Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_398 ID=scaffold_398-JGI_221_v2.0
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: 7944
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.26
Warning! 448 characters in sequence are not A, C, G, or T
Found at i:226 original size:108 final size:106
Alignment explanation
Indices: 2--197 Score: 279
Period size: 108 Copynumber: 1.8 Consensus size: 106
1 T
* * *
2 CAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTTGACTTCTCGTTCC
1 CAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGACTTCACGTTCC
* *
67 ACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGG
66 ACCAAATGACTAAATATCCTCTT--AAAATTTTCAAAATAAGG
* *
110 CAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCACGTT-T
1 CAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGACTTCACGTTCC
174 AGCCAAATTG-CTAAATATCCTCTT
66 A-CCAAA-TGACTAAATATCCTCTT
198 GAATTTTAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 76 0.96
109 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (106 bp):
CAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGACTTCACGTTCC
ACCAAATGACTAAATATCCTCTTAAAATTTTCAAAATAAGG
Found at i:3461 original size:6 final size:6
Alignment explanation
Indices: 3452--3508 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
3442 AAGAAAAAGA
* * * * *
3452 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAATG AAAA-- AAATTA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
3498 AAAATC AAAAT
1 AAAATC AAAAT
3509 AATAAAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
4 3 0.07
6 40 0.93
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:3507 original size:16 final size:15
Alignment explanation
Indices: 3476--3523 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3466 AATCAAAGTC
* *
3476 AAAATGAAAATGAAA
1 AAAATAAAAATCAAA
3491 AAAATTAAAAATCAAA
1 AAAA-TAAAAATCAAA
* *
3507 ATAATAAAAAACAAA
1 AAAATAAAAATCAAA
3522 AA
1 AA
3524 GAAGAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAATAAAAATCAAA
Found at i:4516 original size:7 final size:7
Alignment explanation
Indices: 4504--4562 Score: 95
Period size: 7 Copynumber: 8.7 Consensus size: 7
4494 TAAATTAAAT
4504 AAATGAA
1 AAATGAA
4511 AAATGAA
1 AAATGAA
4518 AAATG-A
1 AAATGAA
4524 AAATGAA
1 AAATGAA
4531 AAATGAA
1 AAATGAA
4538 AAATGAA
1 AAATGAA
4545 AAATG-A
1 AAATGAA
*
4551 AACTGAA
1 AAATGAA
4558 AAATG
1 AAATG
4563 GAGAGGCTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 11 0.23
7 37 0.77
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGAA
Found at i:4529 original size:20 final size:21
Alignment explanation
Indices: 4504--4562 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
4494 TAAATTAAAT
4504 AAATGAAAAATGAAAAATG-A
1 AAATGAAAAATGAAAAATGAA
4524 AAATGAAAAATGAAAAATGAA
1 AAATGAAAAATGAAAAATGAA
*
4545 AAATG-AAACTGAAAAATG
1 AAATGAAAAATGAAAAATG
4563 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 31 0.84
21 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (21 bp):
AAATGAAAAATGAAAAATGAA
Found at i:4534 original size:27 final size:27
Alignment explanation
Indices: 4504--4562 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
4494 TAAATTAAAT
4504 AAATGAAAAATGAAAAATGAAAATGAA
1 AAATGAAAAATGAAAAATGAAAATGAA
*
4531 AAATGAAAAATGAAAAATGAAACTGAA
1 AAATGAAAAATGAAAAATGAAAATGAA
4558 AAATG
1 AAATG
4563 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (27 bp):
AAATGAAAAATGAAAAATGAAAATGAA
Found at i:5941 original size:87 final size:87
Alignment explanation
Indices: 5777--5953 Score: 264
Period size: 87 Copynumber: 2.0 Consensus size: 87
5767 CAGATAAGTA
* * * *
5777 AAGATAGCAGATCTGGCCTTCCTGCATTGACAACGAAGCAGATTGAAAACAAAGCCTTGTCTCTA
1 AAGATAGCAGATCTGGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
5842 TCGGTTATAGTGGAGCTGATTG
66 TCGGTTACAGTGGAGCAGATTG
* *
5864 AAGATAGCAGATCTTGCCTTCCTGCATTAACAACGGAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTGGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
5929 TTGGTTGCAGTGGAGCAGATTG
66 TCGGTTACAGTGGAGCAGATTG
5951 AAG
1 AAG
5954 CCAGAGATCT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (87 bp):
AAGATAGCAGATCTGGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTACAGTGGAGCAGATTG
Found at i:6024 original size:43 final size:43
Alignment explanation
Indices: 5959--6080 Score: 104
Period size: 44 Copynumber: 2.8 Consensus size: 43
5949 TGAAGCCAGA
* *
5959 GATCTTATCTCCCTG-GGATTACAGCGGAGCAGATCAAA-GACAC
1 GATCCTATCTCCCTGAAG-TTACAGCGGAGCAGATCAAATGA-AC
* * * * *
6002 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAAG
1 GATCCTATCTCCCTGAAGTTACAGCGGAGCAGA-TCAAATGAAC
* * * *
6046 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
1 GATCCTATCTCCCTGAAGTTACAGCGGAGCAGATC
6081 GCATCAGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
43 27 0.44
44 32 0.52
45 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
GATCCTATCTCCCTGAAGTTACAGCGGAGCAGATCAAATGAAC
Found at i:6122 original size:54 final size:51
Alignment explanation
Indices: 6047--6181 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 51
6037 AAAATGAAGG
*
6047 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCATCAGATTGAAGCCAGAA
1 ATCTTATCTCCCTGAGA-TTACAGCAGAGTAGATCGCA--A-ATTGAAGCCAGAA
* *
6101 ATCTTATCTCCCTGAGATTACAGC---G--GA--GCAAATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGCAGAGTAGATCGCAAATTGAAGCCAGAA
* *
6145 ATCCTATCTCCCTGAGATTACAGTAGAGTAGATCGCA
1 ATCTTATCTCCCTGAGATTACAGCAGAGTAGATCGCA
6182 CCAGGTCTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
44 33 0.49
45 1 0.01
47 4 0.06
49 4 0.06
51 4 0.06
54 21 0.31
55 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (51 bp):
ATCTTATCTCCCTGAGATTACAGCAGAGTAGATCGCAAATTGAAGCCAGAA
Found at i:6153 original size:44 final size:44
Alignment explanation
Indices: 6085--7079 Score: 393
Period size: 44 Copynumber: 23.0 Consensus size: 44
6075 TAGATCGCAT
* *
6085 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * *
6129 CAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTAGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * * * * *
6173 TAGATCGCA-CCAG--GTCTTATTTCCCTGAGATTGCAGTGGAA
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * * *
6214 CAGACTGAAG-AATTTCAGGTCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCA-GT-A-ATCTTATCTCCCTGAGATTACAGTGGAG
* *
6260 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
** * *** * * * *
6304 TGGATTAAAATGAATGATCTTATCTCGCTGA-AGTTACAGTAGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * **
6348 TAGATCGCA-CCAG--GTCTTATCTCCCTGAGATTACAACGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * *
6389 CAAATTAAAGTC-GATAATCTTATCTCCCTGA-AGTTACAGTGGAG
1 CAGATTGAAGCCAG-TAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * *** * * * * *
6433 CGGATTAAAATAAATGATCTCATCTCTCTGA-AGTTACAGTAGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * * *
6477 TAGATCGCA-TCAG--ATCTTATCTCCTTGAGGTTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* ** ** * *
6518 TAGACCGAA-AAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAG
1 CAGATTGAAGCCA-GT-A-ATCTTATCTCCCTGAGATTACAGTGGAG
* *
6564 CAGATTGAAGTCAG--ATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * *
6606 TAGATTGAAGCTAGTAATCCTATCTCTCTGA-AGTTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * *** * * * * *
6650 TAGATTAAAATAAATGATCTTATCTCTCTGAGGTTACAGTAGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * * *
6694 TAGATCGTA-TCAG--GTC--ATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * *
6733 TAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAA
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * *** * * * * * *
6777 CGGATTAAAATAAATGATCTTATCTCTC-AAAAGTTACAGTAGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * * *
6821 TAGATCGTA-TCAG--GTCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * *
6862 CAAATTGAAGCTAGTAATCCTATCTCCCTGA-AGTTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * *** * * * **
6906 CGGATTAAAATAAAG-GATCTCATCTCTCTGA-AGTTACAGCAGAG
1 CAGATT-GAAGCCAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * *
6950 TAGATCGCA-TCAG--GTCTTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
*** * * * *
6991 CAGACCAAAG-AATTTCAGATCTTATCTCCCTGAGATTATAATGGAG
1 CAGATTGAAGCCA-GT-A-ATCTTATCTCCCTGAGATTACAGTGGAG
* * * *
7037 TAGATTGAAGCTAGTAATCCTATCTCCCTCAGATTACAGTGGA
1 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGA
7080 ACGGATTAAA
Statistics
Matches: 696, Mismatches: 209, Indels: 92
0.70 0.21 0.09
Matches are distributed among these distances:
39 27 0.04
40 2 0.00
41 137 0.20
42 48 0.07
43 17 0.02
44 357 0.51
45 6 0.01
46 99 0.14
47 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:6343 original size:175 final size:169
Alignment explanation
Indices: 6085--6771 Score: 622
Period size: 175 Copynumber: 4.0 Consensus size: 169
6075 TAGATCGCAT
* * * * * * ** * * *
6085 CAGATTGAAGCCAGAAATCTTATCTCCCTG-AGATTACAGCGGAGCAAATTGAAGCTAGTAATCC
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGTAGATT-AAAATAATGATCT
* *
6149 TATCTCCCTG-AGATTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTGCAGTGGA
64 TATCT-CCTGAAG-TTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGA
* * *
6213 ACAGACTGAAGAATTTCAGGTCTTATCTCCCTGAGATTACAGCGGAG
127 GCAGATTGAAG----TCAGATCTTATCTCCCTGAGATTACAGCGGAG
*
6260 CAGATTGAAGCTAGTAATCCTATCTCCCTG-AGATTACAGTGGAGTGGATTAAAATGAATGATCT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAAT-AATGATCT
**
6324 TATCTCGCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAG
64 TATCTC-CTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGAG
* * * *
6389 CAAATTAAAGTCGATAATCTTATCTCCCTGA-AGTTACAGTGGAG
128 CAGATTGAAGTC-A-GATCTTATCTCCCTGAGA-TTACAGCGGAG
* ** * * * * *** *
6433 CGGATT-AAAATAAATGAT-CTCATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCATCA-GATCT
1 CAGATTGAAGCT-AGTAATCCT-ATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAATGATCT
* * * * * * *
6494 TATCTCCTTGAGGTTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTACAG
64 TATCTCC-TGAAGTTACAGTAGAGTAGATCG---CA--CCAGGTCTTATCTCCCTGAGATTACAG
6559 TGGAGCAGATTGAAGTCAGATCTTATCTCCCTGAGATTACAGCGGAG
123 TGGAGCAGATTGAAGTCAGATCTTATCTCCCTGAGATTACAGCGGAG
* *
6606 TAGATTGAAGCTAGTAATCCTATCTCTCTGAAGTTACAGTGGAGTAGATTAAAATAAATGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAAT-AATGATCTT
* * * *
6671 ATCTCTCTGAGGTTACAGTAGAGTAGATCGTATCAGGTC--ATCTCCCTGAGATTACAGTGGAGT
65 ATCTC-CTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGAGC
*
6734 AGATTGAAG-CTAGTAATCCTATCTCCCTGAGATTACAG
129 AGATTGAAGTC-AG--ATCTTATCTCCCTGAGATTACAG
6772 TGGAACGGAT
Statistics
Matches: 421, Mismatches: 66, Indels: 54
0.78 0.12 0.10
Matches are distributed among these distances:
168 1 0.00
169 34 0.08
170 31 0.07
171 31 0.07
172 10 0.02
173 115 0.27
174 16 0.04
175 148 0.35
176 34 0.08
177 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (169 bp):
CAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAATGATCTTA
TCTCCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAG
ATTGAAGTCAGATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:6407 original size:129 final size:129
Alignment explanation
Indices: 6229--6511 Score: 417
Period size: 129 Copynumber: 2.2 Consensus size: 129
6219 TGAAGAATTT
* * * *
6229 CAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTG-AGA
1 CAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAATCCTATCTCCCTGAAG-
* * *
6293 TTACAGTGGAGTGGATTAAAATGAATGATCTTATCTCGCTGAAGTTACAGTAGAGTAGATCGCAC
65 TTACAGTGGAGCGGATTAAAATAAATGATCTCATCTCGCTGAAGTTACAGTAGAGTAGATCGCAC
*
6358 CAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGTCGA-TAATCTTATCTCCCTGAAG
1 CAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAG-CGAGTAATCCTATCTCCCTGAAG
* *
6422 TTACAGTGGAGCGGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 TTACAGTGGAGCGGATTAAAATAAATGATCTCATCTCGCTGAAGTTACAGTAGAGTAGATCGCAC
* * *
6487 CAGATCTTATCTCCTTGAGGTTACA
1 CAGGTCTTATCTCCCTGAGATTACA
6512 GTGGAGTAGA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 135 0.97
130 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (129 bp):
CAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAATCCTATCTCCCTGAAGT
TACAGTGGAGCGGATTAAAATAAATGATCTCATCTCGCTGAAGTTACAGTAGAGTAGATCGCAC
Found at i:6581 original size:129 final size:129
Alignment explanation
Indices: 6233--6610 Score: 383
Period size: 129 Copynumber: 2.9 Consensus size: 129
6223 GAATTTCAGG
* * ** * * *
6233 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTAATCCTATCTCCCTGAGATTAC
1 TCTTATCTCCCTGAGATTACAACGGAGCAAATAAAAGTCGA-TAATCTTATCTCCCTGAGGTTAC
* * * *
6297 AGTGGAGTGGATTAAAATGAATGATCTTATCTCGCTGAAGTTACAGTAGAGTAGATCGCACCAGG
65 AGTGGAGCGGATTAAAATAAATGATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCACCAGA
* *
6362 TCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGTCGATAATCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAACGGAGCAAATAAAAGTCGATAATCTTATCTCCCTGAGGTTACA
* * *
6427 GTGGAGCGGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
66 GTGGAGCGGATTAAAATAAATGATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCACCAGA
* * ** * * *
6491 TCTTATCTCCTTGAGGTTACAGTGGAGTAGACCGA-AAAATTTC-A-GATCTTATCTCCCTGAGG
1 TCTTATCTCCCTGAGATTACAACGGAGCA-A---ATAAAA-GTCGATAATCTTATCTCCCTGAGG
* * * * **
6553 TTACAGTGGAGCAGATTGAAGT-CA-GATCTTATCTCCCTG-AGATTACAGCGGAGTAGAT
61 TTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCCCTGAAG-TTACAGTAGAGTAGAT
6611 TGAAGCTAGT
Statistics
Matches: 212, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
128 2 0.01
129 164 0.77
130 4 0.02
131 35 0.17
132 4 0.02
133 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAACGGAGCAAATAAAAGTCGATAATCTTATCTCCCTGAGGTTACA
GTGGAGCGGATTAAAATAAATGATCTTATCTCCCTGAAGTTACAGTAGAGTAGATCGCACCAGA
Found at i:6598 original size:217 final size:214
Alignment explanation
Indices: 6281--6736 Score: 587
Period size: 217 Copynumber: 2.1 Consensus size: 214
6271 TAGTAATCCT
* ** ** *
6281 ATCTCCCTGAGATTACAGTGGAGTGGA--TTAAAA-TGAATGATCTTATCTCGCTGAAGTTACAG
1 ATCTCCCTGAGATTACAGTGGAGTAGACCGAAAAATTTCA-GATCTTATCTCCCTGAAGTTACAG
* * *
6343 TAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGTCGA-TAAT
65 TAGAGCAGATCGAACCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAG-CGAGTAAT
* *
6407 CTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAG
129 CCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAG
6472 TAGAGTAGATCGCATCAGATC
194 TAGAGTAGATCGCATCAGATC
* * *
6493 TTATCTCCTTGAGGTTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTACA
1 --ATCTCCCTGAGATTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGAAGTTACA
* * * * * * * *
6558 GTGGAGCAGATTGAAGTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAA
64 GTAGAGCAGATCGAA-CCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAA
* * * *
6623 TCCTATCTCTCTGAAGTTACAGTGGAGTAGATTAAAATAAATGATCTTATCTCTCTGAGGTTACA
128 TCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTCATCTCTCTGAAGTTACA
* *
6688 GTAGAGTAGATCGTATCAGGTC
193 GTAGAGTAGATCGCATCAGATC
6710 ATCTCCCTGAGATTACAGTGGAGTAGA
1 ATCTCCCTGAGATTACAGTGGAGTAGA
6737 TTGAAGCTAG
Statistics
Matches: 207, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
214 24 0.12
215 25 0.12
216 38 0.18
217 120 0.58
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (214 bp):
ATCTCCCTGAGATTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGAAGTTACAGT
AGAGCAGATCGAACCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAATCC
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAGTA
GAGTAGATCGCATCAGATC
Found at i:6795 original size:473 final size:474
Alignment explanation
Indices: 6085--7075 Score: 1395
Period size: 473 Copynumber: 2.1 Consensus size: 474
6075 TAGATCGCAT
6085 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCT
1 CAGATTGAAG-CAG-AATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCT
*** ** * * * *
6150 ATCTCCCTGAGATTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCTGAGATTGCAGTGGAAC
64 ATCTCCCTGAGATTACAGTAGAGTAGATAAAAAAAGATCTTATCTCCCTGAGATTACAGTAGAAC
*
6215 AGACTGAAGAATTTCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
129 AGACT-AAG-ATATCAGGTC-TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
** * **
6280 TATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAATGATCTTATCTCGCTGAAGTTACAGTA
191 TATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCAAAAGTTACAGTA
*
6345 GAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGTCGA-TAATCT
256 GAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAG-CGAGTAATCC
* *
6409 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTCATCTCTCTGAAGTTACAGTA
320 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCA
* * *
6474 GAGTAGATCGCATCAGATCTTATCTCCTTGAGGTTACAGTGGAGTAGACCGAAA-AATTTCAGAT
385 GAGTAGATCGCATCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACC-AAAGAATTTCAGAT
* *
6538 CTTATCTCCCTGAGGTTACAGTGGAG
449 CTTATCTCCCTGAGATTACAATGGAG
* *
6564 CAGATTGAAGTCAG-ATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTA
1 CAGATTGAAG-CAGAATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTA
* * * *
6628 TCTCTCTGA-AGTTACAGTGGAGTAGATTAAAATAAATGATCTTATCTCTCTGAGGTTACAGTAG
65 TCTCCCTGAGA-TTACAGTAGAGTAGA-TAAAA-AAA-GATCTTATCTCCCTGAGATTACAGTAG
** * * *
6692 AGTAGA-T-CG-TATCAGGTC-ATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCC
126 AACAGACTAAGATATCAGGTCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
*
6753 TATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCTCAAAAGTTACAGTA
191 TATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCAAAAGTTACAGTA
* * * * *
6818 GAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCT
256 GAGTAGATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAATCCT
6883 ATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAG
321 ATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAG
*
6948 AGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCT
386 AGTAGATCGCATCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCT
*
7013 TATCTCCCTGAGATTATAATGGAG
451 TATCTCCCTGAGATTACAATGGAG
* * *
7037 TAGATTGAAGCTAGTAATCCTATCTCCCTCAGATTACAG
1 CAGATTGAAGC-AG-AATCTTATCTCCCTGAGATTACAG
7076 TGGAACGGAT
Statistics
Matches: 457, Mismatches: 46, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
472 6 0.01
473 308 0.67
475 29 0.06
476 1 0.00
477 71 0.16
478 2 0.00
479 15 0.03
480 25 0.05
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (474 bp):
CAGATTGAAGCAGAATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTAT
CTCCCTGAGATTACAGTAGAGTAGATAAAAAAAGATCTTATCTCCCTGAGATTACAGTAGAACAG
ACTAAGATATCAGGTCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
CCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCAAAAGTTACAGTAGAGTA
GATCGCACCAGGTCTTATCTCCCTGAGATTACAACGGAGCAAATTAAAGCGAGTAATCCTATCTC
CCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAG
ATCGCATCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCT
CCCTGAGATTACAATGGAG
Found at i:6902 original size:129 final size:129
Alignment explanation
Indices: 6535--6994 Score: 674
Period size: 129 Copynumber: 3.6 Consensus size: 129
6525 AAAAATTTCA
* * * * * * *
6535 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTCAGATCTTATCTCCCTGAGATTACA
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTA-TCAGGTCTTATCTCCCTGAGATTACA
* * **
6600 GCGGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAGTTACAGTGGAGTAGATTAAAATAAAT
65 GCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAT
*
6665 GATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGTATCAGGTC--ATCTCCCTGAGATTACAG
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
* * *
6728 TGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTG-AGATTACAGTGGAACGGATTAAAATAAAT
66 CGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATAAAT
**
6792 GATCTTATCTCTCAAAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
* *
6857 CGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
66 CGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAT
* * *
6921 GATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
*
6986 TGGAGCAGA
66 CGGAGCAGA
6995 CCAAAGAATT
Statistics
Matches: 300, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
126 2 0.01
127 116 0.39
129 147 0.49
130 35 0.12
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (129 bp):
GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
CGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAT
Found at i:7046 original size:175 final size:175
Alignment explanation
Indices: 6830--7149 Score: 498
Period size: 175 Copynumber: 1.8 Consensus size: 175
6820 GTAGATCGTA
* *
6830 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAAG
1 TCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATCTCCCT-AAG
*
6895 -TTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
65 ATTACAGTGGAACGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
*
6959 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
130 TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
* * * * *
7005 TCAGATCTTATCTCCCTGAGATTATAATGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTCAGA
1 TCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTAAGA
* * * **
7070 TTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGTTT
66 TTACAGTGGAACGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
7135 CAGATCTTATCTCCC
131 CAGATCTTATCTCCC
7150 AAAGTGGAGC
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
174 2 0.02
175 128 0.98
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (175 bp):
TCAGATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTAAGA
TTACAGTGGAACGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
CAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
Done.