Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004849.1 Hibiscus syriacus cultivar Beakdansim tig00010930_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: 88156
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4035 original size:16 final size:16
Alignment explanation
Indices: 4014--4044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4004 GAAATCAAAA
4014 ATATTAAATATATTAT
1 ATATTAAATATATTAT
*
4030 ATATTATATATATTA
1 ATATTAAATATATTA
4045 AATACATATT
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:0.00, T:0.52
Consensus pattern (16 bp):
ATATTAAATATATTAT
Found at i:6699 original size:2 final size:2
Alignment explanation
Indices: 6692--6731 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6682 ACATACATAC
6692 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
6732 TTTTAATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7879 original size:2 final size:2
Alignment explanation
Indices: 7874--7901 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7864 AAATCACACA
7874 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
7902 TGAAAAATAA
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:10496 original size:21 final size:21
Alignment explanation
Indices: 10447--10497 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
10437 TATGACTATA
10447 GCAATGCGATTTTCCAATTTC
1 GCAATGCGATTTTCCAATTTC
**
10468 GCGTTGCGATTTTCCCAA-TTC
1 GCAATGCGATTTT-CCAATTTC
10489 GCAATGCGA
1 GCAATGCGA
10498 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (21 bp):
GCAATGCGATTTTCCAATTTC
Found at i:10512 original size:20 final size:21
Alignment explanation
Indices: 10487--10538 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
10477 TTTTCCCAAT
*
10487 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
10507 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
10528 TCGCAATGCGA
1 TCGCAATGCGA
10539 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:10552 original size:20 final size:20
Alignment explanation
Indices: 10527--10600 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
10517 AATTTGGAAA
* *
10527 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
10547 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
10567 TTCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
10587 ATCGCAATGAGATA
1 ATCGCAACGAGATA
10601 TTACAGAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:11171 original size:20 final size:20
Alignment explanation
Indices: 11146--11199 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
11136 CAACGGGGAA
11146 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
11166 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
11186 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
11200 TGAAAATCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:11230 original size:14 final size:14
Alignment explanation
Indices: 11211--11264 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
11201 GAAAATCGCA
11211 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
11225 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
11242 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
11258 TTGCGAT
1 TTGCGAT
11265 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:12892 original size:41 final size:42
Alignment explanation
Indices: 12838--12921 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
12828 CCTCTTCAAC
* *
12838 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
12879 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
12921 G
1 G
12922 CTGAAAGGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 20 0.53
42 18 0.47
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:13316 original size:20 final size:20
Alignment explanation
Indices: 13293--13404 Score: 154
Period size: 20 Copynumber: 5.7 Consensus size: 20
13283 AAACTTACTT
13293 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
13313 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
13333 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* *
13353 TCGCAATGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
13373 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
13392 TCGCAACGCGAAA
1 TCGCAACGCGAAA
13405 CACAAATCGC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 15 0.18
20 68 0.82
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:13317 original size:40 final size:40
Alignment explanation
Indices: 13273--13404 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
13263 TAGTTTACTT
* *
13273 TCGCAACAC-AAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGAAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
13313 TCGCAACGCGGAAATGACTATCGCAACGCGAAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
** * * **
13353 TCGCAATGCGAAAATGGCTATCGCAATGCG-AAATGAAAA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
*
13392 TCGCAACGCGAAA
1 TCGCAACACGAAA
13405 CACAAATCGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 18 0.23
40 57 0.73
41 3 0.04
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
Found at i:13366 original size:60 final size:59
Alignment explanation
Indices: 13293--13404 Score: 170
Period size: 60 Copynumber: 1.9 Consensus size: 59
13283 AAACTTACTT
**
13293 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACTATCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTATCGCAACGC-GAAATGAAAATCGCAACGCGAAAATGGCTA
* * *
13353 TCGCAATGCGAAAATGGCTATCGCAATGCGAAATGAAAATCGCAACGCGAAA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAATCGCAACGCGAAA
13405 CACAAATCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 21 0.45
60 26 0.55
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (59 bp):
TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAATCGCAACGCGAAAATGGCTA
Found at i:13433 original size:19 final size:19
Alignment explanation
Indices: 13411--13474 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
13401 GAAACACAAA
13411 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
* *
13430 TCGCGTTGCGA--TTT-TG
1 TCGCATTGCGATTTTTATT
*
13446 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTTATT
13463 TCGCATTGCGAT
1 TCGCATTGCGAT
13475 AGCCATTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 7 0.19
19 17 0.47
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTTATT
Found at i:14077 original size:18 final size:18
Alignment explanation
Indices: 14051--14095 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
14041 GTCGATCAGG
14051 TGATGGCTCTGGGTGAGA
1 TGATGGCTCTGGGTGAGA
* *
14069 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGA
14087 TGATGGCTC
1 TGATGGCTC
14096 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGA
Found at i:15453 original size:19 final size:20
Alignment explanation
Indices: 15417--15458 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
15407 AACAGTTTCT
15417 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
15437 GAAAATGACAA-CGCAACGC
1 GAAAATGAAAATCGCAACAC
15456 GAA
1 GAA
15459 TTTGACTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.52, C:0.21, G:0.19, T:0.07
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:15764 original size:22 final size:22
Alignment explanation
Indices: 15737--15780 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15727 GATGGAGATA
15737 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
15759 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
15781 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:16030 original size:20 final size:20
Alignment explanation
Indices: 15967--16080 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
15957 GATTATGTAT
*
15967 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
15987 TATATCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
16007 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
16027 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
16048 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16068 TATCGCATTGCGA
1 TATCGCGTTGCGA
16081 TTTTCCAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:16084 original size:41 final size:41
Alignment explanation
Indices: 15947--16082 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
15937 CGCTTTGAAA
*
15947 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
** * * *
15988 ATATCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* *
16028 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
16069 ATCGCATTGCGATT
1 ATCGCATTGCGATT
16083 TTCCAAATTA
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.38
41 44 0.56
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:16100 original size:41 final size:40
Alignment explanation
Indices: 16014--16102 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 40
16004 AAGTATCGCG
* ** *
16014 TTGCGAAAGTCAGTATCGCATTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCATTGCGATTTTAAATTA-CGCA
*
16055 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTA-GTA
1 TTGCGATAGTCAGTATCGCATTGCGATTTT--AAATTACGCA
16096 TTGCGAT
1 TTGCGAT
16103 TTACTTATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 37 0.90
43 4 0.10
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCAGTATCGCATTGCGATTTTAAATTACGCA
Found at i:16414 original size:26 final size:26
Alignment explanation
Indices: 16385--16446 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
16375 CGGCTAACAT
*
16385 TTTATAAATTTCTCATCTCTTAAAAC
1 TTTATAAATTTATCATCTCTTAAAAC
* * *
16411 TTTATAAATTTATTATCTTTTAAAAT
1 TTTATAAATTTATCATCTCTTAAAAC
16437 TTTATAAATT
1 TTTATAAATT
16447 CACTTCCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTATAAATTTATCATCTCTTAAAAC
Found at i:19921 original size:23 final size:23
Alignment explanation
Indices: 19895--19939 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19885 CACCACAGCT
*
19895 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
19918 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
19940 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:20188 original size:149 final size:149
Alignment explanation
Indices: 19918--20222 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
19908 CGAAGTGCCC
* *
19918 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
19983 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
20048 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
*
20067 CGTAGACTTGCACCGTAGTGCCATATAATAATGTTCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
20132 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
20197 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
20216 CGTAGAC
1 CGTAGAC
20223 CCTCGACTCT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:21656 original size:21 final size:21
Alignment explanation
Indices: 21632--21676 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21622 TTCTTGTTCG
* *
21632 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
21653 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
21674 TTG
1 TTG
21677 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:26267 original size:50 final size:50
Alignment explanation
Indices: 26166--26270 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
26156 ACTTTCGAAC
*
26166 AGCTATAAAATCACCTCGTCCATTTCGGGATCTGAAGTTTCAGACAGTCA
1 AGCTATAAAATCACCTCGTCCATTTCGGGATCTGAAGTTTCAGACAATCA
* * * * *
26216 AGCTATGACATCACCTTGTTCATTTCGGGGTCTGAA-TTTCCA-AGCAATCA
1 AGCTATAAAATCACCTCGTCCATTTCGGGATCTGAAGTTT-CAGA-CAATCA
26266 AGCTA
1 AGCTA
26271 GCATCATGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 4 0.09
50 43 0.91
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (50 bp):
AGCTATAAAATCACCTCGTCCATTTCGGGATCTGAAGTTTCAGACAATCA
Found at i:26695 original size:20 final size:19
Alignment explanation
Indices: 26651--26705 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 19
26641 TTTATAGAAA
26651 TAATAATATTAAATTATAAT
1 TAATAATATT-AATTATAAT
*
26671 GAATAATATT-ATTATATAT
1 TAATAATATTAATTATA-AT
26690 T--TAATATTAA-TATAAT
1 TAATAATATTAATTATAAT
26706 AAGCTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 2 0.06
17 11 0.35
18 7 0.23
19 2 0.06
20 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATAATATTAATTATAAT
Found at i:26747 original size:23 final size:23
Alignment explanation
Indices: 26721--26765 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
26711 AATAATATTT
26721 TAATAAAG-ATATTTAAAATATAG
1 TAAT-AAGTATATTTAAAATATAG
* *
26744 TAATTAGTATTTTTAAAATATA
1 TAATAAGTATATTTAAAATATA
26766 ACATTATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
TAATAAGTATATTTAAAATATAG
Found at i:26862 original size:20 final size:20
Alignment explanation
Indices: 26837--26875 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
26827 TATAATTTTT
26837 ATTAATAAAATTATAAAAAA
1 ATTAATAAAATTATAAAAAA
26857 ATTAATAAAATTATAAAAA
1 ATTAATAAAATTATAAAAA
26876 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAATAAAATTATAAAAAA
Found at i:26906 original size:27 final size:27
Alignment explanation
Indices: 26876--26927 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
26866 ATTATAAAAA
* *
26876 TAATATTTTAATAATAAATAA-ATTATT
1 TAATAGTTTAAAAAT-AATAATATTATT
26903 TAATAGTTTAAAAATAATAATATTA
1 TAATAGTTTAAAAATAATAATATTA
26928 AGTTTTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAATAGTTTAAAAATAATAATATTATT
Found at i:26952 original size:19 final size:19
Alignment explanation
Indices: 26930--26968 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
26920 TAATATTAAG
26930 TTTTATGATAAATAATATT
1 TTTTATGATAAATAATATT
* **
26949 TTTTATTATATTTAATATT
1 TTTTATGATAAATAATATT
26968 T
1 T
26969 ATAATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTATGATAAATAATATT
Found at i:56609 original size:25 final size:25
Alignment explanation
Indices: 56575--56622 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
56565 GGCCAATAAG
56575 CTTCACATTAATTCGAGGTAATCAT
1 CTTCACATTAATTCGAGGTAATCAT
*
56600 CTTCATATTAATTCGAGGTAATC
1 CTTCACATTAATTCGAGGTAATC
56623 CTGCACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (25 bp):
CTTCACATTAATTCGAGGTAATCAT
Found at i:61485 original size:20 final size:20
Alignment explanation
Indices: 61448--61485 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61438 TCAACGATTT
*
61448 TTATTATTATAATGAAAATA
1 TTATTATTATAATCAAAATA
61468 TTATTA-TATAATTCAAAA
1 TTATTATTATAA-TCAAAA
61486 ACCTTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATTATTATAATCAAAATA
Found at i:69091 original size:192 final size:191
Alignment explanation
Indices: 68663--69111 Score: 568
Period size: 191 Copynumber: 2.3 Consensus size: 191
68653 AACATACACA
* * * *
68663 CCTCTTCTAACTAATTCCAGCACTAAATACTGAAATCATTCAAGAAGTT-ACTGCTAATTGCAGT
1 CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCA-TGATAATTGGAGT
*
68727 AATCAATGCACCACCAAAAAAAACATGACTTAATTGAACCAACTCAAATAACACCCTAATAAATG
65 AATCAATGCACCACCAAAAAAAACAAGACTTAATTGAACCAACTCAAATAACACCCTAATAAATG
* ** * *
68792 AAACAATTCAAGCATGTAACCTTCAGGTCTATAAATGTTTATATTCTGCATCACAAACATCC
130 AAACAATTAAAGCATGTAAAATTCAGGTCTATAAATGTCTATATTCTACATCACAAACATCC
* *
68854 CCTCTTCTGACTAGTTCCAGCACTAAATACTGAAATCGCTCAAGAAGTTCATGATAATTGGAGTA
1 CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGATAATTGGAGTA
* * * * * *
68919 ATCAATGCAGCAGC-AACAAAACAAGACTTAAATTGAATCAACTC-AATAAGATCCC-AATAATT
66 ATCAATGCACCACCAAAAAAAACAAGACTT-AATTGAACCAACTCAAATAACA-CCCTAATAAAT
* * * *
68981 GAAATAATTAAAGGATGTAAAATTGAGGGT-TATAAATGTCTATATTCTACATCATTAAA-ATAC
129 GAAACAATTAAAGCATGTAAAATTCA-GGTCTATAAATGTCTATATTCTACATCA-CAAACAT--
69044 CC
190 CC
* * *
69046 CCTGTTCTGACTAATTCCAGCACTAAATACTGAAATTGTTCAAGAAGTTCCTGATAATTGGAGTA
1 CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGATAATTGGAGTA
69111 A
66 A
69112 CCACAAAAAC
Statistics
Matches: 224, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
190 69 0.31
191 91 0.41
192 64 0.29
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (191 bp):
CCTCTTCTGACTAATTCCAGCACTAAATACTGAAATCGTTCAAGAAGTTCATGATAATTGGAGTA
ATCAATGCACCACCAAAAAAAACAAGACTTAATTGAACCAACTCAAATAACACCCTAATAAATGA
AACAATTAAAGCATGTAAAATTCAGGTCTATAAATGTCTATATTCTACATCACAAACATCC
Found at i:74519 original size:2 final size:2
Alignment explanation
Indices: 74512--74551 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
74502 ATTATTTTGC
74512 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
74552 TAAATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75016 original size:2 final size:2
Alignment explanation
Indices: 75009--75043 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
74999 TGTCTCAATA
75009 TG TG TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
75044 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:75048 original size:2 final size:2
Alignment explanation
Indices: 75043--75136 Score: 127
Period size: 2 Copynumber: 47.5 Consensus size: 2
75033 GTGTGTGTGT
75043 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * *
75085 GA GA GA GA GA GG GA GG GA GA GG GA GA GG GA GA G- GG GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
75126 GA GA GA GA GA G
1 GA GA GA GA GA G
75137 TCCCAATGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
GA
Found at i:78320 original size:35 final size:35
Alignment explanation
Indices: 78229--78443 Score: 108
Period size: 35 Copynumber: 6.2 Consensus size: 35
78219 TGAAAACATT
* * * *
78229 TATATATATAAT-TTTTTTTAAAAATATTTTGAAAA
1 TATATATATTATATATTTTTAAACAT-TTTTAAAAA
* * *
78264 TAAATATAATATATAGTTTTTTAAACCTTTTTAAAAA
1 TATATATATTATATA--TTTTTAAACATTTTTAAAAA
*
78301 TATATATATTATATATTTTTAAAACATTTTGAAAAA
1 TATATATATTATATATTTTT-AAACATTTTTAAAAA
* * *
78337 TATGTAGT-TT-T-TA----AAAACA-TTTTGAAAA
1 TATATA-TATTATATATTTTTAAACATTTTTAAAAA
* * * * *
78365 CATATATATTATATAGTTTTGAATCATTTTGAAAAC
1 TATATATATTATATA-TTTTTAAACATTTTTAAAAA
* * *
78401 T-TATATAATATATAGTTTTAAAAACATTTTTTAAAAC
1 TATATATATTATATA-TTTT-TAAACA-TTTTTAAAAA
78438 TATATA
1 TATATA
78444 ATTTTGAAAA
Statistics
Matches: 136, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
27 1 0.01
28 13 0.10
29 6 0.04
30 2 0.01
34 2 0.01
35 36 0.26
36 31 0.23
37 32 0.24
38 13 0.10
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATATATTATATATTTTTAAACATTTTTAAAAA
Found at i:78345 original size:64 final size:64
Alignment explanation
Indices: 78271--78399 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 64
78261 AAATAAATAT
* * * * *
78271 AATATATAGTTTTTTAAACCTTTTTAAAAATATATATATTATATATTTTTAAAACATTTTGAAA
1 AATATATAGTTTTTAAAAACATTTTAAAAACATATATATTATATAGTTTTAAAACATTTTGAAA
* * * *
78335 AATATGTAGTTTTTAAAAACATTTTGAAAACATATATATTATATAGTTTTGAATCATTTTGAAA
1 AATATATAGTTTTTAAAAACATTTTAAAAACATATATATTATATAGTTTTAAAACATTTTGAAA
78399 A
1 A
78400 CTTATATAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (64 bp):
AATATATAGTTTTTAAAAACATTTTAAAAACATATATATTATATAGTTTTAAAACATTTTGAAA
Found at i:78437 original size:37 final size:35
Alignment explanation
Indices: 78335--78445 Score: 134
Period size: 35 Copynumber: 3.1 Consensus size: 35
78325 CATTTTGAAA
*
78335 AATATGTAGTTTTTAAAAACATTTTGAAAACATATAT
1 AATATATAG-TTTTAAAAACATTTTGAAAAC-TATAT
* * *
78372 ATTATATAGTTTT-GAATCATTTTGAAAACTTATAT
1 AATATATAGTTTTAAAAACATTTTGAAAAC-TATAT
*
78407 AATATATAGTTTTAAAAACATTTTTTAAAACTATAT
1 AATATATAGTTTTAAAAACA-TTTTGAAAACTATAT
78443 AAT
1 AAT
78446 TTTGAAAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 31 0.49
36 16 0.25
37 16 0.25
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (35 bp):
AATATATAGTTTTAAAAACATTTTGAAAACTATAT
Found at i:78453 original size:29 final size:29
Alignment explanation
Indices: 78407--78474 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
78397 AAACTTATAT
* *
78407 AATATATAGTTTTAAAAACATTTTTTAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
* * *
78436 ACTATATAATTTTGAAAATATTTTTAAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
78465 AATATATAAT
1 AATATATAAT
78475 ATATATAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
AATATATAATTTTAAAAACATTTTTAAAA
Found at i:78472 original size:100 final size:101
Alignment explanation
Indices: 78190--78522 Score: 293
Period size: 100 Copynumber: 3.3 Consensus size: 101
78180 TGCAAATGAT
* * * * ***
78190 TTTTGAAAAAATATATATAATATATAGTTTGAAAACA-TTT-ATATATATAATTTTTTTTAAAAA
1 TTTTG-AAAAATATATATAATATATATTTTAAAAACATTTTGAAAAATAT-ATAGATTTTAAAAA
* *
78253 TATTTTGAAAATAA-ATATAATATATAGTTTTTTAAACC
64 TATTTTGAAAA-AATATATAATATATAGTTTTTGAAACA
* * * * * *
78291 TTTTTAAAAATATATATATTATATATTTTTAAAACATTTTGAAAAATATGTAGTTTTTAAAAACA
1 TTTTGAAAAATATATATAATATATATTTTAAAAACATTTTGAAAAATATATAGATTTTAAAAATA
* * *
78356 TTTTGAAAACATATATATTATATAG-TTTTGAATCA
66 TTTTGAAAAAATATATAATATATAGTTTTTGAAACA
* * * *
78391 TTTTGAAAACT-TATATAATATATAGTTTTAAAAACATTTTTTAAAACTATATA-ATTTTGAAAA
1 TTTTGAAAAATATATATAATATATA-TTTTAAAAACA-TTTTGAAAAATATATAGATTTTAAAAA
* * * *
78454 TATTTTTAAAAAATATATAATATATATAATTTTTAAAATA
64 TATTTTGAAAAAATATAT-A-ATATATAGTTTTTGAAACA
* *
78494 CTTTTG-AAAATATATATTATATAGATTTT
1 -TTTTGAAAAATATATATAATATATATTTT
78523 TGGAAAATAA
Statistics
Matches: 187, Mismatches: 35, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
99 12 0.06
100 78 0.42
101 54 0.29
102 12 0.06
103 15 0.08
104 16 0.09
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (101 bp):
TTTTGAAAAATATATATAATATATATTTTAAAAACATTTTGAAAAATATATAGATTTTAAAAATA
TTTTGAAAAAATATATAATATATAGTTTTTGAAACA
Found at i:78484 original size:38 final size:37
Alignment explanation
Indices: 78438--78537 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 37
78428 TTTTTAAAAC
78438 TATATAATTTTGAAAATATTTTTAAAAAATATATAATA
1 TATATAATTTTGAAAATATTTTT-AAAAATATATAATA
* * * *
78476 TATATAATTTTTAAAATACTTTTGAAAATATATATTA
1 TATATAATTTTGAAAATATTTTTAAAAATATATAATA
* *
78513 TATAGATTTTTGGAAAATAATTTTT
1 TATATAATTTT-GAAAAT-ATTTTT
78538 TATATATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
37 21 0.40
38 26 0.50
39 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
TATATAATTTTGAAAATATTTTTAAAAATATATAATA
Found at i:78545 original size:38 final size:35
Alignment explanation
Indices: 78438--78551 Score: 102
Period size: 38 Copynumber: 3.1 Consensus size: 35
78428 TTTTTAAAAC
* * * *
78438 TATATAATTTTGAAAATATTTTTAAAAAATATATAAT
1 TATATAATTTTTAAAATAATTTT-GAATATATAT-AT
* *
78475 ATATATAATTTTTAAAATACTTTTGAAAATATATAT
1 -TATATAATTTTTAAAATAATTTTGAATATATATAT
**
78511 TATATAGATTTTTGGAAAATAATTTTTTATATATATAT
1 TATATA-ATTTTT--AAAATAATTTTGAATATATATAT
78549 TAT
1 TAT
78552 TTGTTTATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
35 6 0.09
36 8 0.12
37 9 0.14
38 43 0.65
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (35 bp):
TATATAATTTTTAAAATAATTTTGAATATATATAT
Found at i:81686 original size:19 final size:19
Alignment explanation
Indices: 81662--81707 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
81652 CATTAGACAT
81662 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
81681 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
81700 TTTGCATT
1 TTTGCATT
81708 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:85551 original size:164 final size:164
Alignment explanation
Indices: 85112--86356 Score: 1396
Period size: 164 Copynumber: 7.6 Consensus size: 164
85102 TTTAAGATAA
* *
85112 CATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* * * * *
85177 TTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAAAGTCCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* * *
85242 CCGAGTTCGATTACACTCAACTTCGAGGGCACAT
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * * *
85276 CATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGTCAACCAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGACTAC
* * * * *
85341 GCTCAGCTCCAATGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * *
85406 CCCGAGTTCGATTACACTCAGCTCCGAGGGCATAA
130 CTCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * **
85441 CATTTTCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTATA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* * * * * * * * * *
85506 TTCAGCTCCTAGGTACATCATTTGCAGCATAGCTAAAGTCGAGAAGTGCTATATGCGAAAGACTC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* *
85571 TCGTGTTCGATTACACTCAGCTTCGAGGGCATAC
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * *
85605 CATTTACAGCATAACTCAAGGCTAGAAGGGTTTTCTGTCACCAAAGACCTTCGAATTCGACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* * * *
85670 CTCAGCTCCAAGGCACATCATTTACATCATAACTCAA-TGCTAGAAGGGTTATCTGTCACCAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT-CGAGAAGGGTTATCTG---CCAAAG
* * * * * * *
85734 ACCTTCGAGTTCTACTACGCTCAGC-TCCAAGGCACAT
127 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * * * * *
85771 CATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCT-TC--CAAAGACCTTCGAGTTCGATTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* * * * *
85833 CTCAGCTCTAAGGTACATCATTTGCAACATAACTTAAGTCGAG-AGGGCTATCTGCC-AAGACCT
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* *
85896 TTGAGTTCGATTACACTCAACTTCGAGGGCATAT
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * * * * *
85930 CATTTGCAGCGTAACTTAAGTCAAGAATGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* * * * * * *
85995 CTCAGCTACGATGCACGTCATTTACAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAAAGACAC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
*
86060 TCGAGTTCGATTACACTCAGCATCGAGGGCATAT
131 TCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* *
86094 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGACTAC
* * * *
86159 GCTCAACTCCCAGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAG
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C--CAAAG
* * * *
86224 ACCTTTGAGTTCGATTACACTCAGC-TCAACGGCATAT
127 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
** * * * * **
86261 CATTTGCAATATAGCTCAAGGCTAGAAGGGTTGTCT-ACTA-AAA-ACCTTCGAGTTTAACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
* **
86323 CTCAACTCCAAGGCACATCATTTATAGCATAACT
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACT
86357 CAAGGAAAAA
Statistics
Matches: 908, Mismatches: 157, Indels: 33
0.83 0.14 0.03
Matches are distributed among these distances:
158 23 0.03
159 41 0.05
160 1 0.00
162 67 0.07
163 116 0.13
164 315 0.35
165 215 0.24
166 38 0.04
167 65 0.07
168 27 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (164 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
TCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
Found at i:85706 original size:83 final size:83
Alignment explanation
Indices: 85112--86361 Score: 1058
Period size: 83 Copynumber: 15.3 Consensus size: 83
85102 TTTAAGATAA
* * * *
85112 CATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
*
85177 TTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * ** * *
85195 CATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTG---CCAAAGTCCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
85257 CTCAACTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * *
85276 CATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGTCAACCAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
* *
85341 GCTCAGCTCCAATGAACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * ** * *
85360 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT-T-T-GCCAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
85422 CTCAGCTCCGAGGGCATAA
66 CTCAGCTCC-AAGGCACAT
* * * * * **
85441 CATTTTCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTATA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
85506 TTCAGCTCCTAGGTACAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * * *
85524 CATTTGCAGCATAGCTAAAGTCGAGAAGTGCTATATG---CGAAAGA-CTCTCGTGTTCGATTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCT-TCGAGTTCGACTAC
* * * * *
85585 ACTCAGCTTCGAGGGCATAC
65 GCTCAGC-TCCAAGGCACAT
* * * *
85605 CATTTACAGCATAACTCAAGGCTAGAAGGGTTTTCTGTCACCAAAGACCTTCGAATTCGACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
85670 CTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * * * *
85688 CATTTACATCATAACTCAATGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCTACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
85753 CTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * * * * *
85771 CATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCT-T--CCAAAGACCTTCGAGTTCGATTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* *
85833 CTCAGCTCTAAGGTACAT
66 CTCAGCTCCAAGGCACAT
* * * * * * *
85851 CATTTGCAACATAACTTAAGTCGAG-AGGGCTATCTG---CC-AAGACCTTTGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * *
85911 CTCAACTTCGAGGGCATAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * *
85930 CATTTGCAGCGTAACTTAAGTCAAGAATGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * *
85995 CTCAGCTACGATGCACGT
66 CTCAGCTCCAAGGCACAT
* * ** *
86013 CATTTACAGCATAACTTAAGTTGAGAAGGGTTATCTG---CCAAAGACAC-TCGAGTTCGATTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGAC-CTTCGAGTTCGACTAC
* * * *
86074 ACTCAGCATCGAGGGCATAT
65 GCTCAGC-TCCAAGGCACAT
* *
86094 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
* * *
86159 GCTCAACTCCCAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * *
86178 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
*
86243 CTCAGCT-CAACGGCATAT
66 CTCAGCTCCAA-GGCACAT
** * * * * * **
86261 CATTTGCAATATAGCTCAAGGCTAGAAGGGTTGTC--T-ACTAAAAACCTTCGAGTTTAACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
*
86323 CTCAACTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
**
86341 CATTTATAGCATAACTCAAGG
1 CATTTGCAGCATAACTCAAGG
86362 AAAAAAGGGC
Statistics
Matches: 933, Mismatches: 203, Indels: 65
0.78 0.17 0.05
Matches are distributed among these distances:
78 25 0.03
79 44 0.05
80 217 0.23
81 150 0.16
82 5 0.01
83 281 0.30
84 161 0.17
85 50 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:86998 original size:33 final size:32
Alignment explanation
Indices: 86960--87288 Score: 187
Period size: 33 Copynumber: 9.8 Consensus size: 32
86950 GCAAATGGTT
*
86960 TTTTGAAAATATATATATATAGTTTTGAAACA
1 TTTTGAAAATATATATATATAGTTTTAAAACA
*
86992 TGTTTGAAAACATTTTATATTATATAGTTTTTTTTAAAAAACA
1 T-TTTG-AAA-A-TATATA-TATATAG----TTTT--AAAACA
*
87035 TTTTGAAAATAAATATAATATAGTTTTTTTAAAACA
1 TTTTGAAAATATATAT-ATATAG---TTTTAAAACA
* *
87071 TTTTTGAAAAAATATATATTGTATA-TTTTTAAACA
1 -TTTTG--AAAATATATA-TATATAGTTTTAAAACA
* *
87106 TTTTGAAAA-ATATGTAT-T--TTTAAAAACA
1 TTTTGAAAATATATATATATAGTTTTAAAACA
*
87134 TTTTGAAAACTATAT-TATATAGTTTTGAAATCA
1 TTTTGAAAA-TATATATATATAGTTTT-AAAACA
87167 TTTTGAAAA-ACTATATATATAGTTTTAAAACA
1 TTTTGAAAATA-TATATATATAGTTTTAAAACA
* * * *
87199 TTTTTAAAA-CTATATA-AT--TTTGAAAATA
1 TTTTGAAAATATATATATATAGTTTTAAAACA
* * *
87227 TTTTAAAAAAATTATAATATATATAATTTTAAAATA
1 TTTT--GAAAA-TAT-ATATATATAGTTTTAAAACA
*
87263 CTTTTGAAAATATAT-TATATATTTTT
1 -TTTTGAAAATATATATATATAGTTTT
87289 GGAAAATATT
Statistics
Matches: 241, Mismatches: 23, Indels: 66
0.73 0.07 0.20
Matches are distributed among these distances:
28 29 0.12
29 4 0.02
30 13 0.05
31 11 0.05
32 35 0.15
33 36 0.15
34 13 0.05
35 14 0.06
36 20 0.08
37 16 0.07
38 8 0.03
39 23 0.10
40 2 0.01
41 7 0.03
42 4 0.02
43 6 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (32 bp):
TTTTGAAAATATATATATATAGTTTTAAAACA
Found at i:87060 original size:39 final size:37
Alignment explanation
Indices: 86959--87115 Score: 116
Period size: 37 Copynumber: 4.3 Consensus size: 37
86949 TGCAAATGGT
* *
86959 TTTTTGAAAATATATAT-ATATAG---TTTTGAAACA
1 TTTTTGAAAAAATATATAATATAGTTTTTTTAAAACA
* * *
86992 TGTTTGAAAACATTTTATATTATATAGTTTTTTTTAAAAAACA
1 TTTTTGAAAA-A--ATATATAATATAG-TTTTTTT--AAAACA
87035 -TTTTGAAAATAA-ATATAATATAGTTTTTTTAAAACA
1 TTTTTGAAAA-AATATATAATATAGTTTTTTTAAAACA
* * *
87071 TTTTTGAAAAAATATATATTGTA-TATTTTT-AAACA
1 TTTTTGAAAAAATATATAATATAGTTTTTTTAAAACA
87106 -TTTTGAAAAA
1 TTTTTGAAAAA
87116 TATGTATTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
33 9 0.09
34 10 0.10
35 5 0.05
36 19 0.19
37 23 0.23
38 7 0.07
39 10 0.10
41 4 0.04
42 9 0.09
43 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAAAATATATAATATAGTTTTTTTAAAACA
Found at i:87149 original size:26 final size:24
Alignment explanation
Indices: 87092--87149 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 24
87082 ATATATATTG
87092 TATATTTTTAAACATTTTGAAAAA
1 TATATTTTTAAACATTTTGAAAAA
*
87116 TATGTATTTTTAAAAACATTTTGAAAAC
1 TA--TATTTTT--AAACATTTTGAAAAA
87144 TATATT
1 TATATT
87150 ATATAGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
26 11 0.38
28 16 0.55
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (24 bp):
TATATTTTTAAACATTTTGAAAAA
Found at i:87283 original size:36 final size:37
Alignment explanation
Indices: 87209--87300 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
87199 TTTTTAAAAC
87209 TATATAATTTTGAAAATATTTTAAAAAAATTATAATA
1 TATATAATTTTGAAAATATTTTAAAAAAATTATAATA
*
87246 TATATAATTTT-AAAATACTTTT--GAAAA-TAT-AT-
1 TATATAATTTTGAAAATA-TTTTAAAAAAATTATAATA
*
87278 TATATATTTTTGGAAAATATTTT
1 TATATAATTTT-GAAAATATTTT
87301 TTATATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 10 0.20
33 6 0.12
34 9 0.18
35 4 0.08
36 6 0.12
37 15 0.30
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TATATAATTTTGAAAATATTTTAAAAAAATTATAATA
Found at i:87294 original size:22 final size:21
Alignment explanation
Indices: 87264--87306 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
87254 TTTAAAATAC
87264 TTTTGAAAATATATTATATAT
1 TTTTGAAAATATATTATATAT
* *
87285 TTTTGGAAAATATTTTTTATAT
1 TTTT-GAAAATATATTATATAT
87307 ATATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTGAAAATATATTATATAT
Found at i:87375 original size:13 final size:13
Alignment explanation
Indices: 87327--87378 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
87317 TTTATTTACC
* *
87327 TTTTTATTTGTTA
1 TTTTCATTTTTTA
*
87340 TTATT-ATTTATTA
1 TT-TTCATTTTTTA
*
87353 ATTTCATTTTTTA
1 TTTTCATTTTTTA
87366 TTTTCATTTTTTA
1 TTTTCATTTTTTA
87379 GGGTCAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 29 0.88
14 2 0.06
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTTTA
Done.