Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000691.1 Hibiscus syriacus cultivar Beakdansim tig00001347_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: 134756
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:462 original size:26 final size:22
Alignment explanation
Indices: 382--479 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 22
372 GTCAAAAAGG
382 TATATTGTATT-TTATATTTA--A
1 TATATT-TATTATTAT-TTTATTA
*
403 TAAATTTATTATTATTTTATTA
1 TATATTTATTATTATTTTATTA
*
425 TATATTT-GTATTATTTTATTA
1 TATATTTATTATTATTTTATTA
** *
446 TATATTCTAAAATTA-TTAATT-
1 TATATT-TATTATTATTTTATTA
467 TATATTTATTATT
1 TATATTTATTATT
480 TGCAGTTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 13 0.20
21 34 0.53
22 13 0.20
23 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTTATTATTATTTTATTA
Found at i:1560 original size:13 final size:14
Alignment explanation
Indices: 1534--1569 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1524 GTAGAGCTAC
1534 ATTTTTTAATTTTA
1 ATTTTTTAATTTTA
1548 ATTTTTTAA-TTTA
1 ATTTTTTAATTTTA
1561 ATGTTTTTA
1 AT-TTTTTA
1570 TATAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
ATTTTTTAATTTTA
Found at i:4367 original size:8 final size:8
Alignment explanation
Indices: 4334--4422 Score: 79
Period size: 8 Copynumber: 11.1 Consensus size: 8
4324 TAGGAGACAT
*
4334 TTTGAGAA
1 TTTGAGAG
4342 TTTGAGAG
1 TTTGAGAG
*
4350 TTTGAAAG
1 TTTGAGAG
4358 TTTGAGAG
1 TTTGAGAG
**
4366 TTACAGAG
1 TTTGAGAG
*
4374 TTTCAGAG
1 TTTGAGAG
*
4382 TTAGAGAG
1 TTTGAGAG
*
4390 TTTGAGAA
1 TTTGAGAG
* *
4398 TTTAAGAT
1 TTTGAGAG
*
4406 TTTAAGAG
1 TTTGAGAG
*
4414 ATTGAGAG
1 TTTGAGAG
4422 T
1 T
4423 CGGGGAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 65 1.00
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (8 bp):
TTTGAGAG
Found at i:5647 original size:59 final size:53
Alignment explanation
Indices: 5578--5710 Score: 140
Period size: 53 Copynumber: 2.4 Consensus size: 53
5568 TAATGTTATT
* * ** * *
5578 TTTTAATTTTATTTTAAATTATTAAATCTATTTTCTTCTTGTCTTAACCTAAAAATATA
1 TTTTATTTTTATTTT-AATT-TTAAATATA-TTTAATCTTATCATAA-C-AAAAA-ATA
*
5637 TTTTATTTTTATTTTAACTTTAAATATATTTAATCTTATCATAACAAAAAATA
1 TTTTATTTTTATTTTAATTTTAAATATATTTAATCTTATCATAACAAAAAATA
*
5690 TTTTATTTTTATCTTAATTTT
1 TTTTATTTTTATTTTAATTTT
5711 TAAAATTATA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
53 22 0.34
54 5 0.08
55 1 0.02
56 12 0.18
57 8 0.12
58 3 0.05
59 14 0.22
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (53 bp):
TTTTATTTTTATTTTAATTTTAAATATATTTAATCTTATCATAACAAAAAATA
Found at i:5773 original size:30 final size:30
Alignment explanation
Indices: 5734--5810 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
5724 TATTTTTATT
* * *
5734 TTAACTTATTACATATATTATATTATTA-A
1 TTAAATTATTAAATATATTATAATATTACA
* * *
5763 CTTAAATTATTAGATATATTTTAATCTTACA
1 -TTAAATTATTAAATATATTATAATATTACA
5794 TTAAATTATTAAATATA
1 TTAAATTATTAAATATA
5811 GTCTGTCCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (30 bp):
TTAAATTATTAAATATATTATAATATTACA
Found at i:5884 original size:31 final size:31
Alignment explanation
Indices: 5818--5888 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
5808 ATAGTCTGTC
5818 CTTA-TTTTAACATAAAATATATATTTTATT
1 CTTATTTTTAACATAAAATATATATTTTATT
* *
5848 CTTATTTTTAACTTAATAATGTATATTTTATT
1 CTTATTTTTAACATAA-AATATATATTTTATT
5880 -TTATTTTTA
1 CTTATTTTTA
5889 TTTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 4 0.11
31 19 0.51
32 14 0.38
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (31 bp):
CTTATTTTTAACATAAAATATATATTTTATT
Found at i:5911 original size:19 final size:18
Alignment explanation
Indices: 5887--5935 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
5877 ATTTTATTTT
5887 TATTTTTATTTTAAAAATA
1 TATTTTTATTTTAAAAA-A
* *
5906 TATTTTAAATTTAAAAAA
1 TATTTTTATTTTAAAAAA
5924 TA-TTTTATTTTA
1 TATTTTTATTTTA
5936 TCTTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTATTTTAAAAAA
Found at i:6031 original size:28 final size:29
Alignment explanation
Indices: 5953--6069 Score: 107
Period size: 27 Copynumber: 4.1 Consensus size: 29
5943 TTAAAATATT
* * * *
5953 ATAAGAATAAATATAAATATTTAAGGTAAG
1 ATAAGAATAAA-ATATATTTTTAAGTTAAA
* *
5983 GTAACAAT-AAA-ATATTTTTAAGTTAATA
1 ATAAGAATAAAATATATTTTTAAGTTAA-A
*
6011 A-AA-ATTAAAATATATTTTTAAGTTAAA
1 ATAAGAATAAAATATATTTTTAAGTTAAA
*
6038 ATAAGAATAAAATATATTTTTAATTTTAAA
1 ATAAGAATAAAATATATTTTTAA-GTTAAA
6068 AT
1 AT
6070 TTTAATTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.03
27 19 0.27
28 18 0.25
29 19 0.27
30 13 0.18
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
ATAAGAATAAAATATATTTTTAAGTTAAA
Found at i:6067 original size:30 final size:30
Alignment explanation
Indices: 5994--6069 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
5984 TAACAATAAA
5994 ATATTTTTAAGTT--AATAAAAATTAAAAT
1 ATATTTTTAAGTTAAAATAAAAATTAAAAT
*
6022 ATATTTTTAAGTTAAAATAAGAA-TAAAAT
1 ATATTTTTAAGTTAAAATAAAAATTAAAAT
*
6051 ATATTTTTAATTTTAAAAT
1 ATATTTTTAA-GTTAAAAT
6070 TTTAATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 13 0.30
29 16 0.37
30 14 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
ATATTTTTAAGTTAAAATAAAAATTAAAAT
Found at i:6768 original size:10 final size:11
Alignment explanation
Indices: 6750--6789 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
6740 TTATATTATT
6750 TAATATTAAAA
1 TAATATTAAAA
6761 TAAT-TTAAAA
1 TAATATTAAAA
*
6771 TAAATAATAAAA
1 T-AATATTAAAA
6783 TAATATT
1 TAATATT
6790 CCTAACCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 7 0.28
11 12 0.48
12 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:8626 original size:13 final size:13
Alignment explanation
Indices: 8608--8647 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
8598 GATAACAGTG
8608 AAAAAATATTAAT
1 AAAAAATATTAAT
* *
8621 AAAAAATAATATT
1 AAAAAATATTAAT
8634 AATAAAATATTAAT
1 AA-AAAATATTAAT
8648 TAATACATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAAATATTAAT
Found at i:8633 original size:16 final size:15
Alignment explanation
Indices: 8608--8640 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
8598 GATAACAGTG
8608 AAAAAATATTAATAA
1 AAAAAATATTAATAA
8623 AAAATAATATTAATAA
1 AAAA-AATATTAATAA
8639 AA
1 AA
8641 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATATTAATAA
Found at i:13822 original size:19 final size:20
Alignment explanation
Indices: 13789--13836 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
13779 AATGATTTTC
*
13789 TTTTG-AAAACAAAAT-TAG
1 TTTTGAAAAACAAAATGAAG
13807 ATTTTGAAAAAC-AAATGAAG
1 -TTTTGAAAAACAAAATGAAG
13827 TTTTGAAAAA
1 TTTTGAAAAA
13837 TGATTTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAG
Found at i:16698 original size:2 final size:2
Alignment explanation
Indices: 16656--16680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16646 TTATTAAATA
16656 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16681 ATTTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17048 original size:2 final size:2
Alignment explanation
Indices: 17041--17078 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17031 TTAAACCATA
17041 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
17079 TGATTAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18979 original size:23 final size:23
Alignment explanation
Indices: 18949--18994 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18939 ATATGGTGAT
18949 GACATTGTTCCTTCATGATGAGG
1 GACATTGTTCCTTCATGATGAGG
18972 GACATTGTTCCTTCATGATGAGG
1 GACATTGTTCCTTCATGATGAGG
18995 AAGTCTAGTC
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:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (23 bp):
GACATTGTTCCTTCATGATGAGG
Found at i:20081 original size:22 final size:22
Alignment explanation
Indices: 20056--20098 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20046 TGAACCCCTC
*
20056 TTTTGTTCTTTTTTCCTTTTTA
1 TTTTGTTATTTTTTCCTTTTTA
* *
20078 TTTTTTTATTTTTTTCTTTTT
1 TTTTGTTATTTTTTCCTTTTT
20099 TTCCCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTGTTATTTTTTCCTTTTTA
Found at i:20084 original size:9 final size:8
Alignment explanation
Indices: 20072--20150 Score: 52
Period size: 8 Copynumber: 9.2 Consensus size: 8
20062 TCTTTTTTCC
20072 TTTTTATT
1 TTTTTATT
20080 TTTTTATT
1 TTTTTATT
*
20088 TTTTTCTT
1 TTTTTATT
*
20096 TTTTTCCCTT
1 TTTTT--ATT
*
20106 TTTTCATT
1 TTTTTATT
*
20114 TTTTCTCCCTT
1 TTTT-T--ATT
20125 TTTTTA-T
1 TTTTTATT
*
20132 TTTTCATT
1 TTTTTATT
20140 TCTTTTATT
1 T-TTTTATT
20149 TT
1 TT
20151 CTTCATGTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.11
8 29 0.52
9 7 0.12
10 8 0.14
11 6 0.11
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:20084 original size:17 final size:17
Alignment explanation
Indices: 20064--20136 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 17
20054 TCTTTTGTTC
20064 TTTTTT-CCTTTTTATT
1 TTTTTTCCCTTTTTATT
20080 TTTTTAT---TTTTT-TCT
1 TTTTT-TCCCTTTTTAT-T
20095 TTTTTTCCCTTTTTTCATT
1 TTTTTTCCC-TTTTT-ATT
*
20114 TTTTCTCCCTTTTT-TT
1 TTTTTTCCCTTTTTATT
*
20130 ATTTTTC
1 TTTTTTC
20137 ATTTCTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
14 2 0.04
15 11 0.24
16 12 0.26
17 1 0.02
18 10 0.22
19 9 0.20
20 1 0.02
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCCCTTTTTATT
Found at i:20108 original size:19 final size:20
Alignment explanation
Indices: 20086--20135 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
20076 TATTTTTTTA
20086 TTTTTTTC-TTTTTT-TCCC
1 TTTTTTTCATTTTTTCTCCC
20104 -TTTTTTCATTTTTTCTCCC
1 TTTTTTTCATTTTTTCTCCC
20123 TTTTTTT-ATTTTT
1 TTTTTTTCATTTTT
20136 CATTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.24
18 6 0.21
19 10 0.34
20 6 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTCATTTTTTCTCCC
Found at i:28813 original size:2 final size:2
Alignment explanation
Indices: 28766--28793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28756 TTAAAATAAT
28766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28794 ATTTTATTAA
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):
TA
Found at i:28834 original size:16 final size:18
Alignment explanation
Indices: 28802--28839 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
28792 TAATTTTATT
28802 AAAATATATATACATAA-
1 AAAATATATATACATAAC
*
28819 AAAATA-ATATATATAAC
1 AAAATATATATACATAAC
28836 AAAA
1 AAAA
28840 ACCTACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATATATACATAAC
Found at i:29166 original size:2 final size:2
Alignment explanation
Indices: 29159--29216 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
29149 TTAAACCATA
29159 AT 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 AT
29201 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
29217 GATTAGATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32196 original size:22 final size:22
Alignment explanation
Indices: 32171--32213 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
32161 TGAACCCCTC
*
32171 TTTTGTTCTTTTTTCCTTTTTA
1 TTTTGTTATTTTTTCCTTTTTA
* *
32193 TTTTTTTATTTTTTTCTTTTT
1 TTTTGTTATTTTTTCCTTTTT
32214 TTCCCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTGTTATTTTTTCCTTTTTA
Found at i:32199 original size:9 final size:8
Alignment explanation
Indices: 32187--32265 Score: 52
Period size: 8 Copynumber: 9.2 Consensus size: 8
32177 TCTTTTTTCC
32187 TTTTTATT
1 TTTTTATT
32195 TTTTTATT
1 TTTTTATT
*
32203 TTTTTCTT
1 TTTTTATT
*
32211 TTTTTCCCTT
1 TTTTT--ATT
*
32221 TTTTCATT
1 TTTTTATT
*
32229 TTTTCTCCCTT
1 TTTT-T--ATT
32240 TTTTTA-T
1 TTTTTATT
*
32247 TTTTCATT
1 TTTTTATT
32255 TCTTTTATT
1 T-TTTTATT
32264 TT
1 TT
32266 CTTCATGTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.11
8 29 0.52
9 7 0.12
10 8 0.14
11 6 0.11
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:32199 original size:17 final size:17
Alignment explanation
Indices: 32179--32251 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 17
32169 TCTTTTGTTC
32179 TTTTTT-CCTTTTTATT
1 TTTTTTCCCTTTTTATT
32195 TTTTTAT---TTTTT-TCT
1 TTTTT-TCCCTTTTTAT-T
32210 TTTTTTCCCTTTTTTCATT
1 TTTTTTCCC-TTTTT-ATT
*
32229 TTTTCTCCCTTTTT-TT
1 TTTTTTCCCTTTTTATT
*
32245 ATTTTTC
1 TTTTTTC
32252 ATTTCTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
14 2 0.04
15 11 0.24
16 12 0.26
17 1 0.02
18 10 0.22
19 9 0.20
20 1 0.02
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCCCTTTTTATT
Found at i:32223 original size:19 final size:20
Alignment explanation
Indices: 32201--32250 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
32191 TATTTTTTTA
32201 TTTTTTTC-TTTTTT-TCCC
1 TTTTTTTCATTTTTTCTCCC
32219 -TTTTTTCATTTTTTCTCCC
1 TTTTTTTCATTTTTTCTCCC
32238 TTTTTTT-ATTTTT
1 TTTTTTTCATTTTT
32251 CATTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.24
18 6 0.21
19 10 0.34
20 6 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTCATTTTTTCTCCC
Found at i:41581 original size:14 final size:14
Alignment explanation
Indices: 41562--41593 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41552 ATAATAAAAC
*
41562 TAAACAAGGGTAAA
1 TAAACAAAGGTAAA
41576 TAAACAAAGGTAAA
1 TAAACAAAGGTAAA
41590 TAAA
1 TAAA
41594 TAAATACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.16, T:0.16
Consensus pattern (14 bp):
TAAACAAAGGTAAA
Found at i:43756 original size:3 final size:3
Alignment explanation
Indices: 43748--43779 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43738 TTCGAAAAAC
43748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43780 CTATCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:55108 original size:17 final size:17
Alignment explanation
Indices: 55074--55111 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55064 ATCAAAATCA
*
55074 TTTTTTAAAATTTCATT
1 TTTTTTAAAATCTCATT
55091 TTTTTTAAAAATCT-ATT
1 TTTTTT-AAAATCTCATT
55108 TTTT
1 TTTT
55112 CTTTCAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTAAAATCTCATT
Found at i:61341 original size:20 final size:22
Alignment explanation
Indices: 61289--61341 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
61279 ACTGAAAGGG
*
61289 AGTATCGATACCATAGTATATA
1 AGTACCGATACCATAGTATATA
*
61311 AGTATCGATACCAT-G-ATA-A
1 AGTACCGATACCATAGTATATA
61330 AGGTACCGATAC
1 A-GTACCGATAC
61342 TATTGAGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 1 0.03
22 14 0.48
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
AGTACCGATACCATAGTATATA
Found at i:70192 original size:54 final size:54
Alignment explanation
Indices: 70108--70526 Score: 561
Period size: 54 Copynumber: 7.8 Consensus size: 54
70098 TACTCTAACA
* *
70108 ATAATGTATTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCTCGGAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
* *
70162 ATAATGTGTTTATGAACGACCGTATTGGCACTAAGTGTGCAGCCCATC-GAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCA-CGGAATTC
* * * *
70216 ATAATGCGTTTATGAACGACTGTATCGACACTAAGTGTGCAACCCAAGGAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
* * * **
70270 ATAATGTGTTTATAAACGACCGTATCGTCACTAAGTTTGCAACCCATAGAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
** * * * **
70324 ATAATGTGTTTATGAACGACCGTATTAGTACTAAGTGTGTAATCCACAAAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
* * * *
70378 ATAATGTGTGTATGAACGACCGCATCGGCACTAAGTGTACAACCCACGAAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
*
70432 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGAAATTC
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
* * * *
70486 ATAATGAGCTTATGAATGACCGTATCGGCACTACGTGTGCA
1 ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCA
70527 CCCTAGAGAA
Statistics
Matches: 320, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 319 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (54 bp):
ATAATGTGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTC
Found at i:77383 original size:54 final size:54
Alignment explanation
Indices: 76919--77369 Score: 652
Period size: 54 Copynumber: 8.4 Consensus size: 54
76909 TGTATTATTA
* * *
76919 GCACTAAGTGTGAAACCCACGAAATTCATAATGTGTTTATGAATGATCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
*
76973 GCACTAAGTGTGTAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
*
77027 GAACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
* * * *
77081 ACAGTAAGTGTGCAACCCACGAAATTCGTAATGTGTTTATGAACGATCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
** *
77135 GCACTAAGTGTATAACCCACGTAATTCATAATGTGTTTATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
* ** * * *
77189 GCACTAAGTGTGCAATCCACGGGATTCATAATGTGTTTATAAATGATCGTATCG
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
* *
77243 GCACTAAGTGTGCAACCCACAAAATTCATAATGTGTTTATGAACGACCGTATCA
1 GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
* * * *
77297 GCACTAAGTGTGCAACCCAC-ATAATTCATAATGAGCTTATGAATGACCGTATTG
1 GCACTAAGTGTGCAACCCACGA-AATTCATAATGTGTTTATGAACGACCGTATCG
* *
77351 GCACTACGTGTGCACCCCA
1 GCACTAAGTGTGCAACCCA
77370 GAGAACTTAT
Statistics
Matches: 356, Mismatches: 40, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 355 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (54 bp):
GCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCG
Found at i:89997 original size:2 final size:2
Alignment explanation
Indices: 89990--90029 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
89980 ATGTTACGTA
89990 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
90030 TTGGTGTATT
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:90196 original size:16 final size:17
Alignment explanation
Indices: 90162--90200 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
90152 TATCCAGATA
* *
90162 ACCCCTCCACAAGTGTC
1 ACCCCTCCAAAAGTATC
90179 ACCCCT-CAAAAGTATC
1 ACCCCTCCAAAAGTATC
90195 ACCCCT
1 ACCCCT
90201 GAATTCTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.28, C:0.46, G:0.08, T:0.18
Consensus pattern (17 bp):
ACCCCTCCAAAAGTATC
Found at i:90582 original size:4 final size:4
Alignment explanation
Indices: 90575--90602 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
90565 AAAAGTTTTG
90575 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
90603 TTTACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:91388 original size:29 final size:29
Alignment explanation
Indices: 91353--91434 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
91343 AAACTAAATT
*
91353 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
91382 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
91411 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
91435 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:96138 original size:29 final size:29
Alignment explanation
Indices: 96103--96184 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
96093 AAACTAAATT
*
96103 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
96132 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
96161 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
96185 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:105605 original size:36 final size:36
Alignment explanation
Indices: 105564--105639 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
105554 ATTTTCGGGA
*
105564 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
105600 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
105636 TTTT
1 TTTT
105640 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:106080 original size:15 final size:15
Alignment explanation
Indices: 106060--106089 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
106050 TATCACAATC
106060 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
106075 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
106090 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:110602 original size:36 final size:36
Alignment explanation
Indices: 110561--110636 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
110551 ATTTTCGGGA
*
110561 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
110597 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
110633 TTTT
1 TTTT
110637 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:111533 original size:22 final size:18
Alignment explanation
Indices: 111489--111525 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
111479 CCATCAAATT
111489 ATATTAATGGATAAAGAG
1 ATATTAATGGATAAAGAG
111507 ATATTAATGGATAAAGAG
1 ATATTAATGGATAAAGAG
111525 A
1 A
111526 GTGTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (18 bp):
ATATTAATGGATAAAGAG
Found at i:119729 original size:3 final size:3
Alignment explanation
Indices: 119721--119789 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
119711 TTAATATATT
*
119721 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
119769 TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA -TAA TA
119790 TGGGTAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:120531 original size:113 final size:113
Alignment explanation
Indices: 120009--121014 Score: 1708
Period size: 113 Copynumber: 8.9 Consensus size: 113
119999 GATAGAGTTA
* *
120009 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * *
120074 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
63 GAACT-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
120125 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
120190 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAA-ATGATGAATTCAGGTAAAAGG
120239 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
120304 CCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAA-ATGATGAATTCAGGTAAAAGG
120353 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
120418 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
120466 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
120531 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
120579 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
120644 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
120692 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
120757 CCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
120805 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
120870 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
120918 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
120983 CTTTCTCTGGAAATGATGATCCATCAAATGAT
66 CTTTCTCTGGAAATGATGATCCATCAAATGAT
121015 AGATTTGAAT
Statistics
Matches: 865, Mismatches: 23, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 602 0.70
114 216 0.25
116 45 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGGTAAAAGG
Found at i:121880 original size:83 final size:83
Alignment explanation
Indices: 121741--122550 Score: 1538
Period size: 83 Copynumber: 9.8 Consensus size: 83
121731 GTAGTTCTTA
*
121741 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
121805 AATTCAATGATTTGTTCTG
65 AATTCAATGATTTGTTCTG
121824 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
121889 ATTCAATGA-TTGTTCTG
66 ATTCAATGATTTGTTCTG
121906 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
121971 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
121989 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
122054 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
122072 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
122137 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
122155 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
122220 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
*
122238 CCAAACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
122303 ATTCAATGATTTGTTCT-
66 ATTCAATGATTTGTTCTG
122320 CTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
1 C-CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTA
122385 AATTCAATGATTTGTTCTG
65 AATTCAATGATTTGTTCTG
122404 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
122469 ATTCAATGATTTGTTCTG
66 ATTCAATGATTTGTTCTG
*
122487 CCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
122551 GTTAATGTTT
Statistics
Matches: 718, Mismatches: 4, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
82 85 0.12
83 630 0.88
84 3 0.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
ATTCAATGATTTGTTCTG
Found at i:123705 original size:15 final size:13
Alignment explanation
Indices: 123683--123735 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 13
123673 CCTTGACCCC
123683 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
123696 ACTCTTTTTCTTTTT
1 -CT-TTTTTCTTTTT
*
123711 CTTTTTTTTTCTTTT
1 C-TTTTTTCT-TTTT
123726 CTTTTTTCTT
1 CTTTTTTCTT
123736 CATTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 16 0.47
15 17 0.50
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:123732 original size:22 final size:22
Alignment explanation
Indices: 123683--123746 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 22
123673 CCTTGACCCC
**
123683 CTTTTTTC-TTTTTACTCTTTTT
1 CTTTTTTCTTTTTTTTTC-TTTT
123705 CTTTTTCT-TTT-TTTTTCTTTT
1 CTTTTT-TCTTTTTTTTTCTTTT
*
123726 CTTTTTTCTTCATTTTTTCTT
1 CTTTTTTCTT-TTTTTTTCTT
123747 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 12 0.35
22 10 0.29
23 11 0.32
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTTCTTTTTTTTTCTTTT
Found at i:134233 original size:15 final size:13
Alignment explanation
Indices: 134201--134238 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
134191 TTTGACAGAA
134201 AAAT-AAATAATG
1 AAATAAAATAATG
134213 AAATAAAATAATTG
1 AAATAAAATAA-TG
134227 CAAATAAAATAA
1 -AAATAAAATAA
134239 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:134332 original size:6 final size:7
Alignment explanation
Indices: 134313--134337 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
134303 TAAATATATA
134313 AATTTTT
1 AATTTTT
134320 AATTTTT
1 AATTTTT
134327 AATTTTT
1 AATTTTT
134334 AATT
1 AATT
134338 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Done.