Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003821.1 Hibiscus syriacus cultivar Beakdansim tig00008195_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: 64185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:12995 original size:19 final size:18
Alignment explanation
Indices: 12971--13028 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
12961 TTAGAAAATT
12971 ATTACTCCTCCTTACTATA
1 ATTACTCC-CCTTACTATA
12990 ATTACTTCCCCTTACTATA
1 ATTAC-TCCCCTTACTATA
13009 ATTACTCCCCTTTACTATA
1 ATTACTCCCC-TTACTATA
13028 A
1 A
13029 CACTTCTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.14
19 29 0.78
20 3 0.08
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTACTCCCCTTACTATA
Found at i:13307 original size:19 final size:19
Alignment explanation
Indices: 13279--13328 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 19
13269 AACATTTAAG
13279 TTCAAACATCCAAAACAAA
1 TTCAAACATCCAAAACAAA
*
13298 TTCAACCATCC---ACAAA
1 TTCAAACATCCAAAACAAA
13314 TTCAAACATCCAAAA
1 TTCAAACATCCAAAA
13329 TGTTAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 15 0.58
19 11 0.42
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (19 bp):
TTCAAACATCCAAAACAAA
Found at i:15312 original size:23 final size:23
Alignment explanation
Indices: 15258--15335 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
15248 CTGAACCCGT
* *
15258 GGAGGGTATCGATACCC--TCAC
1 GGAGGGTATCGGTACCCATTCAA
*
15279 GTGGGGGTATCGGTACCCATTCAA
1 G-GAGGGTATCGGTACCCATTCAA
*
15303 GGAGGGTATCGGTACCCATTTAAA
1 GGAGGGTATCGGTACCCA-TTCAA
15327 GG-GGGTATC
1 GGAGGGTATC
15336 AATACCTCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.02
22 14 0.29
23 23 0.48
24 10 0.21
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (23 bp):
GGAGGGTATCGGTACCCATTCAA
Found at i:15341 original size:23 final size:22
Alignment explanation
Indices: 15281--15335 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 22
15271 ACCCTCACGT
*
15281 GGGGGTATCGGTACCCATTCAA
1 GGGGGTATCGGTACCCATTAAA
15303 GGAGGGTATCGGTACCCATTTAAA
1 GG-GGGTATCGGTACCCA-TTAAA
15327 GGGGGTATC
1 GGGGGTATC
15336 AATACCTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.73
24 6 0.20
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (22 bp):
GGGGGTATCGGTACCCATTAAA
Found at i:19120 original size:21 final size:21
Alignment explanation
Indices: 19079--19117 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19069 AAGACTATTT
19079 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
*
19100 TCATTTTT-TATTTTGAAA
1 TCATTTTTCAATTTTGAAA
19118 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:21124 original size:21 final size:21
Alignment explanation
Indices: 21100--21141 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21090 ATCTTACATA
21100 GGGGTATCAGTACCCTCTGGG
1 GGGGTATCAGTACCCTCTGGG
*
21121 GGGGTATCGGTACCCTCTGGG
1 GGGGTATCAGTACCCTCTGGG
21142 CAATCTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (21 bp):
GGGGTATCAGTACCCTCTGGG
Found at i:22634 original size:35 final size:35
Alignment explanation
Indices: 22588--22662 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
22578 CACAATCATT
*
22588 AATTACATTCTAAACCCCAAAATCT-AAAATACTTC
1 AATTACATTCTAAACCCC-AAATCTCAAAACACTTC
* *
22623 AATTACATTCTAAACCTCAAATTTCAAAACACTTC
1 AATTACATTCTAAACCCCAAATCTCAAAACACTTC
22658 AATTA
1 AATTA
22663 TATGCCCAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATCTCAAAACACTTC
Found at i:22679 original size:35 final size:36
Alignment explanation
Indices: 22588--22680 Score: 91
Period size: 35 Copynumber: 2.6 Consensus size: 36
22578 CACAATCATT
* * * *
22588 AATTACATTCTAAACCCCAAA-ATCTAAAATACTTC
1 AATTACATGCCAAACCCCAAATTTCTAAAACACTTC
* * *
22623 AATTACATTCTAAACCTCAAATTTC-AAAACACTTC
1 AATTACATGCCAAACCCCAAATTTCTAAAACACTTC
* *
22658 AATTATATGCCCAACCCCAAATT
1 AATTACATGCCAAACCCCAAATT
22681 CACAATCTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 47 0.96
36 2 0.04
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (36 bp):
AATTACATGCCAAACCCCAAATTTCTAAAACACTTC
Found at i:23339 original size:29 final size:29
Alignment explanation
Indices: 23307--23440 Score: 133
Period size: 29 Copynumber: 4.6 Consensus size: 29
23297 AAGACTGAAC
* **
23307 TTTTTATAAATTATAATAAATACCAATTT
1 TTTTTATAAATTACAATAAATACCAAAAT
* * * *
23336 TTTTTGTAAATTATAATAAATATCAAAAAC
1 TTTTTATAAATTACAATAAATA-CCAAAAT
* *
23366 TTTATGTAAATTACAATAAATACCAAAAT
1 TTTTTATAAATTACAATAAATACCAAAAT
* * * *
23395 TTTCTAAAAATTACAATAAACACCAAAAC
1 TTTTTATAAATTACAATAAATACCAAAAT
*
23424 TTTTTATATATTACAAT
1 TTTTTATAAATTACAAT
23441 CAAAGGAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 64 0.74
30 23 0.26
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (29 bp):
TTTTTATAAATTACAATAAATACCAAAAT
Found at i:23406 original size:59 final size:58
Alignment explanation
Indices: 23304--23440 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 58
23294 ATCAAGACTG
* ** * ** * *
23304 AACTTTTTATAAATTATAATAAATACCAATTTTTTTTGTAAATTATAATAAATATCAAA
1 AACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACA-CAAA
* * *
23363 AACTTTATGTAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACCAA
1 AACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACAAA
*
23421 AACTTTTTATATATTACAAT
1 AACTTTTTATAAATTACAAT
23441 CAAAGGAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
58 20 0.31
59 44 0.69
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (58 bp):
AACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACAAA
Found at i:26407 original size:18 final size:17
Alignment explanation
Indices: 26368--26420 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
26358 TATGAAATTG
* *
26368 GATTTCAATTCCTGACA
1 GATTTCAATTCCTCATA
26385 GATTTCAATTCCTTCATA
1 GATTTCAATTCC-TCATA
26403 GATTTCAATTCCCTCATA
1 GATTTCAATT-CCTCATA
26421 AACATTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 12 0.38
18 18 0.56
19 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.40
Consensus pattern (17 bp):
GATTTCAATTCCTCATA
Found at i:30247 original size:26 final size:26
Alignment explanation
Indices: 30208--30258 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
30198 GATAAATCGA
* *
30208 AAAGCGAGTTGCTGCGTCTGCGTCGG
1 AAAGCGAATCGCTGCGTCTGCGTCGG
*
30234 AAAGCGAATCGCTGCGTTTGCGTCG
1 AAAGCGAATCGCTGCGTCTGCGTCG
30259 CTGCACGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (26 bp):
AAAGCGAATCGCTGCGTCTGCGTCGG
Found at i:31505 original size:3 final size:3
Alignment explanation
Indices: 31497--31531 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31487 TTTTGATGGA
31497 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
31532 CTCAAGCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31611 original size:21 final size:20
Alignment explanation
Indices: 31582--31629 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
31572 CTTAAAAGTT
31582 TTAAAATTAATTTAAAAATA
1 TTAAAATTAATTTAAAAATA
*
31602 TTAAATATT-A-TTAAAATTA
1 TTAAA-ATTAATTTAAAAATA
31621 -TAAAATTAA
1 TTAAAATTAA
31630 AAAGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 5 0.20
19 8 0.32
20 6 0.24
21 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATTAATTTAAAAATA
Found at i:31620 original size:9 final size:9
Alignment explanation
Indices: 31573--31628 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
31563 TTAAGTTTTC
31573 TTAAAAGTT-
1 TTAAAA-TTA
31582 TTAAAATTAA
1 TTAAAATT-A
*
31592 TTTAAAAATA
1 -TTAAAATTA
31602 TTAAATATTA
1 TTAAA-ATTA
31612 TTAAAATTA
1 TTAAAATTA
31621 -TAAAATTA
1 TTAAAATTA
31629 AAAAGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 10 0.24
9 15 0.37
10 9 0.22
11 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
TTAAAATTA
Found at i:31624 original size:18 final size:18
Alignment explanation
Indices: 31582--31642 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
31572 CTTAAAAGTT
31582 TTAAAATTAATTTAAAAATA
1 TTAAAATT-A-TTAAAAATA
*
31602 TTAAATATTATTAAAATTA
1 TTAAA-ATTATTAAAAATA
**
31621 -TAAAATTAAAAAGAAATA
1 TTAAAATTATTAA-AAATA
31639 TTAA
1 TTAA
31643 TTATTTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 11 0.32
20 6 0.18
21 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAAAATTATTAAAAATA
Found at i:31915 original size:16 final size:17
Alignment explanation
Indices: 31886--31920 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31876 TTTAATAAAG
*
31886 TTTTAATATTTTTATAT
1 TTTTAATATATTTATAT
31903 TTTTAATA-ATTTATAT
1 TTTTAATATATTTATAT
31919 TT
1 TT
31921 AAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATATATTTATAT
Found at i:32129 original size:20 final size:21
Alignment explanation
Indices: 32092--32146 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
32082 TATTTTCTAC
32092 ATATTTTAAT-TTTT-AAATA
1 ATATTTTAATATTTTAAAATA
32111 AT-TTTTAATATTTTAAAATA
1 ATATTTTAATATTTTAAAATA
**
32131 ATATTGGAATATTTTA
1 ATATTTTAATATTTTA
32147 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 7 0.23
21 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
ATATTTTAATATTTTAAAATA
Found at i:35385 original size:11 final size:11
Alignment explanation
Indices: 35371--35396 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35361 GTGTTTTTTG
35371 TTTGTTCGAAA
1 TTTGTTCGAAA
35382 TTTGTTCGAAA
1 TTTGTTCGAAA
35393 TTTG
1 TTTG
35397 ATTTAGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (11 bp):
TTTGTTCGAAA
Found at i:43097 original size:24 final size:24
Alignment explanation
Indices: 43067--43122 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
43057 TAGAAGTTCG
43067 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
43091 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
43115 ATTGAAGC
1 ATTGAAGC
43123 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:43441 original size:63 final size:63
Alignment explanation
Indices: 43372--43499 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
43362 AAGCCCCAAT
43372 TTTTTTTTATTATAGTTATATAATTATATTTATTATTTAATATGTTTTACCTTAAATATTATG
1 TTTTTTTTATTATAGTTATATAATTATATTTATTATTTAATATGTTTTACCTTAAATATTATG
43435 TTTTTTTTATTATAGTTATATAATTATATTTATTATTTAATATGTTTTACCTTAAATATTATG
1 TTTTTTTTATTATAGTTATATAATTATATTTATTATTTAATATGTTTTACCTTAAATATTATG
43498 TT
1 TT
43500 GTAGTTGATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (63 bp):
TTTTTTTTATTATAGTTATATAATTATATTTATTATTTAATATGTTTTACCTTAAATATTATG
Found at i:43704 original size:21 final size:20
Alignment explanation
Indices: 43678--43718 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
43668 TATATAAAAT
*
43678 CCGGTTCAACCGCGGTTGAAC
1 CCGGTTCAACC-CAGTTGAAC
*
43699 CCGGTTGAACCCAGTTGAAC
1 CCGGTTCAACCCAGTTGAAC
43719 TAGTAAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (20 bp):
CCGGTTCAACCCAGTTGAAC
Found at i:43705 original size:10 final size:10
Alignment explanation
Indices: 43678--43718 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
43668 TATATAAAAT
*
43678 CCGGTTCAAC
1 CCGGTTGAAC
43688 CGCGGTTGAAC
1 C-CGGTTGAAC
43699 CCGGTTGAAC
1 CCGGTTGAAC
*
43709 CCAGTTGAAC
1 CCGGTTGAAC
43719 TAGTAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (10 bp):
CCGGTTGAAC
Found at i:44337 original size:18 final size:20
Alignment explanation
Indices: 44298--44345 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
44288 AAATATTTTT
44298 TATTTTATTATATTTACTTAA
1 TATTTTATTATATTTAC-TAA
44319 TATTTTATTAT-TTTA-TAA
1 TATTTTATTATATTTACTAA
44337 TATTTTATT
1 TATTTTATT
44346 TTACTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTATTATATTTACTAA
Found at i:45484 original size:2 final size:2
Alignment explanation
Indices: 45477--45504 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45467 TTTTGATAAG
45477 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
45505 GTTTTAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46619 original size:13 final size:13
Alignment explanation
Indices: 46569--46659 Score: 73
Period size: 13 Copynumber: 7.0 Consensus size: 13
46559 GTTTAGTTTG
46569 TAATGTTTTTATT
1 TAATGTTTTTATT
46582 T-A-GTTTTCT-TT
1 TAATGTTTT-TATT
* *
46593 GTAACGTTTGTATT
1 -TAATGTTTTTATT
*
46607 TAATGTTTATATT
1 TAATGTTTTTATT
*
46620 TAATTGCTTTTATT
1 TAA-TGTTTTTATT
*
46634 TAAT-TTTCTTTTT
1 TAATGTTT-TTATT
46647 TAATGTTTTTATT
1 TAATGTTTTTATT
46660 ATTTAATTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
11 7 0.11
12 5 0.08
13 30 0.48
14 20 0.32
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (13 bp):
TAATGTTTTTATT
Found at i:46635 original size:14 final size:14
Alignment explanation
Indices: 46598--46671 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 14
46588 TCTTTGTAAC
*
46598 GTTTGTATTTAA-T
1 GTTTATATTTAATT
46611 GTTTATATTTAATT
1 GTTTATATTTAATT
46625 GCTTT-TATTTAATT
1 G-TTTATATTTAATT
*
46639 -TTCT-TTTTTAATGT
1 GTT-TATATTTAAT-T
*
46653 TTTTATTATTTAATT
1 GTTTA-TATTTAATT
46668 GTTT
1 GTTT
46672 CAATTGTAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.04
13 19 0.38
14 13 0.26
15 9 0.18
16 7 0.14
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.68
Consensus pattern (14 bp):
GTTTATATTTAATT
Found at i:46811 original size:2 final size:2
Alignment explanation
Indices: 46804--46840 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46794 CATTAAATTG
46804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46841 GAAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49547 original size:18 final size:18
Alignment explanation
Indices: 49524--49572 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
49514 GTAGAATTTT
*
49524 TCCCGAAGGACCACTGTG
1 TCCCGAAGGACCACTATG
49542 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
49560 TCCCGAAGGACCA
1 TCCCGAAGGACCA
49573 TTGATAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:52921 original size:18 final size:18
Alignment explanation
Indices: 52879--52940 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
52869 ATTTTCCCGT
*
52879 AGGACCACTATGTCCCCA
1 AGGACCACTATGTCCCAA
*
52897 A-GACCACTGTGTCCCAA
1 AGGACCACTATGTCCCAA
52914 AGGACCACTATGTCCCAA
1 AGGACCACTATGTCCCAA
52932 AGGACCACT
1 AGGACCACT
52941 GATAATCCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (18 bp):
AGGACCACTATGTCCCAA
Done.