Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1139
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: 2621
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.20
Warning! 468 characters in sequence are not A, C, G, or T
Found at i:1140 original size:20 final size:20
Alignment explanation
Indices: 1114--1306 Score: 148
Period size: 20 Copynumber: 9.9 Consensus size: 20
1104 AGCATGCGAT
*
1114 AAGCAACACATAACACACAC
1 AAGCAACACGTAACACACAC
* * **** *
1134 GAGCAACATGTAACGTTTAA
1 AAGCAACACGTAACACACAC
* * *
1154 AAGCAACACGTAACATATAA
1 AAGCAACACGTAACACACAC
*
1174 AAGCAACA--TATA-GCACAC
1 AAGCAACACGTA-ACACACAC
*
1192 AAGCAACACGT-A-ACACGC
1 AAGCAACACGTAACACACAC
* *
1210 AAGGAACATGT-A-ACACAC
1 AAGCAACACGTAACACACAC
*
1228 AAGCAACACGCAACACACAC
1 AAGCAACACGTAACACACAC
*
1248 AAGCAACACGCAACACACAC
1 AAGCAACACGTAACACACAC
*
1268 AAGCAACACGCAACACACAC
1 AAGCAACACGTAACACACAC
* *
1288 AAGCAACCCGCAACACACA
1 AAGCAACACGTAACACACA
1307 TGCGCAACAC
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
18 40 0.28
19 2 0.01
20 101 0.71
ACGTcount: A:0.49, C:0.32, G:0.12, T:0.07
Consensus pattern (20 bp):
AAGCAACACGTAACACACAC
Found at i:1197 original size:18 final size:18
Alignment explanation
Indices: 1174--1286 Score: 91
Period size: 18 Copynumber: 6.1 Consensus size: 18
1164 TAACATATAA
* *
1174 AAGCAACATATAGCACAC
1 AAGCAACATGTAACACAC
* *
1192 AAGCAACACGTAACACGC
1 AAGCAACATGTAACACAC
*
1210 AAGGAACATGTAACACAC
1 AAGCAACATGTAACACAC
* *
1228 AAGCAACACGCAACACACAC
1 AAGCAACATG-TA-ACACAC
* *
1248 AAGCAACACGCAACACACAC
1 AAGCAACATG-TA-ACACAC
* *
1268 AAGCAACACGCAACACAC
1 AAGCAACATGTAACACAC
1286 A
1 A
1287 CAAGCAACCC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
18 44 0.54
19 2 0.02
20 36 0.44
ACGTcount: A:0.50, C:0.34, G:0.12, T:0.04
Consensus pattern (18 bp):
AAGCAACATGTAACACAC
Found at i:1319 original size:7 final size:7
Alignment explanation
Indices: 1230--1303 Score: 64
Period size: 7 Copynumber: 11.0 Consensus size: 7
1220 TAACACACAA
1230 GCAACAC
1 GCAACAC
1237 GCAACAC
1 GCAACAC
* *
1244 AC-ACAA
1 GCAACAC
1250 GCAACAC
1 GCAACAC
1257 GCAACAC
1 GCAACAC
* *
1264 AC-ACAA
1 GCAACAC
1270 GCAACAC
1 GCAACAC
1277 GCAACAC
1 GCAACAC
* *
1284 AC-ACAA
1 GCAACAC
*
1290 GCAACCC
1 GCAACAC
1297 GCAACAC
1 GCAACAC
1304 ACATGCGCAA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
6 12 0.24
7 38 0.76
ACGTcount: A:0.47, C:0.42, G:0.11, T:0.00
Consensus pattern (7 bp):
GCAACAC
Found at i:1319 original size:20 final size:20
Alignment explanation
Indices: 1222--1306 Score: 161
Period size: 20 Copynumber: 4.2 Consensus size: 20
1212 GGAACATGTA
1222 ACACACAAGCAACACGCAAC
1 ACACACAAGCAACACGCAAC
1242 ACACACAAGCAACACGCAAC
1 ACACACAAGCAACACGCAAC
1262 ACACACAAGCAACACGCAAC
1 ACACACAAGCAACACGCAAC
*
1282 ACACACAAGCAACCCGCAAC
1 ACACACAAGCAACACGCAAC
1302 ACACA
1 ACACA
1307 TGCGCAACAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.49, C:0.41, G:0.09, T:0.00
Consensus pattern (20 bp):
ACACACAAGCAACACGCAAC
Found at i:1374 original size:18 final size:18
Alignment explanation
Indices: 1328--1464 Score: 176
Period size: 18 Copynumber: 7.7 Consensus size: 18
1318 CATCAGTAGA
*
1328 AACATATAACACATAGAT
1 AACATATAACACATAAAT
1346 AACAAATATAACACATAAAT
1 AAC--ATATAACACATAAAT
*
1366 AACATATAACACATAAAA
1 AACATATAACACATAAAT
*
1384 AACATATAACGC----AT
1 AACATATAACACATAAAT
*
1398 AACATATAACACACAAAT
1 AACATATAACACATAAAT
1416 AACATATAACACATAAAT
1 AACATATAACACATAAAT
1434 AACATATAACACATATAA-
1 AACATATAACACATA-AAT
1452 AACATATAACACA
1 AACATATAACACA
1465 CATGCAACAC
Statistics
Matches: 106, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.11
18 75 0.71
19 2 0.02
20 17 0.16
ACGTcount: A:0.61, C:0.18, G:0.01, T:0.20
Consensus pattern (18 bp):
AACATATAACACATAAAT
Found at i:1379 original size:9 final size:9
Alignment explanation
Indices: 1329--1464 Score: 97
Period size: 9 Copynumber: 15.3 Consensus size: 9
1319 ATCAGTAGAA
1329 ACATATAAC
1 ACATATAAC
1338 ACATAGATAAC
1 ACAT--ATAAC
*
1349 AAATATAAC
1 ACATATAAC
*
1358 ACATA-AATA
1 ACATATAA-C
1367 ACATATAAC
1 ACATATAAC
* *
1376 ACATAAAAA
1 ACATATAAC
1385 ACATATAAC
1 ACATATAAC
*
1394 GC--AT-A-
1 ACATATAAC
1399 ACATATAAC
1 ACATATAAC
* *
1408 ACACA-AATA
1 ACATATAA-C
1417 ACATATAAC
1 ACATATAAC
*
1426 ACATA-AATA
1 ACATATAA-C
1435 ACATATAAC
1 ACATATAAC
*
1444 ACATATAAA
1 ACATATAAC
1453 ACATATAAC
1 ACATATAAC
1462 ACA
1 ACA
1465 CATGCAACAC
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
5 1 0.01
6 1 0.01
7 4 0.04
8 7 0.07
9 70 0.72
10 6 0.06
11 8 0.08
ACGTcount: A:0.60, C:0.18, G:0.01, T:0.20
Consensus pattern (9 bp):
ACATATAAC
Found at i:1392 original size:25 final size:25
Alignment explanation
Indices: 1364--1444 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
1354 TAACACATAA
1364 ATAACATATAACACATAAAAAACAT
1 ATAACATATAACACATAAAAAACAT
** * * * *
1389 ATAACGCATAACATATAACACACAA
1 ATAACATATAACACATAAAAAACAT
*
1414 ATAACATATAACACATAAATAACAT
1 ATAACATATAACACATAAAAAACAT
1439 ATAACA
1 ATAACA
1445 CATATAAAAC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.60, C:0.19, G:0.01, T:0.20
Consensus pattern (25 bp):
ATAACATATAACACATAAAAAACAT
Found at i:1410 original size:50 final size:50
Alignment explanation
Indices: 1351--1466 Score: 169
Period size: 50 Copynumber: 2.2 Consensus size: 50
1341 TAGATAACAA
* *
1351 ATATAACACATAAATAACATATAACACATAAAAAACATATAACGCATAAC
1 ATATAACACACAAATAACATATAACACATAAAAAACATATAACACATAAC
*
1401 ATATAACACACAAATAACATATAACACATAAATAACATATAACACATATAAAAC
1 ATATAACACACAAATAACATATAACACATAAAAAACATATAACAC--AT--AAC
1455 ATATAACACACA
1 ATATAACACACA
1467 TGCAACACAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
50 42 0.71
52 2 0.03
54 15 0.25
ACGTcount: A:0.60, C:0.19, G:0.01, T:0.20
Consensus pattern (50 bp):
ATATAACACACAAATAACATATAACACATAAAAAACATATAACACATAAC
Found at i:1437 original size:68 final size:69
Alignment explanation
Indices: 1328--1461 Score: 225
Period size: 68 Copynumber: 1.9 Consensus size: 69
1318 CATCAGTAGA
* *
1328 AACATATAACACATAGATAACAAATATAACACATAAATAACATATAACACATAAAAAACATATAA
1 AACATATAACACACAAATAAC-AATATAACACATAAATAACATATAACACATAAAAAACATATAA
1393 CGCAT
65 CGCAT
*
1398 AACATATAACACACAAATAAC-ATATAACACATAAATAACATATAACACATATAAAACATATAAC
1 AACATATAACACACAAATAACAATATAACACATAAATAACATATAACACATAAAAAACATATAAC
1462 ACACATGCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 42 0.69
70 19 0.31
ACGTcount: A:0.60, C:0.18, G:0.01, T:0.20
Consensus pattern (69 bp):
AACATATAACACACAAATAACAATATAACACATAAATAACATATAACACATAAAAAACATATAAC
GCAT
Done.