Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007797.1 Hibiscus syriacus cultivar Beakdansim tig00110105_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: 397486
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:340362 original size:25 final size:24
Alignment explanation
Indices: 340308--340362 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
340298 TGTTTATTAT
* *
340308 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
340332 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
340358 TGTTT
1 TGTTT
340363 ATTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:341517 original size:18 final size:18
Alignment explanation
Indices: 341491--341535 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
341481 TCCACTTCGG
*
341491 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCTA
*
341509 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCTA
341527 GAGCCATCA
1 GAGCCATCA
341536 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCCATCACCTCACCTA
Found at i:342065 original size:19 final size:20
Alignment explanation
Indices: 342011--342056 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
342001 TAGTTTACTT
*
342011 TCGCAACACGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
342031 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
342051 TCGCAA
1 TCGCAA
342057 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:342085 original size:14 final size:14
Alignment explanation
Indices: 342066--342124 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
342056 ATGCGAAATG
342066 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
342080 AAAATCACAATGCGAAATG
1 AAAATCGCAA--CG--A-C
342099 AAAATCGCAACGAC
1 AAAATCGCAACGAC
342113 AAAATCGCAACG
1 AAAATCGCAACG
342125 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:342096 original size:33 final size:33
Alignment explanation
Indices: 342054--342140 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
342044 ATGGCTATCG
342054 CAATGCGAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
342087 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
342120 CAACGCGAAATG-AAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
342141 TGCGATTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
32 9 0.17
33 43 0.83
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:342175 original size:14 final size:14
Alignment explanation
Indices: 342156--342279 Score: 70
Period size: 14 Copynumber: 7.9 Consensus size: 14
342146 TTTGTGTTCG
342156 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
342170 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
342186 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
* *
342202 CGTTGGGATTTTCATTT
1 CGTTGCGA-TTT--TGT
342219 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
342235 CGTTG-GTATTTTCATTT
1 CGTTGCG-A-TTT--TGT
342252 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
342268 CGTTGCGATTTT
1 CGTTGCGATTTT
342280 CATTTCGCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 32
0.68 0.06 0.25
Matches are distributed among these distances:
13 1 0.01
14 30 0.35
15 6 0.07
16 16 0.19
17 8 0.09
18 15 0.17
19 9 0.10
20 1 0.01
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:342220 original size:33 final size:33
Alignment explanation
Indices: 342152--342295 Score: 247
Period size: 33 Copynumber: 4.4 Consensus size: 33
342142 GCGATTTGTG
*
342152 TTCGCGTTGCGATTTTGTCGTTGCGA-TTTCAT
1 TTCGCATTGCGATTTTGTCGTTGCGATTTTCAT
*
342184 TTCGCATTGCGATTTTGTCGTTGGGATTTTCAT
1 TTCGCATTGCGATTTTGTCGTTGCGATTTTCAT
342217 TTCGCATTGCGATTTTGTCGTTG-GTATTTTCAT
1 TTCGCATTGCGATTTTGTCGTTGCG-ATTTTCAT
342250 TTCGCATTGCGATTTTGTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTGTCGTTGCGATTTTCAT
342283 TTCGCATTGCGAT
1 TTCGCATTGCGAT
342296 AGCCATTTCC
Statistics
Matches: 107, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
32 25 0.23
33 81 0.76
34 1 0.01
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (33 bp):
TTCGCATTGCGATTTTGTCGTTGCGATTTTCAT
Found at i:342331 original size:20 final size:20
Alignment explanation
Indices: 342268--342335 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
342258 GCGATTTTGT
**
342268 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* * * *
342287 CATTGCGATAGCCATTTCCA
1 CGTTGCGATAGTCATTTTCG
*
342307 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
342327 CGTTGCGAT
1 CGTTGCGAT
342336 TTTAAGTTTC
Statistics
Matches: 36, Mismatches: 12, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
19 10 0.28
20 26 0.72
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:345729 original size:32 final size:31
Alignment explanation
Indices: 345688--345788 Score: 123
Period size: 32 Copynumber: 3.2 Consensus size: 31
345678 ACGAGATAAT
*
345688 GAGAATCGCAACGCGGAAATGACTATCGCGAC
1 GAGAATCGCAACGC-GAAATGACTATCGCAAC
345720 GAGAATCGCAACGCGAAATGACTATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
* * *
345751 GAGAGAATTGTAACGCGAAATGA-AATCGCAAC
1 --GAGAATCGCAACGCGAAATGACTATCGCAAC
*
345783 GCGAAT
1 GAGAAT
345789 GAAAATCACA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 5 0.08
31 16 0.26
32 22 0.35
33 19 0.31
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.14
Consensus pattern (31 bp):
GAGAATCGCAACGCGAAATGACTATCGCAAC
Found at i:345801 original size:50 final size:51
Alignment explanation
Indices: 345723--345837 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 51
345713 TCGCGACGAG
** * * *
345723 AATCGCAACGCGAAATGACTATCGCAACGAGAGAATTGTAACGCGAAATG-A
1 AATCGCAACGCG-AATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
*
345774 AATCGCAACGCGAATGAAAATCACAACGAGAGAATCGCAACGTGAAATGAA
1 AATCGCAACGCGAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
*
345825 AATCGCAATGCGA
1 AATCGCAACGCGA
345838 TTTTGGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 31 0.55
51 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (51 bp):
AATCGCAACGCGAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
Found at i:346419 original size:20 final size:21
Alignment explanation
Indices: 346394--346448 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
346384 GCTATGTAAA
346394 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGATAGTAAGTAT
* *
346414 TCGCATTGCGAT-TTACGTAT
1 TCGCATTGCGATAGTAAGTAT
346434 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
346449 CATAATCGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATAGTAAGTAT
Found at i:348172 original size:219 final size:214
Alignment explanation
Indices: 347786--348220 Score: 809
Period size: 219 Copynumber: 2.0 Consensus size: 214
347776 AATTGCATTG
347786 TTTGAAGATTCATCGATGCTTGGGTTCAAATTGCTTGCCCTAGCTTTCCATTGATTGGGGTGATG
1 TTTGAAGATTCATCGATGCTTGGGTTCAAATTGCTTGCCCTAGCTTTCCATTGATTGGGGTGATG
347851 CTTTTGTAACACCTTTACTGACTACATTCGGCAGAGATTGCACTAGGGGATATCCGGATGGTGGG
66 CTTTTGTAACACCTTTACTGACTACATTCGGCAGAGATTGCACTAGGGGATATCCGGATGGTGGG
347916 AGAGAGATGGTTGTGGTTCTTGTGGAAATGGATTGAGTTGCAAGGAGAGT-AATCATGTTGTGAT
131 AGAGAGATGGTTGTGGTTCTTGTGGAAATGGATTGAGTTGCAAGGAGAGTAAATCATGTTGTGAT
347980 GGCAACGGAGTAAAGGATT
196 GGCAACGGAGTAAAGGATT
347999 TTTGAAGATTCAGTCGATGCTTGGGTTCAAATTGCTTGCCCTAGGCTTTCCATTGATTGGGGTGA
1 TTTGAAGATTCA-TCGATGCTTGGGTTCAAATTGCTTGCCCTA-GCTTTCCATTGATTGGGGTGA
348064 TGCTTTTGTAACACCTTTACTGACTACATTCGAGGCAGAGATTGCACTAGGGGAGATATCCGGAT
64 TGCTTTTGTAACACCTTTACTGACTACATTC--GGCAGAGATTGCACTA-GGG-GATATCCGGAT
348129 GGTGGGAGAGAGATGGTTGTGGTTCTTGTGGAAATGGATTGAGTTGCAAGGAGAGTAAATCATGT
125 GGTGGGAGAGAGATGGTTGTGGTTCTTGTGGAAATGGATTGAGTTGCAAGGAGAGTAAATCATGT
348194 TGTGATGGCAACGGAGTAAAGGATT
190 TGTGATGGCAACGGAGTAAAGGATT
348219 TT
1 TT
348221 CGCGGTGATT
Statistics
Matches: 215, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
213 12 0.06
214 30 0.14
215 52 0.24
217 16 0.07
218 3 0.01
219 67 0.31
220 35 0.16
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (214 bp):
TTTGAAGATTCATCGATGCTTGGGTTCAAATTGCTTGCCCTAGCTTTCCATTGATTGGGGTGATG
CTTTTGTAACACCTTTACTGACTACATTCGGCAGAGATTGCACTAGGGGATATCCGGATGGTGGG
AGAGAGATGGTTGTGGTTCTTGTGGAAATGGATTGAGTTGCAAGGAGAGTAAATCATGTTGTGAT
GGCAACGGAGTAAAGGATT
Found at i:357560 original size:2 final size:2
Alignment explanation
Indices: 357513--357550 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
357503 AATATCACTA
357513 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
357551 TTCAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360982 original size:27 final size:28
Alignment explanation
Indices: 360928--360982 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
360918 GTTTCCAAGG
*
360928 GAATATTTATTTTGGCACCCTAATCTTTT
1 GAATATTTATTTT-GCACCCTAAACTTTT
360957 GAATATTTATATTT-C-CCCTAAACTTT
1 GAATATTTAT-TTTGCACCCTAAACTTT
360983 ACCATTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
29 10 0.42
30 3 0.12
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (28 bp):
GAATATTTATTTTGCACCCTAAACTTTT
Found at i:362261 original size:72 final size:71
Alignment explanation
Indices: 362155--362304 Score: 255
Period size: 72 Copynumber: 2.1 Consensus size: 71
362145 AGATGAACAA
* *
362155 TTGAATCGAAAGTGCAATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCAATGATTCCTTCCGTTCACTTTGAATCGAAAGTGCCGACGCTTCCTTTCG
362220 TTCTTC
66 TTCTTC
* *
362226 TTGAATCGAAAGTGTCGATGATTCCTTTCGTTCACTTTGAATCGAAAGTGCCGACGCTTCCTTTC
1 TTGAATCGAAAGTG-CAATGATTCCTTCCGTTCACTTTGAATCGAAAGTGCCGACGCTTCCTTTC
362291 GTTCTTC
65 GTTCTTC
362298 TTGAATC
1 TTGAATC
362305 ACCTTCATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 14 0.19
72 60 0.81
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (71 bp):
TTGAATCGAAAGTGCAATGATTCCTTCCGTTCACTTTGAATCGAAAGTGCCGACGCTTCCTTTCG
TTCTTC
Found at i:362304 original size:36 final size:36
Alignment explanation
Indices: 362155--362294 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 36
362145 AGATGAACAA
* *
362155 TTGAATCGAAAGTG-CAATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
*
362190 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
* *
362225 CTTGAATCGAAAGTGTCGATGATTCCTTTCGTTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
*
362262 TTGAATCGAAAGTGCCGACGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
362295 TTCTTGAATC
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
35 15 0.16
36 77 0.83
37 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
Found at i:364383 original size:21 final size:21
Alignment explanation
Indices: 364359--364398 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
364349 TAGAATAAAA
364359 AAATAAAAATTAAATTAAATT
1 AAATAAAAATTAAATTAAATT
* *
364380 AAATAAAAGTTTAATTAAA
1 AAATAAAAATTAAATTAAA
364399 AGAAAAAAAT
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:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATAAAAATTAAATTAAATT
Found at i:365709 original size:18 final size:18
Alignment explanation
Indices: 365672--365705 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
365662 ACCTAAACCA
365672 AAATAAAAAATAATAAAT
1 AAATAAAAAATAATAAAT
*
365690 AAATAAATAA-AATAAA
1 AAATAAAAAATAATAAA
365706 ATAAGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAATAAAT
Found at i:365740 original size:2 final size:2
Alignment explanation
Indices: 365722--365772 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
365712 ATATTATAAA
* * * *
365722 AT AT TT AT AT AG A- AT AT AT AC AT AT -T CT 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
365762 AT AT AT AT AT A
1 AT AT AT AT AT A
365773 AAGCCGGTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:372689 original size:33 final size:33
Alignment explanation
Indices: 372647--372714 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
372637 GCTTATTAGA
372647 ATCGTGTTACCTTGTGACATAATGTTCTCTACT
1 ATCGTGTTACCTTGTGACATAATGTTCTCTACT
372680 ATCGTGTTACCTTGTGACATAATGTTCTCTACT
1 ATCGTGTTACCTTGTGACATAATGTTCTCTACT
372713 AT
1 AT
372715 ATTATGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (33 bp):
ATCGTGTTACCTTGTGACATAATGTTCTCTACT
Found at i:377948 original size:20 final size:20
Alignment explanation
Indices: 377919--377956 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
377909 CCCCTTCAAA
*
377919 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
377939 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
377957 TGCACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:381796 original size:22 final size:21
Alignment explanation
Indices: 381754--381793 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
381744 AAGTTTGTTT
*
381754 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
381775 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
381794 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:385980 original size:15 final size:15
Alignment explanation
Indices: 385962--385991 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
385952 AATTCTTTCC
385962 ATTTCCTTTCTTATT
1 ATTTCCTTTCTTATT
*
385977 ATTTCTTTTCTTATT
1 ATTTCCTTTCTTATT
385992 CCATTTCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTCCTTTCTTATT
Found at i:386016 original size:12 final size:12
Alignment explanation
Indices: 385975--386019 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
385965 TCCTTTCTTA
*
385975 TTATTTCTTTTC
1 TTATTTCATTTC
*
385987 TTATTCCATTTC
1 TTATTTCATTTC
385999 TTATTTCATTTC
1 TTATTTCATTTC
386011 TTATTTCAT
1 TTATTTCAT
386020 ATTTCCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTCATTTC
Found at i:386026 original size:32 final size:28
Alignment explanation
Indices: 385962--386042 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
385952 AATTCTTTCC
*
385962 ATTTCC-TTTCTTATTATTTCTTTTCTT
1 ATTTCCATTTCTTATTATTTCTTTTCAT
385989 A-TTCCATTTCTTATTTCATTTCTTATTTCAT
1 ATTTCCATTTCTTA-TT-ATTTC-T-TTTCAT
* *
386020 ATTTCCATTT-TAATCATTTCTTT
1 ATTTCCATTTCTTATTATTTCTTT
386043 CTTGTAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.09
27 10 0.22
28 3 0.07
29 10 0.22
30 2 0.04
31 8 0.18
32 8 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTCCATTTCTTATTATTTCTTTTCAT
Found at i:388585 original size:154 final size:154
Alignment explanation
Indices: 388304--388617 Score: 574
Period size: 154 Copynumber: 2.0 Consensus size: 154
388294 TCAGGATTGA
*
388304 CTAAACTAATATGCATACAGCTGGACTGCATAAATTAAAGTGAAGAGATTCAGATAATCTTTTCT
1 CTAAACTAATATGCATACAGCCGGACTGCATAAATTAAAGTGAAGAGATTCAGATAATCTTTTCT
* *
388369 TTCTTCCCAACTAAACTATATATATGTATGTCCATCCTCTGGTCTTTCCCCACACTCGCAAATAA
66 TTCTTCCCAACTAAACTATATATATGTATGTCCATCCTCTGGCCTTTCCCCACACTCACAAATAA
*
388434 TTGATAACATATCCCACTTGCATC
131 TTGATAACATATCCCACTTGAATC
*
388458 CTAAACTAATATGCATACAGCCGGACTGCATAAATTAAAGTGAAGAGATTCAGATAATCTTTTTT
1 CTAAACTAATATGCATACAGCCGGACTGCATAAATTAAAGTGAAGAGATTCAGATAATCTTTTCT
*
388523 TTCTTCCCAACTAAACTATATATATGTATGTCCATCCTCTGGCCTTTCCCTACACTCACAAATAA
66 TTCTTCCCAACTAAACTATATATATGTATGTCCATCCTCTGGCCTTTCCCCACACTCACAAATAA
388588 TTGATAACATATCCCACTTGAATC
131 TTGATAACATATCCCACTTGAATC
388612 CTAAAC
1 CTAAAC
388618 AATGAGATTT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (154 bp):
CTAAACTAATATGCATACAGCCGGACTGCATAAATTAAAGTGAAGAGATTCAGATAATCTTTTCT
TTCTTCCCAACTAAACTATATATATGTATGTCCATCCTCTGGCCTTTCCCCACACTCACAAATAA
TTGATAACATATCCCACTTGAATC
Done.