Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2714
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: 17115
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:1385 original size:3 final size:3
Alignment explanation
Indices: 1340--1373 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1330 AATAAAATGC
*
1340 AAT AAT AAT AAT GAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1374 ATTCAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1392 original size:17 final size:18
Alignment explanation
Indices: 1326--1391 Score: 50
Period size: 20 Copynumber: 3.6 Consensus size: 18
1316 GGTATAAATA
*
1326 AATAAAT-AAAATGCAAT
1 AATAAATAAAAATTCAAT
1343 AAT-AATAATGATAATAT-AAT
1 AATAAATAA--A-AAT-TCAAT
1363 AAT-AATAATAAATTCAAT
1 AATAAATAA-AAATTCAAT
1381 AATAAATAAAA
1 AATAAATAAAA
1392 TGACAGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
16 3 0.08
17 5 0.12
18 11 0.28
19 7 0.17
20 14 0.35
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAAATAAAAATTCAAT
Found at i:2438 original size:12 final size:12
Alignment explanation
Indices: 2416--2444 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2406 GGCCTCGGGT
2416 TTGGG-TTGTAA
1 TTGGGCTTGTAA
2427 TTGGGCTTGTAA
1 TTGGGCTTGTAA
2439 TTGGGC
1 TTGGGC
2445 CGGGCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.07, G:0.38, T:0.41
Consensus pattern (12 bp):
TTGGGCTTGTAA
Found at i:3209 original size:174 final size:173
Alignment explanation
Indices: 2899--3374 Score: 806
Period size: 174 Copynumber: 2.8 Consensus size: 173
2889 AAGATCTGAA
* *
2899 CGATCTACTCTACTGTAAC-TCAGAGAAATAAGAT-CTTTATTTTAATCCGCTCCACTATAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTAATCCGCTCCACTGTAATCT
2962 CAGGGAGATAGGATTACTAGCTTC-ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
65 CAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
3026 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAA-ATAGACCTGGTG
130 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAATA-AGACCTGGTG
*
3070 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTCTAATCCACTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TAATCCGCTCCACTGTAATCT
* * *
3135 CAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT
65 CAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
3200 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAATAAGACCTGGTG
130 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAATAAGACCTGGTG
3244 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC-TT-TTTAATCCGCTCCACTGTAA-C-C
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTAATCCGCTCCACTGTAATCTC
*
3305 AGGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
66 AGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
3370 CTTCG
131 CTTCG
3375 ATCTACTTTG
Statistics
Matches: 289, Mismatches: 11, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
169 67 0.23
170 1 0.00
171 36 0.12
172 18 0.06
173 49 0.17
174 117 0.40
175 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (173 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTAATCCGCTCCACTGTAATCTC
AGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
CTTCGGTCTGTTCCACTGTAATCTCAGGGAATAAGACCTGGTG
Found at i:3354 original size:44 final size:44
Alignment explanation
Indices: 2948--3361 Score: 193
Period size: 44 Copynumber: 9.6 Consensus size: 44
2938 TTTTAATCCG
* * *
2948 CTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTC-ATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
* * * ** *
2991 CTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T-ACCA-GCTTCAATCTA
* * * * * *
3037 TTCCACTGTAATCTCAGGGAAAT-AG---ACCTGGTGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
* * *** *
3077 CTCTACTGTAA-CTTCAGAGAGATAAGA-T-CCTTTATTCTAATCCA
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACC-AGCTTC-AATCTA
* * * *
3121 CTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
* * * ** *
3165 CTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTCTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TT-ACCA-GCTTCAATCTA
* * * * *
3211 TTCCACTGTAATCTCAGGGA-ATAAG---ACCTGGTGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
* * ** * **
3251 CTCTACTGTAA-CTTCAGAGAGATAAGA-T-CC-TTTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACCAGCTTCAATCTA
*
3292 CTCCACTGTAA-C-CAGGGAGATAGGATTACCAGCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
*
3334 CTCCGCTGTAATCTCAGGGAGATAAGAT
1 CTCCACTGTAATCTCAGGGAGATAAGAT
3362 CTGAAATTCT
Statistics
Matches: 274, Mismatches: 70, Indels: 53
0.69 0.18 0.13
Matches are distributed among these distances:
39 13 0.05
40 47 0.17
41 24 0.09
42 20 0.07
43 29 0.11
44 70 0.26
45 20 0.07
46 51 0.19
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTCAATCTA
Found at i:15999 original size:9 final size:10
Alignment explanation
Indices: 15988--16049 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
15978 GGTACAAATA
15988 AATAAATAA-
1 AATAAATAAT
*
15997 AATGCAATAAT
1 AAT-AAATAAT
16008 AATAATGATAAT
1 AATAA--ATAAT
16020 AAT-AATAAT
1 AATAAATAAT
16029 AATAAATTCAAT
1 AATAAA-T-AAT
16041 AATAAATAA
1 AATAAATAA
16050 AATGACAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 11 0.25
10 10 0.23
11 6 0.14
12 17 0.39
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:16045 original size:3 final size:3
Alignment explanation
Indices: 16002--16033 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
15992 AATAAAATGC
*
16002 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16034 ATTCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Done.