Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3526
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: 30297
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:616 original size:30 final size:29
Alignment explanation
Indices: 582--638 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
572 ATAGTATCGT
582 ATCTTGGATTTCTTTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATTC-GGGTTTCTCA
*
612 ATCTTGGATTTCTTTATTCGGTTTTCT
1 ATCTTGGATTTCTTTATTCGGGTTTCT
639 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (29 bp):
ATCTTGGATTTCTTTATTCGGGTTTCTCA
Found at i:3400 original size:46 final size:46
Alignment explanation
Indices: 3348--3523 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
3338 TATTTGGACA
3348 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
3394 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
3439 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
3487 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3524 GTGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 64 0.58
47 28 0.25
48 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:3455 original size:93 final size:93
Alignment explanation
Indices: 3346--3516 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
3336 GATATTTGGA
**
3346 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTT
3411 GAGTCCGAGTTCGTGAGATGTAACTAGG
66 GAGTCCGAGTTCGTGAGATGTAACTAGG
* *
3439 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTT
3504 GAGTCCGAGTTCG
66 GAGTCCGAGTTCG
3517 CTTATGGGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAGG
Found at i:6232 original size:30 final size:29
Alignment explanation
Indices: 6198--6254 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
6188 ATAGTATCGT
6198 ATCTTGGATTTCTTTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATT-TGGGTTTCTCA
*
6228 ATCTTGGATTTCTTTATTTGGTTTTCT
1 ATCTTGGATTTCTTTATTTGGGTTTCT
6255 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (29 bp):
ATCTTGGATTTCTTTATTTGGGTTTCTCA
Found at i:6253 original size:14 final size:14
Alignment explanation
Indices: 6201--6255 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
6191 GTATCGTATC
6201 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
* **
6215 TCTGGGTTTCTCAAT
1 T-TGGATTTCTTTAT
6230 CTTGGATTTCTTTAT
1 -TTGGATTTCTTTAT
*
6245 TTGGTTTTCTT
1 TTGGATTTCTT
6256 GTTATCTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 11 0.34
15 20 0.62
16 1 0.03
ACGTcount: A:0.11, C:0.13, G:0.16, T:0.60
Consensus pattern (14 bp):
TTGGATTTCTTTAT
Found at i:10184 original size:40 final size:40
Alignment explanation
Indices: 10127--10344 Score: 304
Period size: 40 Copynumber: 5.5 Consensus size: 40
10117 ACTCACTCAT
* *
10127 TGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
*
10167 TGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
*
10207 TGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
* *
10247 TGCCTTCGGGGC-TA---AGGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
*
10283 TGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAA
1 TGCCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAA
10324 TGCCTTCGGGACTTAGCCCGG
1 TGCCTTCGGGACTTAGCCCGG
10345 TTATCATCCA
Statistics
Matches: 160, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
36 31 0.19
37 2 0.01
39 3 0.02
40 96 0.60
41 24 0.15
42 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
Found at i:10298 original size:76 final size:78
Alignment explanation
Indices: 10127--10338 Score: 288
Period size: 76 Copynumber: 2.7 Consensus size: 78
10117 ACTCACTCAT
* * * *
10127 TGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATGCCTTCGAGACTTAGCCCGGATAT
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTA--CAGGATAT
10192 AGTAACTCGCACAAA
64 AGTAACTCGCACAAA
* *
10207 TGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGCCTTCGGGGC-TA-AGGATATAG
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTACAGGATATAG
10270 TAACTCGCACAAA
66 TAACTCGCACAAA
*
10283 TGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATGCCTTCGGGACTTA
1 TGCCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATGCCTTCGGGACTTA
10339 GCCCGGTTAT
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
75 1 0.01
76 49 0.41
77 14 0.12
78 6 0.05
79 2 0.02
80 47 0.39
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (78 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTACAGGATATAG
TAACTCGCACAAA
Found at i:12410 original size:46 final size:46
Alignment explanation
Indices: 12358--12533 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
12348 TATTTGGGCA
12358 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
12404 TCCGAACTCGTTGAGTTGAGTCCGAATTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
12449 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
12497 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGA-TTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGG
12534 GTGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:12507 original size:93 final size:93
Alignment explanation
Indices: 12354--12526 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
12344 CGGATATTTG
*
12354 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12419 TTGAGTCCGAATTCGTGAGATGTAACTA
66 TTGAGTCCGAATTCGTGAGATGTAACTA
* * *
12447 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
12512 TTGAGTCCGAGTTCG
66 TTGAGTCCGAATTCG
12527 ATTATGGGTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAATTCGTGAGATGTAACTA
Found at i:17865 original size:14 final size:14
Alignment explanation
Indices: 17846--17893 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
17836 AATCTATGCC
*
17846 AATAAATACTAGAA
1 AATAAATACTAAAA
17860 AATAAATCAC-AAAA
1 AATAAAT-ACTAAAA
* *
17874 AATAAAGAATAAAA
1 AATAAATACTAAAA
17888 AATAAA
1 AATAAA
17894 AAATTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (14 bp):
AATAAATACTAAAA
Found at i:18174 original size:16 final size:17
Alignment explanation
Indices: 18148--18180 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18138 AAATAACTAG
*
18148 ATGCAAAATTATCCTAA
1 ATGCAAAATTAACCTAA
18165 ATGC-AAATTAACCTAA
1 ATGCAAAATTAACCTAA
18181 GTGTGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (17 bp):
ATGCAAAATTAACCTAA
Found at i:20906 original size:28 final size:28
Alignment explanation
Indices: 20841--20991 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
20831 GAGATTGGCG
* * * *
20841 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
20870 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20898 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20926 CTAAGTGTGTGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
20954 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20981 CTGAGTGTGCG
1 CTAAGTGTGCG
20992 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.21
28 74 0.65
29 15 0.13
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:28834 original size:28 final size:28
Alignment explanation
Indices: 28769--28919 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
28759 GAGATTGGCG
* * * *
28769 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
28798 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
28826 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28854 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28882 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
28909 CTGAGTGTGCG
1 CTAAGTGTGCG
28920 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Done.