Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001338.1 Hibiscus syriacus cultivar Beakdansim tig00002612_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: 58465
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4520 original size:77 final size:79
Alignment explanation
Indices: 4366--4607 Score: 237
Period size: 77 Copynumber: 3.1 Consensus size: 79
4356 CGTGATGTTA
* * *
4366 ATCCAACTC-TTTATGTGATGG---ACAGCAAAGGTTGAACAAGTTCATCTCATTATGAACTTCT
1 ATCCAACTCATTT-TGTGATGGAATAGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTGT
* **
4427 TTTTTGGAAATATTG
65 TTATCAGAAATATTG
* * * *
4442 AT-CATCTCATTTTGTGAT-GAATCGAGCAAGGGTTGAACAAGTTCTTCTCATTATGAACCTGTT
1 ATCCAACTCATTTTGTGATGGAATAGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTGTT
* *
4505 TATCAGAATTGTTG
66 TATCAGAAATATTG
* * * * *
4519 ATCCAACTCTTTTTGTGATGGACTAGAGCAAATAG-TGAACAAGTTTTTTTCATTATGAACTTGT
1 ATCCAACTCATTTTGTGATGGAATAGAGCAAA-GGTTGAACAAGTTCTTCTCATTATGAACTTG-
* *
4583 TTTATCGGAAATACTG
64 TTTATCAGAAATATTG
4599 ATCCAACTC
1 ATCCAACTC
4608 CTTCTGATAG
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
74 1 0.01
75 11 0.08
76 5 0.04
77 46 0.35
78 14 0.11
79 34 0.26
80 22 0.17
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (79 bp):
ATCCAACTCATTTTGTGATGGAATAGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTGTT
TATCAGAAATATTG
Found at i:4647 original size:156 final size:153
Alignment explanation
Indices: 4361--4654 Score: 344
Period size: 156 Copynumber: 1.9 Consensus size: 153
4351 TCAAGCGTGA
*
4361 TGTTAATCCAACTCTTTATGTGATGGACAGCAAAGGTTGAACAAGTTCATCTCATTATGAACTTC
1 TGTTAATCCAACTCTTTATGTGATGGACAGCAAAAGTTGAACAAGTTCATCTCATTATGAACTTC
* * * * *
4426 TTTTTTGGAAATATTGATCATCTCATTTTGTGATGAATCGAGCAAGGGTTGAACAAGTTCTTCTC
66 TTTTTCGGAAATACTGATCAACTCATTCTGTGATGAATCGAGAAAGGGTTGAACAAGTTCTTCTC
4491 ATTATGAACCTGTTTATCAGAAT
131 ATTATGAACCTGTTTATCAGAAT
* * ** *
4514 TGTTGATCCAACTCTTTTTGTGATGGACTAGAGCAAATAG-TGAACAAGTTTTTTTCATTATGAA
1 TGTTAATCCAACTCTTTATGTGATGGAC---AGCAAA-AGTTGAACAAGTTCATCTCATTATGAA
* * * * *
4578 CTTGTTTTATCGGAAATACTGATCCAACTCCTTC--TGATAGACTCGAGAAATGG-TGAATAAGT
62 CTTCTTTT-TCGGAAATACTGAT-CAACTCATTCTGTGAT-GAATCGAGAAAGGGTTGAACAAGT
*
4640 TTTTCTCATTATGAA
124 TCTTCTCATTATGAA
4655 TTTCTTCTTC
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
153 26 0.22
156 60 0.51
157 24 0.21
158 7 0.06
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (153 bp):
TGTTAATCCAACTCTTTATGTGATGGACAGCAAAAGTTGAACAAGTTCATCTCATTATGAACTTC
TTTTTCGGAAATACTGATCAACTCATTCTGTGATGAATCGAGAAAGGGTTGAACAAGTTCTTCTC
ATTATGAACCTGTTTATCAGAAT
Found at i:4649 original size:77 final size:77
Alignment explanation
Indices: 4398--4654 Score: 225
Period size: 77 Copynumber: 3.3 Consensus size: 77
4388 CAGCAAAGGT
** * * * *
4398 TGAACAAGTTCATCTCATTATGAACTTCTTTT-TTGGAAATATTGAT-CATCTCATTTTG-TGAT
1 TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCGGAAATATTGATCCAACTCATTCTGAT-A-
* * *
4460 GAATCGAGCAAGGG
64 GACTCGAGAAATGG
* * * * * * *
4474 TTGAACAAGTTCTTCTCATTATGAACCTG-TTTATCAGAATTGTTGATCCAACTCTTTTTGTGAT
1 -TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCGGAAATATTGATCCAACTC--ATTCTGAT
* * *
4538 GGACTAGAGCAAATAG
63 AGACTCGAG-AAATGG
* * *
4554 TGAACAAGTTTTTTTCATTATGAACTTGTTTTATCGGAAATACTGATCCAACTCCTTCTGATAGA
1 TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCGGAAATATTGATCCAACTCATTCTGATAGA
4619 CTCGAGAAATGG
66 CTCGAGAAATGG
*
4631 TGAATAAGTTTTTCTCATTATGAA
1 TGAACAAGTTTTTCTCATTATGAA
4655 TTTCTTCTTC
Statistics
Matches: 143, Mismatches: 30, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
76 3 0.02
77 62 0.43
78 18 0.13
79 31 0.22
80 28 0.20
81 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (77 bp):
TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCGGAAATATTGATCCAACTCATTCTGATAGA
CTCGAGAAATGG
Found at i:9157 original size:22 final size:22
Alignment explanation
Indices: 9132--9182 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
9122 GACTTGACTG
9132 TTGACC-GATCAGACCGTTAACT
1 TTGACCAG-TCAGACCGTTAACT
** *
9154 TTGACCAGTTTGACCGTTGACT
1 TTGACCAGTCAGACCGTTAACT
9176 TTGACCA
1 TTGACCA
9183 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (22 bp):
TTGACCAGTCAGACCGTTAACT
Found at i:10156 original size:27 final size:28
Alignment explanation
Indices: 10114--10178 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
10104 ATTGGAATTA
* *
10114 TAAAACTACCCTTGAAGTGTAAAATGA-C
1 TAAAA-TACCCCTGAAGTGAAAAATGACC
10142 TAAAATACCCCTGAAGTGAAAAATGACC
1 TAAAATACCCCTGAAGTGAAAAATGACC
*
10170 TAAAGTACC
1 TAAAATACC
10179 TCTAAACCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 19 0.58
28 14 0.42
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (28 bp):
TAAAATACCCCTGAAGTGAAAAATGACC
Found at i:10886 original size:57 final size:57
Alignment explanation
Indices: 10798--10925 Score: 229
Period size: 57 Copynumber: 2.2 Consensus size: 57
10788 TATGCAAAAG
*
10798 ATCCTTAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
1 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
*
10855 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTTAATTCATA
1 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
*
10912 ATCTTGAATACCTC
1 ATCCTGAATACCTC
10926 TTATTGTTGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (57 bp):
ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
Found at i:11789 original size:30 final size:31
Alignment explanation
Indices: 11753--11828 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
11743 TAAGGTGACC
* *
11753 CTTGGGTAGGCTCTA-GATCCCGAGAT-CTTT
1 CTTGGGTAGGCTCTATGA-CCCCAAATACTTT
* *
11783 CTTGGGTAGGCCCCATGACCCCAAATAACTTT
1 CTTGGGTAGGCTCTATGACCCCAAAT-ACTTT
11815 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
11829 CGGGCCCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 19 0.51
31 2 0.05
32 16 0.43
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCTCTATGACCCCAAATACTTT
Found at i:13874 original size:17 final size:17
Alignment explanation
Indices: 13854--13888 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13844 CCCGTTGAGC
13854 TGACCAAATCATTGACT
1 TGACCAAATCATTGACT
13871 TGACCAAATCATTGACT
1 TGACCAAATCATTGACT
13888 T
1 T
13889 TGATCAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (17 bp):
TGACCAAATCATTGACT
Found at i:15806 original size:24 final size:23
Alignment explanation
Indices: 15742--15809 Score: 100
Period size: 24 Copynumber: 2.9 Consensus size: 23
15732 CATAATTTAG
*
15742 GTCAGATATCATAACAAAATCCA
1 GTCAGATATCATAACAGAATCCA
15765 GTTCAGATATCATAACAGAATCCA
1 G-TCAGATATCATAACAGAATCCA
*
15789 TGTCAGGTATCATAACAGAAT
1 -GTCAGATATCATAACAGAAT
15810 TCAAATCGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (23 bp):
GTCAGATATCATAACAGAATCCA
Found at i:20240 original size:157 final size:155
Alignment explanation
Indices: 19954--20260 Score: 510
Period size: 157 Copynumber: 2.0 Consensus size: 155
19944 TAAAATTCAG
*
19954 AAACCATAGTAATCCCTCCAGCTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* *
20019 CTATCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
66 CTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTATACTTCCTCCAACAA
20084 TAGCCCCTCAAATAAAACATTTATCAA
131 TA-CCCC-CAAATAAAACATTTATCAA
* *
20111 AAACCATAGTAATCCCTCCAAC-CAAACACGTCATAATGTGTAGGTTCCCCATAACCATACACCC
1 AAACCATAGTAATCCCTCCAACTC-AACACATCATAATGTGTAGGTTCCCCAGAACCATACACCC
*
20175 ACTCTCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTATTA-TTCCTCCAAC
65 ACTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTA-TACTTCCTCCAAC
20239 AATACCCCCAAATAAAACATTT
129 AATACCCCCAAATAAAACATTT
20261 TACATCCGTA
Statistics
Matches: 142, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
155 14 0.10
156 5 0.04
157 121 0.85
158 2 0.01
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (155 bp):
AAACCATAGTAATCCCTCCAACTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
CTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTATACTTCCTCCAACAA
TACCCCCAAATAAAACATTTATCAA
Found at i:20367 original size:24 final size:24
Alignment explanation
Indices: 20305--20350 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20295 ATAATTCAGG
20305 TCAGATATCAGAACAAAATCCAGA
1 TCAGATATCAGAACAAAATCCAGA
*
20329 TCAGATATCAGAACAGAATCCA
1 TCAGATATCAGAACAAAATCCA
20351 TTTCAGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (24 bp):
TCAGATATCAGAACAAAATCCAGA
Found at i:22013 original size:22 final size:22
Alignment explanation
Indices: 21985--22029 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21975 GGTGTTTTTA
21985 TAATTTCACCTAACTGAAGTAT
1 TAATTTCACCTAACTGAAGTAT
22007 TAATTTCACCTAACTGAAGTAT
1 TAATTTCACCTAACTGAAGTAT
22029 T
1 T
22030 CTCTTAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
TAATTTCACCTAACTGAAGTAT
Found at i:23722 original size:18 final size:18
Alignment explanation
Indices: 23688--23722 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23678 AACAACAATA
*
23688 TTTAAGGAAAATAGAAAT
1 TTTAAGGAAAACAGAAAT
*
23706 TTTAAGGAAAACGGAAA
1 TTTAAGGAAAACAGAAA
23723 GAAAAAAATC
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:0.03, G:0.20, T:0.23
Consensus pattern (18 bp):
TTTAAGGAAAACAGAAAT
Found at i:23919 original size:16 final size:17
Alignment explanation
Indices: 23898--23935 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
23888 GCATATCTTA
23898 AAAAAG-GAAAAAAATT
1 AAAAAGAGAAAAAAATT
*
23914 AAAAAGAGAAATAAATT
1 AAAAAGAGAAAAAAATT
23931 AAAAA
1 AAAAA
23936 TAATACATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAAGAGAAAAAAATT
Found at i:29950 original size:3 final size:3
Alignment explanation
Indices: 29932--29988 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
29922 TTTTTATATA
* * * * *
29932 TAT TAT TAA TATT TAT TAT TAT TAT TTT TGT TAT TTT TATT TAA TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
29979 TAT TAT TAT T
1 TAT TAT TAT T
29989 TATGTTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
3 38 0.88
4 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29983 original size:31 final size:30
Alignment explanation
Indices: 29945--30002 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
29935 TATTAATATT
* *
29945 TATTATTATTATTTTTGTTATTTTTATTTAA
1 TATTATTATTATTTATGTT-TTTATATTTAA
29976 TATTATTATTATTTATGTTTTTATATT
1 TATTATTATTATTTATGTTTTTATATT
30003 AATTTTACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (30 bp):
TATTATTATTATTTATGTTTTTATATTTAA
Found at i:29996 original size:28 final size:28
Alignment explanation
Indices: 29941--30005 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
29931 ATATTATTAA
* *
29941 TATTTATTATTATTATTTTTGTTATTTT
1 TATTTAATATTATTATTTTTGATATTTT
*
29969 TATTTAATATTATTATTATTT-ATGTTTT
1 TATTTAATATTATTATT-TTTGATATTTT
29997 TATATTAAT
1 TAT-TTAAT
30006 TTTACAGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TATTTAATATTATTATTTTTGATATTTT
Found at i:31395 original size:32 final size:32
Alignment explanation
Indices: 31359--31494 Score: 236
Period size: 32 Copynumber: 4.2 Consensus size: 32
31349 TTATATTAAC
31359 TACTAACATACTAACTTTTATTTTATTGTTCA
1 TACTAACATACTAACTTTTATTTTATTGTTCA
31391 TACTAACATACTAACTTTTATTTTATTGTTCA
1 TACTAACATACTAACTTTTATTTTATTGTTCA
*
31423 TACTAACATACTCACTTTTATTTTATTGTTCA
1 TACTAACATACTAACTTTTATTTTATTGTTCA
*
31455 TACTAACTTACTAACATTTTATTTTATTGTTCA
1 TACTAACATACTAAC-TTTTATTTTATTGTTCA
*
31488 AACTAAC
1 TACTAAC
31495 CCGCTAACTT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 76 0.77
33 23 0.23
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.49
Consensus pattern (32 bp):
TACTAACATACTAACTTTTATTTTATTGTTCA
Found at i:32501 original size:14 final size:14
Alignment explanation
Indices: 32482--32508 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32472 TTTTTATCTT
32482 TTAAAATTATTTTC
1 TTAAAATTATTTTC
32496 TTAAAATTATTTT
1 TTAAAATTATTTT
32509 AAAAGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:36481 original size:22 final size:20
Alignment explanation
Indices: 36427--36482 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
36417 ATTGTTCATC
*
36427 AGGGTATCGATA-CCCAAGG
1 AGGGTATCGATACCCCAAGA
*
36446 AGGAGTATCAATACCCCAAGAAA
1 AGG-GTATCGATACCCCAAG--A
36469 AGGGTATCGATACC
1 AGGGTATCGATACC
36483 AAGGAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.10
20 8 0.27
21 6 0.20
22 10 0.33
23 3 0.10
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (20 bp):
AGGGTATCGATACCCCAAGA
Found at i:37559 original size:24 final size:24
Alignment explanation
Indices: 37527--37574 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37517 GATCGAATTT
37527 GGGTGCTACACCAATCTTACCTTA
1 GGGTGCTACACCAATCTTACCTTA
37551 GGGTGCTACACCAATCTTACCTTA
1 GGGTGCTACACCAATCTTACCTTA
37575 AAAATGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (24 bp):
GGGTGCTACACCAATCTTACCTTA
Found at i:40870 original size:43 final size:43
Alignment explanation
Indices: 40822--40908 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
40812 AATGATTATA
*
40822 AGATAATATTTGTTTAGAATTTTTCTAAATATGCGCTAATTTC
1 AGATAATATTTATTTAGAATTTTTCTAAATATGCGCTAATTTC
40865 AGATAATATTTATTTAGAATTTTTCTAAATATGCGCTAATTTC
1 AGATAATATTTATTTAGAATTTTTCTAAATATGCGCTAATTTC
40908 A
1 A
40909 ACTTAAATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (43 bp):
AGATAATATTTATTTAGAATTTTTCTAAATATGCGCTAATTTC
Found at i:42281 original size:10 final size:10
Alignment explanation
Indices: 42263--42315 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
42253 TATATCAATT
*
42263 TAAACTATAA
1 TAAAATATAA
42273 TAAAATATAA
1 TAAAATATAA
42283 TAAATAAATATAA
1 T--A-AAATATAA
*
42296 TAAAATACAAA
1 TAAAATA-TAA
42307 TAAAATATA
1 TAAAATATA
42316 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 16 0.44
11 10 0.28
12 1 0.03
13 9 0.25
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAATATAA
Found at i:42291 original size:13 final size:13
Alignment explanation
Indices: 42275--42299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42265 AACTATAATA
42275 AAATATAATAAAT
1 AAATATAATAAAT
42288 AAATATAATAAA
1 AAATATAATAAA
42300 ATACAAATAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAATAAAT
Found at i:42316 original size:23 final size:23
Alignment explanation
Indices: 42263--42310 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
42253 TATATCAATT
*
42263 TAAACTATAATAAAATATAATAAA
1 TAAA-TATAATAAAATAAAATAAA
42287 TAAATATAATAAAATACAAATAAA
1 TAAATATAATAAAATA-AAATAAA
42311 ATATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAATATAATAAAATAAAATAAA
Found at i:45456 original size:18 final size:18
Alignment explanation
Indices: 45433--45471 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
45423 TTTATAAATA
45433 GATACGATAAAATTTTAG
1 GATACGATAAAATTTTAG
45451 GATACGATAAAATTTTAG
1 GATACGATAAAATTTTAG
45469 GAT
1 GAT
45472 GGGCACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (18 bp):
GATACGATAAAATTTTAG
Found at i:47215 original size:24 final size:24
Alignment explanation
Indices: 47164--47218 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
47154 GAACGTTCGG
* *
47164 TTATATTCGTTTATGTTCGTCCGC
1 TTATGTTCGTTTATGTTCGTCCAC
* *
47188 TTATGTTCGTTTATGTTCGTTCAT
1 TTATGTTCGTTTATGTTCGTCCAC
47212 TTATGTT
1 TTATGTT
47219 TAACCCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.16, T:0.56
Consensus pattern (24 bp):
TTATGTTCGTTTATGTTCGTCCAC
Found at i:48381 original size:16 final size:16
Alignment explanation
Indices: 48360--48390 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48350 CAAAAAAAAT
48360 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
48376 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
48391 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:50440 original size:33 final size:33
Alignment explanation
Indices: 50403--50470 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
50393 AAAGAAAAAT
* *
50403 TTATAATTTGAATTTTAAA-TATTTTTCTTATGA
1 TTATAATTTGAATATTAAATTATTTTT-TAATGA
50436 TTATAATTTGAATATTAAATTATTTTTTAATGA
1 TTATAATTTGAATATTAAATTATTTTTTAATGA
50469 TT
1 TT
50471 TCATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (33 bp):
TTATAATTTGAATATTAAATTATTTTTTAATGA
Found at i:50820 original size:20 final size:18
Alignment explanation
Indices: 50804--50840 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
50794 TATAACATAT
*
50804 GTATCATCTCAATAACAA
1 GTATCATATCAATAACAA
*
50822 GTATTATATCAATAACAA
1 GTATCATATCAATAACAA
50840 G
1 G
50841 CGTGAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (18 bp):
GTATCATATCAATAACAA
Found at i:52890 original size:30 final size:27
Alignment explanation
Indices: 52835--52897 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
52825 GTTGATTATT
*
52835 TAAAAATAAAAAATATATTTAAAATTA
1 TAAAAATAAAAAATATATATAAAATTA
*
52862 TAAATAATAACAAATATATAATATAAATTA
1 TAAA-AATAAAAAATATAT-ATA-AAATTA
*
52892 TTAAAA
1 TAAAAA
52898 GAACTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 13 0.43
29 4 0.13
30 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAAATAAAAAATATATATAAAATTA
Done.