Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3070
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: 45539
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:2480 original size:21 final size:22
Alignment explanation
Indices: 2454--2497 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2444 AAAAGGTATC
*
2454 TACAAATTAAATC-TCTAAGAT
1 TACAAATCAAATCTTCTAAGAT
*
2475 TACAAATCATATCTTCTAAGAT
1 TACAAATCAAATCTTCTAAGAT
2497 T
1 T
2498 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCAAATCTTCTAAGAT
Found at i:2495 original size:22 final size:22
Alignment explanation
Indices: 2454--2510 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2444 AAAAGGTATC
* *
2454 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
2475 TACAAATCATATCTTCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
2497 TGCATATCATATCT
1 TACAAATCATATCT
2511 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:11471 original size:48 final size:48
Alignment explanation
Indices: 11413--11717 Score: 493
Period size: 48 Copynumber: 6.3 Consensus size: 48
11403 ATATACACAC
* * *
11413 ATCTCCTACATATTTCACACTAGCTATTCGGCCTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
11461 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
11509 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
* *
11557 ATCTCATACATATTTCACAGTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
*
11605 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCAC--ATATACAT
* * * *
11655 TTCTCATACATATTTCACATTAGCCATTTGGCTTTACCGCATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
*
11703 ATCTCATATATATTT
1 ATCTCATACATATTT
11718 ATCTTGTACA
Statistics
Matches: 244, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
48 199 0.82
50 45 0.18
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCCTTACCACATATACAT
Found at i:20343 original size:82 final size:81
Alignment explanation
Indices: 20227--20382 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
20217 AAATTGTACA
* * * *
20227 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
20291 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20308 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
20373 TGCGAGTTGA
65 TGCGAATTGA
20383 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20350 original size:55 final size:52
Alignment explanation
Indices: 20226--20379 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
20216 TAAATTGTAC
* *
20226 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
20279 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
20334 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
20380 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:20384 original size:27 final size:27
Alignment explanation
Indices: 20227--20382 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
20217 AAATTGTACA
*
20227 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
20254 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
20281 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
20308 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
20336 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
20363 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
20383 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:20393 original size:27 final size:27
Alignment explanation
Indices: 20219--20403 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
20209 GCGGGATTAA
*
20219 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
20246 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
20273 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
20300 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
20328 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
20355 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
20382 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
20404 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:20394 original size:82 final size:81
Alignment explanation
Indices: 20219--20403 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
20209 GCGGGATTAA
* * * *
20219 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
20284 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
20300 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
20364 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
20382 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
20404 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:28428 original size:82 final size:81
Alignment explanation
Indices: 28283--28438 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
28273 AAATTGTACA
* * * *
28283 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACGAAGTGT
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACGAAGTGT
28348 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** * *
28364 GCACTAAGTGTGTGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAGT
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACGAAGT
*
28428 GTGCGACTTGA
64 GTGCGAATTGA
28439 TTGTATAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 17 0.27
82 46 0.73
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACGAAGTGT
GCGAATTGACCATGCG
Found at i:28440 original size:27 final size:27
Alignment explanation
Indices: 28283--28438 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
28273 AAATTGTACA
*
28283 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
28310 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* * *
28337 GCACGAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
28364 GCACTAAGTGTGTGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
28392 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
28419 GCACTAAGTGTGCGACTTGA
1 GCACTAAGTGTGCGAATTGA
28439 TTGTATAGCA
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
27 80 0.77
28 24 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:37973 original size:19 final size:19
Alignment explanation
Indices: 37936--37973 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
37926 ACCTACCAGA
*
37936 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
37955 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
37974 TAAGTTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:43793 original size:48 final size:46
Alignment explanation
Indices: 43730--43900 Score: 161
Period size: 48 Copynumber: 3.6 Consensus size: 46
43720 GTTGAGCATC
43730 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
* * *
43776 CCGAACTCGCGTTGAGTTGAGTCCGAGTTTC-CGT-TGAATG-TAACTAGGCAT
1 CCGAACT--CGTTGAGTTGAGTCCGAG-TTCACTTATGGATGCGAA-T--G--T
* * *
43827 CCGAA-TCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
* *
43872 CCGAGCTCGTTGAGTTTGGGTCCGAGTTC
1 CCGAACTCGTTGAG-TTGAGTCCGAGTTC
43901 TTCATGGGGC
Statistics
Matches: 100, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
45 4 0.04
46 16 0.16
47 23 0.23
48 39 0.39
49 9 0.09
50 3 0.03
51 6 0.06
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
Done.