Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3206
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: 31949
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8195 original size:66 final size:66
Alignment explanation
Indices: 8089--8220 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
8079 TTCTTTTGTC
*
8089 GAACTGAAGACTTGTTGACGGCAGTTCTCTAGGTAAACAGATTCCAACAATGGAAATCCGTGAGA
1 GAACTGAAGACTTGTTGACGGCAGTTCTCTAGGTAAACAGATTCCAACAATGGAAATCCCTGAGA
8154 T
66 T
*
8155 GAACTGAAGACTTGTTGAGGGCAGTTCTCTAGGTAAACAGATTCCAACAATGGAAATCCCTGAGA
1 GAACTGAAGACTTGTTGACGGCAGTTCTCTAGGTAAACAGATTCCAACAATGGAAATCCCTGAGA
8220 T
66 T
8221 AAAGTGTTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (66 bp):
GAACTGAAGACTTGTTGACGGCAGTTCTCTAGGTAAACAGATTCCAACAATGGAAATCCCTGAGA
T
Found at i:9040 original size:21 final size:21
Alignment explanation
Indices: 9016--9057 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9006 TTAATTTTTA
9016 AGTTATTAACTTTTTATATTT
1 AGTTATTAACTTTTTATATTT
9037 AGTTATTAACTTTTTATATTT
1 AGTTATTAACTTTTTATATTT
9058 TTAAATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
AGTTATTAACTTTTTATATTT
Found at i:11903 original size:30 final size:30
Alignment explanation
Indices: 11851--11909 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11841 ACTTCCTTAA
*
11851 TTAATTTTTATTGAATATTATATATATTTT
1 TTAATATTTATTGAATATTATATATATTTT
*
11881 TTAATATTTACTTTAATATATATATATAT
1 TTAATATTTA-TTGAATAT-TATATATAT
11910 ATAACACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 7 0.28
32 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
TTAATATTTATTGAATATTATATATATTTT
Found at i:15945 original size:44 final size:44
Alignment explanation
Indices: 15896--15992 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
15886 ATGATCACAG
*
15896 ACACAGATTTCAGAATATGGAAGCAAAAAAGGGAATGACCAGAA
1 ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
* **
15940 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGATGAGAA
1 ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
15984 ACACAGATT
1 ACACAGATT
15993 CGAGAATTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.51, C:0.11, G:0.23, T:0.15
Consensus pattern (44 bp):
ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
Found at i:16013 original size:44 final size:44
Alignment explanation
Indices: 15896--16013 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
15886 ATGATCACAG
* *
15896 ACACAGATTTC-AGAATATGGAAGCAAAAAAGGGAATGACCAGAA
1 ACACAGA-TTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
* * **
15940 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGATGAGAA
1 ACACAGATTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
*
15984 ACACAGATTCGAGAAT-TAGAAAGCCAAAAA
1 ACACAGATTCGAGAATAT-GAAAGCAAAAAA
16014 CAAAGAGTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 3 0.05
44 62 0.95
ACGTcount: A:0.52, C:0.12, G:0.22, T:0.14
Consensus pattern (44 bp):
ACACAGATTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
Found at i:18635 original size:24 final size:23
Alignment explanation
Indices: 18603--18647 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
18593 AATTTATAAG
18603 ATTTTTAAAAATTAAAAATTATT
1 ATTTTTAAAAATTAAAAATTATT
* *
18626 ATTTTATAAATATTGAAAATTA
1 ATTTT-TAAAAATTAAAAATTA
18648 AATTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTTAAAAATTAAAAATTATT
Found at i:21593 original size:23 final size:24
Alignment explanation
Indices: 21542--21593 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
21532 TATATTATTT
* *
21542 ATTAAAGGTTATTTTAGTGTTATA
1 ATTAAAGGTTAATATAGTGTTATA
21566 A-TAAATGGTTAATATA-TGTTA-A
1 ATTAAA-GGTTAATATAGTGTTATA
21588 ATTAAA
1 ATTAAA
21594 ACTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 13 0.54
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (24 bp):
ATTAAAGGTTAATATAGTGTTATA
Found at i:23771 original size:15 final size:15
Alignment explanation
Indices: 23751--23784 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23741 ATTTTTTTTG
* *
23751 TTATTTTTGCTCGTA
1 TTATTTTTACTCGCA
23766 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
23781 TTAT
1 TTAT
23785 CGTAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Found at i:25784 original size:62 final size:62
Alignment explanation
Indices: 25687--25807 Score: 242
Period size: 62 Copynumber: 2.0 Consensus size: 62
25677 TCTTTTTTTT
25687 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
1 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
25749 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAA
1 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAA
25808 GTACGTCGAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (62 bp):
TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
Found at i:27119 original size:17 final size:17
Alignment explanation
Indices: 27079--27111 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27069 AGTAGAGGCC
27079 AAAAAAAAGAACAAAAA
1 AAAAAAAAGAACAAAAA
27096 ACAAAAAAA-AACAAAA
1 A-AAAAAAAGAACAAAA
27112 GTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAA
Found at i:27581 original size:7 final size:7
Alignment explanation
Indices: 27562--27631 Score: 63
Period size: 7 Copynumber: 9.9 Consensus size: 7
27552 TACTTCACTT
27562 GAAAAAA
1 GAAAAAA
27569 -ACAAAAA
1 GA-AAAAA
27576 GAAAAAGA
1 GAAAAA-A
27584 GAAAAAA
1 GAAAAAA
*
27591 -ATGAAAA
1 GA-AAAAA
*
27598 GAGAAAA
1 GAAAAAA
27605 GAAAAAA
1 GAAAAAA
* *
27612 GAAGAAC
1 GAAAAAA
27619 GAAAAAA
1 GAAAAAA
27626 GAAAAA
1 GAAAAA
27632 GGAGAGGCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
6 2 0.04
7 41 0.79
8 9 0.17
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:27590 original size:22 final size:21
Alignment explanation
Indices: 27562--27631 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
27552 TACTTCACTT
27562 GAAAAAAACAAAAAGAAAAAGA
1 GAAAAAAACAAAAAGAAAAA-A
** *
27584 GAAAAAAATGAAAAGAGAAAA
1 GAAAAAAACAAAAAGAAAAAA
* *
27605 GAAAAAAGA-AGAACGAAAAAA
1 GAAAAAA-ACAAAAAGAAAAAA
27626 GAAAAA
1 GAAAAA
27632 GGAGAGGCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 22 0.55
22 18 0.45
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (21 bp):
GAAAAAAACAAAAAGAAAAAA
Found at i:28670 original size:44 final size:44
Alignment explanation
Indices: 28569--28671 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
28559 GTATTGGCGT
* * * *
28569 GAAGTAGATCGTAGATAGCAGGCCCTGTCTTCCTATATTGGTAG
1 GAAGTAGATCGAAGATAGCAGACCCTGTCTTCCCATACTGGTAG
* * * * *
28613 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGGTTG
1 GAAGTAGATCGAAGATAGCAGACCCTGTCTTCCCATACTGGTAG
28656 CGAAGTAGATCGAAGA
1 -GAAGTAGATCGAAGA
28672 AAACAGATCT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
43 21 0.45
44 26 0.55
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCGAAGATAGCAGACCCTGTCTTCCCATACTGGTAG
Found at i:28901 original size:100 final size:100
Alignment explanation
Indices: 28725--29538 Score: 995
Period size: 100 Copynumber: 8.2 Consensus size: 100
28715 TCAAACGTTT
* * * * * *
28725 TTCTCTGGCAATGCAGTGGGA-CAGATTAAAGCTACGACAGCGAATCTTGCTTCCTCGACATTGC
1 TTCTCTGGCAGTACAGT-GGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* *
28789 AATTAAAGAGATTGAAGCCGCAACGGTGAATCTCAC
65 AATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
28825 TTCTCTGGCAGTACAGTGCAGCAGATTAAAGCTACGACGGTAAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
** *
28890 ATTTAAA-AGATTGAAGCTTCAACGGCGAATCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * *
28925 TT-TATTGGC-GATGCAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTG
1 TTCT-CTGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
* *
28988 CAATTAAAGAGATTGAAGCCACAACAGTGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
29025 TTCTCTGGCAGTACAGTGCAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
* ** *
29090 ATTTAAA-AGATTGAAGCCGCAACAACGAATCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * *
29125 TT-TCTTGGC-GATGCAGTGGATCAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGGCATTG
1 TTCTC-TGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
29188 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
29225 TTCTCTGGCAGTATAGTGCAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
** * *
29290 ATTTAAA-AGATTGAAGCTGCAACGGCAAATCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * *
29325 TT-TCTTGGC-GATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTG
1 TTCTC-TGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
*
29388 CAATTAAAGAGATTGAAGCCACAACGACGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
*
29425 TTCTCTGGCAGTACAGTGGATCAGATTGAAGCTACAACGGTGAATCTTG-TTCCCCGACATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
29489 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
*
29524 TTCTCTAGCAG-ACAG
1 TTCTCTGGCAGTACAG
29539 AACCACAGAT
Statistics
Matches: 615, Mismatches: 80, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
98 4 0.01
99 84 0.14
100 504 0.82
101 23 0.04
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (100 bp):
TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
ATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
Found at i:29078 original size:200 final size:200
Alignment explanation
Indices: 28724--29525 Score: 1259
Period size: 200 Copynumber: 4.0 Consensus size: 200
28714 ATCAAACGTT
* * * *
28724 TTTCTCTGGCAATGCAGTGGGA-CAGATTAAAGCTACGACAGCGAATCTTGCTTCCTCGACATTG
1 TTTCT-TGGCGATGCAGT-GGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTG
* *
28788 CAATTAAAGAGATTGAAGCCGCAACGGTGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTA
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTA
* **
28853 AAGCTACGACGGTAAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCTTCAACGGCGA
129 AAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGA
28918 ATCTTAC
194 ATCTTAC
* * *
28925 TTTATTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
* *
28990 ATTAAAGAGATTGAAGCCACAACAGTGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* **
29055 GCTACGACGGCGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACAACGAAT
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
29120 CTTAC
196 CTTAC
* * *
29125 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGGCATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
*
29190 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTATAGTGCAGCAGATTAAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* *
29255 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCTGCAACGGCAAAT
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
29320 CTTAC
196 CTTAC
*
29325 TTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
* * * *
29390 ATTAAAGAGATTGAAGCCACAACGACGAATCTCACTTCTCTGGCAGTACAGTGGATCAGATTGAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* * * *
29455 GCTACAACGGTGAATCTTG-TTCCCCGACATTGCAA-TTAAAGAGATTGAAGCCACAACGGCGAA
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAA-AGATTGAAGCCGCAACGGCGAA
*
29518 TCTCAC
195 TCTTAC
29524 TT
1 TT
29526 CTCTAGCAGA
Statistics
Matches: 556, Mismatches: 43, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
198 5 0.01
199 43 0.08
200 504 0.91
201 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (200 bp):
TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
CTTAC
Found at i:29776 original size:84 final size:84
Alignment explanation
Indices: 29544--30210 Score: 1040
Period size: 84 Copynumber: 7.9 Consensus size: 84
29534 GACAGAACCA
29544 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGT-G
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
29608 TGGAGCAGACGAAATAAAC
66 TGGAGCAGACGAAAGAAAC
* * * * *
29627 CAG-TCTTATCTCCCTAAGCCGTAATGGAGCAGA-CGAAAGAAACAAGTTTTATCTCCCTAAGCA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAGTCTTATCTCCCTAAGCA
*
29690 GTAGTGGAGCAGACAAAAGAAAC
62 GTAGTGGAGCAGACGAAAGAAAC
* * *
29713 CAGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCACATTAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
29778 TGGAGCAGACAAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
29797 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
29862 TGGAGTAGACGAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
29881 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
29946 T-GAGGCAGACGAAAGAAAC
66 TGGA-GCAGACGAAAGAAAC
29965 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
30030 T-GAGGCAGACGAAAGAAAC
66 TGGA-GCAGACGAAAGAAAC
30049 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
30114 TGGAGTAGACGAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
* * * *
30133 CGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGC
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGC
30197 AGTAGTGGAGCAGA
61 AGTAGTGGAGCAGA
30211 TCACATCAAC
Statistics
Matches: 543, Mismatches: 27, Indels: 23
0.92 0.05 0.04
Matches are distributed among these distances:
81 1 0.00
82 28 0.05
83 6 0.01
84 400 0.74
85 26 0.05
86 22 0.04
87 30 0.06
88 30 0.06
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (84 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
TGGAGCAGACGAAAGAAAC
Found at i:30225 original size:84 final size:82
Alignment explanation
Indices: 29547--30334 Score: 907
Period size: 84 Copynumber: 9.4 Consensus size: 82
29537 AGAACCACAG
*
29547 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGT-GTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGTGG
*
29611 AGCAGACGAAATAAACC
66 AGCAGACGAAAGAAACC
* * * *
29628 AGTCTTATCTCCCTAAGCCGTAATGGAGCAGA-CGAAAGAAACAAGTTTTATCTCCCTAAGCAGT
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAGTCTTATCTCCCTAAGCAGT
*
29692 AGTGGAGCAGACAAAAGAAACC
61 AGTGGAGCAGACGAAAGAAACC
* * **
29714 AGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
*
29779 GGAGCAGACAAAAGAAACC
64 GGAGCAGACGAAAGAAACC
*
29798 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
*
29863 GGAGTAGACGAAAGAAACC
64 GGAGCAGACGAAAGAAACC
*
29882 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
29947 -GAGGCAGACGAAAGAAACC
64 GGA-GCAGACGAAAGAAACC
*
29966 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
30031 -GAGGCAGACGAAAGAAACC
64 GGA-GCAGACGAAAGAAACC
*
30050 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
*
30115 GGAGTAGACGAAAGAAACC
64 GGAGCAGACGAAAGAAACC
* *
30134 GGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCA
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAG-TCTTATCTCCCTAAGCA
* **
30198 GTAGTGGAGCAGATC-ACATCAA-C
59 GTAGTGGAGCAGA-CGAAAGAAACC
** * * * *
30221 -TCTTATCTCCCTAAAAAGTAGTGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAG-TCTTATCTCCCTAAGCAGT
* * **
30284 AGTAGAGCAGATCG-CACCAA--
61 AGTGGAGCAGA-CGAAAGAAACC
*
30304 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
30335 CGAAAAAAAC
Statistics
Matches: 648, Mismatches: 40, Indels: 35
0.90 0.06 0.05
Matches are distributed among these distances:
81 2 0.00
82 28 0.04
83 3 0.00
84 502 0.77
85 26 0.04
86 20 0.03
87 31 0.05
88 35 0.05
89 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (82 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACGAAAGAAACC
Found at i:30227 original size:168 final size:168
Alignment explanation
Indices: 29547--30342 Score: 1002
Period size: 168 Copynumber: 4.7 Consensus size: 168
29537 AGAACCACAG
29547 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGT-GTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGG
* * * *
29611 AGCAGACGAAATAAACCAG-TCTTATCTCCCTAAGCCGTAATGGAGCAGACGAAAGAAACAAGTT
66 AGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACAAGTC
*
29675 TTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACC
130 TTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
* * *
29714 AGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* * *
29779 GGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---ACATCAAG
64 GGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACAAG
*
29841 TCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACC
128 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
29882 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* *
29947 -GAGGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---ACATCAA
64 GGA-GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACAA
30008 GTCTTATCTCCCTAAGCAGTAGT-GAGGCAGACGAAAGAAACC
127 GTCTTATCTCCCTAAGCAGTAGTGGA-GCAGACGAAAGAAACC
30050 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* * *
30115 GGAGTAGACGAAAGAAACCGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAG
64 GGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACAAG
* **
30180 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA-C
128 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
** * * * * *
30221 -TCTTATCTCCCTAAAAAGTAGTGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGCAGT
* *
30284 AGTAGAGCAGATC----G-CACCA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA
61 AGTGGAGCAGA-CGAAAGAAACCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA
30343 ACCAATCTCA
Statistics
Matches: 571, Mismatches: 36, Indels: 42
0.88 0.06 0.06
Matches are distributed among these distances:
167 10 0.02
168 377 0.66
169 61 0.11
170 23 0.04
171 37 0.06
172 59 0.10
173 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (168 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAACAAGTCT
TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
Found at i:30311 original size:252 final size:249
Alignment explanation
Indices: 29530--30334 Score: 1030
Period size: 252 Copynumber: 3.2 Consensus size: 249
29520 TCACTTCTCT
*
29530 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATC
1 AGCAGACAGAAAC-CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATC
* * * *
29595 TCCCTAAGCAGT-GTGGAGCAGACGAAATAAACCAG-TCTTATCTCCCTAAGCCGTAATGGAGCA
65 TCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCA
*
29658 GACGAAAGAAACAAGTTTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCTTAT
130 GACGAAAGAAACAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACC--ATCTTAT
* * **
29723 CTCCCTAAGCAGTAGTAGAGTAGATCACATTA-AGTCTTATCTCCCTAAGCAGTAGTGG
193 CTCCCTAAGCAGTAGTGGAGCAGATCA-AAAACAGTCTTATCTCCCTAAGCAGTAGT-G
29781 AGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTA
1 AGCAGAC---AGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTA
29846 TCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAG
63 TCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * *
29911 CAGATC---A-CATCAAGTCTTATCTCCCTAAGCAGTAGT-GAGGCAGACGAAAGAAACCAGATC
128 CAGA-CGAAAGAAACAAGTCTTATCTCCCTAAGCAGTAGTGGA-GCAGACAAAAGAAACC--ATC
* *
29971 TTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAAGTCTTATCTCCCTAAGCAGTAGTG
189 TTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAAC-AGTCTTATCTCCCTAAGCAGTAGTG
30032 AGGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTT
1 A-GCAGAC---AGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTT
*
30097 ATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCGGATCTTATCTCCCTAAGCAGTAGTGGA
62 ATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGA
* * **
30162 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA-C-TCT
127 GCAGACGAAAGAAACAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAAGAAACCATCT
** * *
30224 TATCTCCCTAAAAAGTAGTGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGTAGTA
190 TATCTCCCTAAGCAGTAGTGGAGCAGATC--AA-AAA-CAG-TCTTATCTCCCTAAGCAGTAGT-
30288 G
249 G
*
30289 AGCAGATC-G-CACCA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 AGCAGA-CAGAAACCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
30335 CGAAAAAAAC
Statistics
Matches: 499, Mismatches: 29, Indels: 51
0.86 0.05 0.09
Matches are distributed among these distances:
250 1 0.00
251 14 0.03
252 290 0.58
253 65 0.13
254 28 0.06
255 36 0.07
256 59 0.12
257 6 0.01
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (249 bp):
AGCAGACAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCT
CCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
ACGAAAGAAACAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCATCTTATCTC
CCTAAGCAGTAGTGGAGCAGATCAAAAACAGTCTTATCTCCCTAAGCAGTAGTG
Done.