Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001414.1 Hibiscus syriacus cultivar Beakdansim tig00002751_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: 81687
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:873 original size:10 final size:11
Alignment explanation
Indices: 849--877 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
839 GAAATAAAAA
849 CTTTAAAATTT
1 CTTTAAAATTT
860 CTTTAAAA-TT
1 CTTTAAAATTT
870 CTTTAAAA
1 CTTTAAAA
878 ATATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (11 bp):
CTTTAAAATTT
Found at i:2150 original size:27 final size:29
Alignment explanation
Indices: 2120--2182 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
2110 AGCATGACTC
*
2120 AAATATCATA-A-A-CCATAATAATCATCA
1 AAATATCATAGATACCCATAA-AAGCATCA
* *
2147 AAATAGCATAGATACCCATAAAAGCATCC
1 AAATATCATAGATACCCATAAAAGCATCA
2176 AAATATC
1 AAATATC
2183 CAAAAGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 9 0.31
28 1 0.03
29 13 0.45
30 6 0.21
ACGTcount: A:0.52, C:0.21, G:0.05, T:0.22
Consensus pattern (29 bp):
AAATATCATAGATACCCATAAAAGCATCA
Found at i:8031 original size:21 final size:20
Alignment explanation
Indices: 8002--8040 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7992 AAAATCATAC
*
8002 TTAACATTTATTTTTTTAATT
1 TTAACATTT-TTTTATTAATT
*
8023 TTAATATTTTTTTATTAA
1 TTAACATTTTTTTATTAA
8041 AAACTTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAACATTTTTTTATTAATT
Found at i:14472 original size:14 final size:14
Alignment explanation
Indices: 14399--14465 Score: 73
Period size: 14 Copynumber: 4.8 Consensus size: 14
14389 TAGGGTTAAA
*
14399 GTTTAGGATTTAGG
1 GTTTATGATTTAGG
*
14413 GTTTATGATTTAAG
1 GTTTATGATTTAGG
* * *
14427 CTTTAAGTTTTAGG
1 GTTTATGATTTAGG
14441 GTTT-TGAGTTTAGG
1 GTTTATGA-TTTAGG
14455 GTTTATGATTT
1 GTTTATGATTT
14466 GAGGTTTGGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
13 1 0.02
14 38 0.90
15 3 0.07
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.51
Consensus pattern (14 bp):
GTTTATGATTTAGG
Found at i:23674 original size:7 final size:7
Alignment explanation
Indices: 23662--23688 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
23652 AATCAAAATA
23662 AAATATT
1 AAATATT
23669 AAATATT
1 AAATATT
23676 AAATATT
1 AAATATT
23683 AAATAT
1 AAATAT
23689 GATTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:23858 original size:13 final size:13
Alignment explanation
Indices: 23840--23873 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
23830 ACATATCATA
23840 TATAAAAACATTT
1 TATAAAAACATTT
23853 TAT-AAAACATTT
1 TATAAAAACATTT
*
23865 TACAAAAAC
1 TATAAAAAC
23874 CGGAGCTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAAACATTT
Found at i:24283 original size:53 final size:52
Alignment explanation
Indices: 24203--24362 Score: 169
Period size: 53 Copynumber: 3.1 Consensus size: 52
24193 ATGCAGACAA
* * *
24203 TGACTCTGCTATACTATTATCTGGTATCACACAACATCATATACTAGCCTCAC
1 TGACTCTGCTATGCTAGTATCTGGTATCACACAACATCAGATACTAGCCT-AC
* * * * *
24256 TGACTCTGCTATGTTAGTATCTGGTATCACACAGCGTCAGATACTAACCGTAA
1 TGACTCTGCTATGCTAGTATCTGGTATCACACAACATCAGATACTAGCC-TAC
** * * * *
24309 TGGGT-TACTATGCTAGTACCTGATATCAAACAACATCAGATACTAGCCTAC
1 TGACTCTGCTATGCTAGTATCTGGTATCACACAACATCAGATACTAGCCTAC
24360 TGA
1 TGA
24363 GAGGGGGTAC
Statistics
Matches: 86, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
51 4 0.05
52 35 0.41
53 46 0.53
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (52 bp):
TGACTCTGCTATGCTAGTATCTGGTATCACACAACATCAGATACTAGCCTAC
Found at i:28634 original size:2 final size:2
Alignment explanation
Indices: 28627--28661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28617 AATAAAATCT
28627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28662 GAATATTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32437 original size:175 final size:175
Alignment explanation
Indices: 32119--32465 Score: 466
Period size: 175 Copynumber: 2.0 Consensus size: 175
32109 TCTAAATCTG
* * * *** * **
32119 TTGCATAGAGAATGAATCAAACTATACCTGAATCCAATCACGAATAACTTTGATAGCCTGTGATT
1 TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
* *
32184 TCAGTTCACTTTCCTAATCACCAAACAGTCCGATAAATCAGCATTTACGCCCCTCAAAAACCTTA
66 TCAGTTCACTTTCCCAATCACCAAACAGTCCGATAAATCAGCATTTAAGCCCCTCAAAAACCTTA
* *
32249 ATTCCAGTGCTTAAACTAACTAAACAAACACTTAGTTCCAATAAC
131 ATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAATAAC
* *
32294 TTGCATAAAGAATGAATCGAACTAAACCTGAATTCAATCACGAAAAAAAATGAGAGCCTACGATT
1 TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
* * *
32359 TCAGTTCACTTTCCCAATCACCAAACAG-CATGATAAATCAGCATTTAAGCTCCTTC-AAAAGCT
66 TCAGTTCACTTTCCCAATCACCAAACAGTC-CGATAAATCAGCATTTAAGC-CCCTCAAAAACCT
* *
32422 GT-ATTCCAATGCTTAAAGTAACTAAGCAAACACTTAGCTCCAAT
129 -TAATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAAT
32466 TACTGGCGAA
Statistics
Matches: 149, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
174 1 0.01
175 143 0.96
176 5 0.03
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (175 bp):
TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
TCAGTTCACTTTCCCAATCACCAAACAGTCCGATAAATCAGCATTTAAGCCCCTCAAAAACCTTA
ATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAATAAC
Found at i:32645 original size:2 final size:2
Alignment explanation
Indices: 32638--32676 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32628 TCGCCTCTTT
32638 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
32677 TTAAGCTCCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:33874 original size:15 final size:16
Alignment explanation
Indices: 33828--33877 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
33818 AAAAAATTAA
33828 AATTGAAAGTTAGAGT
1 AATTGAAAGTTAGAGT
*
33844 GATT-AAA-TTAGGAGT
1 AATTGAAAGTTA-GAGT
33859 AATTGAAAGTTA-AGT
1 AATTGAAAGTTAGAGT
33874 AATT
1 AATT
33878 AAATTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 17 0.59
16 6 0.21
17 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
AATTGAAAGTTAGAGT
Found at i:35741 original size:21 final size:21
Alignment explanation
Indices: 35717--35758 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35707 TGGATGATCA
35717 TTTCATTTTCATGAATACAAT
1 TTTCATTTTCATGAATACAAT
35738 TTTCATTTTCATGAATACAAT
1 TTTCATTTTCATGAATACAAT
35759 GGTCATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTCATTTTCATGAATACAAT
Found at i:35764 original size:21 final size:21
Alignment explanation
Indices: 35719--35764 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
35709 GATGATCATT
**
35719 TCATTTTCATGAATACAATTT
1 TCATTTTCATGAATACAATGG
35740 TCATTTTCATGAATACAATGG
1 TCATTTTCATGAATACAATGG
35761 TCAT
1 TCAT
35765 GTTAAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
TCATTTTCATGAATACAATGG
Found at i:37208 original size:33 final size:33
Alignment explanation
Indices: 37161--37237 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
37151 ACAAAGTTTA
*
37161 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
* **
37193 CGATAAATTTAAATACTTAAAAACTTTTAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
37226 CGAT-AATTGAAA
1 CGATAAATTGAAA
37238 CAAAATTTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:37252 original size:21 final size:21
Alignment explanation
Indices: 37228--37267 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
37218 TTTAAGTTCG
37228 ATAATTGAAACAAAATTTACA
1 ATAATTGAAACAAAATTTACA
* *
37249 ATAATTGAAATAAAGTTTA
1 ATAATTGAAACAAAATTTA
37268 AAAATAAACT
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:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATTGAAACAAAATTTACA
Found at i:39163 original size:177 final size:177
Alignment explanation
Indices: 38771--39462 Score: 1287
Period size: 177 Copynumber: 3.9 Consensus size: 177
38761 TTTTATGGTG
38771 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
*
38836 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACA-TTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
*
38900 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAAAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
*
38947 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATTGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
*
39012 AGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
* *
39077 AAGTAATATTTGTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
39124 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
*
39189 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTCTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
39254 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
*
39301 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAGTCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
* *
39366 CGAGAAATCACTGAAGTCACTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
39431 AAGTAATCTTTTTATTCTCTCTTTTGATTAAT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAAT
39463 ATGTCTACAA
Statistics
Matches: 500, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
176 100 0.20
177 400 0.80
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (177 bp):
TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
Found at i:40395 original size:6 final size:7
Alignment explanation
Indices: 40381--40422 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
40371 TATAAAGTCT
40381 TTAAAAA
1 TTAAAAA
*
40388 ATAAAAA
1 TTAAAAA
40395 TTAAAAA
1 TTAAAAA
40402 TTAAAAA
1 TTAAAAA
*
40409 TTATGAAA
1 TTA-AAAA
40417 TTAAAA
1 TTAAAA
40423 GTTGTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:40759 original size:2 final size:2
Alignment explanation
Indices: 40752--40798 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
40742 AAACAAAATA
40752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40794 AT AT A
1 AT AT A
40799 ATTTTTAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40844 original size:21 final size:22
Alignment explanation
Indices: 40797--40869 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
40787 TATATATATA
* *
40797 TAATTTTTAGTAATTTA-ATTT
1 TAATTTTTAGTATTTTATAGTT
*
40818 TTATTTTTAGTATTTTATA-TT
1 TAATTTTTAGTATTTTATAGTT
*
40839 TAATTTTTTAATATTTATATAGTT
1 TAA-TTTTTAGTATTT-TATAGTT
40863 TGAATTT
1 T-AATTT
40870 AAAATGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 19 0.44
22 12 0.28
23 4 0.09
24 6 0.14
25 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TAATTTTTAGTATTTTATAGTT
Found at i:42835 original size:18 final size:19
Alignment explanation
Indices: 42793--42840 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
42783 CGTCAAATTT
*
42793 TTAATAAAA-ATAAATAAA
1 TTAAAAAAATATAAATAAA
* *
42811 TTTAAAATATATAAAT-AA
1 TTAAAAAAATATAAATAAA
42829 TTAAAAAAATAT
1 TTAAAAAAATAT
42841 TTTTATAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAAAATATAAATAAA
Found at i:49665 original size:14 final size:16
Alignment explanation
Indices: 49606--49667 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 16
49596 CAAAAACTTG
49606 ATTTGATTT-TTTTAT
1 ATTTGATTTATTTTAT
* *
49621 ATTT-ATTTAATTATAG
1 ATTTGATTT-ATTTTAT
*
49637 ATTATGCTTTATTTTAT
1 ATT-TGATTTATTTTAT
49654 ATTTG-TTT-TTTTAT
1 ATTTGATTTATTTTAT
49668 TTTATTTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
14 10 0.26
15 7 0.18
16 9 0.24
17 9 0.24
18 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (16 bp):
ATTTGATTTATTTTAT
Found at i:49670 original size:5 final size:5
Alignment explanation
Indices: 49644--49720 Score: 52
Period size: 5 Copynumber: 14.8 Consensus size: 5
49634 TAGATTATGC
* * *
49644 TTTAT TTTAT ATTT-G TTT-T TTTAT TTTAT TTTAG ATTATT TTTAT TTT-T
1 TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT
49693 TTTAGT TTTAGT TTTAGT TATTAT TTTA
1 TTTA-T TTTA-T TTTA-T T-TTAT TTTA
49721 AGTCTTGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 10 0.17
5 25 0.42
6 22 0.37
7 3 0.05
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:49676 original size:24 final size:25
Alignment explanation
Indices: 49644--49703 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
49634 TAGATTATGC
*
49644 TTTATTTTATATT-TGTTTT-TTTAT
1 TTTATTTTAGATTAT-TTTTATTTAT
*
49668 TTTATTTTAGATTATTTTTATTTTT
1 TTTATTTTAGATTATTTTTATTTAT
49693 TTTAGTTTTAG
1 TTTA-TTTTAG
49704 TTTTAGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 16 0.52
25 9 0.29
26 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTATTTTAGATTATTTTTATTTAT
Found at i:53701 original size:15 final size:15
Alignment explanation
Indices: 53670--53707 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
53660 TTATTTTATA
53670 TTTTATTTTAGATTT
1 TTTTATTTTAGATTT
53685 TTTTAGTTTTAGATTT
1 TTTTA-TTTTAGATTT
*
53701 TGTTATT
1 TTTTATT
53708 ATTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (15 bp):
TTTTATTTTAGATTT
Found at i:61306 original size:2 final size:2
Alignment explanation
Indices: 61301--61328 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61291 GTGTATGTGC
61301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61329 TCTAACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65016 original size:13 final size:13
Alignment explanation
Indices: 64998--65024 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64988 CATAGTTGAA
64998 CAGTCTTCATATG
1 CAGTCTTCATATG
65011 CAGTCTTCATATG
1 CAGTCTTCATATG
65024 C
1 C
65025 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:70130 original size:18 final size:18
Alignment explanation
Indices: 70107--70147 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
70097 TTACCAATCA
70107 ATCTAGGGGTTGAATAAC
1 ATCTAGGGGTTGAATAAC
70125 ATCTAGGGGTTGAATAAC
1 ATCTAGGGGTTGAATAAC
70143 ATCTA
1 ATCTA
70148 AACAAACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (18 bp):
ATCTAGGGGTTGAATAAC
Found at i:81543 original size:24 final size:24
Alignment explanation
Indices: 81516--81591 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
81506 TTATCGACGG
*
81516 TGACTGTCACCAATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
*
81540 TGACTGTCACTGATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
81564 TGACTGTCACCGATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
81588 TGAC
1 TGAC
81592 GGGGGATCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (24 bp):
TGACTGTCACCGATGACCGAACGA
Found at i:81567 original size:11 final size:11
Alignment explanation
Indices: 81528--81591 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
81518 ACTGTCACCA
81528 ATGACCGAACG
1 ATGACCGAACG
* *
81539 ATGACTGTCACTG
1 ATGACCG-AAC-G
81552 ATGACCGAACG
1 ATGACCGAACG
* *
81563 ATGACTGTCACCG
1 ATGACCG--AACG
81576 ATGACCGAACG
1 ATGACCGAACG
81587 ATGAC
1 ATGAC
81592 GGGGGATCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 21 0.51
12 4 0.10
13 16 0.39
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (11 bp):
ATGACCGAACG
Done.