Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_77 ID=scaffold_77-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: 16884
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.29
Warning! 555 characters in sequence are not A, C, G, or T
Found at i:209 original size:17 final size:17
Alignment explanation
Indices: 160--212 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
150 TAATCACTTT
*
160 AATATTAAAT-TTAATTT
1 AATATTAAATCTTAA-TA
*
177 AATATT-TATCTTAATA
1 AATATTAAATCTTAATA
193 AATATTAAATCTTAATA
1 AATATTAAATCTTAATA
210 AAT
1 AAT
213 TAATAGAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 9 0.29
17 22 0.71
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTAAATCTTAATA
Found at i:13748 original size:24 final size:24
Alignment explanation
Indices: 13712--13821 Score: 186
Period size: 24 Copynumber: 4.6 Consensus size: 24
13702 TTTTATGTCC
*
13712 TGAA-ATTACAGTGGATTGAACTT
1 TGAAGATTACAGTGGATTGAACCT
*
13735 TAAAGATTACAGTGGATTGAACCT
1 TGAAGATTACAGTGGATTGAACCT
13759 TGAAGATTACAGTGGATTGAACCT
1 TGAAGATTACAGTGGATTGAACCT
13783 TGAAGATTACAGTGGATTGAACCT
1 TGAAGATTACAGTGGATTGAACCT
*
13807 TGAAGATTATAGTGG
1 TGAAGATTACAGTGG
13822 GGGCAATCAG
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
23 3 0.04
24 79 0.96
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (24 bp):
TGAAGATTACAGTGGATTGAACCT
Found at i:14281 original size:21 final size:21
Alignment explanation
Indices: 14255--14298 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
14245 CTGGCGTTGC
*
14255 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
*
14276 AGTGGAGCAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
14297 AG
1 AG
14299 GCAACGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.32, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:14292 original size:72 final size:72
Alignment explanation
Indices: 14204--14345 Score: 167
Period size: 72 Copynumber: 2.0 Consensus size: 72
14194 CTTGCATTGC
* * ** * * * *
14204 AGTGGAACTGATTAAAGCTAAAGGTAGTGAATCTTGTTTCCCTGGCGTTGCAGTGGAATAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGCAACGAATCTTATCTCCCTGGCCTTGCAGTGGAACAGATTA
14269 AAGCTGA
66 AAGCTGA
* * ** *
14276 AGTGGAGCAGATTAAAGCTGAAGGCAACGAATCTTATCTCTTTGGCCTTGCGGTGGAACAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGCAACGAATCTTATCTCCCTGGCCTTGCAGTGGAACAGATTA
14341 AAGCT
66 AAGCT
14346 AAAGGTAGCA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (72 bp):
AGTGGAACAGATTAAAGCTAAAGGCAACGAATCTTATCTCCCTGGCCTTGCAGTGGAACAGATTA
AAGCTGA
Found at i:14360 original size:51 final size:51
Alignment explanation
Indices: 14276--14421 Score: 157
Period size: 51 Copynumber: 2.9 Consensus size: 51
14266 TTAAAGCTGA
* * * ** *
14276 AGTGGAGCAGATTAAAGCTGAAGGCAACGAATCTTATCTCTTTGGCCTTGC
1 AGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTGACCTTGC
* * * * * **
14327 GGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGATGTTGC
1 AGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTGACCTTGC
* *
14378 AGTGGAGTAGATTAAACCTAAAGGCAGCAAATCTTATCTCCCTG
1 AGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTG
14422 GCGTTAAGAC
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (51 bp):
AGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTGACCTTGC
Found at i:14528 original size:51 final size:51
Alignment explanation
Indices: 14434--14532 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
14424 GTTAAGACTG
14434 AAAGCAGCAAATCTTATTTCCCTGGCATTGCAATAGAACAGATTAAAGCTA
1 AAAGCAGCAAATCTTATTTCCCTGGCATTGCAATAGAACAGATTAAAGCTA
* * * * *
14485 AAAGTAGCGAATCTTGTTTCCCTGGCATTGCAATGGAATAGATTAAAG
1 AAAGCAGCAAATCTTATTTCCCTGGCATTGCAATAGAACAGATTAAAG
14533 ATGAAGTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (51 bp):
AAAGCAGCAAATCTTATTTCCCTGGCATTGCAATAGAACAGATTAAAGCTA
Found at i:14653 original size:261 final size:260
Alignment explanation
Indices: 14185--14953 Score: 1022
Period size: 261 Copynumber: 3.0 Consensus size: 260
14175 ATCCAATAAA
* * * * *
14185 CTTATTTCCCTTGCATTGCAGTGGAACTGATTAAAGCTAAAGGTAGTGAATCTTGTTTCCCTGGC
1 CTTATTTCCCTGGCATTGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGC
* * *
14250 GTTGCAGTGGAATAGATTAAAGCTGAAGTGGAGC-AGATTAAAGCTGAAGGCAACGAATCTTATC
66 GTTGCAATGGAATAGATTAAAGCTGAAGTGGAGCGA-ATTAAAGCTAAAGGCAGCGAATCTTATC
* *
14314 TCTTTGGCCTTGCGGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGATGTTGCA
130 TCTTTGGCCTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGATGTTGCA
* *
14379 GTGGAGTAGATTAAACCTAAAGGCAGCAAATCTTATCTCCCTGGCGTTAAGACTGAAAGCAGCAA
195 GTGGAGTAGATTAAAGCTGAAGGCA-CAAATCTTATCTCCCTGGCGTTAAGACTGAAAGCAGCAA
14444 AT
259 AT
*
14446 CTTATTTCCCTGGCATTGCAATAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGC
1 CTTATTTCCCTGGCATTGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGC
* * * * *
14511 ATTGCAATGGAATAGATTAAAGATGAAGTAGAGCGAATTAAAGCTAAAGGCTGCGAATATTATCT
66 GTTGCAATGGAATAGATTAAAGCTGAAGTGGAGCGAATTAAAGCTAAAGGCAGCGAATCTTATCT
** * * *
14576 CTTTGGATTTACAGTGGAACAGATTAAAGCTAAAGGTAGTGAATCTTGTTTCCCTGACGTTGCAG
131 CTTTGGCCTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGATGTTGCAG
* * ** * * *
14641 TGGAGCAGATTAAAGCTGAAGGCAACAAATCTTATCTCTCTGGTATTATGACTGAAGGCAGCGAA
196 TGGAGTAGATTAAAGCTGAAGGC-ACAAATCTTATCTCCCTGGCGTTAAGACTGAAAGCAGCAAA
14706 T
260 T
* * * *
14707 CTTATTTCCTTGGCGTGGCAGTAGAACAGATTAAAGCTAAGAGTAGCGAATCTTGTTTCCCTGGC
1 CTTATTTCCCTGGCATTGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGC
* * * * *
14772 GTTTCAATGGAATAAATTAAAGCTGAAGCGGAGCGGATTAAAGCTAAAGGCAGCGAATCCTATCT
66 GTTGCAATGGAATAGATTAAAGCTGAAGTGGAGCGAATTAAAGCTAAAGGCAGCGAATCTTATCT
* * * * * * * *
14837 CCTTGGCGTTGCATTAGAATAGA-TCAAGCTAAAGGTAGCGAATCTTGTGTCCCTGATTTTGCAG
131 CTTTGGCCTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGATGTTGCAG
* * * **
14901 CGGAGTAGATT-AAGTTGAAGGCACGAATCTTATCTCCCTAACGTTAAGACTGA
196 TGGAGTAGATTAAAGCTGAAGGCACAAATCTTATCTCCCTGGCGTTAAGACTGA
14954 NNNNNNNNNN
Statistics
Matches: 439, Mismatches: 67, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
258 24 0.05
259 10 0.02
260 45 0.10
261 358 0.82
262 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (260 bp):
CTTATTTCCCTGGCATTGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGC
GTTGCAATGGAATAGATTAAAGCTGAAGTGGAGCGAATTAAAGCTAAAGGCAGCGAATCTTATCT
CTTTGGCCTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGATGTTGCAG
TGGAGTAGATTAAAGCTGAAGGCACAAATCTTATCTCCCTGGCGTTAAGACTGAAAGCAGCAAAT
Found at i:15592 original size:19 final size:19
Alignment explanation
Indices: 15568--15611 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15558 TGCAACAAAC
**
15568 AGCAAAGAAACTGAATGAG
1 AGCAAAGAAACCAAATGAG
*
15587 AGCAAAGAAACCAAATGAT
1 AGCAAAGAAACCAAATGAG
15606 AGCAAA
1 AGCAAA
15612 AAAAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.14, G:0.20, T:0.09
Consensus pattern (19 bp):
AGCAAAGAAACCAAATGAG
Found at i:16447 original size:3 final size:3
Alignment explanation
Indices: 16439--16495 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
16429 TTTAATACTG
16439 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16487 TTA TTA TTA
1 TTA TTA TTA
16496 CTACTACTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16500 original size:3 final size:3
Alignment explanation
Indices: 16494--16543 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16484 TTATTATTAT
16494 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
16542 TA
1 TA
16544 TTATTAGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Done.