Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004552.1 Hibiscus syriacus cultivar Beakdansim tig00010110_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: 86975
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2488 original size:22 final size:22
Alignment explanation
Indices: 2450--2501 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2440 AAAGATATTG
**
2450 GATAATAAATATTTAAA-ATAA
1 GATAATAAATAGCTAAATATAA
*
2471 GATTAATAAATAGCTAAATATAG
1 GA-TAATAAATAGCTAAATATAA
2494 GATAATAA
1 GATAATAA
2502 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (22 bp):
GATAATAAATAGCTAAATATAA
Found at i:4983 original size:97 final size:96
Alignment explanation
Indices: 4858--5104 Score: 275
Period size: 97 Copynumber: 2.5 Consensus size: 96
4848 AGATGATCCT
* * *
4858 TCAAGAGAAACTGTCTCAAGAGATACAAAATTTGTTTCAAGGAAACGA-CTCAAATATG-GTTTT
1 TCAA-AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAACAATCTCAAAGATGTGTTTT
* *
4921 GTTTTAA-GAGAAACAAACTCAAAGATTTTGTGTT
65 GTTTCAATG-GAAACAAACTCAAAGATTTT-T-TC
* * *
4955 TCCAAAGAAACTGCCTCAAGGGAGACAAAATTTGTTTCAATGGAAATAATCTCAAAGATGTTTGT
1 T-CAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GGAAACAATCTCAAAGATG--TGT
*
5020 TTTGTTTCAATGGAAACAGACTCAAAGATTTTTTC
62 TTTGTTTCAATGGAAACAAACTCAAAGATTTTTTC
* *
5055 TCAAATGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAA
1 TCAAA-GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAG-GAAACAA
5105 ACTTACAATT
Statistics
Matches: 126, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
97 33 0.26
98 9 0.07
99 13 0.10
100 24 0.19
101 16 0.13
102 30 0.24
103 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (96 bp):
TCAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAACAATCTCAAAGATGTGTTTTG
TTTCAATGGAAACAAACTCAAAGATTTTTTC
Found at i:5117 original size:64 final size:61
Alignment explanation
Indices: 5020--5172 Score: 155
Period size: 66 Copynumber: 2.4 Consensus size: 61
5010 AGATGTTTGT
** * *
5020 TTTGTTTCAATGGAAACAGACTCAAAGATTTTTTCTC-AAATGAAATTGTCTCAAGAGAGACAAA
1 TTTGTTTCAAAAGAAACA-ACTTACA-ATTTTTTCTCGAAA-GAAATTGTCT--AGAGAGACAAA
5084 A
61 A
* * *
5085 CTTTGTTTCCAGAGAAACAAACTTACAATTTTTTTTTTCGAAAGAAATTGTCTAGAGAGACAAAA
1 -TTTGTTTCAAAAGAAAC-AACTTACAA--TTTTTTCTCGAAAGAAATTGTCTAGAGAGACAAAA
5150 TTTGTTTCAAAAGAAACAACTTA
1 TTTGTTTCAAAAGAAACAACTTA
5173 AAGGATATTG
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
63 6 0.08
64 15 0.20
65 13 0.17
66 19 0.25
67 19 0.25
68 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (61 bp):
TTTGTTTCAAAAGAAACAACTTACAATTTTTTCTCGAAAGAAATTGTCTAGAGAGACAAAA
Found at i:5144 original size:67 final size:64
Alignment explanation
Indices: 5048--5172 Score: 173
Period size: 67 Copynumber: 1.9 Consensus size: 64
5038 GACTCAAAGA
* *
5048 TTTTTTCTCAAATGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAAACTTACAA
1 TTTTTTCTCAAATGAAATTGTCTC-AGAGAGACAAAA-TTTGTTTCAAAAGAAAC-AACTTACAA
5113 TT
63 TT
*
5115 TTTTTTTTCGAAA-GAAATTGTCT-AGAGAGACAAAATTTGTTTCAAAAGAAACAACTTA
1 TTTTTTCTC-AAATGAAATTGTCTCAGAGAGACAAAATTTGTTTCAAAAGAAACAACTTA
5173 AAGGATATTG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
63 6 0.11
64 15 0.28
65 12 0.22
67 18 0.33
68 3 0.06
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (64 bp):
TTTTTTCTCAAATGAAATTGTCTCAGAGAGACAAAATTTGTTTCAAAAGAAACAACTTACAATT
Found at i:6380 original size:13 final size:13
Alignment explanation
Indices: 6346--6438 Score: 64
Period size: 15 Copynumber: 6.8 Consensus size: 13
6336 TTTTACTTTG
*
6346 TTTTTCTTTTGTTC
1 TTTTTCTCTT-TTC
*
6360 -TTTT-TCTTTAC
1 TTTTTCTCTTTTC
*
6371 TTTTTCTCTTTGTTT
1 TTTTTCTC-TT-TTC
6386 TTTTTCTCTTTGCTC
1 TTTTTCTCTTT--TC
*
6401 TTTTTCTCTTTGC
1 TTTTTCTCTTTTC
*
6414 ATTTTTTTCTTTTC
1 -TTTTTCTCTTTTC
*
6428 TTTTTTTCTTT
1 TTTTTCTCTTT
6439 GCTCATTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.03
12 7 0.11
13 19 0.30
14 15 0.23
15 21 0.33
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTCTCTTTTC
Found at i:6391 original size:15 final size:15
Alignment explanation
Indices: 6371--6479 Score: 94
Period size: 15 Copynumber: 7.1 Consensus size: 15
6361 TTTTCTTTAC
6371 TTTTTCTCTTTGTTT
1 TTTTTCTCTTTGTTT
* *
6386 TTTTTCTCTTTGCTC
1 TTTTTCTCTTTGTTT
*
6401 TTTTTCTCTTTGCATT
1 TTTTTCTCTTTG-TTT
* *
6417 TTTTTCTTTTCTTTTT
1 TTTTTCTCTT-TGTTT
* *
6433 TTCTTTGCTCATTATTT
1 TT-TTT-CTCTTTGTTT
**
6450 TTTTT-TCTTTACTT
1 TTTTTCTCTTTGTTT
6464 TTTTTCTCTTTGTTT
1 TTTTTCTCTTTGTTT
6479 T
1 T
6480 GATTGGATCT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
14 12 0.16
15 33 0.44
16 17 0.23
17 10 0.13
18 3 0.04
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTTTCTCTTTGTTT
Found at i:6403 original size:49 final size:48
Alignment explanation
Indices: 6350--6479 Score: 125
Period size: 48 Copynumber: 2.8 Consensus size: 48
6340 ACTTTGTTTT
6350 TCTTTTGTTCTTTTTCTTTAC-TTTTTCTCTTTGTTTTTTTTCTCTTTGC
1 TCTTTT-TTCTTTTTCTTTACTTTTTTCTCTTTGTTTTTTTT-TCTTTGC
* *
6399 TC-TTTTTC----TCTTTGCATTTTTT-TCTTT-TCTTTTTTTCTTTGC
1 TCTTTTTTCTTTTTCTTTAC-TTTTTTCTCTTTGTTTTTTTTTCTTTGC
6441 TCATTATTTT-TTTTTCTTTACTTTTTTTCTCTTTGTTTT
1 TC-TT-TTTTCTTTTTCTTTAC-TTTTTTCTCTTTGTTTT
6480 GATTGGATCT
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
42 9 0.14
43 13 0.20
44 6 0.09
45 9 0.14
47 3 0.05
48 15 0.23
49 7 0.11
50 3 0.05
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.75
Consensus pattern (48 bp):
TCTTTTTTCTTTTTCTTTACTTTTTTCTCTTTGTTTTTTTTTCTTTGC
Found at i:6421 original size:34 final size:32
Alignment explanation
Indices: 6383--6475 Score: 81
Period size: 33 Copynumber: 2.9 Consensus size: 32
6373 TTTCTCTTTG
6383 TTTTTTTTCTCTTTGCTCTTTTTCTCTTTG-C-A
1 TTTTTTTTCTCTTT-CT-TTTTTCTCTTTGCCAA
6415 -TTTTTTTCT-TTTCTTTTTT-TCTTTGCTCATTA
1 TTTTTTTTCTCTTTCTTTTTTCTCTTTGC-CA--A
6447 TTTTTTTT-TCTTTACTTTTTTTCTCTTTG
1 TTTTTTTTCTCTTT-C-TTTTTTCTCTTTG
6476 TTTTGATTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
27 6 0.12
28 5 0.10
29 3 0.06
30 3 0.06
31 9 0.18
32 2 0.04
33 10 0.20
34 1 0.02
35 6 0.12
36 6 0.12
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTTTTTTCTCTTTCTTTTTTCTCTTTGCCAA
Found at i:6479 original size:29 final size:29
Alignment explanation
Indices: 6337--6479 Score: 123
Period size: 29 Copynumber: 4.8 Consensus size: 29
6327 TGTCTTCTCT
*
6337 TTTACTTTGTTTT-TCTTT-TGTTCTTTTTC
1 TTTACTTT-TTTTCTCTTTGT-TTTTTTTTC
6366 TTTAC--TTTTTCTCTTTGTTTTTTTTCTC
1 TTTACTTTTTTTCTCTTTGTTTTTTTT-TC
* * **
6394 TTTGCTCTTTTTCTCTTTGCATTTTTTTC
1 TTTACTTTTTTTCTCTTTGTTTTTTTTTC
* *
6423 TTTTCTTTTTTTCTTTGCTCATTATTTTTTTTTC
1 TTTACTTTTTTTC--T-CT--TTGTTTTTTTTTC
6457 TTTACTTTTTTTCTCTTTGTTTT
1 TTTACTTTTTTTCTCTTTGTTTT
6480 GATTGGATCT
Statistics
Matches: 93, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
26 4 0.04
27 12 0.13
28 7 0.08
29 24 0.26
30 18 0.19
31 3 0.03
32 3 0.03
34 22 0.24
ACGTcount: A:0.04, C:0.16, G:0.05, T:0.75
Consensus pattern (29 bp):
TTTACTTTTTTTCTCTTTGTTTTTTTTTC
Found at i:7893 original size:13 final size:13
Alignment explanation
Indices: 7875--7907 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
7865 TGGATCACTG
7875 CTTCGTCTCGGAT
1 CTTCGTCTCGGAT
7888 CTTCGTCTCGGAT
1 CTTCGTCTCGGAT
7901 CTTCGTC
1 CTTCGTC
7908 ATTGAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.33, G:0.21, T:0.39
Consensus pattern (13 bp):
CTTCGTCTCGGAT
Found at i:10221 original size:40 final size:40
Alignment explanation
Indices: 10166--10257 Score: 184
Period size: 40 Copynumber: 2.3 Consensus size: 40
10156 GTTGTAGCCT
10166 GGGTGCATGGATACACAACAGGGTGCATGGATGCACAGCA
1 GGGTGCATGGATACACAACAGGGTGCATGGATGCACAGCA
10206 GGGTGCATGGATACACAACAGGGTGCATGGATGCACAGCA
1 GGGTGCATGGATACACAACAGGGTGCATGGATGCACAGCA
10246 GGGTGCATGGAT
1 GGGTGCATGGAT
10258 GCACTAATTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.28, C:0.18, G:0.37, T:0.16
Consensus pattern (40 bp):
GGGTGCATGGATACACAACAGGGTGCATGGATGCACAGCA
Found at i:10258 original size:20 final size:20
Alignment explanation
Indices: 10166--10261 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
10156 GTTGTAGCCT
*
10166 GGGTGCATGGATACACAACA
1 GGGTGCATGGATGCACAACA
*
10186 GGGTGCATGGATGCACAGCA
1 GGGTGCATGGATGCACAACA
*
10206 GGGTGCATGGATACACAACA
1 GGGTGCATGGATGCACAACA
*
10226 GGGTGCATGGATGCACAGCA
1 GGGTGCATGGATGCACAACA
10246 GGGTGCATGGATGCAC
1 GGGTGCATGGATGCAC
10262 TAATTGCATT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.28, C:0.20, G:0.36, T:0.16
Consensus pattern (20 bp):
GGGTGCATGGATGCACAACA
Found at i:10302 original size:17 final size:18
Alignment explanation
Indices: 10280--10331 Score: 88
Period size: 17 Copynumber: 2.9 Consensus size: 18
10270 TTCGAAATAG
10280 AGTGCATGGATGCACT-C
1 AGTGCATGGATGCACTGC
10297 AGTGCATGGATGCACTGC
1 AGTGCATGGATGCACTGC
10315 AGGTGCATGGATGCACT
1 A-GTGCATGGATGCACT
10332 TTGACATCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 16 0.48
18 2 0.06
19 15 0.45
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (18 bp):
AGTGCATGGATGCACTGC
Found at i:13766 original size:20 final size:19
Alignment explanation
Indices: 13686--13773 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
13676 TCGAAATGGA
13686 GTGCATGGATGCACT-CAGG
1 GTGCATGGATGCACTACA-G
*
13705 GTGCATCGATGCAC-A-A-
1 GTGCATGGATGCACTACAG
13721 -TGCATGGATGCACTACAG
1 GTGCATGGATGCACTACAG
* *
13739 GTGCATGGATGTACTACGGG
1 GTGCATGGATGCACTAC-AG
*
13759 GTGTATGGATGCACT
1 GTGCATGGATGCACT
13774 TTGACACCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
15 12 0.21
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.49
20 14 0.25
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (19 bp):
GTGCATGGATGCACTACAG
Found at i:14498 original size:21 final size:21
Alignment explanation
Indices: 14449--14498 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
14439 AAGATATTGG
14449 ATAATAAATATTTAAAATAAGA
1 ATAATAAATA-TTAAAATAAGA
* *
14471 TTAATAAATA-TAAATATAGGA
1 ATAATAAATATTAAA-ATAAGA
14492 ATAATAA
1 ATAATAA
14499 TGAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (21 bp):
ATAATAAATATTAAAATAAGA
Found at i:16237 original size:3 final size:3
Alignment explanation
Indices: 16223--16266 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
16213 GCAAAAATTG
*
16223 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16267 TTATAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19306 original size:19 final size:19
Alignment explanation
Indices: 19282--19318 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19272 TGCACAGTCA
19282 TTGTCTGCTGCCCATGTCC
1 TTGTCTGCTGCCCATGTCC
*
19301 TTGTCTGCTGCCCTTGTC
1 TTGTCTGCTGCCCATGTC
19319 TCTGATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.35, G:0.22, T:0.41
Consensus pattern (19 bp):
TTGTCTGCTGCCCATGTCC
Found at i:28484 original size:18 final size:19
Alignment explanation
Indices: 28458--28497 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28448 GGTCGGATTA
* *
28458 AATTTAAAAAAA-TTAATT
1 AATTAAAAAAAAGTAAATT
28476 AATTAAAAAAAAGTAAATT
1 AATTAAAAAAAAGTAAATT
28495 AAT
1 AAT
28498 AATTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATTAAAAAAAAGTAAATT
Found at i:33676 original size:59 final size:59
Alignment explanation
Indices: 33597--33829 Score: 351
Period size: 59 Copynumber: 3.9 Consensus size: 59
33587 AAATTACCAA
* *
33597 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGCGTATAAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
**
33656 AGGGCACTTTGTGCACTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
33715 -GTGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AG-GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * * *
33774 ATGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
33830 ATTGAATTTA
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
58 1 0.01
59 157 0.99
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:34827 original size:16 final size:16
Alignment explanation
Indices: 34806--34846 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
34796 ATGAGTTAAG
*
34806 AAGTTTGGGAGCTCCA
1 AAGTTTAGGAGCTCCA
*
34822 AAGTTTAGGAGCTCCT
1 AAGTTTAGGAGCTCCA
*
34838 GAGTTTAGG
1 AAGTTTAGG
34847 GGAGAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (16 bp):
AAGTTTAGGAGCTCCA
Found at i:40482 original size:59 final size:59
Alignment explanation
Indices: 40409--40580 Score: 263
Period size: 59 Copynumber: 2.9 Consensus size: 59
40399 ATTACCAAAG
*
40409 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAA
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAA
* * *
40468 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATCAATTTCCATATAT
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAA
* * * * *
40527 GGCACTTTGTGTGCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCA
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCA
40581 ATTGAATTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 103 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAA
Found at i:43400 original size:12 final size:12
Alignment explanation
Indices: 43380--43417 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
43370 ATTATAACTA
43380 ATAATATTAAAT
1 ATAATATTAAAT
*
43392 ATTATATTAAAT
1 ATAATATTAAAT
43404 A-AATATTAAAT
1 ATAATATTAAAT
43415 ATA
1 ATA
43418 TTTATGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:46425 original size:8 final size:8
Alignment explanation
Indices: 46412--46452 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
46402 CTCATTTTCA
46412 GAGAATTT
1 GAGAATTT
46420 GAGAATTT
1 GAGAATTT
*
46428 -AGAGTTT
1 GAGAATTT
*
46435 GGGAATTT
1 GAGAATTT
46443 GAGAATTT
1 GAGAATTT
46451 GA
1 GA
46453 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:46745 original size:126 final size:126
Alignment explanation
Indices: 46520--47252 Score: 1403
Period size: 126 Copynumber: 5.8 Consensus size: 126
46510 CTATAATCGG
46520 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
46585 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
46646 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
46711 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
46772 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
46837 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
*
46898 TTCACTATTCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
46963 TCATTGCCATATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
47024 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
47089 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
47150 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--T
47215 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
47253 ATAACTTAAA
Statistics
Matches: 597, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
126 558 0.93
128 39 0.07
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
Found at i:47696 original size:33 final size:34
Alignment explanation
Indices: 47635--47733 Score: 132
Period size: 33 Copynumber: 3.0 Consensus size: 34
47625 AAATTTAATG
*
47635 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
47669 TTAAATTT-GAATAATATTATCTT-TATTTT-TAT
1 TTAAATTTCGAATAATATAAT-TTATATTTTAAAT
*
47701 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
47734 AACATTTATC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
32 12 0.21
33 33 0.59
34 11 0.20
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:48366 original size:21 final size:21
Alignment explanation
Indices: 48258--48360 Score: 154
Period size: 21 Copynumber: 4.9 Consensus size: 21
48248 ATAAAACCCT
48258 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
48279 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
*
48300 GCAGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
*
48321 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGCATGTAA-CCTG
* *
48342 GCGGGCTCGGAATGTAACC
1 GCGGGCTAGGCATGTAACC
48361 CTGCGGAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
20 2 0.03
21 72 0.94
22 3 0.04
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.18
Consensus pattern (21 bp):
GCGGGCTAGGCATGTAACCTG
Found at i:48375 original size:63 final size:63
Alignment explanation
Indices: 48258--48390 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 63
48248 ATAAAACCCT
* * * * *
48258 GCGGGCTAGGCATGTAACCTGGCGGGCTAGGCATGTAACCTGGCAGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCAGGATAGGCATATAAACTG
* *
48321 GCGGGCTAGGAATGTAACCCT-GCGGGCTCGGAATGTAACCCT-GC-GGAGATGGCATATAAACT
1 GCGGGCTAGGAATGTAA-CCTGGCGGGCTAGGAATGTAA-CCTGGCAGGATA-GGCATATAAACT
48383 G
63 G
*
48384 GTGGGCT
1 GCGGGCT
48391 TGGCATATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 3 0.05
63 50 0.85
64 6 0.10
ACGTcount: A:0.22, C:0.23, G:0.36, T:0.20
Consensus pattern (63 bp):
GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCAGGATAGGCATATAAACTG
Found at i:48396 original size:21 final size:21
Alignment explanation
Indices: 48370--48417 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
48360 CCTGCGGAGA
*
48370 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
48391 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
48412 GGGCAT
1 TGGCAT
48418 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:50177 original size:33 final size:31
Alignment explanation
Indices: 50130--50207 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 31
50120 TTAATAATTC
* *
50130 TAAATAAATAATA-TTATATAAATATTATTTTAA
1 TAAAAAAATAATATTTACATAAATA-TA--TTAA
50163 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATATTTACATAAATATATTAA
50194 TATAAAAAATAATA
1 TA-AAAAAATAATA
50208 ACTATTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 14 0.34
34 10 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATATTTACATAAATATATTAA
Found at i:50202 original size:34 final size:33
Alignment explanation
Indices: 50135--50240 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
50125 AATTCTAAAT
*
50135 AAATAATA-TTATATAAATATTATT-TTA-ATAAAA
1 AAATAATATTTA-ATAAATA-TATTAATATA-AAAA
50168 AAATAATATTTACATAAATATATTAATATAAAAA
1 AAATAATATTTA-ATAAATATATTAATATAAAAA
* * *
50202 ATAATAACTATTTAA-AAAAATACTAACATAAAAA
1 A-AATAA-TATTTAATAAATATATTAATATAAAAA
50236 TAAAT
1 -AAAT
50241 TTCTTACCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
33 12 0.19
34 36 0.58
35 8 0.13
36 6 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAATATTTAATAAATATATTAATATAAAAA
Found at i:51795 original size:15 final size:15
Alignment explanation
Indices: 51775--51804 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51765 TATCACAATC
51775 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
51790 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
51805 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:59423 original size:41 final size:41
Alignment explanation
Indices: 59365--59443 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
59355 CAAAATGGTA
* * *
59365 ACTTTAGCCGCGTTTTTATATAAACACTACAATAGAGTAGT
1 ACTTTAGCCGCGTTTTTACAAAAACACCACAATAGAGTAGT
* *
59406 ACTTTAGCGGCAG-TTTTACAAAAACGCCACAATAGAGT
1 ACTTTAGCCGC-GTTTTTACAAAAACACCACAATAGAGT
59444 TAATCTATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
ACTTTAGCCGCGTTTTTACAAAAACACCACAATAGAGTAGT
Found at i:59485 original size:83 final size:83
Alignment explanation
Indices: 59398--59712 Score: 287
Period size: 83 Copynumber: 3.8 Consensus size: 83
59388 ACACTACAAT
* * * *
59398 AGAGTAGTACTTTAGCGGCAGTTTTACAAAAACGCCACAATAGAGTTAATCTATAGTGACATTTT
1 AGAGTAGTACTTTAGCGGCAGTTTTATACAAACGCCACAATAGAGTTCATCTATAGTGATATTTT
* *
59463 TTAAACAAATGCCGCAAC
66 TTCAACAAATACCGCAAC
* * * ** * * * * * *
59481 AGAGTAGTACGTTAGTGG-TGTTTTTATAGTAACACCATAATAGGGTTCATCTATATTGATGTTG
1 AGAGTAGTACTTTAGCGGCAG-TTTTATACAAACGCCACAATAGAGTTCATCTATAGTGATATTT
* *
59545 TCTCAACAAATACCGCAAT
65 TTTCAACAAATACCGCAAC
* * * * *
59564 AGAGTAGTACTTTAGCGGC-GTTTTATGCAAACTCCACAATAGGGTTCATTTATAGTGGT-TTTT
1 AGAGTAGTACTTTAGCGGCAGTTTTATACAAACGCCACAATAGAGTTCATCTATAGTGATATTTT
*
59627 TCTCAACAAACACCGCAAC
66 T-TCAACAAATACCGCAAC
* * * * * * *
59646 ATAGTATTACTTTAGTGGCATTTTTATACAAATGCCGCAATA-AGATTCATCTATAGTGGTATTT
1 AGAGTAGTACTTTAGCGGCAGTTTTATACAAACGCCACAATAGAG-TTCATCTATAGTGATATTT
59710 TTT
65 TTT
59713 GTACAAGCGC
Statistics
Matches: 184, Mismatches: 42, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
81 3 0.02
82 64 0.35
83 112 0.61
84 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (83 bp):
AGAGTAGTACTTTAGCGGCAGTTTTATACAAACGCCACAATAGAGTTCATCTATAGTGATATTTT
TTCAACAAATACCGCAAC
Found at i:59697 original size:165 final size:166
Alignment explanation
Indices: 59394--59700 Score: 366
Period size: 165 Copynumber: 1.9 Consensus size: 166
59384 ATAAACACTA
59394 CAATAGAGTAGTACTTTAGCGGCAGTTTTACAAAAACGCCACAATAGAGTTAATCTATAGTGACA
1 CAATAGAGTAGTACTTTAGCGGCAGTTTTACAAAAACGCCACAATAGAGTTAATCTATAGTGACA
** ** ** * *
59459 TTTTTTAAACAAATGCCGCAACAGAGTAGTACGTTAGTGGTGTTTTTATAGTAACACCATAATAG
66 TTTTTTAAACAAACACCGCAACAGAGTAGTACGTTAGTGGCATTTTTATACAAACACCACAATAA
*
59524 GGTTCATCTATATTGATGTTGTCTCAACAAATACCG
131 GATTCATCTATATTGATGTTGTCTCAACAAATACCG
*** * * * * **
59560 CAATAGAGTAGTACTTTAGCGGC-GTTTTATGCAAACTCCACAATAGGGTTCATTTATAGTG-GT
1 CAATAGAGTAGTACTTTAGCGGCAGTTTTACAAAAACGCCACAATAGAGTTAATCTATAGTGACA
* * * * ** *
59623 TTTTTCTCAACAAACACCGCAACATAGTATTACTTTAGTGGCATTTTTATACAAATGCCGCAATA
66 TTTTT-TAAACAAACACCGCAACAGAGTAGTACGTTAGTGGCATTTTTATACAAACACCACAATA
59688 AGATTCATCTATA
130 AGATTCATCTATA
59701 GTGGTATTTT
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
164 5 0.04
165 87 0.76
166 23 0.20
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (166 bp):
CAATAGAGTAGTACTTTAGCGGCAGTTTTACAAAAACGCCACAATAGAGTTAATCTATAGTGACA
TTTTTTAAACAAACACCGCAACAGAGTAGTACGTTAGTGGCATTTTTATACAAACACCACAATAA
GATTCATCTATATTGATGTTGTCTCAACAAATACCG
Found at i:65569 original size:25 final size:24
Alignment explanation
Indices: 65526--65574 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
65516 TGTTACTAAA
65526 ATATATATAGAGTTAATATATATAT
1 ATATATATAGAGTTAATATA-ATAT
* * *
65551 ATATATATATATTTGATATAATAT
1 ATATATATAGAGTTAATATAATAT
65575 GATTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
ATATATATAGAGTTAATATAATAT
Found at i:68957 original size:21 final size:19
Alignment explanation
Indices: 68931--68988 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 19
68921 TGATTTATTA
68931 TTATGGAGTTCAAGTTGGTTG
1 TTATGGA-TTCAAGTT-GTTG
68952 TTATGGATTTCAAGTCTGTTG
1 TTATGGA-TTCAAGT-TGTTG
68973 TTATGGATGTCAAGTT
1 TTATGGAT-TCAAGTT
68989 TATTGGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (19 bp):
TTATGGATTCAAGTTGTTG
Found at i:72614 original size:19 final size:19
Alignment explanation
Indices: 72590--72626 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
72580 ACCAAACTAA
*
72590 CTTAATAATCTAATATATT
1 CTTAATAAACTAATATATT
72609 CTTAATAAACTAATATAT
1 CTTAATAAACTAATATAT
72627 ATGTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
CTTAATAAACTAATATATT
Found at i:75786 original size:46 final size:46
Alignment explanation
Indices: 75609--75779 Score: 285
Period size: 46 Copynumber: 3.8 Consensus size: 46
75599 ATAAACTGGC
* *
75609 AAATAAGCTTACGAGCTTAT-GGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
75653 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
75699 AAATAAGCTTACTAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
75745 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
75780 AGATTTTATA
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
44 20 0.17
45 15 0.12
46 85 0.71
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
Done.