Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold583
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: 68966
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.23
Warning! 18735 characters in sequence are not A, C, G, or T
Found at i:8787 original size:20 final size:21
Alignment explanation
Indices: 8764--8810 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
8754 GGGTTAAAAT
*
8764 TGAGCTGAA-TTGATCTCGAA-
1 TGAGCTGAACTTGAGCTC-AAG
8784 TGAGCT-AACTTGAGCTCAAG
1 TGAGCTGAACTTGAGCTCAAG
8804 TGAGCTG
1 TGAGCTG
8811 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TGAGCTGAACTTGAGCTCAAG
Found at i:10658 original size:14 final size:14
Alignment explanation
Indices: 10639--10665 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10629 ATGCATCTCC
10639 CATGCATGAATCTA
1 CATGCATGAATCTA
10653 CATGCATGAATCT
1 CATGCATGAATCT
10666 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:51843 original size:11 final size:13
Alignment explanation
Indices: 51825--51859 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
51815 CAATTTCACA
51825 GAAAAATTTCG-T
1 GAAAAATTTCGTT
51837 G-AAAATTTCGTT
1 GAAAAATTTCGTT
51849 GAAAAATTTCG
1 GAAAAATTTCG
51860 ACGTTTCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 9 0.43
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (13 bp):
GAAAAATTTCGTT
Found at i:55761 original size:16 final size:17
Alignment explanation
Indices: 55740--55772 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55730 ATTATTGAGC
55740 TAGCTA-AATTTATTAT
1 TAGCTATAATTTATTAT
*
55756 TAGCTATATTTTATTAT
1 TAGCTATAATTTATTAT
55773 GTGTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TAGCTATAATTTATTAT
Found at i:57020 original size:17 final size:17
Alignment explanation
Indices: 56970--57020 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
56960 ATTGTAATTG
*
56970 AAAAAAAATTGAAGTA-
1 AAAAAAAAGTGAAGTAT
56986 AAAAAAAAGTTCG-AGTAT
1 AAAAAAAAG-T-GAAGTAT
57004 AAAAAAAAGTGAAGTAT
1 AAAAAAAAGTGAAGTAT
57021 TGGAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.30
17 11 0.37
18 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.16, T:0.20
Consensus pattern (17 bp):
AAAAAAAAGTGAAGTAT
Found at i:58042 original size:20 final size:20
Alignment explanation
Indices: 58019--58072 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
58009 AGTTTTTCCC
*
58019 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
58039 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
58059 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
58073 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:58054 original size:30 final size:30
Alignment explanation
Indices: 58019--58092 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
58009 AGTTTTTCCC
58019 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
58049 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
58079 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
58093 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:58082 original size:20 final size:20
Alignment explanation
Indices: 58019--58083 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
58009 AGTTTTTCCC
* * * *
58019 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
58039 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
58058 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
58079 AGCTC
1 AGCTC
58084 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:60224 original size:16 final size:16
Alignment explanation
Indices: 60203--60240 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
60193 CCGTATGCAA
60203 TTTTTTTCTTTC-AAT
1 TTTTTTTCTTTCGAAT
60218 TTTTTTTCTTTCGAAT
1 TTTTTTTCTTTCGAAT
60234 TTTTTTT
1 TTTTTTT
60241 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTTTCGAAT
Found at i:60247 original size:23 final size:23
Alignment explanation
Indices: 60220--60264 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
60210 CTTTCAATTT
*
60220 TTTTTCTTTCGAATTTTTTTTTG
1 TTTTTCTTTCAAATTTTTTTTTG
*
60243 TTTTTTTTTCAAATTTTTTTTT
1 TTTTTCTTTCAAATTTTTTTTT
60265 CAAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTCAAATTTTTTTTTG
Found at i:60260 original size:14 final size:14
Alignment explanation
Indices: 60201--60276 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 14
60191 GACCGTATGC
60201 AATTTTTTTCTTTCA
1 AATTTTTTT-TTTCA
* *
60216 ATTTTTTTTCTTTCG
1 AATTTTTTT-TTTCA
60231 AA-TTTTTTTTT--
1 AATTTTTTTTTTCA
*
60242 --GTTTTTTTTTCA
1 AATTTTTTTTTTCA
60254 AA-TTTTTTTTTCA
1 AATTTTTTTTTTCA
60267 AACTTTTTTT
1 AA-TTTTTTT
60277 ACGTACCTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
10 9 0.18
13 16 0.31
14 6 0.12
15 20 0.39
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (14 bp):
AATTTTTTTTTTCA
Found at i:60261 original size:15 final size:14
Alignment explanation
Indices: 60200--60241 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
60190 AGACCGTATG
*
60200 CAATTTTTTTCTTT
1 CAATTTTTTTTTTT
60214 CAATTTTTTTTCTTT
1 CAATTTTTTTT-TTT
60229 CGAATTTTTTTTT
1 C-AATTTTTTTTT
60242 GTTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 5 0.20
16 10 0.40
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (14 bp):
CAATTTTTTTTTTT
Found at i:60268 original size:13 final size:13
Alignment explanation
Indices: 60204--60276 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
60194 CGTATGCAAT
*
60204 TTTTTTCTTTCAATT
1 TTTTTT-TTTCAA-A
*
60219 TTTTTTCTTTCGAA
1 TTTTTT-TTTCAAA
*
60233 TTTTTTTTT---G
1 TTTTTTTTTCAAA
60243 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
60256 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
60269 CTTTTTTT
1 -TTTTTTT
60277 ACGTACCTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
10 9 0.18
13 16 0.32
14 13 0.26
15 12 0.24
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:60604 original size:22 final size:22
Alignment explanation
Indices: 60574--60617 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
60564 TTTGGTATTT
*
60574 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
*
60596 GGGATTTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
60618 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Done.