Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005978.1 Hibiscus syriacus cultivar Beakdansim tig00014052_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: 77456
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1618 original size:12 final size:12
Alignment explanation
Indices: 1580--1655 Score: 66
Period size: 12 Copynumber: 6.3 Consensus size: 12
1570 ATTTCCGACT
1580 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
1592 TG-ATATATGACC
1 TGAAT-TCTGTTC
1604 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
1616 TGATTTCTGATC
1 TGAATTCTGTTC
*
1628 TGGATTCTGTTC
1 TGAATTCTGTTC
1640 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
1652 TGAA
1 TGAA
1656 GCCTGTTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
11 4 0.08
12 42 0.86
13 3 0.06
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:1655 original size:48 final size:50
Alignment explanation
Indices: 1566--1675 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 50
1556 AAATATTTTA
* **
1566 TCTGATTTCCGA-CTTGAATTCTGTTCTGATATATGACCTGAATTCTG-T
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAAGCCTGTT
* * **
1614 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGTTCTGAAGCCTGTT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAAGCCTGTT
*
1663 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1676 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
48 38 0.73
49 14 0.27
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.47
Consensus pattern (50 bp):
TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAAGCCTGTT
Found at i:1662 original size:24 final size:24
Alignment explanation
Indices: 1580--1655 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
1570 ATTTCCGACT
* *
1580 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
1604 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
1628 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
1652 TGAA
1 TGAA
1656 GCCTGTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:5140 original size:24 final size:24
Alignment explanation
Indices: 5055--5127 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
5045 CTAGAAGGCC
5055 GGTTGATTTTCAAATTAAGGGGCT
1 GGTTGATTTTCAAATTAAGGGGCT
* * *
5079 GGTTGATTTTCAAACTAAAGGGTT
1 GGTTGATTTTCAAATTAAGGGGCT
5103 GGTTGATTTTCAAATTAAGGGGCT
1 GGTTGATTTTCAAATTAAGGGGCT
5127 G
1 G
5128 CTTTGAATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (24 bp):
GGTTGATTTTCAAATTAAGGGGCT
Found at i:9688 original size:24 final size:24
Alignment explanation
Indices: 9660--9732 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
9650 TTCTAGAAGA
9660 CCGGTTGATTTTCAAATTAAGGGG
1 CCGGTTGATTTTCAAATTAAGGGG
*
9684 CCGGTTGATTTTCAAACTAAGGGG
1 CCGGTTGATTTTCAAATTAAGGGG
** *
9708 TTGGTTGATTTTTAAATTAAGGGG
1 CCGGTTGATTTTCAAATTAAGGGG
9732 C
1 C
9733 TGCTTTGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.36
Consensus pattern (24 bp):
CCGGTTGATTTTCAAATTAAGGGG
Found at i:12365 original size:22 final size:21
Alignment explanation
Indices: 12326--12385 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
12316 AAATCAGTAC
*
12326 AAATATTATTTAAT-AATTAAAT
1 AAATATT-TTTATTAAATT-AAT
*
12348 AAATA-TTTTATATAAATTTAT
1 AAATATTTTTAT-TAAATTAAT
12369 AAATATTTTTATTAAAT
1 AAATATTTTTATTAAAT
12386 ATTTTGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 15 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATTTTTATTAAATTAAT
Found at i:12370 original size:21 final size:21
Alignment explanation
Indices: 12346--12385 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12336 TAATAATTAA
12346 ATAAATA-TTTTATATAAATTT
1 ATAAATATTTTTAT-TAAATTT
12367 ATAAATATTTTTATTAAAT
1 ATAAATATTTTTATTAAAT
12386 ATTTTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATATTTTTATTAAATTT
Found at i:12913 original size:14 final size:14
Alignment explanation
Indices: 12894--12947 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
12884 AATATATTTG
12894 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
12908 TTTATGTTCGTTTA
1 TTTATGTTCGTTCA
*
12922 CTTT-CGTTCGTTCA
1 -TTTATGTTCGTTCA
12936 TTTATGTTCGTT
1 TTTATGTTCGTT
12948 TATGTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 28 0.82
15 3 0.09
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:13047 original size:14 final size:14
Alignment explanation
Indices: 13028--13081 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
13018 TTAATATTTG
13028 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
13042 TTTATGTTCGTTTA
1 TTTATGTTCGTTCA
*
13056 CTTT-CGTTCGTTCA
1 -TTTATGTTCGTTCA
13070 TTTATGTTCGTT
1 TTTATGTTCGTT
13082 TATGTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 28 0.82
15 3 0.09
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:13050 original size:134 final size:134
Alignment explanation
Indices: 12887--13160 Score: 548
Period size: 134 Copynumber: 2.0 Consensus size: 134
12877 ATTCGATAAT
12887 ATATTTGTTTATGTTCGTTCATTTATGTTCGTTTACTTTCGTTCGTTCATTTATGTTCGTTTATG
1 ATATTTGTTTATGTTCGTTCATTTATGTTCGTTTACTTTCGTTCGTTCATTTATGTTCGTTTATG
12952 TTTAACCTAATATCTCTATACTCATTTAATATATTAAGGCCCAATAAATTTTATGGACGATTCTC
66 TTTAACCTAATATCTCTATACTCATTTAATATATTAAGGCCCAATAAATTTTATGGACGATTCTC
13017 ATTA
131 ATTA
13021 ATATTTGTTTATGTTCGTTCATTTATGTTCGTTTACTTTCGTTCGTTCATTTATGTTCGTTTATG
1 ATATTTGTTTATGTTCGTTCATTTATGTTCGTTTACTTTCGTTCGTTCATTTATGTTCGTTTATG
13086 TTTAACCTAATATCTCTATACTCATTTAATATATTAAGGCCCAATAAATTTTATGGACGATTCTC
66 TTTAACCTAATATCTCTATACTCATTTAATATATTAAGGCCCAATAAATTTTATGGACGATTCTC
13151 ATTA
131 ATTA
13155 ATATTT
1 ATATTT
13161 TAAAATTCAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 140 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.50
Consensus pattern (134 bp):
ATATTTGTTTATGTTCGTTCATTTATGTTCGTTTACTTTCGTTCGTTCATTTATGTTCGTTTATG
TTTAACCTAATATCTCTATACTCATTTAATATATTAAGGCCCAATAAATTTTATGGACGATTCTC
ATTA
Found at i:13329 original size:22 final size:24
Alignment explanation
Indices: 13301--13357 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
13291 GTTTATTTAC
13301 GTTCGTTTATGTT-AATTA-TTGT
1 GTTCGTTTATGTTCAATTATTTGT
**
13323 GTTCGTTTATGTTCGTTTATTTGT
1 GTTCGTTTATGTTCAATTATTTGT
13347 GTTCGTTTATG
1 GTTCGTTTATG
13358 ATTTAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 13 0.42
23 3 0.10
24 15 0.48
ACGTcount: A:0.12, C:0.07, G:0.21, T:0.60
Consensus pattern (24 bp):
GTTCGTTTATGTTCAATTATTTGT
Found at i:23150 original size:12 final size:12
Alignment explanation
Indices: 23133--23166 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
23123 GTATCGTAAA
23133 TTCGCGTTGCAT
1 TTCGCGTTGCAT
23145 TTCGCGTTGCAT
1 TTCGCGTTGCAT
23157 TTCGCGTTGC
1 TTCGCGTTGC
23167 GATAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:23206 original size:21 final size:21
Alignment explanation
Indices: 23182--23272 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
23172 TTGAAAATCG
23182 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
23203 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
23224 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
23242 CGCGTGCGATAGTCTACAGTGT
1 CG-TTGCGATAGTCTACAGTGT
23264 CGTTGCGAT
1 CGTTGCGAT
23273 TTTCCATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.07
19 10 0.17
21 40 0.69
22 4 0.07
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:23256 original size:40 final size:41
Alignment explanation
Indices: 23203--23295 Score: 179
Period size: 40 Copynumber: 2.3 Consensus size: 41
23193 TCTACAGTGT
23203 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
23244 CG-TGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
23284 CGTTGCGATAGT
1 CGTTGCGATAGT
23296 TGAAAATCGC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 40 0.78
41 11 0.22
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:23289 original size:20 final size:20
Alignment explanation
Indices: 23224--23292 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
23214 TCTACAGTGT
23224 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
23244 CG-TGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
23263 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
23284 CGTTGCGAT
1 CGTTGCGAT
23293 AGTTGAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 11 0.30
20 15 0.41
21 11 0.30
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:23306 original size:61 final size:62
Alignment explanation
Indices: 23154--23356 Score: 227
Period size: 61 Copynumber: 3.3 Consensus size: 62
23144 TTTCGCGTTG
* *
23154 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT--TTTC
* * ** **
23218 CA-GT-GTCGTTGCGAT-TTTCCATTTCGCG-TGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCG-CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
** *
23277 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGAAC-GTGTCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
* *
23338 CATCTCGCATTGCGATAGT
1 CATTTCGCGTTGCGATAGT
23357 GTACAGTGTC
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
59 4 0.03
60 10 0.09
61 69 0.60
62 20 0.17
63 10 0.09
64 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (62 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:23366 original size:41 final size:41
Alignment explanation
Indices: 23302--23437 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
23292 TAGTTGAAAA
* *
23302 TCGCGTTGCGATAGTGAAC-GTGTCATTGCGATTTTCCATC
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
* *
23342 TCGCATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
* * *
23383 TCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTCCA-A
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
23423 T-GTCGTTGCGATAGT
1 TCG-CGTTGCGATAGT
23438 CTATAGTAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 30 0.35
41 55 0.64
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
Found at i:23373 original size:21 final size:21
Alignment explanation
Indices: 23347--23437 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 21
23337 CCATCTCGCA
* *
23347 TTGCGATAGTGTACAGTGTCG
1 TTGCGATAGTTTACAATGTCG
* *
23368 TTGCGAT--TTT-CCATTTCGCG
1 TTGCGATAGTTTACAATGT--CG
*
23388 TTGCGATAGTCTACAATGTCG
1 TTGCGATAGTTTACAATGTCG
*
23409 TTGCGAT--TTTCCAATGTCG
1 TTGCGATAGTTTACAATGTCG
23428 TTGCGATAGT
1 TTGCGATAGT
23438 CTATAGTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.06
19 19 0.35
20 9 0.17
21 17 0.31
22 2 0.04
23 4 0.07
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
TTGCGATAGTTTACAATGTCG
Found at i:23411 original size:102 final size:102
Alignment explanation
Indices: 23179--23415 Score: 354
Period size: 102 Copynumber: 2.3 Consensus size: 102
23169 TAGTTGAAAA
* * * *
23179 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATAGTCTACAATGTCGTTGCGATAGTCAACAGTGTCATTGCGATTTTCCATCTCG
23244 CGTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
66 CGTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
23281 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATAGTGAAC-GTGTCATTGCGATTTTCCATCT
1 TCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATAGTCAACAGTGTCATTGCGATTTTCCATCT
* *
23343 CGCATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
64 CGC-GTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
23383 TCGCGTTGCGATAGTCTACAATGTCGTTGCGAT
1 TCGCGTTGCGATAGTCTACAATGTCGTTGCGAT
23416 TTTCCAATGT
Statistics
Matches: 121, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
101 25 0.21
102 94 0.78
103 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (102 bp):
TCGCGTTGCGATAGTCTACAATGTCGTTGCGATAGTCAACAGTGTCATTGCGATTTTCCATCTCG
CGTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:23545 original size:6 final size:6
Alignment explanation
Indices: 23536--23583 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
23526 CATTACCATT
23536 ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23581 ACC
1 ACC
23584 CGAGACGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.35, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:23591 original size:10 final size:10
Alignment explanation
Indices: 23544--23591 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
23534 TTACCACGAC
23544 CACGACCACGA
1 CACGACC-CGA
23555 CCACGACCACGA
1 -CACGACC-CGA
*
23567 CACGACACGA
1 CACGACCCGA
23577 CACGACCCGA
1 CACGACCCGA
*
23587 GACGA
1 CACGA
23592 GACGGCGGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 16 0.48
11 6 0.18
12 11 0.33
ACGTcount: A:0.35, C:0.44, G:0.21, T:0.00
Consensus pattern (10 bp):
CACGACCCGA
Found at i:24091 original size:6 final size:6
Alignment explanation
Indices: 24080--24115 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
24070 TCTCGTCTCG
24080 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24116 ACGTGTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:28674 original size:15 final size:15
Alignment explanation
Indices: 28651--28708 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
28641 TGGGTGGGAG
*
28651 GATGTGGGGCGGGCA
1 GATGCGGGGCGGGCA
28666 GATGCGGGGCGGGCA
1 GATGCGGGGCGGGCA
* *
28681 AATGCGGGGCGGGAA
1 GATGCGGGGCGGGCA
28696 GATGCGGGGCGGG
1 GATGCGGGGCGGG
28709 TAATGTCTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.16, C:0.16, G:0.60, T:0.09
Consensus pattern (15 bp):
GATGCGGGGCGGGCA
Found at i:41571 original size:27 final size:26
Alignment explanation
Indices: 41509--41572 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
41499 TATGTAATAA
*
41509 AATTTTCTAATAGTTATATTTTAATTT
1 AATTTT-TAATAGTTATATTTTAATCT
*
41536 AATTATTTAATAGTTATTTGTTTATATCT
1 AATT-TTTAATAGTTATAT-TTTA-ATCT
41565 -ATTTTTAA
1 AATTTTTAA
41573 AAAATTAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 20 0.62
28 9 0.28
29 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (26 bp):
AATTTTTAATAGTTATATTTTAATCT
Found at i:56202 original size:20 final size:20
Alignment explanation
Indices: 56190--56227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56180 AAACTTTAGG
56190 GAAAGTTTTGAAACTCTTAA
1 GAAAGTTTTGAAACTCTTAA
* *
56210 GATAGTTTTGAAAATCTT
1 GAAAGTTTTGAAACTCTT
56228 GAACAGTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (20 bp):
GAAAGTTTTGAAACTCTTAA
Found at i:60157 original size:19 final size:19
Alignment explanation
Indices: 60135--60185 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
60125 TTGGTTAGTG
60135 ACCAAAATGTAAAATTTAA
1 ACCAAAATGTAAAATTTAA
60154 ACCAAAATGTAAAATTTAA
1 ACCAAAATGTAAAATTTAA
60173 ACCAAAATGTAAA
1 ACCAAAATGTAAA
60186 TTTTGAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (19 bp):
ACCAAAATGTAAAATTTAA
Found at i:61455 original size:19 final size:20
Alignment explanation
Indices: 61412--61457 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
61402 TAATATGCTG
* *
61412 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
*
61432 GAAATTGATTTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
61451 GAAATTG
1 GAAATTG
61458 GATCATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:65981 original size:38 final size:38
Alignment explanation
Indices: 65930--66002 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
65920 CTCCTTTTCA
*
65930 TTCTGTCCGTGTATTTCTAACTAGGTTGAAAAATACTG
1 TTCTGTCCGTGTATTTATAACTAGGTTGAAAAATACTG
*
65968 TTCTGTCTGTGTATTTATAACTAGGTTGAAAAATA
1 TTCTGTCCGTGTATTTATAACTAGGTTGAAAAATA
66003 ATTGTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (38 bp):
TTCTGTCCGTGTATTTATAACTAGGTTGAAAAATACTG
Found at i:66877 original size:30 final size:30
Alignment explanation
Indices: 66838--66986 Score: 226
Period size: 30 Copynumber: 5.0 Consensus size: 30
66828 AAGCCCAAGC
*
66838 AACCGGAGAAGCCGAAAGAGGCTGAGAAGA
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
* * *
66868 AACCCGAGAAGTCGAAAGAGGCTGAGAAGA
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
* * * *
66898 AACCCGAGAAGCCTAAGGAAGCCGAGAAGA
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
66928 AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
66958 AACCGGAGAAGCCGAAAGAGGCCGAGAAG
1 AACCGGAGAAGCCGAAAGAGGCCGAGAAG
66987 CCTAAGGAGT
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 108 1.00
ACGTcount: A:0.43, C:0.19, G:0.35, T:0.03
Consensus pattern (30 bp):
AACCGGAGAAGCCGAAAGAGGCCGAGAAGA
Found at i:66956 original size:18 final size:18
Alignment explanation
Indices: 66933--66988 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
66923 GAAGAAACCG
66933 GAGAAGCCGAAAGAGGCC
1 GAGAAGCCGAAAGAGGCC
66951 GAGAA---G-AA-A--CC
1 GAGAAGCCGAAAGAGGCC
66962 GGAGAAGCCGAAAGAGGCC
1 -GAGAAGCCGAAAGAGGCC
66981 GAGAAGCC
1 GAGAAGCC
66989 TAAGGAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
11 2 0.07
12 5 0.17
13 1 0.03
14 2 0.07
15 2 0.07
16 2 0.07
17 1 0.03
18 13 0.43
19 2 0.07
ACGTcount: A:0.41, C:0.21, G:0.38, T:0.00
Consensus pattern (18 bp):
GAGAAGCCGAAAGAGGCC
Found at i:67903 original size:179 final size:182
Alignment explanation
Indices: 67677--68058 Score: 593
Period size: 183 Copynumber: 2.1 Consensus size: 182
67667 TTTTCTAATT
* * *
67677 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
*
67741 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAA-T-TA-T-ATTTAAGTTTAAAAGTTATTG
66 TATAAAATAAAAAATTTAGAT-AATTTTTTAATTAATTATATTGATTTAAGTTTAAAAGTTATTG
*
67802 GATCTTAAATTATTAATT-GAGTTTTAAAT-AGTTTGGGCTT-AGCCCATATTTTA
130 GATCTTAAATTATTAATTAG-GTTTTAAATGA-TTTGGG-TTGAGCCCATATGTTA
67855 TATATAATATATTTAATATTTTTTAATT-AAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
*
67919 TTATAAAATAAAAAATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TTATAAAATAAAAAATTTAGATAATTTTTTAATTAATT-ATATTGATTTAAGTTTAAAAGTTATT
67984 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
129 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
68038 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
68059 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
178 27 0.14
179 67 0.36
181 2 0.01
182 3 0.02
183 87 0.46
184 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAATTTTTTAATTAATTATATTGATTTAAGTTTAAAAGTTATTGG
ATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:77085 original size:119 final size:118
Alignment explanation
Indices: 76839--77065 Score: 334
Period size: 119 Copynumber: 1.9 Consensus size: 118
76829 TTAATTTTCA
*
76839 AAATCTCATTACTTATCACACAACTCAAAGTTTTAAAGGTAAAACAATTAAATATTTTTATTTCA
1 AAATCTCATTACTTATAACACAACTCAAAGTTTTAAAGGTAAAACAATTAAATATTTTTATTTCA
* *
76904 CATAATTAGATTTTTTCTCCTTTATTGAATTCCAATTTCCCATAACTATATTC
66 CATAATTAAATTTTTTCTCCTTCATTGAATTCCAATTTCCCATAACTATATTC
* * *
76957 AAATCTCATTAACTTATAACGCAACTCAAAGTTTTAACGGTAAAATAATTAAATATTTTTAGTTT
1 AAATCTCATT-ACTTATAACACAACTCAAAGTTTTAAAGGTAAAACAATTAAATATTTTTA-TTT
* * *
77022 CCCATAATTAAATTTTTT-T-C-TCATTGAATTCCAGTTTCTCATAA
64 CACATAATTAAATTTTTTCTCCTTCATTGAATTCCAATTTCCCATAA
77066 TTAGATTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
117 21 0.21
118 11 0.11
119 47 0.48
120 19 0.19
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (118 bp):
AAATCTCATTACTTATAACACAACTCAAAGTTTTAAAGGTAAAACAATTAAATATTTTTATTTCA
CATAATTAAATTTTTTCTCCTTCATTGAATTCCAATTTCCCATAACTATATTC
Done.