Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1361
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: 31415
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Found at i:119 original size:45 final size:46
Alignment explanation
Indices: 65--292 Score: 325
Period size: 46 Copynumber: 5.0 Consensus size: 46
55 TTTCTGTCAT
** * * *
65 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTTAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
** ** *
111 G-TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTC-CGTCAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
*
155 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAAATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
201 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
**
247 GTTGCCATAATATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
293 AGAGCACACT
Statistics
Matches: 169, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
44 4 0.02
45 72 0.43
46 93 0.55
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
Found at i:185 original size:90 final size:91
Alignment explanation
Indices: 49--291 Score: 344
Period size: 90 Copynumber: 2.7 Consensus size: 91
39 GTCCTTACTC
** * *
49 ATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTTACG-T
1 ATTCA-TTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTT
113 GCCATGGTATCTTTCAACCATGGTCTT
65 GCCATGGTATCTTTCAACCATGGTCTT
* * *
140 ATTCATTTCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAAATCAGGTTG
1 ATTCATTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTG
205 CCATGGTATCTTTCAACCATGGTCTT
66 CCATGGTATCTTTCAACCATGGTCTT
** * * **
231 ACACATTTCATATCAGGTTGCCATAATATCTTTCAACCATGGTCTTACACATTTCATATCA
1 ATTCATTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
292 GAGAGCACAC
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
90 50 0.37
91 40 0.30
92 45 0.33
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (91 bp):
ATTCATTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTG
CCATGGTATCTTTCAACCATGGTCTT
Found at i:2361 original size:16 final size:16
Alignment explanation
Indices: 2342--2380 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2332 AATTTTTCCC
*
2342 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
2358 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
2374 TCTTTCC
1 TTTTTCC
2381 CTGCTCTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:2600 original size:25 final size:25
Alignment explanation
Indices: 2572--2623 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2562 TACTTTTACT
2572 TAATAATAATAA-TAAATTAATA-ATA
1 TAAT-ATAATAAGTAAATT-ATACATA
2597 TAATATAATAAGTAAATTATACATA
1 TAATATAATAAGTAAATTATACATA
2622 TA
1 TA
2624 TTTTAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
TAATATAATAAGTAAATTATACATA
Found at i:4470 original size:52 final size:53
Alignment explanation
Indices: 4366--4471 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 53
4356 AAAAAGAAGT
* *
4366 ATAGTTCTATATGGATTTTACTTTTATTTTATTTTATCACTGTATTTTATTTA
1 ATAGTTCTATATCGATTTTACTTTTATTTTATTTTATAACTGTATTTTATTTA
4419 ATAGTTCTATATACGA-TTTACTTTTA-TTTATTTTATAACTGTATTTTATTTA
1 ATAGTTCTATAT-CGATTTTACTTTTATTTTATTTTATAACTGTATTTTATTTA
4471 A
1 A
4472 CAAAGATTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
52 26 0.52
53 22 0.44
54 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (53 bp):
ATAGTTCTATATCGATTTTACTTTTATTTTATTTTATAACTGTATTTTATTTA
Found at i:6099 original size:18 final size:18
Alignment explanation
Indices: 6076--6180 Score: 88
Period size: 18 Copynumber: 5.6 Consensus size: 18
6066 TCATTATAGC
6076 ATTATTCAGTAACAGTCA
1 ATTATTCAGTAACAGTCA
*
6094 ATTATTCAGCTCAATAACG-C-
1 ATTATTCAG-T-AA-CA-GTCA
6114 ATTATATCAGATAACAGTCA
1 ATTAT-TCAG-TAACAGTCA
* *
6134 TTTATTCAGTAACAGTTA
1 ATTATTCAGTAACAGTCA
**
6152 ATTATTCAGTAGTAGTCA
1 ATTATTCAGTAACAGTCA
*
6170 GTTATTCAGTA
1 ATTATTCAGTA
6181 CATTTAATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
18 42 0.60
19 7 0.10
20 13 0.19
21 7 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
ATTATTCAGTAACAGTCA
Found at i:8317 original size:39 final size:41
Alignment explanation
Indices: 8273--8365 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
8263 GTTTTTAGGG
* *
8273 TAAATCCTATCCACCTT-AAGTTACTATAGTGAATCAAG-A
1 TAAATCCTATCCACCTTAAAATTACCATAGTGAATCAAGAA
*
8312 TAAATCTCTATTCA-CTTAAAATTACCATAGTGAATCAAGAA
1 TAAATC-CTATCCACCTTAAAATTACCATAGTGAATCAAGAA
*
8353 CAAATCCT-TCCAC
1 TAAATCCTATCCAC
8366 TTTTGAGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
39 12 0.27
40 27 0.60
41 6 0.13
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.30
Consensus pattern (41 bp):
TAAATCCTATCCACCTTAAAATTACCATAGTGAATCAAGAA
Found at i:9977 original size:16 final size:17
Alignment explanation
Indices: 9946--9978 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9936 TTCATAAGTA
9946 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
9963 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
9979 GCTTCATCAT
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:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:10574 original size:46 final size:46
Alignment explanation
Indices: 10259--10566 Score: 406
Period size: 46 Copynumber: 6.7 Consensus size: 46
10249 TTATCTTTAA
* * * * * *
10259 CATGATGCCATAGTGTCTTTCAACTACGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
* *
10305 CATGTTGTCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* *
10351 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* *
10397 CACGTTGCCATGGTATCTTTCAACCATGGTTTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * *
10443 CACGTTGCCATGGTATC-TTCAACCATAGTCTT-TTCATTTCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* ** *
10487 CATGTTGCTATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
*
10533 CATGTTGCCATGGTATCTTTCAACCACGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
10567 CACATTTCTT
Statistics
Matches: 235, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
44 26 0.11
45 31 0.13
46 178 0.76
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:12362 original size:11 final size:11
Alignment explanation
Indices: 12346--12393 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
12336 CTTTATATAC
12346 TAATAAAATAA
1 TAATAAAATAA
12357 TAATAAAATATA
1 TAATAAAATA-A
* *
12369 TTATTAAAATAT
1 -TAATAAAATAA
12381 TAATAAAATAA
1 TAATAAAATAA
12392 TA
1 TA
12394 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 21 0.68
12 1 0.03
13 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:12376 original size:24 final size:24
Alignment explanation
Indices: 12340--12395 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
12330 TTCTTTCTTT
*
12340 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* *
12364 ATATATTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
12388 ATAATATT
1 AT-ATATT
12396 TATCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:15674 original size:3 final size:3
Alignment explanation
Indices: 15666--15697 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
15656 CATATATTTT
15666 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
15698 TCCATTCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:18936 original size:11 final size:11
Alignment explanation
Indices: 18917--18961 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
18907 TAAATATTTA
18917 TAATAAAATAT
1 TAATAAAATAT
*
18928 TAGTAAAATAT
1 TAATAAAATAT
*
18939 CTCATTAAAATAT
1 -T-AATAAAATAT
18952 TAATAAAATA
1 TAATAAAATA
18962 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 18 0.62
12 2 0.07
13 9 0.31
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Done.