Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1238
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: 67949
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:94 original size:40 final size:40
Alignment explanation
Indices: 49--209 Score: 191
Period size: 40 Copynumber: 4.0 Consensus size: 40
39 GGATTTAGCC
* *
49 GATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
1 GATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCG
**
89 GATATAGTCACTAGCATGAATGCCTTCGGGACTTAGCCCG
1 GATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
* *
129 GATATAGTCACTAGCACAAATGCCTTCAGGACTTATCCCG
1 GATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
* *
169 GGTATAG-CAACTACTCGCACAAATGCCTTCGTGACTTAGCC
1 GATATAGTC-ACTA---GCACAAATGCCTTCGGGACTTAGCC
210 TAACATTCAA
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 80 0.77
41 1 0.01
43 22 0.21
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:7291 original size:40 final size:40
Alignment explanation
Indices: 7217--7389 Score: 217
Period size: 40 Copynumber: 4.3 Consensus size: 40
7207 AAGTATCTTT
* *
7217 GGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
* **
7256 GGGTCTTAGCCCGGATATAGTCACTAGCATGAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
*
7296 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTA
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
*
7336 GGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGCCTTC
7379 GGGACTTAGCC
1 GGGACTTAGCC
7390 TAACGTTCAA
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
39 8 0.07
40 84 0.72
41 1 0.01
43 24 0.21
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
Found at i:18274 original size:29 final size:29
Alignment explanation
Indices: 18232--18288 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
18222 GGACATTTGC
18232 ATTGTATTGTGATTACATGTAAGACCATG
1 ATTGTATTGTGATTACATGTAAGACCATG
* *
18261 ATTGTATTGTGATTACGTGTGAGACCAT
1 ATTGTATTGTGATTACATGTAAGACCAT
18289 ATTTGGGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (29 bp):
ATTGTATTGTGATTACATGTAAGACCATG
Found at i:18341 original size:43 final size:43
Alignment explanation
Indices: 18268--18378 Score: 116
Period size: 43 Copynumber: 2.6 Consensus size: 43
18258 ATGATTGTAT
* * * * * *
18268 TGTGATTACGTGTGAGACCATATTTGGGACATTGGCATCGTTA
1 TGTGATTACGTGTAAGACCATATCTAGGACAGTGACATCGATA
* *
18311 T-TCGATTACGTGTAAGACCCTGTCTAGGACAGTGACATCGATA
1 TGT-GATTACGTGTAAGACCATATCTAGGACAGTGACATCGATA
* *
18354 TGTGATAACATGTAAGACCATATCT
1 TGTGATTACGTGTAAGACCATATCT
18379 GTGATATGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 1 0.02
43 52 0.96
44 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATATCTAGGACAGTGACATCGATA
Found at i:31186 original size:24 final size:24
Alignment explanation
Indices: 31153--31220 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
31143 GTGAAATTCC
31153 AAAGGCTGAAAAGCCAAAAAGCCG
1 AAAGGCTGAAAAGCCAAAAAGCCG
* *
31177 AAAGGGTGAAAAGCCGAAAAGCCG
1 AAAGGCTGAAAAGCCAAAAAGCCG
*
31201 AAAGGCTGAAAAGCTAAAAA
1 AAAGGCTGAAAAGCCAAAAA
31221 AGTGGGTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.26, T:0.06
Consensus pattern (24 bp):
AAAGGCTGAAAAGCCAAAAAGCCG
Found at i:31195 original size:8 final size:8
Alignment explanation
Indices: 31160--31214 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
31150 TCCAAAGGCT
31160 GAAAAGCC
1 GAAAAGCC
*
31168 AAAAAGCC
1 GAAAAGCC
* **
31176 GAAAGGGT
1 GAAAAGCC
31184 GAAAAGCC
1 GAAAAGCC
31192 GAAAAGCC
1 GAAAAGCC
* *
31200 GAAAGGCT
1 GAAAAGCC
31208 GAAAAGC
1 GAAAAGC
31215 TAAAAAAGTG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.49, C:0.18, G:0.29, T:0.04
Consensus pattern (8 bp):
GAAAAGCC
Found at i:37208 original size:154 final size:154
Alignment explanation
Indices: 36984--37261 Score: 351
Period size: 154 Copynumber: 1.8 Consensus size: 154
36974 CGCTATTTGC
* * * * * * * * *
36984 TTCACCTTTTGCGGCGTTTTAGGAAAAACGCCACTAATTCTTGATATATTGCGGCGTTTACTGGA
1 TTCACCTATTGCGGCATTTTAGAAAAAACACCACTAATTCTCGATATATTGCAGCATTCACAGGA
* *
37049 GGCGCCGCTAAAGCCTCTATAGCTCACCAATGCACGACATAATATTT-CTCAAAACTTTTGTGGC
66 AGCGCCGCTAAAGCCTCTATAGCTCACCAATACACGACATAAT-TTTCCTCAAAACTTTTGTGGC
37113 GTTTTTAAACAACCGCCACTAATGG
130 GTTTTTAAACAACCGCCACTAATGG
* * * *
37138 TTCACCTATTGTGGCATTTTAGAAAAAACACCGCTAATTGTCGATATATTGCAGCATTCGCAGGA
1 TTCACCTATTGCGGCATTTTAGAAAAAACACCACTAATTCTCGATATATTGCAGCATTCACAGGA
* ** * * *
37203 AGCGCCGCTAATGCCTCTATAGCTTTCCAATACACGGCGTCATTTTCCTCAAAACTTTT
66 AGCGCCGCTAAAGCCTCTATAGCTCACCAATACACGACATAATTTTCCTCAAAACTTTT
37262 ACGGCATTTT
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
153 3 0.03
154 99 0.97
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (154 bp):
TTCACCTATTGCGGCATTTTAGAAAAAACACCACTAATTCTCGATATATTGCAGCATTCACAGGA
AGCGCCGCTAAAGCCTCTATAGCTCACCAATACACGACATAATTTTCCTCAAAACTTTTGTGGCG
TTTTTAAACAACCGCCACTAATGG
Found at i:52108 original size:43 final size:43
Alignment explanation
Indices: 52041--52212 Score: 138
Period size: 43 Copynumber: 4.0 Consensus size: 43
52031 TAAGCTTGTA
* ** * *
52041 CAATGCCA-TATCCCAGATGTGGTCTTACATGTTATCACATAT
1 CAATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATAT
*
52083 CAATGCCACTGTCCCAGACAAGGTCTTACACGTAATCA-ATTAAT
1 CAATGCCACTGTCCCAGACATGGTCTTACACGTAATCACA-T-AT
* * * *
52127 -GATGCCAAC-GTCCCGGACATGGTATTACACGTAATCTCA-AT
1 CAATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATAT
* * * * *
52168 ACAATGCCAATGTCCCAAACATGGTCTGACATGTAATTACATAT
1 -CAATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATAT
52212 C
1 C
52213 GATAACCTAA
Statistics
Matches: 101, Mismatches: 20, Indels: 17
0.73 0.14 0.12
Matches are distributed among these distances:
41 2 0.02
42 10 0.10
43 82 0.81
44 7 0.07
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (43 bp):
CAATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATAT
Found at i:59311 original size:55 final size:55
Alignment explanation
Indices: 59250--59360 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
59240 CGTGTCAATC
* * * *
59250 TAACAGGTTCGACCACG-GTTGTTAGACACGGGCGTGTCACACGTCCGTGCTGTTT
1 TAACAGGTTCAACCACGTG-TCTTACACACGGACGTGTCACACGTCCGTGCTGTTT
* * *
59305 TAACAGGTTCAACCACGTGTCTTCCACACGGACGTGTCGCACGTCCGTGTTGTTT
1 TAACAGGTTCAACCACGTGTCTTACACACGGACGTGTCACACGTCCGTGCTGTTT
59360 T
1 T
59361 GGCAAGCTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 47 0.98
56 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (55 bp):
TAACAGGTTCAACCACGTGTCTTACACACGGACGTGTCACACGTCCGTGCTGTTT
Found at i:63081 original size:14 final size:13
Alignment explanation
Indices: 63058--63087 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
63048 GGGATATCAA
63058 AACAATAATTAAG
1 AACAATAATTAAG
63071 AACACATAATTAAG
1 AACA-ATAATTAAG
63085 AAC
1 AAC
63088 TAGTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AACAATAATTAAG
Done.