Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3021
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: 43739
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:43 original size:1 final size:1
Alignment explanation
Indices: 37--87 Score: 84
Period size: 1 Copynumber: 51.0 Consensus size: 1
27 TTATGTGTAA
* *
37 TTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
88 GTGATTAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:71 original size:25 final size:25
Alignment explanation
Indices: 37--87 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
27 TTATGTGTAA
37 TTTTTTTTTTTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTGTTT
62 TTTTTTTTTTTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTGTTT
87 T
1 T
88 GTGATTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTTTTTTGTTT
Found at i:677 original size:35 final size:37
Alignment explanation
Indices: 605--677 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
595 GATAGTGTAG
605 AATGAAAATGAATAAATACAAAGAAGATCAGGTATGT
1 AATGAAAATGAATAAATACAAAGAAGATCAGGTATGT
*
642 AATGAAAATGAATAAATAC-AGGAA-ATCAGGTATGT
1 AATGAAAATGAATAAATACAAAGAAGATCAGGTATGT
677 A
1 A
678 TGATACCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 12 0.34
36 4 0.11
37 19 0.54
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.22
Consensus pattern (37 bp):
AATGAAAATGAATAAATACAAAGAAGATCAGGTATGT
Found at i:8016 original size:68 final size:67
Alignment explanation
Indices: 7944--8093 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
7934 CATCATGTGT
* * * *
7944 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
8006 ATGTAG
62 ATGTAG
** * *
8012 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
8077 AG
66 AG
8079 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
8094 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:8049 original size:64 final size:64
Alignment explanation
Indices: 7968--8151 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
7958 AGACATTATG
* *
7968 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
8032 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
8097 AA
63 AA
* * * *
8099 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
8152 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:10691 original size:19 final size:20
Alignment explanation
Indices: 10667--10718 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
10657 ACTATAGCAA
10667 CACACAATTT-CAA-TTATTT
1 CACAC-ATTTACAACTTATTT
10686 CACACATTTACAACTTATTT
1 CACACATTTACAACTTATTT
*
10706 TACA-ACTTTACAA
1 CACACA-TTTACAA
10719 AATAGCACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 16 0.55
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
CACACATTTACAACTTATTT
Found at i:13846 original size:10 final size:10
Alignment explanation
Indices: 13833--13858 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13823 TATATAAATA
13833 AAAAATATTC
1 AAAAATATTC
13843 AAAAATATTC
1 AAAAATATTC
13853 AAAAAT
1 AAAAAT
13859 TAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATTC
Found at i:13858 original size:52 final size:52
Alignment explanation
Indices: 13756--13913 Score: 257
Period size: 52 Copynumber: 3.0 Consensus size: 52
13746 TATAAAATAC
13756 AAATTAATTAAAATTACATAAATGAAAAAATATTAAACAATATTCAAAAATTA
1 AAATTAATTAAAATTACATAAAT-AAAAAATATTAAACAATATTCAAAAATTA
*
13809 AAATTAATTAAAATTATATAAATAAAAAATATTCAAA-AATATTCAAAAATTA
1 AAATTAATTAAAATTACATAAATAAAAAATATT-AAACAATATTCAAAAATTA
* *
13861 AAATTAATTAAAATTACATAAAT-AAAAATATTAAATAATATTCAAAATTTA
1 AAATTAATTAAAATTACATAAATAAAAAATATTAAACAATATTCAAAAATTA
13912 AA
1 AA
13914 GTAAACCGTT
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
50 3 0.03
51 25 0.25
52 47 0.47
53 25 0.25
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (52 bp):
AAATTAATTAAAATTACATAAATAAAAAATATTAAACAATATTCAAAAATTA
Found at i:14441 original size:17 final size:18
Alignment explanation
Indices: 14421--14455 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14411 ATTTCTTGTA
14421 AACTTTTA-AAATTTTAT
1 AACTTTTATAAATTTTAT
*
14438 AACTTTTATATATTTTAT
1 AACTTTTATAAATTTTAT
14456 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
AACTTTTATAAATTTTAT
Found at i:17548 original size:13 final size:13
Alignment explanation
Indices: 17530--17560 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
17520 GAGAAAAAAA
17530 TAAATTAATTAAT
1 TAAATTAATTAAT
17543 TAAATTAATTAAT
1 TAAATTAATTAAT
17556 TAAAT
1 TAAAT
17561 GTCTAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTAATTAAT
Found at i:21080 original size:23 final size:23
Alignment explanation
Indices: 21037--21080 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21027 AACAATAAAA
* *
21037 TTTTAGTATTAATAATTATATTG
1 TTTTAGTATTAAAAATAATATTG
21060 TTTTA-TATTCAAAAATAATAT
1 TTTTAGTATT-AAAAATAATAT
21081 ATACATGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTTAGTATTAAAAATAATATTG
Found at i:27283 original size:49 final size:47
Alignment explanation
Indices: 27149--27641 Score: 745
Period size: 47 Copynumber: 10.3 Consensus size: 47
27139 GTATATTTGA
*
27149 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATATG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
27196 ATGAATGTGAAAGTGTATATATGTGATAAGG-CTGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTG
* *
27243 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
*
27292 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATATG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
27341 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
* *
27390 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATATG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
27437 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
27484 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
27533 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * *
27580 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
27627 ATGGATGTGATAAGT
1 ATGAATGTGA-AAGT
27642 CCCGAAGGGC
Statistics
Matches: 417, Mismatches: 22, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.00
47 227 0.54
48 4 0.01
49 183 0.44
50 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:27283 original size:96 final size:94
Alignment explanation
Indices: 27149--27641 Score: 745
Period size: 96 Copynumber: 5.1 Consensus size: 94
27139 GTATATTTGA
*
27149 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATATGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
27214 ATATGTGATAAGG-CTGAATGGCCAATGTG
66 ATATGTGATAAGGCCT-AATGGCCGATGTG
* *
27243 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-
*
27308 ATATATATGTGATAAGGCCTAATGGCCGATATG
63 -TATATATGTGATAAGGCCTAATGGCCGATGTG
27341 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* *
27406 ATATATGTGATAAGGCCTAATAGCCGATATG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
* *
27437 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
27502 ATATATGTGATAAGGCCTAATGGCCGATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
27533 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * *
27598 ATATGTGACAGGGCCGAGTGGCCAACGTG
66 ATATGTGATAAGGCCTAATGGCCGATGTG
*
27627 ATGGATGTGATAAGT
1 ATGAATGTGA-AAGT
27642 CCCGAAGGGC
Statistics
Matches: 370, Mismatches: 21, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
94 95 0.26
95 4 0.01
96 180 0.49
98 89 0.24
99 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:32053 original size:93 final size:93
Alignment explanation
Indices: 31940--32111 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31930 CGCCCATAAG
* *
31940 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
32005 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
32033 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
32098 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
32112 TCAATCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:32108 original size:46 final size:46
Alignment explanation
Indices: 31933--32108 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
31923 TGTAACCCGC
* *
31933 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
31979 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
32029 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
32072 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
32109 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.58
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:39569 original size:47 final size:47
Alignment explanation
Indices: 39495--39669 Score: 196
Period size: 47 Copynumber: 3.8 Consensus size: 47
39485 TACCGCCCAA
*
39495 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCAC
1 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCATCCAC
* * * * *
39542 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TTACATC
1 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCATCCA-C
* * **
39590 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA-
1 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCATCCAC
* *
39635 TAAGTGAACTCGGACTC-ACTCAACGAGTTCGGATG
1 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGATG
39670 CTCAATCATC
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 18 0.17
46 14 0.13
47 68 0.65
48 5 0.05
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (47 bp):
TAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCATCCAC
Done.