Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5175.1
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: 30666
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.28
Warning! 2557 characters in sequence are not A, C, G, or T
Found at i:281 original size:30 final size:30
Alignment explanation
Indices: 198--292 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
188 AACTAAAATT
* *
198 AGCTAAGCTTTAGCTCGTAAGCTAAAGTTG
1 AGCTAAGATTTAGCTCGTAAGCTGAAGTTG
* * ** *
228 AGCTGAGATTAAAATCCTAAGCTGAAGTTG
1 AGCTAAGATTTAGCTCGTAAGCTGAAGTTG
* *
258 AGCTAAGGTTTAGCTCGTGAGCTGAA-TATG
1 AGCTAAGATTTAGCTCGTAAGCTGAAGT-TG
288 AGCTA
1 AGCTA
293 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (30 bp):
AGCTAAGATTTAGCTCGTAAGCTGAAGTTG
Found at i:929 original size:19 final size:19
Alignment explanation
Indices: 905--944 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
895 AGCTCCCATG
905 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
924 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
943 TA
1 TA
945 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:1391 original size:71 final size:71
Alignment explanation
Indices: 1307--1448 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
1297 CTCTTAGGTG
1307 CATGTTCGGCCAAGTGCATGTAGGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCATTC
1 CATGTTCGGCCAAGTGCATGTAGGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCATTC
1372 ATGTAT
66 ATGTAT
*
1378 CATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCATTC
1 CATGTTCGGCCAAGTGCATGTAGGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCATTC
1443 ATGTAT
66 ATGTAT
1449 GGTGTGCTAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (71 bp):
CATGTTCGGCCAAGTGCATGTAGGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCATTC
ATGTAT
Found at i:2279 original size:14 final size:14
Alignment explanation
Indices: 2257--2304 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2247 ACCTAAACCG
* *
2257 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
2271 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
2285 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
2299 ACCATT
1 ACCATT
2305 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:3185 original size:22 final size:22
Alignment explanation
Indices: 3160--3213 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
3150 TAAAGATGTG
*
3160 TAATGCT-CTCTTTAATTGATG-A
1 TAATGCTCCT-TTTAA-TGAAGAA
3182 TAATAGCTCCTTTTAATGAAGAA
1 TAAT-GCTCCTTTTAATGAAGAA
3205 TAATGCTCC
1 TAATGCTCC
3214 CCTTTGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 13 0.46
23 13 0.46
24 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (22 bp):
TAATGCTCCTTTTAATGAAGAA
Found at i:9615 original size:19 final size:19
Alignment explanation
Indices: 9567--9606 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
9557 AAAGTAAACC
9567 TCACCACAAAACCTCACAA
1 TCACCACAAAACCTCACAA
9586 TCACCACAAAACCTCACAA
1 TCACCACAAAACCTCACAA
9605 TC
1 TC
9607 TCTCGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.12
Consensus pattern (19 bp):
TCACCACAAAACCTCACAA
Found at i:13690 original size:20 final size:20
Alignment explanation
Indices: 13643--13690 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
13633 AGTAAGCTCG
13643 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
13663 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
13683 GTTGAGCT
1 GTTGAGCT
13691 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:15385 original size:13 final size:12
Alignment explanation
Indices: 15369--15488 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
15359 TTTTTTCGCT
15369 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
15382 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
15396 TTTTCTTTTTC-
1 TTTTCTTTTTCA
* *
15407 TTTCACTTTTTTGA
1 TTT-TC-TTTTTCA
15421 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
15431 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
15444 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
15456 TTTTCTTTTT-G
1 TTTTCTTTTTCA
15467 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
15477 ATTTCTTTTTCA
1 TTTTCTTTTTCA
15489 ATCTCTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 17 0.20
12 30 0.35
13 19 0.22
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:15398 original size:14 final size:14
Alignment explanation
Indices: 15369--15405 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
15359 TTTTTTCGCT
15369 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
15382 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
15396 TTTTCTTTTT
1 TTTTCTTTTT
15406 CTTTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:15405 original size:15 final size:15
Alignment explanation
Indices: 15369--15408 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
15359 TTTTTTCGCT
15369 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTAA
*
15382 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTAA
15396 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
15409 TCACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 6 0.26
15 7 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCTTAA
Found at i:15487 original size:6 final size:6
Alignment explanation
Indices: 15367--15474 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
15357 TCTTTTTTCG
* * **
15367 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
15418 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
15466 -GTTTT CTTT
1 CTTTTT CTTT
15475 CAATTTCTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 5 0.07
6 58 0.76
7 10 0.13
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:16552 original size:12 final size:11
Alignment explanation
Indices: 16537--16578 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
16527 TTTTCTTTTC
16537 TTTTTTTTTGA
1 TTTTTTTTTGA
16548 TTTTTTTTTGAA
1 TTTTTTTTTG-A
* *
16560 TTTTTTCTCG-
1 TTTTTTTTTGA
16570 TTTTTTTTT
1 TTTTTTTTT
16579 AAATCCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 7 0.27
11 10 0.38
12 9 0.35
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:16659 original size:12 final size:13
Alignment explanation
Indices: 16642--16672 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16632 CAACTCAAAA
16642 TTTTTTTT-GATT
1 TTTTTTTTGGATT
16654 TTTTTTTTGGATT
1 TTTTTTTTGGATT
16667 TTTTTT
1 TTTTTT
16673 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGGATT
Found at i:23393 original size:14 final size:14
Alignment explanation
Indices: 23346--23393 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
23336 GTACGAATGG
*
23346 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
23360 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
23374 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
23388 ATTGGT
1 AATGGT
23394 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:24699 original size:30 final size:30
Alignment explanation
Indices: 24614--24710 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
24604 TAAACTAAAA
* *
24614 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
24644 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
24674 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
24703 ATGAGCTA
1 -TGAGCTA
24711 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Done.