Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006244.1 Hibiscus syriacus cultivar Beakdansim tig00014886_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: 57665
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:5214 original size:54 final size:53
Alignment explanation
Indices: 5155--5323 Score: 162
Period size: 54 Copynumber: 3.1 Consensus size: 53
5145 TTCTTTGGGG
* * * *
5155 TGCACACGTAGTGCTGATACAGTTATTCATAATCTCATTATGAATTTCGTAGG-T
1 TGCACACTTAGTGCT-ATACAGTCATTCATAAGCACATTATGAATTTCGT-GGTT
* *
5209 TGCACACTTAGTGCCTATACGGTCGTTCATAAGCACATTATGAATTTCGTGGTT
1 TGCACACTTAGTG-CTATACAGTCATTCATAAGCACATTATGAATTTCGTGGTT
** * * * * *
5263 TGCACACTTAGTGCCTATATGGTCGTTCATCAA-CATATGATGAATTTTGTGGGT
1 TGCACACTTAGTG-CTATACAGTCATTCAT-AAGCACATTATGAATTTCGTGGTT
5317 TGCACAC
1 TGCACAC
5324 ATAATGCATA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.02
54 95 0.94
55 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (53 bp):
TGCACACTTAGTGCTATACAGTCATTCATAAGCACATTATGAATTTCGTGGTT
Found at i:5336 original size:54 final size:54
Alignment explanation
Indices: 5194--5492 Score: 343
Period size: 54 Copynumber: 5.5 Consensus size: 54
5184 TAATCTCATT
* * * * * * *
5194 ATGAATTTCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCAT-AAGCACATT
1 ATGAATTCCGTGGGTTGCACACATAGTGCATATACGGTTGTTCATCAA-CATATG
* * * * * *
5248 ATGAATTTCGTGGTTTGCACACTTAGTGCCTATATGGTCGTTCATCAACATATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCATATACGGTTGTTCATCAACATATG
** * *
5302 ATGAATTTTGTGGGTTGCACACATAATGCATATATGGTTGTTCATCAACATATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCATATACGGTTGTTCATCAACATATG
* * * *
5356 AAGAATTCTGTGGGTTGCACACATAGTGCCA-AAACGGTTGTTCATCAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTG-CATATACGGTTGTTCATCAACATATG
* *
5410 ATGAATTCCGTGGGTTGCACACATAGTGC-TAAAACGGTTGTTCATCAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCAT-ATACGGTTGTTCATCAACATATG
5464 ATGAATTCCGTGGGTTGCACACATAGTGC
1 ATGAATTCCGTGGGTTGCACACATAGTGC
5493 CAAAAGTACA
Statistics
Matches: 222, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.00
54 217 0.98
55 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (54 bp):
ATGAATTCCGTGGGTTGCACACATAGTGCATATACGGTTGTTCATCAACATATG
Found at i:11447 original size:25 final size:25
Alignment explanation
Indices: 11410--11468 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
11400 ACGCATAGCT
*
11410 ATGAAAAT-TTCAGGATGAAACCAA
1 ATGAAGATATTCAGGATGAAACCAA
11434 ATGAAGATATTCAGGATGAAACCAA
1 ATGAAGATATTCAGGATGAAACCAA
11459 ATGAAGATAT
1 ATGAAGATAT
11469 CAAAGCTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (25 bp):
ATGAAGATATTCAGGATGAAACCAA
Found at i:16113 original size:21 final size:21
Alignment explanation
Indices: 16087--16126 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16077 CCCCCTTTGA
*
16087 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
16108 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
16127 TGGGGTTCTT
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:16841 original size:21 final size:21
Alignment explanation
Indices: 16817--16856 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16807 ACCGTCAACC
*
16817 AAATCCATTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
* *
16838 AAATCTAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
16857 AATCCAATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:20960 original size:52 final size:53
Alignment explanation
Indices: 20808--21171 Score: 279
Period size: 54 Copynumber: 6.6 Consensus size: 53
20798 TAATCTCATT
* * * * * * * ** *
20808 ATGAATTTTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATAAACACATT
1 ATGAATTATGTGGGTTGAACACATAGTG-CAAAACGGTTGTTCATCAACTTATG
* * * * * * *
20862 ATGAATTCTGTGGTTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATG
1 ATGAATTATGTGGGTTGAACACATAGTG-CAAAACGGTTGTTCATCAACTTATG
* * * *
20916 ATGAATTTTGTGGG-T-AATATATAGTGCATATACGGTTGTTCATCAA-TATATG
1 ATGAATTATGTGGGTTGAACACATAGTGCA-AAACGGTTGTTCATCAACT-TATG
*
20968 ATGAATTATGTGGGTTGCACACATAGTGGCATAGTGCCAAAATGGTTGTTCATCAACTTATG
1 ATGAATTATGTGGGTTG-A-AC--A----CATAGTG-CAAAACGGTTGTTCATCAACTTATG
* *
21030 ATGAATT-TCGTGGGTTGCACACATAGTTCAAAAACGGTTGTTCATCAACTTATG
1 ATGAATTAT-GTGGGTTGAACACATAGTGC-AAAACGGTTGTTCATCAACTTATG
* * *
21084 ATGAATTCTGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTTTG
1 ATGAATTATGTGGGTTGAACACATAGTG-CAAAACGGTTGTTCATCAACTTATG
*
21138 ATGAATTATGTGGGTT-ACACAAATAGTGCCAAAA
1 ATGAATTATGTGGGTTGA-ACACATAGTG-CAAAA
21172 GTACACATAA
Statistics
Matches: 264, Mismatches: 27, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
51 1 0.00
52 41 0.16
53 3 0.01
54 167 0.63
55 3 0.01
56 1 0.00
58 2 0.01
60 2 0.01
61 1 0.00
62 40 0.15
63 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (53 bp):
ATGAATTATGTGGGTTGAACACATAGTGCAAAACGGTTGTTCATCAACTTATG
Found at i:21097 original size:116 final size:114
Alignment explanation
Indices: 20883--21111 Score: 307
Period size: 116 Copynumber: 2.0 Consensus size: 114
20873 GGTTTGCACA
* * * * * * *
20883 CATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTAATATATAGTGCATATA
1 CATAGTGCCAAAACGGTCGTTCATCAACATATGATGAATTTCGTGGGTAACACATAGTGCAAAAA
20948 CGGTTGTTCATCAATATATGATGAATTATGTGGGTTGCACACATAGTGG
66 CGGTTGTTCATCAATATATGATGAATTATGTGGGTTGCACACATAGTGG
* * * * *
20997 CATAGTGCCAAAATGGTTGTTCATCAACTTATGATGAATTTCGTGGGTTGCACACATAGTTCAAA
1 CATAGTGCCAAAACGGTCGTTCATCAACATATGATGAATTTCGTGGG-T-AACACATAGTGCAAA
*
21062 AACGGTTGTTCATCAACT-TATGATGAATTCTGTGGGTTGCACACATAGTG
64 AACGGTTGTTCATCAA-TATATGATGAATTATGTGGGTTGCACACATAGTG
21112 CCAAAACGGT
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
114 41 0.41
115 1 0.01
116 56 0.57
117 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (114 bp):
CATAGTGCCAAAACGGTCGTTCATCAACATATGATGAATTTCGTGGGTAACACATAGTGCAAAAA
CGGTTGTTCATCAATATATGATGAATTATGTGGGTTGCACACATAGTGG
Found at i:23960 original size:21 final size:21
Alignment explanation
Indices: 23934--23978 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23924 GATTTCTGGG
* *
23934 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
23955 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
23976 CAA
1 CAA
23979 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:25846 original size:23 final size:23
Alignment explanation
Indices: 25802--25846 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25792 ATCATTATAT
*
25802 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
25825 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
25847 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:29335 original size:26 final size:26
Alignment explanation
Indices: 29285--29335 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
29275 TTCACTTACT
***
29285 TAAAATTTTATAAGTTTGTTTTTTTC
1 TAAAATTTTATAAGTTTGAACTTTTC
*
29311 TAAAATTTTATACGTTTGAACTTTT
1 TAAAATTTTATAAGTTTGAACTTTT
29336 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (26 bp):
TAAAATTTTATAAGTTTGAACTTTTC
Found at i:30563 original size:21 final size:20
Alignment explanation
Indices: 30539--30596 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
30529 ATTTTTAATG
30539 TTAATTTTTTATTTTTTTTT
1 TTAATTTTTTATTTTTTTTT
* *
30559 CTTAATATTTTATTTTATTTT
1 -TTAATTTTTTATTTTTTTTT
30580 TT-ATTTTCTTAGTTTTT
1 TTAATTTT-TTA-TTTTT
30597 AATATTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.13
20 5 0.16
21 22 0.71
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (20 bp):
TTAATTTTTTATTTTTTTTT
Found at i:32311 original size:11 final size:11
Alignment explanation
Indices: 32297--32321 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32287 TTTTAGTTTT
32297 TTTATTTATTA
1 TTTATTTATTA
32308 TTTATTTATTA
1 TTTATTTATTA
32319 TTT
1 TTT
32322 CTTATCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:34856 original size:95 final size:94
Alignment explanation
Indices: 34684--34879 Score: 295
Period size: 95 Copynumber: 2.1 Consensus size: 94
34674 TATAATATTA
* *
34684 TATATATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGA
1 TATATATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGATTTATGGA
* *
34749 TAATATTCAGCTAGCCTGATAAAGGTGAT
66 TAAGATTCAGCTAACCTGATAAAGGTGAT
* *
34778 TATACTATATAATAAAGCTTGAGTTGTCCCTCTA-AGACAATTGGTTAAACGCCCCGGATTTATG
1 TATA-TATACAATAAAGCCTGAGTTGTCCCTCTAGAG-CAATTGGTTAAACGCCCCGGATTTATG
*
34842 GATAAGATTCAGCTAACCTGATAAAGGTGTT
64 GATAAGATTCAGCTAACCTGATAAAGGTGAT
*
34873 TACATAT
1 TATATAT
34880 TGAGCTGTCC
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 9 0.10
95 83 0.90
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGATTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTGAT
Found at i:36257 original size:42 final size:41
Alignment explanation
Indices: 36198--36277 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
36188 CAAAGTTTTT
* *
36198 TCTCTCTTGAGACAGTTTCTCTTTAAACAAATTTTGTCTTTG
1 TCTCTCTTAAGACAGTTTCTCTTGAAACAAA-TTTGTCTTTG
36240 TCTCTCTTAAGACAGTTTCTCTTGAAACAAATTTGTCT
1 TCTCTCTTAAGACAGTTTCTCTTGAAACAAATTTGTCT
36278 CTCTTGAGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (41 bp):
TCTCTCTTAAGACAGTTTCTCTTGAAACAAATTTGTCTTTG
Found at i:36470 original size:36 final size:36
Alignment explanation
Indices: 36320--36521 Score: 201
Period size: 36 Copynumber: 5.4 Consensus size: 36
36310 TTGAATATGT
* *
36320 TTTC-CTTGAAACAAATTTCT-TCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTT-TGTCTCTCTTGAGACAG
* * * * * *
36355 TTTCTTTTGGAACTAAGTTTTGTCCCTCTTGATATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
36392 TTTCTCTTGAAACAAATTTTGTCTTTGACTCTCTTGATACAG
1 TTTCTCTTGAAACAAATTTTG----T--CTCTCTTGAGACAG
*
36434 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
36470 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
36506 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
36522 ATCTTTGAAT
Statistics
Matches: 140, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.03
36 76 0.54
37 26 0.19
38 1 0.01
40 1 0.01
42 32 0.23
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:36505 original size:21 final size:21
Alignment explanation
Indices: 36436--36505 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
36426 TGATACAGTT
*
36436 TCTCTTGAAATAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
36457 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
36474 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
36493 TCTCTTGAGACAA
1 TCTCTTGAAACAA
36506 TTTCCCTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 7 0.19
16 1 0.03
17 3 0.08
18 4 0.11
19 3 0.08
20 1 0.03
21 18 0.49
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:36538 original size:216 final size:209
Alignment explanation
Indices: 36185--36695 Score: 722
Period size: 216 Copynumber: 2.4 Consensus size: 209
36175 AATTTACTCA
* * *
36185 AAACAAAGTTTTTTCTCTCTTGAGACAGTTTCTCTTTA-AACAAATTTTGTCTTTGTCTCTCTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTC-CCTTAGAACAAA-----T-TTTGTCTCTCTTG
* *
36249 AGACAGTTTCTCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTGTTGA
58 AGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATTGTTGA
*
36314 ATATGTTTTCCTTGAAACAAATTTCTTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTC
123 ATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTC
* *
36379 CCTCTTGATATAGTTTCTCTTG
188 CCTCTTGAGACAGTTTCTCTTG
* * *
36401 AAACAAATTTTGTCTTTGACTCTCTTGATACAGTTTCTCTT-GAAATAAATTTTGTCTCTCTTGA
1 AAACAAATTTTG----T--CTCTCTTGAGACAGTTTCCCTTAG-AACAAATTTTGTCTCTCTTGA
36465 GACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCT-TTG
59 GACAGTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAAT-TGTTG
*
36529 AATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGT
122 AATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGT
*
36594 CTCTCTTGAGACAGTTTCTCTTG
187 CCCTCTTGAGACAGTTTCTCTTG
*
36617 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAGAACAAATTTTGTTTCTCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAGAACAAATTTTGTCTCTCTTGAGACAGTT
36682 TCCCTTGAAACAAA
66 TCCCTTGAAACAAA
36696 ATCTTTGAAT
Statistics
Matches: 267, Mismatches: 17, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
210 60 0.22
211 1 0.00
212 1 0.00
215 37 0.14
216 142 0.53
217 1 0.00
219 1 0.00
220 2 0.01
221 22 0.08
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (209 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAGAACAAATTTTGTCTCTCTTGAGACAGTT
TCCCTTGAAACAAATTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATTGTTGAATATGTTT
TCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCCCTCTTGA
GACAGTTTCTCTTG
Found at i:36635 original size:36 final size:36
Alignment explanation
Indices: 36534--36695 Score: 218
Period size: 36 Copynumber: 4.5 Consensus size: 36
36524 CTTTGAATAT
* * *
36534 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
36570 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
36607 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
36643 GTTTCCCTT-AGAACAAATTTTGTTTCTCTTGAGACA
1 GTTTCCCTTGA-AACAAATTTTGTCTCTCTTGAGACA
36679 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
36696 ATCTTTGAAT
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.01
36 78 0.70
37 32 0.29
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:36638 original size:174 final size:173
Alignment explanation
Indices: 36415--36839 Score: 760
Period size: 174 Copynumber: 2.4 Consensus size: 173
36405 AAATTTTGTC
* * *
36415 TTTGACTCTCTTGATACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-A
36480 AACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGA
65 AACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGA
36545 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
130 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
36589 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAG
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA-
* *
36654 AACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGA
65 AACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGA
36719 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
130 AACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
*
36763 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCCA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCT-TA
36828 AACAAAATTTTG
65 AAC-AAATTTTG
36840 CCTCCCTCGT
Statistics
Matches: 242, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
173 1 0.00
174 232 0.96
175 9 0.04
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (173 bp):
TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAA
ACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAA
ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
Found at i:36694 original size:72 final size:73
Alignment explanation
Indices: 36534--36858 Score: 271
Period size: 73 Copynumber: 4.6 Consensus size: 73
36524 CTTTGAATAT
* ** * *
36534 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAACTAAATTTTGTCTCTC
36599 TTGAGACA
66 TTGAGACA
* * * *
36607 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAGAAC-AAATTTTGTTTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAACTAAATTTTGTCTCTC
36671 TTGAGACA
66 TTGAGACA
* * * *
36679 GTTTCCCTTGAAACAAA----ATCT---TTGA-ATATGTTTTCCTT-GAAAC-AAATTTCGTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA-GTTTCCCTTAG-AACTAAATTTTGTCTC
*
36734 CCTTGAGACA
64 TCTTGAGACA
** * * * * *
36744 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAAC-AAATTTTGTCTC
1 GTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCCCTTAG-AACTAAATTTTGTCTC
36807 TCTTGAGACA
64 TCTTGAGACA
** * * * *
36817 GTTTCCCTCCAAACAAAATTTTGCCTCCCTCGTGACAGTTTC
1 GTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTC
36859 TCTGGAAACA
Statistics
Matches: 204, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
64 3 0.01
65 45 0.22
66 2 0.01
68 3 0.01
70 3 0.01
72 36 0.18
73 110 0.54
74 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (73 bp):
GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAACTAAATTTTGTCTCTC
TTGAGACA
Found at i:36766 original size:138 final size:136
Alignment explanation
Indices: 36592--36839 Score: 390
Period size: 138 Copynumber: 1.8 Consensus size: 136
36582 ACTAAGTTTT
*
36592 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AGAA
1 GTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA-AA
* **
36656 CAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAA
65 CAAATTTTGTCTCTCTTGAGACAGTTTCCCTCCAAACAAAAT-TTTGAATATGTTTTCCTTGAAA
36721 CAAATTTC
129 CAAATTTC
* * * *
36729 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
36794 CAAATTTTGTCTCTCTTGAGACAGTTTCCCTCCAAACAAAATTTTG
65 CAAATTTTGTCTCTCTTGAGACAGTTTCCCTCCAAACAAAATTTTG
36840 CCTCCCTCGT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
137 30 0.30
138 70 0.69
139 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (136 bp):
GTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAATTTTGTCTCTCTTGAGACAGTTTCCCTCCAAACAAAATTTTGAATATGTTTTCCTTGAAACA
AATTTC
Found at i:36796 original size:102 final size:102
Alignment explanation
Indices: 36608--36797 Score: 292
Period size: 102 Copynumber: 1.9 Consensus size: 102
36598 CTTGAGACAG
* * *
36608 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAGAACAAATTTTGTTTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAACAAATTTTGTCTCTCTT
36673 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
** * *
36710 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAAC-AAATTTTGTCTCTCT
*
36774 TGAGACAGTTTCTCTTGAAACAAA
65 TGAGACAGTTTCCCTTGAAACAAA
36798 TTTTGTCTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 39 0.49
102 40 0.51
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTAGAACAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
Found at i:36809 original size:36 final size:36
Alignment explanation
Indices: 36710--36868 Score: 176
Period size: 37 Copynumber: 4.4 Consensus size: 36
36700 TTGAATATGT
*
36710 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * *
36745 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
*
36782 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* ** * * *
36818 TTTCCCTCCAAACAAAATTTTGCCTCCCTCGTGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
*
36855 TTTCTCTGGAAACA
1 TTTCTCTTGAAACA
36869 CAAAAAACCT
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
35 4 0.04
36 39 0.38
37 60 0.58
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:36917 original size:36 final size:35
Alignment explanation
Indices: 36854--36941 Score: 128
Period size: 36 Copynumber: 2.5 Consensus size: 35
36844 CCTCGTGACA
*
36854 GTTTCTCTGGAAACAC--AAAAAACCTTTG-AAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
36886 CGTTTCTCTTGAAACACAAAAAAAACCCTTTGAAAAT
1 -GTTTCTCTTGAAACACAAAAAAAA-CCTTTGAAAAT
36923 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
36942 GACCTTCGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 15 0.30
35 6 0.12
36 25 0.50
37 4 0.08
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:37222 original size:83 final size:83
Alignment explanation
Indices: 36938--37383 Score: 414
Period size: 80 Copynumber: 5.5 Consensus size: 83
36928 TCTTGAAACA
* * *
36938 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGGC
* *
37003 TAGAAGGGTTATCTG---C
65 AAGAAGGGCTATCTGTCAC
* * * * * *
37019 CAAAGACCTTAGAGTTCGATTCCATTCAGCTCAAAGGCGCA-CATTTTGCAGCATAACTTAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA-TTTACAGCATAACTCAAGGC
37083 AAGAAGGGCTATC--T-AC
65 AAGAAGGGCTATCTGTCAC
* * *
37099 CAAAGACC-TCGAGTTCGATTACACTCAGCTTCGATGGCACATCATTTACAGCATAACTCAATGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGGC
* * *
37163 TAGAAGGGTTATTTGTCAC
65 AAGAAGGGCTATCTGTCAC
* * * *** * **
37182 CAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACATCATTCGTAGCATAGC-CTAAATC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTC-AAGGC
* *
37246 GAGAAGGGCTATCTGTCAT
65 AAGAAGGGCTATCTGTCAC
* * * *
37265 CAAAGACCTTCGAGTTCGATTCCATTCAGCTC-AAGGCACATCATTCACAGCATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCA
* *
37329 AGAAGGGCTATTTGTCAA
66 AGAAGGGCTATCTGTCAC
* * * *
37347 C-AATA-TTATCGAGTTCGATTCCATTCAGCTC-AAGGCA
1 CAAAGACCT-TCGAGTTCGATTACACTCAGCTCAAAGGCA
37384 AGAATGACTA
Statistics
Matches: 301, Mismatches: 52, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
79 20 0.07
80 82 0.27
81 60 0.20
82 44 0.15
83 77 0.26
84 18 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCA
AGAAGGGCTATCTGTCAC
Found at i:37402 original size:55 final size:55
Alignment explanation
Indices: 37318--37432 Score: 167
Period size: 55 Copynumber: 2.1 Consensus size: 55
37308 TTCACAGCAT
* * *
37318 AGCTCAAGGCAAGAAGGGCTATTTGTCAACAATATTATCGAGTTCGATTCCATTC
1 AGCTCAAGGCAAGAAGGACTATCTGTCAACAAAATTATCGAGTTCGATTCCATTC
* * * *
37373 AGCTCAAGGCAAGAATGACTATCTGTCAACAAAATTGTCGAGTTTGATTTCATTC
1 AGCTCAAGGCAAGAAGGACTATCTGTCAACAAAATTATCGAGTTCGATTCCATTC
37428 AGCTC
1 AGCTC
37433 GATGACAACG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
AGCTCAAGGCAAGAAGGACTATCTGTCAACAAAATTATCGAGTTCGATTCCATTC
Found at i:37674 original size:9 final size:9
Alignment explanation
Indices: 37662--37700 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
37652 TTATTTATGA
37662 TTATTATTT
1 TTATTATTT
*
37671 TTATTATTA
1 TTATTATTT
*
37680 TTAATATTT
1 TTATTATTT
37689 TTATTAATTT
1 TTATT-ATTT
37699 TT
1 TT
37701 TTCTTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTATTT
Found at i:37682 original size:18 final size:18
Alignment explanation
Indices: 37647--37694 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
37637 GTTTTAAAAA
*
37647 AATATTTAT-TTATGATT
1 AATATTTTTATTATGATT
* *
37664 ATTATTTTTATTATTATT
1 AATATTTTTATTATGATT
37682 AATATTTTTATTA
1 AATATTTTTATTA
37695 ATTTTTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
AATATTTTTATTATGATT
Found at i:39226 original size:9 final size:8
Alignment explanation
Indices: 39212--39248 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
39202 CATTATTACA
39212 TTTTTTATT
1 TTTTTTA-T
39221 TTTTTTAT
1 TTTTTTAT
39229 TTTTTTAT
1 TTTTTTAT
39237 TTTTTTAT
1 TTTTTTAT
39245 TTTT
1 TTTT
39249 ATTTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:39232 original size:16 final size:16
Alignment explanation
Indices: 39211--39252 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
39201 TCATTATTAC
39211 ATTTTTTATTTTTTTT
1 ATTTTTTATTTTTTTT
39227 ATTTTTT-TATTTTTTT
1 ATTTTTTAT-TTTTTTT
39243 A-TTTTTATTT
1 ATTTTTTATTT
39253 AATATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (16 bp):
ATTTTTTATTTTTTTT
Found at i:39260 original size:25 final size:25
Alignment explanation
Indices: 39212--39263 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39202 CATTATTACA
* *
39212 TTTTTTATTTTTTTTATTTTTTTAT
1 TTTTTTATTTTTTTTATATATTTAT
39237 TTTTTTATTTTTATTTA-ATATTTAT
1 TTTTTTATTTTT-TTTATATATTTAT
39262 TT
1 TT
39264 ATTATTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTTATTTTTTTTATATATTTAT
Found at i:40880 original size:20 final size:20
Alignment explanation
Indices: 40838--40880 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40828 TTTTTAATTT
* *
40838 TTTTAATAATAAAAATATTA
1 TTTTAAAAATAAAAATATAA
40858 TTTTAAAAATTAAAAA-ATAA
1 TTTTAAAAA-TAAAAATATAA
40878 TTT
1 TTT
40881 ATTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATAAAAATATAA
Found at i:47431 original size:20 final size:21
Alignment explanation
Indices: 47386--47430 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
47376 GAGGTTTTAA
47386 TTTTTGAGTGTTTAGAAGATT
1 TTTTTGAGTGTTTAGAAGATT
*
47407 TTTTTG-GTGTTTA-AATATT
1 TTTTTGAGTGTTTAGAAGATT
47426 TTTTT
1 TTTTT
47431 TATGCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.62
Consensus pattern (21 bp):
TTTTTGAGTGTTTAGAAGATT
Found at i:48015 original size:27 final size:28
Alignment explanation
Indices: 47957--48022 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
47947 GATCAACTGT
47957 TGACGTCGTTCGTCTTCTAGCCAACTCC
1 TGACGTCGTTCGTCTTCTAGCCAACTCC
* * *
47985 -GACGTCGTTTGTCTTCTCGTCAAC-CC
1 TGACGTCGTTCGTCTTCTAGCCAACTCC
*
48011 TGACGCCGTTCG
1 TGACGTCGTTCG
48023 CCTTTTCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.12, C:0.35, G:0.21, T:0.32
Consensus pattern (28 bp):
TGACGTCGTTCGTCTTCTAGCCAACTCC
Found at i:52809 original size:23 final size:23
Alignment explanation
Indices: 52762--52809 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
52752 AATAACATAT
* * **
52762 TAGGTATCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
52785 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
52808 TA
1 TA
52810 AGCATTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:52871 original size:87 final size:87
Alignment explanation
Indices: 52725--52887 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
52715 TATGTTATAT
* * *
52725 CATTTAACCGAAAATATTATTAAGTACAATAACATATTAGGTATCGTTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
52790 AGCGCTTATATAATAAAATAAG
66 AGCGCTTATATAATAAAATAAG
*
52812 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
52877 AGCGCTTATAT
66 AGCGCTTATAT
52888 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAAG
Found at i:53568 original size:200 final size:197
Alignment explanation
Indices: 52882--53606 Score: 878
Period size: 199 Copynumber: 3.6 Consensus size: 197
52872 TAGGTAGCGC
* * * * *
52882 TTATATTGACCTATTTTATAAGTAAACCGATATATTTATACCGGTAACATTGCAAATTTACCTAT
1 TTATGTTGACATATTTTCTAA-T-AACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
* * *
52947 TACATTATAATTATCGGTTTCGATGTTTTTTTGGATCGATACAATTTT--AAATGTTTTGACACT
64 TACATTATAATTATCGGTTTCGATGTTTTTTGGGATCGATAC--TTTTAAAAATGTATCGACACT
* * *
53010 TTATGCGTGCACCTCG-TTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAA-AGAGTG
127 TTATGCGTGCACCT-GTTTGGGCATTCATTATGGACAAAAGTATCGACACAAACTTAACA-AGTG
*
53073 TTGATACA
190 TCGATACA
* * * *
53081 TTAT-TTAGACTTATTTTTTCATAA-AACCGATATATTTCTATCGGGTACATTGTAAATTTACCT
1 TTATGTT-GAC--ATATTTTC-TAATAACCGATATATTTATACCGGTTACATTGTAAATTTACCT
* * * * * *
53144 ATCATATTGTAATTATCGGTTTCGATG-TTTTTGAGATCAATACTTTTAATAAATGTATCGACTC
62 ATTACATTATAATTATCGGTTTCGATGTTTTTTGGGATCGATACTTTTAA-AAATGTATCGACAC
*
53208 TTTATGCGTGCACCTGTTT-GGCATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTG
126 TTTATGCGTGCACCTGTTTGGGCATTCATTATGGACAAAA-GTATCGACACAAACTTAACAAGTG
*
53272 TCGATACT
190 TCGATACA
* * * * *
53280 TTATGATGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACATAT
1 TTATGTTGACATATTTTCT-A-ATAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
* * *
53345 TACATTATAATTATCGATTTCGAT-TTTATTGGGATCGATACTTTTAATAATTGTATCGACACTT
64 TACATTATAATTATCGGTTTCGATGTTTTTTGGGATCGATACTTTTAA-AAATGTATCGACACTT
53409 TATGCGTGCACCTGGTTTGGGCATTCATTATGGACAATAAGTATCGACACAAA-TTACACAAGTG
128 TATGCGTGCACCT-GTTTGGGCATTCATTATGGACAA-AAGTATCGACACAAACTTA-ACAAGTG
53473 TCGATACA
190 TCGATACA
* *
53481 TTATGTTGACATGTTTTCTAATTAACCGATATATTTATACCGGTTACATTGTTAATTTACCTATT
1 TTATGTTGACATATTTTCTAA-TAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATT
*
53546 ACATTATAATTATTGGTTTCGATGTTTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
65 ACATTATAATTATCGGTTTCGATGTTTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
53607 ATATTTAGGT
Statistics
Matches: 452, Mismatches: 52, Indels: 43
0.83 0.10 0.08
Matches are distributed among these distances:
196 5 0.01
197 7 0.02
198 34 0.08
199 231 0.51
200 95 0.21
201 75 0.17
202 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TTATGTTGACATATTTTCTAATAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTA
CATTATAATTATCGGTTTCGATGTTTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTTAT
GCGTGCACCTGTTTGGGCATTCATTATGGACAAAAGTATCGACACAAACTTAACAAGTGTCGATA
CA
Done.