Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold727
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: 51767
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:10911 original size:132 final size:132
Alignment explanation
Indices: 10674--11415 Score: 1247
Period size: 132 Copynumber: 5.6 Consensus size: 132
10664 TTGAAGTCAT
*
10674 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
*
10739 ACATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
10804 CA
131 CA
*
10806 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
* *
10871 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
10936 CA
131 CA
*
10938 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
* *
11003 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
11068 CA
131 CA
* * * *
11070 GAAAGCAGATTTTTTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCTT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
*
11135 ATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
11200 CA
131 CA
* *
11202 GAAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
11267 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGT-G-GAAGTAGATCG
66 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
*
11330 AA
131 CA
* * * * **
11332 GGAAGCAGATCTTGTATTCATATATTGGTGTGGAA-TAGATCGAAGATAGCAGATCCTGCCTTCC
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGT-GAAGTAGATCGAAGATAGCAGATCCTATCTTCC
*
11396 TATATTGGTAGGAAGTGGAT
65 TATATTGATAGGAAGTGGAT
11416 TGAAAAACAG
Statistics
Matches: 581, Mismatches: 28, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
130 83 0.14
131 4 0.01
132 494 0.85
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCT
ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
CA
Found at i:11616 original size:40 final size:40
Alignment explanation
Indices: 11567--11883 Score: 318
Period size: 40 Copynumber: 7.8 Consensus size: 40
11557 AAGATTTCAG
* * *
11567 GTCTTATCTCCCTAAGTAATAGTAGAGCAGATCGCATCAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* ** *
11607 GTCTCATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAACCACA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GCATCA-A
*
11648 GATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* *
11689 GTCTTATCTCCCTAAGCAGTAGTGGAG-AGGA-CGAAACCACA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCG-CATCA-A
11730 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* * * * *
11771 GTCTTATCTCCTTAAGCAGTAGCGGAGCAGA-AGAAACCACA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-CATCA-A
* * * *
11812 GATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACACCCA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* **
11853 GTCTTATCTCTCTAAATAGTAGTGGAGCAGA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
11884 CTAAAAACAC
Statistics
Matches: 232, Mismatches: 31, Indels: 28
0.80 0.11 0.10
Matches are distributed among these distances:
39 5 0.02
40 119 0.51
41 12 0.05
42 92 0.40
43 4 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (40 bp):
GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
Found at i:11659 original size:82 final size:82
Alignment explanation
Indices: 11568--11899 Score: 470
Period size: 82 Copynumber: 4.0 Consensus size: 82
11558 AGATTTCAGG
* * *
11568 TCTTATCTCCCTAAGTAATAGTAGAGCAGATCGCATCAAGTCTCATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
11633 GCAGACAAAACCACAGA
66 GCAGACAAAACCACAGA
11650 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
*
11715 G-AGGACGAAACCACAGA
66 GCA-GACAAAACCACAGA
* * *
11732 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCTTAAGCAGTAGCGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
11797 GCAGA-AGAAACCACAGA
66 GCAGACA-AAACCACAGA
* * * * * * **
11814 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACACCCAGTCTTATCTCTCTAAATAGTAGTGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
* *
11879 GCAGACTAAAAACACAAA
66 GCAGAC-AAAACCACAGA
11897 TCT
1 TCT
11900 CATCCCCATG
Statistics
Matches: 226, Mismatches: 19, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
81 1 0.00
82 212 0.94
83 12 0.05
84 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (82 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
GCAGACAAAACCACAGA
Found at i:12373 original size:15 final size:15
Alignment explanation
Indices: 12353--12384 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12343 ATGCGTGGCC
12353 CCCTCGTCTGCCACG
1 CCCTCGTCTGCCACG
12368 CCCTCGTCTGCCACG
1 CCCTCGTCTGCCACG
12383 CC
1 CC
12385 TCCAACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.56, G:0.19, T:0.19
Consensus pattern (15 bp):
CCCTCGTCTGCCACG
Found at i:12967 original size:10 final size:10
Alignment explanation
Indices: 12942--12974 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12932 GGGAGTTTCC
12942 CTTTATTTTTT
1 CTTT-TTTTTT
12953 C-TTTTTTTT
1 CTTTTTTTTT
12962 CTTTTTTTTT
1 CTTTTTTTTT
12972 CTT
1 CTT
12975 CTTGCGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 13 0.62
11 1 0.05
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:13478 original size:16 final size:16
Alignment explanation
Indices: 13459--13489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13449 TATTGTTATC
*
13459 TATTTATTTATATTTA
1 TATTTATTTAAATTTA
13475 TATTTATTTAAATTT
1 TATTTATTTAAATTT
13490 TCAGTACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTAAATTTA
Found at i:14869 original size:16 final size:17
Alignment explanation
Indices: 14848--14880 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14838 ATGATGGAGC
14848 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
14864 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
14881 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:24301 original size:21 final size:21
Alignment explanation
Indices: 24277--24318 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24267 TCAGAAAATA
24277 ATAACAAGATTAGTCTTAGGT
1 ATAACAAGATTAGTCTTAGGT
24298 ATAACAAGATTAGTCTTAGGT
1 ATAACAAGATTAGTCTTAGGT
24319 TTCATTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
ATAACAAGATTAGTCTTAGGT
Found at i:31893 original size:40 final size:40
Alignment explanation
Indices: 31839--31955 Score: 200
Period size: 40 Copynumber: 3.0 Consensus size: 40
31829 GGGAAAAATA
31839 TATAA-CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
31878 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGAGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
31918 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
31956 GTTACATCCG
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 5 0.07
40 68 0.93
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:39859 original size:40 final size:40
Alignment explanation
Indices: 39804--39916 Score: 208
Period size: 40 Copynumber: 2.8 Consensus size: 40
39794 GAAAAATATA
*
39804 TATAATCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
39844 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
39884 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGC
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGC
39917 TAGTTGTTAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:42466 original size:19 final size:19
Alignment explanation
Indices: 42438--42486 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
42428 CTAGTTGTTT
* *
42438 TCCCTCTTGATTAGCATTC
1 TCCCTTTTGATTAGCAGTC
42457 TCCCTTTTGATTAGCAGTC
1 TCCCTTTTGATTAGCAGTC
42476 TCCCTTTTGAT
1 TCCCTTTTGAT
42487 CTTATTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.12, T:0.45
Consensus pattern (19 bp):
TCCCTTTTGATTAGCAGTC
Found at i:43873 original size:17 final size:16
Alignment explanation
Indices: 43841--43872 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43831 ATAATGTTGA
43841 ATTCAGTGGATTTTTT
1 ATTCAGTGGATTTTTT
43857 ATTCAGTGGATTTTTT
1 ATTCAGTGGATTTTTT
43873 TGCATTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (16 bp):
ATTCAGTGGATTTTTT
Found at i:44976 original size:20 final size:20
Alignment explanation
Indices: 44948--44987 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44938 ATTTAGTTTT
* *
44948 TGCTTTAAAAAATCAAAGAA
1 TGCTCTAAAAAATAAAAGAA
44968 TGCTCTAAAAAATAAAAGAA
1 TGCTCTAAAAAATAAAAGAA
44988 AATTTTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (20 bp):
TGCTCTAAAAAATAAAAGAA
Found at i:49676 original size:3 final size:3
Alignment explanation
Indices: 49668--49717 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
49658 TTGTATTTCA
* *
49668 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49715 TAT
1 TAT
49718 ATGTATATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Done.