Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007628.1 Hibiscus syriacus cultivar Beakdansim tig00023397_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: 74180
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:3922 original size:18 final size:18
Alignment explanation
Indices: 3901--3940 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3891 TTGAAAAATC
*
3901 ATTATATATTATTATAAT
1 ATTATATATCATTATAAT
3919 ATTATATATCATTATAAT
1 ATTATATATCATTATAAT
3937 ATTA
1 ATTA
3941 AAGAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATATCATTATAAT
Found at i:5594 original size:23 final size:22
Alignment explanation
Indices: 5550--5591 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5540 ATAATCCTAT
5550 TATTTCAAAATATATTAATTTA
1 TATTTCAAAATATATTAATTTA
5572 TATTT-AAAATAT-TT-ATTTA
1 TATTTCAAAATATATTAATTTA
5591 T
1 T
5592 TTAGAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 7 0.35
22 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTCAAAATATATTAATTTA
Found at i:5962 original size:22 final size:19
Alignment explanation
Indices: 5946--5989 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
5936 GAACAAAAGT
5946 AATTAAATATATAAACATATAA
1 AATTAAA-ATATAAACA-A-AA
*
5968 AATTAAAATATAAATAAAA
1 AATTAAAATATAAACAAAA
5987 AAT
1 AAT
5990 GACTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 1 0.05
21 8 0.38
22 7 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAATATAAACAAAA
Found at i:7303 original size:3 final size:3
Alignment explanation
Indices: 7283--7337 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
7273 ATTTATTTAT
* * *
7283 TAA TAA TATA TAA CAA TAA TAA TAA T-A TAA TAA TAA CAA TTA -AA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7327 TAA TAA -AA TAA
1 TAA TAA TAA TAA
7338 AAGTAAACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 5 0.12
3 34 0.81
4 3 0.07
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:7615 original size:76 final size:76
Alignment explanation
Indices: 7464--8029 Score: 958
Period size: 76 Copynumber: 7.5 Consensus size: 76
7454 GATGAAAATG
* * * * *
7464 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
7529 TCCCGAAGGCTT
65 TCCCGAAGGCTT
7541 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
7606 CCTGAAGGCTT
66 CCCGAAGGCTT
*
7617 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
7682 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
7693 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
7757 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
7768 TTTGGAAACATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
7832 CCCAAAGGCTT
66 CCCGAAGGCTT
*
7843 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
7908 CCCGAAGGCTTT
66 CCCGAAGGC-TT
*
7920 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
7984 CCCGAAGGCTT
66 CCCGAAGGCTT
*
7995 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
8030 TGGGAAATAG
Statistics
Matches: 466, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 179 0.38
76 190 0.41
77 97 0.21
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:8197 original size:138 final size:139
Alignment explanation
Indices: 8034--8308 Score: 439
Period size: 138 Copynumber: 2.0 Consensus size: 139
8024 CAGATGTGGG
*
8034 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATTGTTTTCTTACGTTTCAACAATTTCATTTCTA
1 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACGTTTCAACAATTTCATTT-TA
**
8099 GAAAAGATTGAATGAGAAACTATGGAAA-TCGTTTTCTC-ATTA-TTTTTCAAAATAACATGTTG
65 GAAAAGATAAAATGAGAAACTATGGAAATTC-TTTTCTCTATTATTTTTTCAAAATAACATGTTG
8161 ATTGGGTTTGT
129 ATTGGGTTTGT
*
8172 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAG
1 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACGTTTCAACAATTTCATTTTAG
**
8237 AAAAGATAAAATGAGAAACTATGGAAATTCTTTTCTCATTATTATTTTTTTGAAATAACATGTTG
66 AAAAGATAAAATGAGAAACTATGGAAATTCTTTTCTC--TATTATTTTTTCAAAATAACATGTTG
8302 ATTGGGT
129 ATTGGGT
8309 AACATGACCC
Statistics
Matches: 126, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
137 35 0.28
138 62 0.49
140 4 0.03
141 25 0.20
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (139 bp):
AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACGTTTCAACAATTTCATTTTAG
AAAAGATAAAATGAGAAACTATGGAAATTCTTTTCTCTATTATTTTTTCAAAATAACATGTTGAT
TGGGTTTGT
Found at i:8870 original size:22 final size:22
Alignment explanation
Indices: 8845--8899 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8835 CATAAAGCTT
* *
8845 TCATCTTTGAAAAGAGAATGTA
1 TCATCTTTGAAAAGAAAATCTA
* *
8867 TCATATTTAAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
8889 TCATCTTTGAA
1 TCATCTTTGAA
8900 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:11601 original size:114 final size:114
Alignment explanation
Indices: 11434--11653 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
11424 GATCATGCAG
* * * *
11434 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
11499 ACACTTCCAGAAGATTCTATTCGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
*
11548 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
11613 ACACTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTA
11654 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:15841 original size:14 final size:14
Alignment explanation
Indices: 15824--15862 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
15814 TAAAAGTATG
15824 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
15838 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
15853 AATG-AAAATG
1 AATGCAAAATG
15863 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:18271 original size:20 final size:21
Alignment explanation
Indices: 18221--18271 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18211 TAAATATTAT
* *
18221 GAAAATCATAAAAAATTGAAA
1 GAAAATAATTAAAAATTGAAA
18242 GAAAATAATTAAAAATT-AAA
1 GAAAATAATTAAAAATTGAAA
18262 -AAAATGAATT
1 GAAAAT-AATT
18272 TTTAATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (21 bp):
GAAAATAATTAAAAATTGAAA
Found at i:18937 original size:143 final size:142
Alignment explanation
Indices: 18711--18967 Score: 347
Period size: 143 Copynumber: 1.8 Consensus size: 142
18701 ATTATTTCAA
* * * *
18711 AATATATTAATTTATATATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGC
1 AATATATTAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGC
* *
18776 CTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACATTTTTATAAAAAT
66 CTTAAGACAGCTCCTTTCTT-AATATTAAAAAATAAATAAATAATTAAAACATTTTTATAAAAAT
18841 AATAATAATATAT
130 AATAATAATATAT
** * *
18854 AATATA-TAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGGCATCCAGTT
1 AATATATTAATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGT
* * * *
18918 GCTTTAAGACTG-TCCTTTCTTAATATTGAAAAATAAATAAATATTTAAAA
64 GCCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATAATTAAAA
18968 AATTATTACT
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
142 34 0.35
143 46 0.47
144 18 0.18
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (142 bp):
AATATATTAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGC
CTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATAATTAAAACATTTTTATAAAAATA
ATAATAATATAT
Found at i:19405 original size:13 final size:13
Alignment explanation
Indices: 19387--19411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19377 AAATTATAAT
19387 AAAACTGAATTAG
1 AAAACTGAATTAG
19400 AAAACTGAATTA
1 AAAACTGAATTA
19412 CAAGGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
AAAACTGAATTAG
Found at i:20451 original size:3 final size:3
Alignment explanation
Indices: 20431--20485 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
20421 ATTTATTTAT
* * *
20431 TAA TAA TATA TAA CAA TAA TAA T-A TTA TAA TAA TAA TAA TTA -AA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20475 TAA TAA -AA TAA
1 TAA TAA TAA TAA
20486 AAGTAAACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20462 original size:14 final size:14
Alignment explanation
Indices: 20431--20480 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
20421 ATTTATTTAT
*
20431 TAATAAT-ATATAA
1 TAATAATAATATTA
*
20444 CAATAATAATATTA
1 TAATAATAATATTA
20458 TAATAATAATAATTA
1 TAATAATAAT-ATTA
20473 -AATAATAA
1 TAATAATAA
20481 AATAAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.19
14 22 0.69
15 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATAATATTA
Found at i:20465 original size:17 final size:16
Alignment explanation
Indices: 20431--20470 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
20421 ATTTATTTAT
20431 TAATAATATATAACAA
1 TAATAATATATAACAA
*
20447 TAATAATATTATAATAA
1 TAATAATA-TATAACAA
20464 TAATAAT
1 TAATAAT
20471 TAAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATATATAACAA
Found at i:22839 original size:64 final size:65
Alignment explanation
Indices: 22768--22916 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 65
22758 CTAGGGGTGC
* * *
22768 ATCGGTACACTAATTACATTCGATGTTTC-AAAGAGCCATGAGTGCATCGATGCATGG-TATGTG
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-TGTG
22831 A
65 A
** * * ** * *
22832 ATCGGTACACAAAATGTATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCTTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
*
22897 ATCGGTACACAAAATGCATT
1 ATCGGTACACAAAATACATT
22917 AGATATGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 24 0.34
65 46 0.65
66 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
Found at i:23282 original size:12 final size:13
Alignment explanation
Indices: 23256--23290 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
23246 TAAGATTTTC
23256 TTTGAAAATCAAT
1 TTTGAAAATCAAT
23269 TTTGAAAA-CAAT
1 TTTGAAAATCAAT
23281 TTTGCAAAAT
1 TTTG-AAAAT
23291 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:28666 original size:2 final size:2
Alignment explanation
Indices: 28659--28688 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28649 TTAATTCTTG
28659 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
28689 TATTTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31221 original size:20 final size:22
Alignment explanation
Indices: 31178--31222 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31168 ATAAGATTAT
*
31178 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
31200 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
31220 TAA
1 TAA
31223 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:31458 original size:18 final size:18
Alignment explanation
Indices: 31435--31492 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
31425 AAAATAAAAG
31435 TATAATATTATATATAAT
1 TATAATATTATATATAAT
31453 TATAATATTACATAATATAA-
1 TATAATATT--AT-ATATAAT
* *
31473 TATCATATTAT-TAGAAT
1 TATAATATTATATATAAT
31490 TAT
1 TAT
31493 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 11 0.32
20 10 0.29
21 6 0.18
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATAATATTATATATAAT
Found at i:34377 original size:2 final size:2
Alignment explanation
Indices: 34370--34409 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34360 CAGCATTCTA
34370 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
34410 TCCAAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41793 original size:24 final size:24
Alignment explanation
Indices: 41763--41832 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
41753 ATACATTACC
*
41763 TGAATTCTGTTATGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* * *
41787 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTATGATTTCTGATA
*
41811 TGAATTCTGTTTTGATTTCTGA
1 TGAATTCTGTTATGATTTCTGA
41833 AACCTCCGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:41803 original size:48 final size:48
Alignment explanation
Indices: 41727--41832 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
41717 ATATTTTATC
* *
41727 TGATTTCTGACTTGAATTATGTTATGATA-CATTACCTGAATTCTGTTA
1 TGATTTCTGACTTGAATTATGTTATGATATC-TGACATGAATTCTGTTA
* * * * *
41775 TGATTTCTGA-TCTGGATTCTGTTCTGATATCTGATATGAATTCTGTTT
1 TGATTTCTGACT-TGAATTATGTTATGATATCTGACATGAATTCTGTTA
41823 TGATTTCTGA
1 TGATTTCTGA
41833 AACCTCCGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (48 bp):
TGATTTCTGACTTGAATTATGTTATGATATCTGACATGAATTCTGTTA
Found at i:41830 original size:12 final size:12
Alignment explanation
Indices: 41767--41831 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
41757 ATTACCTGAA
41767 TTCTGTTATGAT
1 TTCTGTTATGAT
* *
41779 TTCTGATCTGGA-
1 TTCTGTTAT-GAT
*
41791 TTCTGTTCTGAT
1 TTCTGTTATGAT
* * *
41803 ATCTGATATGAA
1 TTCTGTTATGAT
*
41815 TTCTGTTTTGAT
1 TTCTGTTATGAT
41827 TTCTG
1 TTCTG
41832 AAACCTCCGT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 36 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.52
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:43951 original size:13 final size:13
Alignment explanation
Indices: 43933--43957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43923 GGTCACAACC
43933 TGACCCGACCCGT
1 TGACCCGACCCGT
43946 TGACCCGACCCG
1 TGACCCGACCCG
43958 ACCCATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:43957 original size:18 final size:18
Alignment explanation
Indices: 43934--43988 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
43924 GTCACAACCT
43934 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
* *
43952 GACCCGACCCATTTACCC
1 GACCCGACCCGTTGACCC
* *
43970 GACCCAAACCGTTGACCC
1 GACCCGACCCGTTGACCC
43988 G
1 G
43989 TTGACCGTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.47, G:0.18, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:43998 original size:7 final size:7
Alignment explanation
Indices: 43977--44007 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
43967 CCCGACCCAA
43977 ACCGTTG
1 ACCGTTG
43984 ACCCGTTG
1 A-CCGTTG
43992 ACCGTTG
1 ACCGTTG
43999 ACCGTTG
1 ACCGTTG
44006 AC
1 AC
44008 TGGCGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (7 bp):
ACCGTTG
Found at i:46518 original size:24 final size:24
Alignment explanation
Indices: 46448--46554 Score: 92
Period size: 24 Copynumber: 4.5 Consensus size: 24
46438 ATATTTTATC
46448 TGATTTCTGA-CTTGAATTCTGTTA
1 TGATTTCTGATC-TGAATTCTGTTA
* * * *
46472 TGA-TACATTACCTGAATTTTGTTA
1 TGATTTC-TGATCTGAATTCTGTTA
* *
46496 TGATTTCTGATCTGGATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTA
* * * *
46520 TTATATCTGATATGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTA
46544 TGATTTCTGAT
1 TGATTTCTGAT
46555 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.03
24 60 0.92
25 3 0.05
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.51
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTA
Found at i:65140 original size:28 final size:26
Alignment explanation
Indices: 65089--65158 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
65079 TTTATTGAAA
65089 AATA-ATTATATATTA-AAATAAAAG
1 AATATATTATATATTATAAATAAAAG
* *
65113 TATAATATTATATATTATAATATTAAAG
1 AAT-ATATTATATATTATAA-ATAAAAG
* *
65141 AATATAATACATATTATA
1 AATATATTATATATTATA
65159 GAATTATGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 2 0.05
25 1 0.03
26 11 0.30
27 15 0.41
28 8 0.22
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (26 bp):
AATATATTATATATTATAAATAAAAG
Found at i:68059 original size:27 final size:28
Alignment explanation
Indices: 67986--68059 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
67976 TTTATTGAAA
*
67986 AATAATTATATATTATTAAAATAAAAGTAT
1 AATAA-TATATATTA-TAAAATAAAAGAAT
* * *
68016 AATATTATATCATTATAATATTAAAGAAT
1 AATAATATAT-ATTATAAAATAAAAGAAT
68045 -ATAATATATATTATA
1 AATAATATATATTATA
68060 GAATTATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 6 0.16
28 8 0.21
29 16 0.42
30 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
AATAATATATATTATAAAATAAAAGAAT
Found at i:68095 original size:15 final size:16
Alignment explanation
Indices: 68070--68099 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
68060 GAATTATGAG
68070 TAAATATTTTAATAAT
1 TAAATATTTTAATAAT
68086 TAAA-ATTTTAATAA
1 TAAATATTTTAATAA
68100 AATGTTAATA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATTTTAATAAT
Found at i:73730 original size:19 final size:18
Alignment explanation
Indices: 73699--73734 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
73689 AGTTTTGTAA
*
73699 TTTATGAATAATATTATT
1 TTTATGAAAAATATTATT
73717 TTTATTGAAAAATATTAT
1 TTTA-TGAAAAATATTAT
73735 ATATTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTATGAAAAATATTATT
Found at i:73746 original size:19 final size:19
Alignment explanation
Indices: 73703--73746 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
73693 TTGTAATTTA
* *
73703 TGAATAATATTATTTTTAT
1 TGAAAAATATTATTATTAT
73722 TGAAAAATATTATATATTAT
1 TGAAAAATATTAT-TATTAT
73742 T-AAAA
1 TGAAAA
73747 TAAAAGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
TGAAAAATATTATTATTAT
Done.