Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003210.1 Hibiscus syriacus cultivar Beakdansim tig00006760_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: 127762
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2346 original size:21 final size:20
Alignment explanation
Indices: 2316--2355 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2306 AATAATTTTT
* *
2316 TTTATTATTATACACATATG
1 TTTATTATTAAACAAATATG
2336 TTTATTTATTAAACAAATAT
1 TTTA-TTATTAAACAAATAT
2356 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTATTATTAAACAAATATG
Found at i:4447 original size:24 final size:24
Alignment explanation
Indices: 4420--4465 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4410 CCCTCGTTAC
*
4420 CACTCTCACCTTCACCTTCATCTT
1 CACTATCACCTTCACCTTCATCTT
* **
4444 CACTATCATCTTCGTCTTCATC
1 CACTATCACCTTCACCTTCATC
4466 ATCTTCATCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.41, G:0.02, T:0.39
Consensus pattern (24 bp):
CACTATCACCTTCACCTTCATCTT
Found at i:12093 original size:24 final size:23
Alignment explanation
Indices: 12042--12097 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
12032 TATATTGTTC
*
12042 TATTAAAAAACACTTTTTTCACA
1 TATTAAAATACACTTTTTTCACA
*
12065 CATTAAAATACACATTTTTTCA-A
1 TATTAAAATACAC-TTTTTTCACA
12088 TTATTAAAAT
1 -TATTAAAAT
12098 GTTAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (23 bp):
TATTAAAATACACTTTTTTCACA
Found at i:21466 original size:19 final size:19
Alignment explanation
Indices: 21442--21478 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
21432 ACGAACACAT
21442 GTAAACGAACACAATAAAC
1 GTAAACGAACACAATAAAC
21461 GTAAACGAACACAATAAA
1 GTAAACGAACACAATAAA
21479 TGAACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (19 bp):
GTAAACGAACACAATAAAC
Found at i:21468 original size:33 final size:33
Alignment explanation
Indices: 21429--21504 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
21419 TGAGCGAACA
* *
21429 TAAACGAACACATGTAAACGAACA-CAATAAACG
1 TAAACGAACACA-ATAAACGAACATAAATAAACG
* *
21462 TAAACGAACACAATAAATGAACATAAATTAACG
1 TAAACGAACACAATAAACGAACATAAATAAACG
*
21495 TAAACAAACA
1 TAAACGAACA
21505 TAAATGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 9 0.24
33 28 0.76
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.14
Consensus pattern (33 bp):
TAAACGAACACAATAAACGAACATAAATAAACG
Found at i:21478 original size:13 final size:14
Alignment explanation
Indices: 21428--21461 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21418 ATGAGCGAAC
21428 ATAAACGAACACAT
1 ATAAACGAACACAT
*
21442 GTAAACGAACACA-
1 ATAAACGAACACAT
21455 ATAAACG
1 ATAAACG
21462 TAAACGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (14 bp):
ATAAACGAACACAT
Found at i:28204 original size:17 final size:17
Alignment explanation
Indices: 28177--28245 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
28167 AAAATAACAT
*
28177 AAATATAAATT-TTAAA
1 AAATATTAATTATTAAA
*
28193 AGAATATTAATTATTATA
1 A-AATATTAATTATTAAA
28211 AAATATTAATGATATTATTAA
1 AAATATTAAT--TATTA--AA
*
28232 AAATATCAATTATT
1 AAATATTAATTATT
28246 GATCTATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.02
17 18 0.42
18 5 0.12
19 9 0.21
21 10 0.23
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATATTAATTATTAAA
Found at i:28228 original size:19 final size:18
Alignment explanation
Indices: 28195--28245 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
28185 ATTTTAAAAG
28195 AATATTAATTATTA-TAA
1 AATATTAATTATTATTAA
28212 AATATTAATGATATTATTAAA
1 AATATTAAT--TATTATT-AA
*
28233 AATATCAATTATT
1 AATATTAATTATT
28246 GATCTATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
19 9 0.31
20 1 0.03
21 10 0.34
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATTAATTATTATTAA
Found at i:28455 original size:13 final size:13
Alignment explanation
Indices: 28439--28472 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
28429 TTGGGAAGGA
28439 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
*
28452 AAAAGAAAAAAAG
1 AAAAGAGAAAAAG
28465 AAAA-AGAA
1 AAAAGAGAA
28473 GATTAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:35548 original size:12 final size:12
Alignment explanation
Indices: 35533--35590 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
35523 TCTTCATTAC
35533 TTATATATTTTA
1 TTATATATTTTA
*
35545 TTAT-TA--CTA
1 TTATATATTTTA
* *
35554 TTATAGATTATA
1 TTATATATTTTA
*
35566 TTAAATATTTTA
1 TTATATATTTTA
*
35578 TTTTATATTTTA
1 TTATATATTTTA
35590 T
1 T
35591 ATTTTTAGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
9 6 0.17
10 1 0.03
11 2 0.06
12 26 0.74
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATATATTTTA
Found at i:46202 original size:1 final size:1
Alignment explanation
Indices: 46196--46220 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
46186 TCCTAAGTTG
46196 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
46221 CGTTTGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:47271 original size:106 final size:106
Alignment explanation
Indices: 47017--47691 Score: 1115
Period size: 106 Copynumber: 6.4 Consensus size: 106
47007 AGGTTTTACC
*
47017 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
* * *
47082 ACGAAGGGACCGCTGGTTGTCAACGAA-CATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
47122 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
47187 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
47228 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
47293 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
* *
47334 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
*
47399 GCGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
* *
47440 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
47505 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
* * * *
47546 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCAC--AAGCTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-G-ACGTAAGTTCAACTTCA
* ** * * *
47609 CGACGAAGGG-GCGACTGACTGTCAACAAACAATTTCCCAGTTC
64 CGACGAAGGGACCG-CTGGTTGTCAACAAATAATTTCCCAATTT
*
47652 CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
47692 TGAACAATAC
Statistics
Matches: 547, Mismatches: 19, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
105 92 0.17
106 452 0.83
107 1 0.00
108 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
Found at i:52566 original size:2 final size:2
Alignment explanation
Indices: 52559--52588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52549 ATGCCTGGGA
52559 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
52589 GCTTACAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61194 original size:3 final size:3
Alignment explanation
Indices: 61186--61212 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
61176 TTGGCATTTA
61186 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
61213 TTAATTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:63254 original size:17 final size:17
Alignment explanation
Indices: 63221--63273 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
63211 ATGTTATGTC
*
63221 AAAAATAATTTAAAATT-
1 AAAAAT-ATTAAAAATTG
63238 ATAAAATATTAAAAATTG
1 A-AAAATATTAAAAATTG
63256 AAAAGATATATAAAAATT
1 AAAA-ATAT-TAAAAATT
63274 CAATACTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 13 0.42
18 10 0.32
19 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAAATATTAAAAATTG
Found at i:69762 original size:19 final size:19
Alignment explanation
Indices: 69734--69786 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
69724 TTAATTTTAT
*
69734 AAATATAAAAAAATCAGAA
1 AAATACAAAAAAATCAGAA
*
69753 AAATACAAAAAAATCTGAA
1 AAATACAAAAAAATCAGAA
69772 AAATTACAAAAAAAT
1 AAA-TACAAAAAAAT
69787 TAGTATGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.17
Consensus pattern (19 bp):
AAATACAAAAAAATCAGAA
Found at i:81027 original size:60 final size:60
Alignment explanation
Indices: 80926--81095 Score: 155
Period size: 60 Copynumber: 2.9 Consensus size: 60
80916 GATAAATTGA
* ** * *** * *
80926 AATATTCAAAAGTTTGGGGACTAATTTAGAATGATGGTCATAGTTTGGGGATGAAACTAG
1 AATACTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAG
* * ** * * *
80986 AATGA-TCAAAAGTTTAAGGACTAGTTTAAAATGAAATTCATAAATTAAGAATAAAATTAG
1 AAT-ACTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAG
* *
81046 AATACTCAAAAG-TTAAGGACCAATTTAAAATAAAAATCATAGTTTAGGGA
1 AATACTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGA
81096 CATATGATTC
Statistics
Matches: 86, Mismatches: 22, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
59 31 0.36
60 54 0.63
61 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (60 bp):
AATACTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAG
Found at i:84883 original size:2 final size:2
Alignment explanation
Indices: 84872--84924 Score: 58
Period size: 2 Copynumber: 27.0 Consensus size: 2
84862 ATTGACTCTG
*
84872 TA TA -A TA TA TA TA TCA CA TA TGA -A TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA
84913 TA TA TA TA TA TA
1 TA TA TA TA TA TA
84925 CTGCATATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 3 0.07
2 39 0.89
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:86189 original size:2 final size:2
Alignment explanation
Indices: 86182--86214 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86172 TCATAAAATT
86182 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 T
86215 TTTACAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92467 original size:29 final size:31
Alignment explanation
Indices: 92399--92464 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
92389 CGTTCAAAGT
* *
92399 TTGGCTACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
92432 TTGGCCACCAACCAAGATGAAATTTCC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
92462 TTG
1 TTG
92465 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:93031 original size:21 final size:21
Alignment explanation
Indices: 92992--93032 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
92982 GTCTGCTGAA
* *
92992 GCTCCACCTGTTTTAGAGTAT
1 GCTCCACCTGCTGTAGAGTAT
*
93013 GCTCCACCTGCTGTGGAGTA
1 GCTCCACCTGCTGTAGAGTA
93033 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (21 bp):
GCTCCACCTGCTGTAGAGTAT
Found at i:95815 original size:35 final size:35
Alignment explanation
Indices: 95708--95817 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 35
95698 TTTTAGGGAT
* *
95708 CAAATATGGAATTCCCATGATCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
* * *
95743 CTACCAA-A-GAATTTTCCAATGTGT-ACAAG-TTAGCCAC
1 C-A--AATATGAA-ATTCCCATGT-TCA-AAGTTTGGCCAC
95780 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
95815 CAA
1 CAA
95818 CCAAGATGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
34 6 0.11
35 21 0.37
36 7 0.12
37 17 0.30
38 6 0.11
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (35 bp):
CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
Found at i:95875 original size:29 final size:31
Alignment explanation
Indices: 95807--95872 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 31
95797 TGTTCAAAGT
*
95807 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
95840 TTGGCCACCAACCAAGATGAAATTTCC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
95870 TTG
1 TTG
95873 CCAACTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.16
33 27 0.84
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:96763 original size:55 final size:54
Alignment explanation
Indices: 96680--96787 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 54
96670 AATAATGTAC
*
96680 AAATGCAACCACCAGTCAATAAATTTGATCATAACAAATCTCTTAGATTTACCT
1 AAATGCAACCACCAGTCAATAAATTTGATCATAACAAATCTCTTAAATTTACCT
* *
96734 AAATGCAACCCACTAGTCAATAAATTTGATCATAATAAATCTCTTAAATTTACC
1 AAATGCAA-CCACCAGTCAATAAATTTGATCATAACAAATCTCTTAAATTTACC
96788 ATAAGGTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
54 8 0.16
55 42 0.84
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (54 bp):
AAATGCAACCACCAGTCAATAAATTTGATCATAACAAATCTCTTAAATTTACCT
Found at i:98488 original size:16 final size:16
Alignment explanation
Indices: 98463--98493 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
98453 ATTTATACAG
98463 AACATCTGAATCATTT
1 AACATCTGAATCATTT
*
98479 AACATTTGAATCATT
1 AACATCTGAATCATT
98494 CAGTGCTTAA
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:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (16 bp):
AACATCTGAATCATTT
Found at i:102779 original size:23 final size:23
Alignment explanation
Indices: 102753--102798 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102743 TCGGTACCCT
102753 CTTAGCCCCCTTAATTGACTTTC
1 CTTAGCCCCCTTAATTGACTTTC
102776 CTTAGCCCCCTTAATTGACTTTC
1 CTTAGCCCCCTTAATTGACTTTC
102799 AACAATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.09, T:0.39
Consensus pattern (23 bp):
CTTAGCCCCCTTAATTGACTTTC
Found at i:112807 original size:24 final size:24
Alignment explanation
Indices: 112769--112838 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
112759 CAAAACAGAG
* *
112769 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
112793 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
112817 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
112839 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:113574 original size:29 final size:28
Alignment explanation
Indices: 113532--113605 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
113522 ATCAAACATT
*
113532 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* *
113561 TTACCAATATAGCACCCTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
113590 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
113606 AAAACCAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.87
30 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:113692 original size:10 final size:10
Alignment explanation
Indices: 113672--113715 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
113662 TCGGGTCGTG
113672 ACCGGTC-AA
1 ACCGGTCAAA
113681 ACCGGTCAAA
1 ACCGGTCAAA
*
113691 ACCGGT-TAA
1 ACCGGTCAAA
*
113700 ACCAGTCAAA
1 ACCGGTCAAA
113710 ACCGGT
1 ACCGGT
113716 TTCCAGTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:113716 original size:19 final size:19
Alignment explanation
Indices: 113672--113716 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
113662 TCGGGTCGTG
* *
113672 ACCGGTCAAACCGGTCAAA
1 ACCGGTTAAACCAGTCAAA
113691 ACCGGTTAAACCAGTCAAA
1 ACCGGTTAAACCAGTCAAA
113710 ACCGGTT
1 ACCGGTT
113717 TCCAGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCAGTCAAA
Found at i:119820 original size:24 final size:24
Alignment explanation
Indices: 119782--119851 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
119772 CAAAACAGAG
* *
119782 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
119806 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
119830 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
119852 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:120585 original size:29 final size:28
Alignment explanation
Indices: 120543--120616 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
120533 GTCAAACATT
*
120543 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* *
120572 TTACCAATATAGCACCCTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
120601 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
120617 AAAACCAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.87
30 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:120678 original size:17 final size:18
Alignment explanation
Indices: 120652--120693 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
120642 CACCGGTCAA
*
120652 CGGGTTGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
120669 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
120687 CGGGTCG
1 CGGGTCG
120694 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:122265 original size:44 final size:44
Alignment explanation
Indices: 122212--122297 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
122202 AATTTAAAAT
*
122212 ATATTTATTTATTTAATTATTTAAAAATAATTATATATGATAAG
1 ATATATATTTATTTAATTATTTAAAAATAATTATATATGATAAG
*
122256 ATATATATTTATTTAATTATTTAAAAATAATTATATGTGATA
1 ATATATATTTATTTAATTATTTAAAAATAATTATATATGATA
122298 GAATCTACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (44 bp):
ATATATATTTATTTAATTATTTAAAAATAATTATATATGATAAG
Found at i:123809 original size:3 final size:3
Alignment explanation
Indices: 123796--123839 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
123786 AAATGACTAT
*
123796 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
123840 GTAACAGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.