Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2164
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: 8341
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2329 original size:10 final size:11
Alignment explanation
Indices: 2306--2345 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
2296 TTATTAATAT
2306 TAATT-TTAAG
1 TAATTATTAAG
2316 TAATTATTAA-
1 TAATTATTAAG
2326 TAATT-TTAAG
1 TAATTATTAAG
2336 TAATTATTAA
1 TAATTATTAA
2346 TATTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 15 0.56
11 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
TAATTATTAAG
Found at i:2352 original size:10 final size:10
Alignment explanation
Indices: 2306--2352 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
2296 TTATTAATAT
2306 TAATT-TTAA
1 TAATTATTAA
2315 GTAATTATTAA
1 -TAATTATTAA
2326 TAATT-TTAA
1 TAATTATTAA
2335 GTAATTATTAA
1 -TAATTATTAA
*
2346 TATTTAT
1 TAATTAT
2353 ATTAATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 4 0.12
10 21 0.64
11 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (10 bp):
TAATTATTAA
Found at i:2357 original size:23 final size:22
Alignment explanation
Indices: 2296--2349 Score: 85
Period size: 20 Copynumber: 2.5 Consensus size: 22
2286 GTTATTAATG
2296 TTATTAATATTAATTTTAAGTAA
1 TTATTAATATT-ATTTTAAGTAA
2319 TTATTAATA--ATTTTAAGTAA
1 TTATTAATATTATTTTAAGTAA
2339 TTATTAATATT
1 TTATTAATATT
2350 TATATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 20 0.69
23 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
TTATTAATATTATTTTAAGTAA
Found at i:2411 original size:21 final size:21
Alignment explanation
Indices: 2385--2454 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 21
2375 TCGATTTCGA
2385 AATCTATATTTCTATATTATT
1 AATCTATATTTCTATATTATT
2406 AATCTATATTTCTAATTTCTATATTATT
1 AATC--TA----T-ATTTCTATATTATT
2434 AATCTATATTTCTATATTATT
1 AATCTATATTTCTATATTATT
2455 TATATTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
21 18 0.43
22 1 0.02
23 2 0.05
26 2 0.05
27 1 0.02
28 18 0.43
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
AATCTATATTTCTATATTATT
Found at i:2413 original size:13 final size:13
Alignment explanation
Indices: 2395--2443 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
2385 AATCTATATT
2395 TCTATATTATTAA
1 TCTATATTATTAA
2408 TCTATATT-TCTAA
1 TCTATATTAT-TAA
2421 TTTCTATATTATTAA
1 --TCTATATTATTAA
2436 TCTATATT
1 TCTATATT
2444 TCTATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (13 bp):
TCTATATTATTAA
Found at i:2428 original size:28 final size:29
Alignment explanation
Indices: 2387--2463 Score: 129
Period size: 28 Copynumber: 2.7 Consensus size: 29
2377 GATTTCGAAA
2387 TCTATATTTCTATATTATTAATCTATATT
1 TCTATATTTCTATATTATTAATCTATATT
2416 TCTA-ATTTCTATATTATTAATCTATATT
1 TCTATATTTCTATATTATTAATCTATATT
*
2444 TCTATATTATTTATATTATT
1 TCTATATT-TCTATATTATT
2464 TATTAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 28 0.62
29 7 0.16
30 10 0.22
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (29 bp):
TCTATATTTCTATATTATTAATCTATATT
Found at i:2483 original size:49 final size:49
Alignment explanation
Indices: 2385--2518 Score: 144
Period size: 49 Copynumber: 2.7 Consensus size: 49
2375 TCGATTTCGA
* * * *
2385 AATCTATATTTCTATATTATTAATCTATATTT-CTAATTTCTATATTATT
1 AATCTATATTTCTATATTATTTATAT-TATTTACTAATATATATATTATT
*
2434 AATCTATATTTCTATATTATTTATATTATTTATTAATATATAATATATTATT
1 AATCTATATTTCTATATTATTTATATTATTTACT-A-ATAT-ATATATTATT
* * *
2486 ATTATATTATTTATATATTATTTATATTATTTA
1 AATCTA-TATTTCTATATTATTTATATTATTTA
2519 AATATTATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
48 5 0.07
49 25 0.35
50 1 0.01
51 3 0.04
52 13 0.18
53 25 0.35
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (49 bp):
AATCTATATTTCTATATTATTTATATTATTTACTAATATATATATTATT
Found at i:2484 original size:31 final size:31
Alignment explanation
Indices: 2425--2558 Score: 100
Period size: 34 Copynumber: 4.3 Consensus size: 31
2415 TTCTAATTTC
* *
2425 TATATTATTAATCT-ATAT-TTCTATATTATT
1 TATATTATTTAT-TAATATATTATATATTATT
*
2455 TATATTATTTATTAATATATAATATATTATTAT
1 TATATTATTTATTAATATATTATATATTA-T-T
* **
2488 TATATTATTTATATATTAT-TTATATTATTTAAA
1 TATATTATTTAT-TAATATATTATA-TA-TTATT
2521 TATTATTATTTATTTAA-ATATTAT-TATTATT
1 TA-TATTATTTA-TTAATATATTATATATTATT
2552 TA-ATTAT
1 TATATTAT
2559 ATTTAAATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
29 6 0.07
30 15 0.18
31 13 0.15
32 3 0.04
33 21 0.25
34 22 0.26
35 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (31 bp):
TATATTATTTATTAATATATTATATATTATT
Found at i:2493 original size:11 final size:11
Alignment explanation
Indices: 2448--2561 Score: 65
Period size: 11 Copynumber: 11.1 Consensus size: 11
2438 TATATTTCTA
2448 TATTATTTATAT
1 TATTA-TTATAT
2460 TATTTATTA-A-
1 TA-TTATTATAT
*
2470 TATATAATATAT
1 TAT-TATTATAT
2482 TATTATTATAT
1 TATTATTATAT
2493 TA-T-TTATA-
1 TATTATTATAT
2501 TATTATT-TA-
1 TATTATTATAT
*
2510 TATTATT-TAAA
1 TATTATTAT-AT
2521 TATTATTAT-T
1 TATTATTATAT
*
2531 TATT-TAAATAT
1 TATTAT-TATAT
2542 TATTATTAT-T
1 TATTATTATAT
2552 TA--ATTATAT
1 TATTATTATAT
2561 T
1 T
2562 TAAATTATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
8 7 0.08
9 20 0.24
10 19 0.23
11 25 0.30
12 10 0.12
13 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2542 original size:60 final size:59
Alignment explanation
Indices: 2438--2620 Score: 185
Period size: 60 Copynumber: 3.0 Consensus size: 59
2428 ATTATTAATC
* *
2438 TATATT-TCTATATTATTT--ATATTATTTATTAATATATAATATATTATTATTATATTATTTA
1 TATATTATTTATATTATTTAAATATTA-TTATT--TATTTAA-ATATTATTATTAT-TTATTTA
*
2499 TATATTATTTATATTATTTAAATATTATTATTTATTTAAATATTATTATTATTTAATTA
1 TATATTATTTATATTATTTAAATATTATTATTTATTTAAATATTATTATTATTTATTTA
* * * * *
2558 TAT-TTAAATTATTTATATTTAAATATTATTTTTTATTTAAATTATTATTTTTTTTTTATTTA
1 TATATT-ATTTATAT-TATTTAAATATTATTATTTATTTAAA-TATTA-TTATTATTTATTTA
2620 T
1 T
2621 TTTTTTTTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
58 2 0.02
59 15 0.14
60 38 0.36
61 17 0.16
62 23 0.22
63 5 0.05
64 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (59 bp):
TATATTATTTATATTATTTAAATATTATTATTTATTTAAATATTATTATTATTTATTTA
Found at i:2568 original size:25 final size:28
Alignment explanation
Indices: 2482--2588 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 28
2472 TATAATATAT
*
2482 TATTATTATATTATTTATATATTATTT--A
1 TATTATT-TA-TATTTAAATATTATTTAAA
* *
2510 TATTATTTAAATATT-ATTATTTATTTAAA
1 TATTATTTATAT-TTAAATA-TTATTTAAA
*
2539 TATTA-TTATTATTTAATTA-TATTT-AA
1 TATTATTTA-TATTTAAATATTATTTAAA
2565 -ATTATTTATATTTAAATATTATTT
1 TATTATTTATATTTAAATATTATTT
2589 TTTATTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
25 13 0.20
26 14 0.21
27 15 0.23
28 12 0.18
29 12 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTATTTATATTTAAATATTATTTAAA
Found at i:2575 original size:15 final size:15
Alignment explanation
Indices: 2555--2603 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
2545 TATTATTTAA
2555 TTATATTTAAATTAT
1 TTATATTTAAATTAT
2570 TTATATTTAAATATTATT
1 TTATATTT-AA-ATTA-T
*
2588 TTTTATTTAAATTAT
1 TTATATTTAAATTAT
2603 T
1 T
2604 ATTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.33
16 6 0.20
17 6 0.20
18 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTTAAATTAT
Found at i:2625 original size:17 final size:18
Alignment explanation
Indices: 2581--2636 Score: 78
Period size: 17 Copynumber: 3.1 Consensus size: 18
2571 TATATTTAAA
*
2581 TATTATTTTTTATTTAAAT
1 TATTATTTTTT-TTTAATT
*
2600 TATTATTTTTTTTTTATT
1 TATTATTTTTTTTTAATT
2618 TATT-TTTTTTTTTAATT
1 TATTATTTTTTTTTAATT
2635 TA
1 TA
2637 AGTTAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 14 0.41
18 9 0.26
19 11 0.32
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTATTTTTTTTTAATT
Found at i:2678 original size:43 final size:45
Alignment explanation
Indices: 2594--2678 Score: 102
Period size: 43 Copynumber: 1.9 Consensus size: 45
2584 TATTTTTTAT
* * ** **
2594 TTAAATTATTATTTTTTTTTTATTTATTTTTTTTTTTAATTTAAG
1 TTAAATTATTATTTTTATTTTATTAATTTTAATTTCGAATTTAAG
2639 TTAAA-TA-TATTTTTATTTTATTAATTTTAATTTCGAATTT
1 TTAAATTATTATTTTTATTTTATTAATTTTAATTTCGAATTT
2679 GATTTTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 27 0.79
44 2 0.06
45 5 0.15
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (45 bp):
TTAAATTATTATTTTTATTTTATTAATTTTAATTTCGAATTTAAG
Found at i:6914 original size:15 final size:15
Alignment explanation
Indices: 6894--6927 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
6884 ATACAATATC
6894 AATATTAAATTAAAT
1 AATATTAAATTAAAT
6909 AATATTAAATTAAAT
1 AATATTAAATTAAAT
6924 AATA
1 AATA
6928 GGTAATAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATTAAATTAAAT
Done.