus size: 86
53748 CGTTTGCGCT
* * * ** * * *
53758 AAAAACGCCGCTAAATC-TCAATACCTATTGCAGCGTTTGTGATAAAAACGCCGTTAAATATCAA
1 AAAAACGCCGCTAAA-CATCAACACCTACTGCGGCGTTTGTGGGAAAAATGCCGCTAAAAATCAA
*
53822 CATCTACTGCGGCATTTGTGGG
65 CACCTACTGCGGCATTTGTGGG
* * *
53844 AAAAACGCCACTAAACATCAATACCTACTGCGGCGTTTGTGGGAAAAATGTCGCTAAAAATCAAC
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAATGCCGCTAAAAATCAAC
***
53909 ACCTACTGCGGCATTAACGGG
66 ACCTACTGCGGCATTTGTGGG
* * *
53930 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTAGCGGGAAAAATGCCGC-AAAACATCAA
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAATGCCGCTAAAA-ATCAA
* **
53994 CACCTACTGCGGCGTTTGTGAA
65 CACCTACTGCGGCATTTGTGGG
* *
54016 AAAAATGCCGCTAAACATCAACACCTATTGCGGCGTTT
1 AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTT
54054 TTTGTTGAAA
Statistics
Matches: 179, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 5 0.03
86 174 0.97
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (86 bp):
AAAAACGCCGCTAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAATGCCGCTAAAAATCAAC
ACCTACTGCGGCATTTGTGGG
Found at i:53913 original size:129 final size:129
Alignment explanation
Indices: 53744--54053 Score: 350
Period size: 129 Copynumber: 2.4 Consensus size: 129
53734 CATATATTTA
* ** * ** * * ** *
53744 GCGGCGTTTGCGCTAAAAACGCCGCTAAATCTCAATACCTATTGCAGCGTTTGTGATAAAAACGC
1 GCGGCGTTTGTGAAAAAAATGCCGCTAAAAATCAACACCTATTGCGGCGTTTACGAGAAAAACGC
** * * * * * *
53809 CGTTAAATATCAACATCTACTGCGGCATTTGTGGGAAAAACGCCACTAAACATCAATACCTACT
66 CGCAAAACATCAACACCTACTGCGGCATTAGCGGGAAAAACGCCACAAAACATCAACACCTACT
** * * * * *
53873 GCGGCGTTTGTGGGAAAAATGTCGCTAAAAATCAACACCTACTGCGGCATTAACGGGAAAAACGC
1 GCGGCGTTTGTGAAAAAAATGCCGCTAAAAATCAACACCTATTGCGGCGTTTACGAGAAAAACGC
* * *
53938 CGCAAAACATCAACACCTACTGCGGCGTTAGCGGGAAAAATGCCGCAAAACATCAACACCTACT
66 CGCAAAACATCAACACCTACTGCGGCATTAGCGGGAAAAACGCCACAAAACATCAACACCTACT
*
54002 GCGGCGTTTGTGAAAAAAATGCCGCTAAACATCAACACCTATTGCGGCGTTT
1 GCGGCGTTTGTGAAAAAAATGCCGCTAAAAATCAACACCTATTGCGGCGTTT
54054 TTTGTTGAAA
Statistics
Matches: 147, Mismatches: 34, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
129 147 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (129 bp):
GCGGCGTTTGTGAAAAAAATGCCGCTAAAAATCAACACCTATTGCGGCGTTTACGAGAAAAACGC
CGCAAAACATCAACACCTACTGCGGCATTAGCGGGAAAAACGCCACAAAACATCAACACCTACT
Found at i:55664 original size:3 final size:3
Alignment explanation
Indices: 55651--55685 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
55641 ATATATATAA
*
55651 TAT TAAT TAT TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55686 TAATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56687 original size:60 final size:60
Alignment explanation
Indices: 56594--56738 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
56584 CATATGTCTC
* * * ** *
56594 CAAACTATGACCCTTATT-TAAATTAGTCCTTAAA-TTTCTAAACATTTTAATTTTATCC-
1 CAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTT-TAAACATTCCAATTTCATCCT
* * * *
56652 CTAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTGAGCATTCCAATTTCATCTT
1 C-AAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCT
56713 CAAACTATGACTCTCATTCTAAATTA
1 CAAACTATGACTCTCATTCTAAATTA
56739 GTTCAAAGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 14 0.19
60 53 0.74
61 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
CAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCT
Found at i:62921 original size:2 final size:2
Alignment explanation
Indices: 62914--62946 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62904 AAAGAAAGGT
62914 TA 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 TA T
62947 TAACCATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64176 original size:22 final size:22
Alignment explanation
Indices: 64151--64217 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
64141 CACCACAGCT
*
64151 CGTATAATGCACCGAAGTGCCA
1 CGTAGAATGCACCGAAGTGCCA
* * * *
64173 CGTAGAATTACACAGGAGTGCCG
1 CGTAGAA-TGCACCGAAGTGCCA
* *
64196 CATAGAATGCACCGTAGTGCCA
1 CGTAGAATGCACCGAAGTGCCA
64218 TATAATAGGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAATGCACCGAAGTGCCA
Done.