Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1266
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: 43340
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3291 original size:72 final size:71
Alignment explanation
Indices: 3157--3291 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 71
3147 TCATTTATTA
* *
3157 AATTTAATATAAGAGATTAATTTATAATTATTTTTTTAATTATATTTTAATTCTTTTGTAATAGA
1 AATTTAATATAAGAGATTAATTTATAATTAATTTTTTAA-TATATTGTAATTCTTTTGTAATAGA
3222 ATCATTG
65 ATCATTG
* *
3229 AATTTAATATAATATATTAATTTTATTAATTAATTTTTTAA-ATGAGTTGTAATT-TTTT-TAAT
1 AATTTAATATAAGAGATTAA-TTTA-TAATTAATTTTTTAATAT-A-TTGTAATTCTTTTGTAAT
3291 A
62 A
3292 AAATTTTAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
72 25 0.45
73 9 0.16
74 21 0.38
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (71 bp):
AATTTAATATAAGAGATTAATTTATAATTAATTTTTTAATATATTGTAATTCTTTTGTAATAGAA
TCATTG
Found at i:4226 original size:1 final size:1
Alignment explanation
Indices: 4215--4249 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
4205 CTCAATTAAT
* *
4215 AAAAGAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4250 TGGGACAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:4233 original size:13 final size:13
Alignment explanation
Indices: 4215--4249 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4205 CTCAATTAAT
4215 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
4228 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
4241 AAAA-AAAAA
1 AAAAGAAAAA
4250 TGGGACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:4241 original size:18 final size:18
Alignment explanation
Indices: 4215--4249 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4205 CTCAATTAAT
*
4215 AAAAGAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAG
4233 AAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAA
4250 TGGGACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAG
Found at i:7370 original size:19 final size:20
Alignment explanation
Indices: 7339--7380 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
7329 CAAATCGAAC
*
7339 AGATAACAAGAA-GTAAGAA
1 AGATAACAAGAAGGGAAGAA
7358 AGATAA-AAGGAAGGGAAGAA
1 AGATAACAA-GAAGGGAAGAA
7378 AGA
1 AGA
7381 AGCCAAAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 9 0.45
20 9 0.45
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07
Consensus pattern (20 bp):
AGATAACAAGAAGGGAAGAA
Found at i:12540 original size:1 final size:1
Alignment explanation
Indices: 12534--12585 Score: 68
Period size: 1 Copynumber: 52.0 Consensus size: 1
12524 AGAGATATAT
* * * *
12534 AAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAGAGAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12586 CGAGAAACCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.92, C:0.02, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:12590 original size:21 final size:19
Alignment explanation
Indices: 12534--12592 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 19
12524 AGAGATATAT
12534 AAAAAAAAAAAAAAA-A-A
1 AAAAAAAAAAAAAAAGAGA
*
12551 AAAAAAAACAAAAAAGAGA
1 AAAAAAAAAAAAAAAGAGA
12570 AAAAAAAAAAAGAAAACGAGA
1 AAAAAAAAAAA-AAAA-GAGA
12591 AA
1 AA
12593 CCATAAGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 14 0.39
18 1 0.03
19 11 0.31
20 4 0.11
21 6 0.17
ACGTcount: A:0.88, C:0.03, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGAGA
Found at i:13519 original size:16 final size:16
Alignment explanation
Indices: 13484--13521 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
13474 GGTTTTTGTT
*
13484 CTTTTTTTTTTTTTAA
1 CTTTTTGTTTTTTTAA
13500 -TTTTTGTTTTTTTAA
1 CTTTTTGTTTTTTTAA
13515 CTTTTTG
1 CTTTTTG
13522 AATTTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.79
Consensus pattern (16 bp):
CTTTTTGTTTTTTTAA
Found at i:14766 original size:29 final size:29
Alignment explanation
Indices: 14733--14788 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
14723 AATATGCATG
14733 AAAA-TAAATACTATTAA-TTTTTATTTATC
1 AAAATTAAATA-TA-TAATTTTTTATTTATC
*
14762 AAAATTAGATATATAATTTTTTATTTA
1 AAAATTAAATATATAATTTTTTATTTA
14789 AGTTATGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (29 bp):
AAAATTAAATATATAATTTTTTATTTATC
Found at i:15780 original size:1 final size:1
Alignment explanation
Indices: 15774--15810 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
15764 CCCGTCCCTC
*
15774 AAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15811 GAAGAGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:15800 original size:21 final size:21
Alignment explanation
Indices: 15774--15813 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
15764 CCCGTCCCTC
15774 AAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAGAAAA
15795 AAAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAGAA
15814 GAGAAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAGAAAA
Found at i:17236 original size:15 final size:15
Alignment explanation
Indices: 17198--17246 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
17188 TATTAATTAG
17198 TAAATTTATAAATAA-
1 TAAATTTATAAA-AAT
*
17213 TAAATATTTTAAAATAT
1 TAAAT-TTATAAAA-AT
17230 TAAATTTATAAAAAT
1 TAAATTTATAAAAAT
17245 TA
1 TA
17247 CTATCCTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 10 0.34
16 14 0.48
17 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTTATAAAAAT
Found at i:35125 original size:17 final size:18
Alignment explanation
Indices: 35074--35137 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
35064 ACCACTTTTC
35074 TTTTATT-ATTATAATTA
1 TTTTATTAATTATAATTA
* *
35091 TTATTTTATAATTTTAATT-
1 TT-TTAT-TAATTATAATTA
35110 TTTTATTAATTATAATTAA
1 TTTTATTAATTATAATT-A
35129 TATTTATTA
1 T-TTTATTA
35138 TATCCGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 12 0.32
18 6 0.16
19 4 0.11
20 15 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTAATTATAATTA
Found at i:36270 original size:2 final size:2
Alignment explanation
Indices: 36263--36291 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36253 CTTTAAGTTC
36263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36292 AGTCAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36768 original size:20 final size:18
Alignment explanation
Indices: 36745--36788 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
36735 TATTTTTTAA
36745 AATTATGAAAATTTATTTTT
1 AATTATGAAAA-TTA-TTTT
*
36765 AATTAATTAAAATTATTTT
1 AATT-ATGAAAATTATTTT
36784 AATTA
1 AATTA
36789 ATTCGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 8 0.36
20 7 0.32
21 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTATGAAAATTATTTT
Found at i:38079 original size:21 final size:21
Alignment explanation
Indices: 38053--38092 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38043 TGATCAGGGC
*
38053 TCGAACTCTTCTTCGTTCTCT
1 TCGAACTCCTCTTCGTTCTCT
*
38074 TCGAACTCCTCTTGGTTCT
1 TCGAACTCCTCTTCGTTCT
38093 GGTTGTACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.12, T:0.45
Consensus pattern (21 bp):
TCGAACTCCTCTTCGTTCTCT
Found at i:38934 original size:2 final size:2
Alignment explanation
Indices: 38917--38962 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
38907 CAAAATCTGC
*
38917 AT AT A- AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38958 AT AT A
1 AT AT A
38963 GAAGAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39114 original size:14 final size:14
Alignment explanation
Indices: 39093--39132 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39083 ATATTTTTAT
*
39093 TTAA-ATTTAAATA
1 TTAATATTTAAAAA
39106 TTAATATTTAAAAA
1 TTAATATTTAAAAA
*
39120 ATAATATTTAAAA
1 TTAATATTTAAAA
39133 TAAAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:39774 original size:21 final size:20
Alignment explanation
Indices: 39744--39798 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
39734 TTAAAAATAT
*
39744 ATAAAAATAATTTTATTCTTA
1 ATAAATATAATTTTATT-TTA
39765 ATAAATATAATTATTTATTTTA
1 ATAAATATAA-T-TTTATTTTA
*
39787 ATATATA-AATTT
1 ATAAATATAATTT
39799 ATATATTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 1 0.03
21 11 0.37
22 10 0.33
23 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATATAATTTTATTTTA
Found at i:39800 original size:22 final size:23
Alignment explanation
Indices: 39755--39797 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
39745 TAAAAATAAT
39755 TTTATTCTTAATAAATATAATTA
1 TTTATTCTTAATAAATATAATTA
*
39778 TTTATT-TTAATATATA-AATT
1 TTTATTCTTAATAAATATAATT
39798 TATATATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTATTCTTAATAAATATAATTA
Found at i:39805 original size:22 final size:23
Alignment explanation
Indices: 39744--39805 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
39734 TTAAAAATAT
*
39744 ATAAAAATAATT-T-TATTCTTA
1 ATAAATATAATTATATATTCTTA
*
39765 ATAAATATAATTATTTATT-TTA
1 ATAAATATAATTATATATTCTTA
*
39787 ATATATA-AATTTATATATT
1 ATAAATATAA-TTATATATT
39806 ACCATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 13 0.37
22 18 0.51
23 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAAATATAATTATATATTCTTA
Found at i:41721 original size:2 final size:2
Alignment explanation
Indices: 41714--41750 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41704 TTTGGTGGAT
41714 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41751 CAAGAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.