Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1683
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: 46685
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Found at i:2100 original size:39 final size:37
Alignment explanation
Indices: 2057--2232 Score: 158
Period size: 40 Copynumber: 4.5 Consensus size: 37
2047 TACTCGTTCG
*
2057 AATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACA
1 AATGCCTTCGGACTTAGCCCGG--ATAGTAACTCGCACA
* * *
2096 AATGCCTTCGGGACTTA-ACCGGATTGTATACTCACACA
1 AATGCCTTC-GGACTTAGCCCGGATAGTA-ACTCGCACA
* *
2134 AATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGACTTAGCCCGG-A-TAGTAACTCGCACA
* * *
2173 AATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACA
1 AATGCCTTCGGA-CTTAGCCCGGATA--GTAAC-TCGCACA
2214 AA-GCCTTCGGGACTTAGCC
1 AATGCCTTC-GGACTTAGCC
2233 GGACATCATT
Statistics
Matches: 112, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
37 11 0.10
38 23 0.21
39 33 0.29
40 34 0.30
41 11 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (37 bp):
AATGCCTTCGGACTTAGCCCGGATAGTAACTCGCACA
Found at i:2140 original size:38 final size:40
Alignment explanation
Indices: 2057--2235 Score: 153
Period size: 39 Copynumber: 4.6 Consensus size: 40
2047 TACTCGTTCG
* * * *
2057 AATGCCTTC-GGACATAGCCCGGTTATAGTA-ACTCGCACA
1 AATGCCTTCGGGACTTAGACCGGAT-TAGTATACTCACACA
2096 AATGCCTTCGGGACTTA-ACCGGATT-GTATACTCACACA
1 AATGCCTTCGGGACTTAGACCGGATTAGTATACTCACACA
* *
2134 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAT-CTCGCACA
1 AATGCCTTCGGGACTTAGACCGG-ATTAGTATACTCACACA
* * * *
2173 AATGCCTTC-GGATCTTAGTCCGGATATGGT-CACTTAGCACA
1 AATGCCTTCGGGA-CTTAGACCGGAT-TAGTATACTCA-CACA
2214 AA-GCCTTCGGGACTTAG-CCGGA
1 AATGCCTTCGGGACTTAGACCGGA
2236 CATCATTCAA
Statistics
Matches: 118, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
37 7 0.06
38 27 0.23
39 40 0.34
40 35 0.30
41 9 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGACCGGATTAGTATACTCACACA
Found at i:7849 original size:78 final size:78
Alignment explanation
Indices: 7694--7944 Score: 361
Period size: 78 Copynumber: 3.2 Consensus size: 78
7684 CGGATGATAA
* * * *
7694 CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTA-ATTCCGGGCTAAG-CCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
7757 GTGCGAGTTA-TATAT
65 GTGC-AG-TACTATAT
7772 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
7837 TGCAGTACTATAT
66 TGCAGTACTATAT
*
7850 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
7915 AGCA-TAGCTATAT
66 TGCAGTA-CTATAT
*
7928 CC-GGCTAA-ACCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
7945 TACTTGGTTG
Statistics
Matches: 162, Mismatches: 7, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
76 8 0.05
77 10 0.06
78 126 0.78
79 18 0.11
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCAGTACTATAT
Found at i:7855 original size:38 final size:40
Alignment explanation
Indices: 7694--7914 Score: 353
Period size: 40 Copynumber: 5.6 Consensus size: 40
7684 CGGATGATAA
* * * *
7694 CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
7734 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTA-TATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7772 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7812 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
7850 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7890 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
7915 AGCATAGCTA
Statistics
Matches: 171, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
38 49 0.29
39 47 0.27
40 75 0.44
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:7902 original size:118 final size:118
Alignment explanation
Indices: 7694--7914 Score: 367
Period size: 118 Copynumber: 1.9 Consensus size: 118
7684 CGGATGATAA
7694 CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
*
7759 GCGAGTTATATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
66 GCGAGTTATATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7812 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTAAT-TCCGGGCTAAG-CCCGAAGGCATTT
7874 GTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
64 GTGCGAGTTA-TATAACCGGGCTAAGTCCCGAAGGCATTTG
7915 AGCATAGCTA
Statistics
Matches: 97, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
115 2 0.02
116 14 0.14
117 26 0.27
118 55 0.57
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (118 bp):
CCGGGCTAAGTCCCAAAGGCATCTGTGCAAGTAACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
GCGAGTTATATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:15961 original size:40 final size:40
Alignment explanation
Indices: 15856--16111 Score: 308
Period size: 40 Copynumber: 6.5 Consensus size: 40
15846 CGGATGATAA
* * *
15856 CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
15896 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
15935 CCGGGCTATGTCCCAAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
15975 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
* * * *
16015 CCGAGCTAAGTCCCGAAGGAATTTGCGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
16055 CCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
16094 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
16112 TACTTCGTTG
Statistics
Matches: 188, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
38 16 0.09
39 42 0.22
40 128 0.68
41 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:16093 original size:119 final size:119
Alignment explanation
Indices: 15856--16111 Score: 335
Period size: 119 Copynumber: 2.2 Consensus size: 119
15846 CGGATGATAA
* *
15856 CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTAATTCCGAGCTAAGCCCGAAGGCAATTGC
* * * *
15921 GCGAGTTATTATATCCGGGCTATGTCCCAAAGGCATTTGTGCAAGTTACTATAT
66 GCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCATTTGAGCAAGTTACTATAT
*
15975 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACT-ATATCCGAGCTAAGTCCCGAAGG-AAT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGC-AAGTGACTAAT-TCCGAGCTAAG-CCCGAAGGCAA-
*
16037 TTGCGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
62 TTGCGCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCATTTGAGCAAGTTA-CTATAT
**
16094 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
16112 TACTTCGTTG
Statistics
Matches: 122, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
118 18 0.15
119 52 0.43
120 52 0.43
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTAATTCCGAGCTAAGCCCGAAGGCAATTGC
GCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCATTTGAGCAAGTTACTATAT
Found at i:24613 original size:29 final size:29
Alignment explanation
Indices: 24570--24635 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
24560 CATGATTATG
*
24570 AATGTGA-CTGGGCCTAACGGGCCATATA
1 AATGTGATTTGGGCCTAACGGGCCATATA
* *
24598 AATGTGATTTGGGCCTAATGGGCCATATG
1 AATGTGATTTGGGCCTAACGGGCCATATA
*
24627 AATATGATT
1 AATGTGATT
24636 AGGCTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAACGGGCCATATA
Found at i:35195 original size:15 final size:15
Alignment explanation
Indices: 35175--35209 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
35165 CCAAGGGAAG
35175 TATGTGGGTGCAAGC
1 TATGTGGGTGCAAGC
35190 TATGTGGGTGCAAGC
1 TATGTGGGTGCAAGC
35205 TATGT
1 TATGT
35210 TAGAAGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.37, T:0.31
Consensus pattern (15 bp):
TATGTGGGTGCAAGC
Found at i:36064 original size:7 final size:8
Alignment explanation
Indices: 36043--36078 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
36033 GTTGTAACGC
36043 TCCCAAAA
1 TCCCAAAA
36051 TCCCAAAA
1 TCCCAAAA
36059 -CCCAAAAA
1 TCCC-AAAA
36067 TCCCAAAA
1 TCCCAAAA
36075 TCCC
1 TCCC
36079 GAACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 3 0.12
8 20 0.77
9 3 0.12
ACGTcount: A:0.47, C:0.42, G:0.00, T:0.11
Consensus pattern (8 bp):
TCCCAAAA
Found at i:37517 original size:29 final size:28
Alignment explanation
Indices: 37473--37591 Score: 121
Period size: 29 Copynumber: 4.2 Consensus size: 28
37463 CATGATTATG
* *
37473 AATGTGACTGGGCCTAACGGGCCATATA
1 AATGTGATTGGGCCTAATGGGCCATATA
*
37501 AATGTGATTCGGGCCTAATAGGCCATATA
1 AATGTGATT-GGGCCTAATGGGCCATATA
* * *
37530 CAGGTGATTTGGGCCTAATGGGCCATATG
1 AATGTGA-TTGGGCCTAATGGGCCATATA
* * * *
37559 AATATGATTAGGCTTAATGGGCCAGATA
1 AATGTGATTGGGCCTAATGGGCCATATA
*
37587 TATGT
1 AATGT
37592 ATGTGAAATT
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
28 28 0.38
29 43 0.59
30 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCATATA
Found at i:39410 original size:40 final size:39
Alignment explanation
Indices: 39326--39509 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
39316 TCGAATGATG
* * * *
39326 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
39366 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
39406 TCCGGGCTAAG-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39444 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
39485 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
39510 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Done.