Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01784.F2
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: 4688
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Found at i:114 original size:14 final size:14
Alignment explanation
Indices: 95--122 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
85 GCAGAGCCGA
95 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
109 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
123 GCAGCGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
AGGGAGAGGGAGAG
Found at i:2389 original size:24 final size:24
Alignment explanation
Indices: 2357--2616 Score: 78
Period size: 24 Copynumber: 10.0 Consensus size: 24
2347 CTCTTCCTCT
2357 TCTCTCCTTC-GAGCATCCTCTTCC
1 TCTCTCCTTCTG-GCATCCTCTTCC
*
2381 TCTCTCCTTCTGGCCTCCTCTTCC
1 TCTCTCCTTCTGGCATCCTCTTCC
* * * *
2405 TCT-TCCGTCCTAGCTTCTTCTTCCTCC
1 TCTCTCC-TTCTGGCATC--C-TCTTCC
* *
2432 TCTCTCCTCCTGGCCTCTTCTTCCTCCTCC
1 TCTCTCCTTCTGGCATC--C-T-CT--TCC
* * *
2462 TCTCTCCTTCTGGCCTCCTTTTCT
1 TCTCTCCTTCTGGCATCCTCTTCC
* *
2486 TCTCTTCTCTTAGCT-TCTTCCTCTTCC
1 TCTC-TC-CTT--CTGGCATCCTCTTCC
* *
2513 TCTCTCCTTCTCTTAGCTTCTTCCTCTTCC
1 TCTCTCC-T-TC-T-G--GCATCCTCTTCC
* * **
2543 TCTCTCCTTCTGGCCTCCTTTTTT
1 TCTCTCCTTCTGGCATCCTCTTCC
* *
2567 TCTCTTCTCTTAGCT-TCTTCCTCTTCC
1 TCTC-TC-CTT--CTGGCATCCTCTTCC
*
2594 TCTCTCCTTCTGGCTTCCTCTTC
1 TCTCTCCTTCTGGCATCCTCTTC
2617 TTCTTCCCTT
Statistics
Matches: 185, Mismatches: 26, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
23 5 0.03
24 58 0.31
25 10 0.05
26 15 0.08
27 47 0.25
28 11 0.06
29 1 0.01
30 38 0.21
ACGTcount: A:0.02, C:0.44, G:0.07, T:0.47
Consensus pattern (24 bp):
TCTCTCCTTCTGGCATCCTCTTCC
Found at i:2401 original size:51 final size:52
Alignment explanation
Indices: 2346--2627 Score: 168
Period size: 51 Copynumber: 5.3 Consensus size: 52
2336 CTTGTAGCTC
* *
2346 CCTCTTCCTCTTCTC-TCCTTCGAGCATCCTCTTCCTCTCTCCTTCTGGCCT
1 CCTCTTCCTCTTCTCTTCCTTAGAGCTTCCTCTTCCTCTCTCCTTCTGGCCT
* ** * * *
2397 CCTCTTCCTCTTC-CGTCC-TAGCTTCTTCTTCCTCCTCTCTCCTCCTGGCCT
1 CCTCTTCCTCTTCTCTTCCTTAG-AGCTTCCTCTTCCTCTCTCCTTCTGGCCT
* * * * * * * *
2448 CTTCTTCCTCCTCCTCTCTCCTTCTG-GCCTCCTTTTCTTCTCTTCTCTTAGCT-TCTT
1 CCTCTTCCT-CTTCTCT-TCCTT-AGAGCTTCCTCTTCCTCTC-TC-CTT--CTGGCCT
**
2505 CCTCTTCCTC-TCTCCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCTTCTGGCCT
1 CCTCTTCCTCTTCT-CTTC-CTTAG-AGCTTCCTCTTCCTCTCTCCTTCTGGCCT
* ** *
2559 CCT-TT--TTTTCTCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCTTCTGGCTT
1 CCTCTTCCTCTTCTCTTC-CTTAG-AGCTTCCTCTTCCTCTCTCCTTCTGGCCT
* *
2610 CCTCTTCTTCTTCCCTTC
1 CCTCTTCCTCTTCTCTTC
2628 TCTTTTGGGC
Statistics
Matches: 178, Mismatches: 33, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
50 3 0.02
51 90 0.51
52 8 0.04
53 5 0.03
54 26 0.15
55 11 0.06
56 11 0.06
57 22 0.12
58 2 0.01
ACGTcount: A:0.02, C:0.45, G:0.06, T:0.47
Consensus pattern (52 bp):
CCTCTTCCTCTTCTCTTCCTTAGAGCTTCCTCTTCCTCTCTCCTTCTGGCCT
Found at i:2430 original size:30 final size:29
Alignment explanation
Indices: 2396--2478 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 29
2386 CCTTCTGGCC
* *
2396 TCCTCTTCCTCTTCCGTCCTAGCTTCTTCT
1 TCCTCCTCCTCTTCC-TCCTAGCCTCTTCT
*
2426 TCCTCCT-CTC-TCCTCCTGGCCTCTTCT
1 TCCTCCTCCTCTTCCTCCTAGCCTCTTCT
* *
2453 TCCTCCTCCTCTCTCCTTCTGGCCTC
1 TCCTCCTCCTCT-TCCTCCTAGCCTC
2479 CTTTTCTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 19 0.41
28 6 0.13
29 3 0.07
30 18 0.39
ACGTcount: A:0.01, C:0.49, G:0.07, T:0.42
Consensus pattern (29 bp):
TCCTCCTCCTCTTCCTCCTAGCCTCTTCT
Found at i:2432 original size:27 final size:27
Alignment explanation
Indices: 2378--2469 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
2368 AGCATCCTCT
* * *
2378 TCCTCTCTCCTTCTGGCCTCCTCTTCC
1 TCCTCTCTCCTCCTAGCCTCTTCTTCC
* *
2405 T-CT-TC-CGTCCTAGCTTCTTCTTCC
1 TCCTCTCTCCTCCTAGCCTCTTCTTCC
*
2429 TCCTCTCTCCTCCTGGCCTCTTCTTCC
1 TCCTCTCTCCTCCTAGCCTCTTCTTCC
2456 TCCTC-CTCTCTCCT
1 TCCTCTCTC-CTCCT
2470 TCTGGCCTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 7 0.13
27 27 0.51
ACGTcount: A:0.01, C:0.50, G:0.07, T:0.42
Consensus pattern (27 bp):
TCCTCTCTCCTCCTAGCCTCTTCTTCC
Found at i:2458 original size:17 final size:15
Alignment explanation
Indices: 2430--2478 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2420 TCTTCTTCCT
2430 CCTCTCTCCTCCTGG
1 CCTCTCTCCTCCTGG
2445 CCTCTTCTTCCTCCT--
1 CCTC-TC-TCCTCCTGG
*
2460 CCTCTCTCCTTCTGG
1 CCTCTCTCCTCCTGG
2475 CCTC
1 CCTC
2479 CTTTTCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 12 0.41
16 2 0.07
17 7 0.24
ACGTcount: A:0.00, C:0.53, G:0.08, T:0.39
Consensus pattern (15 bp):
CCTCTCTCCTCCTGG
Found at i:2500 original size:81 final size:82
Alignment explanation
Indices: 2372--2700 Score: 356
Period size: 81 Copynumber: 4.1 Consensus size: 82
2362 CCTTCGAGCA
* * *
2372 TCCTCTTCCTCTCTCCTTCTGGCCTCCTCTTC--CTCTTCCGTCCTAGCTTCTTCTTCCTCCTCT
1 TCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCC-TCTTAGCTTCTTCCTCCTCCTCT
* *
2435 CTCCTCCTGGCCTCTTCT
65 CTCCTTCTGGCCTCCTCT
* *
2453 TCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTT-CTCTTAGCTTCTTCCTCTTCCTCTC
1 TCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCCTCTTAGCTTCTTCCTCCTCCTCTC
* *
2517 TCCTTCT--CTTAGCTTCT
66 TCCTTCTGGCCT--CCTCT
* *
2534 TCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTT-CTCTTAGCTTCTTCCTCTTCCTCTC
1 TCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCCTCTTAGCTTCTTCCTCCTCCTCTC
*
2598 TCCTTCTGGCTTCCTCT
66 TCCTTCTGGCCTCCTCT
* * **
2615 TCTTCTTCC-CT-TCTCTTTTGGGCCT-CTTCTTCCGCT-TTCCTCTTAGCTTCTTCCTCCT-CT
1 TCCTCTTCCTCTCTC-CTTCT-GGCCTCCTT-TTCTTCTCTTCCTCTTAGCTTCTTCCTCCTCCT
* *
2675 CTTTTCTTTCTGGCCTCCTCT
63 C-TCTCCTTCTGGCCTCCTCT
2696 TCCTC
1 TCCTC
2701 CTCTTTCCTC
Statistics
Matches: 217, Mismatches: 20, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
79 4 0.02
80 14 0.06
81 190 0.88
82 1 0.00
83 8 0.04
ACGTcount: A:0.02, C:0.43, G:0.07, T:0.48
Consensus pattern (82 bp):
TCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCCTCTTAGCTTCTTCCTCCTCCTCTC
TCCTTCTGGCCTCCTCT
Found at i:2525 original size:30 final size:30
Alignment explanation
Indices: 2489--2553 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
2479 CTTTTCTTCT
2489 CTTCTCTTAGCTTCTTCCTCTTCCTCTCTC
1 CTTCTCTTAGCTTCTTCCTCTTCCTCTCTC
2519 CTTCTCTTAGCTTCTTCCTCTTCCTCTCTC
1 CTTCTCTTAGCTTCTTCCTCTTCCTCTCTC
2549 CTTCT
1 CTTCT
2554 GGCCTCCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.03, C:0.43, G:0.03, T:0.51
Consensus pattern (30 bp):
CTTCTCTTAGCTTCTTCCTCTTCCTCTCTC
Found at i:2628 original size:24 final size:24
Alignment explanation
Indices: 2532--2616 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
2522 CTCTTAGCTT
2532 CTTCCTCTTCCTCTCTCCTTCTGG
1 CTTCCTCTTCCTCTCTCCTTCTGG
* * ** *
2556 CCTCCTTTTTTTCTCTTCTCTTAGCT-T
1 CTTCCTCTTCCTCTC-TC-CTT--CTGG
2583 CTTCCTCTTCCTCTCTCCTTCTGG
1 CTTCCTCTTCCTCTCTCCTTCTGG
2607 CTTCCTCTTC
1 CTTCCTCTTC
2617 TTCTTCCCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
23 2 0.04
24 21 0.46
25 5 0.11
26 5 0.11
27 11 0.24
28 2 0.04
ACGTcount: A:0.01, C:0.42, G:0.06, T:0.51
Consensus pattern (24 bp):
CTTCCTCTTCCTCTCTCCTTCTGG
Found at i:2641 original size:51 final size:49
Alignment explanation
Indices: 2535--2643 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 49
2525 TTAGCTTCTT
* **
2535 CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAGCTTCTT
1 CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCCCTTCTCTTA--TTCGG
* *
2586 CCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCTTCTTCCCTTCTCTT-TTGGG
1 CCTCTTCCTCTCTCCTTCTGGCCTCCT-TT-TT-TTCCCTTCTCTTATTCGG
2637 CCTCTTC
1 CCTCTTC
2644 TTCCGCTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
51 35 0.70
52 2 0.04
53 2 0.04
54 11 0.22
ACGTcount: A:0.01, C:0.41, G:0.07, T:0.50
Consensus pattern (49 bp):
CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCCCTTCTCTTATTCGG
Found at i:2724 original size:30 final size:30
Alignment explanation
Indices: 2418--2737 Score: 83
Period size: 30 Copynumber: 11.7 Consensus size: 30
2408 TCCGTCCTAG
* * *
2418 CTTCTTCTTCCTCCTCTCTCCTCCTGGCCT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
* * * *
2448 CTTCTTCCTCCTCCTCTCTCCTTCTGGC--
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
* * * *
2476 C-TCCT-TTTCTTCTC-TT-CTCTTAGCTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
* * *
2502 CTTCCTCTTCCTCTCTCCTT-CTCTTAGCTT
1 CTTCCTCTTCCTC-CTCTTTCCTCCTGGCTT
*
2532 CTTCCTCTTCCT-CTC--TCCTTCTGGC--
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
** * * *
2557 C-TCCT-TTTTTTCTC-TT-CTCTTAGCTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
*
2583 CTTCCTCTTCCT-CTC--TCCTTCTGGCTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
* * * *
2610 CCTCTTCTTCTTCC-C-TT-CT-CT--TTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
*** * * * *
2634 GGGCCTCTTCTTCCGCTTTCCTCTTAGCTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
* * *
2664 CTTCCTCCT-CT-CT-TTTCTTTCTGGC--
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
2689 C-TCCTCTTCCTCCTCTTTCCTCCTGGCTT
1 CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
*
2718 CTTCCTCTTCCTTC-CTTTCC
1 CTTCCTCTTCCTCCTCTTTCC
2738 CTTTCAATTT
Statistics
Matches: 213, Mismatches: 49, Indels: 57
0.67 0.15 0.18
Matches are distributed among these distances:
23 3 0.01
24 35 0.16
25 7 0.03
26 16 0.08
27 58 0.27
28 15 0.07
29 11 0.05
30 68 0.32
ACGTcount: A:0.01, C:0.43, G:0.06, T:0.49
Consensus pattern (30 bp):
CTTCCTCTTCCTCCTCTTTCCTCCTGGCTT
Done.