Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006392.1 Hibiscus syriacus cultivar Beakdansim tig00015401_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: 55361
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12599 original size:21 final size:21
Alignment explanation
Indices: 12573--12614 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12563 CTAGAATGGG
*
12573 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
12594 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
12615 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:12770 original size:34 final size:35
Alignment explanation
Indices: 12730--12813 Score: 134
Period size: 34 Copynumber: 2.4 Consensus size: 35
12720 CCATGCAGGA
12730 GAGAATCTGTACCCGGGGAATCGATA-CCCCTGGG
1 GAGAATCTGTACCCGGGGAATCGATACCCCCTGGG
*
12764 GAGAATCTGTTCCCGGGGAATCGATACCCCCCTGGG
1 GAGAATCTGTACCCGGGGAATCGATA-CCCCCTGGG
*
12800 GGGAATCTGTACCC
1 GAGAATCTGTACCC
12814 TCTGGACAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 25 0.56
36 20 0.44
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (35 bp):
GAGAATCTGTACCCGGGGAATCGATACCCCCTGGG
Found at i:13696 original size:29 final size:29
Alignment explanation
Indices: 13654--13713 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
13644 ATACAGTGGT
13654 CTTGGAGGTCGCCATGCCATCCGGGCGAC
1 CTTGGAGGTCGCCATGCCATCCGGGCGAC
*
13683 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGCCATCCGGGCGAC
13712 CT
1 CT
13714 GTGTGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.33, G:0.35, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGCCATCCGGGCGAC
Found at i:13790 original size:33 final size:33
Alignment explanation
Indices: 13753--13866 Score: 153
Period size: 33 Copynumber: 3.5 Consensus size: 33
13743 ATGCAATCAA
13753 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
* *
13786 CATGGGACGTGGGAATGCAT-GGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
13818 CATGGG--GTGGGAATGCATGGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGGAGGGGA---TG
*
13852 CATTGGACGTGGGAA
1 CATGGGACGTGGGAA
13867 AACCTTCCTC
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.17
31 8 0.11
32 16 0.23
33 20 0.29
34 7 0.10
36 7 0.10
ACGTcount: A:0.21, C:0.09, G:0.53, T:0.18
Consensus pattern (33 bp):
CATGGGACGTGGGAATGCATGGGGGAGGGGATG
Found at i:13814 original size:15 final size:15
Alignment explanation
Indices: 13761--13839 Score: 113
Period size: 15 Copynumber: 5.1 Consensus size: 15
13751 AACATGGGAC
13761 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
13777 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
13792 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
13809 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
13824 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
13839 G
1 G
13840 GAGGGGATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
15 34 0.60
16 10 0.18
17 13 0.23
ACGTcount: A:0.20, C:0.08, G:0.54, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:14425 original size:21 final size:21
Alignment explanation
Indices: 14400--14443 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
14390 AATCTAGTTA
14400 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
14421 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
14442 AT
1 AT
14444 ATATATTAGT
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:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:14457 original size:34 final size:34
Alignment explanation
Indices: 14419--14516 Score: 99
Period size: 38 Copynumber: 2.7 Consensus size: 34
14409 TTAGTATAAA
* *
14419 TTATTAGTTTGTTAGTTTAAGTTATATATATTAG
1 TTATTAGTTTGTTAGTTTAAGTTATAAAAATTAG
*
14453 TTATTAGTTTAAGTTATTATTATA-TATATAAAAATTAG
1 TTATTAGTTT--GTTAGT-TTA-AGT-TATAAAAATTAG
*
14491 TTAATTAGTTTCTTAGTTTAAGTTAT
1 TT-ATTAGTTTGTTAGTTTAAGTTAT
14517 TAAATATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
34 10 0.19
35 4 0.08
36 9 0.17
37 8 0.15
38 13 0.25
39 8 0.15
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (34 bp):
TTATTAGTTTGTTAGTTTAAGTTATAAAAATTAG
Found at i:14467 original size:13 final size:13
Alignment explanation
Indices: 14430--14471 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
14420 TATTAGTTTG
14430 TTAGTTTAAGTTA
1 TTAGTTTAAGTTA
14443 TATA-TATT-AGTTA
1 T-TAGT-TTAAGTTA
14456 TTAGTTTAAGTTA
1 TTAGTTTAAGTTA
14469 TTA
1 TTA
14472 TTATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (13 bp):
TTAGTTTAAGTTA
Found at i:14548 original size:41 final size:46
Alignment explanation
Indices: 14456--14548 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 46
14446 ATATTAGTTA
*
14456 TTAGTTTAAGTTATTATTATATATATAAAAATTAGTTAATTAGTTTC
1 TTAGTTTAAGTTATTA-TATATATATAAAAATTAGTTAATTAATTTC
*
14503 TTAGTTTAAGTTATTA-A-ATATA-AAAAA-TA-TTAATTAATTTG
1 TTAGTTTAAGTTATTATATATATATAAAAATTAGTTAATTAATTTC
14544 TTAGT
1 TTAGT
14549 GTCTTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
41 15 0.34
42 2 0.05
43 5 0.11
44 5 0.11
45 1 0.02
47 16 0.36
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (46 bp):
TTAGTTTAAGTTATTATATATATATAAAAATTAGTTAATTAATTTC
Found at i:15311 original size:26 final size:25
Alignment explanation
Indices: 15282--15340 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
15272 AAATCATATT
*
15282 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
15308 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
15334 ATTATTA
1 ATTATTA
15341 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:18386 original size:124 final size:124
Alignment explanation
Indices: 18166--18752 Score: 1070
Period size: 124 Copynumber: 4.8 Consensus size: 124
18156 ATGTATTTAT
18166 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18231 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
18290 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18355 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
18414 TAATCATTATAAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18479 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
18538 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18603 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
18662 TAATCA-T-T----AT-A---AA-AATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* *
18716 TTGATAATAATCATTATAATAATGATTTTATAATAAT
66 TTGATAATAATCATTATAGTAATGATTTGATAATAAT
18753 TATTTAGTTA
Statistics
Matches: 459, Mismatches: 4, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
113 76 0.17
114 2 0.00
117 1 0.00
118 2 0.00
122 1 0.00
123 1 0.00
124 376 0.82
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:18404 original size:150 final size:144
Alignment explanation
Indices: 18221--18564 Score: 401
Period size: 150 Copynumber: 2.3 Consensus size: 144
18211 TTTGATGATT
* *
18221 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT-
* * *
18286 GTAATAATCATTATAAA-AATGATTTAATAATGATTTA-AAT-ATTTAATGATTTGATGATT-TA
63 -TAATAATCATT-TAAATAATGA-TT--TAATGATTTAGAATGATTTAAT-A-ATAATCATTATA
18347 GTAATGATTTGATAATAATCATTA
121 GTAATGATTTGATAATAATCATTA
18371 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* * *
18436 ATAATGATTTAAATTTTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATCATTTAAA----TAATGATTTAATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
18501 TGATTTGATAATAATCATTA
125 TGATTTGATAATAATCATTA
* *
18521 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
18565 GATTTAAATA
Statistics
Matches: 172, Mismatches: 10, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
146 4 0.02
147 10 0.06
148 9 0.05
149 10 0.06
150 127 0.74
151 12 0.07
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (144 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATCATTTAAATAATGATTTAATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATTT
GATAATAATCATTA
Found at i:18475 original size:19 final size:19
Alignment explanation
Indices: 18428--18483 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
18418 CATTATAAAA
18428 ATGATTTAATAATGATTT-
1 ATGATTTAATAATGATTTG
* *
18446 A-AATTT-TTAATGATTTG
1 ATGATTTAATAATGATTTG
*
18463 ATGATTTAGTAATGATTTG
1 ATGATTTAATAATGATTTG
18482 AT
1 AT
18484 AATAATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
ATGATTTAATAATGATTTG
Found at i:18683 original size:26 final size:26
Alignment explanation
Indices: 18224--18682 Score: 404
Period size: 26 Copynumber: 18.3 Consensus size: 26
18214 GATGATTTAG
*
18224 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18250 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18276 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18302 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
18325 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
18348 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18374 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18400 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18426 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
** * * * * * *
18449 TTTTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
18472 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18498 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18524 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18550 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
18573 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
18596 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18622 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18648 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
*
18674 AAATGATTT
1 TAATGATTT
18683 AAATATTTAA
Statistics
Matches: 356, Mismatches: 52, Indels: 50
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.03
22 9 0.03
23 34 0.10
24 21 0.06
25 22 0.06
26 255 0.72
27 3 0.01
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:18985 original size:17 final size:17
Alignment explanation
Indices: 18960--18992 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18950 ACTAAATATT
*
18960 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
18977 TAATGATTTGATACTA
1 TAATGATTTGATACTA
18993 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:18985 original size:25 final size:23
Alignment explanation
Indices: 18906--18985 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
18896 GATTTATTGT
18906 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
18927 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
18954 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
18976 GTAATGATTT
1 -TAAT-ATTT
18986 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:21165 original size:15 final size:14
Alignment explanation
Indices: 21142--21172 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
21132 TACAACACTA
21142 AACTTTAATATAAT
1 AACTTTAATATAAT
21156 AACTTATAATATAAT
1 AACTT-TAATATAAT
21171 AA
1 AA
21173 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:21180 original size:16 final size:16
Alignment explanation
Indices: 21147--21193 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
21137 CACTAAACTT
*
21147 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
21162 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
21178 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
21194 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:21509 original size:41 final size:40
Alignment explanation
Indices: 21421--21509 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
21411 TTAACAAAAC
* *
21421 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
21462 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
21503 AAACTAA
1 AAACTAA
21510 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:21674 original size:21 final size:21
Alignment explanation
Indices: 21644--21696 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
21634 CCCTTTCCTC
*
21644 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
21665 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
21686 TTCTTTCTTTC
1 TTCTTTCTTTC
21697 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:21687 original size:17 final size:16
Alignment explanation
Indices: 21667--21698 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
21657 TTCTCCCTTT
21667 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
21684 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
21699 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:21731 original size:23 final size:23
Alignment explanation
Indices: 21701--21746 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21691 TCTTTCTCGG
21701 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
21724 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
21747 TCTTTCTTTT
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:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:21787 original size:25 final size:25
Alignment explanation
Indices: 21759--21810 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
21749 TTTCTTTTAT
21759 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
21784 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
21809 AA
1 AA
21811 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:22000 original size:13 final size:13
Alignment explanation
Indices: 21982--22013 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
21972 GGCTGCATGT
21982 GAATGGATGATGG
1 GAATGGATGATGG
21995 GAATGGATGATGG
1 GAATGGATGATGG
22008 GAATGG
1 GAATGG
22014 CGCCGGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (13 bp):
GAATGGATGATGG
Found at i:22047 original size:29 final size:29
Alignment explanation
Indices: 22014--22151 Score: 215
Period size: 29 Copynumber: 4.8 Consensus size: 29
22004 ATGGGAATGG
22014 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
22043 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
22072 CGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
22101 CGTCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
22130 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
22152 CTCTATTCCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 100 0.98
30 2 0.02
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:22210 original size:26 final size:26
Alignment explanation
Indices: 22174--22228 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
22164 GCATGGCCAC
22174 CTCGCATGGGGAGAACGCTCATATGG
1 CTCGCATGGGGAGAACGCTCATATGG
*
22200 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCATATGG
22226 CTC
1 CTC
22229 CTATGCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCATATGG
Found at i:22262 original size:35 final size:35
Alignment explanation
Indices: 22216--22303 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
22206 TGGGGAGAAC
*
22216 GCTCGTATGGCTCCTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
22251 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
22286 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
22304 TCACCCCGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:22315 original size:12 final size:12
Alignment explanation
Indices: 22298--22339 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
22288 TCGTATGGCT
22298 CGTATGTCACCC
1 CGTATGTCACCC
*
22310 CGTATGTCAACC
1 CGTATGTCACCC
22322 CGTATGTCACCC
1 CGTATGTCACCC
22334 CGTATG
1 CGTATG
22340 GCCACCTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:22382 original size:30 final size:32
Alignment explanation
Indices: 22348--22413 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 32
22338 TGGCCACCTC
22348 GCATGGGGAGAA-C-GCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
22378 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACC--T-GCTCGTATGGCTCGTAT
22413 G
1 G
22414 TCAACCCGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 12 0.39
31 1 0.03
35 18 0.58
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (32 bp):
GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
Found at i:22725 original size:2 final size:2
Alignment explanation
Indices: 22718--22763 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
22708 ACGAATTACC
*
22718 TA TA TA TA TA CA TA 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 TA TA TA TA TA TA TA
22760 TA TA
1 TA TA
22764 AACCATCCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29200 original size:19 final size:19
Alignment explanation
Indices: 29173--29215 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
29163 TAGGTCTCTA
*
29173 GGAGTACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
29192 GGAGCACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
29211 GGAGC
1 GGAGC
29216 TGCAACAGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.35, T:0.12
Consensus pattern (19 bp):
GGAGCACACGGCGACCTAT
Found at i:31804 original size:69 final size:69
Alignment explanation
Indices: 31688--31825 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
31678 TTATTAATGA
* * *
31688 GGCGTGCTAATACATGTATAAGTCAATATTGGTAGTTTAATAAATGAAATGATTAACTTACACCG
1 GGCGAGCTAATACAGGTATAAGTCAATATTAGTAGTTTAATAAATGAAATGATTAACTTACACCG
31753 GTGT
66 GTGT
31757 GGCGAGCTAATACAGGTATAAGTCAATATTAGTAGTTTAATAAATGAAATGATTAACTTACACCG
1 GGCGAGCTAATACAGGTATAAGTCAATATTAGTAGTTTAATAAATGAAATGATTAACTTACACCG
31822 GTGT
66 GTGT
31826 AAGTCAATTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (69 bp):
GGCGAGCTAATACAGGTATAAGTCAATATTAGTAGTTTAATAAATGAAATGATTAACTTACACCG
GTGT
Found at i:35147 original size:60 final size:60
Alignment explanation
Indices: 35020--35147 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
35010 AAATGATCCT
* * * * * *
35020 CTGACTATATGGTGTTGCTTTGTTAAGTTCTTTAACTATTGAAAGTTAAAAAATAGTCAC
1 CTGACTATAGGGTGTTGCTTTGTTAAGTCCATCAACTATTAAAAGTTAAAAAATAATCAC
* * *
35080 CTAACTATAGGGTGTTGCTTTGTTGAGTCCATCAACTATTAAAAGTTACAAAATAATCAC
1 CTGACTATAGGGTGTTGCTTTGTTAAGTCCATCAACTATTAAAAGTTAAAAAATAATCAC
*
35140 TTGACTAT
1 CTGACTAT
35148 TATGTAGTAG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (60 bp):
CTGACTATAGGGTGTTGCTTTGTTAAGTCCATCAACTATTAAAAGTTAAAAAATAATCAC
Found at i:42792 original size:19 final size:20
Alignment explanation
Indices: 42748--42794 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
42738 TGATATGAGT
42748 TATGTGATATGAAAATATGAC
1 TATGTGATATG-AAATATGAC
*
42769 CATGTGATATG-AATATGTA-
1 TATGTGATATGAAATATG-AC
42788 TATGTGA
1 TATGTGA
42795 CAAACATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 10 0.43
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (20 bp):
TATGTGATATGAAATATGAC
Found at i:42923 original size:21 final size:21
Alignment explanation
Indices: 42897--42957 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
42887 ATATGTGTTA
*
42897 TATGTGGTCCTCCGGGACATC
1 TATGTGGTCCTTCGGGACATC
42918 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCCTTCGGGACATC
*
42939 TATGTGGTCATTCGGGACA
1 TATGTGGTCCTTCGGGACA
42958 AATTATGCGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.31
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATC
Found at i:43206 original size:2 final size:2
Alignment explanation
Indices: 43201--43230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43191 TGTGATTTTG
43201 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
43231 GAGTATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45781 original size:9 final size:9
Alignment explanation
Indices: 45759--45827 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
45749 TCGGTTTTCA
45759 ACCGGTTCTG
1 ACCGGTT-TG
45769 ACCGGTTTG
1 ACCGGTTTG
*
45778 ACCGGTTCG
1 ACCGGTTTG
45787 AACCGGTTTG
1 -ACCGGTTTG
*
45797 ACCGGTCTG
1 ACCGGTTTG
*
45806 AACCGATTTG
1 -ACCGGTTTG
*
45816 ACCGGTCTG
1 ACCGGTTTG
45825 ACC
1 ACC
45828 CAATCGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 28 0.56
10 22 0.44
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:45783 original size:19 final size:19
Alignment explanation
Indices: 45759--45825 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
45749 TCGGTTTTCA
45759 ACCGGTTCTG-ACCGGTTTG
1 ACCGG-TCTGAACCGGTTTG
45778 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
*
45797 ACCGGTCTGAACCGATTTG
1 ACCGGTCTGAACCGGTTTG
45816 ACCGGTCTGA
1 ACCGGTCTGA
45826 CCCAATCGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 1 0.02
18 2 0.05
19 40 0.91
20 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:45848 original size:9 final size:9
Alignment explanation
Indices: 45836--45881 Score: 56
Period size: 9 Copynumber: 4.7 Consensus size: 9
45826 CCCAATCGAC
45836 CCGACCCGA
1 CCGACCCGA
45845 CCGACCCGA
1 CCGACCCGA
45854 CCCGACCCGA
1 -CCGACCCGA
45864 CCGTTGACCCGA
1 CC---GACCCGA
45876 CCGACC
1 CCGACC
45882 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 15 0.45
10 9 0.27
12 9 0.27
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.04
Consensus pattern (9 bp):
CCGACCCGA
Found at i:45849 original size:14 final size:14
Alignment explanation
Indices: 45832--45881 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
45822 CTGACCCAAT
45832 CGACCCGACCCGAC
1 CGACCCGACCCGAC
45846 CGACCCGACCCGACC
1 CGACCCGACCCGA-C
*
45861 CGACCGTTGACCCGAC
1 CGACC--CGACCCGAC
45877 CGACC
1 CGACC
45882 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 13 0.41
15 6 0.19
16 6 0.19
17 7 0.22
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.04
Consensus pattern (14 bp):
CGACCCGACCCGAC
Found at i:45877 original size:5 final size:5
Alignment explanation
Indices: 45832--45865 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
45822 CTGACCCAAT
45832 CGACC CGACC CGA-C CGACC CGACC CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC
45866 GTTGACCCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:45881 original size:16 final size:16
Alignment explanation
Indices: 45838--45888 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
45828 CAATCGACCC
*
45838 GACCCGACCGACC--C
1 GACCCGACCGACCGTT
45852 GACCCGACCCGACCGTT
1 GACCCGA-CCGACCGTT
45869 GACCCGACCGACCGTT
1 GACCCGACCGACCGTT
45885 GACC
1 GACC
45889 GTTGACTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 7 0.21
15 6 0.18
16 13 0.39
17 7 0.21
ACGTcount: A:0.20, C:0.49, G:0.24, T:0.08
Consensus pattern (16 bp):
GACCCGACCGACCGTT
Found at i:53056 original size:9 final size:9
Alignment explanation
Indices: 53036--53093 Score: 71
Period size: 9 Copynumber: 6.1 Consensus size: 9
53026 TCGTTTTCAA
53036 CGGTTCTGAC
1 CGGTT-TGAC
53046 CGGTTTGAC
1 CGGTTTGAC
53055 CGGTTTCGAC
1 CGGTTT-GAC
*
53065 CGGTTCGAAC
1 CGGTTTG-AC
53075 CGGTTTGAC
1 CGGTTTGAC
*
53084 CGGTCTGAC
1 CGGTTTGAC
53093 C
1 C
53094 CGACCGACCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 22 0.51
10 21 0.49
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.28
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:53065 original size:19 final size:18
Alignment explanation
Indices: 53036--53093 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
53026 TCGTTTTCAA
53036 CGGTTCTGACCGGTTTGAC
1 CGGTT-TGACCGGTTTGAC
*
53055 CGGTTTCGACCGGTTCGAAC
1 CGGTTT-GACCGGTTTG-AC
*
53075 CGGTTTGACCGGTCTGAC
1 CGGTTTGACCGGTTTGAC
53093 C
1 C
53094 CGACCGACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 22 0.65
20 8 0.24
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.28
Consensus pattern (18 bp):
CGGTTTGACCGGTTTGAC
Found at i:53126 original size:22 final size:21
Alignment explanation
Indices: 53097--53140 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
53087 TCTGACCCGA
53097 CCGACCGACCCGACCGTTGAC
1 CCGACCGACCCGACCGTTGAC
53118 CCGACCCGACCCGACCGTTGAC
1 CCGA-CCGACCCGACCGTTGAC
53140 C
1 C
53141 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.09
Consensus pattern (21 bp):
CCGACCGACCCGACCGTTGAC
Found at i:53142 original size:7 final size:7
Alignment explanation
Indices: 53130--53160 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
53120 GACCCGACCC
53130 GACCGTT
1 GACCGTT
53137 GACCGTT
1 GACCGTT
53144 GACCGTT
1 GACCGTT
53151 GACCGTT
1 GACCGTT
53158 GAC
1 GAC
53161 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Done.