Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1204
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: 34992
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Found at i:209 original size:104 final size:104
Alignment explanation
Indices: 3--316 Score: 518
Period size: 101 Copynumber: 3.1 Consensus size: 104
1 TG
*
3 ATCCACCATATCTTTGAAATGTG--AAGGGGCTGCTATGTGCTGATT--CCCGA-GGGTTGCTAA
1 ATCCACCATATCTTTGAAATGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
63 GTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT
66 GTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGAT
103 ATCCACCATATCTTTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTA
1 ATCCACCATATCTTTGAAATGTGAAAA-GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTA
168 AGTGCTGATTCCCCGA-TCATTGGTGGTGCTAAGTGCGAT
65 AGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT
*
207 ATCCACCATATCTTTGAAA--TAAAAAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
1 ATCCACCATATCTTTGAAATGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* *
270 GTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAG
66 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT
309 ATCCACCA
1 ATCCACCA
317 ATAACGGTTA
Statistics
Matches: 203, Mismatches: 4, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
100 23 0.11
101 53 0.26
102 36 0.18
103 19 0.09
104 42 0.21
105 5 0.02
106 25 0.12
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (104 bp):
ATCCACCATATCTTTGAAATGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT
Found at i:273 original size:27 final size:27
Alignment explanation
Indices: 231--282 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
221 TGAAATAAAA
*
231 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
258 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
283 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:7620 original size:26 final size:26
Alignment explanation
Indices: 7585--7636 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
7575 AATGTGAAAG
*
7585 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
7611 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
7637 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:7647 original size:103 final size:102
Alignment explanation
Indices: 7507--7872 Score: 610
Period size: 103 Copynumber: 3.6 Consensus size: 102
7497 TGTATATAAA
** * * *
7507 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
7571 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
7610 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
7675 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAGGGGGTTGCTATGTGCTGATT-CCCCG
7713 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
7778 TGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
* *
7815 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCG-GATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
7873 ATAACGGTTA
Statistics
Matches: 252, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
101 8 0.03
102 77 0.31
103 166 0.66
104 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:7825 original size:26 final size:26
Alignment explanation
Indices: 7790--7841 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
7780 AAATAAAAAG
*
7790 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
7816 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
7842 TTCAGTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:13705 original size:50 final size:50
Alignment explanation
Indices: 13641--13835 Score: 241
Period size: 50 Copynumber: 3.9 Consensus size: 50
13631 TGATGTTAGG
* *
13641 GATATATGAAAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGCCTC
1 GATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTC
* * *
13691 GAGATATGATAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-C
1 GATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTC
* * * * *
13741 GATAGATGAGAGCCAGTATAAGACCAATGTATGAGACATGGCATCAGCCTC
1 GATATATGAGAGCTAGTGTAAGACC-ATGTCTGGGACATGGCATCAGCCTC
* *
13792 GATATACGAGAG-TCAGTGTAATACCATGTCTGGGACATGGCATC
1 GATATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATC
13836 GACTTTGATG
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
50 82 0.67
51 40 0.33
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (50 bp):
GATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTC
Found at i:19968 original size:17 final size:17
Alignment explanation
Indices: 19946--19978 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19936 CAATCTCTTT
19946 TTACATATAACATCATA
1 TTACATATAACATCATA
*
19963 TTACATATAAGATCAT
1 TTACATATAACATCAT
19979 CCATAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (17 bp):
TTACATATAACATCATA
Found at i:20516 original size:41 final size:41
Alignment explanation
Indices: 20358--20539 Score: 192
Period size: 40 Copynumber: 4.5 Consensus size: 41
20348 GGAGTATAAC
* * *
20358 CAGGGGCACGGAAGTGCAA--CCAGAGGTACCAAAGTACAAA
1 CAGGGGCACGTAAGTGCAATTCAAG-GGTACCGAAGTACAAA
* * * * * * *
20398 TAGGGGAACATAGGTGGAA-TCAAGAGTGCCGAAGTACAAA
1 CAGGGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAAA
*
20438 TAGGGGCACGTAAGTGCAATT-AAGGGTACCGAAGTACAAA
1 CAGGGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAAA
* *
20478 CAGGGGCATGTAAGTGCAATTCAAGGGTACCGAAGTACAAT
1 CAGGGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAAA
* *
20519 CAGAGGCACGCAAGTGCAATT
1 CAGGGGCACGTAAGTGCAATT
20540 TAGGTATAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
40 77 0.66
41 40 0.34
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (41 bp):
CAGGGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAAA
Found at i:20535 original size:81 final size:80
Alignment explanation
Indices: 20382--20539 Score: 192
Period size: 81 Copynumber: 2.0 Consensus size: 80
20372 TGCAACCAGA
* * * * *
20382 GGTACCAAAGTACAAATAGGGGAACATAGGTGGAATCAAGAGTGCCGAAGTACAAATAGGGGCAC
1 GGTACCAAAGTACAAACAGGGGAACATAAGTGCAATCAAGAGTACCGAAGTACAAATAGAGGCAC
*
20447 GTAAGTGCAATTAAG
66 GCAAGTGCAATTAAG
* * ** *
20462 GGTACCGAAGTACAAACAGGGGCATGTAAGTGCAATTCAAGGGTACCGAAGTAC-AATCAGAGGC
1 GGTACCAAAGTACAAACAGGGGAACATAAGTGCAA-TCAAGAGTACCGAAGTACAAAT-AGAGGC
20526 ACGCAAGTGCAATT
64 ACGCAAGTGCAATT
20540 TAGGTATAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 31 0.48
81 34 0.52
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.16
Consensus pattern (80 bp):
GGTACCAAAGTACAAACAGGGGAACATAAGTGCAATCAAGAGTACCGAAGTACAAATAGAGGCAC
GCAAGTGCAATTAAG
Found at i:25216 original size:40 final size:40
Alignment explanation
Indices: 25156--25339 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
25146 TATTCGAATG
*
25156 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
25196 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
25236 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
25276 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* *
25316 ATATCCGAGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
25340 CTTGTGCGAG
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 121 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:25289 original size:80 final size:80
Alignment explanation
Indices: 25156--25339 Score: 255
Period size: 80 Copynumber: 2.3 Consensus size: 80
25146 TATTCGAATG
* * *
25156 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
25220 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
25236 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
25301 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
*
25316 ATATCCGAGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
25340 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 90 0.97
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:33559 original size:39 final size:38
Alignment explanation
Indices: 33455--33660 Score: 206
Period size: 39 Copynumber: 5.3 Consensus size: 38
33445 TTATTCGATG
*
33455 ATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGTG--
1 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCTAGTGCT
* *
33491 ACTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCT
1 A-TATCCGGGCTAAGA-CCGAAGGCATTTGTGCTAG-TGCT
*
33532 ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAGTG-CT
* * * *
33571 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTACC
1 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCTAGTGCT
* * *
33610 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCTAGT-GCT
33649 ATATCC-GGCTAA
1 ATATCCGGGCTAA
33661 ATCCCGAAGA
Statistics
Matches: 142, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.01
37 20 0.14
38 24 0.17
39 65 0.46
40 31 0.22
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAGTGCT
Done.