Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2580
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: 17515
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:514 original size:1 final size:1
Alignment explanation
Indices: 508--532 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
498 GTTATTTGAC
508 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
533 CCGGGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3282 original size:16 final size:16
Alignment explanation
Indices: 3261--3292 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3251 TAAGGCCTTG
3261 CCATTCACTCTTGATT
1 CCATTCACTCTTGATT
3277 CCATTCACTCTTGATT
1 CCATTCACTCTTGATT
3293 ACGATAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (16 bp):
CCATTCACTCTTGATT
Found at i:4550 original size:19 final size:20
Alignment explanation
Indices: 4513--4551 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4503 TATCAATATA
*
4513 TTTTTATAATATTTTAAAAT
1 TTTTTATAATATTTAAAAAT
*
4533 TTTTTATTA-ATTTAAAAAT
1 TTTTTATAATATTTAAAAAT
4552 ACATATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTATAATATTTAAAAAT
Found at i:4594 original size:16 final size:17
Alignment explanation
Indices: 4567--4601 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4557 TTTACTTTTA
4567 TATTATAAAATAAAATT
1 TATTATAAAATAAAATT
*
4584 TATTA-AAAATAGAATT
1 TATTATAAAATAAAATT
4600 TA
1 TA
4602 ACTCGATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TATTATAAAATAAAATT
Found at i:5512 original size:2 final size:2
Alignment explanation
Indices: 5505--5562 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5495 TGACAAAATC
5505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5547 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
5563 AAAGAATCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8590 original size:155 final size:154
Alignment explanation
Indices: 8410--9460 Score: 856
Period size: 154 Copynumber: 6.8 Consensus size: 154
8400 ATAGTAATAC
* * *
8410 TAAAAGACAC-AAAATGA-ATAGAAAAAGGACAAACTTATCCTAAATGCACACCTTTGGCAT-GT
1 TAAAAGACACGAAAATGATATA-AAAAA-GATAAACCTATCCTAAATGTACACCTTTGGCATAG-
* * * *
8472 AAGCGACTCGATGACTATCTAGGACTTGATTCTAAG-AAAATTACGAAAGTGCCTTTAAGGTATA
63 AAGCGACTCGGTGACTACCTAAGACTTGATTCT-AGTAAAATTACGAAAATGCCTTTAA-GTATA
* * *
8536 CATTCAACT-TTAAAGTATCTCACTAACCT
126 CTTTCAA-TGTGAAAGTATCTCAGTAACCT
* *
8565 TAAAAGACACGAAAATGACATAAAAAAGATAAACCTATCCTAAATATACACCTTTGGCATAGAAG
1 TAAAAGACACGAAAATGATATAAAAAAGATAAACCTATCCTAAATGTACACCTTTGGCATAGAAG
* * * * * * * * *
8630 TGACT-TGTGACTGCCTAAAACCTT-ATTATAATAAAATTACAAAAATATCCTTCAAGTATACTT
66 CGACTCGGTGACTACCTAAGA-CTTGATTCTAGTAAAATTACGAAAAT-GCCTTTAAGTATACTT
* *
8693 TCGATGTGAAAGTATTTCAGTAACCT
129 TCAATGTGAAAGTATCTCAGTAACCT
* * * *
8719 TAAAGGACAC-AACAATGATATAAAAAATAAAAACCTATCCTAAATGTACAACTTTGGCATAGAA
1 TAAAAGACACGAA-AATGATATAAAAAAGATAAACCTATCCTAAATGTACACCTTTGGCATAGAA
* * * * * * *
8783 GCAAC-CTGGTGACTACTTAAGACTTGATTCTAGTAAAATTATGAAAATACCCTTGAGGTATATT
65 GCGACTC-GGTGACTACCTAAGACTTGATTCTAGTAAAATTACGAAAAT-GCCTTTAAGTATACT
* * *
8847 TTCAACGTGAAAATATC-CCGATAACCT
128 TTCAATGTGAAAGTATCTCAG-TAACCT
* * * * * *
8874 TAAAGGATACGAAAATGATAT-AAAAAGATGAACCTAGCATAAATGTACA-CTTTCGCATAGAAG
1 TAAAAGACACGAAAATGATATAAAAAAGATAAACCTATCCTAAATGTACACCTTTGGCATAGAAG
* *
8937 CGACTCGGTGACTACCTAAGA-TCTAATTCTAGTAAAATTACGAAAATGCCTTTGAAGTATACCT
66 CGACTCGGTGACTACCTAAGACT-TGATTCTAGTAAAATTACGAAAATGCCTTT-AAGTATACTT
* *
9001 TCGATGTGAAAGTATCTTAGTAACCT
129 TCAATGTGAAAGTATCTCAGTAACCT
* * * * * **
9027 TAAAAGACACGAAAATAATA-ATAAAAATATGAACCTATTCTAAATGTAC-CCTTTTCGTGTAGA
1 TAAAAGACACGAAAATGATATA-AAAAAGATAAACCTATCCTAAATGTACACC-TTTGGCATAGA
* * * * * * ** *
9090 AACGAC-CTGTTGACTACTTAAGA-TCTGATTCTAATAAAATTACAAAAATGCCATTGGGTATAT
64 AGCGACTC-GGTGACTACCTAAGACT-TGATTCTAGTAAAATTACGAAAATGCCTTTAAGTATAC
* * *
9153 TTTCAACGTGAAAGTAT-TCTGATAACCC
127 TTTCAATGTGAAAGTATCTCAG-TAACCT
* * * **
9181 TAAATGATATGCAAAA-GATATAAAAAAGACGAACCTAGT-CTAAATGTACACCTTTGGCATAGA
1 TAAAAGACACG-AAAATGATATAAAAAAGATAAACCTA-TCCTAAATGTACACCTTTGGCATAGA
* * * * * *
9244 AGCAACTCGGTGACTACCTAAGACCTAATTCTAGT-AAATTATGAAAATACC-CTAATGGTATAC
64 AGCGACTCGGTGACTACCTAAGACTTGATTCTAGTAAAATTACGAAAATGCCTTTAA--GTATA-
* * *
9307 CTTT-TACGTGAAAGTATCTCAATAACC-
126 CTTTCAATGTGAAAGTATCTCAGTAACCT
* * * *
9334 TAAAAGATACGAAAATGATA-ATAAAAAGATGAACCTATCCTAAATGTAAACTTTTGGCATAGAA
1 TAAAAGACACGAAAATGATATA-AAAAAGATAAACCTATCCTAAATGTACACCTTTGGCATAGAA
* * ** * * * * *
9398 GCGACCCGGTGACTACTTAAGACCCGGTTTTAGTAAAATTACAAAAATACCTTGAAGATATAC
65 GCGACTCGGTGACTACCTAAGACTTGATTCTAGTAAAATTACGAAAATGCCTTTAAG-TATAC
9461 CATCGACATA
Statistics
Matches: 722, Mismatches: 135, Indels: 80
0.77 0.14 0.09
Matches are distributed among these distances:
152 12 0.02
153 193 0.27
154 296 0.41
155 203 0.28
156 15 0.02
157 3 0.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (154 bp):
TAAAAGACACGAAAATGATATAAAAAAGATAAACCTATCCTAAATGTACACCTTTGGCATAGAAG
CGACTCGGTGACTACCTAAGACTTGATTCTAGTAAAATTACGAAAATGCCTTTAAGTATACTTTC
AATGTGAAAGTATCTCAGTAACCT
Found at i:9073 original size:308 final size:308
Alignment explanation
Indices: 8445--9452 Score: 1050
Period size: 308 Copynumber: 3.3 Consensus size: 308
8435 AGGACAAACT
* * * *
8445 TATCCTAAATGCAC-ACCTTTGGCAT-GTAAGCGA-CTCGATGACTA-TCTAGGACTTGATTCTA
1 TATCCTAAATGTACAACTTTTGGCATAG-AAGCGACCT-GGTGACTACT-TAAGACTTGATTCT-
* * * * * ** * * * *
8506 AG-AAAATTACGAAAGTGCCTTTAAGGTATACATTCAACTTTAAAGTATCTC-ACTAACCTTAAA
62 AGTAAAATTACAAAAATACCCTTGAGGTATATTTTCAACGTGAAAATATCCCGA-TAACCTTAAA
* * * * * *
8569 AGACACGAAAATGACATAAAAAAGATAAACCTATCCTAAATATACACCTTTGGCATAGAAGTGAC
126 AGATACGAAAATGATATAAAAAAGATGAACCTA-GCTAAATGTACACCTTTGGCATAGAAGCGAC
* * * * * * * *
8634 T-TGTGACTGCCTAAAACCTTATTATAATAAAATTACAAAAATATCCTTCAAGTATACTTTCGAT
190 TCGGTGACTACCTAAGACCTAATTCTAGTAAAATTACGAAAATA-CCTT-AAGTATACCTTCGAT
* **
8698 GTGAAAGTAT-TTCAGTAACCTTAAAGGACAC-AACAATGAT-ATAAAAAATAAAAACC
253 GTGAAAGTATCTT-AGTAACCTTAAAAGACACGAA-AATGATAAT-AAAAATATGAACC
*
8754 TATCCTAAATGTACAAC-TTTGGCATAGAAGCAACCTGGTGACTACTTAAGACTTGATTCTAGTA
1 TATCCTAAATGTACAACTTTTGGCATAGAAGCGACCTGGTGACTACTTAAGACTTGATTCTAGTA
** *
8818 AAATTATGAAAATACCCTTGAGGTATATTTTCAACGTGAAAATATCCCGATAACCTTAAAGGATA
66 AAATTACAAAAATACCCTTGAGGTATATTTTCAACGTGAAAATATCCCGATAACCTTAAAAGATA
*
8883 CGAAAATGATAT-AAAAAGATGAACCTAGCATAAATGTACA-CTTTCGCATAGAAGCGACTCGGT
131 CGAAAATGATATAAAAAAGATGAACCTAGC-TAAATGTACACCTTTGGCATAGAAGCGACTCGGT
* *
8946 GACTACCTAAGATCTAATTCTAGTAAAATTACGAAAATGCCTTTGAAGTATACCTTCGATGTGAA
195 GACTACCTAAGACCTAATTCTAGTAAAATTACGAAAATACC-TT-AAGTATACCTTCGATGTGAA
*
9011 AGTATCTTAGTAACCTTAAAAGACACGAAAATAATAATAAAAATATGAACC
258 AGTATCTTAGTAACCTTAAAAGACACGAAAATGATAATAAAAATATGAACC
* * * ** * * *
9062 TATTCTAAATGTAC-CCTTTTCGTGTAGAAACGACCTGTTGACTACTTAAGA-TCTGATTCTAAT
1 TATCCTAAATGTACAACTTTTGGCATAGAAGCGACCTGGTGACTACTTAAGACT-TGATTCTAGT
* * * * * * *
9125 AAAATTACAAAAATGCCATTG-GGTATATTTTCAACGTGAAAGTATTCTGATAACCCTAAATGAT
65 AAAATTACAAAAATACCCTTGAGGTATATTTTCAACGTGAAAATATCCCGATAACCTTAAAAGAT
* * *
9189 ATGCAAAA-GATATAAAAAAGACGAACCTAGTCTAAATGTACACCTTTGGCATAGAAGCAACTCG
130 ACG-AAAATGATATAAAAAAGATGAACCTAG-CTAAATGTACACCTTTGGCATAGAAGCGACTCG
* * ** *
9253 GTGACTACCTAAGACCTAATTCTAGT-AAATTATGAAAATACCCTAATGGTATACCTTTTACGTG
193 GTGACTACCTAAGACCTAATTCTAGTAAAATTACGAAAATACCTTAA--GTATACCTTCGATGTG
* * * *
9317 AAAGTATCTCAATAACC-TAAAAGATACGAAAATGATAATAAAAAGATGAACC
256 AAAGTATCTTAGTAACCTTAAAAGACACGAAAATGATAATAAAAATATGAACC
* ** * *
9369 TATCCTAAATGTA-AACTTTTGGCATAGAAGCGACCCGGTGACTACTTAAGACCCGGTTTTAGTA
1 TATCCTAAATGTACAACTTTTGGCATAGAAGCGACCTGGTGACTACTTAAGACTTGATTCTAGTA
9433 AAATTACAAAAATA-CCTTGA
66 AAATTACAAAAATACCCTTGA
9453 AGATATACCA
Statistics
Matches: 589, Mismatches: 87, Indels: 48
0.81 0.12 0.07
Matches are distributed among these distances:
306 6 0.01
307 162 0.28
308 255 0.43
309 159 0.27
310 7 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (308 bp):
TATCCTAAATGTACAACTTTTGGCATAGAAGCGACCTGGTGACTACTTAAGACTTGATTCTAGTA
AAATTACAAAAATACCCTTGAGGTATATTTTCAACGTGAAAATATCCCGATAACCTTAAAAGATA
CGAAAATGATATAAAAAAGATGAACCTAGCTAAATGTACACCTTTGGCATAGAAGCGACTCGGTG
ACTACCTAAGACCTAATTCTAGTAAAATTACGAAAATACCTTAAGTATACCTTCGATGTGAAAGT
ATCTTAGTAACCTTAAAAGACACGAAAATGATAATAAAAATATGAACC
Found at i:9396 original size:462 final size:460
Alignment explanation
Indices: 8410--9480 Score: 1149
Period size: 462 Copynumber: 2.3 Consensus size: 460
8400 ATAGTAATAC
* * ** * *
8410 TAAAAGACAC-AAAATGAATAGAAAAAGGACAAACTTATCCTAAATGCACACCTTTGGCAT-GTA
1 TAAAAGATACGAAAATG-ATATAAAAA-GATGAACCTATCCTAAATGTACA-CTTTGGCATAG-A
* * * *
8473 AGCGACTCGATGACTATCTAGGACTTGATTCTAAG-AAAATTACGAAAGTGCCTTT-AAGGTATA
62 AGCGACTCGGTGACTACCTAAGAC-TGATTCT-AGTAAAATTACGAAAATGCCTTTGAA-GTATA
* * *
8536 CATTCAACTTTAAAGTATCTCACTAACCTTAAAAGACACGAAAATGACATAAAAAAGATAAACCT
124 CCTTCGACTTGAAAGTATCTCACTAACCTTAAAAGACACGAAAATGACATAAAAAAGATAAACCT
* ** * * *
8601 ATCCTAAATATACACCTTTGGCATAGAAGTGACTTGTGACTGCCTAAAACCTTATTATAATAAAA
189 ATCCTAAATATACACCTTTCGCATAGAAACGACCTGTGACTACCTAAAACCTGATTATAATAAAA
* * * *
8666 TTACAAAAATATCCTTCAAGTATACTTTCGATGTGAAAGTATTTCAGTAACCTTAAAGGACACAA
254 TTACAAAAATAGCCTTCAAGTATACTTTCAACGTGAAAGTATTTCAGTAACCCTAAAGGACACAA
*
8731 CAATGATATAAAAAATAAAAACCTATCCTAAATGTACAACTTTGGCATAGAAGCAACCTGGTGAC
319 CAATGATATAAAAAAGAAAAACCTATCCTAAATGTACAACTTTGGCATAGAAGCAACCTGGTGAC
* * * *
8796 TACTTAAGACTTGATTCTAGTAAAATTATGAAAATACCCTTGAGGTATATTTTCAACGTGAAAAT
384 TACCTAAGACCTAATTCTAGTAAAATTATGAAAATACCCTTAAGGTATATTTT-AACGTGAAAAT
*
8861 ATCCCGATAACCT
448 ATCCCAATAACCT
* * * *
8874 TAAAGGATACGAAAATGATATAAAAAGATGAACCTAGCATAAATGTACACTTTCGCATAGAAGCG
1 TAAAAGATACGAAAATGATATAAAAAGATGAACCTATCCTAAATGTACACTTTGGCATAGAAGCG
*
8939 ACTCGGTGACTACCTAAGATCTAATTCTAGTAAAATTACGAAAATGCCTTTGAAGTATACCTTCG
66 ACTCGGTGACTACCTAAGA-CTGATTCTAGTAAAATTACGAAAATGCCTTTGAAGTATACCTTCG
* *
9004 A-TGTGAAAGTATCTTAGTAACCTTAAAAGACACGAAAAT-A-ATAATAAAA-ATATGAACCTAT
130 ACT-TGAAAGTATCTCACTAACCTTAAAAGACACGAAAATGACATAA-AAAAGATA--AACCTAT
* * ** * * * *
9065 TCTAAATGTAC-CCTTTTCGTGTAGAAACGACCTGTTGACTACTTAAGATCTGATTCTAATAAAA
191 CCTAAATATACACC-TTTCGCATAGAAACGACCTG-TGACTACCTAAAACCTGATTATAATAAAA
** * * * *
9129 TTACAAAAAT-GCCATT-GGGTATATTTTCAACGTGAAAGTA-TTCTGATAACCCTAAATGATAT
254 TTACAAAAATAGCC-TTCAAGTATACTTTCAACGTGAAAGTATTTCAG-TAACCCTAAAGGACA-
** *
9191 GCAA-AA-GATATAAAAAAGACGAACCTAGT-CTAAATGTACACCTTTGGCATAGAAGCAA-CTC
316 -CAACAATGATATAAAAAAGAAAAACCTA-TCCTAAATGTACAACTTTGGCATAGAAGCAACCT-
9252 GGTGACTACCTAAGACCTAATTCTAGT-AAATTATGAAAATACCC-TAATGGTATACCTTTT-AC
378 GGTGACTACCTAAGACCTAATTCTAGTAAAATTATGAAAATACCCTTAA-GGTATA--TTTTAAC
* *
9314 GTGAAAGTATCTCAATAACC-
440 GTGAAAATATCCCAATAACCT
*
9334 TAAAAGATACGAAAATGATAATAAAAAGATGAACCTATCCTAAATGTAAACTTTTGGCATAGAAG
1 TAAAAGATACGAAAATGAT-ATAAAAAGATGAACCTATCCTAAATGTACAC-TTTGGCATAGAAG
* * * * * * * *
9399 CGACCCGGTGACTACTTAAGACCCGGTTTTAGTAAAATTACAAAAATACC-TTGAAGATATACCA
64 CGACTCGGTGACTACCTAAGA-CTGATTCTAGTAAAATTACGAAAATGCCTTTGAAG-TATACCT
* *
9463 TCGACATAAAAGTATCTC
127 TCGACTTGAAAGTATCTC
9481 CGTAATCCTA
Statistics
Matches: 510, Mismatches: 73, Indels: 50
0.81 0.12 0.08
Matches are distributed among these distances:
460 27 0.05
461 92 0.18
462 303 0.59
463 63 0.12
464 19 0.04
465 6 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (460 bp):
TAAAAGATACGAAAATGATATAAAAAGATGAACCTATCCTAAATGTACACTTTGGCATAGAAGCG
ACTCGGTGACTACCTAAGACTGATTCTAGTAAAATTACGAAAATGCCTTTGAAGTATACCTTCGA
CTTGAAAGTATCTCACTAACCTTAAAAGACACGAAAATGACATAAAAAAGATAAACCTATCCTAA
ATATACACCTTTCGCATAGAAACGACCTGTGACTACCTAAAACCTGATTATAATAAAATTACAAA
AATAGCCTTCAAGTATACTTTCAACGTGAAAGTATTTCAGTAACCCTAAAGGACACAACAATGAT
ATAAAAAAGAAAAACCTATCCTAAATGTACAACTTTGGCATAGAAGCAACCTGGTGACTACCTAA
GACCTAATTCTAGTAAAATTATGAAAATACCCTTAAGGTATATTTTAACGTGAAAATATCCCAAT
AACCT
Found at i:11861 original size:23 final size:24
Alignment explanation
Indices: 11810--11864 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
11800 ATGAAACTAG
11810 TTAAAA-TATAAAATACAATAAAA
1 TTAAAATTATAAAATACAATAAAA
* *
11833 TAAAAATTCTAAAATA-AA-AAATA
1 TTAAAATTATAAAATACAATAAA-A
11856 TTAAAATTA
1 TTAAAATTA
11865 AAATTAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAATTATAAAATACAATAAAA
Found at i:13889 original size:13 final size:13
Alignment explanation
Indices: 13871--13895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13861 ATGTTGCACA
13871 GTATCGATACATT
1 GTATCGATACATT
13884 GTATCGATACAT
1 GTATCGATACAT
13896 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:13908 original size:20 final size:21
Alignment explanation
Indices: 13883--13935 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
13873 ATCGATACAT
**
13883 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
13903 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
13924 TGTATCGATACA
1 TGTATCGATACA
13936 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Done.