Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006952.1 Hibiscus syriacus cultivar Beakdansim tig00017868_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: 59503
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:828 original size:14 final size:14
Alignment explanation
Indices: 809--841 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
799 TGATTGTTTA
809 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
823 ATGA-TTGTAAAAG
1 ATGATTTGTAAAAG
*
836 TTGATT
1 ATGATT
842 CAATAGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (14 bp):
ATGATTTGTAAAAG
Found at i:880 original size:82 final size:84
Alignment explanation
Indices: 752--924 Score: 280
Period size: 82 Copynumber: 2.1 Consensus size: 84
742 TGGCTGCAAT
* * ***
752 AGTTGATACAATAGTAGATGAGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTAA-TGATTT
1 AGTTGATTCAATAGTAGATGAAGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
816 GTAAAAGATGA-TTGTAAA
66 GTAAAAGATGATTTGTAAA
834 AGTTGATTCAATAGTAGAT-AAGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
1 AGTTGATTCAATAGTAGATGAAGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
898 GTAAAAGATGATTTGTAAA
66 GTAAAAGATGATTTGTAAA
917 AGTTGATT
1 AGTTGATT
925 TGTTTAATTG
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
81 34 0.40
82 35 0.42
83 15 0.18
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (84 bp):
AGTTGATTCAATAGTAGATGAAGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
GTAAAAGATGATTTGTAAA
Found at i:911 original size:14 final size:14
Alignment explanation
Indices: 892--927 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
882 ATTGTTTAAT
892 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
906 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
920 TGATTTGT
1 TGATTTGT
928 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1073 original size:33 final size:32
Alignment explanation
Indices: 1031--1161 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 32
1021 AAAAATGACT
1031 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
1064 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
1096 ATCGCAATGCGAAATGAAAATCGCAATCCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--C-G--A-G-AA
1135 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGC-GAAATGAAAATCGCAA
1162 TGCGAAATGA
Statistics
Matches: 90, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
32 27 0.30
33 31 0.34
34 1 0.01
35 1 0.01
37 1 0.01
38 1 0.01
39 12 0.13
40 16 0.18
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:1131 original size:20 final size:19
Alignment explanation
Indices: 1031--1212 Score: 191
Period size: 19 Copynumber: 10.4 Consensus size: 19
1021 AAAAATGACT
1031 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1050 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1064 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1083 ATCGCAA--CG--A-G-AA
1 ATCGCAATGCGAAATGAAA
1096 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1115 ATCGCAATCCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1135 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1155 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1174 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1188 ATCGCAATGCGAAA-AAAA
1 ATCGCAATGCGAAATGAAA
1206 ATCGCAA
1 ATCGCAA
1213 CGAGAGAATC
Statistics
Matches: 140, Mismatches: 7, Indels: 33
0.78 0.04 0.18
Matches are distributed among these distances:
13 9 0.06
14 21 0.15
15 5 0.04
16 4 0.03
17 7 0.05
18 12 0.09
19 44 0.31
20 38 0.27
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1192 original size:14 final size:14
Alignment explanation
Indices: 1173--1226 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1163 GCGAAATGAA
1173 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1187 AATCGCAATGCGAAAAAA
1 AATCGCAA--CG--AGAG
1205 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1219 AATCGCAA
1 AATCGCAA
1227 TGCGATTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
16 4 0.12
18 10 0.31
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1212 original size:32 final size:33
Alignment explanation
Indices: 1154--1231 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 33
1144 CGGAAATGAA
*
1154 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATAAAAATCGCAACGAGAG
1187 AATCGCAATGCGAAA-AAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATAAAAATCGCAACGAGAG
1219 AATCGCAATGCGA
1 AATCGCAATGCGA
1232 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAATGCGAAATAAAAATCGCAACGAGAG
Found at i:1304 original size:20 final size:19
Alignment explanation
Indices: 1221--1417 Score: 225
Period size: 20 Copynumber: 10.7 Consensus size: 19
1211 AACGAGAGAA
*
1221 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1240 TCGCATTGGGATTCTCA--
1 TCGCATTGCGATTTTCATT
1257 -CG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1273 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1292 TCCACATTACGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1312 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1332 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1351 TCCGCGTTGCGATTTTCATAT
1 T-CGCATTGCGATTTTCAT-T
1372 TCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATT
*
1389 T-G--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATT
1405 TCGCATTGCGATT
1 TCGCATTGCGATT
1418 CTCTCGTTGC
Statistics
Matches: 152, Mismatches: 13, Indels: 26
0.80 0.07 0.14
Matches are distributed among these distances:
14 21 0.14
16 4 0.03
17 4 0.03
19 55 0.36
20 66 0.43
21 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1344 original size:39 final size:38
Alignment explanation
Indices: 1221--1417 Score: 225
Period size: 39 Copynumber: 5.3 Consensus size: 38
1211 AACGAGAGAA
* * *
1221 TCGCAATGCGATTTTCATTTCGCATTGGGATTCTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1257 -CG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
1292 TCCACATTACGATTTTCATTTCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
1332 TCGCATTGCGATTTTCATTTCCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCAT-T
*
1372 TCGCATTGCGATTTTCA--T-G--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1405 TCGCATTGCGATT
1 TCGCATTGCGATT
1418 CTCTCGTTGC
Statistics
Matches: 144, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
33 42 0.29
34 12 0.08
35 2 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 48 0.33
40 37 0.26
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1351 original size:59 final size:59
Alignment explanation
Indices: 1259--1389 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 59
1249 GATTCTCACG
1259 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCAT-TTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATT-CGCA
* * *
1318 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCGTTGCGATTTTCATATTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATTCGCA
1377 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1390 GTTGCGGTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 66 0.97
60 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.47
Consensus pattern (59 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATTCGCA
Found at i:1439 original size:33 final size:34
Alignment explanation
Indices: 1318--1450 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 34
1308 CATTTCCGCA
*
1318 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCA--T---CG
*
1357 TTGCGATTTTCATATTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCAT-TTCGCATTGCGATTCTCATCG
*
1391 TTGCGGTTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCATCG
* * *
1424 TTGCGATTGTAATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
1451 AGTCATTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
32 1 0.01
33 29 0.34
34 23 0.27
38 1 0.01
39 13 0.15
40 18 0.21
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATCG
Found at i:1496 original size:20 final size:20
Alignment explanation
Indices: 1423--1496 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1413 CGATTCTCTC
* * *
1423 GTTGCGATTGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
**
1443 GTTGCGATAGTCA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
1463 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
1484 GTTGCGATAGTCA
1 GTTGCGATAGTCA
1497 AATGCATGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.55
21 13 0.31
22 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:3973 original size:24 final size:24
Alignment explanation
Indices: 3939--3992 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3929 CTGAAACATC
*
3939 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
3963 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3987 ATCAAA
1 ATCAAA
3993 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4703 original size:20 final size:20
Alignment explanation
Indices: 4678--4949 Score: 312
Period size: 20 Copynumber: 13.4 Consensus size: 20
4668 AAATTTCAGT
*
4678 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
4698 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
4718 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCTC
*
4738 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
4758 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
4778 GTTGCGATTTACGGATACAT-
1 GTTGCGATTTACGGATTC-TC
* *
4798 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
4819 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
4839 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
4860 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
4880 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
4901 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
4921 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATTCTC
4942 GTTGCGAT
1 GTTGCGAT
4950 AGTAAGAATC
Statistics
Matches: 214, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
20 147 0.69
21 67 0.31
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:4822 original size:41 final size:41
Alignment explanation
Indices: 4676--4949 Score: 330
Period size: 41 Copynumber: 6.8 Consensus size: 41
4666 CAAAATTTCA
*
4676 GTGTTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTA-
1 GTGTTGCGATTTTAC-GTATTGTCGTTGCGATTTACGGA-TAC
* * *
4716 -TCGTTGCGA-TTTACAG-ATTATCGTTGCGATTTACAGATTC
1 GT-GTTGCGATTTTAC-GTATTGTCGTTGCGATTTACGGATAC
* *
4756 -TCGTTGCGA-TTTACGGATTATCGTTGCGATTTACGGATAC
1 GT-GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
4796 ATGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
4837 GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
4878 GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
* * **
4919 GCGTTGCGATTTTACGGATACTCGTTGCGAT
1 GTGTTGCGATTTTACGTATTGTCGTTGCGAT
4950 AGTAAGAATC
Statistics
Matches: 217, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.01
40 76 0.35
41 138 0.64
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (41 bp):
GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
Found at i:4884 original size:82 final size:82
Alignment explanation
Indices: 4678--5010 Score: 387
Period size: 82 Copynumber: 4.1 Consensus size: 82
4668 AAATTTCAGT
* * *
4678 GTTGCGA-TTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGA-TTTACAG-ATTATCG
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGA-TACGCGTTGCGATTTTAC-GTATTGTCG
* *
4739 TTGCGATTTACAGATTCTC
64 TTGCGATTTACAGATACGC
* **
4758 GTTGCGA-TTTACGGATTATCGTTGCGATTTACGGATACATGTTGCGATTTTACGTATTGTCGTT
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
*
4822 GCGATTTACGGATACGC
66 GCGATTTACAGATACGC
* *
4839 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
*
4904 GCGATTTACGGATACGC
66 GCGATTTACAGATACGC
* * * *
4921 GTTGCGATTTTACGGATACTCGTTGCGATAGTAAGAAT-CGCGTTGCGATTTATA--TATTCG-C
1 GTTGCGATTTTACGGATTCTCGTTGCGAT-TTACGGATACGCGTTGCGATTT-TACGTATT-GTC
* * *
4982 GTTGCGATTTTCATATTCGC
63 GTTGCGATTTACAGATACGC
5002 GTTGCGATT
1 GTTGCGATT
5011 CTGGAAACTG
Statistics
Matches: 224, Mismatches: 22, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
79 2 0.01
80 41 0.18
81 64 0.29
82 110 0.49
83 7 0.03
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (82 bp):
GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
GCGATTTACAGATACGC
Found at i:4981 original size:20 final size:20
Alignment explanation
Indices: 4958--5010 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
4948 ATAGTAAGAA
4958 TCGCGTTGCGATTTAT-ATAT
1 TCGCGTTGCGATTT-TCATAT
4978 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
4998 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5011 CTGGAAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:17099 original size:21 final size:22
Alignment explanation
Indices: 17056--17153 Score: 76
Period size: 23 Copynumber: 4.4 Consensus size: 22
17046 GAAATTTGAA
17056 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAGAATGTC
*
17078 CCGAAGGACCACATA-TATGTC
1 CCGAAGGACCACATAGAATGTC
* *
17099 CCGAAGGACTGA-GTAGAAATGTC
1 CCGAAGGAC-CACATAG-AATGTC
* ** *
17122 CCAAAATACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAA-TGTC
17145 CCGAAGGAC
1 CCGAAGGAC
17154 TGCGTAGAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
21 17 0.29
22 17 0.29
23 25 0.42
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:17159 original size:23 final size:23
Alignment explanation
Indices: 17094--17162 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
17084 GACCACATAT
*
17094 ATGTCCCGAAGGACTGAGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
* ** **
17117 ATGTCCCAAAATACCACGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
*
17140 TTGTCCCGAAGGACTGCGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
17163 CCCTCGACTC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
ATGTCCCGAAGGACTGCGTAGAA
Found at i:18722 original size:23 final size:23
Alignment explanation
Indices: 18688--18840 Score: 107
Period size: 23 Copynumber: 6.8 Consensus size: 23
18678 GAGTTGAGGG
*
18688 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
18711 TTCTACGTGGTCCTTCGAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* * *
18734 TTCTACGTGATCATTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* * * * *
18757 TTCTACGCGATCATTCGAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*** *
18780 TTCTATACGGTCTTTCGGGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
* *
18802 -TATATGTGGTCCTTCGGGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
*
18823 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
18841 TGCAAATTTC
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.17
22 14 0.13
23 77 0.71
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:18797 original size:46 final size:44
Alignment explanation
Indices: 18695--18802 Score: 126
Period size: 46 Copynumber: 2.4 Consensus size: 44
18685 GGGTTCTACG
* * * * *
18695 CGGTCCTTCGGGACAATTCTACGTGGTCCTTCGAGACATTTCTA
1 CGGTCATTCGGGACATTTCTACGCGATCATTCGAGACATTTCTA
18739 CGTGATCATTCGGGACATTTCTACGCGATCATTCGAGACATTTCTATA
1 CG-G-TCATTCGGGACATTTCTACGCGATCATTCGAGACATTTC--TA
*
18787 CGGTCTTTCGGGACAT
1 CGGTCATTCGGGACAT
18803 ATATGTGGTC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.04
45 1 0.02
46 46 0.85
47 1 0.02
48 4 0.07
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (44 bp):
CGGTCATTCGGGACATTTCTACGCGATCATTCGAGACATTTCTA
Found at i:26531 original size:2 final size:2
Alignment explanation
Indices: 26519--26548 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
26509 TAATACGATA
26519 AT AT GAT 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 AT AT A
26549 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27086 original size:2 final size:2
Alignment explanation
Indices: 27075--27129 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
27065 ATTAATCAAT
27075 TA TA -A TA TA TA 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
27116 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
27130 ATTTCATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28054 original size:60 final size:60
Alignment explanation
Indices: 27931--28043 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
27921 CACCTATGTT
* ** * * * *
27931 CTATAGGGAGTTTCTTTGTTGAGTCCCTTGACTATTAAAAGTCATAAAATGGTAGCCCGA
1 CTATAGGGAGTTGCTTTGTTGAGTCCCTCAAATATTAAAAGTCACAAAATGATAGCCCAA
*
27991 CTATAGGGAGTTGCTTTGTTGAGTCCCTCAAATATTAAAAGTTACAAAATGAT
1 CTATAGGGAGTTGCTTTGTTGAGTCCCTCAAATATTAAAAGTCACAAAATGAT
28044 CACTCAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (60 bp):
CTATAGGGAGTTGCTTTGTTGAGTCCCTCAAATATTAAAAGTCACAAAATGATAGCCCAA
Found at i:28345 original size:29 final size:29
Alignment explanation
Indices: 28252--28345 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 29
28242 GAACATAATG
*
28252 AATAGTCG-GGTGACCATTTTGTAACTTTT
1 AATAGTCGAGG-GACCATTTTATAACTTTT
** **** *
28281 AATAGTCGAATGACTCAACAAAACAACTTCTT
1 AATAGTCGAGGGAC-C-ATTTTATAACTT-TT
28313 -ATAGTCGAGGGACCATTTTATAACTTTT
1 AATAGTCGAGGGACCATTTTATAACTTTT
28341 AATAG
1 AATAG
28346 CCACTGACTC
Statistics
Matches: 45, Mismatches: 15, Indels: 10
0.64 0.21 0.14
Matches are distributed among these distances:
28 2 0.04
29 22 0.49
30 2 0.04
31 17 0.38
32 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (29 bp):
AATAGTCGAGGGACCATTTTATAACTTTT
Found at i:29891 original size:15 final size:15
Alignment explanation
Indices: 29871--29900 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29861 AATCTATCTG
29871 AAAATTCAAAACATT
1 AAAATTCAAAACATT
29886 AAAATTCAAAACATT
1 AAAATTCAAAACATT
29901 CTGCAACAGC
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:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATTCAAAACATT
Found at i:30733 original size:32 final size:32
Alignment explanation
Indices: 30687--30754 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
30677 TATGTGAGTG
30687 AAGACTCTGCTTAACCTATGAACAAAAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
* *
30719 AAGACTCTGGTTAACCTATGAACAACAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
30751 AAGA
1 AAGA
30755 GACCATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (32 bp):
AAGACTCTGCTTAACCTATGAACAAAAATTTA
Found at i:32457 original size:37 final size:37
Alignment explanation
Indices: 32404--32477 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
32394 ATTCCCACCA
*
32404 TGGGAAAGCATGGTGCTGAATATTATGCATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
32441 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
32478 GGTACTGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (37 bp):
TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
Found at i:34069 original size:13 final size:13
Alignment explanation
Indices: 34051--34085 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
34041 TGCTATACTA
34051 TAAATATACAATG
1 TAAATATACAATG
34064 TAAATATACAATG
1 TAAATATACAATG
34077 TAAATATAC
1 TAAATATAC
34086 TATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (13 bp):
TAAATATACAATG
Found at i:34779 original size:115 final size:116
Alignment explanation
Indices: 34577--34808 Score: 353
Period size: 115 Copynumber: 2.0 Consensus size: 116
34567 TCCTTCGTTG
*
34577 TGAAGTTGAAATCCTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
1 TGAAGTTGAAATCCTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
*
34642 GTGAAGTTGAAATCCAATCTTGTAAATTGAATCGCTTT-GAGATT-AATATC
66 GTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAG-TTCAATATC
**
34692 TGAAGTTGAAATTGT-GGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGT
1 TGAAGTTGAAATCCTAGG-TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGT
* * * *
34756 TGTGAAGTTGAAATTCACTCTTGTGAATTGTATCACTTTCGAGTTCAATATC
65 TGTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAGTTCAATATC
34808 T
1 T
34809 TTCGCTGTGA
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
114 2 0.02
115 94 0.89
116 10 0.09
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (116 bp):
TGAAGTTGAAATCCTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
GTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAGTTCAATATC
Found at i:43799 original size:23 final size:23
Alignment explanation
Indices: 43768--43818 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
43758 GGAATCGTTA
43768 CCCCC-TTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
43790 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
43813 CCCCCT
1 CCCCCT
43819 GTAAGGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:49365 original size:22 final size:22
Alignment explanation
Indices: 49339--49422 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
49329 TTGGTACAGA
*
49339 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
49361 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGA-TACCCCC-TTGAAG
*
49385 GGG-ACCGAT-TCCCC-TGTAA-
1 GGGAACCGATACCCCCTTG-AAG
* *
49404 GGGAATCGATACCTCCTTG
1 GGGAACCGATACCCCCTTG
49423 GGGTTCTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
19 5 0.10
20 7 0.14
21 7 0.14
22 11 0.22
23 11 0.22
24 9 0.18
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:49391 original size:23 final size:23
Alignment explanation
Indices: 49350--49398 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
49340 GGAATCGATA
49350 CCCCCTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
49373 CCCCCTTTGAAGGGG-ACCGATTC
1 CCCCC-TTGAAGGGGAACCGATTC
49396 CCC
1 CCC
49399 TGTAAGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.18, C:0.39, G:0.24, T:0.18
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:58223 original size:18 final size:18
Alignment explanation
Indices: 58200--58245 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
58190 AAAAGTTATT
*
58200 TTTAAATAAAAGATAAGA
1 TTTAAATAAAAGAAAAGA
*
58218 TTTAAATAAAAGAAAATA
1 TTTAAATAAAAGAAAAGA
*
58236 ATTAAATAAA
1 TTTAAATAAA
58246 TAATCTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
TTTAAATAAAAGAAAAGA
Found at i:59220 original size:22 final size:23
Alignment explanation
Indices: 59179--59221 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
59169 CAAAAAATGC
* *
59179 TTTCAAAACCATATATTATATAT
1 TTTCAAAAACATATACTATATAT
59202 TTTCAAAAAC-TATACTATAT
1 TTTCAAAAACATATACTATAT
59222 TGATACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTCAAAAACATATACTATATAT
Found at i:59324 original size:13 final size:12
Alignment explanation
Indices: 59296--59330 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
59286 CAAGCCATAC
59296 CATATTTTTAGT
1 CATATTTTTAGT
*
59308 CATATTTATTTGT
1 CATATTT-TTAGT
59321 CATATTTTTA
1 CATATTTTTA
59331 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (12 bp):
CATATTTTTAGT
Done.