Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_720
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: 49355
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1531 original size:40 final size:40
Alignment explanation
Indices: 1433--1695 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
1423 TCCTCGTTCA
* * * * *
1433 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
1472 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1512 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1552 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
1592 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
1632 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
1672 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1696 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:1704 original size:41 final size:41
Alignment explanation
Indices: 1627--1704 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1617 TTAGTATCTC
* * *
1627 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1668 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1705 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:13718 original size:40 final size:40
Alignment explanation
Indices: 13663--13848 Score: 277
Period size: 40 Copynumber: 4.7 Consensus size: 40
13653 TTGAATGATG
* * *
13663 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
13703 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
13743 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
13783 TCCGGGTGAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
13824 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
13849 AATGAGTAGC
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 126 0.93
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17771 original size:46 final size:46
Alignment explanation
Indices: 17721--17896 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
17711 TGGTTGAGCA
17721 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
17767 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
*
17812 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
17860 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17897 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
42 6 0.05
43 5 0.05
45 3 0.03
46 59 0.53
47 26 0.23
48 2 0.02
50 4 0.04
51 6 0.05
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:17877 original size:93 final size:93
Alignment explanation
Indices: 17718--17887 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
17708 GGATGGTTGA
*
17718 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
17783 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
*
17811 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGAG
17875 TTGAGTCCGAGTT
65 TTGAGTCCGAGTT
17888 CGCTTATGGG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:25186 original size:46 final size:46
Alignment explanation
Indices: 25136--25307 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
25126 TGAGAATCCA
25136 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
25182 AACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGGCATCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G--TCCG
* *
25229 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG-CTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-CG
* *
25275 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25308 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
42 6 0.06
43 5 0.05
45 3 0.03
46 53 0.51
47 24 0.23
48 2 0.02
50 4 0.04
51 6 0.06
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:40149 original size:20 final size:20
Alignment explanation
Indices: 40103--40149 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40093 GTAAGCTCGG
40103 TTGAGCTCAAATGAGATGAA
1 TTGAGCTCAAATGAGATGAA
*** *
40123 ACAAGCTCAAATGAGCTGAA
1 TTGAGCTCAAATGAGATGAA
40143 TTGAGCT
1 TTGAGCT
40150 GGATAGAGCT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (20 bp):
TTGAGCTCAAATGAGATGAA
Found at i:42907 original size:5 final size:5
Alignment explanation
Indices: 42893--42991 Score: 51
Period size: 5 Copynumber: 19.2 Consensus size: 5
42883 TATATAAAAC
* * * * * *
42893 AATAT AATAT CATAT AACAT AATAA AATTT AAT-T ACATAT AATTT AAAAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT
* *
42943 AAATGAT AATA- AATAT AATAT GATGGAT AATAT AAAAAT AATAT -ATAT
1 -AAT-AT AATAT AATAT AATAT AAT--AT AATAT -AATAT AATAT AATAT
42991 A
1 A
42992 TGTCATTTTA
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
4 10 0.14
5 43 0.61
6 11 0.16
7 6 0.09
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:44623 original size:86 final size:85
Alignment explanation
Indices: 44467--44672 Score: 317
Period size: 86 Copynumber: 2.4 Consensus size: 85
44457 CTTTGATCGG
* * * *
44467 CTCTCCGTCAAACACAAAGATACCAAATCATCTTGATTTGCTTCACGTAAACAGTGAAAGCTAAA
1 CTCTCCGTCGAACATAGAGATGCCAAATCATCTTGATTTGCTTCACGTAAACAGTGAAAGCTAAA
44532 TCAGCTATGTCTTCGATCTA
66 TCAGCTATGTCTTCGATCTA
44552 CTCTCCGTCGAACATAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTG-AAG-T
1 CTCTCCGTCGAACATAGAGATGCCAAATCATCTT-GATTTGCTTC-ACGTAAACA-GTGAAAGCT
*
44615 AAATCAGCTATGTCTTCGATCTG
63 AAATCAGCTATGTCTTCGATCTA
*
44638 CTCTCCGTCGAACATAGAGATGTCAAATCATCTTG
1 CTCTCCGTCGAACATAGAGATGCCAAATCATCTTG
44673 GATGTGCCTC
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
85 31 0.28
86 66 0.59
87 12 0.11
88 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (85 bp):
CTCTCCGTCGAACATAGAGATGCCAAATCATCTTGATTTGCTTCACGTAAACAGTGAAAGCTAAA
TCAGCTATGTCTTCGATCTA
Found at i:44788 original size:45 final size:43
Alignment explanation
Indices: 44735--45045 Score: 195
Period size: 44 Copynumber: 7.3 Consensus size: 43
44725 GAATATAGAA
*
44735 AGAT-AGATCTGTCATCTTGGGATCTACTCTCCATCCATTAAGAG
1 AGATAAGATCTGTCATCTT-GGATCTACTC-CCGTCCATTAAGAG
* *
44779 AGATAAGATCTGT-ATCTTGGATTTACTCCCCGT-CATTACGGGAG
1 AGATAAGATCTGTCATCTTGGATCTACT-CCCGTCCATTA--AGAG
*
44823 AGATAAG-TCTGTCATCTTGGATCTACTCCTCGTCCATTTCAGAG
1 AGATAAGATCTGTCATCTTGGATCTACTCC-CGTCCA-TTAAGAG
* *
44867 AGATAAGATCTGTCATCTTGGATCTGC-CCCTGTCC-TTCAGAG
1 AGATAAGATCTGTCATCTTGGATCTACTCCC-GTCCATTAAGAG
* * *
44909 AGATAA-ATCCG-CATCTTGAATCTGC-CCCG---A-T--GA-
1 AGATAAGATCTGTCATCTTGGATCTACTCCCGTCCATTAAGAG
* * * * * * *
44942 AGGTCAGATCTGTTATGTCTTCGATCTGCTTCCTGTCCGAATACAGAG
1 AGATAAGATCTGTCA--TCTTGGATCTAC-TCCCGTCC-ATTA-AGAG
* * * *
44990 AGATAAGATCTATTATCTTGGATCTGCTCCCCGTCCATTTCAGAG
1 AGATAAGATCTGTCATCTTGGATCTACT-CCCGTCCA-TTAAGAG
45035 AGATAAGATCT
1 AGATAAGATCT
45046 ACTATTTTTT
Statistics
Matches: 216, Mismatches: 23, Indels: 55
0.73 0.08 0.19
Matches are distributed among these distances:
33 4 0.02
34 6 0.03
35 1 0.00
36 1 0.00
37 10 0.05
39 4 0.02
40 16 0.07
41 4 0.02
42 18 0.08
43 20 0.09
44 53 0.25
45 45 0.21
46 20 0.09
47 2 0.01
48 12 0.06
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (43 bp):
AGATAAGATCTGTCATCTTGGATCTACTCCCGTCCATTAAGAG
Found at i:45016 original size:46 final size:47
Alignment explanation
Indices: 44959--45101 Score: 143
Period size: 46 Copynumber: 3.1 Consensus size: 47
44949 ATCTGTTATG
*
44959 TCTTCGATCTGCTTCCTGTCCGAATACAGAGAGATAAGATCTATTA-
1 TCTTCGATCTGCTTCCTGTCCGAATACAGAGAGATAAGATCTACTAT
* * * * *
45005 TCTTGGATCTGCTCCCCGTCC-ATTTCAGAGAGATAAGATCTACTAT
1 TCTTCGATCTGCTTCCTGTCCGAATACAGAGAGATAAGATCTACTAT
* * * *
45051 TTTTTGATCTG-TTCCCTGT-CGAATACAAGAGAAATAAGATCTGCTA-
1 TCTTCGATCTGCTT-CCTGTCCGAATAC-AGAGAGATAAGATCTACTAT
45097 TCTTC
1 TCTTC
45102 AACTTGTTCC
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
45 23 0.30
46 37 0.48
47 17 0.22
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (47 bp):
TCTTCGATCTGCTTCCTGTCCGAATACAGAGAGATAAGATCTACTAT
Found at i:48200 original size:40 final size:40
Alignment explanation
Indices: 48116--48340 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
48106 TTGAATGATG
* * * *
48116 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
48156 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48196 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48235 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48275 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
48316 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
48341 AATGAGGAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 121 0.74
41 9 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:48362 original size:119 final size:119
Alignment explanation
Indices: 48116--48373 Score: 265
Period size: 119 Copynumber: 2.2 Consensus size: 119
48106 TTGAATGATG
* *
48116 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
48181 GTACGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
48235 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
48298 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-GAGCTATA
64 TTGTACGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
48355 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
48374 TACGTGATTT
Statistics
Matches: 115, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
118 3 0.03
119 82 0.71
120 30 0.26
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Done.