Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold640
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: 14402
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:8182 original size:44 final size:43
Alignment explanation
Indices: 8134--8482 Score: 182
Period size: 44 Copynumber: 8.2 Consensus size: 43
8124 AGCCACCAGC
* * * * *
8134 CTTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGCAGAT
** *** * * *
8178 CTTATCTGTCTAAATTGCAGTAGAGCAGATCG--CAT-CA-AGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGCAGA-T
** **
8218 CTTATCTCCCTAAGCAGTAGTGGAGCAGAAAGAAGAAACTA-AT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGC-AGAT
* * * *
8261 CTTATCTCTCTAAACAGTAGTGGAGCAGATCGAA-A-GCACCAAC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGCA--GAT
* * * * * ** *
8304 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGCAGAT
**
8348 CTTATCTCCCTACA-CAGTAGTGGAGCAGATCGAA-A-GCA-CC
1 CTTATCTCCCTA-AGCAGTAGTGGAGCAGATCGAAGATGCAGAT
* * * * * *
8388 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGCAGAT
* *
8432 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAAGCT-CAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGATGCAGAT
8475 CTTATCTC
1 CTTATCTC
8483 TCTGAAGTTG
Statistics
Matches: 223, Mismatches: 64, Indels: 37
0.69 0.20 0.11
Matches are distributed among these distances:
39 2 0.01
40 53 0.24
41 5 0.02
42 3 0.01
43 73 0.33
44 81 0.36
45 4 0.02
46 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGCAGAT
Found at i:8376 original size:170 final size:170
Alignment explanation
Indices: 8050--8468 Score: 421
Period size: 170 Copynumber: 2.4 Consensus size: 170
8040 GCAGATCCTG
** * * *
8050 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT-TCCTAAGGTAGTAGTGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-AACTAATCTTATCTCT-CTAA-GCAGTAGTGG
* ** * * * *
8114 AACAGAT-TTAAGCCACCAGCCTTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATTGTAGAT
63 AGCAGATCGAAAG-CACCAACCTTATCTCCCTAAGCAGCAGCAGAGTAGGTTAAAGATTGTAGAT
** ** * * **
8178 CTTATCTGTCTAAATTGCAGTAGAGCAGATCG-CATCAAGTCTTA
127 CTTATCTCCCTAAACAGCAGTAGAGCAGATCGAAAGC-ACCCTTA
** *
8222 TCTCCCTAAGCAGTAGTGGAGCAGAAAGAAGAAACTAATCTTATCTCTCTAAACAGTAGTGGAGC
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAACTAATCTTATCTCTCTAAGCAGTAGTGGAGC
* *
8287 AGATCGAAAGCACCAACCTTATCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAGATCTTA
66 AGATCGAAAGCACCAACCTTATCTCCCTAAGCAGCAGCAGAGTAGGTTAAAGATTGTAGATCTTA
* * *
8352 TCTCCCTACACAGTAGTGGAGCAGATCGAAAGCACCCTTA
131 TCTCCCTAAACAGCAGTAGAGCAGATCGAAAGCACCCTTA
* * * * * *** *
8392 TCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAACTA-ATCTTATCTCTCTAAGCAGTAGTGGAG
*
8457 TAGATCGAAAGC
65 CAGATCGAAAGC
8469 TCAGATCTTA
Statistics
Matches: 202, Mismatches: 41, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
170 115 0.57
171 56 0.28
172 31 0.15
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (170 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAACTAATCTTATCTCTCTAAGCAGTAGTGGAGC
AGATCGAAAGCACCAACCTTATCTCCCTAAGCAGCAGCAGAGTAGGTTAAAGATTGTAGATCTTA
TCTCCCTAAACAGCAGTAGAGCAGATCGAAAGCACCCTTA
Found at i:8431 original size:84 final size:85
Alignment explanation
Indices: 8259--8468 Score: 334
Period size: 84 Copynumber: 2.4 Consensus size: 85
8249 GAAGAAACTA
*
8259 ATCTTATCTCTCTAAACAGTAGTGGAGCAGATCGAAAGCACCAACCTTATCTCCCTGAGCAGCAG
1 ATCTTATCTCCCT-AACAGTAGTGGAGCAGATCGAAAGCACC-ACCTTATCTCCCTGAGCAGCAG
*
8324 CGGAGTAGGTTAAAGATTGTAG
64 CGGAGTAGGTCAAAGATTGTAG
8346 ATCTTATCTCCCTACACAGTAGTGGAGCAGATCGAAAGCA-C-CCTTATCTCCCTGAGCAGCAGC
1 ATCTTATCTCCCTA-ACAGTAGTGGAGCAGATCGAAAGCACCACCTTATCTCCCTGAGCAGCAGC
*
8409 GGAGTAGGTCGAAGATTGTAG
65 GGAGTAGGTCAAAGATTGTAG
*
8430 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAAGC
1 ATCTTATCTCCCTAA-CAGTAGTGGAGCAGATCGAAAGC
8469 TCAGATCTTA
Statistics
Matches: 117, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
83 1 0.01
84 77 0.66
86 2 0.02
87 37 0.32
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (85 bp):
ATCTTATCTCCCTAACAGTAGTGGAGCAGATCGAAAGCACCACCTTATCTCCCTGAGCAGCAGCG
GAGTAGGTCAAAGATTGTAG
Found at i:8476 original size:43 final size:42
Alignment explanation
Indices: 8212--8482 Score: 169
Period size: 43 Copynumber: 6.3 Consensus size: 42
8202 GCAGATCGCA
** *
8212 TCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAAAGAAGAAAC
1 TCAA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-A-AAGC
* *
8257 T-AATCTTATCTCTCTAAACAGTAGTGGAGCAGATCGAAAGC
1 TCAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAGC
* * * * * * * * *
8298 ACCAACCTTATCTCCCTGAGCAGCAGCGGAGTAGGT-TAAAGAT
1 -TCAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAG-C
*
8341 TGTAGATCTTATCTCCCTACA-CAGTAGTGGAGCAGATCGAAAG-
1 T-CA-ATCTTATCTCCCTA-AGCAGTAGTGGAGCAGATCGAAAGC
** * * * * *
8384 -CACCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTG-
1 TCAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-A--GC
*
8427 T-AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAAGC
1 TCA-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAGC
8469 TCAGATCTTATCTC
1 TCA-ATCTTATCTC
8483 TCTGAAGTTG
Statistics
Matches: 172, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.01
40 27 0.16
41 6 0.03
42 6 0.03
43 70 0.41
44 56 0.33
45 6 0.03
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (42 bp):
TCAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAGC
Found at i:8574 original size:44 final size:44
Alignment explanation
Indices: 8477--8579 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
8467 GCTCAGATCT
* * *
8477 TATCTCTCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
1 TATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAACCAAACC
* ** *
8521 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAA-AACCACAAACC
1 TATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAAC-CAAACC
8565 TCATC-CCCTAAAGTT
1 T-ATCTCCCTAAAGTT
8580 ACGGTAGAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 3 0.06
44 44 0.88
45 3 0.06
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (44 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAACCAAACC
Found at i:9579 original size:9 final size:10
Alignment explanation
Indices: 9556--9581 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9546 TAATTTGGAT
9556 TTTTTTATTA
1 TTTTTTATTA
9566 TTTTTTATTA
1 TTTTTTATTA
9576 TTTTTT
1 TTTTTT
9582 TTAAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTA
Done.