Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001223.1 Hibiscus syriacus cultivar Beakdansim tig00002412_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: 67200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4693 original size:26 final size:26
Alignment explanation
Indices: 4663--4751 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 26
4653 GTCATAACCC
*
4663 GACCCGACCCGTTTACCTGACCCGTT
1 GACCCGACCCGTTGACCTGACCCGTT
* *
4689 GACCCGAACCGACCTGTTGACCCGACTCGTT
1 GACCCG-A-C--CC-GTTGACCTGACCCGTT
*
4720 GACCCGACACGTTGACCGTTGACCCGTT
1 GACCCGACCCGTTGACC--TGACCCGTT
4748 GACC
1 GACC
4752 GTCGTTGACT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
26 13 0.26
27 2 0.04
28 12 0.24
29 1 0.02
30 3 0.06
31 19 0.38
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.20
Consensus pattern (26 bp):
GACCCGACCCGTTGACCTGACCCGTT
Found at i:4694 original size:31 final size:31
Alignment explanation
Indices: 4659--4727 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
4649 ACCGGTCATA
* *
4659 ACCCGACCCGACCCGTTTACCTGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
* * *
4690 ACCCGAACCGACCTGTTGACCCGACTCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
4721 ACCCGAC
1 ACCCGAC
4728 ACGTTGACCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.43, G:0.20, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:4720 original size:13 final size:13
Alignment explanation
Indices: 4704--4736 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4694 GAACCGACCT
*
4704 GTTGACCCGACTC
1 GTTGACCCGACAC
4717 GTTGACCCGACAC
1 GTTGACCCGACAC
4730 GTTGACC
1 GTTGACC
4737 GTTGACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.21
Consensus pattern (13 bp):
GTTGACCCGACAC
Found at i:7254 original size:24 final size:24
Alignment explanation
Indices: 7227--7317 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
7217 TCAAATTTGA
* * *
7227 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTAG
*
7251 ATTCTGATATGATA-TTGACATAG
1 ATTCTGATATGATACTTGACCTAG
* *
7274 ATTCTGATCTGATACATGACCTAG
1 ATTCTGATATGATACTTGACCTAG
7298 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
7318 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.33
24 38 0.67
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTAG
Found at i:7287 original size:47 final size:48
Alignment explanation
Indices: 7227--7317 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
7217 TCAAATTTGA
* * *
7227 ATTCTGTTATGATACCTGACCTGGATTCTGATATGATA-TTGACATAG
1 ATTCTGATATGATACATGACCTAGATTCTGATATGATACTTGACATAG
*
7274 ATTCTGATCTGATACATGACCTAGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTAGATTCTGATATGATACTTGAC
7318 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTAGATTCTGATATGATACTTGACATAG
Found at i:15066 original size:20 final size:20
Alignment explanation
Indices: 15041--15078 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15031 GAGAATGAGG
*
15041 AACCGATTTCCAGGTCTTCC
1 AACCGATTTACAGGTCTTCC
15061 AACCGATTTACAGGTCTT
1 AACCGATTTACAGGTCTT
15079 TCAAACAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (20 bp):
AACCGATTTACAGGTCTTCC
Found at i:25659 original size:22 final size:22
Alignment explanation
Indices: 25631--25676 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
25621 TTGGTACGTA
*
25631 TTATTTTATGTTTAT-GACATAT
1 TTATTTTATCTTTATGGA-ATAT
*
25653 TTATTTTGTCTTTATGGAATAT
1 TTATTTTATCTTTATGGAATAT
25675 TT
1 TT
25677 TCAAATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (22 bp):
TTATTTTATCTTTATGGAATAT
Found at i:27541 original size:21 final size:21
Alignment explanation
Indices: 27512--27564 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
27502 ATTCTGACTA
27512 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
27533 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
27554 TCGCAATGCGA
1 TCGCATTGCGA
27565 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:27807 original size:22 final size:22
Alignment explanation
Indices: 27782--27843 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 22
27772 GGTGACATTC
27782 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
27804 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
27822 GTCTCCATCTCCGGCAAAATCA
1 GTCCCCATCTCCGACGAAATCA
27844 TTCACGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 16 0.52
22 15 0.48
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:28217 original size:33 final size:34
Alignment explanation
Indices: 28169--28241 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
28159 ACTATCGCAA
** *
28169 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
28202 TGCGATTCT-TACGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
28236 TGCGAT
1 TGCGAT
28242 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:28238 original size:20 final size:20
Alignment explanation
Indices: 28213--28261 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28203 GCGATTCTTA
28213 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
28233 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
28253 TGTTGCGAT
1 CGTTGCGAT
28262 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:28267 original size:20 final size:20
Alignment explanation
Indices: 28229--28283 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
28219 GATAGTCAAA
* **
28229 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
28249 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
28269 TTCGTATTGCGATTT
1 TTCGTGTTGCGATTT
28284 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:28291 original size:20 final size:20
Alignment explanation
Indices: 28248--28291 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28238 CGATAGTCAT
* ** *
28248 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTAAAG
28268 TTTCGTATTGCGATTTAAAG
1 TTTCGTATTGCGATTTAAAG
28288 TTTC
1 TTTC
28292 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGATTTAAAG
Found at i:30179 original size:20 final size:20
Alignment explanation
Indices: 30154--30219 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
30144 AGAATAGTTT
30154 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
30174 ACTATCGCAA--TG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
30190 A--ATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
30208 ACTATCGCAACG
1 ACTATCGCAACG
30220 AAAGAATCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
14 7 0.20
16 3 0.09
17 4 0.11
18 3 0.09
20 18 0.51
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:30203 original size:34 final size:34
Alignment explanation
Indices: 30157--30238 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
30147 ATAGTTTACT
* * *
30157 ATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
30191 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
30225 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
30239 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:30248 original size:19 final size:18
Alignment explanation
Indices: 30190--30255 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
30180 GCAATGAGAG
30190 AATCGCAATGCGAAAATGA
1 AATCGCAATGCG-AAATGA
*
30209 CTATCGCAA--CGAAA-G-
1 -AATCGCAATGCGAAATGA
30224 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
30243 AATCGCATTGCGA
1 AATCGCAATGCGA
30256 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.18
16 6 0.16
17 4 0.11
18 2 0.05
19 12 0.32
20 7 0.18
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:30289 original size:20 final size:20
Alignment explanation
Indices: 30264--30364 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 20
30254 GATTCTCTCG
**
30264 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
30284 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
30304 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
*
30318 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
30338 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
30358 TTGCGAT
1 TTGCGAT
30365 TTTAAGTTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
18 1 0.01
20 54 0.79
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:30308 original size:54 final size:54
Alignment explanation
Indices: 30245--30365 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
30235 GAAATGAAAA
* *
30245 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTTATTT
1 TCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
** *
30299 TCGCATTGCGATTCTCTCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
*
30353 TCGCGTTGCGATT
1 TCGCATTGCGATT
30366 TTAAGTTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (54 bp):
TCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
Found at i:30374 original size:20 final size:20
Alignment explanation
Indices: 30318--30374 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
30308 GATTCTCTCA
* *
30318 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTAAGTTTCGCG
* *
30338 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTAAGTTTCGCG
**
30358 TTGCGATTTTAAGTTTC
1 TTGCGATAGTAAGTTTC
30375 AGATTCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTAAGTTTCGCG
Found at i:32352 original size:14 final size:14
Alignment explanation
Indices: 32333--32368 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
32323 ATTGTTTAAT
32333 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
32347 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
32361 TGATTTGT
1 TGATTTGT
32369 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32596 original size:33 final size:34
Alignment explanation
Indices: 32544--32614 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 34
32534 AGAGTTTTCG
32544 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
32578 CGTTGCGGTTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
32611 CGTT
1 CGTT
32615 ATGATAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:32626 original size:33 final size:33
Alignment explanation
Indices: 32559--32639 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
32549 CGATTTTCAT
* * **
32559 TTTCGCATTGCGATTCACTCGTTGCGGTTTTCA
1 TTTCGCATTGCGATTCACTCGTTACGATAGTCA
* *
32592 TTTCGCATTGCGATTCTCTCGTTATGATAGTCA
1 TTTCGCATTGCGATTCACTCGTTACGATAGTCA
*
32625 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
32640 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCGTTACGATAGTCA
Found at i:32640 original size:20 final size:20
Alignment explanation
Indices: 32617--32684 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
32607 CTCTCGTTAT
32617 GATAGTCATTTCCGCGTTGC
1 GATAGTCATTTCCGCGTTGC
*
32637 GATAGTCATTTCCGTGTTGC
1 GATAGTCATTTCCGCGTTGC
32657 GATAGTCATATT-CGCGTTGC
1 GATAGTCAT-TTCCGCGTTGC
32677 GATAGTCA
1 GATAGTCA
32685 AATGAATGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
GATAGTCATTTCCGCGTTGC
Found at i:35057 original size:24 final size:24
Alignment explanation
Indices: 35023--35076 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
35013 CTGAAAAATC
35023 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
35047 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
35071 ATCAAA
1 ATCAAA
35077 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:35961 original size:20 final size:20
Alignment explanation
Indices: 35938--36104 Score: 248
Period size: 20 Copynumber: 8.3 Consensus size: 20
35928 TAGAATCTCG
35938 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
35958 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
35978 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
35998 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
36018 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
36038 TTGCGATTTACGTAATCGTA
1 TTGCGATTTACGTATTCGCA
*
36058 TTGCGATTTTC-TAAATTCGCA
1 TTGCGATTTACGT--ATTCGCA
*
36079 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATTCGCA
36099 TTGCGA
1 TTGCGA
36105 ATTAGGAAAA
Statistics
Matches: 134, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
19 2 0.01
20 117 0.87
21 14 0.10
22 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:35964 original size:40 final size:39
Alignment explanation
Indices: 35917--36088 Score: 174
Period size: 40 Copynumber: 4.3 Consensus size: 39
35907 GAAATTCAGT
35917 ATTGCGATAGTTA-GAATCTCGTTGCGATTTACAG-ATTCGC
1 ATTGCGAT--TTACGAATCTCGTTGCGATTTAC-GTATTCGC
*
35957 ATTGCGATTTACGTAT-TCGCATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGAATCTCG--TTGCGATTTACGTATTCGC
* *
35997 ATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGC
1 ATTGCGATTTACG-AATCTCGTTGCGATTTACGTATTCGC
* *
36037 ATTGCGATTTACGTAATCGT-ATTGCGATTTTC-TAAATTCGC
1 ATTGCGATTTACG-AATC-TCGTTGCGATTTACGT--ATTCGC
36078 ATTGCGATTTA
1 ATTGCGATTTA
36089 TGTATTCGCA
Statistics
Matches: 117, Mismatches: 6, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
38 6 0.05
39 5 0.04
40 86 0.74
41 19 0.16
42 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (39 bp):
ATTGCGATTTACGAATCTCGTTGCGATTTACGTATTCGC
Found at i:36127 original size:21 final size:21
Alignment explanation
Indices: 36101--36146 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
36091 TATTCGCATT
*
36101 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
36122 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
36143 GCGA
1 GCGA
36147 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:39505 original size:127 final size:127
Alignment explanation
Indices: 39276--39909 Score: 1090
Period size: 127 Copynumber: 5.0 Consensus size: 127
39266 GTACTATTCA
* ** *
39276 CGTGAAAGCGCGTTCCCGGGGGCGCATCTTCCATTATTTTGTCAGAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
* *
39341 TATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAT
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
39403 CGTGAAGGCGCGTTCTCGGGGGCGCGCATTCCATTATTTTGTCAGAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
*
39468 TATTATGTCACTTATGTCCCCCGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
39530 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATTATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
39595 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
39657 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
*
39722 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
39784 CGTGAAGGCGCGTTTCCGGGGG-GCGCCTTCCATTATTTTGTCAGAAAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
* **
39848 TATTATGTCACATATGTCCCCCAAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
39910 TTTAAGGCGT
Statistics
Matches: 487, Mismatches: 20, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
126 101 0.21
127 386 0.79
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATTATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:40384 original size:34 final size:34
Alignment explanation
Indices: 40346--40446 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
40336 GAATTTAATG
40346 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATACTATAATTTATATTTTAAAT
* * * * *
40380 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTTGAATACTATAATTTATATTTTAAAT
40414 TTAAATTTTGAATACTATAA-TTATTATTTTAAA
1 TTAAATTTTGAATACTATAATTTA-TATTTTAAA
40447 AATATTTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 2 0.04
34 54 0.96
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTTGAATACTATAATTTATATTTTAAAT
Found at i:40999 original size:21 final size:20
Alignment explanation
Indices: 40970--41039 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
40960 GGTATAAAAC
* *
40970 CCTGTGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
40990 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
41011 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
41032 CCCTGCGG
1 -CCTGCGG
41040 ATATGACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:42820 original size:16 final size:17
Alignment explanation
Indices: 42793--42824 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42783 TAACTGTAGA
42793 CAAAAAATAATAATTAG
1 CAAAAAATAATAATTAG
42810 CAAAAAA-AATAATTA
1 CAAAAAATAATAATTA
42825 ATTAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (17 bp):
CAAAAAATAATAATTAG
Found at i:42879 original size:30 final size:30
Alignment explanation
Indices: 42813--42908 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
42803 TAATTAGCAA
* * *
42813 AAAAAATAATTA-ATTAATA-AATTTAAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
*
42841 AAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
* * *
42871 AAAAAATAA-TATTTATATAATTATATTAAT
1 AAAAAATAATTATATAAAT-ATTATTTTAAT
*
42901 ATAAAATA
1 AAAAAATA
42909 TAATAACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.20
29 13 0.23
30 32 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATTATATAAATATTATTTTAAT
Found at i:43260 original size:61 final size:60
Alignment explanation
Indices: 43118--43261 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
43108 AATGAAAGGA
* * ** *
43118 GCGTCCCCGGGGATGCGCCTTTCACACGTGGCAATTGAATCAGCAAAATAAAGGTAAAGC
1 GCGTCCCCGGAGATGCGCCTTTCACACGTGACAATCAAATCAGCAAAATAAAGATAAAGC
*
43178 GCGTCCCC-GAGGATGCGCCTTTCACACGTGAC-ATCAAACTCAGCGTAAAAT-CAGATAAAGC
1 GCGTCCCCGGA-GATGCGCCTTTCACACGTGACAATCAAA-TCAGC--AAAATAAAGATAAAGC
*
43239 GCGTCCCCGGAAATGCGCCTTTC
1 GCGTCCCCGGAGATGCGCCTTTC
43262 GTCACCTCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
59 5 0.07
60 33 0.46
61 27 0.38
62 7 0.10
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (60 bp):
GCGTCCCCGGAGATGCGCCTTTCACACGTGACAATCAAATCAGCAAAATAAAGATAAAGC
Found at i:44687 original size:23 final size:23
Alignment explanation
Indices: 44661--44706 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
44651 TATCGTAAAT
44661 TTTAAA-AAAATATATTA-ATTTTA
1 TTTAAATAAAA-A-ATTACATTTTA
44684 TTTAAATAAAAAATTACATTTTA
1 TTTAAATAAAAAATTACATTTTA
44707 AAGAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATAAAAAATTACATTTTA
Found at i:45679 original size:21 final size:21
Alignment explanation
Indices: 45655--45694 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45645 AGTCAAACTC
* *
45655 AAAATTTTATTGTTATAAATT
1 AAAATTTTAATGGTATAAATT
45676 AAAATTTTAATGGTATAAA
1 AAAATTTTAATGGTATAAA
45695 CTATACATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
AAAATTTTAATGGTATAAATT
Found at i:56515 original size:10 final size:10
Alignment explanation
Indices: 56488--56519 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56478 TCTTTGGGTG
56488 TTATATAAGC
1 TTATATAAGC
56498 TTAT-TAAGC
1 TTATATAAGC
56507 TTATATAAGC
1 TTATATAAGC
56517 TTA
1 TTA
56520 AAACATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (10 bp):
TTATATAAGC
Found at i:56996 original size:24 final size:24
Alignment explanation
Indices: 56969--57027 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
56959 ACATAGGCAG
56969 TGTACCGATACACCAATGAAGGGA
1 TGTACCGATACACCAATGAAGGGA
*
56993 TGTACCGATACACCAGTGAAGGGA
1 TGTACCGATACACCAATGAAGGGA
57017 TGTACCGATAC
1 TGTACCGATAC
57028 CCTATAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (24 bp):
TGTACCGATACACCAATGAAGGGA
Found at i:57679 original size:15 final size:15
Alignment explanation
Indices: 57659--57688 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57649 GTGAATGATA
*
57659 TGATAAGAAGCTATG
1 TGATAAGAAGATATG
57674 TGATAAGAAGATATG
1 TGATAAGAAGATATG
57689 AGTTTATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (15 bp):
TGATAAGAAGATATG
Found at i:57919 original size:18 final size:18
Alignment explanation
Indices: 57896--57930 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57886 GTTCTTAAGG
57896 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
57914 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
57931 AATTCAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Done.