Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1821
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: 32792
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:945 original size:30 final size:30
Alignment explanation
Indices: 911--1007 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
901 AGCTCACTCC
911 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
941 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
971 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
1001 TAGCTCA
1 TAGCTCA
1008 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:3506 original size:37 final size:37
Alignment explanation
Indices: 3455--3525 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3445 CATTCTTGTA
3455 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
3492 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
3526 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:3525 original size:6 final size:6
Alignment explanation
Indices: 3465--3514 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
3455 AAGAGAAAAC
*
3465 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
3514 A
1 A
3515 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3607 original size:11 final size:12
Alignment explanation
Indices: 3575--3605 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3565 TTGAGAGAAC
3575 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3587 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3599 TTGAAAA
1 TTGAAAA
3606 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:5755 original size:30 final size:30
Alignment explanation
Indices: 5721--5817 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5711 AGCTCACTCC
5721 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
5751 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
5781 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
5811 TAGCTCA
1 TAGCTCA
5818 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:11950 original size:23 final size:22
Alignment explanation
Indices: 11899--11950 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
11889 TCCTCGTCTT
*
11899 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
11921 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
11944 TTCTTTT
1 TTCTTTT
11951 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:15282 original size:25 final size:25
Alignment explanation
Indices: 15253--15309 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
15243 ATTAAGTCAA
15253 GTTAGTTTAATTATGTAACTTTCAT
1 GTTAGTTTAATTATGTAACTTTCAT
15278 GTTAGTTTAATTATGTAACTTTCAT
1 GTTAGTTTAATTATGTAACTTTCAT
15303 GTTAGTT
1 GTTAGTT
15310 AAAATTGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (25 bp):
GTTAGTTTAATTATGTAACTTTCAT
Found at i:15441 original size:26 final size:26
Alignment explanation
Indices: 15391--15441 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
15381 TCATCTTAGT
* * *
15391 TTTAATTAATAAGTTTTTTTTTTAAC
1 TTTAATTAATAAGTGTTGTTATTAAC
*
15417 TTTATTTAATAAGTGTTGTTATTAA
1 TTTAATTAATAAGTGTTGTTATTAA
15442 TTAATCTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (26 bp):
TTTAATTAATAAGTGTTGTTATTAAC
Found at i:25168 original size:27 final size:27
Alignment explanation
Indices: 25138--25315 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
25128 ATATTAAGTC
* * *
25138 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
25165 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
25193 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
25220 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
25247 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
25274 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
25301 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25316 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:25222 original size:55 final size:54
Alignment explanation
Indices: 25138--25315 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
25128 ATATTAAGTC
* * *
25138 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
25193 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
25247 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
25301 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25316 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:25304 original size:81 final size:82
Alignment explanation
Indices: 25159--25314 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
25149 TGCTATATAA
* *
25159 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
25224 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
25241 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
25304 ACACTTAGTGC
65 ACACTTAGTGC
25315 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:26161 original size:20 final size:21
Alignment explanation
Indices: 26123--26162 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
26113 AAATTGTATC
*
26123 TTATAATCATTTTTTTAAAAT
1 TTATAATCATTTTTCTAAAAT
*
26144 TTATAATGA-TTTTCTAAAA
1 TTATAATCATTTTTCTAAAA
26163 ACAGAACAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTATAATCATTTTTCTAAAAT
Found at i:26163 original size:21 final size:21
Alignment explanation
Indices: 26123--26163 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
26113 AAATTGTATC
* *
26123 TTATAATCATTTTTTTAAAAT
1 TTATAATCATTTTCTAAAAAT
*
26144 TTATAATGATTTTCTAAAAA
1 TTATAATCATTTTCTAAAAA
26164 CAGAACAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATAATCATTTTCTAAAAAT
Done.