Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003474.1 Hibiscus syriacus cultivar Beakdansim tig00007347_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: 114989
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2852 original size:31 final size:31
Alignment explanation
Indices: 2816--2890 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2806 AATATTATGT
* * * *
2816 TCTAAAGTGCTGACATGACACATGTCACGTG
1 TCTAAAGTGATGACATAAAACATGTCACATG
*
2847 TCTAAAGTGATGACATAAAACATGTTACATG
1 TCTAAAGTGATGACATAAAACATGTCACATG
*
2878 TCTAAAATGATGA
1 TCTAAAGTGATGA
2891 TGTGGTACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (31 bp):
TCTAAAGTGATGACATAAAACATGTCACATG
Found at i:16242 original size:21 final size:21
Alignment explanation
Indices: 16216--16259 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16206 TCCTTCTCGC
* *
16216 CTCTCTTTCGATCGACTTCTT
1 CTCTCTTTCCATCAACTTCTT
16237 CTCTCTTTCCATCAACTTCTT
1 CTCTCTTTCCATCAACTTCTT
16258 CT
1 CT
16260 GATGAATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.36, G:0.05, T:0.48
Consensus pattern (21 bp):
CTCTCTTTCCATCAACTTCTT
Found at i:16399 original size:58 final size:59
Alignment explanation
Indices: 16251--16410 Score: 207
Period size: 58 Copynumber: 2.7 Consensus size: 59
16241 CTTTCCATCA
*
16251 ACTTCTTCTGATGAATATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGCCG
1 ACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGCCG
* ** * ** * **
16310 CCGCCTTCTGATGAACATCGAACTAGTTTTCAAACCCCAAGATG-CTCTGTTTCGGTTG
1 ACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGCCG
16368 ACTTCTTCTGATGAACATCGAACTAGTTTTCAAA-AGCCAAGAT
1 ACTTCTTCTGATGAACATCGAACTAGTTTTCAAACA-CCAAGAT
16411 ACCCTGTACA
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 47 0.55
59 39 0.45
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (59 bp):
ACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGCCG
Found at i:21510 original size:13 final size:14
Alignment explanation
Indices: 21470--21511 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
21460 TATACATTAA
*
21470 AAATTATAAAATAAT
1 AAATTATTAAA-AAT
21485 AAATTATTAAAAAT
1 AAATTATTAAAAAT
*
21499 AAA-TATTGAAAAT
1 AAATTATTAAAAAT
21512 CATATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
14 6 0.24
15 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATTATTAAAAAT
Found at i:25880 original size:21 final size:21
Alignment explanation
Indices: 25836--25880 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25826 GATTTCTGGG
* *
25836 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCACT
*
25857 CAAGGGGAATCGATACCCCCT
1 CAAGGGGAATCGATACCCACT
25878 CAA
1 CAA
25881 ACGAACATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCACT
Found at i:27108 original size:32 final size:31
Alignment explanation
Indices: 27066--27193 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
27056 AGAGTCGAGG
*
27066 GTTTACCTATGTTCTACGGAACATATGAACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
27097 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
27129 GTATACCTATGTTCTAAGGAACATGTGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
27160 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
27191 GTT
1 GTT
27194 ACCGAGGATC
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:27213 original size:30 final size:30
Alignment explanation
Indices: 27179--27337 Score: 257
Period size: 30 Copynumber: 5.3 Consensus size: 30
27169 GGTTCTTCGG
*
27179 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
27209 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
27239 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
27269 GACCTCTGGACAATTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
27299 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
27328 GACCGCTGGA
1 GACCTCTGGA
27338 TAGGTCCTTC
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 17 0.14
30 105 0.86
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:27622 original size:2 final size:2
Alignment explanation
Indices: 27610--27645 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
27600 GTATGCGTGG
*
27610 AT AT GT 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
27646 GAAAGGTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30509 original size:21 final size:21
Alignment explanation
Indices: 30465--30509 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30455 GATTTCTGGG
* * *
30465 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
30486 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
30507 CAA
1 CAA
30510 ACGAACATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:31715 original size:32 final size:31
Alignment explanation
Indices: 31673--31800 Score: 105
Period size: 31 Copynumber: 4.1 Consensus size: 31
31663 AGAGTCGAGG
31673 GTTTACCTATGTTCTACGAAACATATGGACAA
1 GTTTACCTATGTTCTACGAAACATATGGAC-A
* * ***
31705 TTTTACCTATG-TCTTTCGAGGTATATGGACA
1 GTTTACCTATGTTC-TACGAAACATATGGACA
* * * *
31736 GTATACCTATGTTCTAAGGAAGATATGGACA
1 GTTTACCTATGTTCTACGAAACATATGGACA
* * ** *
31767 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGAAACATATGGACA
31798 GTT
1 GTT
31801 ACCGAGGATC
Statistics
Matches: 74, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
31 50 0.68
32 24 0.32
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGAAACATATGGACA
Found at i:31820 original size:30 final size:30
Alignment explanation
Indices: 31786--31944 Score: 257
Period size: 30 Copynumber: 5.3 Consensus size: 30
31776 GGTTCTTCGG
*
31786 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
31816 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
31846 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
31876 GACCTCTGTACAGTTACCGATGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
31906 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
31935 GACCTCTGGA
1 GACCTCTGGA
31945 TAGGTCCTTC
Statistics
Matches: 121, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 17 0.14
30 104 0.86
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:32229 original size:2 final size:2
Alignment explanation
Indices: 32217--32250 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
32207 GTATGCGTGG
*
32217 AT AT GT 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
32251 GAAAGGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33485 original size:75 final size:75
Alignment explanation
Indices: 33362--33512 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 75
33352 TCTGTGCACG
**
33362 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCTTGTACGTGAACATCCAGCATGGTGACCA
1 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
33427 TCATCCTCAT
66 TCATCCTCAT
* * * * *
33437 CAACTTTGAAAAGCAAATAGAGCTCCACCTAGGCCCCGGTATGTGAACATCCGGTATGGTGACCC
1 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
33502 TCATCCTCAT
66 TCATCCTCAT
33512 C
1 C
33513 TTAATGCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (75 bp):
CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
TCATCCTCAT
Found at i:42237 original size:4 final size:4
Alignment explanation
Indices: 42228--42278 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
42218 CAAAATTACG
* * *
42228 TACA TACA TACA TATA TACA TACA TACA GACA TACA TA-G TGACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T-ACA TACA
42276 TAC
1 TAC
42279 CTTGTGAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:42753 original size:8 final size:8
Alignment explanation
Indices: 42740--42769 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
42730 AGACTCGTCA
42740 ATGTATAC
1 ATGTATAC
42748 ATGTATAC
1 ATGTATAC
*
42756 ATGTATAA
1 ATGTATAC
42764 ATGTAT
1 ATGTAT
42770 GCTTAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (8 bp):
ATGTATAC
Found at i:42778 original size:12 final size:12
Alignment explanation
Indices: 42761--42785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42751 TATACATGTA
42761 TAAATGTATGCT
1 TAAATGTATGCT
42773 TAAATGTATGCT
1 TAAATGTATGCT
42785 T
1 T
42786 GATTGGCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAATGTATGCT
Found at i:56785 original size:13 final size:13
Alignment explanation
Indices: 56767--56791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56757 CATTCAGAAA
56767 GATAAGGAAACAG
1 GATAAGGAAACAG
56780 GATAAGGAAACA
1 GATAAGGAAACA
56792 TTAAACCCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (13 bp):
GATAAGGAAACAG
Found at i:63082 original size:69 final size:69
Alignment explanation
Indices: 62971--63109 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
62961 GGTGATCTAT
62971 ATCTGTACCTTATGTTTTGATCTTATTTATACCTTGCAATGGAACATTAAAACTGAGAGAGAAAG
1 ATCTGTACCTTATGTTTTGATCTTATTTATACCTTGCAATGGAACATTAAAACTGAGAGAGAAAG
63036 ATAA
66 ATAA
* *
63040 ATCTGTACCTTATGTTTTGATGTTATTTATACCTTGCGATGGAACATTAAAACTGAGAGAGAAAG
1 ATCTGTACCTTATGTTTTGATCTTATTTATACCTTGCAATGGAACATTAAAACTGAGAGAGAAAG
63105 ATAA
66 ATAA
63109 A
1 A
63110 CCATTTACTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (69 bp):
ATCTGTACCTTATGTTTTGATCTTATTTATACCTTGCAATGGAACATTAAAACTGAGAGAGAAAG
ATAA
Found at i:65485 original size:2 final size:2
Alignment explanation
Indices: 65478--65503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65468 TCATGTGTCA
65478 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
65504 TGAATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70088 original size:20 final size:20
Alignment explanation
Indices: 70063--70103 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
70053 TAGCATATGT
70063 TATCACTTTTGATGCAATCG
1 TATCACTTTTGATGCAATCG
70083 TATCACTTTTGATGCAATCG
1 TATCACTTTTGATGCAATCG
70103 T
1 T
70104 GTTCATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (20 bp):
TATCACTTTTGATGCAATCG
Found at i:70912 original size:56 final size:56
Alignment explanation
Indices: 70823--70992 Score: 232
Period size: 56 Copynumber: 3.0 Consensus size: 56
70813 GATTTCGGGG
* * * ** *
70823 TTATGCTTCTTAATGGCAATAACTGATATATATACTCGATTTCGGGGTCTCTATTT
1 TTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGAGACCCCTATTT
* *
70879 TTATTCTTCTTAATGGCAACAATTGATAGATATACTCGATTTCGAGACCCCTATTT
1 TTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGAGACCCCTATTT
* * * *
70935 TTATGCTTATTAATGGCAACAACTGATAGATATATTCGATTTTGAGGCCCCTATTT
1 TTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGAGACCCCTATTT
70991 TT
1 TT
70993 TGGGGGCTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 100 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (56 bp):
TTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGAGACCCCTATTT
Found at i:71329 original size:20 final size:20
Alignment explanation
Indices: 71304--71341 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
71294 TTTGGTTCAC
71304 AGAATGTAAGATTACCAGTG
1 AGAATGTAAGATTACCAGTG
71324 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
71342 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTG
Found at i:71554 original size:37 final size:39
Alignment explanation
Indices: 71499--71571 Score: 107
Period size: 37 Copynumber: 1.9 Consensus size: 39
71489 GTTAGAAAAT
71499 ATTTATATAATATTTATATAT-TTTCTTTAAAAAATTTAA
1 ATTTATATAATATTTATATATATTT-TTTAAAAAATTTAA
*
71538 ATTTATA-AA-ATTTATATATATTTTTTACAAAATT
1 ATTTATATAATATTTATATATATTTTTTAAAAAATT
71572 GAAAATAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 20 0.62
38 5 0.16
39 7 0.22
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (39 bp):
ATTTATATAATATTTATATATATTTTTTAAAAAATTTAA
Found at i:71585 original size:37 final size:37
Alignment explanation
Indices: 71510--71585 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
71500 TTTATATAAT
* * *
71510 ATTTATATATTTTCTTTAAAAAATTTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAATATAAAAA
*
71547 ATTTATATATATTT-TTTACAAAATTGAAA-ATAGAAAA
1 ATTTATATAT-TTTCTTTAAAAAATTGAAATATA-AAAA
71584 AT
1 AT
71586 GTTTAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
36 2 0.06
37 28 0.85
38 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAATATAAAAA
Found at i:81057 original size:18 final size:19
Alignment explanation
Indices: 81034--81070 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
81024 CTAGTAATCC
81034 TATTCCCA-GGTAATCTTT
1 TATTCCCACGGTAATCTTT
81052 TATTCCCACTGGTAATCTT
1 TATTCCCAC-GGTAATCTT
81071 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (19 bp):
TATTCCCACGGTAATCTTT
Found at i:82595 original size:18 final size:19
Alignment explanation
Indices: 82558--82597 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
82548 TCAAGATATT
82558 TAATAAAAATAATATCTTA
1 TAATAAAAATAATATCTTA
* *
82577 TAATTAAAAT-ATATTTTA
1 TAATAAAAATAATATCTTA
82595 TAA
1 TAA
82598 CTTTTAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAAAAATAATATCTTA
Found at i:83699 original size:66 final size:65
Alignment explanation
Indices: 83560--83720 Score: 191
Period size: 66 Copynumber: 2.5 Consensus size: 65
83550 TGCACTAAGA
* * * * * *
83560 GTGCAACGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGTATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAAACCAGAGTGCATCGATGCATGGCTT
* *
83624 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAAACACTGAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAAAC-CAGAGTGCATCGATGCATGGCT
83688 AT
65 -T
* * *
83690 GTGCCTCGATGAATAAAATGCATTCAATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
83721 CAATTAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 26 0.31
65 11 0.13
66 46 0.55
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAAACCAGAGTGCATCGATGCATGGCTT
Found at i:89852 original size:49 final size:49
Alignment explanation
Indices: 89782--89881 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 49
89772 AACAGAATTA
* * *
89782 TTGACGTAATAACTTTGTATTTTTCTCTGAATTATGACATGATATTATC
1 TTGACGTAATAACTTTGTATTTTTATCTCAATGATGACATGATATTATC
* * *
89831 TTGATGTAATGACTTTTTATTTTTATCTCAATGATGACATGATATTATC
1 TTGACGTAATAACTTTGTATTTTTATCTCAATGATGACATGATATTATC
89880 TT
1 TT
89882 ATGATGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (49 bp):
TTGACGTAATAACTTTGTATTTTTATCTCAATGATGACATGATATTATC
Found at i:92087 original size:17 final size:18
Alignment explanation
Indices: 92052--92087 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
92042 AGAGAAAAAG
*
92052 TTTTATTTAATTATTAAC
1 TTTTAATTAATTATTAAC
92070 TTTTAATTAATT-TTAAC
1 TTTTAATTAATTATTAAC
92087 T
1 T
92088 ATATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATTAATTATTAAC
Found at i:102673 original size:59 final size:60
Alignment explanation
Indices: 102568--102707 Score: 187
Period size: 60 Copynumber: 2.4 Consensus size: 60
102558 ATATACATAG
* * *
102568 AGTTT-GGGATGAAATTAGAATGTTCAAAAATTTTGGGGACCAATTTAGAATG-CAGTCAT
1 AGTTTAGGGATGAAATTA-AATGTTCAAAAATTTTAGAGACCAATTTAGAATGACAATCAT
* *
102627 AGTTTAGGGATGAAATTGAAATGTTC-AAAATTTTAGAGACTAATTTAGAATGATAATCAT
1 AGTTTAGGGATGAAATT-AAATGTTCAAAAATTTTAGAGACCAATTTAGAATGACAATCAT
*
102687 AGTTTAGGGATAAAATTAAAT
1 AGTTTAGGGATGAAATTAAAT
102708 TAAAAGTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
59 32 0.44
60 39 0.54
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (60 bp):
AGTTTAGGGATGAAATTAAATGTTCAAAAATTTTAGAGACCAATTTAGAATGACAATCAT
Done.