Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004551.1 Hibiscus syriacus cultivar Beakdansim tig00010106_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: 74396
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1944 original size:27 final size:28
Alignment explanation
Indices: 1914--1988 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
1904 AAAAGTATAC
*
1914 TTTTTTATAAATTATGATAAAGGACAAT
1 TTTTTTATAAATTATAATAAAGGACAAT
* *
1942 TTTTTTATAAAATACAATAAAGGACAA-
1 TTTTTTATAAATTATAATAAAGGACAAT
* * *
1969 CTTCTCATAAATTATAATAA
1 TTTTTTATAAATTATAATAA
1989 TACTATCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 15 0.38
28 24 0.62
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.39
Consensus pattern (28 bp):
TTTTTTATAAATTATAATAAAGGACAAT
Found at i:2179 original size:22 final size:22
Alignment explanation
Indices: 2140--2221 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
2130 GTACGGATGG
*
2140 TGGAAGAAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
* * *
2162 TGGAAGTAGGTTGTACGAATGT
1 TGGAAGTAGGCTGCACGAATGC
*
2184 TGAAAGTAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
**
2206 TGGAAGCGGGCTGCAC
1 TGGAAGTAGGCTGCAC
2222 AGCCACTGAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.28, C:0.16, G:0.37, T:0.20
Consensus pattern (22 bp):
TGGAAGTAGGCTGCACGAATGC
Found at i:6575 original size:20 final size:20
Alignment explanation
Indices: 6550--6588 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6540 GGGTGGTGTG
6550 CATCATTAGTGGAGTTGGTA
1 CATCATTAGTGGAGTTGGTA
6570 CATCATTAGTGGAGTTGGT
1 CATCATTAGTGGAGTTGGT
6589 GGAATTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (20 bp):
CATCATTAGTGGAGTTGGTA
Found at i:8320 original size:21 final size:21
Alignment explanation
Indices: 8296--8335 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8286 AAAAATTATC
* *
8296 TAAAATATTATTATTTTTACT
1 TAAAACATCATTATTTTTACT
*
8317 TAAAACATCATTTTTTTTA
1 TAAAACATCATTATTTTTA
8336 TATTTTCGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAACATCATTATTTTTACT
Found at i:8412 original size:29 final size:30
Alignment explanation
Indices: 8350--8414 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
8340 TTCGGTCATA
*
8350 TTTTAACGCCTAATAATATTTTCAGATATT
1 TTTTAACACCTAATAATATTTTCAGATATT
*
8380 TTTTAACACCTAATAATA-TTTCCGATTATT
1 TTTTAACACCTAATAATATTTTCAGA-TATT
8410 TTTTA
1 TTTTA
8415 TCAATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTAACACCTAATAATATTTTCAGATATT
Found at i:13656 original size:14 final size:14
Alignment explanation
Indices: 13616--13656 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
13606 AATCTGGAAT
*
13616 GAGTCAACTCGTCC
1 GAGTCAACTCGTTC
*
13630 GAGTCAAATCGTTC
1 GAGTCAACTCGTTC
*
13644 GAGTCAACCCGTT
1 GAGTCAACTCGTT
13657 GACTTTGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (14 bp):
GAGTCAACTCGTTC
Found at i:19338 original size:3 final size:3
Alignment explanation
Indices: 19330--19430 Score: 60
Period size: 3 Copynumber: 31.7 Consensus size: 3
19320 ATATTTAACT
* * *
19330 ATA ATA AT- ATA ATTA ATA ATA GTA ACTA ATA ATT ATAA ATA CTA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA
* * * * *
19377 ATTA ATG ATA ATA ATA ATC ATA AGCA ATTA ATA ATTA TTA ATA TTA ATA
1 A-TA ATA ATA ATA ATA ATA ATA A-TA A-TA ATA A-TA ATA ATA ATA ATA
19426 ATA AT
1 ATA AT
19431 TCGAATAAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
2 2 0.03
3 55 0.74
4 17 0.23
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:19363 original size:20 final size:17
Alignment explanation
Indices: 19338--19382 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 17
19328 CTATAATAAT
19338 ATAATTAATAATAGTAACTA
1 ATAATTAATAA-A-T-ACTA
19358 ATAATT-ATAAATACTA
1 ATAATTAATAAATACTA
19374 ATAATTAAT
1 ATAATTAAT
19383 GATAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.42
17 3 0.12
18 1 0.04
19 4 0.17
20 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAATTAATAAATACTA
Found at i:19424 original size:16 final size:16
Alignment explanation
Indices: 19356--19427 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
19346 TAATAGTAAC
* *
19356 TAATAATTATAAATAC
1 TAATAATTATTAATAT
* * *
19372 TAATAATTAATGATAA
1 TAATAATTATTAATAT
* *
19388 TAATAATCA-TAAGCAAT
1 TAATAATTATTAA--TAT
19405 TAATAATTATTAATAT
1 TAATAATTATTAATAT
19421 TAATAAT
1 TAATAAT
19428 AATTCGAATA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
15 2 0.05
16 29 0.67
17 9 0.21
18 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATAATTATTAATAT
Found at i:19703 original size:16 final size:17
Alignment explanation
Indices: 19670--19707 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19660 TCTATTAAAA
19670 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
* *
19687 ATTTT-AATTTTTTTAT
1 ATTTTAAATTATTATAT
19703 ATTTT
1 ATTTT
19708 TATTGATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:19742 original size:26 final size:25
Alignment explanation
Indices: 19715--19767 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
19705 TTTTATTGAT
*
19715 AATTTATTTTTATCTTTAAAATTTATA
1 AATTTATCTTT-TC-TTAAAATTTATA
19742 AATTTATCTTTTCTTAAAATTT-TA
1 AATTTATCTTTTCTTAAAATTTATA
19766 AA
1 AA
19768 AATTCACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 9 0.36
26 2 0.08
27 10 0.40
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTATCTTTTCTTAAAATTTATA
Found at i:19770 original size:26 final size:27
Alignment explanation
Indices: 19715--19771 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
19705 TTTTATTGAT
* *
19715 AATTTATTTTTATCTTTAAAATTTATA
1 AATTTATCTTTATCTTTAAAATTTAAA
19742 AATTTATCTTT-TC-TTAAAATTTTAAA
1 AATTTATCTTTATCTTTAAAA-TTTAAA
19768 AATT
1 AATT
19772 CACTTTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 11 0.41
27 10 0.37
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTTATCTTTATCTTTAAAATTTAAA
Found at i:19777 original size:25 final size:25
Alignment explanation
Indices: 19730--19777 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19720 ATTTTTATCT
* *
19730 TTAAAATTTATAAATTTATCTTTTC
1 TTAAAATTTAAAAATTCATCTTTTC
19755 TTAAAATTTTAAAAATTCA-CTTT
1 TTAAAA-TTTAAAAATTCATCTTT
19778 AACATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAAATTTAAAAATTCATCTTTTC
Found at i:20920 original size:26 final size:26
Alignment explanation
Indices: 20872--20921 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20862 TTAATTATTA
*
20872 TATTTTAATTTAACATATGATTAGAT
1 TATTTTAATTTAACATATCATTAGAT
*
20898 TATTTTAGTTTAA-AGTATCATTAG
1 TATTTTAATTTAACA-TATCATTAG
20922 TTCCTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (26 bp):
TATTTTAATTTAACATATCATTAGAT
Found at i:21511 original size:18 final size:18
Alignment explanation
Indices: 21484--21521 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21474 CGGAGTTTGT
*
21484 TTTGAATATGTTTAAATG
1 TTTGAATATGATTAAATG
*
21502 TTTGAGTATGATTAAATG
1 TTTGAATATGATTAAATG
21520 TT
1 TT
21522 ACTTAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTGAATATGATTAAATG
Found at i:21740 original size:18 final size:18
Alignment explanation
Indices: 21713--21750 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21703 CGGAGTTTGT
*
21713 TTTGAATATGTTTAAATG
1 TTTGAATATGATTAAATG
*
21731 TTTGAGTATGATTAAATG
1 TTTGAATATGATTAAATG
21749 TT
1 TT
21751 ACTTAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTGAATATGATTAAATG
Found at i:21851 original size:229 final size:229
Alignment explanation
Indices: 21444--21903 Score: 893
Period size: 229 Copynumber: 2.0 Consensus size: 229
21434 AGTCAACACG
*
21444 GATGGTGCTCGTAGACTTAACATGTGTTTACGGAGTTTGTTTTGAATATGTTTAAATGTTTGAGT
1 GATGGCGCTCGTAGACTTAACATGTGTTTACGGAGTTTGTTTTGAATATGTTTAAATGTTTGAGT
*
21509 ATGATTAAATGTTACTTAACAGACATAATATTCATTTGATTTTATTTATAAAGTTTTTTAGTTTT
66 ATGATTAAATGTTACTTAACAGACATAATATTCATTTGATTTTACTTATAAAGTTTTTTAGTTTT
21574 ATTATCAGGAGTTAATTGTATCACATGTACTCAAATTATGACTCTTATATTAAGGTAGTCCTTAA
131 ATTATCAGGAGTTAATTGTATCACATGTACTCAAATTATGACTCTTATATTAAGGTAGTCCTTAA
21639 ACTTTTAAATATTTTAATTTAATTCCTAAACTAT
196 ACTTTTAAATATTTTAATTTAATTCCTAAACTAT
21673 GATGGCGCTCGTAGACTTAACATGTGTTTACGGAGTTTGTTTTGAATATGTTTAAATGTTTGAGT
1 GATGGCGCTCGTAGACTTAACATGTGTTTACGGAGTTTGTTTTGAATATGTTTAAATGTTTGAGT
21738 ATGATTAAATGTTACTTAACAGACATAATATTCATTTGATTTTACTTATAAAGTTTTTTAGTTTT
66 ATGATTAAATGTTACTTAACAGACATAATATTCATTTGATTTTACTTATAAAGTTTTTTAGTTTT
*
21803 ATTCTCAGGAGTTAATTGTATCACATGTACTCAAATTATGACTCTTATATTAAGGTAGTCCTTAA
131 ATTATCAGGAGTTAATTGTATCACATGTACTCAAATTATGACTCTTATATTAAGGTAGTCCTTAA
21868 ACTTTTAAATATTTTAATTTAATTCCTAAACTAT
196 ACTTTTAAATATTTTAATTTAATTCCTAAACTAT
21902 GA
1 GA
21904 ATATCATTCT
Statistics
Matches: 228, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 228 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (229 bp):
GATGGCGCTCGTAGACTTAACATGTGTTTACGGAGTTTGTTTTGAATATGTTTAAATGTTTGAGT
ATGATTAAATGTTACTTAACAGACATAATATTCATTTGATTTTACTTATAAAGTTTTTTAGTTTT
ATTATCAGGAGTTAATTGTATCACATGTACTCAAATTATGACTCTTATATTAAGGTAGTCCTTAA
ACTTTTAAATATTTTAATTTAATTCCTAAACTAT
Found at i:24498 original size:419 final size:418
Alignment explanation
Indices: 23720--24553 Score: 1256
Period size: 419 Copynumber: 2.0 Consensus size: 418
23710 ATAATGCCAC
** *
23720 GACATCTCCTCTCAGTCTCAACTATGGCAGCCTATGCTATTTACAAAAACCACCCCTCTTAGTCA
1 GACATCTCCTCTCAGTCTCAACTATGGCAGCCTACACTATTGACAAAAACCACCCCTCTTAGTCA
* *
23785 TTAAAATCCTATCTTACTCTCTCTCAAGCACTAAGGGGTTAGGATATATTATTACTAGGCCAGTT
66 TTAAAATCCTATCTTACTCTCTCTCAAGCACTAAGGGATTAGGATATAGTATTACTAGGCCAGTT
* * * * *
23850 CTAATCTTAAGAAAATACTACACCCCATTGCTTATGTGGATCTTTCTTGTATTTCTCTCGAATAA
131 CAAAGCTCAAGAAAATACTACACCCCATTGCTTATGCGGATCTTACTTGTATTTCTCTCGAATAA
* *
23915 TACAAGTATTAATGACTAAGTTTCTCTCGAACACCTAGCCTTCATCTAAGTAATGGACACTCTCA
196 TACAAGTATTAATGACTAAGTTTCTCTCGAACACATAGCCTTCATATAAGTAATGGACACTCTCA
* ** * *
23980 TGCCTCCTACAAACTTAGGCGATGAAGCATTCATAAGAAAAACAAGTAAATACAAAAGATAACTA
261 TGACTCCTACAAACTTAGAAGATGAAACATTCATAAGAAAAACAAGTAAATACAAAAGATAAATA
* * * *
24045 TAAATCCACCATTAAAATAATGTTAAACATCCATAAAATCAACTCCACCAAATAAGGTTAGTTCA
326 TAAATACACCATTAAAATAATATCAAACATCCATAAAATCAACCCCACCAAATAAGGTTAG-TCA
24110 TGGTGGGGTTCGAATCATCCATGAAACAA
390 TGGTGGGGTTCGAATCATCCATGAAACAA
* *
24139 GACATCTCCTCTCAGTCTCAACTATGGCAGCCTACACTATTGATAAAAACTACCCCTCTTAGTCA
1 GACATCTCCTCTCAGTCTCAACTATGGCAGCCTACACTATTGACAAAAACCACCCCTCTTAGTCA
* * * * * *
24204 TTGAAATCCTATCTTAGTCTCTCTTAAGCACTAAGGGATTAGGATATAGTATTATTATGCCGGTT
66 TTAAAATCCTATCTTACTCTCTCTCAAGCACTAAGGGATTAGGATATAGTATTACTAGGCCAGTT
* * * * *
24269 CAAAGCTCAAGAAATTACTATACCCCATTGTTTATGCGGATCTTACTTGTGTTTCTCTCGAATAC
131 CAAAGCTCAAGAAAATACTACACCCCATTGCTTATGCGGATCTTACTTGTATTTCTCTCGAATAA
* * *
24334 TACAAGTATTAAT-AGCTAAGTTTCTTTTGATCACATAGCCTTCATATAAGTAATGGACACTCTC
196 TACAAGTATTAATGA-CTAAGTTTCTCTCGAACACATAGCCTTCATATAAGTAATGGACACTCTC
* *
24398 ATGACTCCTACAAACTTAGAAGATGAAACATTCATAAGCAAAACAAGTAAATGCAAAAGATAAAT
260 ATGACTCCTACAAACTTAGAAGATGAAACATTCATAAGAAAAACAAGTAAATACAAAAGATAAAT
* *
24463 TTAAATATACCATTAAAATAATATCAAACATCCATAAAATCAACCCCACCAAATAAGGTTAGTCA
325 ATAAATACACCATTAAAATAATATCAAACATCCATAAAATCAACCCCACCAAATAAGGTTAGTCA
* *
24528 TGGTGGGGTTCGAATTATCTATGAAA
390 TGGTGGGGTTCGAATCATCCATGAAA
24554 TAAAACATGA
Statistics
Matches: 371, Mismatches: 43, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
418 28 0.08
419 343 0.92
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (418 bp):
GACATCTCCTCTCAGTCTCAACTATGGCAGCCTACACTATTGACAAAAACCACCCCTCTTAGTCA
TTAAAATCCTATCTTACTCTCTCTCAAGCACTAAGGGATTAGGATATAGTATTACTAGGCCAGTT
CAAAGCTCAAGAAAATACTACACCCCATTGCTTATGCGGATCTTACTTGTATTTCTCTCGAATAA
TACAAGTATTAATGACTAAGTTTCTCTCGAACACATAGCCTTCATATAAGTAATGGACACTCTCA
TGACTCCTACAAACTTAGAAGATGAAACATTCATAAGAAAAACAAGTAAATACAAAAGATAAATA
TAAATACACCATTAAAATAATATCAAACATCCATAAAATCAACCCCACCAAATAAGGTTAGTCAT
GGTGGGGTTCGAATCATCCATGAAACAA
Found at i:28729 original size:46 final size:46
Alignment explanation
Indices: 28235--28712 Score: 688
Period size: 46 Copynumber: 10.4 Consensus size: 46
28225 AAATGAAGGA
* * *
28235 ATAAAAGAAAATGCATAACGGTGCATTATCAGCATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** * *
28281 ATAAATGAAAATGTATAACAATGCATTGTCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
28327 ATAAATGAAAATGCATAACAGTGTATTATCAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
28373 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
28419 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGTATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** *
28465 ACAAATGAAAATGCATAACGGTGCATTATCAACATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
28511 ATAAATAAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
28557 ATAAATGAAAATGCATAACGGTGCATTATTGGCATGAAAGGATGCA
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
28603 ATAAATAAAAACGCATAACGGTGCATTATCGGCGTGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
28649 ATAAATGAAAATGCATAACGGTGTA-TATTCGGCATGAAAGAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTA-TCGGCATGAAAGGATGCC
* *
28695 ACAAATGAAAATACATAA
1 ATAAATGAAAATGCATAA
28713 TGGTATATTA
Statistics
Matches: 386, Mismatches: 45, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
45 2 0.01
46 384 0.99
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:31327 original size:244 final size:243
Alignment explanation
Indices: 30890--31422 Score: 798
Period size: 244 Copynumber: 2.2 Consensus size: 243
30880 TAACCTTTCG
* * * *
30890 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGTATAATTGGTACCTTTATACCAATTTC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTATACCAATTGC
* * * *
30955 ACAGTTAGGTCGTTATTCTTTTACTCAACGGTATTTAACCGTTCATGTAACTGGCATAATTGGTA
66 ACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGGTA
* * * * *
31020 CCTTTCTACCAATTGTACATTTAGGCCATTATTCTTTTACTCAACGACATTTAACTATTCATCTA
131 CATTTCTACCAATTGCACAGTTAGACCATTATTCTTTTACTCAACGACATTTAACCATTCATCTA
*
31085 ACTGGA-ATAATTGGTACCTTTCTACCAATTGCAATAGTTAGACCATTAT
196 ACT-GATATAATTGGTACCTTTCTACCAATTGC-ACAGTTAGACCATTAT
*
31134 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTATACCAATTGC
* *
31199 ACAGTTAGGCCATTATTTTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATGATTGGTA
66 ACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGGTA
* * * ** *
31264 CATTTCTACTAATTGCATAGTTAGACCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTA
131 CATTTCTACCAATTGCACAGTTAGACCATTATTCTTTTACTCAACGACATTTAACCATTCATCTA
* *
31329 ACTGATATAATTGGTACCTTTTTACCAATTGCACAGTTAGGCCATTAT
196 ACTGATATAATTGGTACCTTTCTACCAATTGCACAGTTAGACCATTAT
* *
31377 TCTTTTACTCAACTGTATTTAACCATTCATCTAACTGGCATAATTG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
31423 AAACCTTTTT
Statistics
Matches: 261, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
243 60 0.23
244 201 0.77
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (243 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTATACCAATTGC
ACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGGTA
CATTTCTACCAATTGCACAGTTAGACCATTATTCTTTTACTCAACGACATTTAACCATTCATCTA
ACTGATATAATTGGTACCTTTCTACCAATTGCACAGTTAGACCATTAT
Found at i:31452 original size:81 final size:81
Alignment explanation
Indices: 30890--31422 Score: 787
Period size: 81 Copynumber: 6.6 Consensus size: 81
30880 TAACCTTTCG
* * * *
30890 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGTATAATTGGTACCTTTATACCAATTTC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
* *
30955 ACAGTTAGGTCGTTAT
66 ACAGTTAGGCCATTAT
* *
30971 TCTTTTACTCAACGGTATTTAACCGTTCATGTAACTGGCATAATTGGTACCTTTCTACCAATTGT
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
*
31036 ACATTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
** ** *
31052 TCTTTTACTCAACGACATTTAACTATTCATCTAACTGGAATAATTGGTACCTTTCTACCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
* *
31117 AATAGTTAGACCATTAT
66 -ACAGTTAGGCCATTAT
*
31134 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
31199 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * * * *
31215 TTTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATGATTGGTACATTTCTACTAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
* *
31280 ATAGTTAGACCATTAT
66 ACAGTTAGGCCATTAT
* ** *
31296 TCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGATATAATTGGTACCTTTTTACCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
31361 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* *
31377 TCTTTTACTCAACTGTATTTAACCATTCATCTAACTGGCATAATTG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
31423 AAACCTTTTT
Statistics
Matches: 402, Mismatches: 49, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
81 330 0.82
82 72 0.18
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGC
ACAGTTAGGCCATTAT
Found at i:31900 original size:58 final size:58
Alignment explanation
Indices: 31774--31901 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 58
31764 CTTATTTCGT
* *
31774 ACACCTAGTGCCCATACGAAAATTCATACACTTAGTATGAATTTCTTAATATTTTAGC
1 ACACATAGTGCCCATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGC
* * *
31832 ACACAAAGTGCCCAATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTT-GC
1 ACACATAGTGCCC-ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGC
*
31890 ACACTTAGTGCC
1 ACACATAGTGCC
31902 ATTTGGTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 23 0.37
59 39 0.63
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (58 bp):
ACACATAGTGCCCATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGC
Found at i:32386 original size:19 final size:19
Alignment explanation
Indices: 32364--32409 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
32354 ACTATGATAC
*
32364 CGATACCACCTTCTGGCAT
1 CGATACCACCTTATGGCAT
* *
32383 CGATACCCCCTTATGGTAT
1 CGATACCACCTTATGGCAT
32402 CGATACCA
1 CGATACCA
32410 GTTTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (19 bp):
CGATACCACCTTATGGCAT
Found at i:39065 original size:20 final size:20
Alignment explanation
Indices: 39040--39078 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39030 AAAGCTTTAA
* *
39040 GATCATTATTTTCTTTTGAT
1 GATCATCATTTACTTTTGAT
39060 GATCATCATTTACTTTTGA
1 GATCATCATTTACTTTTGA
39079 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (20 bp):
GATCATCATTTACTTTTGAT
Found at i:45450 original size:81 final size:81
Alignment explanation
Indices: 45306--45595 Score: 409
Period size: 81 Copynumber: 3.6 Consensus size: 81
45296 TTAACCTTTC
* * *
45306 TTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTAGCATAATTGATACCTTTCTACCAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG
* **
45371 CACAGTTAGGTCGCTA
66 CACAGTTAGGCCATTA
* * ** *
45387 TTCGTTTAGTCAACATTATTTAACCGTTCATCTAACCGGCATAATTGGTACCTTTCTACCAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG
* *
45452 TACATTTAGGCCATTA
66 CACAGTTAGGCCATTA
* * * * *
45468 TTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGTAAAATTGGCACCTTTCTACTAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG
45533 CACAGTTAGGCCATTA
66 CACAGTTAGGCCATTA
*
45549 TTCTTTTACTCAACGGTATTTAACCCTTCATCTAACTGGCATAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
45596 ACACAATTAT
Statistics
Matches: 181, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 181 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG
CACAGTTAGGCCATTA
Found at i:45616 original size:81 final size:81
Alignment explanation
Indices: 45306--45637 Score: 403
Period size: 81 Copynumber: 4.1 Consensus size: 81
45296 TTAACCTTTC
* * *
45306 TTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTAGCATAATTGATACCTTTCTACCAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTG
* **
45371 CACAGTTAGGTCGCTA
66 CACAGTTAGGCCATTA
* * ** * **
45387 TTCGTTTAGTCAACATTATTTAACCGTTCATCTAACCGGCATAATTGGTACCTTTCTACCAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTG
* *
45452 TACATTTAGGCCATTA
66 CACAGTTAGGCCATTA
* * * * *
45468 TTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGTAAAATTGGCACCTTTCTACTAATTG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTG
45533 CACAGTTAGGCCATTA
66 CACAGTTAGGCCATTA
* ** * ** *
45549 TTCTTTTACTCAACGGTATTTAACCCTTCATCTAACTGGCATAATTGACACAATTATGTCAAATG
1 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTG
45614 CACAGTTAGGCCTATTA
66 CACAGTTAGGCC-ATTA
*
45631 ATCTTTT
1 TTCTTTT
45638 GTTTTAGAGC
Statistics
Matches: 213, Mismatches: 37, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
81 203 0.95
82 10 0.05
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTG
CACAGTTAGGCCATTA
Found at i:46451 original size:95 final size:96
Alignment explanation
Indices: 46326--46552 Score: 257
Period size: 95 Copynumber: 2.4 Consensus size: 96
46316 TATGGCTCTA
* * * * * *
46326 TAGTATCGATACTAC-TA-CACTAGTACCGATACTTCTATACTATGGTATCGATACCTCCTTCT-
1 TAGTATCGATACT-CTTACCA-TAGTATCGATACTACCATACTATGGTACCAATACCCCCTTCTA
* * *
46388 GATATCGATA-CTGATTTTAGGTTCGATG-TTGCC
64 G-TATCGATATCAG-TTTTAGATTCAATGTTTGCC
*
46421 TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGGTACCAATACCCCCTTCTAGT
1 TAGTATCGATACTCTTACCATAGTATCGATACTACCATACTATGGTACCAATACCCCCTTCTAGT
*
46486 ATCGATATCAGTTTTAGATTCAATGTTTTCC
66 ATCGATATCAGTTTTAGATTCAATGTTTGCC
* * *
46517 TAGTATCGATACCCTTACCATTGTATCGATATTACC
1 TAGTATCGATACTCTTACCATAGTATCGATACTACC
46553 TAGTCTGTAT
Statistics
Matches: 113, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
94 1 0.01
95 70 0.62
96 42 0.37
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (96 bp):
TAGTATCGATACTCTTACCATAGTATCGATACTACCATACTATGGTACCAATACCCCCTTCTAGT
ATCGATATCAGTTTTAGATTCAATGTTTGCC
Found at i:47867 original size:46 final size:46
Alignment explanation
Indices: 47790--48059 Score: 308
Period size: 46 Copynumber: 5.9 Consensus size: 46
47780 TAGTTAATAT
* * ** * *
47790 ACCATTACGTATTTTCATTGGTGGCATCCTTTCATGCCAATTATGC
1 ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGC
* * * *
47836 ACCGTTAAGCATTTTCATTTATGACATCCTTTCATGCCTATAATGT
1 ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGC
** * *
47882 ACCATTATGCATTTTCATTTATGGTATCCTTTCATGCCGATGATGC
1 ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGC
* * * *
47928 ACCGTTATGCATTTTTATTTATGACAACCTTTCATGCCTATAATGC
1 ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGC
** *
47974 ACCATTATGCATTTTCATTTATGGA-ATCCTTTCATATCGATAATGC
1 ACCATTATGCATTTTCATTTAT-GACATCCTTTCATGCCAATAATGC
* * *
48020 ACCATTATGTATTTTCATTTATGGCATCTTTTCATGCCAA
1 ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAA
48060 AGACATGTAA
Statistics
Matches: 187, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
45 1 0.01
46 184 0.98
47 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (46 bp):
ACCATTATGCATTTTCATTTATGACATCCTTTCATGCCAATAATGC
Found at i:48079 original size:92 final size:92
Alignment explanation
Indices: 47784--48057 Score: 368
Period size: 92 Copynumber: 3.0 Consensus size: 92
47774 GATATGTAGT
* * * ** * * * *
47784 TAATATACCATTACGTATTTTCATTGGTGGCATCCTTTCATGCCAATTATGCACCGTTAAGCATT
1 TAATGTACCATTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCACCGTTATGCATT
47849 TTCATTTATGACATCCTTTCATGCCTA
66 TTCATTTATGACATCCTTTCATGCCTA
* *
47876 TAATGTACCATTATGCATTTTCATTTATGGTATCCTTTCATGCCGATGATGCACCGTTATGCATT
1 TAATGTACCATTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCACCGTTATGCATT
* *
47941 TTTATTTATGACAACCTTTCATGCCTA
66 TTCATTTATGACATCCTTTCATGCCTA
* ** * *
47968 TAATGCACCATTATGCATTTTCATTTATGGAATCCTTTCATATCGATAATGCACCATTATGTATT
1 TAATGTACCATTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCACCGTTATGCATT
* *
48033 TTCATTTATGGCATCTTTTCATGCC
66 TTCATTTATGACATCCTTTCATGCC
48058 AAAGACATGT
Statistics
Matches: 160, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 160 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (92 bp):
TAATGTACCATTATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCACCGTTATGCATT
TTCATTTATGACATCCTTTCATGCCTA
Found at i:48155 original size:81 final size:81
Alignment explanation
Indices: 48067--48599 Score: 814
Period size: 81 Copynumber: 6.6 Consensus size: 81
48057 CAAAGACATG
* * * *
48067 TAACCTTTCATTTAACTAGCATGATTGACACCTTTCAGTCAAATGCACAACTAGGAAATTAATCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
48132 TTTACTCAAAGGTATT
66 TTTACTCAAAGGTATT
* * * *
48148 TAACCTTTCATCTAACTGGCATGATTGATACCTTTATGTCAAATGCACAACTAAGCAATTAGTCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
48213 TTTACTCAAAGGTATT
66 TTTACTCAAAGGTATT
*** *
48229 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAAATAATTAGTCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
48294 TTTACTCAAAGGTATT
66 TTTACTCAAAGGTATT
** * * * *
48310 TAACCTTTCATCTAACTAACATGATTGACACCTTTTTTTCAAATGCATAGCTAGGCAATTAATCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
48375 TTTACTCAAAGGTATT
66 TTTACTCAAAGGTATT
* *
48391 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTTGGCAATTAATCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
*
48456 TTTACTCAAATGTATT
66 TTTACTCAAAGGTATT
* * * *
48472 TAACCTTTCATCTAATTGGCATGATTGACACATTTCTGTCAAATACACAACTAGTCAATTAATCT
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
*
48537 TTTACTCAAAGATATT
66 TTTACTCAAAGGTATT
* *
48553 TAACCTTTCATCTAACTCGTATGATTGACACCTTTCTGTCAAATGCA
1 TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCA
48600 GAAAAAAGCG
Statistics
Matches: 410, Mismatches: 42, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 410 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (81 bp):
TAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCT
TTTACTCAAAGGTATT
Found at i:61993 original size:21 final size:21
Alignment explanation
Indices: 61960--62002 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
61950 CATCTAGGTA
*
61960 TTTGTAGACGCCATGAATTCT
1 TTTGTAGACGCCATAAATTCT
* *
61981 TTTGTCGAGGCCATAAATTCT
1 TTTGTAGACGCCATAAATTCT
62002 T
1 T
62003 GCAAGGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
TTTGTAGACGCCATAAATTCT
Found at i:63575 original size:21 final size:19
Alignment explanation
Indices: 63537--63582 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
63527 AATTAATCCT
63537 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
63557 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
63578 A-TAAT
1 ACTAAT
63583 GATTTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Done.