Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004607.1 Hibiscus syriacus cultivar Beakdansim tig00010297_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: 89805
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7965 original size:2 final size:2
Alignment explanation
Indices: 7958--8010 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
7948 GAAAAAGGAA
7958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8000 AT AT AT AT AT A
1 AT AT AT AT AT A
8011 CATCAAAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8064 original size:34 final size:36
Alignment explanation
Indices: 8003--8074 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
7993 TATATATATA
*
8003 TATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
8039 TATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATACAACAAAGTATTAATAAAATAGAAAAGC
8073 TA
1 TA
8075 CCCTCTCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 12 0.36
35 7 0.21
36 14 0.42
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (36 bp):
TATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:8584 original size:17 final size:18
Alignment explanation
Indices: 8551--8586 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8541 ATATATATGT
*
8551 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
8569 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
8586 A
1 A
8587 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:9003 original size:35 final size:35
Alignment explanation
Indices: 8964--9035 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
8954 CTAAAAAACC
8964 CTATTTTAAACTAATATTTGAGTCCTAATCCAACT
1 CTATTTTAAACTAATATTTGAGTCCTAATCCAACT
* *
8999 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAAACTAATATTTGAGTCCTAATCCAACT
9034 CT
1 CT
9036 TCTTTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (35 bp):
CTATTTTAAACTAATATTTGAGTCCTAATCCAACT
Found at i:23501 original size:23 final size:21
Alignment explanation
Indices: 23449--23510 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
23439 TTTTGGTGCA
*
23449 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
23469 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
23490 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
23511 ACAGGGGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:23518 original size:21 final size:21
Alignment explanation
Indices: 23492--23531 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23482 CCCCCTTTGA
*
23492 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
23513 AGGGGAAGCGATACCCCCC
1 AGGGGAACCGATACCCCCC
23532 TGGGGTTCTG
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:0.28, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:27640 original size:220 final size:220
Alignment explanation
Indices: 27254--27893 Score: 624
Period size: 220 Copynumber: 2.9 Consensus size: 220
27244 AAGATGTTTT
* *
27254 TAATGATTTGTGAGACAAATGAGAAAACGATTTTCAAAGTTT-TTCATTTAATA-TTTTAGAAAA
1 TAAT-ATTTGTGA-AAAAATGAGAAAATGATTTTCAAAGTTTCTT-ATTTAATATTTTTAGAAAA
** * * * * * *
27317 TG-AAATTTTAGAAAATTAAGAAAACAATTTCCAAATTTTCTTGCCTAATTGATTCTTTTCAAAA
63 TGAAAATTTT-GAAAATTAAGAAAATGATTTCTAAAGTTTCTTACCTAGTAGATTATTTTCAAAA
* * * * * * *
27381 TCAGTAAGTCCTTCGAGCCATTAATAAATCTTTCGAGCATGATGATTAAGATCTCTGGGCCATCT
127 TTAGTAAGTTCTTCGAGTCATCAGTAAGTCTTTCGAGCATGATGATTAA-ATCT-TGGGTCATCT
*
27446 ATAAGACCTTT-G-T-TCATGATGCTTTTAA
190 ATAAGACCTTTAGATGGCATGATGCTTTTAA
* *
27474 TAATATTTGTGAAAAAATGAGAAAAATGATTTTCAAAATTTCTTAATTAATATTTTTAGAAAATG
1 TAATATTTGTGAAAAAATGAG-AAAATGATTTTCAAAGTTTCTTATTTAATATTTTTAGAAAATG
* * *
27539 AAAATTTTGAAAATTAAGAAAATGATTTCTAAAGTTTCTTACTTAGCAGATTAATTTCAAAATTA
65 AAAATTTTGAAAATTAAGAAAATGATTTCTAAAGTTTCTTACCTAGTAGATTATTTTCAAAATTA
*
27604 GTAAGTTCTTC-AGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTTT
130 GTAAGTTCTTCGA-GTCATCAGTAAGTCTTTCGAGCATGATGATTAAATC-TT-GGGTCATCTAT
* *** *
27668 TAGTTTTTTGAGCAAGATAGGGCATGATGTTTTTAA
192 AAGACCTTT-----AGAT--GGCATGATGCTTTTAA
* * * *
27704 -AGATATTTGCGAAAACAATTAG--AATAATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAAT
1 TA-ATATTTGTGAAAA-AATGAGAAAATGATTTTCAAAGTTTCTTATTTAATATTTTTAGAAAAT
* * *
27766 GAAATTTTTGAAAAGT--GAAAATGATTT-TCAAAGTTTCTTACCTAGTAAATTATTTTCAAAAT
64 GAAAATTTTGAAAATTAAGAAAATGATTTCT-AAAGTTTCTTACCTAGTAGATTATTTTCAAAAT
* * *
27828 TAGTAAG-TCATTCGAGTCAACTGTAAGCCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCT
128 TAGTAAGTTC-TTCGAGTCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-C-TTGGGTCATCT
27892 AT
190 AT
27894 CACTCTTTCG
Statistics
Matches: 351, Mismatches: 46, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
218 8 0.02
219 37 0.11
220 117 0.33
221 7 0.02
225 3 0.01
226 93 0.26
227 5 0.01
228 50 0.14
229 1 0.00
230 25 0.07
231 5 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (220 bp):
TAATATTTGTGAAAAAATGAGAAAATGATTTTCAAAGTTTCTTATTTAATATTTTTAGAAAATGA
AAATTTTGAAAATTAAGAAAATGATTTCTAAAGTTTCTTACCTAGTAGATTATTTTCAAAATTAG
TAAGTTCTTCGAGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTGGGTCATCTATAAGA
CCTTTAGATGGCATGATGCTTTTAA
Found at i:27778 original size:15 final size:17
Alignment explanation
Indices: 27753--27785 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27743 CTCATTTAAT
27753 ATTTTTAGAAAA-TGAA
1 ATTTTTAGAAAAGTGAA
27769 ATTTTT-GAAAAGTGAA
1 ATTTTTAGAAAAGTGAA
27785 A
1 A
27786 ATGATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATTTTTAGAAAAGTGAA
Found at i:28580 original size:15 final size:15
Alignment explanation
Indices: 28560--28593 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28550 AAATTGGCGA
28560 ATTCATCTTTGCTTC
1 ATTCATCTTTGCTTC
28575 ATTCATCTTTGCTTC
1 ATTCATCTTTGCTTC
28590 ATTC
1 ATTC
28594 TCGTTCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTCATCTTTGCTTC
Found at i:30583 original size:18 final size:18
Alignment explanation
Indices: 30560--30601 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
30550 TAAACAACTG
*
30560 CACCTTCCTCTCATACAT
1 CACCTTCCTCTCATACAA
30578 CACCTTCCTCTCATACAA
1 CACCTTCCTCTCATACAA
30596 CACCTT
1 CACCTT
30602 AATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.31
Consensus pattern (18 bp):
CACCTTCCTCTCATACAA
Found at i:33238 original size:20 final size:21
Alignment explanation
Indices: 33215--33254 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33205 AAAAAGTAAA
*
33215 AGTTAA-AATGAAATAGAAAG
1 AGTTAAGAATGAAAGAGAAAG
*
33235 AGTTAAGGATGAAAGAGAAA
1 AGTTAAGAATGAAAGAGAAA
33255 ATAAAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (21 bp):
AGTTAAGAATGAAAGAGAAAG
Found at i:43614 original size:31 final size:31
Alignment explanation
Indices: 43579--43646 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
43569 AAAATATTTT
*
43579 AAATTTGTGATGGAATATATGGACCCATCAC
1 AAATTTGTGATGGAACATATGGACCCATCAC
* * *
43610 AAATTTGTGTTGGAACATGTGGACCCCTCAC
1 AAATTTGTGATGGAACATATGGACCCATCAC
43641 AAATTT
1 AAATTT
43647 CTGACAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
AAATTTGTGATGGAACATATGGACCCATCAC
Found at i:43736 original size:31 final size:31
Alignment explanation
Indices: 43637--43715 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
43627 TGTGGACCCC
43637 TCACAAATTTCTGACAGATTCACCTATTCTG
1 TCACAAATTTCTGACAGATTCACCTATTCTG
43668 TCACAAATTTCTGACAGATTCACCTATTCTG
1 TCACAAATTTCTGACAGATTCACCTATTCTG
43699 TCACAAATTTCTGACAG
1 TCACAAATTTCTGACAG
43716 GTCCACATGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (31 bp):
TCACAAATTTCTGACAGATTCACCTATTCTG
Found at i:44975 original size:167 final size:168
Alignment explanation
Indices: 44669--45327 Score: 817
Period size: 167 Copynumber: 4.0 Consensus size: 168
44659 ATACTAACGG
* * * * * * *
44669 ATTTTCGTCAATAAATTTCTGACGGACTAGTTTATGTCCTTGGAAATGTTGGTTTCGATCAAAGT
1 ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCGATCAACGT
* * * * *
44734 TTTACCGACTACTCTCTTCAATCATAAATTCCATCATAAATTTTCTTAGAAATTACATCAACAAT
66 TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAAATTACATCAACAAT
* *
44799 TACACATTTTTTTGTAGTGTGTGGCCACAATGACTTTC
131 TACACATTTTTTTGTAGTGCGTGGCCACAATGACTTTT
* *
44837 ATTTCCGTC-ATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCAATCAGCGT
1 ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCGATCAACGT
* *
44901 TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAGATTACATGAACAAT
66 TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAAATTACATCAACAAT
* * *
44966 TATACA--TTTTTGTAGTGAGTGGCCTCAATGACTTTT
131 TACACATTTTTTTGTAGTGCGTGGCCACAATGACTTTT
* * * * ** * *
45002 ATTTTCGTCAGTATATTTTTGACGGACTATTTTATGTCAACGAAAATGTTGGTTTCGATCAACGT
1 ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCGATCAACGT
* ** *
45067 TTTACTGACTACTCTATTCAATCATAAATTTTGTCATAAAATCTCTCAAAAATTACATCAACAAT
66 TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAAATTACATCAACAAT
** * *
45132 TTTACATTTTTTTTGTAATGCGTGGCCACAATAACTTTT
131 TACACA-TTTTTTTGTAGTGCGTGGCCACAATGACTTTT
* * *** *
45171 ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCAGAAACATAAATTTCGATCAACAT
1 ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCGATCAACGT
* * * * * *
45236 TTTACTGACTA--CTCTTCCAGCAGAAATTCCGTCATAAATTTTCTCAAAAATTCCATCAGCAAT
66 TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAAATTACATCAACAAT
*
45299 TACATATTTTTTT-TAGTGCGTGGCCACAA
131 TACACATTTTTTTGTAGTGCGTGGCCACAA
45328 CGACAGTTAT
Statistics
Matches: 418, Mismatches: 69, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
165 50 0.12
166 117 0.28
167 155 0.37
168 8 0.02
169 88 0.21
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (168 bp):
ATTTCCGTCAATATATTTTTGACGAACTAGTTTATGTCCTCGGAAATATTGGTTTCGATCAACGT
TTTACTGACTACTCTCTTCAATCATAAATTCCGTCATAAATTCTCTCAAAAATTACATCAACAAT
TACACATTTTTTTGTAGTGCGTGGCCACAATGACTTTT
Found at i:45275 original size:333 final size:332
Alignment explanation
Indices: 44669--45283 Score: 872
Period size: 333 Copynumber: 1.8 Consensus size: 332
44659 ATACTAACGG
*** *
44669 ATTTTCGTCAATAAATTTCTGACGGACTAGTTTATGTCCTTGGAAATGTTGGTTTCGATCAAAGT
1 ATTTTCGTCAATAAATTTCTGACGGACTAGTTTATGTCAACGAAAATGTTGGTTTCGATCAAAGT
* * * * *
44734 TTTACCGACTACTCTCTTCAATCATAAATTCCATCATAAATTTTCTTAGAAATTACATCAACAAT
66 TTTACCGACTACTCTATTCAATCATAAATTCCATCATAAAATCTCTCAAAAATTACATCAACAAT
* * *
44799 TACACATTTTTTTGTAGTGTGTGGCCACAATGACTTTCATTTCCGTCATATATTTTTGACGAACT
131 TACACATTTTTTTGTAATGCGTGGCCACAATAACTTTCATTTCCGTCATATATTTTTGACGAACT
* * *** * * * *
44864 AGTTTATGTCCTCGGAAATATTGGTTTCAATCAGCGTTTTACTGACTACTCTCTTCAATCATAAA
196 AGTTTATGTCCTCAGAAACATAAATTTCAATCAACATTTTACTGACTAC-CTCTTCAAGCAGAAA
44929 TTCCGTCATAAATTCTCTCAAAGATTACATGAACAATTATACATTTTTGTAGTGAGTGGCCTCAA
260 TTCCGTCATAAATTCTCTCAAAGATTACATGAACAATTATACATTTTTGTAGTGAGTGGCCTCAA
44994 TGACTTTT
325 TGACTTTT
* * * * *
45002 ATTTTCGTCAGTATATTTTTGACGGACTATTTTATGTCAACGAAAATGTTGGTTTCGATCAACGT
1 ATTTTCGTCAATAAATTTCTGACGGACTAGTTTATGTCAACGAAAATGTTGGTTTCGATCAAAGT
* ***
45067 TTTACTGACTACTCTATTCAATCATAAATTTTGTCATAAAATCTCTCAAAAATTACATCAACAAT
66 TTTACCGACTACTCTATTCAATCATAAATTCCATCATAAAATCTCTCAAAAATTACATCAACAAT
** *
45132 TTTACATTTTTTTTGTAATGCGTGGCCACAATAACTTTTATTTCCGTCAATATATTTTTGACGAA
131 TACACA-TTTTTTTGTAATGCGTGGCCACAATAACTTTCATTTCCGTC-ATATATTTTTGACGAA
* *
45197 CTAGTTTATGTCCTCAGAAACATAAATTTCGATCAACATTTTACTGACTA-CTCTTCCAGCAGAA
194 CTAGTTTATGTCCTCAGAAACATAAATTTCAATCAACATTTTACTGACTACCTCTTCAAGCAGAA
*
45261 ATTCCGTCATAAATTTTCTCAAA
259 ATTCCGTCATAAATTCTCTCAAA
45284 AATTCCATCA
Statistics
Matches: 244, Mismatches: 36, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
333 149 0.61
334 37 0.15
335 58 0.24
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (332 bp):
ATTTTCGTCAATAAATTTCTGACGGACTAGTTTATGTCAACGAAAATGTTGGTTTCGATCAAAGT
TTTACCGACTACTCTATTCAATCATAAATTCCATCATAAAATCTCTCAAAAATTACATCAACAAT
TACACATTTTTTTGTAATGCGTGGCCACAATAACTTTCATTTCCGTCATATATTTTTGACGAACT
AGTTTATGTCCTCAGAAACATAAATTTCAATCAACATTTTACTGACTACCTCTTCAAGCAGAAAT
TCCGTCATAAATTCTCTCAAAGATTACATGAACAATTATACATTTTTGTAGTGAGTGGCCTCAAT
GACTTTT
Found at i:47307 original size:32 final size:33
Alignment explanation
Indices: 47251--47313 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
47241 TCTAAACTCA
*
47251 ACTTTTAGATTTTTTAAATATGAAATTAAACCC
1 ACTTTTAGAATTTTTAAATATGAAATTAAACCC
*
47284 ACTTTTA-AATTTTTAAATTTGAAATTAAAC
1 ACTTTTAGAATTTTTAAATATGAAATTAAAC
47314 TCGACATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (33 bp):
ACTTTTAGAATTTTTAAATATGAAATTAAACCC
Found at i:51251 original size:19 final size:19
Alignment explanation
Indices: 51227--51275 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
51217 ATGCCAGATT
* *
51227 GGTATCGGTACTTTGAGGA
1 GGTATCGATACTTTAAGGA
51246 GGTATCGATACTTTAAGGA
1 GGTATCGATACTTTAAGGA
51265 GGTATCGATAC
1 GGTATCGATAC
51276 CCCTGAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.31
Consensus pattern (19 bp):
GGTATCGATACTTTAAGGA
Found at i:51944 original size:21 final size:22
Alignment explanation
Indices: 51882--52007 Score: 93
Period size: 21 Copynumber: 5.8 Consensus size: 22
51872 TCGAGGGTCT
* * *
51882 TATGTGGTCCTTCGG-GAAAAA
1 TATGTGGTACTTCGGTGCAAAC
* *
51903 TATGTGGTCCTTCAGG-ACAAA-
1 TATGTGGTACTTC-GGTGCAAAC
51924 TATGTGGTACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAA-C
*
51947 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAA-C
*
51970 TATGTGGT-CATTC-GTG-AGAAT
1 TATGTGGTAC-TTCGGTGCA-AAC
*
51991 TATGTGGCACTTCGGTG
1 TATGTGGTACTTCGGTG
52008 AAAATTACGA
Statistics
Matches: 89, Mismatches: 8, Indels: 15
0.79 0.07 0.13
Matches are distributed among these distances:
20 2 0.02
21 40 0.45
22 15 0.17
23 32 0.36
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (22 bp):
TATGTGGTACTTCGGTGCAAAC
Found at i:51958 original size:23 final size:23
Alignment explanation
Indices: 51924--52007 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
51914 TCAGGACAAA
*
51924 TATGTGGTACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
51947 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
51970 TATGTGGTCA-TTC-GTG-AGAA-T
1 TATGTGG-CACTTCGGTGCA-AACC
51991 TATGTGGCACTTCGGTG
1 TATGTGGCACTTCGGTG
52008 AAAATTACGA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.04
21 11 0.20
22 8 0.15
23 32 0.58
24 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:52491 original size:27 final size:28
Alignment explanation
Indices: 52444--52500 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
52434 TATTAACTGG
*
52444 TTATTTTATTAAAAAGGTTT-ATGTTGT
1 TTATTTTATTAAAAAGCTTTAATGTTGT
* *
52471 TTATTTTGTTATAAAA-CTTTAATTTTGT
1 TTATTTTATTA-AAAAGCTTTAATGTTGT
52499 TT
1 TT
52501 GTAATTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.60
Consensus pattern (28 bp):
TTATTTTATTAAAAAGCTTTAATGTTGT
Found at i:66572 original size:53 final size:53
Alignment explanation
Indices: 66471--66606 Score: 166
Period size: 53 Copynumber: 2.5 Consensus size: 53
66461 GTAGTATCAA
* * *
66471 TACCTTAAGGATGATATCGATA-CCTTGAAACATCGAATGCTAGATTGGTATCGG
1 TACCTTGAGGA-GGTATCGATACCCTTG-AACATCGAACGCTAGATTGGTATCGG
* **
66525 TACCTTGAGGAGGTATCGATACCCTTGAACATTGAACGCTATTTTGGTATCGG
1 TACCTTGAGGAGGTATCGATACCCTTGAACATCGAACGCTAGATTGGTATCGG
* * *
66578 TACCATGAGGGGGTATGGATACCCTTGAA
1 TACCTTGAGGAGGTATCGATACCCTTGAA
66607 GGGAAGTATC
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
53 57 0.79
54 15 0.21
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (53 bp):
TACCTTGAGGAGGTATCGATACCCTTGAACATCGAACGCTAGATTGGTATCGG
Found at i:67235 original size:23 final size:22
Alignment explanation
Indices: 67155--67259 Score: 67
Period size: 23 Copynumber: 4.8 Consensus size: 22
67145 TTTAGGGTCT
67155 TATGTGGTC-CTTCGG-GATAAA-
1 TATGTGG-CACTTCGGTGA-AAAC
*
67176 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTG-AAAAC
* * *
67199 AATATGGCATTTCGGTGTAAAAC
1 TATGTGGCACTTCGGTG-AAAAC
* *
67222 TATGTGGTCA-TTCGG-GACAAT
1 TATGTGG-CACTTCGGTGAAAAC
*
67243 TATGTGGAACTTCGGTG
1 TATGTGGCACTTCGGTG
67260 CAAATTACGA
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
20 2 0.03
21 28 0.42
22 5 0.08
23 29 0.44
24 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGAAAAC
Found at i:69310 original size:13 final size:13
Alignment explanation
Indices: 69279--69303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69269 ATATCTTTTA
69279 AAATAATTTTAAG
1 AAATAATTTTAAG
69292 AAATAATTTTAA
1 AAATAATTTTAA
69304 AAGATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATAATTTTAAG
Found at i:72244 original size:134 final size:134
Alignment explanation
Indices: 72004--72294 Score: 402
Period size: 134 Copynumber: 2.2 Consensus size: 134
71994 GATTCATTCC
* * ** *
72004 ATTGAATCGAGATAGACTTGTTCCACTGTTACTCATGGAAGATCAAACCTTGAAAGAGAGGGATT
1 ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
* ** * * *
72069 TGTTCTGCTTCTTCTTGAGTTAAAATCATATATGGGGATGTTGATTCATTCCATTATTCTTCAGA
66 TGTTATGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGA
72134 GAAG
131 GAAG
* * * *
72138 ATTGAATCGAGGTAGAATTGTTCCACTGTCACTCAAAGAATATCAAATCTTGAAAGGGAGGGATC
1 ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
* * * *
72203 TGTTATGCTTCTTCTTGAGGGAAAATCAGATCTTAGGATGTTGATTCATTCCACTCTTCTTCAGG
66 TGTTATGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGA
72268 GAAG
131 GAAG
*
72272 ATTTAATCGAGGTAGACTTGTTC
1 ATTGAATCGAGGTAGACTTGTTC
72295 TTCTTGTTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (134 bp):
ATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAAGAAGATCAAACCTTGAAAGAGAGGGATC
TGTTATGCTTCTTCTTGAGGGAAAATCAGATATGAGGATGTTGATTCATTCCACTATTCTTCAGA
GAAG
Found at i:72979 original size:15 final size:15
Alignment explanation
Indices: 72959--72988 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72949 CATGTTTTCG
72959 AGTTAATCTACATGT
1 AGTTAATCTACATGT
72974 AGTTAATCTACATGT
1 AGTTAATCTACATGT
72989 TTTTATTCTT
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:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
AGTTAATCTACATGT
Found at i:73542 original size:9 final size:9
Alignment explanation
Indices: 73521--73587 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
73511 ATTTATTCTC
73521 TTTTTCTTT
1 TTTTTCTTT
73530 TTTTT-TTT
1 TTTTTCTTT
73538 CTTTTT-TTT
1 -TTTTTCTTT
*
73547 CTTTTTCCTT
1 -TTTTTCTTT
73557 TTTTTCATTT
1 TTTTTC-TTT
*
73567 TATTTCTTT
1 TTTTTCTTT
*
73576 CTTTTCTTT
1 TTTTTCTTT
73585 TTT
1 TTT
73588 CATTTTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 3 0.06
9 37 0.76
10 9 0.18
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:73573 original size:34 final size:33
Alignment explanation
Indices: 73530--73600 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
73520 CTTTTTCTTT
* * *
73530 TTTTTTTTCTTTTTTTTCTTTTTCCTTTTTTTCA
1 TTTTATTTCTTTCTTTTCTTTTTCC-ATTTTTCA
*
73564 TTTTATTTCTTTCTTTTCTTTTTTCATTTTTCA
1 TTTTATTTCTTTCTTTTCTTTTTCCATTTTTCA
73597 TTTT
1 TTTT
73601 TCATTCTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (33 bp):
TTTTATTTCTTTCTTTTCTTTTTCCATTTTTCA
Found at i:73593 original size:7 final size:7
Alignment explanation
Indices: 73577--73610 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
73567 TATTTCTTTC
*
73577 TTTTCTT
1 TTTTCAT
73584 TTTTCAT
1 TTTTCAT
73591 TTTTCAT
1 TTTTCAT
73598 TTTTCAT
1 TTTTCAT
*
73605 TCTTCA
1 TTTTCA
73611 GGCGAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:73594 original size:9 final size:8
Alignment explanation
Indices: 73527--73587 Score: 63
Period size: 8 Copynumber: 7.4 Consensus size: 8
73517 TCTCTTTTTC
73527 TTTT-TTT
1 TTTTCTTT
73534 TTTTCTTT
1 TTTTCTTT
73542 TTTT-TCTT
1 TTTTCT-TT
*
73550 TTTCCTTT
1 TTTTCTTT
73558 TTTTCATTT
1 TTTTC-TTT
73567 TATTTCTTT
1 T-TTTCTTT
73576 CTTTTCTTT
1 -TTTTCTTT
73585 TTT
1 TTT
73588 CATTTTTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 5 0.11
8 21 0.46
9 15 0.33
10 5 0.11
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:78498 original size:26 final size:26
Alignment explanation
Indices: 78462--78512 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
78452 ATACGAGCCC
78462 ACCATAATACACATAAGGTCATGCCT
1 ACCATAATACACATAAGGTCATGCCT
* *
78488 ACCATAATACATATAAGGTCGTGCC
1 ACCATAATACACATAAGGTCATGCC
78513 CACTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (26 bp):
ACCATAATACACATAAGGTCATGCCT
Found at i:87743 original size:23 final size:24
Alignment explanation
Indices: 87705--87749 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
87695 TAAATAGTGC
87705 AATAAAAAAATGAAAACAAAATAA
1 AATAAAAAAATGAAAACAAAATAA
* *
87729 AATAAAAAGAT-AAAAGAAAAT
1 AATAAAAAAATGAAAACAAAAT
87750 TAGTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (24 bp):
AATAAAAAAATGAAAACAAAATAA
Found at i:89744 original size:17 final size:17
Alignment explanation
Indices: 89722--89762 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
89712 ATATACCTAC
89722 ATATAATACAATAA-AAT
1 ATATAATAC-ATAACAAT
*
89739 ATATAATACATAACCAT
1 ATATAATACATAACAAT
89756 ATATAAT
1 ATATAAT
89763 TATCATGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAATACATAACAAT
Done.