Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2151
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: 43254
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8914 original size:29 final size:28
Alignment explanation
Indices: 8882--8955 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
8872 GCAAGACTTT
*
8882 TCACTTTTTTTTTAACTTGATTTTTTTGC
1 TCACTTTTTTTTT-ACTTCATTTTTTTGC
* *
8911 TCACTTTTTTTTTCCTTCTTTTTTTTGC
1 TCACTTTTTTTTTACTTCATTTTTTTGC
*
8939 TCGA-TTTTTTTTCACTT
1 TC-ACTTTTTTTTTACTT
8956 TTTTTTGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 25 0.64
29 14 0.36
ACGTcount: A:0.09, C:0.18, G:0.05, T:0.68
Consensus pattern (28 bp):
TCACTTTTTTTTTACTTCATTTTTTTGC
Found at i:8919 original size:14 final size:15
Alignment explanation
Indices: 8902--8950 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
8892 TTTAACTTGA
8902 TTTTTTTGCTC-ACT
1 TTTTTTTGCTCGACT
* **
8916 TTTTTTTTC-CTTCT
1 TTTTTTTGCTCGACT
8930 TTTTTTTGCTCGA-T
1 TTTTTTTGCTCGACT
8944 TTTTTTT
1 TTTTTTT
8951 CACTTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTTTTTGCTCGACT
Found at i:8958 original size:12 final size:13
Alignment explanation
Indices: 8879--8961 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 13
8869 CTCGCAAGAC
8879 TTTTCAC-TTTTT
1 TTTTCACTTTTTT
*
8891 TTTTAACTTGATTTT
1 TTTTCACTT--TTTT
8906 TTTGCTCAC-TTTTT
1 TTT--TCACTTTTTT
8920 TTTTC-CTTCTTTT
1 TTTTCACTT-TTTT
* **
8933 TTTTGCTCGATTTT
1 TTTT-CACTTTTTT
8947 TTTTCACTTTTTT
1 TTTTCACTTTTTT
8960 TT
1 TT
8962 GAATTCTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
11 1 0.02
12 9 0.16
13 17 0.31
14 16 0.29
15 8 0.15
16 1 0.02
17 3 0.05
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (13 bp):
TTTTCACTTTTTT
Found at i:11463 original size:22 final size:22
Alignment explanation
Indices: 11435--11478 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11425 TTTTGAACCA
11435 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
11457 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
11479 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:13254 original size:21 final size:23
Alignment explanation
Indices: 13209--13255 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
13199 TCACCTGCAA
* *
13209 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
13232 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
13253 TAA
1 TAA
13256 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:14832 original size:11 final size:11
Alignment explanation
Indices: 14813--14856 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
14803 TAGTAGTTTC
*
14813 TTCAAAAAAAT
1 TTCAAAAAAAA
*
14824 TTGAAAAAAAA
1 TTCAAAAAAAA
14835 TTCAAAAAAAA
1 TTCAAAAAAAA
14846 TTCAAAAAAAA
1 TTCAAAAAAAA
14857 AATTTGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:14833 original size:12 final size:12
Alignment explanation
Indices: 14816--14862 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
14806 TAGTTTCTTC
14816 AAAAAAATTTGA
1 AAAAAAATTTGA
*
14828 AAAAAAA-TTCA
1 AAAAAAATTTGA
**
14839 AAAAAAATTCAAA
1 AAAAAAATT-TGA
14852 AAAAAAATTTG
1 AAAAAAATTTG
14863 GTTTCCTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 10 0.36
12 8 0.29
13 10 0.36
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:14920 original size:14 final size:15
Alignment explanation
Indices: 14898--14938 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
14888 GATATCAAGT
14898 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
14913 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
14928 TGAAAAAAAAA
1 TGAAAAAAAAA
14939 GAAGAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:25445 original size:22 final size:21
Alignment explanation
Indices: 25419--25468 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
25409 AAATATTTAC
* *
25419 ATAAAAATTAAACTAAGTAAAA
1 ATAAAAAATAAA-TAAATAAAA
25441 ATAAATAAATAAATAAATAAAA
1 ATAAA-AAATAAATAAATAAAA
25463 ATAAAA
1 ATAAAA
25469 CTTTACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAAAAATAAATAAATAAAA
Found at i:25464 original size:18 final size:19
Alignment explanation
Indices: 25419--25467 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
25409 AAATATTTAC
*
25419 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
25439 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
25457 ATAAAAATAAA
1 ATAAAAATAAA
25468 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:26042 original size:20 final size:21
Alignment explanation
Indices: 26007--26045 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
25997 CAGCTCGTTG
26007 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
26028 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
26046 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:26453 original size:13 final size:13
Alignment explanation
Indices: 26435--26460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26425 TGTGTCCTAA
26435 TATGAATTAAATT
1 TATGAATTAAATT
26448 TATGAATTAAATT
1 TATGAATTAAATT
26461 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:27588 original size:10 final size:10
Alignment explanation
Indices: 27573--27619 Score: 67
Period size: 10 Copynumber: 4.5 Consensus size: 10
27563 GTAAGTGATT
27573 AAAAAAATAA
1 AAAAAAATAA
27583 AAAAAAATTGAA
1 AAAAAAA-T-AA
27595 AAAAAAATAA
1 AAAAAAATAA
*
27605 AAAAAAGTAA
1 AAAAAAATAA
27615 AAAAA
1 AAAAA
27620 TTCGTGGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 23 0.68
11 2 0.06
12 9 0.26
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:27618 original size:22 final size:22
Alignment explanation
Indices: 27573--27619 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
27563 GTAAGTGATT
**
27573 AAAAAAATAAAAAAAAATTGAA
1 AAAAAAATAAAAAAAAATAAAA
*
27595 AAAAAAATAAAAAAAAGTAAAA
1 AAAAAAATAAAAAAAAATAAAA
27617 AAA
1 AAA
27620 TTCGTGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (22 bp):
AAAAAAATAAAAAAAAATAAAA
Found at i:31507 original size:70 final size:70
Alignment explanation
Indices: 31389--31525 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
31379 TTGCATGCCC
31389 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
31454 TGTTG
66 TGTTG
* *
31459 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
31524 TG
66 TG
31526 ATTTAATTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:36347 original size:11 final size:10
Alignment explanation
Indices: 36333--36378 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
36323 AAAATTTTGA
36333 AAAAAAAATAG
1 AAAAAAAAT-G
*
36344 AAAAAAAATC
1 AAAAAAAATG
*
36354 AAAAAAATTG
1 AAAAAAAATG
36364 -AAAAAAA-G
1 AAAAAAAATG
36372 AAAAAAA
1 AAAAAAA
36379 TTGATACGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 1 0.03
9 12 0.40
10 8 0.27
11 9 0.30
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.09
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:36367 original size:18 final size:18
Alignment explanation
Indices: 36334--36382 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
36324 AAATTTTGAA
*
36334 AAAAAAATAGAAAAAAAATC
1 AAAAAAATTG-AAAAAAA-C
*
36354 AAAAAAATTGAAAAAAAG
1 AAAAAAATTGAAAAAAAC
36372 AAAAAAATTGA
1 AAAAAAATTGA
36383 TACGAGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 7 0.26
20 9 0.33
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (18 bp):
AAAAAAATTGAAAAAAAC
Found at i:36377 original size:20 final size:20
Alignment explanation
Indices: 36331--36378 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
36321 AAAAAATTTT
36331 GAAAAAAAAATAGAAAAAAA
1 GAAAAAAAAATAGAAAAAAA
* *
36351 -ATCAAAAAAATTGAAAAAAA
1 GA-AAAAAAAATAGAAAAAAA
36371 GAAAAAAA
1 GAAAAAAA
36379 TTGATACGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.08
Consensus pattern (20 bp):
GAAAAAAAAATAGAAAAAAA
Done.