Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005272.1 Hibiscus syriacus cultivar Beakdansim tig00011920_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: 69013
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4436 original size:21 final size:22
Alignment explanation
Indices: 4387--4448 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
4377 CCCTTGAATA
*
4387 ACTAAAGTGCCTTAGCACTAAT
1 ACTAAAGTGCATTAGCACTAAT
*
4409 A-TGAAAGTGCATT-GCATTAAT
1 ACT-AAAGTGCATTAGCACTAAT
*
4430 ACTAAAGTGCCTTAGCACT
1 ACTAAAGTGCATTAGCACT
4449 GCTGAGATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (22 bp):
ACTAAAGTGCATTAGCACTAAT
Found at i:5494 original size:20 final size:22
Alignment explanation
Indices: 5448--5502 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
5438 ATACTTAGAA
* *
5448 GGTATCGGTACCATAGATTAGG
1 GGTATCGATACCATAGATGAGG
5470 GGTATCGATACCAT-GATGA-G
1 GGTATCGATACCATAGATGAGG
5490 GGTATCGATACCA
1 GGTATCGATACCA
5503 GGTTACTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
22 13 0.42
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (22 bp):
GGTATCGATACCATAGATGAGG
Found at i:5595 original size:21 final size:21
Alignment explanation
Indices: 5541--5622 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
5531 ATACATGAAG
* *
5541 GGGGTATCGATACCCTAA-TG
1 GGGGTATCGATACCATAAGTA
*
5561 GGGTAGTATTGATACCATAAGTA
1 GGG--GTATCGATACCATAAGTA
*
5584 GGGGTATCGATACCATAAGCA
1 GGGGTATCGATACCATAAGTA
5605 GGGGTATCGATACC-TAAG
1 GGGGTATCGATACCATAAG
5623 GGCTGGAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 7 0.13
21 30 0.56
22 13 0.24
23 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.24
Consensus pattern (21 bp):
GGGGTATCGATACCATAAGTA
Found at i:6068 original size:59 final size:59
Alignment explanation
Indices: 5940--6284 Score: 525
Period size: 59 Copynumber: 5.9 Consensus size: 59
5930 TACCAAAGGT
*
5940 CACTTTGTGTGCTAAAATTGTAAGGAAATCATACTA--TGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
* *
5997 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCTAGACAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
* *
6056 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAGTTTCCAGATGGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
**
6115 CACTTTGTGTGCTAAAATATTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
*
6174 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
* ** ** * *
6233 AACACTGTGTGCTAAAA-GGATAAGGAAATCATACCGTTTGTATGAAATTCCA
1 CACTTTGTGTGCTAAAATGG-TAAGGAAATCATACTATGTGTATGAATTTCCA
6285 ATTGAATTTA
Statistics
Matches: 263, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
57 35 0.13
58 2 0.01
59 226 0.86
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (59 bp):
CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGATAGGG
Found at i:12553 original size:21 final size:20
Alignment explanation
Indices: 12497--12558 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
12487 TGATACATAA
*
12497 AGGGGTATCGATACCCTAA-T
1 AGGGATATCGATA-CCTAAGT
* *
12517 GGGGTAGTATCAATACCATAAGT
1 AGGG-A-TATCGATACC-TAAGT
12540 AGGGATATCGATACCTAAG
1 AGGGATATCGATACCTAAG
12559 GGTTGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.21
21 11 0.33
22 11 0.33
23 4 0.12
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (20 bp):
AGGGATATCGATACCTAAGT
Found at i:12604 original size:19 final size:19
Alignment explanation
Indices: 12580--12626 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
12570 TTAAGTTAGG
12580 GCTGATAATGTTATAGGAA
1 GCTGATAATGTTATAGGAA
12599 GCTGATAATGTTATAGGAA
1 GCTGATAATGTTATAGGAA
*
12618 GTTGATAAT
1 GCTGATAAT
12627 AAATATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (19 bp):
GCTGATAATGTTATAGGAA
Found at i:12975 original size:59 final size:59
Alignment explanation
Indices: 12891--13241 Score: 524
Period size: 59 Copynumber: 5.9 Consensus size: 59
12881 GAATTACCAA
* * * *
12891 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTATGTCTATGAATTTCCATAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
* * * *
12950 AGGGAACTTTATGTGCTAAACTGGTAAGGAAATCATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
* *
13009 AGGGAACTTTGTGTGCTAAAATGGTAAGAAAATTATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
* *
13068 AGGGCACTTTGTGTGCTAAAATTGTAAGAAAATCATACTATGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
*
13127 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
* * * * *
13186 AGGGCACTCTGTGTGCTAAAA-GGATAAGGAAATCATACTGTTTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGG-TAAGAAAATCATACTATGTGTATGAATTTCCA
13242 ATTGAATTTA
Statistics
Matches: 268, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 2 0.01
59 266 0.99
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTATGTGTATGAATTTCCAGAT
Found at i:15275 original size:11 final size:12
Alignment explanation
Indices: 15254--15301 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
15244 GGATATCCGA
15254 TTATA-TTTATT
1 TTATATTTTATT
15265 TT-TATTTTATT
1 TTATATTTTATT
*
15276 TTAT-TTTTAAT
1 TTATATTTTATT
*
15287 TTATATTATATT
1 TTATATTTTATT
15299 TTA
1 TTA
15302 GAAAAATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 2 0.06
11 20 0.65
12 9 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATATTTTATT
Found at i:15280 original size:16 final size:16
Alignment explanation
Indices: 15254--15301 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
15244 GGATATCCGA
*
15254 TTATATTTATTTTTATT
1 TTAT-TTTATTTTTAAT
15271 TTATTTTATTTTTAAT
1 TTATTTTATTTTTAAT
*
15287 TTATATTATATTTTA
1 TTATTTTAT-TTTTA
15302 GAAAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTATTTTTAAT
Found at i:16838 original size:7 final size:7
Alignment explanation
Indices: 16826--16850 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16816 TATTTAAACT
16826 TAAAATA
1 TAAAATA
16833 TAAAATA
1 TAAAATA
16840 TAAAATA
1 TAAAATA
16847 TAAA
1 TAAA
16851 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAATA
Found at i:19853 original size:12 final size:12
Alignment explanation
Indices: 19820--19877 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 12
19810 GTCACAACCC
19820 GACCTGACCCGTT
1 GACC-GACCCGTT
*
19833 TACCCGACCCGTT
1 GA-CCGACCCGTT
19846 GACCGACCCGTT
1 GACCGACCCGTT
19858 GACCGTTGACCCGTT
1 GACC---GACCCGTT
19873 GACCG
1 GACCG
19878 GAGTTGACCA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 15 0.38
13 10 0.26
14 2 0.05
15 12 0.31
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.21
Consensus pattern (12 bp):
GACCGACCCGTT
Found at i:19870 original size:15 final size:13
Alignment explanation
Indices: 19820--19879 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
19810 GTCACAACCC
*
19820 GACCTGACCCGTT
1 GACCGGACCCGTT
* *
19833 TACCCGACCCGTT
1 GACCGGACCCGTT
19846 GACC-GACCCGTT
1 GACCGGACCCGTT
19858 GACCGTTGACCCGTT
1 GACCG--GACCCGTT
19873 GACCGGA
1 GACCGGA
19880 GTTGACCACT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 12 0.29
13 16 0.39
15 13 0.32
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (13 bp):
GACCGGACCCGTT
Found at i:22361 original size:48 final size:48
Alignment explanation
Indices: 22309--22440 Score: 128
Period size: 48 Copynumber: 2.8 Consensus size: 48
22299 AATATTTTAC
*
22309 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
22357 CTGA-TATCTGACATGGA-TTCTAATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
22405 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
22441 CTGATTTATG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
47 5 0.07
48 58 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:22447 original size:24 final size:24
Alignment explanation
Indices: 22326--22440 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
22316 TCGATTTGAT
22326 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
22350 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
22374 TTCTAATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
22398 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
22421 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
22441 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:24583 original size:9 final size:9
Alignment explanation
Indices: 24569--24616 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
24559 AAGGTAAAAG
24569 TGACCGGTT
1 TGACCGGTT
24578 TGACCGGTTT
1 TGACCGG-TT
* *
24588 TGGAACTGTTT
1 T-G-ACCGGTT
24599 TGACCGGTT
1 TGACCGGTT
24608 TGACCGGTT
1 TGACCGGTT
24617 ACAACCCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 21 0.66
10 4 0.12
11 4 0.12
12 3 0.09
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (9 bp):
TGACCGGTT
Found at i:24647 original size:13 final size:13
Alignment explanation
Indices: 24624--24658 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24614 GTTACAACCC
*
24624 GACCTGACCCGTT
1 GACCCGACCCGTT
*
24637 TACCCGACCCGTT
1 GACCCGACCCGTT
24650 GACCCGACC
1 GACCCGACC
24659 TGACCCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:24653 original size:8 final size:8
Alignment explanation
Indices: 24642--24686 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
24632 CCGTTTACCC
24642 GACCCGTT
1 GACCCGTT
*
24650 GACCCGACCT
1 GACCCG--TT
24660 GACCCGTT
1 GACCCGTT
24668 GA-CCGTT
1 GACCCGTT
24675 GACCCGTT
1 GACCCGTT
24683 GACC
1 GACC
24687 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 7 0.22
8 18 0.56
10 7 0.22
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:24658 original size:31 final size:32
Alignment explanation
Indices: 24620--24686 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
24610 ACCGGTTACA
*
24620 ACCCGACCTGACCCGTTTACC-CGACCCGTTG
1 ACCCGACCTGACCCGTTGACCGCGACCCGTTG
*
24651 ACCCGACCTGACCCGTTGACCGTTGACCCGTTG
1 ACCCGACCTGACCCGTTGACCG-CGACCCGTTG
24684 ACC
1 ACC
24687 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.62
33 12 0.38
ACGTcount: A:0.16, C:0.43, G:0.21, T:0.19
Consensus pattern (32 bp):
ACCCGACCTGACCCGTTGACCGCGACCCGTTG
Found at i:24679 original size:15 final size:15
Alignment explanation
Indices: 24659--24687 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24649 TGACCCGACC
24659 TGACCCGTTGACCGT
1 TGACCCGTTGACCGT
24674 TGACCCGTTGACCG
1 TGACCCGTTGACCG
24688 GAGTTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (15 bp):
TGACCCGTTGACCGT
Found at i:24696 original size:33 final size:35
Alignment explanation
Indices: 24642--24706 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
24632 CCGTTTACCC
24642 GACCCGTTGACCCGACCTGACC-C-GTTGACCGTT
1 GACCCGTTGACCCGACCTGACCACTGTTGACCGTT
* **
24675 GACCCGTTGACCGGAGTTGACCACTGTTGACC
1 GACCCGTTGACCCGACCTGACCACTGTTGACC
24707 AAAACTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 19 0.70
34 1 0.04
35 7 0.26
ACGTcount: A:0.17, C:0.35, G:0.26, T:0.22
Consensus pattern (35 bp):
GACCCGTTGACCCGACCTGACCACTGTTGACCGTT
Found at i:27171 original size:48 final size:48
Alignment explanation
Indices: 27119--27250 Score: 128
Period size: 48 Copynumber: 2.8 Consensus size: 48
27109 AATATTTTAC
*
27119 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
27167 CTGA-TATCTGACATGGA-TTCTAATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
27215 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
27251 CTGATTTATG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
47 5 0.07
48 58 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:27257 original size:24 final size:24
Alignment explanation
Indices: 27136--27250 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
27126 TCGATTTGAT
27136 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
27160 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
27184 TTCTAATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
27208 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
27231 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
27251 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:29702 original size:15 final size:16
Alignment explanation
Indices: 29671--29701 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29661 CTATATATCC
29671 TAATAGTTTTATAAAA
1 TAATAGTTTTATAAAA
*
29687 TAATATTTTTATAAA
1 TAATAGTTTTATAAA
29702 TCAAATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATAGTTTTATAAAA
Found at i:38837 original size:3 final size:3
Alignment explanation
Indices: 38829--38874 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
38819 GGAATTCCAA
38829 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38875 TTTTGGGACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42360 original size:20 final size:20
Alignment explanation
Indices: 42335--42384 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
42325 CTTTCAAAGG
42335 GTATCGATACTC-G-GGGTCCA
1 GTATCGATACTCAGAGGGT--A
42355 GTATCGATACTCAGAGGGTA
1 GTATCGATACTCAGAGGGTA
42375 GTATCGATAC
1 GTATCGATAC
42385 CATTAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 23 0.82
21 1 0.04
22 4 0.14
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCAGAGGGTA
Found at i:42447 original size:18 final size:19
Alignment explanation
Indices: 42424--42467 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42414 ATTTTGGTAC
*
42424 CGATACTCAAGGG-AGTAT
1 CGATACTCAAGGGAAATAT
42442 CGATAC-CAAGGGTAAATAT
1 CGATACTCAAGGG-AAATAT
42461 CGATACT
1 CGATACT
42468 ACTGGAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (19 bp):
CGATACTCAAGGGAAATAT
Found at i:42830 original size:89 final size:89
Alignment explanation
Indices: 42679--42858 Score: 324
Period size: 89 Copynumber: 2.0 Consensus size: 89
42669 TTTAGGAAAT
42679 GTTGGGAGTCACCACCAACCATTTTAAGGTGTGATTGGAACACCATAAAATCGGGTAATTTTAAT
1 GTTGGGAGTCACCACCAACCATTTTAAGGTGTGATTGGAACACCATAAAATCGGGTAATTTTAAT
* *
42744 AAAATGTTTTATTTTTATCAAAAC
66 AAAATATTTTAATTTTATCAAAAC
* *
42768 GTTGGGAGTCACCACCAACCATTTTAAGGTGTGATTGGAACATCATAAAATTGGGTAATTTTAAT
1 GTTGGGAGTCACCACCAACCATTTTAAGGTGTGATTGGAACACCATAAAATCGGGTAATTTTAAT
42833 AAAATATTTTAATTTTATCAAAAC
66 AAAATATTTTAATTTTATCAAAAC
42857 GT
1 GT
42859 CAGGTTTAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (89 bp):
GTTGGGAGTCACCACCAACCATTTTAAGGTGTGATTGGAACACCATAAAATCGGGTAATTTTAAT
AAAATATTTTAATTTTATCAAAAC
Found at i:43622 original size:20 final size:20
Alignment explanation
Indices: 43597--43647 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43587 ATGTGAAAAG
*
43597 TCTAAAGCTAAGGGACTAAA
1 TCTAAAACTAAGGGACTAAA
*
43617 TCTAAAATTAAGGGACTAAA
1 TCTAAAACTAAGGGACTAAA
* *
43637 CCTATAACTAA
1 TCTAAAACTAA
43648 AGGTTCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.24
Consensus pattern (20 bp):
TCTAAAACTAAGGGACTAAA
Found at i:43943 original size:13 final size:13
Alignment explanation
Indices: 43924--43970 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
43914 TTAAATAATC
43924 TAATTAAAATAAA
1 TAATTAAAATAAA
43937 -AATTTAAAATAAA
1 TAA-TTAAAATAAA
*
43950 TAAATAAAATAAA
1 TAATTAAAATAAA
*
43963 TAAATAAA
1 TAATTAAA
43971 CAAAGCTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATTAAAATAAA
Found at i:44224 original size:17 final size:16
Alignment explanation
Indices: 44204--44246 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
44194 TAATTACATG
44204 AATTAAACT-AATGACTA
1 AATTAAA-TAAATG-CTA
44221 AATTGAAATAAATGCTA
1 AATT-AAATAAATGCTA
44238 AATTAAATA
1 AATTAAATA
44247 TGAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 7 0.29
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (16 bp):
AATTAAATAAATGCTA
Found at i:48101 original size:19 final size:19
Alignment explanation
Indices: 48077--48128 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
48067 AGTGCATTTG
48077 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
48096 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
48115 ATGCATCGATGCAC
1 ATGCATCGATGCAC
48129 TCTGGCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:52201 original size:20 final size:20
Alignment explanation
Indices: 52172--52233 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
52162 ATGCAAAATG
*
52172 AGTATTGATACTGCTACAGT
1 AGTATCGATACTGCTACAGT
*
52192 AGTATCGATACTGCTGCAGT
1 AGTATCGATACTGCTACAGT
52212 AGTATCGATACTGCTACAGT
1 AGTATCGATACTGCTACAGT
52232 AG
1 AG
52234 AATCAAGCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTGCTACAGT
Found at i:54313 original size:27 final size:25
Alignment explanation
Indices: 54259--54330 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 25
54249 TAAATTATAA
*
54259 TTTT-AAAATTATATATTATATATG
1 TTTTAAAAACTATATATTATATATG
54283 TTTTAAAAAACTATATATATATATATG
1 TTTT-AAAAACTATATAT-TATATATG
*
54310 TTTTCAAAACTATATATTATA
1 TTTTAAAAACTATATATTATA
54331 ATTTGAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 4 0.09
25 4 0.09
26 23 0.53
27 12 0.28
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (25 bp):
TTTTAAAAACTATATATTATATATG
Found at i:54325 original size:20 final size:20
Alignment explanation
Indices: 54300--54354 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
54290 AAACTATATA
54300 TATATATATGTTTTCAAAAC
1 TATATATATGTTTTCAAAAC
** * *
54320 TATATATTATAATTTGAAAAT
1 TATATA-TATGTTTTCAAAAC
*
54341 TACATATATGTTTT
1 TATATATATGTTTT
54355 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TATATATATGTTTTCAAAAC
Found at i:54482 original size:21 final size:21
Alignment explanation
Indices: 54369--54484 Score: 65
Period size: 21 Copynumber: 5.4 Consensus size: 21
54359 TTTTAAAAAG
* *
54369 AACTATATATCATAATTTCAA
1 AACTATATTTTATAATTTCAA
* ** *
54390 GAA-TATATTATATGTTTTGAA
1 -AACTATATTTTATAATTTCAA
* *
54411 AACTATATATTA-AAGTTCCAA
1 AACTATATTTTATAA-TTTCAA
* * * *
54432 AACTATATATATGTACATGTTTAG
1 AACTATAT-TTTATA-AT-TTCAA
54456 AACTATATTTTATAATTTCAA
1 AACTATATTTTATAATTTCAA
54477 AACTATAT
1 AACTATAT
54485 ATATATATAT
Statistics
Matches: 66, Mismatches: 22, Indels: 13
0.65 0.22 0.13
Matches are distributed among these distances:
20 2 0.03
21 42 0.64
22 5 0.08
23 6 0.09
24 11 0.17
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.41
Consensus pattern (21 bp):
AACTATATTTTATAATTTCAA
Found at i:54511 original size:22 final size:22
Alignment explanation
Indices: 54486--54542 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
54476 AAACTATATA
54486 TATATATATATATATTAAAACC-
1 TATAT-TATATATATTAAAACCG
*
54508 TATATGT-TATAATTTTAAAACCG
1 TATAT-TATAT-ATATTAAAACCG
54531 TATATTATATAT
1 TATATTATATAT
54543 GTTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 3 0.10
22 19 0.63
23 8 0.27
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATTATATATATTAAAACCG
Found at i:55531 original size:20 final size:18
Alignment explanation
Indices: 55503--55547 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55493 TCCTAATTTT
*
55503 GTTTGTGTTCAAATTCTAGG
1 GTTTATGTTCAAA-T-TAGG
*
55523 GTTTATGTTCACATTAGG
1 GTTTATGTTCAAATTAGG
55541 GTTTATG
1 GTTTATG
55548 GAATTGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47
Consensus pattern (18 bp):
GTTTATGTTCAAATTAGG
Found at i:57548 original size:59 final size:59
Alignment explanation
Indices: 57471--57658 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 59
57461 TGCATATTTA
* * *
57471 GGATTGCACTAAAGTATAACTAGTGCATATGGTAGGCATGACCTTATGTGTCATATTCG
1 GGATTACACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCG
* * * *
57530 GGATTACACTAAAGTATAACTAGTCCGTATGGTGGGCACGACCTTATGTGTCATGTTCA
1 GGATTACACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCG
* * * * * * * *
57589 GAACTGCACTAATGTATAACTAGTGTAGATTGTGGGCACGACCTTATGTGTCATACTCG
1 GGATTACACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCG
57648 GG-TTAGCACTA
1 GGATTA-CACTA
57659 CAATGCATAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
58 1 0.01
59 105 0.99
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (59 bp):
GGATTACACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCG
Found at i:58930 original size:16 final size:16
Alignment explanation
Indices: 58905--58958 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
58895 CATAAACTGA
*
58905 ATATATACACACACAC
1 ATATAGACACACACAC
58921 ATATAGACACACAAACAC
1 ATATAGACACAC--ACAC
*
58939 ATACATGCACACACACAC
1 ATATA-G-ACACACACAC
58957 AT
1 AT
58959 TTATAGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 11 0.34
18 14 0.44
19 1 0.03
20 6 0.19
ACGTcount: A:0.50, C:0.31, G:0.04, T:0.15
Consensus pattern (16 bp):
ATATAGACACACACAC
Found at i:63172 original size:15 final size:15
Alignment explanation
Indices: 63152--63180 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
63142 AATTTTGCTT
63152 CTTTTTTTTCTTTTC
1 CTTTTTTTTCTTTTC
63167 CTTTTTTTTCTTTT
1 CTTTTTTTTCTTTT
63181 TGTTTGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTCTTTTC
Found at i:64194 original size:18 final size:18
Alignment explanation
Indices: 64171--64233 Score: 117
Period size: 18 Copynumber: 3.5 Consensus size: 18
64161 TTTCCTAAAC
64171 TAGAAGTGGTGTTGAGTT
1 TAGAAGTGGTGTTGAGTT
64189 TAGAAGTGGTGTTGAGTT
1 TAGAAGTGGTGTTGAGTT
64207 TAGAAGTGGTGTTGAGTT
1 TAGAAGTGGTGTTGAGTT
*
64225 TAGACGTGG
1 TAGAAGTGG
64234 GAACGTCGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.37
Consensus pattern (18 bp):
TAGAAGTGGTGTTGAGTT
Done.