Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000823.1 Hibiscus syriacus cultivar Beakdansim tig00001591_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: 113787
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4589 original size:137 final size:137
Alignment explanation
Indices: 4370--4701 Score: 427
Period size: 137 Copynumber: 2.4 Consensus size: 137
4360 AGGTGCCGAA
* **
4370 TTAATTATTCGATAGTCCATAATTGATTAAAATTAATTAGGATTAATGCTAGAGCCTCCATCTTA
1 TTAATTATTCGA-AGTCAATAATT-ATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTA
* * * *
4435 GGCCTAATTTTATATTTAATCCTTAAATTAGGTGAACTCTTAATTTGGTCATCGCTTTTACTTGA
64 GGCCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGA
4500 GATTCCAA-T
129 GATT-CAACT
* *
4509 TTAATTATTCGAA-TCGATAATATATTAAAATTAATTAGGATTAATATTAAAGCCTCCATCTTAG
1 TTAATTATTCGAAGTCAATAAT-TATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAG
* * * * *
4573 GCTTAATTTCACATTTAGTCCTTAAATTAGGAGGATTCTTAATTTGGTCATCGCTTTTTCTCGAG
65 GCCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGAG
*
4638 GTTCAACT
130 ATTCAACT
* * *
4646 TTAATTATTCGAATTGCAATAATGATTAAAATTAATTTAAG-TTAATATTAGAGCCT
1 TTAATTATTCGAAGT-CAATAATTATTAAAATTAA-TTAGGATTAATATTAGAGCCT
4702 ATATTTTCAG
Statistics
Matches: 170, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
136 3 0.02
137 117 0.69
138 28 0.16
139 22 0.13
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (137 bp):
TTAATTATTCGAAGTCAATAATTATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGG
CCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGAGA
TTCAACT
Found at i:7100 original size:2 final size:2
Alignment explanation
Indices: 7093--7117 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7083 TTGAGTTATC
7093 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 T
7118 GTATGTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18528 original size:18 final size:18
Alignment explanation
Indices: 18501--18586 Score: 136
Period size: 18 Copynumber: 4.8 Consensus size: 18
18491 AATGCATTTT
* *
18501 ATGCACCGATGCACAACC
1 ATGCATCGATGCACAGCC
18519 ATGCATCGATGCACAGCC
1 ATGCATCGATGCACAGCC
* *
18537 ATGCATCTATGCACATCC
1 ATGCATCGATGCACAGCC
18555 ATGCATCGATGCACAGCC
1 ATGCATCGATGCACAGCC
18573 ATGCATCGATGCAC
1 ATGCATCGATGCAC
18587 TGAAGATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGCATCGATGCACAGCC
Found at i:18689 original size:65 final size:64
Alignment explanation
Indices: 18559--18697 Score: 156
Period size: 65 Copynumber: 2.2 Consensus size: 64
18549 ACATCCATGC
* * ** * **
18559 ATCGATGCACAGCCATGCATCGATGCACTGAAGATTTTATTAAAACATCGAATTGATTTTTTGT
1 ATCGATGCACAACCATGCATCGATGCACTCAAGATAGTATTAAAACATCGAATTGAATTAATGT
* *
18623 ATTGATGCACATACCATGCATCGATGCACTACAAGATAGT-TTGAAACATCGAA-TGCAATTAAT
1 ATCGATGCACA-ACCATGCATCGATGCACT-CAAGATAGTATTAAAACATCGAATTG-AATTAAT
18686 GT
63 GT
18688 ATCGATGCAC
1 ATCGATGCAC
18698 CCTTAGTGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 12 0.19
65 44 0.71
66 6 0.10
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (64 bp):
ATCGATGCACAACCATGCATCGATGCACTCAAGATAGTATTAAAACATCGAATTGAATTAATGT
Found at i:26507 original size:19 final size:20
Alignment explanation
Indices: 26485--26523 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
26475 TGCTTTCTGA
*
26485 TTGTTTTGGATG-TTTGAAT
1 TTGTTTTGAATGCTTTGAAT
26504 TTGTTTTGAATGCTTTGAAT
1 TTGTTTTGAATGCTTTGAAT
26524 GATTGTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.03, G:0.23, T:0.56
Consensus pattern (20 bp):
TTGTTTTGAATGCTTTGAAT
Found at i:27303 original size:65 final size:64
Alignment explanation
Indices: 27183--27309 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 64
27173 TTTCAAATGC
* *
27183 ATTTTATGCACCGATGCACAACCATGCATCGATGTACTCAGGATTTTATTAAAACATCGAATTG
1 ATTTTATGCACCGATGCACAACCATGCATCGATGCACTCAGGATATTATTAAAACATCGAATTG
* * * * *
27247 ATTTTTTGTACCGATGCACATACCATGCATCGATGCACTACATGCTATT-TTGAAACATCGAAT
1 ATTTTATGCACCGATGCACA-ACCATGCATCGATGCACT-CAGGATATTATTAAAACATCGAAT
27310 GCAATTAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 18 0.33
65 30 0.56
66 6 0.11
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (64 bp):
ATTTTATGCACCGATGCACAACCATGCATCGATGCACTCAGGATATTATTAAAACATCGAATTG
Found at i:33070 original size:19 final size:20
Alignment explanation
Indices: 33046--33091 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
33036 CTTTAATTTG
33046 TTTATTTAATTATT-TTTCT
1 TTTATTTAATTATTATTTCT
* *
33065 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTCT
33085 TTTATTT
1 TTTATTT
33092 TAAAAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTAATTATTATTTCT
Found at i:33183 original size:23 final size:24
Alignment explanation
Indices: 33140--33185 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
33130 ACTATTACTA
*
33140 TTTATTATTATATTATTTTTTAAT
1 TTTATTATTATATTATCTTTTAAT
33164 TTTATT-TTA-ATATATCTTTTAA
1 TTTATTATTATAT-TATCTTTTAA
33186 ACTTCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 12 0.60
24 6 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATTATTATATTATCTTTTAAT
Found at i:39316 original size:22 final size:23
Alignment explanation
Indices: 39281--39325 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
39271 TTCAATGTTC
*
39281 CAAAAAAAATCGAA-AATAAAAA
1 CAAAAAAAATCGAAGAAAAAAAA
39303 CAAAAAATAA-CGAAGAAAAAAAA
1 CAAAAAA-AATCGAAGAAAAAAAA
39326 TACCATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.78, C:0.09, G:0.07, T:0.07
Consensus pattern (23 bp):
CAAAAAAAATCGAAGAAAAAAAA
Found at i:42134 original size:19 final size:20
Alignment explanation
Indices: 42106--42156 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
42096 AATCCCTTTA
*
42106 ATTT-TTTTATTTAATTGTT
1 ATTTCTTTTATTTAATTCTT
42125 -TTTCTTTTATTTAATTCTT
1 ATTTCTTTTATTTAATTCTT
*
42144 ATTTTTTTTATTT
1 ATTTCTTTTATTT
42157 TAAAAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 14 0.50
20 11 0.39
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
ATTTCTTTTATTTAATTCTT
Found at i:42248 original size:5 final size:5
Alignment explanation
Indices: 42205--42250 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
42195 ACTATTAATA
*
42205 TTTAT TATTAT ATTATT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT T-TTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
42251 ATATATCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 29 0.78
6 8 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:45016 original size:23 final size:22
Alignment explanation
Indices: 44976--45019 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44966 TAAAACTATC
44976 ATATGATATTTAAAACATATAT
1 ATATGATATTTAAAACATATAT
44998 ATATG-TATATTAAATACATATA
1 ATATGATAT-TTAAA-ACATATA
45020 CTCAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 10 0.50
23 7 0.35
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
ATATGATATTTAAAACATATAT
Found at i:45537 original size:25 final size:25
Alignment explanation
Indices: 45503--45556 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
45493 TCGTAGTGCT
45503 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
45528 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
45553 TACA
1 TACA
45557 TTTAGTGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.20
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCACCATA
Found at i:45906 original size:24 final size:24
Alignment explanation
Indices: 45874--45921 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
45864 TCTTTCTGAT
45874 GATGTATAAAACATCTATGCACAA
1 GATGTATAAAACATCTATGCACAA
*
45898 GATGTATAAAACATTTATGCACAA
1 GATGTATAAAACATCTATGCACAA
45922 TGTCATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (24 bp):
GATGTATAAAACATCTATGCACAA
Found at i:46496 original size:31 final size:29
Alignment explanation
Indices: 46461--46524 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
46451 CATTCACAAC
* * *
46461 TTTTCCAAAATTGTCGAATTGGTCCCCTAAA
1 TTTTCAAAAATTATAGAA-TGGTCCCC-AAA
*
46492 TTTTCAAAAATTATATAATGGTCCCCAAA
1 TTTTCAAAAATTATAGAATGGTCCCCAAA
46521 TTTT
1 TTTT
46525 TCTAAGGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.24
30 8 0.28
31 14 0.48
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (29 bp):
TTTTCAAAAATTATAGAATGGTCCCCAAA
Found at i:51903 original size:20 final size:21
Alignment explanation
Indices: 51878--51929 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
51868 TTATCTCAAG
51878 TAAAAC-TATCATATG-ATATT
1 TAAAACATAT-ATATGTATATT
51898 TAAAACATATATATGTATA-T
1 TAAAACATATATATGTATATT
51918 TAAATACATATA
1 TAAA-ACATATA
51930 CTCAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAACATATATATGTATATT
Found at i:54524 original size:29 final size:32
Alignment explanation
Indices: 54440--54525 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 32
54430 GCCAAAATCT
* * *
54440 AACTTTT-TAAAA-TTACCATTTTGGTCCCTA
1 AACTTTTCCAAAATTTATCATTTTGGTCACTA
*
54470 AACTTTTCCAAAATTTAT-ACTTTGGTCACTA
1 AACTTTTCCAAAATTTATCATTTTGGTCACTA
*
54501 AAC-TTT-CAATATTT-TCATTTTGGTC
1 AACTTTTCCAAAATTTATCATTTTGGTC
54526 GCTATTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 15 0.32
30 10 0.21
31 18 0.38
32 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (32 bp):
AACTTTTCCAAAATTTATCATTTTGGTCACTA
Found at i:57074 original size:27 final size:30
Alignment explanation
Indices: 57043--57112 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
57033 TTAATTATGC
57043 TTTTATTTATTTTG-A-ATTAACCACTG-A
1 TTTTATTTATTTTGCATATTAACCACTGCA
* *
57070 TTTTATTT-TCTTGCATTTTAACCACTGCTA
1 TTTTATTTATTTTGCATATTAACCACTGC-A
57100 TATTTATTTATTT
1 T-TTTATTTATTT
57113 ATAATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.12
27 9 0.26
28 10 0.29
30 2 0.06
31 7 0.21
32 2 0.06
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTTATTTATTTTGCATATTAACCACTGCA
Found at i:57615 original size:17 final size:18
Alignment explanation
Indices: 57584--57623 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
57574 TTCTATCTTG
57584 TATTT-TGATTCTTATGT
1 TATTTATGATTCTTATGT
*
57601 TATTTATGATT-TTATTT
1 TATTTATGATTCTTATGT
57618 TATTTA
1 TATTTA
57624 AGAACTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (18 bp):
TATTTATGATTCTTATGT
Found at i:64706 original size:18 final size:16
Alignment explanation
Indices: 64657--64714 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
64647 GAATAAGTAA
64657 AAAAGAAGAAAAAAATG
1 AAAA-AAGAAAAAAATG
*
64674 AAAAAAAAATAAAAAATG
1 -AAAAAAGA-AAAAAATG
*
64692 AAGAAAAGAAGAAAAAGG
1 AA-AAAAGAA-AAAAATG
64710 AAAAA
1 AAAAA
64715 CAAAAAGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAAGAAAAAAATG
Found at i:71640 original size:16 final size:16
Alignment explanation
Indices: 71619--71651 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
71609 GTAAAATGTT
71619 AAAACA-TTGAACAAAA
1 AAAACACTT-AACAAAA
71635 AAAACACTTAACAAAA
1 AAAACACTTAACAAAA
71651 A
1 A
71652 CATACTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAACACTTAACAAAA
Found at i:75222 original size:300 final size:300
Alignment explanation
Indices: 74491--75382 Score: 1289
Period size: 300 Copynumber: 3.0 Consensus size: 300
74481 TCTAATACCA
* *
74491 CTAAATGTAACACCCTAATCTAGTCTGACCCGAAGATCCATGGATTACAATGTTACACGAGACTA
1 CTAAATGTAACACCCTAATCCAGTCTGACCCGAAGATCCATGGATTACAATGTTACACGGGACTA
* * *
74556 CCGAAATAGTGACCCAAAAAATTTATTTGAAATCTGGTTTTAAAACAATTGATAAAAATAATCCA
66 CCGAAATAGTGACCCAAAAAA-TTATTTGAAATCTGGTTGTAAAACAACTGATAATAATAATCCA
* * *
74621 TA-TCATTTAAAATAAAACATGATGATAATGATATGGGTTTACAAAATATCGGGAGC-TCCCAAA
130 TAGT-AGTTAAAATAAAACATGATGATAATAATATGGGTTTACAAAATATCGGGAGCTTCCAAAA
* * *
74684 -ATATATCCAAAATAATACAAATACTGAGTACAAATCAAGTTACGGCTGAATACATATAAAGGTC
194 TATATATCCAAAATAATACAAATACTGAGTACAAATCAAGTTACGACTGAATACACATAAGGGTC
* * *
74748 CATAAATAGTACATGCCCTATTAGAATGACTCAAGACGTACT
259 CATAAATAGTACATGCCCTCTAAGAATGACTCAAGACATACT
* * *
74790 CTAAATTTAACA-CCTAATCCAGTCTGACTCGAAGATCCATGGATTACAATGTTACATGGGACTA
1 CTAAATGTAACACCCTAATCCAGTCTGACCCGAAGATCCATGGATTACAATGTTACACGGGACTA
*** * *
74854 CCGAAATAGTGACCCAAATTTTTTTTTAAAATCTGGTTGTAAAACAACTGATAATAATAATCCAT
66 CCGAAATAGTGACCCAAAAAATTATTTGAAATCTGGTTGTAAAACAACTGATAATAATAATCCAT
* *
74919 AGTAGTTAAAATAAAACATGATGATAATAATCTGGGTTTACAAAATATGGGGAGCTTCCAAAATA
131 AGTAGTTAAAATAAAACATGATGATAATAATATGGGTTTACAAAATATCGGGAGCTTCCAAAATA
* * *
74984 TATATCCAAAATAATACAAATACCGAGTACAAATCAAGTTACGTCAT-AATACACATAAGGGTTC
196 TATATCCAAAATAATACAAATACTGAGTACAAATCAAGTTACGAC-TGAATACACATAAGGGTCC
*
75048 ATAAATAGTACAAT-CCCTCCAAGAATGACTCAAGACATACT
260 ATAAATAGTAC-ATGCCCTCTAAGAATGACTCAAGACATACT
* *
75089 CTAAATGTAACACCCTAATCCAGT-TCGACCCTAAGATCCATGAATTACAATGTTACACGGGACT
1 CTAAATGTAACACCCTAATCCAGTCT-GACCCGAAGATCCATGGATTACAATGTTACACGGGACT
* * * *
75153 ACCAAAAAAGTGACCCAAAAAATTATTTGAAATCTGGTTGTAAAACAACTAATAATAATAATTCA
65 ACCGAAATAGTGACCCAAAAAATTATTTGAAATCTGGTTGTAAAACAACTGATAATAATAATCCA
* * * *
75218 TAGTAGTTAAAATAAAACATGATAATAATAATATATGGGTTTACAAAATATTGGAAGCTTCGAAA
130 TAGTAGTTAAAATAAAACATGATGATAAT-A-ATATGGGTTTACAAAATATCGGGAGCTTCCAAA
* * *
75283 ATATATA--CAAAATAATTCAAATATTGAGTACAAATCAAGTTACGACTGAATACACAAAAGGGT
193 ATATATATCCAAAATAATACAAATACTGAGTACAAATCAAGTTACGACTGAATACACATAAGGGT
75346 CCATAAATAGTACATGCCCTCTAAGAATGACTCAAGA
258 CCATAAATAGTACATGCCCTCTAAGAATGACTCAAGA
75383 TGTACTCTGA
Statistics
Matches: 529, Mismatches: 53, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
297 88 0.17
298 73 0.14
299 118 0.22
300 213 0.40
301 1 0.00
302 36 0.07
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (300 bp):
CTAAATGTAACACCCTAATCCAGTCTGACCCGAAGATCCATGGATTACAATGTTACACGGGACTA
CCGAAATAGTGACCCAAAAAATTATTTGAAATCTGGTTGTAAAACAACTGATAATAATAATCCAT
AGTAGTTAAAATAAAACATGATGATAATAATATGGGTTTACAAAATATCGGGAGCTTCCAAAATA
TATATCCAAAATAATACAAATACTGAGTACAAATCAAGTTACGACTGAATACACATAAGGGTCCA
TAAATAGTACATGCCCTCTAAGAATGACTCAAGACATACT
Found at i:76132 original size:20 final size:20
Alignment explanation
Indices: 76109--76158 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
76099 CGATCCTTCA
76109 GTATCGATACTAAACCT-TTG
1 GTATCGATAC-AAACCTGTTG
** *
76129 GTATTTATACACACCTGTTG
1 GTATCGATACAAACCTGTTG
76149 GTATCGATAC
1 GTATCGATAC
76159 CCCCTGACTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (20 bp):
GTATCGATACAAACCTGTTG
Found at i:76237 original size:22 final size:18
Alignment explanation
Indices: 76212--76261 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
76202 CCTAGGTTGA
76212 GTATTGATACTATGGTATTGGG
1 GTATTGATACT-T-G-ATT-GG
*
76234 GTATCGATACTTGATTGG
1 GTATTGATACTTGATTGG
76252 GTATTGATAC
1 GTATTGATAC
76262 CAAATTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 1 0.04
21 1 0.04
22 10 0.38
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (18 bp):
GTATTGATACTTGATTGG
Found at i:88974 original size:18 final size:17
Alignment explanation
Indices: 88949--88982 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
88939 TATTCGAATA
88949 ATTTAATCGAATATAAT
1 ATTTAATCGAATATAAT
88966 ATTTGAATCGAATATAA
1 ATTT-AATCGAATATAA
88983 AATCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
ATTTAATCGAATATAAT
Found at i:89458 original size:26 final size:25
Alignment explanation
Indices: 89402--89454 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
89392 CAAAACATCC
*
89402 AAACAACCAAATATTCAAATTTGTT
1 AAACAACCAAATATTCAAATATGTT
89427 AAACAACCAAATCCA-TCAAA-ATGTT
1 AAACAACCAAAT--ATTCAAATATGTT
89452 AAA
1 AAA
89455 ACAATGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 19 0.76
26 5 0.20
27 1 0.04
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.25
Consensus pattern (25 bp):
AAACAACCAAATATTCAAATATGTT
Found at i:97019 original size:13 final size:13
Alignment explanation
Indices: 97001--97025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96991 TTTGAATTGA
97001 TCAAACTTGTTGC
1 TCAAACTTGTTGC
97014 TCAAACTTGTTG
1 TCAAACTTGTTG
97026 TTTAAGGCTT
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:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
TCAAACTTGTTGC
Found at i:97675 original size:18 final size:18
Alignment explanation
Indices: 97658--97691 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
97648 TATTCAAATA
97658 ATTT-AATCGAATATAAT
1 ATTTGAATCGAATATAAT
97675 ATTTGAATCGAATATAA
1 ATTTGAATCGAATATAA
97692 AATCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (18 bp):
ATTTGAATCGAATATAAT
Found at i:98730 original size:5 final size:5
Alignment explanation
Indices: 98706--98744 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
98696 GTAGGAGACT
98706 AGTCC AGTTCC AGTTCC AGTCC AGTCCC AGTCC AGTCC A
1 AGTCC AG-TCC AG-TCC AGTCC AGT-CC AGTCC AGTCC A
98745 TGATCCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 16 0.50
6 16 0.50
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (5 bp):
AGTCC
Found at i:98742 original size:11 final size:11
Alignment explanation
Indices: 98709--98743 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
98699 GGAGACTAGT
*
98709 CCAGTTCCAGTT
1 CCAG-TCCAGTC
98721 CCAGTCCAGTC
1 CCAGTCCAGTC
98732 CCAGTCCAGTC
1 CCAGTCCAGTC
98743 C
1 C
98744 ATGATCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (11 bp):
CCAGTCCAGTC
Found at i:102319 original size:16 final size:16
Alignment explanation
Indices: 102298--102373 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
102288 ATCGACAGTG
102298 GAATCGCCAAAGATGA
1 GAATCGCCAAAGATGA
*
102314 GAATCG--ACAG-TG-
1 GAATCGCCAAAGATGA
102326 GAATCGCCAAAGATGA
1 GAATCGCCAAAGATGA
*
102342 GAATCG--ACAG-TG-
1 GAATCGCCAAAGATGA
102354 GAATCGCCAAAGATGA
1 GAATCGCCAAAGATGA
102370 GAAT
1 GAAT
102374 AGAGTTGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
12 12 0.25
13 4 0.08
14 12 0.25
15 4 0.08
16 16 0.33
ACGTcount: A:0.41, C:0.17, G:0.28, T:0.14
Consensus pattern (16 bp):
GAATCGCCAAAGATGA
Found at i:102328 original size:28 final size:28
Alignment explanation
Indices: 102288--102373 Score: 172
Period size: 28 Copynumber: 3.1 Consensus size: 28
102278 TATTTCCGGT
102288 ATCGACAGTGGAATCGCCAAAGATGAGA
1 ATCGACAGTGGAATCGCCAAAGATGAGA
102316 ATCGACAGTGGAATCGCCAAAGATGAGA
1 ATCGACAGTGGAATCGCCAAAGATGAGA
102344 ATCGACAGTGGAATCGCCAAAGATGAGA
1 ATCGACAGTGGAATCGCCAAAGATGAGA
102372 AT
1 AT
102374 AGAGTTGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (28 bp):
ATCGACAGTGGAATCGCCAAAGATGAGA
Found at i:102331 original size:12 final size:12
Alignment explanation
Indices: 102288--102359 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 12
102278 TATTTCCGGT
102288 ATCGACAGTGGA
1 ATCGACAGTGGA
*
102300 ATCGCCAAAGATGAGA
1 ATCG--ACAG-TG-GA
102316 ATCGACAGTGGA
1 ATCGACAGTGGA
*
102328 ATCGCCAAAGATGAGA
1 ATCG--ACAG-TG-GA
102344 ATCGACAGTGGA
1 ATCGACAGTGGA
102356 ATCG
1 ATCG
102360 CCAAAGATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
12 16 0.33
13 4 0.08
14 12 0.25
15 4 0.08
16 12 0.25
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (12 bp):
ATCGACAGTGGA
Found at i:106024 original size:25 final size:25
Alignment explanation
Indices: 105991--106044 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
105981 TCTTGTAAAT
*
105991 GGGCCTGTGTGCCTTACTTTGTAAC
1 GGGCATGTGTGCCTTACTTTGTAAC
106016 GGGCATGTGTGCCTTACTTTGTAAC
1 GGGCATGTGTGCCTTACTTTGTAAC
106041 GGGC
1 GGGC
106045 CTTCGTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.13, C:0.22, G:0.31, T:0.33
Consensus pattern (25 bp):
GGGCATGTGTGCCTTACTTTGTAAC
Found at i:107729 original size:42 final size:42
Alignment explanation
Indices: 107670--107753 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
107660 ATCATATATA
*
107670 GAAATGTTGGTTCATTCCA-TATTCTTGAGAGAAGATTGAATC
1 GAAATGTTGATTCATTCCACTATTCTTGAGAG-AGATTGAATC
* * *
107712 GAAATGTTGATTCATTCCACTGTTCTTTAGAGATATTGAATC
1 GAAATGTTGATTCATTCCACTATTCTTGAGAGAGATTGAATC
107754 AAGGCAGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (42 bp):
GAAATGTTGATTCATTCCACTATTCTTGAGAGAGATTGAATC
Found at i:109219 original size:24 final size:24
Alignment explanation
Indices: 109187--109234 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
109177 TGTTTCATTT
*
109187 TTTTATTTTCATTGTTCTTTCTTC
1 TTTTATTTTCATTGTTATTTCTTC
* *
109211 TTTTATTTTTATTTTTATTTCTTC
1 TTTTATTTTCATTGTTATTTCTTC
109235 AGGCGAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTTTCATTGTTATTTCTTC
Done.