Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008851.1 Hibiscus syriacus cultivar Beakdansim tig00112062_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: 70161
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:6395 original size:31 final size:32
Alignment explanation
Indices: 6360--6429 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
6350 CTTTTAAAAC
* *
6360 TTGCAATAAT-GTCCCAAAATATTTAGTCTGT
1 TTGCAATAATGGTCCCAAAACATTTAGTCCGT
**
6391 TTGCAAT-ATGGTCCCCTAACATTTAGTCCGT
1 TTGCAATAATGGTCCCAAAACATTTAGTCCGT
6422 TTGCAATA
1 TTGCAATA
6430 TGTTCCCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (32 bp):
TTGCAATAATGGTCCCAAAACATTTAGTCCGT
Found at i:8923 original size:30 final size:31
Alignment explanation
Indices: 8850--8912 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
8840 GTTATGTCGA
8850 GGACCATA-T-TACAACAGACTAAATGTTAGG
1 GGACCATATTGTA-AACAGACTAAATGTTAGG
*
8880 GGACCATATTGTAAACAGACT-AATGTTGGG
1 GGACCATATTGTAAACAGACTAAATGTTAGG
8910 GGA
1 GGA
8913 TTGTATTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 19 0.63
31 9 0.30
32 2 0.07
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (31 bp):
GGACCATATTGTAAACAGACTAAATGTTAGG
Found at i:19441 original size:36 final size:36
Alignment explanation
Indices: 19394--19483 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
19384 GTACATTCAC
*
19394 AGGGCACTGAATGTGACGCATCTACGGT-GCAATCAA
1 AGGGCACTGAATGTGACACATCTACGGTAG-AATCAA
* * *
19430 AGGGCATTGAATGTGTCACATCTACGGTAGAATCAC
1 AGGGCACTGAATGTGACACATCTACGGTAGAATCAA
*
19466 ATGGCACTGAATGTGACA
1 AGGGCACTGAATGTGACA
19484 TACCTATTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (36 bp):
AGGGCACTGAATGTGACACATCTACGGTAGAATCAA
Found at i:20126 original size:34 final size:33
Alignment explanation
Indices: 20083--20149 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 33
20073 GCCCCGATTA
20083 TATATATATAATATTTTATATTTTGTATATTAAT
1 TATATATATAATATTTTATATTTT-TATATTAAT
20117 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
20150 AACAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 9 0.27
34 24 0.73
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:20163 original size:33 final size:34
Alignment explanation
Indices: 20092--20166 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
20082 ATATATATAT
* * * *
20092 AATATTTTATATTTTGTATATTAATTATATATAT
1 AATATTTTATATTTTGTATATTAATAACAAATAA
20126 AATATTTTATATTTT-TATATTAATAACAAATAA
1 AATATTTTATATTTTGTATATTAATAACAAATAA
20159 AATATTTT
1 AATATTTT
20167 CGGGTTCGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
AATATTTTATATTTTGTATATTAATAACAAATAA
Found at i:21017 original size:28 final size:31
Alignment explanation
Indices: 20958--21019 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
20948 TTTCATAGAA
20958 ATTAGAAAATAAAATCCATAAGTAATCACAAT
1 ATTAGAAAATAAAATCCATAAGTAAT-ACAAT
*
20990 ATTAGAAAATAAAATTCATAATGTCAATAC
1 ATTAGAAAATAAAATCCATAA-GT-AATAC
21020 TTCATAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 20 0.74
33 4 0.15
34 3 0.11
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.27
Consensus pattern (31 bp):
ATTAGAAAATAAAATCCATAAGTAATACAAT
Found at i:21224 original size:32 final size:32
Alignment explanation
Indices: 21188--21249 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
21178 TCACAAATCT
*
21188 CTAGCTTTATTTTAACATTCAGTCGTGTCTCC
1 CTAGCTTTACTTTAACATTCAGTCGTGTCTCC
* *
21220 CTAGCTTTGCTTTAACATTCAGTCTTGTCT
1 CTAGCTTTACTTTAACATTCAGTCGTGTCT
21250 TCCATGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (32 bp):
CTAGCTTTACTTTAACATTCAGTCGTGTCTCC
Found at i:21345 original size:3 final size:3
Alignment explanation
Indices: 21337--21439 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
21327 ATATTATAAA
* * *
21337 TAT TAT TAT TAT TGT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
21385 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21432 TAT TAT TA
1 TAT TAT TA
21440 AATATATTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 89 0.98
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:23588 original size:15 final size:13
Alignment explanation
Indices: 23568--23605 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
23558 ATTTATATGT
23568 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
23583 TTATTTTATTTCA
1 TTATTTTATTTCA
23596 TTA-TTTATTT
1 TTATTTTATTT
23606 TGTCAGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:34135 original size:17 final size:17
Alignment explanation
Indices: 34110--34171 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
34100 ATGCTTGAAG
* *
34110 GAAAAAAAAAGAGAGAA
1 GAAAAAAAAAGAAAAAA
* *
34127 GAGAAAAAAGGAAAAAA
1 GAAAAAAAAAGAAAAAA
34144 GAAAAAAAAAGAAAAAA
1 GAAAAAAAAAGAAAAAA
34161 GAAAAAAAAAG
1 GAAAAAAAAAG
34172 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAGAAAAAA
Found at i:34171 original size:10 final size:10
Alignment explanation
Indices: 34138--34170 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
34128 AGAAAAAAGG
34138 AAAAAAGAAA
1 AAAAAAGAAA
34148 AAAAAAGAAA
1 AAAAAAGAAA
34158 AAAGAAA-AAA
1 AAA-AAAGAAA
34168 AAA
1 AAA
34171 GGGGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:35423 original size:83 final size:83
Alignment explanation
Indices: 35284--35900 Score: 1004
Period size: 83 Copynumber: 7.4 Consensus size: 83
35274 ATATCCCAGT
*
35284 CCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
35349 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGCAGAA
35367 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
35432 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGCAGAA
*
35450 CCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
35515 TGATCTGG-TTGGACAGAA
66 TGATCTGGTTTGG-CAGAA
* * ** * * *
35533 TCAATTATTGAATTTAAAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
35598 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGCAGAA
35616 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
35681 TGATCTGGTTTGGTAGAA
66 TGATCTGGTTTGGCAGAA
*
35699 CCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
35764 TGATCTGG-TTGGACAGAA
66 TGATCTGGTTTGG-CAGAA
* * * * * * * *
35782 TCAATTATTAAATTTAGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
35847 TAATCTGGTTTGGCAGAA
66 TGATCTGGTTTGGCAGAA
* *
35865 CCAATCATTGAATTTGGAAGATGAATTTGCTCATAG
1 CCAATCATTGAATTTGGAAGATGAATGTACTCATAG
35901 TAGAAATAAG
Statistics
Matches: 494, Mismatches: 36, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
82 8 0.02
83 478 0.97
84 8 0.02
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAA
Found at i:35728 original size:249 final size:249
Alignment explanation
Indices: 35316--35900 Score: 1107
Period size: 249 Copynumber: 2.3 Consensus size: 249
35306 GAATGTATTC
35316 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
35381 TGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
66 TGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
35446 AGAACCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
131 AGAACCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
35511 TATCTGATCTGGTTGGACAGAATCAATTATTGAATTTAAAAGATGAATTTGCTA
196 TATCTGATCTGGTTGGACAGAATCAATTATTAAATTTAAAAGATGAATTTGCTA
35565 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
35630 TGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
66 TGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
35695 AGAACCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
131 AGAACCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
35760 TATCTGATCTGGTTGGACAGAATCAATTATTAAATTTAGAAGATGAATTTGCTA
196 TATCTGATCTGGTTGGACAGAATCAATTATTAAATTTAAAAGATGAATTTGCTA
* *
35814 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
35879 TGGAAGATGAATTTGCTCATAG
66 TGGAAGATGAATGTACTCATAG
35901 TAGAAATAAG
Statistics
Matches: 329, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
249 329 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (249 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TGGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
AGAACCAATCATTGAATTTGGAAGATGAATGTATTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTGGACAGAATCAATTATTAAATTTAAAAGATGAATTTGCTA
Found at i:36900 original size:114 final size:114
Alignment explanation
Indices: 36700--37251 Score: 824
Period size: 114 Copynumber: 4.8 Consensus size: 114
36690 CAAATCTATC
* * *
36700 AATTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGA
1 AATTGATGGATT-ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
36764 AGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACTTGAATTCATCA
65 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCA
*
36814 AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAA
1 AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
*
36879 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTCATCA
66 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCA
36928 AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
36993 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCA
66 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCA
* *
37042 AATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAA
1 AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * * *
37107 GAAGTTCATAATGAGAAGAACTTT-TTCAATCTTTTGCTTGAAATCAT-A
66 GAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTACCTGAATTCATCA
* * * * * * *
37155 ATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTAGTCATATGAAGAAGGA
1 AATTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAAC---TCATCTGAAGAAGGA
* *
37219 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
37252 TAATTCTATC
Statistics
Matches: 407, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
112 2 0.00
113 38 0.09
114 321 0.79
115 5 0.01
116 41 0.10
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (114 bp):
AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCA
Found at i:37586 original size:3 final size:3
Alignment explanation
Indices: 37578--37678 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
37568 ATATTATAAA
* *
37578 TAT TAT TAT TAT TGT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
37626 CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37674 TAT TA
1 TAT TA
37679 AATATATTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39116 original size:13 final size:13
Alignment explanation
Indices: 39100--39146 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
39090 ATATAATAAA
39100 TAAATATTTATTT
1 TAAATATTTATTT
*
39113 TAAATAAATTATTT
1 TAAAT-ATTTATTT
39127 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
39140 TCAATAT
1 TAAATAT
39147 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:40433 original size:37 final size:37
Alignment explanation
Indices: 40388--40462 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40378 AAAATGTGCA
40388 ACCAACCAACTACTTTCCACACAATCTAATACATGTG
1 ACCAACCAACTACTTTCCACACAATCTAATACATGTG
*
40425 ACCAACCAACTACTTTCCACATAATCTAATACATGTG
1 ACCAACCAACTACTTTCCACACAATCTAATACATGTG
40462 A
1 A
40463 TCAGTGACAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.25
Consensus pattern (37 bp):
ACCAACCAACTACTTTCCACACAATCTAATACATGTG
Found at i:41027 original size:15 final size:15
Alignment explanation
Indices: 41007--41038 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40997 CTACTAACGG
*
41007 TGACAAAATTATATT
1 TGACAAAATTAAATT
41022 TGACAAAATTAAATT
1 TGACAAAATTAAATT
41037 TG
1 TG
41039 TCACAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:42211 original size:15 final size:15
Alignment explanation
Indices: 42192--42238 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
42182 GATTTTTAAT
42192 TCTTTTCAATTTATTC
1 TCTTTT-AATTTATTC
42208 -CTTTTTAATTTGAATTC
1 TC-TTTTAATTT--ATTC
42225 TCTTTTAATTTATT
1 TCTTTTAATTTATT
42239 TATTTATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
15 9 0.33
16 4 0.15
17 13 0.48
18 1 0.04
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.64
Consensus pattern (15 bp):
TCTTTTAATTTATTC
Found at i:42263 original size:27 final size:26
Alignment explanation
Indices: 42228--42306 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
42218 TGAATTCTCT
*
42228 TTTAATTTATTT-ATTTATTTGATATTG
1 TTTATTTTATTTAATTTATTT--TATTG
42255 TTTATTTTATTTTAATTTATTTTATTG
1 TTTATTTTA-TTTAATTTATTTTATTG
*
42282 TTTATTATTAATTTGATTTATTTTA
1 TTTATT-TT-ATTTAATTTATTTTA
42307 GGGCAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 19 0.41
28 18 0.39
29 9 0.20
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTATTTTATTTAATTTATTTTATTG
Found at i:49456 original size:18 final size:20
Alignment explanation
Indices: 49420--49457 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
49410 TTCTTATCAC
49420 CGTATATTTACTTTGTTTAA
1 CGTATATTTACTTTGTTTAA
*
49440 CGTAT-TTTAGTTT-TTTAA
1 CGTATATTTACTTTGTTTAA
49458 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (20 bp):
CGTATATTTACTTTGTTTAA
Found at i:51340 original size:21 final size:21
Alignment explanation
Indices: 51314--51360 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
51304 AGAGGAAAGT
51314 AGAAAATATTGCCACGACAAC
1 AGAAAATATTGCCACGACAAC
*
51335 AGAAAATGTTGCCACGACAAC
1 AGAAAATATTGCCACGACAAC
51356 AGAAA
1 AGAAA
51361 TCTGCTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (21 bp):
AGAAAATATTGCCACGACAAC
Found at i:66173 original size:13 final size:14
Alignment explanation
Indices: 66155--66187 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
66145 GATAGCATAT
66155 TATATAGTGTA-AG
1 TATATAGTGTATAG
66168 TATATAGTGTATAG
1 TATATAGTGTATAG
66182 TATATA
1 TATATA
66188 TACTATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (14 bp):
TATATAGTGTATAG
Found at i:66225 original size:7 final size:7
Alignment explanation
Indices: 66184--66284 Score: 68
Period size: 7 Copynumber: 14.1 Consensus size: 7
66174 GTGTATAGTA
*
66184 TATATAC
1 TATATAT
66191 TATATACT
1 TATATA-T
*
66199 TACACTA-
1 TATA-TAT
66206 TATATATT
1 TATATA-T
66214 TATATAT
1 TATATAT
66221 TATATAT
1 TATATAT
66228 TATTATAGT
1 TA-TATA-T
*
66237 TTTATAT
1 TATATAT
66244 GGTATATA-
1 --TATATAT
66252 T-TATAT
1 TATATAT
66258 TATAT-T
1 TATATAT
*
66264 T-TACAT
1 TATATAT
66270 TATATAT
1 TATATAT
66277 TATATAT
1 TATATAT
66284 T
1 T
66285 TATTATTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
5 6 0.08
6 8 0.11
7 35 0.47
8 17 0.23
9 9 0.12
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:66294 original size:4 final size:4
Alignment explanation
Indices: 66276--66330 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
66266 ACATTATATA
* * *
66276 TTAT ATAT TTA- TTAT TTAT TTAT TTAT TTAC TTATT TTGT TTCAT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TT-AT TTAT
66324 TTAT TTA
1 TTAT TTA
66331 GGTCCAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 6 0.15
4 30 0.73
5 5 0.12
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:67759 original size:21 final size:21
Alignment explanation
Indices: 67717--67758 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
67707 CTCAATATAT
67717 ATATATATATATTCTTTAAAA
1 ATATATATATATTCTTTAAAA
* *
67738 ATATAT-TATCTTTTTTAAAA
1 ATATATATATATTCTTTAAAA
67758 A
1 A
67759 ACTATGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATATATATTCTTTAAAA
Found at i:69864 original size:49 final size:49
Alignment explanation
Indices: 69782--69947 Score: 269
Period size: 49 Copynumber: 3.4 Consensus size: 49
69772 GAGTGGCAAT
* ** *
69782 TTTTATGTCGAAATGCACCGTTATGTGTTTAACTTTCATTTGAGGCACC
1 TTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
* *
69831 TTTAATGCCAAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
1 TTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
*
69880 TTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
1 TTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
69929 TTTTATGCCGAAATGCACC
1 TTTTATGCCGAAATGCACC
69948 TATGATTCTT
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 107 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (49 bp):
TTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTGTGGCACC
Done.