Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3183
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: 29766
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:1256 original size:33 final size:33
Alignment explanation
Indices: 1218--1280 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1208 GATTACTCAC
1218 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
1251 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
1281 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:1307 original size:21 final size:21
Alignment explanation
Indices: 1278--1333 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
1268 CAAGCTCTCT
*
1278 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
1299 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
1320 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
1334 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:1326 original size:14 final size:14
Alignment explanation
Indices: 1277--1333 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1267 TCAAGCTCTC
1277 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
1290 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
1304 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
1318 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
1332 TT
1 TT
1334 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:1361 original size:18 final size:18
Alignment explanation
Indices: 1340--1397 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
1330 TTTTCTCTCA
1340 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
1358 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
1376 CTTTTT-GTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
1393 GTTTT
1 CTTTT
1398 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:1388 original size:11 final size:11
Alignment explanation
Indices: 1372--1401 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1362 TGCAATTTCT
1372 TTTTCTTTTTG
1 TTTTCTTTTTG
1383 TTTTCTTTTTG
1 TTTTCTTTTTG
1394 TTTTCTTT
1 TTTTCTTT
1402 CAATTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:1414 original size:6 final size:6
Alignment explanation
Indices: 1295--1401 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
1285 TCTTTTTTCG
* * * **
1295 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
1346 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
1393 -GTTTT CTTT
1 CTTTTT CTTT
1402 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
5 8 0.11
6 52 0.72
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:2480 original size:24 final size:25
Alignment explanation
Indices: 2436--2495 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
2426 TTAAACTTGA
*
2436 TTTTTTTTTGCTCACCTTTTTTTTTC
1 TTTTTTTTTGCTCA-CATTTTTTTTC
2462 TTTTTTTTTGCTCA-ATTTTTTTTC
1 TTTTTTTTTGCTCACATTTTTTTTC
**
2486 ACTTTTTTTG
1 TTTTTTTTTG
2496 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 17 0.55
26 14 0.45
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (25 bp):
TTTTTTTTTGCTCACATTTTTTTTC
Found at i:2480 original size:25 final size:27
Alignment explanation
Indices: 2436--2494 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
2426 TTAAACTTGA
* *
2436 TTTTTTTTTGCTCACCTTTTTTTT-TC
1 TTTTTTTTTGCTCACATTTTTTTTCAC
2462 TTTTTTTTTGCTCA-ATTTTTTTTCAC
1 TTTTTTTTTGCTCACATTTTTTTTCAC
2488 TTTTTTT
1 TTTTTTT
2495 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTGCTCACATTTTTTTTCAC
Found at i:2491 original size:11 final size:11
Alignment explanation
Indices: 2452--2507 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
2442 TTTGCTCACC
*
2452 TTTTTTTTTCT
1 TTTTTTTTTCA
2463 TTTTTTTTGCTCA
1 TTTTTTTT--TCA
*
2476 ATTTTTTTTCA
1 TTTTTTTTTCA
* *
2487 -CTTTTTTTGA
1 TTTTTTTTTCA
2497 TTTTTTTTTCA
1 TTTTTTTTTCA
2508 ATCAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.22
11 19 0.53
13 9 0.25
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:2492 original size:35 final size:35
Alignment explanation
Indices: 2453--2520 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2443 TTGCTCACCT
**
2453 TTTTTTTTCTTTTTTTTTGC-TCAATTTTTTTTCAC
1 TTTTTTTGATTTTTTTTT-CATCAATTTTTTTTCAC
2488 TTTTTTTGATTTTTTTTTCAATCAATTTTTTTT
1 TTTTTTTGATTTTTTTTTC-ATCAATTTTTTTT
2521 TTCGAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 1 0.03
35 16 0.55
36 12 0.41
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (35 bp):
TTTTTTTGATTTTTTTTTCATCAATTTTTTTTCAC
Found at i:4509 original size:16 final size:16
Alignment explanation
Indices: 4490--4522 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4480 TCTTTTTCTT
*
4490 TTTTTTTAATTCTGAA
1 TTTTTTTAATACTGAA
4506 TTTTTTTAATACTGAA
1 TTTTTTTAATACTGAA
4522 T
1 T
4523 ACACAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTTTTAATACTGAA
Found at i:22135 original size:19 final size:19
Alignment explanation
Indices: 22111--22150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22101 AGCTCCCATG
22111 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
22130 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
22149 TA
1 TA
22151 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:22609 original size:20 final size:20
Alignment explanation
Indices: 22563--22609 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22553 AGCTCGTTTC
*
22563 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
22583 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
22603 CAGCTCA
1 CAGCTCA
22610 ATCCTAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:24150 original size:9 final size:9
Alignment explanation
Indices: 24138--24173 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
24128 AAAAAAGTGC
*
24138 AAAAAAAGAA
1 AAAAAAA-AG
24148 AAAAAAAAG
1 AAAAAAAAG
24157 AAAAAAAAG
1 AAAAAAAAG
24166 AAAAAAAA
1 AAAAAAAA
24174 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:24152 original size:11 final size:11
Alignment explanation
Indices: 24124--24176 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
24114 TGAAATTCAA
24124 AAAAAAAAAAG
1 AAAAAAAAAAG
***
24135 TGCAAAAAAAG
1 AAAAAAAAAAG
24146 AAAAAAAAAAG
1 AAAAAAAAAAG
24157 --AAAAAAAAG
1 AAAAAAAAAAG
24166 AAAAAAAAAAG
1 AAAAAAAAAAG
24177 TGAAAAGTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 9 0.26
11 25 0.74
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:24182 original size:11 final size:11
Alignment explanation
Indices: 24126--24182 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
24116 AAATTCAAAA
*
24126 AAAAAAAAGTG
1 AAAAAAAAGAG
*
24137 CAAAAAAAGA-
1 AAAAAAAAGAG
24147 AAAAAAAA-AG
1 AAAAAAAAGAG
*
24157 AAAAAAAAGAA
1 AAAAAAAAGAG
*
24168 AAAAAAAAGTG
1 AAAAAAAAGAG
24179 AAAA
1 AAAA
24183 GTCTTGTGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 1 0.03
10 15 0.39
11 22 0.58
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:24182 original size:20 final size:20
Alignment explanation
Indices: 24124--24182 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
24114 TGAAATTCAA
24124 AAAAAAAAAAGTGCAAAAAAAG
1 AAAAAAAAAAGTG--AAAAAAG
**
24146 AAAAAAAAAAGAAAAAAAAG
1 AAAAAAAAAAGTGAAAAAAG
24166 AAAAAAAAAAGTGAAAA
1 AAAAAAAAAAGTGAAAA
24183 GTCTTGTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 22 0.67
22 11 0.33
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAGTGAAAAAAG
Found at i:25280 original size:48 final size:47
Alignment explanation
Indices: 25201--25306 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
25191 GAGTGTCATG
*
25201 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
25249 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
25297 GAAAAAGAAA
1 GAAAAAGAAA
25307 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:27022 original size:20 final size:20
Alignment explanation
Indices: 26976--27022 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
26966 AGCTCGTTTC
*
26976 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
26996 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27016 CAGCTCA
1 CAGCTCA
27023 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.