Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2023
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: 21191
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:7306 original size:21 final size:21
Alignment explanation
Indices: 7280--7331 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
7270 AAAAGACAAC
7280 TTGATTTATAATTCT-ACTTAA
1 TTGATTTATAATT-TAACTTAA
*
7301 TTGATTTATAATTTAATTTAA
1 TTGATTTATAATTTAACTTAA
7322 TTGATTTATA
1 TTGATTTATA
7332 TAATAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (21 bp):
TTGATTTATAATTTAACTTAA
Found at i:7338 original size:21 final size:21
Alignment explanation
Indices: 7280--7341 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
7270 AAAAGACAAC
* *
7280 TTGATTTATAAT-TCTACTTAA
1 TTGATTTATAATAT-AATTTAA
*
7301 TTGATTTATAATTTAATTTAA
1 TTGATTTATAATATAATTTAA
7322 TTGATTTAT-ATAATAATTTA
1 TTGATTTATAAT-ATAATTTA
7342 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTGATTTATAATATAATTTAA
Found at i:7380 original size:13 final size:14
Alignment explanation
Indices: 7362--7394 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
7352 ATATTTAATA
7362 AATTTTAAATTT-T
1 AATTTTAAATTTAT
*
7375 AATTTTATATTTAT
1 AATTTTAAATTTAT
7389 AATTTT
1 AATTTT
7395 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTAAATTTAT
Found at i:7393 original size:14 final size:14
Alignment explanation
Indices: 7352--7400 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
7342 TAAAAAATTA
7352 ATATTTAATAAATTTT
1 ATATTT-AT-AATTTT
*
7368 AAATTT-TAATTTT
1 ATATTTATAATTTT
7381 ATATTTATAATTTT
1 ATATTTATAATTTT
*
7395 TTATTT
1 ATATTT
7401 TTTAAATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 11 0.38
14 13 0.45
16 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTATAATTTT
Found at i:10506 original size:40 final size:40
Alignment explanation
Indices: 10462--10542 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
10452 CAGATTCATA
10462 AGCATTTTATTGGATTATAGTAACAATTAAAATACCTATG
1 AGCATTTTATTGGATTATAGTAACAATTAAAATACCTATG
10502 AGCATTTTATTGGATTATAGTAACAATTAAAATACCTATG
1 AGCATTTTATTGGATTATAGTAACAATTAAAATACCTATG
10542 A
1 A
10543 ACTGTATTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (40 bp):
AGCATTTTATTGGATTATAGTAACAATTAAAATACCTATG
Found at i:15167 original size:14 final size:14
Alignment explanation
Indices: 15150--15184 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
15140 TAATTAATTA
15150 ATTTAAATAAAAAT
1 ATTTAAATAAAAAT
* *
15164 ATTTTAATAAATAT
1 ATTTAAATAAAAAT
15178 ATTTAAA
1 ATTTAAA
15185 AGTTAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTAAATAAAAAT
Found at i:15474 original size:23 final size:24
Alignment explanation
Indices: 15448--15492 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
15438 ACTTTAGGTT
*
15448 AGTGATTATTTTT-TAAAGATTAG
1 AGTGAGTATTTTTATAAAGATTAG
15471 AGTGAGTATTTTTATAAAGATT
1 AGTGAGTATTTTTATAAAGATT
15493 TAAAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (24 bp):
AGTGAGTATTTTTATAAAGATTAG
Found at i:17192 original size:15 final size:16
Alignment explanation
Indices: 17160--17192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17150 TATAATTTTA
17160 AAAAAAATTTAAATAT
1 AAAAAAATTTAAATAT
*
17176 AAAAAATTTTAAA-AT
1 AAAAAAATTTAAATAT
17191 AA
1 AA
17193 TTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAAATTTAAATAT
Found at i:20481 original size:11 final size:11
Alignment explanation
Indices: 20465--20501 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
20455 ATTATTACTT
20465 TTATTTATAAA
1 TTATTTATAAA
* *
20476 TTATTTTTAAT
1 TTATTTATAAA
20487 TTATTTATAAA
1 TTATTTATAAA
20498 TTAT
1 TTAT
20502 ACCAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:21149 original size:40 final size:39
Alignment explanation
Indices: 21100--21186 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 39
21090 TAAATATTAT
21100 TTTAATTTTA-TTAAAAATAA-TAATAATAAACTATTTTTAA
1 TTTAATTTTATTTAAAAATAATTAAT-ATAAA-T-TTTTTAA
21140 TTTAATTTTATTTTAAAAATAATTAATATAAATTTTTTAA
1 TTTAATTTTA-TTTAAAAATAATTAATATAAATTTTTTAA
*
21180 ATTAATT
1 TTTAATT
21187 AAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
40 23 0.53
41 1 0.02
42 15 0.35
43 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
TTTAATTTTATTTAAAAATAATTAATATAAATTTTTTAA
Found at i:21163 original size:107 final size:108
Alignment explanation
Indices: 20946--21145 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
20936 AATGTTATTT
* *
20946 TTTTAATTTATTAATGTAAAATTTTTTAAAATTTAATTAAATATCATTTTTATTTATTAAAAAAT
1 TTTTAATTTATTAATGT-AAATTTTTTAAAACTTAATTAAATATCATTTTAATTTATTAAAAAAT
* * * * *
21011 AATACTAATAAATACTTTTTATTTTTATAAAAATATATAATTAA
65 AATAATAATAAATACTTTTTAATTTAATAAAAATATAAAAATAA
* *
21055 TTTTAATTTGTTAAATGT-AATTTTTT-AAACTTAATTAAATATTATTTTAATTTTATT-AAAAA
1 TTTTAATTTATT-AATGTAAATTTTTTAAAACTTAATTAAATATCATTTTAA-TTTATTAAAAAA
21117 TAATAATAATAAACTA-TTTTTAATTTAAT
64 TAATAATAATAAA-TACTTTTTAATTTAAT
21146 TTTATTTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
107 49 0.60
108 16 0.20
109 11 0.14
110 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.52
Consensus pattern (108 bp):
TTTTAATTTATTAATGTAAATTTTTTAAAACTTAATTAAATATCATTTTAATTTATTAAAAAATA
ATAATAATAAATACTTTTTAATTTAATAAAAATATAAAAATAA
Done.