Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003680.1 Hibiscus syriacus cultivar Beakdansim tig00007860_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: 106805
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3123 original size:29 final size:28
Alignment explanation
Indices: 3083--3142 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3073 TAAAAGTATA
*
3083 AAAAGATTATA-TTAATTATTATTTAAAT
1 AAAAGATTATATTTAATAATT-TTTAAAT
* *
3111 AAAATATTAATATTTAATAATTTTTATAT
1 AAAAGATT-ATATTTAATAATTTTTAAAT
3140 AAA
1 AAA
3143 TCGATAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 12 0.44
30 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAAAGATTATATTTAATAATTTTTAAAT
Found at i:9660 original size:15 final size:15
Alignment explanation
Indices: 9640--9669 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9630 GATTAGTATA
9640 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
9655 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
9670 ATATAATTTG
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:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:18685 original size:34 final size:34
Alignment explanation
Indices: 18647--18728 Score: 164
Period size: 34 Copynumber: 2.4 Consensus size: 34
18637 CCTCCCTAGT
18647 TTCTCTCGAACACTAAGGATGTGCTACTTAGATA
1 TTCTCTCGAACACTAAGGATGTGCTACTTAGATA
18681 TTCTCTCGAACACTAAGGATGTGCTACTTAGATA
1 TTCTCTCGAACACTAAGGATGTGCTACTTAGATA
18715 TTCTCTCGAACACT
1 TTCTCTCGAACACT
18729 TAGTAATCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (34 bp):
TTCTCTCGAACACTAAGGATGTGCTACTTAGATA
Found at i:42506 original size:12 final size:12
Alignment explanation
Indices: 42486--42519 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42476 GTAATTTTCA
*
42486 ATTTCAAAATTG
1 ATTTTAAAATTG
42498 ATTTTAAAATTG
1 ATTTTAAAATTG
*
42510 ATTTTCAAAT
1 ATTTTAAAAT
42520 CTTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (12 bp):
ATTTTAAAATTG
Found at i:43978 original size:15 final size:15
Alignment explanation
Indices: 43958--43987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43948 GATTAGTATC
43958 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
43973 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
43988 ATATAATTTG
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:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:44527 original size:17 final size:17
Alignment explanation
Indices: 44470--44551 Score: 76
Period size: 17 Copynumber: 4.7 Consensus size: 17
44460 TTATGGTTGC
*
44470 CATTTTAAGTTGCAACC-
1 CATTTTAGGTTGC-ACCA
* * *
44487 TATTTTATGGTGGCGCCA
1 CATTTTA-GGTTGCACCA
44505 CATTTTAGGTTGCACCA
1 CATTTTAGGTTGCACCA
* *
44522 CTTTTTCAAGTTGCACCA
1 CATTTT-AGGTTGCACCA
44540 CATTTTAGGTTG
1 CATTTTAGGTTG
44552 TAACTCCTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
17 26 0.51
18 25 0.49
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (17 bp):
CATTTTAGGTTGCACCA
Found at i:44563 original size:18 final size:17
Alignment explanation
Indices: 44542--44580 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
44532 TTGCACCACA
44542 TTTTAGGTTGTAACTCCT
1 TTTTAGGTTGTAAC-CCT
*
44560 TTTTATGTTGTAACCCT
1 TTTTAGGTTGTAACCCT
44577 TTTT
1 TTTT
44581 CAAGGTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.56
Consensus pattern (17 bp):
TTTTAGGTTGTAACCCT
Found at i:44759 original size:26 final size:26
Alignment explanation
Indices: 44730--44779 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
44720 TTTTATTAAA
44730 AAATAAATGTAATAAAAATATATATT
1 AAATAAATGTAATAAAAATATATATT
* * * *
44756 AAATTATTTTATTAAAAATATATA
1 AAATAAATGTAATAAAAATATATA
44780 AATTAGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AAATAAATGTAATAAAAATATATATT
Found at i:46132 original size:27 final size:27
Alignment explanation
Indices: 46094--46148 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
46084 ATTAAGTTCT
46094 TTTATTCAAAGAAAAATGCATCTTACA
1 TTTATTCAAAGAAAAATGCATCTTACA
46121 TTTATTCAAAGAAAAATGCATCTTACA
1 TTTATTCAAAGAAAAATGCATCTTACA
46148 T
1 T
46149 AAGAGGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (27 bp):
TTTATTCAAAGAAAAATGCATCTTACA
Found at i:50062 original size:28 final size:27
Alignment explanation
Indices: 50028--50155 Score: 94
Period size: 28 Copynumber: 4.6 Consensus size: 27
50018 TAAAATTTTC
* *
50028 GTTTCGGAATTTATTTCCAAAATGTCTT
1 GTTTCGGAATTAATTT-CAAAATGTCAT
*
50056 GTTTCGGAATTAAATTTTAAAATGTCAT
1 GTTTCGGAATT-AATTTCAAAATGTCAT
* * * *
50084 GTTTCAGAATTAATTTATAAAATATCCT
1 GTTTCGGAATTAATTT-CAAAATGTCAT
** * * *
50112 GTTTCAAAATTAAATTTTTAAAAGGTCAC
1 GTTTCGGAATT-AA-TTTCAAAATGTCAT
*
50141 GTTTTGGAATTAATT
1 GTTTCGGAATTAATT
50156 CTTTTATTGT
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
27 7 0.09
28 51 0.62
29 21 0.26
30 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (27 bp):
GTTTCGGAATTAATTTCAAAATGTCAT
Found at i:50094 original size:56 final size:57
Alignment explanation
Indices: 50027--50155 Score: 143
Period size: 56 Copynumber: 2.3 Consensus size: 57
50017 TTAAAATTTT
* * * * * ** *
50027 CGTTTCGGAATTTATTTCCAAAATGTCTTGTTTCGGAATTAAA-TTTTAAAATGTCA
1 CGTTTCAGAATTAATTTACAAAATATCCTGTTTCAAAATTAAATTTTTAAAAGGTCA
* *
50083 TGTTTCAGAATTAATTTATAAAATATCCTGTTTCAAAATTAAATTTTTAAAAGGTCA
1 CGTTTCAGAATTAATTTACAAAATATCCTGTTTCAAAATTAAATTTTTAAAAGGTCA
**
50140 CGTTTTGGAATTAATT
1 CGTTTCAGAATTAATT
50156 CTTTTATTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
56 34 0.58
57 25 0.42
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (57 bp):
CGTTTCAGAATTAATTTACAAAATATCCTGTTTCAAAATTAAATTTTTAAAAGGTCA
Found at i:50330 original size:28 final size:28
Alignment explanation
Indices: 50298--50391 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 28
50288 CACTGTTTCA
50298 GAATTAATTAGT-AAAATATCCAATCTTG
1 GAATTAATTA-TAAAAATATCCAATCTTG
* * * * *
50326 GAATTAGTTATGACAATATCCAGTGCTCG
1 GAATTAATTATAAAAATATCCAAT-CTTG
* * *
50355 GAATTGATTATTAAAAATAT-C-ATTTTA
1 GAATTAATTA-TAAAAATATCCAATCTTG
50382 GAATTAATTA
1 GAATTAATTA
50392 AACTGTCCGT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
27 11 0.22
28 20 0.40
29 12 0.24
30 7 0.14
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (28 bp):
GAATTAATTATAAAAATATCCAATCTTG
Found at i:50477 original size:28 final size:29
Alignment explanation
Indices: 50446--50501 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
50436 GTATTAACTA
*
50446 TTATAATA-CCAGTGTTCAGAATTAATTT
1 TTATAATATCCAGTGTCCAGAATTAATTT
* *
50474 TTATGATATCCAGTGTCCGGAATTAATT
1 TTATAATATCCAGTGTCCAGAATTAATT
50502 ACTAACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (29 bp):
TTATAATATCCAGTGTCCAGAATTAATTT
Found at i:50541 original size:28 final size:27
Alignment explanation
Indices: 50510--50563 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
50500 TTACTAACAT
50510 ATCAGCTAGCGGAATTAATTGTTGAAAC
1 ATCAGCTAGC-GAATTAATTGTTGAAAC
** *
50538 ATCATTTATCGAATTAATTGTTGAAA
1 ATCAGCTAGCGAATTAATTGTTGAAA
50564 TGTCCTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (27 bp):
ATCAGCTAGCGAATTAATTGTTGAAAC
Found at i:51017 original size:117 final size:114
Alignment explanation
Indices: 50884--51159 Score: 297
Period size: 117 Copynumber: 2.4 Consensus size: 114
50874 ATATACAGTT
* *
50884 TTCCGAATTAATTATTATAATATCCACTGTTTCCAATTAATTATGAAAACATATAGTATCCTAAA
1 TTCCGAATTAATTATTA-AATATCCAGTGTTTCCAATTAATTATGAAAACATACA-TATCCTAAA
* * * *
50949 CTAATTAGTAAAATACCCAGTAAGTTGAATTAATTAGTAAGATA-TCTATTTG
64 CTAATTAGCAAAATACCCAGTAAGTCGAATTAATTAGTAAAATATTCGA--TG
* * * * * * * * *
51001 TTCCGAATTAATTATTACGATGTTCAGTATTGCCAATTAATTATGAAAATATGCATTTCCTGAAC
1 TTCCGAATTAATTATTA-AATATCCAGTGTTTCCAATTAATTATGAAAACATACATATCCTAAAC
* * *
51066 TAATTAGCAAAATATCCAGTAGGTCGATTTAATTAGTAAAATATTCGATG
65 TAATTAGCAAAATACCCAGTAAGTCGAATTAATTAGTAAAATATTCGATG
51116 TTCTC-AATTAATTATTAAGATATCCAGTG-TTCCGAATTAATTAT
1 TTC-CGAATTAATTATTAA-ATATCCAGTGTTTCC-AATTAATTAT
51160 TATGAAGTCA
Statistics
Matches: 131, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
114 3 0.02
115 34 0.26
116 46 0.35
117 48 0.37
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (114 bp):
TTCCGAATTAATTATTAAATATCCAGTGTTTCCAATTAATTATGAAAACATACATATCCTAAACT
AATTAGCAAAATACCCAGTAAGTCGAATTAATTAGTAAAATATTCGATG
Found at i:51146 original size:29 final size:29
Alignment explanation
Indices: 51094--51196 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
51084 GTAGGTCGAT
* * * *
51094 TTAATTAGTAAAATATTCGATGTTCTCAA
1 TTAATTATTAAGATATCCAATGTTCTCAA
*
51123 TTAATTATTAAGATATCCAGTGTTC-CGAA
1 TTAATTATTAAGATATCCAATGTTCTC-AA
* *
51152 TTAATTATTATGA-AGT-CAATGTTGTCAA
1 TTAATTATTAAGATA-TCCAATGTTCTCAA
* *
51180 TTAATTATGAAAATATC
1 TTAATTATTAAGATATC
51197 AGTTTCCTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
28 21 0.36
29 37 0.64
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41
Consensus pattern (29 bp):
TTAATTATTAAGATATCCAATGTTCTCAA
Found at i:51216 original size:143 final size:143
Alignment explanation
Indices: 50976--51281 Score: 420
Period size: 143 Copynumber: 2.1 Consensus size: 143
50966 CAGTAAGTTG
* * * * *
50976 AATTAATTAGTAAGATATCTATTTGTTCCGAATTAATTATTACGATGTTCAGTATTGCCAATTAA
1 AATTAATTATTAAGATATCCATGTGTTCCGAATTAATTATTACGAAGTTCAATATTGCCAATTAA
* * *
51041 TTATGAAAATATGCATTTCCTGAACTAATTAGCAAAATATCCAGTAGGTCGATTTAATTAGTAAA
66 TTATGAAAATATGCATTTCCTGAACTAATTAGCAAAATAT-CAATAAGTAGATTTAATTAGT-AA
* *
51106 ATATTCGATGTTCTC
129 ATATCCCATGTTCTC
* * *
51121 AATTAATTATTAAGATATCCA-GTGTTCCGAATTAATTATTATGAAG-TCAATGTTGTCAATTAA
1 AATTAATTATTAAGATATCCATGTGTTCCGAATTAATTATTACGAAGTTCAATATTGCCAATTAA
*
51184 TTATGAAAATAT-CAGTTTCCTGAACTAATTAGCAATATATCAATAAGTAGATTTAATTAGTAAA
66 TTATGAAAATATGCA-TTTCCTGAACTAATTAGCAAAATATCAATAAGTAGATTTAATTAGTAAA
* *
51248 TATCCCCTGTTCTG
130 TATCCCATGTTCTC
51262 AATTAATTATTAAGATATCC
1 AATTAATTATTAAGATATCC
51282 TGTTTTTAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
141 33 0.23
142 20 0.14
143 50 0.35
144 22 0.15
145 19 0.13
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (143 bp):
AATTAATTATTAAGATATCCATGTGTTCCGAATTAATTATTACGAAGTTCAATATTGCCAATTAA
TTATGAAAATATGCATTTCCTGAACTAATTAGCAAAATATCAATAAGTAGATTTAATTAGTAAAT
ATCCCATGTTCTC
Found at i:51293 original size:28 final size:28
Alignment explanation
Indices: 51236--51492 Score: 125
Period size: 28 Copynumber: 9.2 Consensus size: 28
51226 ATAAGTAGAT
* *
51236 TTAATTAGT-AAATATCCCCTGTTCT-GAA
1 TTAATTATTAAAATAT--CCTGTTTTGGAA
* **
51264 TTAATTATTAAGATATCCTGTTTTTAAA
1 TTAATTATTAAAATATCCTGTTTTGGAA
* * *
51292 TTAATTATTAAAATCTCCGGTTTCGGAA
1 TTAATTATTAAAATATCCTGTTTTGGAA
*
51320 CTAATTATTAAAATATCCT-TTCTTGGAA
1 TTAATTATTAAAATATCCTGTT-TTGGAA
* * * *
51348 TTAATTATCAAAATGTCCTATTGCT-GAA
1 TTAATTATTAAAATATCCTGTT-TTGGAA
* * ** * * *
51376 TTAATTTTTAAGACGTCTTGTGTCGGAA
1 TTAATTATTAAAATATCCTGTTTTGGAA
* * * **
51404 TTAATT-TTTAAATATTCTATTTAAGAA
1 TTAATTATTAAAATATCCTGTTTTGGAA
* * *
51431 GTAATT-TCTAAAATGTCCTG-TTTCGAA
1 TTAATTAT-TAAAATATCCTGTTTTGGAA
* *
51458 GTTAATTTTTAAGAAT-TCCTGTTTCGGAA
1 -TTAATTATTAA-AATATCCTGTTTTGGAA
51487 TTAATT
1 TTAATT
51493 CTTTTATTCG
Statistics
Matches: 171, Mismatches: 48, Indels: 20
0.72 0.20 0.08
Matches are distributed among these distances:
27 31 0.18
28 123 0.72
29 17 0.10
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (28 bp):
TTAATTATTAAAATATCCTGTTTTGGAA
Found at i:51381 original size:56 final size:56
Alignment explanation
Indices: 51259--51386 Score: 141
Period size: 56 Copynumber: 2.3 Consensus size: 56
51249 ATCCCCTGTT
* * * * *
51259 CTGAATTAATTATTAAGATATCCTGTTTTTAAATTAATTATTAAAATCTCCGGTTT
1 CTGAATTAATTATTAAAATATCCTGTTTTGAAATTAATTATCAAAATCTCCGATTG
* * * * *
51315 CGGAACTAATTATTAAAATATCCT-TTCTTGGAATTAATTATCAAAATGTCCTATTG
1 CTGAATTAATTATTAAAATATCCTGTT-TTGAAATTAATTATCAAAATCTCCGATTG
*
51371 CTGAATTAATTTTTAA
1 CTGAATTAATTATTAA
51387 GACGTCTTGT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
55 2 0.03
56 56 0.97
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (56 bp):
CTGAATTAATTATTAAAATATCCTGTTTTGAAATTAATTATCAAAATCTCCGATTG
Found at i:51693 original size:21 final size:21
Alignment explanation
Indices: 51630--51687 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
51620 TTTTCTGAAA
51630 TTCCTTTTTCAAAATTAACTTT
1 TTCC-TTTTCAAAATTAACTTT
51652 TTCC-TTTCAAAATTAACTTT
1 TTCCTTTTCAAAATTAACTTT
*
51672 TTCCTTTTGAAAATTA
1 TTCCTTTTCAAAATTA
51688 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 20 0.59
21 10 0.29
22 4 0.12
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (21 bp):
TTCCTTTTCAAAATTAACTTT
Found at i:53554 original size:36 final size:36
Alignment explanation
Indices: 53508--53751 Score: 362
Period size: 36 Copynumber: 6.8 Consensus size: 36
53498 ATTTCATCTA
*
53508 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * * *
53544 CACTTCCGATTTAAGTCGAACGGAAGGAGGCACCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
53580 CACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* *
53616 CACTTCCAATTCAAGTCGAACGGAAGGAGGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
**
53652 CACTTCCGATTCAAGAGGAACGGAAGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
53688 CACTTCCGATTCAAGTCAAACGGAAGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * *
53724 TACTTCCAATTCAAGTTGAACGGAAGGA
1 CACTTCCGATTCAAGTCGAACGGAAGGA
53752 TGTAGCGCAT
Statistics
Matches: 190, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 190 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
Found at i:63522 original size:43 final size:43
Alignment explanation
Indices: 63475--63588 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 43
63465 TTAGCTCAAT
* * *
63475 TGCAGTAAAAATGGCAGAAACAAGAGGTGCTTAAGAGACTAAA
1 TGCAGTAAAAATGGCAGAAACAAGAGATGATTAAGAGACCAAA
* * * *
63518 TGCAGCATAAATGGCATAAATC-AGAGATGATTAAGAGACCAAT
1 TGCAGTAAAAATGGCAGAAA-CAAGAGATGATTAAGAGACCAAA
* * * *
63561 TGCAGTGAAAATAGAAGAAACAGGAGAT
1 TGCAGTAAAAATGGCAGAAACAAGAGAT
63589 TATCAAAGGA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
42 1 0.02
43 53 0.96
44 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.18
Consensus pattern (43 bp):
TGCAGTAAAAATGGCAGAAACAAGAGATGATTAAGAGACCAAA
Found at i:64423 original size:10 final size:10
Alignment explanation
Indices: 64408--64450 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
64398 TCACCACACT
64408 AAATCTTCTC
1 AAATCTTCTC
64418 AAATCTTCTC
1 AAATCTTCTC
*
64428 TAAT-TCTCTC
1 AAATCT-TCTC
*
64438 AAATCATCTC
1 AAATCTTCTC
64448 AAA
1 AAA
64451 AAACAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 1 0.04
10 27 0.96
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATCTTCTC
Found at i:64504 original size:17 final size:18
Alignment explanation
Indices: 64484--64517 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
64474 TTTATAAGGT
64484 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
64501 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
64518 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:64534 original size:13 final size:13
Alignment explanation
Indices: 64513--64572 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
64503 ATTTTGTTAG
64513 TATTTTATTTAAT
1 TATTTTATTTAAT
*
64526 TATTGTA-TTACAT
1 TATTTTATTTA-AT
* *
64539 AATTTT-TTT-AG
1 TATTTTATTTAAT
64550 TATTTTATTTAAT
1 TATTTTATTTAAT
64563 TATTTTATTT
1 TATTTTATTT
64573 TTTTACAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 6 0.16
12 6 0.16
13 25 0.68
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:64577 original size:21 final size:21
Alignment explanation
Indices: 64490--64569 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
64480 AGGTATATTT
* *
64490 TATTATATTTAATATTTTGTTAG
1 TATTTTATTTAAT-TATT-TTAG
64513 TATTTTATTTAATTA--TT-G
1 TATTTTATTTAATTATTTTAG
** *
64531 TA--TTACATAATTTTTTTAG
1 TATTTTATTTAATTATTTTAG
64550 TATTTTATTTAATTATTTTA
1 TATTTTATTTAATTATTTTA
64570 TTTTTTTACA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
16 8 0.18
18 5 0.11
19 5 0.11
21 13 0.30
22 1 0.02
23 12 0.27
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTTATTTAATTATTTTAG
Found at i:67328 original size:28 final size:28
Alignment explanation
Indices: 67297--67352 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
67287 ATGTTATCTG
67297 TCATGAGAGCTAGAGGTATAGTTGGCAT
1 TCATGAGAGCTAGAGGTATAGTTGGCAT
67325 TCATGAGAGCTAGAGGTATAGTTGGCAT
1 TCATGAGAGCTAGAGGTATAGTTGGCAT
67353 GCCAAGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (28 bp):
TCATGAGAGCTAGAGGTATAGTTGGCAT
Found at i:69121 original size:263 final size:265
Alignment explanation
Indices: 68630--69160 Score: 1048
Period size: 263 Copynumber: 2.0 Consensus size: 265
68620 CAGGAGTCAG
68630 TTACGCGCGGGGAAGGATTAGCACCCCCACAAGCGCCCAAATATTGGTACCTAGTTGGTTACCCT
1 TTACGCGCGGGGAAGGATTAGCACCCCCACAAGCGCCCAAATATTGGTACCTAGTTGGTTACCCT
68695 ATATTTAAAATCAGAAAATTTTGAGTTTGATATATTTAACTTAAAAATAATTACGGATGCAAAGT
66 ATATTTAAAATCAGAAAATTTTGAGTTTGATATATTTAACTTAAAAATAATTACGGATGCAAAGT
68760 TGAAAAGGATATTAGTTTATCGAGACCGATAGATTTCACTCCCGAGCGTTAATGCGGAAGATCAA
131 TGAAAAGGATATTAGTTTATCGAGACCGATAGATTTCACTCCCGAGCGTTAATGCGGAAGATCAA
68825 CTATTGTGCCTAATAACCGAACATTGCATCGTTTTAGAAAACATGATGCGGTTTTG-AAAGGATG
196 CTATTGTGCCTAATAACCGAACATTGCATCGTTTTAGAAAACATGATGCGGTTTTGAAAAGGATG
68889 TCGAC
261 TCGAC
68894 TTACGCGCGGGGAAGGATTAGCA-CCCCACAAGCGCCCAAATATTGGTACCTAGTTGGTTACCCT
1 TTACGCGCGGGGAAGGATTAGCACCCCCACAAGCGCCCAAATATTGGTACCTAGTTGGTTACCCT
68958 ATATTTAAAATCAGAAAATTTTGAGTTTGATATATTTAACTTAAAAATAATTACGGATGCAAAGT
66 ATATTTAAAATCAGAAAATTTTGAGTTTGATATATTTAACTTAAAAATAATTACGGATGCAAAGT
69023 TGAAAAGGATATTAGTTTATCGAGACCGATAGATTTCACTCCCGAGCGTTAATGCGGAAGATCAA
131 TGAAAAGGATATTAGTTTATCGAGACCGATAGATTTCACTCCCGAGCGTTAATGCGGAAGATCAA
69088 CTATTGTGCCTAATAACCGAACATTGCATCGTTTTAGAAAACATGATGCGGTTTTGAAAAGGATG
196 CTATTGTGCCTAATAACCGAACATTGCATCGTTTTAGAAAACATGATGCGGTTTTGAAAAGGATG
69153 TCGAC
261 TCGAC
69158 TTA
1 TTA
69161 TTTAGGGAAT
Statistics
Matches: 266, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
263 227 0.85
264 39 0.15
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (265 bp):
TTACGCGCGGGGAAGGATTAGCACCCCCACAAGCGCCCAAATATTGGTACCTAGTTGGTTACCCT
ATATTTAAAATCAGAAAATTTTGAGTTTGATATATTTAACTTAAAAATAATTACGGATGCAAAGT
TGAAAAGGATATTAGTTTATCGAGACCGATAGATTTCACTCCCGAGCGTTAATGCGGAAGATCAA
CTATTGTGCCTAATAACCGAACATTGCATCGTTTTAGAAAACATGATGCGGTTTTGAAAAGGATG
TCGAC
Found at i:70485 original size:91 final size:91
Alignment explanation
Indices: 70378--70734 Score: 561
Period size: 91 Copynumber: 3.9 Consensus size: 91
70368 AATCACCCAA
* * * *
70378 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGGGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
70443 CTCCCCACTGGAAATGTTGATGCAAG
66 CTCCCCACTGGAAATGTTGATGCAAG
*
70469 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * **
70534 CTCTCCACTGAAAATCTTGAACCAAG
66 CTCCCCACTGGAAATGTTGATGCAAG
* * *
70560 GTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATCATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
70625 CTCTCTACTGGAAATGTTGATGCAAG
66 CTCCCCACTGGAAATGTTGATGCAAG
70651 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
*
70716 CTCCCTACTGGAAAATGTT
66 CTCCCCACTGG-AAATGTT
70735 AATCCACCTC
Statistics
Matches: 242, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
91 235 0.97
92 7 0.03
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCCCCACTGGAAATGTTGATGCAAG
Found at i:76284 original size:23 final size:23
Alignment explanation
Indices: 76236--76284 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
76226 ATTGAAATAA
* *
76236 AAAAATATATAACAAAAAACATT
1 AAAAATATAAAACAAAAAACAAT
*
76259 AAAAATATAAAATAAAATAA-AAT
1 AAAAATATAAAACAAAA-AACAAT
76282 AAA
1 AAA
76285 GACCTAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAAATATAAAACAAAAAACAAT
Found at i:86491 original size:43 final size:42
Alignment explanation
Indices: 86440--86718 Score: 280
Period size: 42 Copynumber: 6.6 Consensus size: 42
86430 AGTAGGCTGT
* *
86440 AATCCCACTTTTTACTTTTATAATTGATGTCTCTAATTTTTTC
1 AATCCCACTTTTTACTTTTATAATTGA-GGCCCTAATTTTTTC
* * * *
86483 AACCCCACTTTTTACATTTATAATTAGAGCCCCT-AGTTTTTC
1 AATCCCACTTTTTACTTTTATAATT-GAGGCCCTAATTTTTTC
*
86525 AATCCCAATTTTTAGC-TTTATAATTGAGGCCCTAAATTTTTT-
1 AATCCCACTTTTTA-CTTTTATAATTGAGGCCCT-AATTTTTTC
* * * *
86567 AATCTCACTTTATACCTTTATAATTGATGCCCTAATTTTTTTC
1 AATCCCACTTTTTACTTTTATAATTGAGGCCCTAA-TTTTTTC
* * * *
86610 AATCTCACTTTCTACCTTTATAATTGAGGCCCTAACTTTTT-
1 AATCCCACTTTTTACTTTTATAATTGAGGCCCTAATTTTTTC
* * * *
86651 AATCTCACTTTTTACTTCTATAATTTAAGTCCCTAA-TTTTTC
1 AATCCCACTTTTTACTTTTATAA-TTGAGGCCCTAATTTTTTC
*
86693 AATCCCATTTTTTACTTTTTATAATT
1 AATCCCACTTTTTAC-TTTTATAATT
86719 TAAGCCCTGA
Statistics
Matches: 202, Mismatches: 24, Indels: 21
0.82 0.10 0.09
Matches are distributed among these distances:
41 35 0.17
42 91 0.45
43 74 0.37
44 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (42 bp):
AATCCCACTTTTTACTTTTATAATTGAGGCCCTAATTTTTTC
Found at i:86608 original size:85 final size:81
Alignment explanation
Indices: 86440--86710 Score: 294
Period size: 85 Copynumber: 3.2 Consensus size: 81
86430 AGTAGGCTGT
* * * * *
86440 AATCCCACTTTTTACTTTTATAATTGATGTCTCTAATTTTTTCAACCCCACTTTTTACATTTATA
1 AATCCCACTTTTTAC-TTTATAATTGA-GGCCCTAATTTTTT-AATCTCACTTTTTACCTTTATA
*
86505 ATTAGAGCCCCTAGTTTTTC
63 ATT-GAGCCCCTAATTTTTC
* *
86525 AATCCCAATTTTTAGCTTTATAATTGAGGCCCTAAATTTTTTAATCTCACTTTATACCTTTATAA
1 AATCCCACTTTTTA-CTTTATAATTGAGGCCCT-AATTTTTTAATCTCACTTTTTACCTTTATAA
86590 TTGATG-CCCTAATTTTTTTC
64 TTGA-GCCCCTAA--TTTTTC
* * *
86610 AATCTCACTTTCTACCTTTATAATTGAGGCCCTAACTTTTTAATCTCACTTTTTA-CTTCTATAA
1 AATCCCACTTTTTA-CTTTATAATTGAGGCCCTAATTTTTTAATCTCACTTTTTACCTT-TATAA
* *
86674 TTTAAGTCCCTAATTTTTC
64 -TTGAGCCCCTAATTTTTC
*
86693 AATCCCATTTTTTACTTT
1 AATCCCACTTTTTACTTT
86711 TTATAATTTA
Statistics
Matches: 160, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
82 4 0.03
83 27 0.17
84 52 0.32
85 76 0.47
86 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (81 bp):
AATCCCACTTTTTACTTTATAATTGAGGCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATT
GAGCCCCTAATTTTTC
Found at i:86726 original size:127 final size:127
Alignment explanation
Indices: 86440--86718 Score: 334
Period size: 127 Copynumber: 2.2 Consensus size: 127
86430 AGTAGGCTGT
* *
86440 AATCCCACTTTTTACTTTTATAATTGATGTCTCTAA-TTTTTTCAACCCCACTTTTTACATTTAT
1 AATCCCACTTTTTACTTTTATAATTGATG-CCCTAATTTTTTTCAACCCCACTTTCTACATTTAT
* * *
86504 AATTAGAGCCCCTAGTTTTTCAATCCCAATTTTTAGCTTTATAATTGAGGCCCTAAATTTTTT
65 AATTAGAGCCCCTACTTTTTCAATCCCAATTTTTAGCTTTATAATTAAGGCCCTAAATTTTTC
* * * * * *
86567 AATCTCACTTTATACCTTTATAATTGATGCCCTAATTTTTTTCAATCTCACTTTCTACCTTTATA
1 AATCCCACTTTTTACTTTTATAATTGATGCCCTAATTTTTTTCAACCCCACTTTCTACATTTATA
* * * *
86632 ATT-GAGGCCCTAACTTTTT-AATCTCACTTTTTA-CTTCTATAATTTAAGTCCCT-AATTTTTC
66 ATTAGAGCCCCT-ACTTTTTCAATCCCAATTTTTAGCTT-TATAA-TTAAGGCCCTAAATTTTTC
*
86693 AATCCCATTTTTTACTTTTTATAATT
1 AATCCCACTTTTTAC-TTTTATAATT
86719 TAAGCCCTGA
Statistics
Matches: 128, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
125 3 0.02
126 48 0.38
127 77 0.60
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (127 bp):
AATCCCACTTTTTACTTTTATAATTGATGCCCTAATTTTTTTCAACCCCACTTTCTACATTTATA
ATTAGAGCCCCTACTTTTTCAATCCCAATTTTTAGCTTTATAATTAAGGCCCTAAATTTTTC
Found at i:87991 original size:75 final size:75
Alignment explanation
Indices: 87910--88051 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
87900 GGCAGACACA
* *
87910 AATAAAATTTCAGGGTGGGAACCTTCAGTAAAATGAACAACTAATATAAAGAAATTTGAATTCCA
1 AATAAAATTTCAGGGTGGGAACCTTCAGTAAAATGAACAACTAATATAAACAAATTCGAATTCCA
87975 GGGTGGGCAC
66 GGGTGGGCAC
* * * * * * *
87985 AATAAAATTTTAGGGTGGGCACCTTTAGTGAAATGAACAACTAGTATACACAAATTCGGATTCCA
1 AATAAAATTTCAGGGTGGGAACCTTCAGTAAAATGAACAACTAATATAAACAAATTCGAATTCCA
88050 GG
66 GG
88052 ATATGCACGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (75 bp):
AATAAAATTTCAGGGTGGGAACCTTCAGTAAAATGAACAACTAATATAAACAAATTCGAATTCCA
GGGTGGGCAC
Found at i:88173 original size:32 final size:32
Alignment explanation
Indices: 88134--88228 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 32
88124 CTGACTGTAT
*
88134 CTACTGTGCATTATCTAAATGCGACACTGACA
1 CTACTGTGCATTATCTAAATGCAACACTGACA
* * * *
88166 CTCCTGTGCAATATCTAAATGCAACCCTGACT
1 CTACTGTGCATTATCTAAATGCAACACTGACA
* * * *
88198 CTATTATGCATTATTTGAATGCAACACTGAC
1 CTACTGTGCATTATCTAAATGCAACACTGAC
88229 TAGTATCTGG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (32 bp):
CTACTGTGCATTATCTAAATGCAACACTGACA
Found at i:94101 original size:32 final size:32
Alignment explanation
Indices: 94020--94113 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
94010 CTGCTACACC
* * * * *
94020 TTATCTAACTGCATTACTAGCTCTATTGTGCA
1 TTATCTAAATGCAATATTAACTCTGTTGTGCA
* *
94052 TTATCTGAATGCCATATTAACTCTGTTGTGCA
1 TTATCTAAATGCAATATTAACTCTGTTGTGCA
* *
94084 TTATCTAAATGCAATATTGACTCCGTTGTG
1 TTATCTAAATGCAATATTAACTCTGTTGTG
94114 ACTCATACAC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (32 bp):
TTATCTAAATGCAATATTAACTCTGTTGTGCA
Found at i:100399 original size:20 final size:20
Alignment explanation
Indices: 100374--100412 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
100364 GATGTAGTAT
100374 GGTCTTGGTAGTTGCAATAA
1 GGTCTTGGTAGTTGCAATAA
100394 GGTCTTGGTAGTTGCAATA
1 GGTCTTGGTAGTTGCAATA
100413 TAATCTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (20 bp):
GGTCTTGGTAGTTGCAATAA
Found at i:100419 original size:20 final size:20
Alignment explanation
Indices: 100376--100421 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
100366 TGTAGTATGG
*
100376 TCTTGGTAGTTGCAATAAGG
1 TCTTGGTAGTTGCAATAAGA
100396 TCTTGGTAGTTGCAATATA-A
1 TCTTGGTAGTTGCAATA-AGA
100416 TCTTGG
1 TCTTGG
100422 ATCGTGGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (20 bp):
TCTTGGTAGTTGCAATAAGA
Found at i:103193 original size:31 final size:32
Alignment explanation
Indices: 103155--103217 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
103145 CACTTGTTGG
103155 AAATACAACTGGCCACTTG-AAAAAATATATT
1 AAATACAACTGGCCACTTGAAAAAAATATATT
103186 AAATACAACTGGCCACTTGAAAAAAATATATT
1 AAATACAACTGGCCACTTGAAAAAAATATATT
103218 CTTTGTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (32 bp):
AAATACAACTGGCCACTTGAAAAAAATATATT
Found at i:104337 original size:2 final size:2
Alignment explanation
Indices: 104330--104362 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
104320 ATTGTGGTAT
104330 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104363 TGAAAGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.