Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007045.1 Hibiscus syriacus cultivar Beakdansim tig00018268_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: 64874
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4162 original size:19 final size:19
Alignment explanation
Indices: 4138--4198 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
4128 AAACCGAAAC
4138 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
*
4157 CGGTTTTTT---TAACGGTT
1 CGGTTTTTTCGGT-TCGGTT
*
4174 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
4193 CGGTTT
1 CGGTTT
4199 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTCGGTTCGGTT
Found at i:4197 original size:18 final size:18
Alignment explanation
Indices: 4142--4205 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
4132 CGAAACCGGT
4142 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
4160 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
4178 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
4196 TTTATCGGTT
1 TTTTTCGGTT
4206 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 23 0.59
19 6 0.15
21 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:6507 original size:12 final size:13
Alignment explanation
Indices: 6463--6506 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
6453 GCCCCGATTA
6463 CCCGATTACCCGC
1 CCCGATTACCCGC
6476 CCCGATTACCCGC
1 CCCGATTACCCGC
6489 CCCGA-TACCCGC
1 CCCGATTACCCGC
6501 CCCGAT
1 CCCGAT
6507 AAATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.16, C:0.55, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:6638 original size:12 final size:12
Alignment explanation
Indices: 6614--6659 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
6604 CGATTCCCAG
6614 CCCAATA-CCGA
1 CCCAATACCCGA
6625 CCCAATACCCGA
1 CCCAATACCCGA
* *
6637 CCCAATACCTGG
1 CCCAATACCCGA
6649 CCCAATACCCG
1 CCCAATACCCG
6660 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:6641 original size:23 final size:24
Alignment explanation
Indices: 6614--6659 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6604 CGATTCCCAG
6614 CCCAATACC-GACCCAATACCCGA
1 CCCAATACCTGACCCAATACCCGA
*
6637 CCCAATACCTGGCCCAATACCCG
1 CCCAATACCTGACCCAATACCCG
6660 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (24 bp):
CCCAATACCTGACCCAATACCCGA
Found at i:13104 original size:29 final size:31
Alignment explanation
Indices: 13051--13109 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
13041 GTCTTATTTT
* *
13051 TGTTTGAAATTGTATTGGTTTTTTATTAGTA
1 TGTTTAAAATTGTATTGGTTATTTATTAGTA
13082 TGTTTAAAATT-TATT-GTTATTTATTAGT
1 TGTTTAAAATTGTATTGGTTATTTATTAGT
13110 TGAAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 4 0.15
31 10 0.38
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.59
Consensus pattern (31 bp):
TGTTTAAAATTGTATTGGTTATTTATTAGTA
Found at i:15390 original size:44 final size:44
Alignment explanation
Indices: 15340--15439 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
15330 CAACTCAACG
** * **
15340 GTATCGATATTGTCCAAG-GAATATCGATACTACTCTATGCAGTA
1 GTATCGATACCGTCC-AGTGAATATCGATACTACTATATAAAGTA
* *
15384 GTATCGATACCGTCCAGTGAGTATCGATACTACTATGTAAAGTA
1 GTATCGATACCGTCCAGTGAATATCGATACTACTATATAAAGTA
15428 GTATCGATACCG
1 GTATCGATACCG
15440 AACATGGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.04
44 46 0.96
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
GTATCGATACCGTCCAGTGAATATCGATACTACTATATAAAGTA
Found at i:21049 original size:28 final size:28
Alignment explanation
Indices: 21013--21073 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
21003 AATTATGGCT
21013 AATCCCATTTGAATTACAAAAATCAGTA
1 AATCCCATTTGAATTACAAAAATCAGTA
*
21041 AATCTCATTTGAATTACAAAAATCAGTA
1 AATCCCATTTGAATTACAAAAATCAGTA
21069 AATCC
1 AATCC
21074 AAGATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.30
Consensus pattern (28 bp):
AATCCCATTTGAATTACAAAAATCAGTA
Found at i:22324 original size:20 final size:21
Alignment explanation
Indices: 22286--22324 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22276 TTTTTCTTCA
* *
22286 AAATCTTTTATTTTGACTTGC
1 AAATCTTTAATCTTGACTTGC
22307 AAATCTTTAATCTT-ACTT
1 AAATCTTTAATCTTGACTT
22325 TCGAGTTCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (21 bp):
AAATCTTTAATCTTGACTTGC
Found at i:24348 original size:24 final size:24
Alignment explanation
Indices: 24321--24399 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
24311 CTGTCCAGGG
24321 AGTATCGATACTACTCTGTGCAGT
1 AGTATCGATACTACTCTGTGCAGT
*
24345 AGTATCG--A-TAC-C-GTCCAGT
1 AGTATCGATACTACTCTGTGCAGT
* *
24364 GAGTATCGATACTACTATGTGAAGT
1 -AGTATCGATACTACTCTGTGCAGT
*
24389 AGTATCAATAC
1 AGTATCGATAC
24400 CAAACATGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 6 0.14
20 8 0.18
21 3 0.07
22 2 0.05
23 3 0.07
24 17 0.39
25 5 0.11
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (24 bp):
AGTATCGATACTACTCTGTGCAGT
Found at i:24368 original size:44 final size:44
Alignment explanation
Indices: 24302--24400 Score: 153
Period size: 44 Copynumber: 2.2 Consensus size: 44
24292 CAACTCAACG
* * *
24302 GTATCGATACTGTCCAGGGAGTATCGATACTACTCTGTGCAGTA
1 GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTGAAGTA
*
24346 GTATCGATACCGTCCAGTGAGTATCGATACTACTATGTGAAGTA
1 GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTGAAGTA
*
24390 GTATCAATACC
1 GTATCGATACC
24401 AAACATGGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
GTATCGATACCGTCCAGGGAGTATCGATACTACTATGTGAAGTA
Found at i:24370 original size:20 final size:20
Alignment explanation
Indices: 24302--24375 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
24292 CAACTCAACG
* *
24302 GTATCGATACTGTCCAGGGA
1 GTATCGATACCGTCCAGTGA
*
24322 GTATCGATACTACTCTGTGCAGT-A
1 GTATCG--A-TAC-C-GTCCAGTGA
24346 GTATCGATACCGTCCAGTGA
1 GTATCGATACCGTCCAGTGA
24366 GTATCGATAC
1 GTATCGATAC
24376 TACTATGTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 6 0.14
20 18 0.41
21 3 0.07
22 2 0.05
23 3 0.07
24 7 0.16
25 5 0.11
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (20 bp):
GTATCGATACCGTCCAGTGA
Found at i:24770 original size:18 final size:18
Alignment explanation
Indices: 24749--24801 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
24739 CTAATAATTG
* *
24749 AATCGAATATAATATTTA
1 AATCGAATATAAAATCTA
24767 AATCGAATATAAAATCTA
1 AATCGAATATAAAATCTA
*
24785 AATAGAATATAAAATCT
1 AATCGAATATAAAATCT
24802 TAAAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (18 bp):
AATCGAATATAAAATCTA
Found at i:26562 original size:2 final size:2
Alignment explanation
Indices: 26555--26586 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26545 ATACTACATC
*
26555 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26587 CGAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27118 original size:22 final size:22
Alignment explanation
Indices: 27088--27135 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
27078 ATGGCATGGC
* *
27088 CCCTGCACCGACCTAGCCCCTG
1 CCCTACACCCACCTAGCCCCTG
27110 CCCTACACCCACCTAGCCCCTG
1 CCCTACACCCACCTAGCCCCTG
27132 CCCT
1 CCCT
27136 GCCCTGCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.58, G:0.12, T:0.15
Consensus pattern (22 bp):
CCCTACACCCACCTAGCCCCTG
Found at i:28066 original size:26 final size:24
Alignment explanation
Indices: 28016--28066 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
28006 AGTTCTATTT
*
28016 AATATATATATAATTTTTTGAAAA
1 AATATATATATAATGTTTTGAAAA
28040 AATATATATAATATATAGTTTTGAAAA
1 AATATATAT-ATA-AT-GTTTTGAAAA
28067 CATTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 2 0.09
27 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (24 bp):
AATATATATATAATGTTTTGAAAA
Found at i:28108 original size:37 final size:37
Alignment explanation
Indices: 28038--28576 Score: 681
Period size: 37 Copynumber: 14.4 Consensus size: 37
28028 ATTTTTTGAA
28038 AAAATATATATAATATATAG-TTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
28074 AAAACATATATAATATATAATTTTTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
28111 AAAATACATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
28148 AAAATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
28185 AAAATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
28222 AATATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
28259 AAAATATATATAATATATAGTTTCTGAAAATATGTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
28296 AAAAAATATATTTAATATATAATTTTTGAAAACATTTTG
1 --AAAATATATATAATATATAGTTTTTGAAAACATTTTG
*
28335 AAAATATATATATAATATATAATTTTTGAAAACATTTTG
1 -AAA-ATATATATAATATATAGTTTTTGAAAACATTTTG
* *
28374 AATATATGTATAATATATATAGTTTTTGAAAACATTTTG
1 AAAATATATAT-A-ATATATAGTTTTTGAAAACATTTTG
* **
28413 AAAATATATATAATATATAGTTTTTAAAAACATTTCA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
28450 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
*
28487 AAAATATAT-TTATAATATAGTTTTTGAAAACATTTT-
1 AAAATATATATAAT-ATATAGTTTTTGAAAACATTTTG
** * * * **
28523 TTAACATATATAATAT-TTGGTTTTGAAAGTATTTTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACA-TTTT-G
28561 AAAATATATATAATAT
1 AAAATATATATAATAT
28577 CATTTTTTAA
Statistics
Matches: 450, Mismatches: 42, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
35 11 0.02
36 33 0.07
37 287 0.64
38 21 0.05
39 98 0.22
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTGAAAACATTTTG
Found at i:28624 original size:22 final size:21
Alignment explanation
Indices: 28599--28653 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
28589 TATAATGCCA
28599 TTTTATTTATTTATTTTCATTT
1 TTTTATTTATTTATTTTC-TTT
*
28621 TTTTATTTATCTATTTTCTTT
1 TTTTATTTATTTATTTTCTTT
*
28642 TTTTCTTT-TTTA
1 TTTTATTTATTTA
28654 GGGATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 3 0.10
21 10 0.33
22 17 0.57
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTTATTTATTTTCTTT
Found at i:30609 original size:2 final size:2
Alignment explanation
Indices: 30597--30640 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
30587 TGTGAACAAG
30597 AT AT GAT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30639 AT
1 AT
30641 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30879 original size:22 final size:22
Alignment explanation
Indices: 30851--30994 Score: 243
Period size: 22 Copynumber: 6.5 Consensus size: 22
30841 CAAGAATCGA
*
30851 GGGACATATACAGTGGTTATTC
1 GGGACATATACAGTGGTCATTC
30873 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
30895 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
*
30917 GGGACATATACAGTGGTCCTTC
1 GGGACATATACAGTGGTCATTC
* * *
30939 GAGACATATACAATGGTCCTTC
1 GGGACATATACAGTGGTCATTC
30961 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
30983 GGGACATATACA
1 GGGACATATACA
30995 TAAATTTCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 115 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (22 bp):
GGGACATATACAGTGGTCATTC
Found at i:43740 original size:2 final size:2
Alignment explanation
Indices: 43733--43782 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
43723 TGTACATTAG
43733 AT AT AT AT AT AT 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 AT AT AT AT AT AT
43775 AT AT AT AT
1 AT AT AT AT
43783 CATCCCTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44419 original size:45 final size:45
Alignment explanation
Indices: 44389--44603 Score: 270
Period size: 45 Copynumber: 4.8 Consensus size: 45
44379 ACTCTAACGT
* *
44389 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * *
44434 CTTTTATGTTGATAATGTACCCATATACATCTCAAC-CATAATATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* ** * *
44479 ATTTTCTGTTGATAATATACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* **
44524 CTTTTCTATTGATAATGCATACATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
44569 CTTTTCTGTTGATAATGCACCCATATGCATCTCAA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAA
44604 ATCTGGCATC
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 143 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:44639 original size:90 final size:87
Alignment explanation
Indices: 44389--44644 Score: 235
Period size: 90 Copynumber: 2.8 Consensus size: 87
44379 ACTCTAACGT
* * * * *
44389 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCA---TGATAATGTAC
* *
44454 CCATATACATCTCAACCATAATATA
63 CCATATGCATTTCAACCATAATATA
* ** * * * *
44479 ATTTTCTGTTGATAATATACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGCAT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT-CCTTTC-A-TGATAATGTAC
* *
44544 ACATATGCATTTCAACTC-TAGTATA
63 CCATATGCATTTCAAC-CATAATATA
* * * *
44569 CTTTTCTGTTGATAATGCACCCATATGCATCTCAAATCTGGCATCCTTTCATGCCAATAATTTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATG---ATAATGTAC
44634 CCATATGCATT
63 CCATATGCATT
44645 ATTCTGTTAT
Statistics
Matches: 132, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
87 2 0.02
88 1 0.01
89 5 0.04
90 119 0.90
91 4 0.03
92 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (87 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGATAATGTACCCA
TATGCATTTCAACCATAATATA
Found at i:48235 original size:99 final size:99
Alignment explanation
Indices: 48051--48240 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 99
48041 TTATAATATT
* * *
48051 ATATGTATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAATAGCCCCGTCTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAACAGCCCAGTCTTTATGG
48116 ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
* * * * * *
48150 ATATATATGCAATAAATCTTTAGCTGTCTCTCTAGAGCAATTGGTTAAACATCCCAG-CTTTATG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTT-AACAGCCCAGTCTTTATG
* *
48214 GATAAGATTTAGCTAGCCTGATAAAGG
65 GATAAGATTCAGCTAGACTGATAAAGG
48241 CAAATTACAA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 72 0.91
100 7 0.09
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAACAGCCCAGTCTTTATGG
ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
Found at i:56850 original size:20 final size:20
Alignment explanation
Indices: 56825--56864 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56815 TTTTGAAACA
*
56825 TTTTGAAAAAATATATATAT
1 TTTTGAAAAAATATACATAT
*
56845 TTTTGAAAATATATACATAT
1 TTTTGAAAAAATATACATAT
56865 ATAGTCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTGAAAAAATATACATAT
Found at i:56882 original size:55 final size:57
Alignment explanation
Indices: 56778--56896 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 57
56768 TATTTAATAT
* * * *
56778 ATATAAATTTTTTTGAATATATATATATATATATAGTTTTTGAAACATTTTGAAAAA
1 ATATATATATTTTTGAATATATATATACATATATAGTTCTTGAAACATTTTGAAAAA
*
56835 ATATATATATTTTTGAA-A-ATATATACATATATAG-TCTTGAAAACATTTTGAAAAT
1 ATATATATATTTTTGAATATATATATACATATATAGTTCTTG-AAACATTTTGAAAAA
56890 ATATATA
1 ATATATA
56897 ATATATAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 4 0.07
55 36 0.64
56 1 0.02
57 15 0.27
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (57 bp):
ATATATATATTTTTGAATATATATATACATATATAGTTCTTGAAACATTTTGAAAAA
Found at i:56964 original size:38 final size:37
Alignment explanation
Indices: 56845--57051 Score: 237
Period size: 36 Copynumber: 5.6 Consensus size: 37
56835 ATATATATAT
* *
56845 TTTTGAAAATATATA-CATATATAG-TCTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
56880 TTTTGAAAATATATATAATATATAGTTTTTGAAAAC-
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
56916 TTTTCAAAAATATATATAATATATAGTTTTTTGAAAACA
1 TTTT-GAAAATATATATAATATATAG-TTTTTGAAAACA
*
56955 TTTTGAAAATATATATATAATATATAGTTTTTGTAAACA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
* * * *
56994 TTTTTG--AACACATATAATATAT-GGTTTTGAAAGCA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
57029 TTTTTTGAAAATATATATAATAT
1 --TTTTGAAAATATATATAATAT
57052 CATTTTAAAA
Statistics
Matches: 149, Mismatches: 12, Indels: 19
0.83 0.07 0.11
Matches are distributed among these distances:
35 25 0.17
36 31 0.21
37 30 0.20
38 23 0.15
39 18 0.12
40 22 0.15
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:57082 original size:4 final size:4
Alignment explanation
Indices: 57073--57117 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
57063 ATATATACAT
* *
57073 TTTA TTTA TTTCT TTTCA TTTA TTTA TTTA TTTA TTTA TTCA TTT
1 TTTA TTTA TTT-A TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTT
57118 TTATTTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
4 29 0.81
5 7 0.19
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:58463 original size:5 final size:5
Alignment explanation
Indices: 58455--58495 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
58445 ATTTCAACTC
* *
58455 TTTAT TTTAT TTTAT TTTAT TTTAT CTTAT TTTAT TCTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
58496 CTTTAACCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:58475 original size:15 final size:15
Alignment explanation
Indices: 58404--58495 Score: 69
Period size: 15 Copynumber: 5.9 Consensus size: 15
58394 ATTTATCCAA
*
58404 ATTTTATTTAATTTT
1 ATTTTATTTTATTTT
* *
58419 ACTTTATTTT-TTGT
1 ATTTTATTTTATTTT
* *
58433 CTTTAATATTTTATTTCA
1 ATTT--TATTTTATTT-T
58451 ACTCTTTATTTTATTTT
1 A-T-TTTATTTTATTTT
*
58468 ATTTTATTTTATCTT
1 ATTTTATTTTATTTT
*
58483 ATTTTATTCTATT
1 ATTTTATTTTATT
58496 CTTTAACCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 5 0.08
15 31 0.53
16 7 0.12
17 3 0.05
18 10 0.17
19 1 0.02
20 2 0.03
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTATTTT
Found at i:60061 original size:21 final size:21
Alignment explanation
Indices: 60027--60066 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60017 GCCCCTTCTC
*
60027 CCTCCCAGCTGCCTGCTCCTT
1 CCTCCCAGCTGCCTCCTCCTT
60048 CCTCCCACGC-GCCTCCTCC
1 CCTCCCA-GCTGCCTCCTCC
60067 GCCTTCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.05, C:0.60, G:0.12, T:0.23
Consensus pattern (21 bp):
CCTCCCAGCTGCCTCCTCCTT
Found at i:60831 original size:30 final size:29
Alignment explanation
Indices: 60795--60857 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
60785 TTAAAAGAGA
60795 AAAATATAATATAATGAAATAAAATAAAAT
1 AAAATATAATATAATGAAA-AAAATAAAAT
* *
60825 AAAATATAATATAATGAAAAAACTAAATT
1 AAAATATAATATAATGAAAAAAATAAAAT
60854 AAAA
1 AAAA
60858 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATATAATATAATGAAAAAAATAAAAT
Found at i:61726 original size:36 final size:38
Alignment explanation
Indices: 61656--61726 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
61646 TTTGCTTGGT
* *
61656 TTGCTGTTAGGATTTTCTTGGTTTTTTGTGGTGTTCGG
1 TTGCTGTTAGGATTTTCTGGGTTTTTGGTGGTGTTCGG
61694 TTGCTGTT-GGTATTTT-TGGGTTTTTGGT-GTGTT
1 TTGCTGTTAGG-ATTTTCTGGGTTTTTGGTGGTGTT
61727 GTGTTTGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 5 0.17
37 12 0.40
38 13 0.43
ACGTcount: A:0.04, C:0.06, G:0.32, T:0.58
Consensus pattern (38 bp):
TTGCTGTTAGGATTTTCTGGGTTTTTGGTGGTGTTCGG
Found at i:62130 original size:16 final size:16
Alignment explanation
Indices: 62109--62165 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 16
62099 ACCTATTCCA
62109 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
62125 AAATAAAAAATGAAATAAAT
1 AAAT-AAAAAT--AA-AAAT
62145 AAAT-AAAAT-AAAAT
1 AAATAAAAATAAAAAT
62159 -AATAAAA
1 AAATAAAA
62166 TGTAATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.08
14 7 0.19
15 1 0.03
16 4 0.11
17 6 0.17
18 5 0.14
19 2 0.06
20 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:62153 original size:13 final size:12
Alignment explanation
Indices: 62108--62166 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 12
62098 GACCTATTCC
62108 AAAATAAAA-ATA
1 AAAATAAAATA-A
62120 AAAAT-AAATAA
1 AAAATAAAATAA
*
62131 AAAATGAAATAA
1 AAAATAAAATAA
62143 ATAAATAAAATAA
1 A-AAATAAAATAA
62156 AATAATAAAAT
1 AA-AATAAAAT
62167 GTAATAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 9 0.21
12 14 0.33
13 19 0.45
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:62172 original size:13 final size:13
Alignment explanation
Indices: 62114--62176 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
62104 TTCCAAAATA
62114 AAAAT-AAA-AAT
1 AAAATAAAATAAT
62125 -AAATAAAA-AAT
1 AAAATAAAATAAT
*
62136 GAAAT-AAATAAAT
1 AAAATAAAAT-AAT
62149 AAAATAAAATAAT
1 AAAATAAAATAAT
**
62162 AAAATGTAATAAT
1 AAAATAAAATAAT
62175 AA
1 AA
62177 CAACTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.09
11 9 0.20
12 4 0.09
13 23 0.52
14 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:62308 original size:35 final size:35
Alignment explanation
Indices: 62224--62587 Score: 384
Period size: 35 Copynumber: 10.4 Consensus size: 35
62214 GTTTTTTAAA
*
62224 TATATATTATACG-TTTCAAAATCA-TTTAAAAAC
1 TATATATTATACGTTTTCAAAACCATTTTAAAAAC
* * *
62257 -ATATATT-TAC-ATTTCAAAACCGTTTTGAAAAC
1 TATATATTATACGTTTTCAAAACCATTTTAAAAAC
* *
62289 TATAT-TATATATGTTTTCAAAACCGTTTTTAAAAAAC
1 TATATAT-TATACGTTTTCAAAACC-ATTTT-AAAAAC
* * *
62326 TATATATTATATGTTTTCAAAACTATTTTTAAAAC
1 TATATATTATACGTTTTCAAAACCATTTTAAAAAC
* *
62361 ATATATATTATACGTTTTCCAAACTATTTTAAAAAAC
1 -TATATATTATACGTTTTCAAAACCATTTT-AAAAAC
* * * *
62398 TATATACTATATGTTTTCGAAACCGTTTTAAAAAC
1 TATATATTATACGTTTTCAAAACCATTTTAAAAAC
*
62433 TATATATTATACGTTTTCAAAACTATTTTTAAAAAC
1 TATATATTATACGTTTTCAAAACCA-TTTTAAAAAC
* * *
62469 TATATATTATACATTTTCCAAACTATTTTGAAAAA-
1 TATATATTATACGTTTTCAAAACCATTTT-AAAAAC
* * * *
62504 TATATACTATATGTTTTCAAAATCGTTTTAAAAAC
1 TATATATTATACGTTTTCAAAACCATTTTAAAAAC
*
62539 TATATATTATACG-TTTCTAAAACTATTTTAAAAAC
1 TATATATTATACGTTTTC-AAAACCATTTTAAAAAC
62574 TATATATTATACGT
1 TATATATTATACGT
62588 GTTTTGCAAA
Statistics
Matches: 278, Mismatches: 37, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
31 12 0.04
32 16 0.06
33 5 0.02
34 11 0.04
35 105 0.38
36 97 0.35
37 31 0.11
38 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (35 bp):
TATATATTATACGTTTTCAAAACCATTTTAAAAAC
Found at i:62443 original size:71 final size:71
Alignment explanation
Indices: 62191--62587 Score: 399
Period size: 71 Copynumber: 5.7 Consensus size: 71
62181 TATATAGTAT
* * * **
62191 TATATTATATGTTTTCGAAAAATGTTTTTTAAA-TATATATTATACG-TTTCAAAA-TCA-TTT-
1 TATATTATACGTTTTC-AAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACT-ATTTTA
62251 AAAAAC-A
64 AAAAACTA
* ** * *
62258 TATATT-TAC-ATTTCAAAACCGTTTTGAAAACTATAT-TATATATGTTTTCAAAACCGT-TTTT
1 TATATTATACGTTTTCAAAACTATTTTAAAAACTATATAT-TATACGTTTTCAAAA-C-TATTTT
62319 AAAAAACTA
63 AAAAAACTA
* * *
62328 TATATTATATGTTTTCAAAACTATTTTTAAAACATATATATTATACGTTTTCCAAACTATTTTAA
1 TATATTATACGTTTTCAAAACTATTTTAAAAAC-TATATATTATACGTTTTCAAAACTATTTTAA
62393 AAAACTA
65 AAAACTA
* * * ** *
62400 TATACTATATGTTTTCGAAACCGTTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAA
1 TATATTATACGTTTTCAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTAAA
62465 AAACTA
66 AAACTA
* * * * *
62471 TATATTATACATTTTCCAAACTATTTTGAAAAA-TATATACTATATGTTTTCAAAA-TCGTTTT-
1 TATATTATACGTTTTCAAAACTATTTT-AAAAACTATATATTATACGTTTTCAAAACT-ATTTTA
62533 AAAAACTA
64 AAAAACTA
62541 TATATTATACG-TTTCTAAAACTATTTTAAAAACTATATATTATACGT
1 TATATTATACGTTTTC-AAAACTATTTTAAAAACTATATATTATACGT
62588 GTTTTGCAAA
Statistics
Matches: 278, Mismatches: 34, Indels: 33
0.81 0.10 0.10
Matches are distributed among these distances:
64 13 0.05
65 14 0.05
66 10 0.04
67 6 0.02
68 3 0.01
69 16 0.06
70 48 0.17
71 84 0.30
72 65 0.23
73 18 0.06
74 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (71 bp):
TATATTATACGTTTTCAAAACTATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTAAA
AAACTA
Done.