Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2759
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: 32710
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7641 original size:13 final size:13
Alignment explanation
Indices: 7623--7648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7613 CAATTTTTTG
7623 TGTATCGATACAT
1 TGTATCGATACAT
7636 TGTATCGATACAT
1 TGTATCGATACAT
7649 ACTTGGTGTA
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:7663 original size:32 final size:33
Alignment explanation
Indices: 7603--7666 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
7593 TACAAGCCAA
** *
7603 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
7636 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
7667 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:9180 original size:3 final size:3
Alignment explanation
Indices: 9162--9195 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9152 CATCAAGGAC
* *
9162 GAT GAA GAT AAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
9196 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:9402 original size:24 final size:25
Alignment explanation
Indices: 9369--9415 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
9359 TTTGATTGTC
*
9369 CAAACCTAAAGAAGAAAGGCATGAG
1 CAAACCTAAAGAAGAAAGCCATGAG
9394 CAAA-CTAAAGAAGAAAGCCATG
1 CAAACCTAAAGAAGAAAGCCATG
9416 CTAGCCACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.53, C:0.17, G:0.21, T:0.09
Consensus pattern (25 bp):
CAAACCTAAAGAAGAAAGCCATGAG
Found at i:15220 original size:193 final size:193
Alignment explanation
Indices: 14891--15278 Score: 758
Period size: 193 Copynumber: 2.0 Consensus size: 193
14881 ACCGGCCAAA
14891 GACCTAACATTGCCTACTTCATCTTTACCGATATTGTCCGAGATTTAAAAGGCAATTCGACAATC
1 GACCTAACATTGCCTACTTCATCTTTACCGATATTGTCCGAGATTTAAAAGGCAATTCGACAATC
14956 CTTCATGGTATGATCCTTAGTCATTTCTTCGAGGTTAGTGGCATTGATTTGTCATGGGATGCCGG
66 CTTCATGGTATGATCCTTAGTCATTTCTTCGAGGTTAGTGGCATTGATTTGTCATGGGATGCCGG
*
15021 GATTCCTATCTCTCGACCTCGCATCATCGGTTCCAAATCCATGGCCAAGATTGGCTATGAGGT
131 GATTCCTATCTCTCGACCTCGCATCATCGGTTCCAAATCCATGGCCAAGATTGGCTATGAAGT
*
15084 GACCTAACCTTGCCTACTTCATCTTTACCGATATTGTCCGAGATTTAAAAGGCAATTCGACAATC
1 GACCTAACATTGCCTACTTCATCTTTACCGATATTGTCCGAGATTTAAAAGGCAATTCGACAATC
15149 CTTCATGGTATGATCCTTAGTCATTTCTTCGAGGTTAGTGGCATTGATTTGTCATGGGATGCCGG
66 CTTCATGGTATGATCCTTAGTCATTTCTTCGAGGTTAGTGGCATTGATTTGTCATGGGATGCCGG
15214 GATTCCTATCTCTCGACCTCGCATCATCGGTTCCAAATCCATGGCCAAGATTGGCTATGAAGT
131 GATTCCTATCTCTCGACCTCGCATCATCGGTTCCAAATCCATGGCCAAGATTGGCTATGAAGT
15277 GA
1 GA
15279 GAAACCGAAC
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (193 bp):
GACCTAACATTGCCTACTTCATCTTTACCGATATTGTCCGAGATTTAAAAGGCAATTCGACAATC
CTTCATGGTATGATCCTTAGTCATTTCTTCGAGGTTAGTGGCATTGATTTGTCATGGGATGCCGG
GATTCCTATCTCTCGACCTCGCATCATCGGTTCCAAATCCATGGCCAAGATTGGCTATGAAGT
Found at i:16413 original size:13 final size:13
Alignment explanation
Indices: 16395--16419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16385 ATAATGCACA
16395 GTATCGATACATT
1 GTATCGATACATT
16408 GTATCGATACAT
1 GTATCGATACAT
16420 GACTATTGTA
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:16526 original size:13 final size:13
Alignment explanation
Indices: 16508--16535 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16498 ACATACAAGA
16508 TGTATCGATACAT
1 TGTATCGATACAT
16521 TGTATCGATACAT
1 TGTATCGATACAT
16534 TG
1 TG
16536 GCTTGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17504 original size:18 final size:19
Alignment explanation
Indices: 17472--17523 Score: 79
Period size: 18 Copynumber: 2.7 Consensus size: 19
17462 ATGATATAAA
*
17472 TATATATATAATAATTTTT
1 TATATATATATTAATTTTT
17491 TATA-ATATATTAATTTTT
1 TATATATATATTAATTTTT
17509 TATATCATATATTAA
1 TATAT-ATATATTAA
17524 ATGTGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 17 0.57
19 4 0.13
20 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATATATTAATTTTT
Found at i:20188 original size:34 final size:34
Alignment explanation
Indices: 20150--20215 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
20140 ATCCCTATTC
* *
20150 GGTTAAACACATCAAAAATCATTAAATCCTATAT
1 GGTTAAACACATAAAAAATCAGTAAATCCTATAT
20184 GGTTAAACACATAAAAAATCAGTAAATCCTAT
1 GGTTAAACACATAAAAAATCAGTAAATCCTAT
20216 GGAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (34 bp):
GGTTAAACACATAAAAAATCAGTAAATCCTATAT
Found at i:20853 original size:11 final size:11
Alignment explanation
Indices: 20826--20874 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
20816 AAGGGTTTAG
20826 CTTTTTT-TTT
1 CTTTTTTCTTT
* *
20836 CTATTTTCTCT
1 CTTTTTTCTTT
20847 CTTTTTTCTTT
1 CTTTTTTCTTT
20858 C-TTTTTCTTT
1 CTTTTTTCTTT
20868 CTTTTTT
1 CTTTTTT
20875 TCTCTCTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:20877 original size:22 final size:21
Alignment explanation
Indices: 20826--20874 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
20816 AAGGGTTTAG
20826 CTTTTTT-TTTCTATTTTCTCT
1 CTTTTTTCTTTCT-TTTTCTCT
*
20847 CTTTTTTCTTTCTTTTTCTTT
1 CTTTTTTCTTTCTTTTTCTCT
20868 CTTTTTT
1 CTTTTTT
20875 TCTCTCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (21 bp):
CTTTTTTCTTTCTTTTTCTCT
Found at i:20882 original size:22 final size:21
Alignment explanation
Indices: 20826--20887 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
20816 AAGGGTTTAG
20826 CTTTTTTT-TTCTATTTTCTCT
1 CTTTTTTTCTTCT-TTTTCTCT
*
20847 C-TTTTTTCTTTCTTTTTCTTT
1 CTTTTTTTC-TTCTTTTTCTCT
20868 CTTTTTTTCTCTCTTATTTC
1 CTTTTTTTCT-TCTT-TTTC
20888 CTCCACCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 6 0.17
21 10 0.29
22 15 0.43
23 4 0.11
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
CTTTTTTTCTTCTTTTTCTCT
Found at i:20887 original size:11 final size:11
Alignment explanation
Indices: 20826--20887 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
20816 AAGGGTTTAG
*
20826 CTTTTTT-TTT
1 CTTTTTTCTCT
*
20836 CTATTTTCTCT
1 CTTTTTTCTCT
*
20847 CTTTTTTCTTT
1 CTTTTTTCTCT
*
20858 C-TTTTTCTTT
1 CTTTTTTCTCT
20868 CTTTTTTTCTCT
1 C-TTTTTTCTCT
*
20880 CTTATTTC
1 CTTTTTTC
20888 CTCCACCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 16 0.37
11 18 0.42
12 9 0.21
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (11 bp):
CTTTTTTCTCT
Found at i:23231 original size:20 final size:21
Alignment explanation
Indices: 23191--23232 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
23181 AAATATTGAT
23191 TAAAACTAAAACTTCACACTA
1 TAAAACTAAAACTTCACACTA
23212 TAAAA-TAAATACTTCA-ACTA
1 TAAAACTAAA-ACTTCACACTA
23232 T
1 T
23233 TATTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAACTAAAACTTCACACTA
Found at i:30575 original size:13 final size:13
Alignment explanation
Indices: 30557--30582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30547 CAAATTTTTG
30557 TGTATCGATACAT
1 TGTATCGATACAT
30570 TGTATCGATACAT
1 TGTATCGATACAT
30583 ACTTGGTGTA
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:30597 original size:32 final size:33
Alignment explanation
Indices: 30537--30600 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
30527 TACAAGCCAA
* *
30537 TGTATCGATACAAATTTTTGTGTATCGATACAT
1 TGTATCGATACAAATCTTGGTGTATCGATACAT
*
30570 TGTATCGATACATA-CTTGGTGTATCGATACA
1 TGTATCGATACAAATCTTGGTGTATCGATACA
30601 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAAATCTTGGTGTATCGATACAT
Done.