Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2626
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: 34844
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1878 original size:16 final size:17
Alignment explanation
Indices: 1847--1879 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1837 TTAAAGGACG
1847 ACCAAGCACCGGCGGGT
1 ACCAAGCACCGGCGGGT
*
1864 ACCAA-CACTGGCGGGT
1 ACCAAGCACCGGCGGGT
1880 TGACAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.09
Consensus pattern (17 bp):
ACCAAGCACCGGCGGGT
Found at i:9348 original size:6 final size:6
Alignment explanation
Indices: 9330--9362 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
9320 AATGGGAATG
9330 AATAGAA AA-AAA AATAAA AATAAA AATAAA AAT
1 AATA-AA AATAAA AATAAA AATAAA AATAAA AAT
9363 GAACATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.16
6 19 0.76
7 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:12354 original size:22 final size:22
Alignment explanation
Indices: 12326--12380 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
12316 TGGACATGTT
12326 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
12348 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
12370 AAAAATGCATG
1 AAAAATGCATG
12381 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:13338 original size:20 final size:20
Alignment explanation
Indices: 13291--13365 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
13281 AAAAAGACAT
*
13291 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
13310 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
13331 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
13351 AATGCATCGATACAT
1 AATGTATCGATACAT
13366 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:13360 original size:40 final size:39
Alignment explanation
Indices: 13288--13365 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
13278 GGTAAAAAGA
* * *
13288 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
13327 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
13366 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:22270 original size:20 final size:21
Alignment explanation
Indices: 22223--22264 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22213 AGAGAGTTTT
*
22223 AATTGTTTTATCAAGGGGGAG
1 AATTATTTTATCAAGGGGGAG
*
22244 AATTATTTTATTAAGGGGGAG
1 AATTATTTTATCAAGGGGGAG
22265 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (21 bp):
AATTATTTTATCAAGGGGGAG
Found at i:22978 original size:13 final size:13
Alignment explanation
Indices: 22960--22989 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22950 GATACATGGG
*
22960 ACATTGTATTGAT
1 ACATTGTATCGAT
22973 ACATTGTATCGAT
1 ACATTGTATCGAT
22986 ACAT
1 ACAT
22990 GGTAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:23007 original size:33 final size:33
Alignment explanation
Indices: 22944--23012 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
22934 CTAAGTGAAA
* ** *
22944 TGTATCGATACATGGGACATTGTATTGATACAT
1 TGTATCGATACATGGGAAAAAGTATCGATACAT
*
22977 TGTATCGATACATGGTAAAAAGTATCGATACAT
1 TGTATCGATACATGGGAAAAAGTATCGATACAT
23010 TGT
1 TGT
23013 GCCCAACAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGGGAAAAAGTATCGATACAT
Found at i:23924 original size:19 final size:20
Alignment explanation
Indices: 23900--23953 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
23890 ACGTTATGCT
**
23900 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCACAA
23919 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
23939 TTGTATCGATACATG
1 TTGTATCGATACATG
23954 AATCTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:26691 original size:22 final size:21
Alignment explanation
Indices: 26661--26706 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
26651 CTAGACAAGT
26661 ATAAATG-TTTTCAAGGCTTAAA
1 ATAAATGTTTTTCAA-G-TTAAA
*
26683 ATAAGTGTTTTTCAAGTTAAA
1 ATAAATGTTTTTCAAGTTAAA
26704 ATA
1 ATA
26707 TATAAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (21 bp):
ATAAATGTTTTTCAAGTTAAA
Found at i:26843 original size:13 final size:13
Alignment explanation
Indices: 26825--26849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26815 AGATTGCACA
26825 GTATCGATACATT
1 GTATCGATACATT
26838 GTATCGATACAT
1 GTATCGATACAT
26850 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:26968 original size:13 final size:13
Alignment explanation
Indices: 26950--26975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26940 ACACACAATA
26950 TGTATCGATACAT
1 TGTATCGATACAT
26963 TGTATCGATACAT
1 TGTATCGATACAT
26976 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26970 original size:32 final size:33
Alignment explanation
Indices: 26930--26997 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
26920 CCTTAATTGT
*
26930 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
26962 TTGTATCGATACATCCCAAAATGTATTGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
26995 TTG
1 TTG
26998 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:33038 original size:20 final size:21
Alignment explanation
Indices: 33008--33046 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
32998 CTGGAAAAAT
33008 TTCAGAATGTATCGATACAGG
1 TTCAGAATGTATCGATACAGG
33029 TTCA-AATGTATCGATACA
1 TTCAGAATGTATCGATACA
33047 TCTGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (21 bp):
TTCAGAATGTATCGATACAGG
Found at i:33334 original size:21 final size:21
Alignment explanation
Indices: 33308--33364 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
33298 AAAAATTCCA
33308 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
33329 AATGTATTGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
33350 AATGTATCGATACAT
1 AATGTATCGATACAT
33365 CCTACAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:33444 original size:19 final size:19
Alignment explanation
Indices: 33420--33487 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
33410 AATTCAACAA
33420 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
33439 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
33454 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
33471 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
33488 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:33465 original size:32 final size:32
Alignment explanation
Indices: 33422--33484 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
33412 TTCAACAATT
* *
33422 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
33454 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
33485 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:33545 original size:13 final size:13
Alignment explanation
Indices: 33527--33552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33517 CATTTTTCTG
33527 TGTATCGATACAT
1 TGTATCGATACAT
33540 TGTATCGATACAT
1 TGTATCGATACAT
33553 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:33549 original size:33 final size:33
Alignment explanation
Indices: 33507--33573 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
33497 GCCAAGGAAA
***
33507 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
33540 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
33573 T
1 T
33574 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.