Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold67
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: 428520
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:407222 original size:79 final size:79
Alignment explanation
Indices: 406981--407239 Score: 331
Period size: 79 Copynumber: 3.3 Consensus size: 79
406971 TAAAGCTTCG
* * *
406981 ATTTTCCACAATCGGGGATACTCCAACCCCT-TTATTTTCGAGGGGATACTACAACCCCGATTTT
1 ATTTTCCATAATCAGGGATACTCCAA-CCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTT
* *
407045 ATTTTTAAAACGTCG
65 ATTTTCAAAACGTCA
*** * *
407060 ATTTTTTGTAATCAAGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTCCATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
* *
407125 TTTTCAAAATGTCT
66 TTTTCAAAACGTCA
* *
407139 ATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCTGATTTTA
1 ATTTTCCATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
* **
407204 TTTTCAGAACACCA
66 TTTTCAAAACGTCA
**
407218 ATTTTCCATAATTGGGGATACT
1 ATTTTCCATAATCAGGGATACT
407240 TTAGCCCCGT
Statistics
Matches: 155, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
78 3 0.02
79 152 0.98
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (79 bp):
ATTTTCCATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
TTTTCAAAACGTCA
Found at i:416900 original size:92 final size:91
Alignment explanation
Indices: 416449--416889 Score: 498
Period size: 92 Copynumber: 4.8 Consensus size: 91
416439 GATTATAAAG
* * * * * *
416449 GTGCCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATGA-AGATGCCTGCCAGTATG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTTAAAGATGAGA-AAG-GTGCCAATATG
*
416513 CT-AGTTTAAGGCCAACGATATTGGGCTT
64 CTGA-TTCAAGGCCAACGATATTGGGCTT
* * *
416541 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAAATGAGAAAGGTGCCAATATGC
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTT-AAAGATGAGAAAGGTGCCAATATGC
* * *
416606 TGATTTAAGGCTACCGATATTGGGCTT
65 TGATTCAAGGCCAACGATATTGGGCTT
* * * * *
416633 ATGCCAATGTGCTAATTCAAAGCCAACGACATTGGTCC-TAAAGAT--GAAA-CTGCCAATATGC
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG-CCTTAAAGATGAGAAAGGTGCCAATATGC
* * *
416694 TGATTCAAGGCCAGCGATATATTAGGCAT
65 TGATTCAAGGCCAACG--ATATTGGGCTT
* * * *
416723 GTGCCAATGTGTTGATTCAAGGCCAGTGACATTGGCCTTAAAGATGAAAAAGGTGCCAATATACT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTTAAAGATGAGAAAGGTGCCAATATGCT
* *
416788 AATTCAGGGCCAACGATATTGGGCTT
66 GATTCAAGGCCAACGATATTGGGCTT
* * *
416814 GTGCTAATATGCTGATTCAAGGCCAGTGACATTGGCCTTCAAAGATGAGAAAGGTGCCAATATGC
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTT-AAAGATGAGAAAGGTGCCAATATGC
416879 TGATTCAAGGC
65 TGATTCAAGGC
416890 TAGCAATATT
Statistics
Matches: 297, Mismatches: 41, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
88 24 0.08
89 6 0.02
90 45 0.15
91 50 0.17
92 137 0.46
93 34 0.11
94 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (91 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTTAAAGATGAGAAAGGTGCCAATATGCT
GATTCAAGGCCAACGATATTGGGCTT
Found at i:417103 original size:27 final size:27
Alignment explanation
Indices: 417072--417125 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
417062 AAGAAAAATA
*
417072 TGCCACAGAGTTGTGGGCTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
417099 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGG
417126 AAAAAAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (27 bp):
TGCCACAGAGTTGTGGACTTAAAAGGG
Found at i:417203 original size:34 final size:34
Alignment explanation
Indices: 417164--417228 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
417154 TGGAAAAAAT
* *
417164 GTGCCATAAAGTTGTGGGCTTTGAAAAGAGAAAG
1 GTGCCATAAAGTTGTGGACTTAGAAAAGAGAAAG
**
417198 GTGCCATGGAGTTGTGGACTTAGAAAAGAGA
1 GTGCCATAAAGTTGTGGACTTAGAAAAGAGA
417229 TGCCACTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (34 bp):
GTGCCATAAAGTTGTGGACTTAGAAAAGAGAAAG
Found at i:417233 original size:30 final size:30
Alignment explanation
Indices: 417206--417404 Score: 177
Period size: 30 Copynumber: 6.3 Consensus size: 30
417196 AGGTGCCATG
*
417206 GAGTTGTGGACTTAGAAAAGAGATGCCACT
1 GAGTCGTGGACTTAGAAAAGAGATGCCACT
* *
417236 GAGTCATGGACTTTGAAAAGAGATGCCACT
1 GAGTCGTGGACTTAGAAAAGAGATGCCACT
* * * *
417266 GAGTCGTGGACTTTGGGAAAGAAATGCCATT
1 GAGTCGTGGAC-TTAGAAAAGAGATGCCACT
*
417297 GAGTCGTGGACTTGGAAGAAAAAAGATGCCACT
1 GAGTCGTGGACTT---AGAAAAGAGATGCCACT
*
417330 GAGTTGTGGACTTGGAAGTAAAAGGAGGATGCCACT
1 GAGTCGTGGACTT---AG-AAAA-GA-GATGCCACT
* *
417366 GAGTAGTGGACTTTTAGAAAAG-G-TGCCACG
1 GAGTCGTGGAC--TTAGAAAAGAGATGCCACT
417396 GAGTCGTGG
1 GAGTCGTGG
417405 GCTTTTAGAA
Statistics
Matches: 142, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
30 53 0.37
31 27 0.19
33 30 0.21
34 8 0.06
35 3 0.02
36 19 0.13
38 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.23
Consensus pattern (30 bp):
GAGTCGTGGACTTAGAAAAGAGATGCCACT
Found at i:417250 original size:64 final size:63
Alignment explanation
Indices: 417182--417379 Score: 176
Period size: 61 Copynumber: 3.1 Consensus size: 63
417172 AAGTTGTGGG
417182 CTTTGAAAAGAGAAAGGTGCCA-TGGAGTTGTGGACTTAGAAAAGAGATGCCACTGAGTCATGGA
1 CTTTGAAAAGAGAAA-GTGCCACT-GAGTTGTGGACTTAGAAAAGAGATGCCACTGAGTCATGGA
* * * * * *
417246 CTTTGAAAAGAG--A-TGCCACTGAGTCGTGGACTTTGGGAAAGAAATGCCATTGAGTCGTGGA
1 CTTTGAAAAGAGAAAGTGCCACTGAGTTGTGGAC-TTAGAAAAGAGATGCCACTGAGTCATGGA
*
417307 CTTGGAAGAA-A-AAAGATGCCACTGAGTTGTGGACTTGGAAGTAAAAGGAGGATGCCACTGAGT
1 CTTTGAA-AAGAGAAAG-TGCCACTGAGTTGTGGACTT---AG-AAAA-GA-GATGCCACTGAGT
417370 -AGTGGA
58 CA-TGGA
417376 CTTT
1 CTTT
417380 TAGAAAAGGT
Statistics
Matches: 106, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
60 15 0.14
61 32 0.30
62 4 0.04
63 2 0.02
64 29 0.27
66 1 0.01
67 3 0.03
68 2 0.02
69 18 0.17
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.23
Consensus pattern (63 bp):
CTTTGAAAAGAGAAAGTGCCACTGAGTTGTGGACTTAGAAAAGAGATGCCACTGAGTCATGGA
Found at i:418069 original size:29 final size:29
Alignment explanation
Indices: 418010--418096 Score: 120
Period size: 29 Copynumber: 2.9 Consensus size: 29
418000 AAAGGGCTTG
* * *
418010 TTTGGCAATAAAGATGACATGGTTTGATTTA
1 TTTGACAAGAAAGATGA-A-GGTTTGTTTTA
418041 TTTGACAAGAAAGATGAAGGTTTGTTTTA
1 TTTGACAAGAAAGATGAAGGTTTGTTTTA
*
418070 TTTGACAAGAAAGATGATGGTTTGTTT
1 TTTGACAAGAAAGATGAAGGTTTGTTT
418097 CCAACAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 36 0.69
30 1 0.02
31 15 0.29
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (29 bp):
TTTGACAAGAAAGATGAAGGTTTGTTTTA
Found at i:418342 original size:17 final size:17
Alignment explanation
Indices: 418320--418357 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
418310 AGTTAAAAGG
418320 TTTTGTTTTGTTGTT-TT
1 TTTTGTTTT-TTGTTATT
418337 TTTTGTTTTTTGTTATT
1 TTTTGTTTTTTGTTATT
418354 TTTT
1 TTTT
418358 TTATGTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (17 bp):
TTTTGTTTTTTGTTATT
Found at i:425769 original size:21 final size:19
Alignment explanation
Indices: 425722--425776 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
425712 GCAGGACAGC
425722 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
425741 TATGTATCGATACATTTACT
1 TTTGTATCGATACA-ACACT
425761 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
425777 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:427055 original size:164 final size:161
Alignment explanation
Indices: 426811--427113 Score: 414
Period size: 164 Copynumber: 1.9 Consensus size: 161
426801 GGGACACCTT
* * *
426811 TTTTTGCCCTTTGTCCTCAAGAAGCAGGACACATTCCTTTTTTCCTTTTTCTTTTGTCCTTAAGG
1 TTTTTGCCCTTTATCCTCAAGAAGCAGGACACATTCCTTTTTTCCTTTTTCCTTTGTCCTCAAGG
* * *
426876 AGCAGGACGCATTTCATTTCATT-TTTTGGCCTTTGTCCTCAAAGAGTAGGACGCACT-TCTTTT
66 AGCAGGACCCATTTCA-TT-ATTCTTTT-CCCTTTATCCTCAAAGAGTAGGACGCACTCT-TTTT
426939 CCTTTTGTCCTCAAGGAGCAAGATGTGCTTTATCTC
127 CC-TTTGTCCTCAAGGAGCAAGATGTGCTTTATCTC
* *
426975 TTTTT-CCCTTTTATCCTCAAGGAGTAGGACACATTCCTTTTTTCCTTTTTCCTTTGTCCTCAAG
1 TTTTTGCCC-TTTATCCTCAAGAAGCAGGACACATTCCTTTTTTCCTTTTTCCTTTGTCCTCAAG
* * * *
427039 GAGCATGACCCATTTCATTATTCTTTTCCCTTTATCCTTAAAGAGTAGGATGTACTCTTTTTCCT
65 GAGCAGGACCCATTTCATTATTCTTTTCCCTTTATCCTCAAAGAGTAGGACGCACTCTTTTTCCT
*
427104 TTGTCTTCAA
130 TTGTCCTCAA
427114 AGAGTAGGAC
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
161 10 0.08
162 33 0.27
163 10 0.08
164 70 0.57
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (161 bp):
TTTTTGCCCTTTATCCTCAAGAAGCAGGACACATTCCTTTTTTCCTTTTTCCTTTGTCCTCAAGG
AGCAGGACCCATTTCATTATTCTTTTCCCTTTATCCTCAAAGAGTAGGACGCACTCTTTTTCCTT
TGTCCTCAAGGAGCAAGATGTGCTTTATCTC
Found at i:427105 original size:34 final size:35
Alignment explanation
Indices: 427060--427189 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 35
427050 ATTTCATTAT
* **
427060 TCTTTTCCCTTTATCCTTAAAGAGTAGG-ATGTAC
1 TCTTTTTCCTTTATCCTTAAAGAGTAGGAACCTAC
*
427094 TCTTTTTCCTTTGT-CTTCAAAGAGTAGGACACCTAC
1 TCTTTTTCCTTTATCCTT-AAAGAGTAGGA-ACCTAC
* * * *
427130 TCCTTTTT-CTTTGTCCTCAAAGAGCAGGACACCCAC
1 T-CTTTTTCCTTTATCCTTAAAGAGTAGGA-ACCTAC
*
427166 TCTTTTTCCTTTATCCTGAAAGAG
1 TCTTTTTCCTTTATCCTTAAAGAG
427190 CAAAATGCCT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
33 3 0.04
34 22 0.27
35 6 0.07
36 42 0.52
37 8 0.10
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (35 bp):
TCTTTTTCCTTTATCCTTAAAGAGTAGGAACCTAC
Found at i:427142 original size:36 final size:35
Alignment explanation
Indices: 427091--427191 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 35
427081 GAGTAGGATG
* *
427091 TACTCTTTTTCCTTTGTCTTCAAAGAGTAGGACACC
1 TACTCTTTTT-CTTTGTCCTCAAAGAGCAGGACACC
427127 TACTCCTTTTTCTTTGTCCTCAAAGAGCAGGACACC
1 TACT-CTTTTTCTTTGTCCTCAAAGAGCAGGACACC
* * *
427163 CACTCTTTTTCCTTTATCCTGAAAGAGCA
1 TACTCTTTTT-CTTTGTCCTCAAAGAGCA
427192 AAATGCCTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 6 0.10
36 46 0.79
37 6 0.10
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (35 bp):
TACTCTTTTTCTTTGTCCTCAAAGAGCAGGACACC
Found at i:427209 original size:36 final size:36
Alignment explanation
Indices: 427091--427212 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 36
427081 GAGTAGGATG
* * * * **
427091 TACTCTTTTTCCTTTGTCTTCAAAGAGTAGGACACC
1 TACTCCTTTTCCTTTATCCTCAAAGAGCAAAACACC
* * **
427127 TACTCCTTTTTCTTTGTCCTCAAAGAGCAGGACACC
1 TACTCCTTTTCCTTTATCCTCAAAGAGCAAAACACC
* * * **
427163 CACTCTTTTTCCTTTATCCTGAAAGAGCAAAATGCC
1 TACTCCTTTTCCTTTATCCTCAAAGAGCAAAACACC
427199 TACTCCTTTTCCTT
1 TACTCCTTTTCCTT
427213 CCTCTTTTCT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (36 bp):
TACTCCTTTTCCTTTATCCTCAAAGAGCAAAACACC
Found at i:427295 original size:31 final size:31
Alignment explanation
Indices: 427223--427320 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 31
427213 CCTCTTTTCT
* *
427223 AAGCCCACACAAGCTGGTGGCACCTAAGTCTAA
1 AAGCCCACACAAGCTAGTGACACCTAAGTC--A
* * *
427256 GTGTAAGCCCGCACGAGTTAGTGACACCTAAGTCA
1 ----AAGCCCACACAAGCTAGTGACACCTAAGTCA
* *
427291 AAGCCCACACAAGCTATTGGCACCTAAGTC
1 AAGCCCACACAAGCTAGTGACACCTAAGTC
427321 TGAGTCAAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
31 25 0.49
35 1 0.02
37 25 0.49
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (31 bp):
AAGCCCACACAAGCTAGTGACACCTAAGTCA
Found at i:427337 original size:37 final size:37
Alignment explanation
Indices: 427286--427358 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
427276 GTGACACCTA
**
427286 AGTCAAAGCCCACACAAGCTATTGGCACCTAAGTCTG
1 AGTCAAAGCCCACACAAGCTAGGGGCACCTAAGTCTG
* *
427323 AGTCAAAGCGCACACAAGCTGGGGGCACCTAAGTCT
1 AGTCAAAGCCCACACAAGCTAGGGGCACCTAAGTCT
427359 AAATCTAGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (37 bp):
AGTCAAAGCCCACACAAGCTAGGGGCACCTAAGTCTG
Found at i:427352 original size:68 final size:68
Alignment explanation
Indices: 427223--427357 Score: 162
Period size: 68 Copynumber: 2.0 Consensus size: 68
427213 CCTCTTTTCT
* ** * * * *
427223 AAGCCCACACAAGCTGGTGGCACCTAAGTCTAAGTGTAAGCCCGCACGAGTTAGTGACACCTAAG
1 AAGCCCACACAAGCTAGTGGCACCTAAGTCTAAGTCAAAGCCCACACAAGCTAGGGACACCTAAG
427288 TCA
66 TCA
* * * * *
427291 AAGCCCACACAAGCTATTGGCACCTAAGTCTGAGTCAAAGCGCACACAAGCTGGGGGCACCTAAG
1 AAGCCCACACAAGCTAGTGGCACCTAAGTCTAAGTCAAAGCCCACACAAGCTAGGGACACCTAAG
427356 TC
66 TC
427358 TAAATCTAGC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (68 bp):
AAGCCCACACAAGCTAGTGGCACCTAAGTCTAAGTCAAAGCCCACACAAGCTAGGGACACCTAAG
TCA
Done.