Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6347.1
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: 12235
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Found at i:10349 original size:44 final size:44
Alignment explanation
Indices: 10282--11181 Score: 323
Period size: 44 Copynumber: 19.7 Consensus size: 44
10272 GAAGAATTTC
*
10282 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
** * * *
10326 AGATCTTATCTTTCTGAGATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* * *** *
10370 TA-ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* ** * * * *
10413 AGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAG
* * * * ** * *
10457 -G-TCTTATCACCCT-AGGTTACAATGGAGTAGACCGAAG-AATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA---G
* *
10500 AGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* * * *
10544 AGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* * * *** *
10588 TA-ATCCTATCTCTCTGA-AGTTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAG
*
10631 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGT-G-G-AG-------CAGATTGAAGCCAG
* ** ** *
10686 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAA-AAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA---G
* * **
10732 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* * ** *** *
10776 TA-ATCCTATCTGCCTGAGATTACAGTGGAGTGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
*
10819 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGT-G-G-AG-------CAGATTGAAGCCAG
* ** ** *
10874 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAA-AAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA---G
* * **
10920 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* * ** *** *
10964 TA-ATCCTATCTGCCTGAGATTACAGTGGAGTGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
*
11007 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGT-G-G-AG-------CAGATTGAAGCCAG
* ** ** *
11062 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAA-AAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCA---G
* * **
11108 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
* *
11152 TA-ATCCTATCTGCCTGAGATTACAGTGGAG
1 -AGATCTTATCTCCCTGAGATTACAGTGGAG
11182 TGGATTAAAA
Statistics
Matches: 644, Mismatches: 137, Indels: 150
0.69 0.15 0.16
Matches are distributed among these distances:
40 17 0.03
41 10 0.02
42 5 0.01
43 25 0.04
44 326 0.51
45 20 0.03
46 125 0.19
47 13 0.02
51 3 0.00
52 3 0.00
53 3 0.00
54 79 0.12
55 15 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
Found at i:10612 original size:88 final size:86
Alignment explanation
Indices: 10519--11230 Score: 422
Period size: 90 Copynumber: 7.7 Consensus size: 86
10509 CTCCCTAAGG
** *
10519 TTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAG
1 TTACAGTGGAGCAGATTGAA-AAAAAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAG
10584 CTAGTAATCCTATCTCTCTGA-A
65 CTAGTAATCCTATCTC-CTGAGA
* *
10606 GTTACAGTGGAGCGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCA
1 -TTACAGTGGAGCAGATTGAAAA-AAA-GATCTTATCTCTCTGAGA-TTACAG-CG-G-AG----
* *
10669 CATCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGA
55 --T-AGATTGAAGCTAGTA-ATCCTATCT-CCTGAGA
* ** * *
10705 TTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGA
1 TTACAGTGGAGCAGATTGAAAAA---AAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGA
*
10770 AGATAGTAATCCTATCTGCCTGAGA
63 AGCTAGTAATCCTATCT-CCTGAGA
** *
10795 TTACAGTGGAGTGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCAC
1 TTACAGTGGAGCAGATTGAAAA-AAA-GATCTTATCTCTCTGAGA-TTACAG-CG-G-AG-----
* *
10858 ATCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGA
55 -T-AGATTGAAGCTAGTA-ATCCTATCT-CCTGAGA
* ** * *
10893 TTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGA
1 TTACAGTGGAGCAGATTGAAAAA---AAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGA
*
10958 AGATAGTAATCCTATCTGCCTGAGA
63 AGCTAGTAATCCTATCT-CCTGAGA
** *
10983 TTACAGTGGAGTGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCAC
1 TTACAGTGGAGCAGATTGAAAA-AAA-GATCTTATCTCTCTGAGA-TTACAG-CG-G-AG-----
* *
11046 ATCAGATTGAAGCCAG-AGATCTTATCTCCCTGAGA
55 -T-AGATTGAAGCTAGTA-ATCCTATCT-CCTGAGA
* ** * *
11081 TTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGA
1 TTACAGTGGAGCAGATTGAAAAA---AAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGA
*
11146 AGATAGTAATCCTATCTGCCTGAGA
63 AGCTAGTAATCCTATCT-CCTGAGA
** **
11171 TTACAGTGGAGTGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 TTACAGTGGAGCAGATTGAAAA-AAA-GATCTTATCTCTCTGAGA-TTACAGCGGAGTAGAT
11231 CACAGCAGAC
Statistics
Matches: 484, Mismatches: 75, Indels: 130
0.70 0.11 0.19
Matches are distributed among these distances:
87 11 0.02
88 109 0.23
89 15 0.03
90 120 0.25
91 12 0.02
97 12 0.02
98 119 0.25
99 17 0.04
100 63 0.13
101 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (86 bp):
TTACAGTGGAGCAGATTGAAAAAAAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAGC
TAGTAATCCTATCTCCTGAGA
Found at i:10650 original size:218 final size:218
Alignment explanation
Indices: 10272--10674 Score: 745
Period size: 218 Copynumber: 1.8 Consensus size: 218
10262 AGACCAAAAA
*
10272 GAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 GAAGAATTTCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
*
10337 TTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCG
66 CTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCG
*
10402 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCAC
131 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCAC
10467 CCTAGGTTACAATGGAGTAGACC
196 CCTAGGTTACAATGGAGTAGACC
10490 GAAGAATTTCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 GAAGAATTTCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
*
10555 CTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGA-AGTTACAGTGGAGC
66 CTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGA-TTACAGTGGAGC
*
10619 GGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
130 GGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAG
10675 ATTGAAGCCA
Statistics
Matches: 179, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
217 1 0.01
218 178 0.99
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (218 bp):
GAAGAATTTCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
CTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCG
GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCAC
CCTAGGTTACAATGGAGTAGACC
Found at i:10815 original size:188 final size:188
Alignment explanation
Indices: 10544--11263 Score: 1329
Period size: 188 Copynumber: 3.8 Consensus size: 188
10534 TTGAAGCCAG
* *
10544 AGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCT-CTCTGA-AG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGC-CTGAGA-
*
10607 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
64 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
10672 CAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
129 CAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
10732 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
10797 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
66 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
10862 GATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
131 GATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
10920 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
10985 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
66 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
11050 GATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
131 GATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
11108 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
*
11173 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAGCA
66 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
** * *
11238 GA-CAAAACCACAGATCTTATCTCCCT
131 GATTGAAGCCAGAGATCTTATCTCCCT
11264 AAGCAGTTAG
Statistics
Matches: 522, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
187 20 0.04
188 500 0.96
189 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (188 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATT
ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
GATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTC
Found at i:11206 original size:44 final size:44
Alignment explanation
Indices: 11063--11230 Score: 119
Period size: 44 Copynumber: 3.8 Consensus size: 44
11053 TGAAGCCAGA
* ** ** *
11063 GATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAA-ATTT
1 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATA-GT
*
11107 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGT
1 --GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAGT
* * * * *
11153 AATCCTATCTGCCTGAGATTACAGTGGAGTGGATT-AAAATAAAG-
1 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAAT--AGT
* **
11197 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGTAGAT
11231 CACAGCAGAC
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
43 5 0.05
44 56 0.57
45 2 0.02
46 35 0.35
47 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAGT
Found at i:11710 original size:8 final size:8
Alignment explanation
Indices: 11699--11723 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11689 CACCTACCCC
11699 CCCACTTG
1 CCCACTTG
11707 CCCACTTG
1 CCCACTTG
11715 CCCACTTG
1 CCCACTTG
11723 C
1 C
11724 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:12223 original size:13 final size:12
Alignment explanation
Indices: 12187--12224 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
12177 CCTTTCCCCC
12187 TCCCTTCTCTC-
1 TCCCTTCTCTCT
12198 TCCCTTCTCTCT
1 TCCCTTCTCTCT
12210 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
12223 TC
1 TC
12225 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Done.