Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: XM_021443909.1
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: 3140
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Found at i:2327 original size:30 final size:30
Alignment explanation
Indices: 2292--2395 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 30
2282 AACCACAGCT
*
2292 ACAGCAGCAACAGCTGCCGCAACTGCAACA
1 ACAGCAGCAACAGCTGCCACAACTGCAACA
* * * *
2322 GCAGCAGCAGCAGCTTCCACAGCTGCAACA
1 ACAGCAGCAACAGCTGCCACAACTGCAACA
* ** * *
2352 ACAGCAGCAGCCCCTTCCACAGCTGCAACA
1 ACAGCAGCAACAGCTGCCACAACTGCAACA
*
2382 ACAGCAGCAGCAGC
1 ACAGCAGCAACAGC
2396 AGCAGCTTCC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.33, C:0.38, G:0.21, T:0.08
Consensus pattern (30 bp):
ACAGCAGCAACAGCTGCCACAACTGCAACA
Found at i:2356 original size:27 final size:27
Alignment explanation
Indices: 2326--2690 Score: 160
Period size: 27 Copynumber: 13.2 Consensus size: 27
2316 GCAACAGCAG
2326 CAGCAGCAGCTTCCACAGCTGCAACAA
1 CAGCAGCAGCTTCCACAGCTGCAACAA
2353 CAGCAGCAGCCCCTTCCACAGCTGCAACAACAGCAGCA
1 CAGCAGCAG---CTTCCACAGCTG---C-A-A-CA--A
*
2391 GCAGCAGCAGCTTCCACAGTTGCAACAA
1 -CAGCAGCAGCTTCCACAGCTGCAACAA
* * *
2419 CA--A-CAGCTCCCTCA-CTTG---CAG
1 CAGCAGCAGCTTCCACAGC-TGCAACAA
* * *
2440 CAGCAACAGCTCCCTCAGCTGCAACAGCA
1 CAGCAGCAGCTTCCACAGCTGCAACA--A
* * *
2469 GCAGCAGCATCAGCTCCCTCAGCTGCAACAG
1 -CAGCAG---CAGCTTCCACAGCTGCAACAA
* * * *
2500 CAGCAGCAGCATCCACAGCTACAGCAG
1 CAGCAGCAGCTTCCACAGCTGCAACAA
* * ** * * * *
2527 CAGCATCCGCAGCTACAGCAGCAGCAG
1 CAGCAGCAGCTTCCACAGCTGCAACAA
*
2554 CAGCAGCAGCTTCCACAGCT---ACAG
1 CAGCAGCAGCTTCCACAGCTGCAACAA
2578 CAGCAGCAGCTATCC-CAGCTGCAACAA
1 CAGCAGCAGCT-TCCACAGCTGCAACAA
* * * *
2605 CAACAGCAG-TTGCCCCAGATGCAGCAA
1 CAGCAGCAGCTT-CCACAGCTGCAACAA
* * * *
2632 CAGCAGCAACTTCCACAACTGCAGCAG
1 CAGCAGCAGCTTCCACAGCTGCAACAA
* *
2659 CAGCCGCAGCTTCCCCAGCTGCAACAA
1 CAGCAGCAGCTTCCACAGCTGCAACAA
2686 CAGCA
1 CAGCA
2691 ATTACCTCAG
Statistics
Matches: 262, Mismatches: 43, Indels: 66
0.71 0.12 0.18
Matches are distributed among these distances:
21 4 0.02
23 1 0.00
24 43 0.16
25 6 0.02
26 3 0.01
27 128 0.49
28 3 0.01
30 25 0.10
31 1 0.00
32 1 0.00
33 22 0.08
34 1 0.00
35 1 0.00
36 13 0.05
38 1 0.00
39 9 0.03
ACGTcount: A:0.31, C:0.38, G:0.20, T:0.11
Consensus pattern (27 bp):
CAGCAGCAGCTTCCACAGCTGCAACAA
Found at i:2446 original size:66 final size:65
Alignment explanation
Indices: 2320--2447 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 65
2310 GCAACTGCAA
* * *
2320 CAGCAGCAGCAGCAGCTTCCACAGCTGCAACAACAGCAGCAGCCCCTTCCACAGCTGCAACAACA
1 CAGCAGCAGCAGCAGCTTCCACAGCTGCAACAACAACAGCACCCCCTT-CACAGCAGCAACAACA
2385 G
65 G
* * *
2386 CAGCAGCAGCAGCAGCTTCCACAGTTGCAACAACAACAGCTCCCTCACTT-GCAGCAGCAACA
1 CAGCAGCAGCAGCAGCTTCCACAGCTGCAACAACAACAGCACCC-C-CTTCACAGCAGCAACA
2448 GCTCCCTCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
66 50 0.93
67 1 0.02
68 3 0.06
ACGTcount: A:0.32, C:0.38, G:0.19, T:0.11
Consensus pattern (65 bp):
CAGCAGCAGCAGCAGCTTCCACAGCTGCAACAACAACAGCACCCCCTTCACAGCAGCAACAACAG
Found at i:2458 original size:18 final size:18
Alignment explanation
Indices: 2437--2500 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
2427 CCCTCACTTG
2437 CAGCAGCAACAGCTCCCT
1 CAGCAGCAACAGCTCCCT
* **
2455 CAGCTGCAACAG---CAG
1 CAGCAGCAACAGCTCCCT
*
2470 CAGCAGCATCAGCTCCCT
1 CAGCAGCAACAGCTCCCT
*
2488 CAGCTGCAACAGC
1 CAGCAGCAACAGC
2501 AGCAGCAGCA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
15 11 0.32
18 23 0.68
ACGTcount: A:0.28, C:0.41, G:0.20, T:0.11
Consensus pattern (18 bp):
CAGCAGCAACAGCTCCCT
Found at i:2467 original size:24 final size:24
Alignment explanation
Indices: 2383--2473 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2373 GCTGCAACAA
* * * * *
2383 CAGCAGCAGCAGCAGCAGCTTCCA
1 CAGCTGCAACAGCAACAGCTCCCT
* *
2407 CAGTTGCAACAACAACAGCTCCCT
1 CAGCTGCAACAGCAACAGCTCCCT
*
2431 CA-CTTGCAGCAGCAACAGCTCCCT
1 CAGC-TGCAACAGCAACAGCTCCCT
*
2455 CAGCTGCAACAGCAGCAGC
1 CAGCTGCAACAGCAACAGC
2474 AGCATCAGCT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.30, C:0.38, G:0.20, T:0.12
Consensus pattern (24 bp):
CAGCTGCAACAGCAACAGCTCCCT
Found at i:2511 original size:33 final size:33
Alignment explanation
Indices: 2436--2512 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
2426 TCCCTCACTT
*
2436 GCAGCAGCAACAGCTCCCTCAGCTGCAACAGCA
1 GCAGCAGCATCAGCTCCCTCAGCTGCAACAGCA
2469 GCAGCAGCATCAGCTCCCTCAGCTGCAACAGCA
1 GCAGCAGCATCAGCTCCCTCAGCTGCAACAGCA
2502 GCAGCAGCATC
1 GCAGCAGCATC
2513 CACAGCTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.29, C:0.39, G:0.22, T:0.10
Consensus pattern (33 bp):
GCAGCAGCATCAGCTCCCTCAGCTGCAACAGCA
Found at i:2526 original size:21 final size:21
Alignment explanation
Indices: 2500--2552 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2490 GCTGCAACAG
2500 CAGCAGCAGCATCCACAGCTA
1 CAGCAGCAGCATCCACAGCTA
*
2521 CAGCAGCAGCATCCGCAGCTA
1 CAGCAGCAGCATCCACAGCTA
2542 CAGCAGCAGCA
1 CAGCAGCAGCA
2553 GCAGCAGCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.38, G:0.23, T:0.08
Consensus pattern (21 bp):
CAGCAGCAGCATCCACAGCTA
Found at i:2558 original size:33 final size:33
Alignment explanation
Indices: 2521--2587 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2511 TCCACAGCTA
*
2521 CAGCAGCAGCATCCGCAGCTACAGCAGCAGCAG
1 CAGCAGCAGCATCCACAGCTACAGCAGCAGCAG
*
2554 CAGCAGCAGCTTCCACAGCTACAGCAGCAGCAG
1 CAGCAGCAGCATCCACAGCTACAGCAGCAGCAG
2587 C
1 C
2588 TATCCCAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.37, G:0.25, T:0.07
Consensus pattern (33 bp):
CAGCAGCAGCATCCACAGCTACAGCAGCAGCAG
Found at i:2559 original size:21 final size:21
Alignment explanation
Indices: 2500--2560 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
2490 GCTGCAACAG
2500 CAGCAGCAGCATCCA-CAGCTA
1 CAGCAGCAGCA-CCAGCAGCTA
2521 CAGCAGCAGCATCC-GCAGCTA
1 CAGCAGCAGCA-CCAGCAGCTA
*
2542 CAGCAGCAGCAGCAGCAGC
1 CAGCAGCAGCACCAGCAGC
2561 AGCTTCCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.31, C:0.38, G:0.25, T:0.07
Consensus pattern (21 bp):
CAGCAGCAGCACCAGCAGCTA
Found at i:2562 original size:24 final size:24
Alignment explanation
Indices: 2496--2589 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
2486 CTCAGCTGCA
*
2496 ACAGCAGCAGCAGCATCCA-CAGCT
1 ACAGCAGCAGCAGCA-GCAGCAGCT
*
2520 ACAGCAGCAGCATC--C-GCAGCT
1 ACAGCAGCAGCAGCAGCAGCAGCT
2541 ACAGCAGCAGCAGCAGCAGCAGCTT
1 ACAGCAGCAGCAGCAGCAGCAGC-T
*
2566 CCA-CAGCTA-CAGCAGCAGCAGCT
1 ACAGCAGC-AGCAGCAGCAGCAGCT
2589 A
1 A
2590 TCCCAGCTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
21 19 0.32
23 2 0.03
24 35 0.58
25 4 0.07
ACGTcount: A:0.32, C:0.36, G:0.23, T:0.09
Consensus pattern (24 bp):
ACAGCAGCAGCAGCAGCAGCAGCT
Found at i:2583 original size:3 final size:3
Alignment explanation
Indices: 2464--2563 Score: 62
Period size: 3 Copynumber: 33.3 Consensus size: 3
2454 TCAGCTGCAA
* ** ** * * *
2464 CAG CAG CAG CAG CAT CAG CTC CCT CAG CTG CAA CAG CAG CAG CAG CATC
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA-G
* *
2513 CA- CAG CTA- CAG CAG CAG CAT CCG CAG CTA- CAG CAG CAG CAG CAG
1 CAG CAG C-AG CAG CAG CAG CAG CAG CAG C-AG CAG CAG CAG CAG CAG
2557 CAG CAG C
1 CAG CAG C
2564 TTCCACAGCT
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
2 4 0.05
3 66 0.89
4 4 0.05
ACGTcount: A:0.30, C:0.38, G:0.24, T:0.08
Consensus pattern (3 bp):
CAG
Found at i:2612 original size:81 final size:82
Alignment explanation
Indices: 2383--2687 Score: 215
Period size: 81 Copynumber: 3.8 Consensus size: 82
2373 GCTGCAACAA
* * * * * * *
2383 CAGCAGCAGCAGCAGCAGCTTCCACAGTTGCA-A-CAACAACAGCTCCCTCA-CTTGCAGCAGCA
1 CAGCAGCAGCAGCAGCAGCTTCCACAGCT-CACAGCAGCAGCAGCTTCCACAGC-TGCAACAACA
* * *
2445 ACAGC-TCCCTCAGCTGCAA
64 ACAGCAT-CCGCAGCTACAG
* * * * *
2464 CAGCAGCAGCAGCATCAGCTCCCTCAGCTGCAACAGCAGCAGCAGCATCCACAGCT---ACAGCA
1 CAGCAGCAGCAGCAGCAGCTTCCACAGCT-C-ACAGCAGCAGCAGCTTCCACAGCTGCAACAACA
*
2526 GCAGCATCCGCAGCTACAG
64 ACAGCATCCGCAGCTACAG
2545 CAGCAGCAGCAGCAGCAGCTTCCACAGCT-ACAGCAGCAGCAGCTATCC-CAGCTGCAACAACAA
1 CAGCAGCAGCAGCAGCAGCTTCCACAGCTCACAGCAGCAGCAGCT-TCCACAGCTGCAACAACAA
* *
2608 CAGCAGT-TGC--C-CCAG
65 CAGCA-TCCGCAGCTACAG
* * * * *
2623 -ATGCAGCAACAGCAGCAACTTCCACAACTGCAGCAGCAGCCGCAGCTTCCCCAGCTGCAACAAC
1 CA-GCAGCAGCAGCAGCAGCTTCCACAGCT-CA-CAGCAGCAGCAGCTTCCACAGCTGCAACAAC
2687 A
63 A
2688 GCAATTACCT
Statistics
Matches: 183, Mismatches: 26, Indels: 30
0.77 0.11 0.13
Matches are distributed among these distances:
77 1 0.01
78 46 0.25
79 4 0.02
80 4 0.02
81 110 0.60
82 3 0.02
83 1 0.01
84 13 0.07
85 1 0.01
ACGTcount: A:0.30, C:0.38, G:0.20, T:0.11
Consensus pattern (82 bp):
CAGCAGCAGCAGCAGCAGCTTCCACAGCTCACAGCAGCAGCAGCTTCCACAGCTGCAACAACAAC
AGCATCCGCAGCTACAG
Done.