Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006452.1 Hibiscus syriacus cultivar Beakdansim tig00015629_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: 61530
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1190 original size:35 final size:34
Alignment explanation
Indices: 1145--1381 Score: 214
Period size: 35 Copynumber: 6.7 Consensus size: 34
1135 ACATATAACG
* *
1145 TATATAATATATAGTTTAAAAAAATATTTTTTAAA
1 TATATAATATATAGTTT-TAAAAATATTTTTGAAA
*
1180 TATATAATATATAGTTTTAAAAATATTTTAGAAA
1 TATATAATATATAGTTTTAAAAATATTTTTGAAA
* **
1214 -ATATATATAATATAATTTTGAAAACA-ATTTTCAAATATA
1 TATATA-AT-ATATAGTTTT-AAAA-ATATTTT-TGA-A-A
*
1253 TATATAATATATAGTTTTGAAAATATTTTTCGAGAA
1 TATATAATATATAGTTTTAAAAATATTTTT-GA-AA
*
1289 TATATAATATATAGTTTTGAAAATATTTTTGAAA
1 TATATAATATATAGTTTTAAAAATATTTTTGAAA
*
1323 -ATATATATAATATAGTTTTGAAAAAT-TTTTCGAAA
1 TATATA-AT-ATATAGTTTT-AAAAATATTTTTGAAA
*
1358 TATAT-ATAATATATGTTTTGAAAA
1 TATATAAT-ATATA-GTTTTAAAAA
1382 GCATATAATA
Statistics
Matches: 174, Mismatches: 13, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
33 10 0.06
34 32 0.18
35 51 0.29
36 50 0.29
37 13 0.07
38 10 0.06
39 3 0.02
40 5 0.03
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (34 bp):
TATATAATATATAGTTTTAAAAATATTTTTGAAA
Found at i:1320 original size:12 final size:12
Alignment explanation
Indices: 1303--1362 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1293 TAATATATAG
1303 TTTTGAAAATAT
1 TTTTGAAAATAT
1315 TTTTGAAAATAT
1 TTTTGAAAATAT
* * * *
1327 ATAT-AATATAG
1 TTTTGAAAATAT
1338 TTTTGAAAA-AT
1 TTTTGAAAATAT
1349 TTTTCGAAATATAT
1 TTTT-GAAA-ATAT
1363 ATAATATATG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
11 12 0.33
12 21 0.58
13 1 0.03
14 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:14056 original size:36 final size:36
Alignment explanation
Indices: 14003--14274 Score: 365
Period size: 36 Copynumber: 7.6 Consensus size: 36
13993 CATATAACGC
* *
14003 ATATAATATATAATTTTGAAAACATTTTTTGAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
*
14039 ATATAATGTATAGTTTTGAAAACATTTTTTGAAAAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
*
14075 ATAT-ATAGTATA-TTTTGAAAACATTTTTCGAAAAT
1 ATATAATA-TATAGTTTTGAAAACATTTTTTGAAAAT
* *
14110 ATATAATATATAGTTTTGAAAACATTTTTCGAGAAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
* *
14146 ATATAAATATATAGATTTAAAAACA-TTTTTG-AAAT
1 ATAT-AATATATAGTTTTGAAAACATTTTTTGAAAAT
*
14181 ATATATATATATAGTTTTGAAAACTTTTTTTGAAAAT
1 ATATA-ATATATAGTTTTGAAAACATTTTTTGAAAAT
* **
14218 ATAT-ATATATAGTTTTGAAAACACTTTTCAAAAAT
1 ATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
*
14253 ATATAATATATACTTTTGAAAA
1 ATATAATATATAGTTTTGAAAA
14275 GCGTATATAA
Statistics
Matches: 210, Mismatches: 18, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
34 1 0.00
35 86 0.41
36 97 0.46
37 26 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
Found at i:14091 original size:35 final size:35
Alignment explanation
Indices: 14003--14274 Score: 343
Period size: 35 Copynumber: 7.7 Consensus size: 35
13993 CATATAACGC
* *
14003 ATATA-ATATATAATTTTGAAAACATTTTTTGAAT
1 ATATATATATATAGTTTTGAAAACATTTTTTGAAA
*
14037 ATATATAATGTATAGTTTTGAAAACATTTTTTGAAA
1 ATATAT-ATATATAGTTTTGAAAACATTTTTTGAAA
*
14073 ATATATATAGTATA-TTTTGAAAACATTTTTCGAAA
1 ATATATATA-TATAGTTTTGAAAACATTTTTTGAAA
*
14108 ATATATAATATATAGTTTTGAAAACATTTTTCGAGAA
1 ATATAT-ATATATAGTTTTGAAAACATTTTTTGA-AA
* * *
14145 TATATAAATATATAGATTTAAAAACA-TTTTTGAAA
1 -ATATATATATATAGTTTTGAAAACATTTTTTGAAA
*
14180 TATATATATATATAGTTTTGAAAACTTTTTTTGAAA
1 -ATATATATATATAGTTTTGAAAACATTTTTTGAAA
* **
14216 ATATATATATATAGTTTTGAAAACACTTTTCAAAA
1 ATATATATATATAGTTTTGAAAACATTTTTTGAAA
*
14251 ATATATAATATATACTTTTGAAAA
1 ATATAT-ATATATAGTTTTGAAAA
14275 GCGTATATAA
Statistics
Matches: 211, Mismatches: 18, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
34 5 0.02
35 93 0.44
36 89 0.42
37 19 0.09
38 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
ATATATATATATAGTTTTGAAAACATTTTTTGAAA
Found at i:14096 original size:71 final size:71
Alignment explanation
Indices: 14003--14274 Score: 372
Period size: 71 Copynumber: 3.8 Consensus size: 71
13993 CATATAACGC
* * * *
14003 ATATA-ATATATAATTTTGAAAACATTTTTTGAATATATATAATGTATAGTTTTGAAAACATTTT
1 ATATATATATATAGTTTTGAAAACATTTTTCGAAAATATATAATATATAGTTTTGAAAACATTTT
14067 TTGAAA
66 TTGAAA
14073 ATATATATAGTATA-TTTTGAAAACATTTTTCGAAAATATATAATATATAGTTTTGAAAACATTT
1 ATATATATA-TATAGTTTTGAAAACATTTTTCGAAAATATATAATATATAGTTTTGAAAACATTT
*
14137 TTCGAGAA
65 TTTGA-AA
* * * *
14145 TATATAAATATATAGATTTAAAAACATTTTT-G-AAATATATATATATATAGTTTTGAAAACTTT
1 -ATATATATATATAGTTTTGAAAACATTTTTCGAAAATATATA-ATATATAGTTTTGAAAACATT
14208 TTTTGAAA
64 TTTTGAAA
* * *
14216 ATATATATATATAGTTTTGAAAACACTTTTCAAAAATATATAATATATACTTTTGAAAA
1 ATATATATATATAGTTTTGAAAACATTTTTCGAAAATATATAATATATAGTTTTGAAAA
14275 GCGTATATAA
Statistics
Matches: 179, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
70 31 0.17
71 81 0.45
72 45 0.25
73 22 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (71 bp):
ATATATATATATAGTTTTGAAAACATTTTTCGAAAATATATAATATATAGTTTTGAAAACATTTT
TTGAAA
Found at i:14336 original size:11 final size:11
Alignment explanation
Indices: 14320--14377 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
14310 TGAGAACACA
*
14320 TTTTATATATT
1 TTTTATTTATT
**
14331 TTTTATTTACA
1 TTTTATTTATT
*
14342 TTATATTTATT
1 TTTTATTTATT
*
14353 ATTTATTTATT
1 TTTTATTTATT
14364 TATTTATTTATT
1 T-TTTATTTATT
14376 TT
1 TT
14378 GTTTACTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 26 0.70
12 11 0.30
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:14352 original size:4 final size:4
Alignment explanation
Indices: 14321--14376 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
14311 GAGAACACAT
*
14321 TTTA TATA TTT- TTTA TTTACA TTATA TTTA -TTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTT--A TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
14370 TTTA TTT
1 TTTA TTT
14377 TGTTTACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 6 0.13
4 32 0.71
5 3 0.07
6 3 0.07
7 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:21282 original size:47 final size:45
Alignment explanation
Indices: 21212--21337 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
21202 TATAAAATCT
*
21212 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
21257 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
21304 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
21338 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:21484 original size:40 final size:40
Alignment explanation
Indices: 21440--21561 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
21430 ACCGTAGTGC
*
21440 TACACATAAGGTCGTGCCTACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
21480 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
21520 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
21560 TA
1 TA
21562 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:25446 original size:2 final size:2
Alignment explanation
Indices: 25423--25478 Score: 85
Period size: 2 Copynumber: 26.5 Consensus size: 2
25413 TTATGCTCAT
25423 TA TA TGA TA TGA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
25466 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
25479 GGATGACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 45 0.88
3 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26637 original size:14 final size:14
Alignment explanation
Indices: 26614--26652 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
26604 AAGTTATGAT
*
26614 AATTTGTGAAAATA
1 AATTTGTGAAAAAA
*
26628 AATTTTTGAAAAAA
1 AATTTGTGAAAAAA
26642 AA-TTGTGAAAA
1 AATTTGTGAAAA
26653 CTAAAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (14 bp):
AATTTGTGAAAAAA
Found at i:27133 original size:22 final size:22
Alignment explanation
Indices: 27105--27159 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
27095 TTTTGTTTTG
27105 TGGGTTCTTCTAGTCGAATGGT
1 TGGGTTCTTCTAGTCGAATGGT
27127 TGGGTTCTTCTAGTCGAATGGT
1 TGGGTTCTTCTAGTCGAATGGT
27149 TGGGTTCTTCT
1 TGGGTTCTTCT
27160 TTGGTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.11, C:0.15, G:0.31, T:0.44
Consensus pattern (22 bp):
TGGGTTCTTCTAGTCGAATGGT
Found at i:28767 original size:37 final size:36
Alignment explanation
Indices: 28707--28826 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
28697 ATCCCATTAT
* **
28707 CATTTTTC-AACAAACATCAACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
28743 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
28779 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
28814 CATATTTTCAAAG
1 CAT-TTTTCAAAG
28827 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:33393 original size:37 final size:36
Alignment explanation
Indices: 33345--33453 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
33335 ATTTTTCTAC
* *
33345 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
33382 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
33417 AAACATTTACTAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
33454 TTGGTTACCA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 6 0.09
37 27 0.40
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:33409 original size:21 final size:21
Alignment explanation
Indices: 33385--33445 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
33375 TTCAAAGAAA
33385 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
33406 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
33420 CATTTACTAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
33441 CATTT
1 CATTT
33446 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.33
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:33467 original size:35 final size:36
Alignment explanation
Indices: 33352--33480 Score: 133
Period size: 35 Copynumber: 3.6 Consensus size: 36
33342 TACAAACATC
* *
33352 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AACAGT
*
33389 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
* ***
33424 TACTAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
33459 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
33481 AATACTTTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
34 14 0.17
35 42 0.51
37 26 0.32
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Found at i:36535 original size:15 final size:15
Alignment explanation
Indices: 36518--36547 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
36508 ATCTTTCTTT
36518 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
36534 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
36548 GATCTGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:37799 original size:37 final size:37
Alignment explanation
Indices: 37740--37853 Score: 155
Period size: 35 Copynumber: 3.2 Consensus size: 37
37730 ATCCCATTAT
*
37740 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
* *
37776 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
* *
37812 CA-TTTTCAAATAAACATTTACTAAACTTT-AAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
37847 CATTTTT
1 CATTTTT
37854 TTAAAGTTGG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
35 32 0.46
36 17 0.25
37 20 0.29
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (37 bp):
CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
Found at i:40777 original size:3 final size:3
Alignment explanation
Indices: 40769--40795 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40759 AATTAATTTA
40769 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
40796 TTGTAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41838 original size:10 final size:10
Alignment explanation
Indices: 41825--41867 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
41815 AAAGAACACA
41825 AAAAAGAGAG
1 AAAAAGAGAG
*
41835 AAAAAAAGGAG
1 AAAAAGA-GAG
41846 AAAAAGAGAG
1 AAAAAGAGAG
*
41856 AAAAAGAAAG
1 AAAAAGAGAG
41866 AA
1 AA
41868 TAGTCACCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAAAGAGAG
Found at i:41838 original size:11 final size:11
Alignment explanation
Indices: 41824--41860 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41814 AAAAGAACAC
41824 AAAAAAGAGAG
1 AAAAAAGAGAG
41835 AAAAAA-AG-G
1 AAAAAAGAGAG
41844 AGAAAAAGAGAG
1 A-AAAAAGAGAG
41856 AAAAA
1 AAAAA
41861 GAAAGAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:41946 original size:3 final size:3
Alignment explanation
Indices: 41938--41989 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
41928 AGGTAATTCT
41938 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41986 TTA T
1 TTA T
41990 ATTTATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42121 original size:3 final size:3
Alignment explanation
Indices: 42113--42142 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42103 AGGGTTCTCG
42113 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42143 GAAATGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42340 original size:3 final size:3
Alignment explanation
Indices: 42332--42372 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42322 GGACAACCAT
42332 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42373 TTGGTCAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42705 original size:45 final size:46
Alignment explanation
Indices: 42625--42715 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
42615 TTTGCCACTT
42625 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
1 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
42671 GCTTTTTTTAATTTGATTTTGTTTTGTTA-TTTTTTTCATTTATTA
1 GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
42716 ATATAATGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 16 0.36
46 29 0.64
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.71
Consensus pattern (46 bp):
GCTTTTTTTAATTTGATTTTGTTTTGTTATTTTTTTTCATTTATTA
Found at i:49385 original size:31 final size:32
Alignment explanation
Indices: 49311--49384 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
49301 TAAGAGTATG
*
49311 CTCATAATAAAAATTATTGGAAAAAGATAGAC
1 CTCATAATAAAAAGTATTGGAAAAAGATAGAC
*
49343 CTC-TAATAAAAAGTATT-GAAAAA-ATTATA-
1 CTCATAATAAAAAGTATTGGAAAAAGA-TAGAC
49372 CTCATAATAAAAA
1 CTCATAATAAAAA
49385 ATAAATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 4 0.11
30 18 0.47
31 13 0.34
32 3 0.08
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (32 bp):
CTCATAATAAAAAGTATTGGAAAAAGATAGAC
Found at i:53884 original size:20 final size:20
Alignment explanation
Indices: 53855--53953 Score: 146
Period size: 20 Copynumber: 5.0 Consensus size: 20
53845 ATAAACGTGA
*
53855 TTTTAGTTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
53875 TTTTATTTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
* *
53895 TTTCATGTTT-GCGTTGCAAT
1 TTTTAT-TTTCGCGTTGCGAT
*
53915 TTTCATTTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
53935 TTTTATTTTCGCGTTGCGA
1 TTTTATTTTCGCGTTGCGA
53954 ATTTAAGTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 3 0.04
20 66 0.92
21 3 0.04
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.52
Consensus pattern (20 bp):
TTTTATTTTCGCGTTGCGAT
Found at i:53964 original size:20 final size:20
Alignment explanation
Indices: 53854--53964 Score: 120
Period size: 20 Copynumber: 5.5 Consensus size: 20
53844 AATAAACGTG
53854 ATTTTAGTTTCGCGTTGCGA
1 ATTTTAGTTTCGCGTTGCGA
* *
53874 TTTTTATTTTCGCGTTGCG-
1 ATTTTAGTTTCGCGTTGCGA
53893 ATTTTCATGTTT-GCGTTGC-A
1 ATTTT-A-GTTTCGCGTTGCGA
*
53913 ATTTTCATTTTCGCGTTGCGA
1 ATTTT-AGTTTCGCGTTGCGA
* *
53934 TTTTTATTTTCGCGTTGCGA
1 ATTTTAGTTTCGCGTTGCGA
*
53954 ATTTAAGTTTC
1 ATTTTAGTTTC
53965 AGAAACTACT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
19 7 0.09
20 62 0.81
21 8 0.10
ACGTcount: A:0.14, C:0.15, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTTTAGTTTCGCGTTGCGA
Found at i:56032 original size:21 final size:21
Alignment explanation
Indices: 56006--56066 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
55996 TTGCCCTATC
*
56006 ATCGTTCAAGAGGCGCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
56027 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
*
56047 CATC-ATCGAAGAGGCCCCTC
1 -ATCGTTC-AAGAGGCCCCTC
56067 TCACCATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:56079 original size:21 final size:21
Alignment explanation
Indices: 56031--56080 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
56021 CCTCCTATCG
*
56031 TTCAAGAGGCCCCTCTCATCA
1 TTCAAGAGGCCCCTCTCACCA
56052 -TCGAAGAGGCCCCTCTCACCA
1 TTC-AAGAGGCCCCTCTCACCA
56073 TTCAAGAG
1 TTCAAGAG
56081 ACCCTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCACCA
Found at i:57609 original size:20 final size:20
Alignment explanation
Indices: 57584--57636 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
57574 TCGTTGTGAT
57584 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCAAA
*
57604 AGTCAAATTCGCAACGTAAA
1 AGTCAAATTCGCAACGCAAA
57624 AGTCAAATTCGCA
1 AGTCAAATTCGCA
57637 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAA
Found at i:57722 original size:74 final size:74
Alignment explanation
Indices: 57540--57722 Score: 240
Period size: 74 Copynumber: 2.5 Consensus size: 74
57530 GTACACTTTT
* ** *
57540 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCTCGTTGTGATAGTCAAATTCGCAACGCAAAA
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
57605 GTCAAATTC
66 GTCAAATTC
** * * * * **
57614 GCAACGTAAAAGTCAAATTCGCATTGCGATTTTCGCGTTACGATAGTCAAATTTGCAATATTAAA
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
*
57679 GTTAAATTC
66 GTCAAATTC
*
57688 GCAACGCGAAAGTCAAATTCGCGTTGTGAATTTCG
1 GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCG
57723 GTTTGCGATT
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 91 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (74 bp):
GCAACGCGAAAGTCAAATTCGCGTTGTGATTTTCGCGTTACGATAGTCAAATTCGCAACACAAAA
GTCAAATTC
Found at i:57748 original size:20 final size:20
Alignment explanation
Indices: 57725--57801 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
57715 GAATTTCGGT
* *
57725 TTGCGATTTTAATTTTCGCG
1 TTGCGAATTTAACTTTCGCG
*
57745 TTGCGAATTTTAA-TTTTGCG
1 TTGCGAA-TTTAACTTTCGCG
* * *
57765 TTACGAATTTGACTTTCGCA
1 TTGCGAATTTAACTTTCGCG
57785 TTGCGAATTTAACTTTC
1 TTGCGAATTTAACTTTC
57802 ACAACAATCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 4 0.09
20 38 0.81
21 5 0.11
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTAACTTTCGCG
Found at i:58078 original size:18 final size:18
Alignment explanation
Indices: 58055--58090 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58045 AAGCCGGTTG
*
58055 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
58073 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
58091 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:61210 original size:27 final size:27
Alignment explanation
Indices: 61172--61355 Score: 131
Period size: 27 Copynumber: 6.7 Consensus size: 27
61162 GAACCGACCC
* *
61172 GACACTTTGGGAATTATTTGAAAAGGT
1 GACATTTTGGGAATTATTTGAAAATGT
61199 GACATTTTGGGAATTATTTTGAAAAATGT
1 GACATTTTGGGAATTA-TTTG-AAAATGT
*
61228 GACATTTTGGGAACTATTTTG-AAA-GT
1 GACATTTTGGGAATTA-TTTGAAAATGT
* * * **
61254 GACATTTTGGGATTTTTTTAAAAACAAT
1 GACATTTTGGGAATTATTTGAAAA-TGT
* * ** **
61282 -ACATTCTGGTAATTATTTTTAAACAT
1 GACATTTTGGGAATTATTTGAAAATGT
* *
61308 GACATTTTGAGAATTATTTGTAAAACTTT
1 GACATTTTGGGAATTATTTG-AAAA-TGT
* *
61337 GATATTTTGGTAATTATTT
1 GACATTTTGGGAATTATTT
61356 TTAATAAAGG
Statistics
Matches: 124, Mismatches: 25, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.02
26 20 0.16
27 50 0.40
28 8 0.06
29 43 0.35
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (27 bp):
GACATTTTGGGAATTATTTGAAAATGT
Found at i:61234 original size:29 final size:28
Alignment explanation
Indices: 61172--61326 Score: 151
Period size: 27 Copynumber: 5.7 Consensus size: 28
61162 GAACCGACCC
* *
61172 GACACTTTGGGAATTA-TTTGAAAAGGT
1 GACATTTTGGGAATTATTTTGAAAAAGT
61199 GACATTTTGGGAATTATTTTGAAAAATGT
1 GACATTTTGGGAATTATTTTGAAAAA-GT
*
61228 GACATTTTGGGAACTATTTTG--AAAGT
1 GACATTTTGGGAATTATTTTGAAAAAGT
* * *
61254 GACATTTTGGG-ATTTTTTTAAAAACAAT
1 GACATTTTGGGAATTATTTTGAAAA-AGT
* * * *
61282 -ACATTCTGGTAATTATTTTTAAACA-T
1 GACATTTTGGGAATTATTTTGAAAAAGT
*
61308 GACATTTTGAGAATTATTT
1 GACATTTTGGGAATTATTT
61327 GTAAAACTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
25 6 0.06
26 14 0.13
27 44 0.42
28 20 0.19
29 22 0.21
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (28 bp):
GACATTTTGGGAATTATTTTGAAAAAGT
Done.