Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold581
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: 64553
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4680 original size:109 final size:109
Alignment explanation
Indices: 4489--4708 Score: 413
Period size: 109 Copynumber: 2.0 Consensus size: 109
4479 ATGAGGCCTA
*
4489 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAGATTTGT
1 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
*
4554 TTAAGTGTAGAATTCTCTTTTAGTTTTTCTCCAAGAATTCTCTC
66 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
*
4598 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAATCAAAAAATTTCAAATTTGT
1 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
4663 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
66 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
4707 TT
1 TT
4709 GAGTTTTCTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (109 bp):
TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
Found at i:13414 original size:24 final size:24
Alignment explanation
Indices: 13362--13408 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
13352 TGTTTAAGTA
13362 TAGAATTCTCCTTGAGTTTTCTCC
1 TAGAATTCTCCTTGAGTTTTCTCC
*
13386 AAGAATTCTCTCTTGAGTTTTCT
1 TAGAATTCTC-CTTGAGTTTTCT
13409 TTAGAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (24 bp):
TAGAATTCTCCTTGAGTTTTCTCC
Found at i:13585 original size:30 final size:32
Alignment explanation
Indices: 13551--13612 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
13541 TTAGGACTTA
13551 TCTTTT-AATT-T-CTTGCTGTCAATTTTTATT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTTATT
*
13581 TCTTTTAAATTCTGCTTGTGTCGATTTTTATT
1 TCTTTTAAATTCTGCTTGTGTCAATTTTTATT
13613 AGCTAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 4 0.14
32 14 0.50
33 4 0.14
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (32 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTTATT
Found at i:24549 original size:23 final size:22
Alignment explanation
Indices: 24498--24549 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
24488 CCTCGTCTTT
*
24498 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
24520 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
24543 TTCTTTT
1 TTCTTTT
24550 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:24558 original size:12 final size:12
Alignment explanation
Indices: 24507--24561 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
24497 TTTCTTTTGT
24507 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
24520 -TCATTTTC-TC
1 TTCTTTTTCAAC
24530 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
24543 TTCTTTTTCAAT
1 TTCTTTTTCAAC
24555 TTCTTTT
1 TTCTTTT
24562 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:24568 original size:17 final size:18
Alignment explanation
Indices: 24543--24580 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
24533 TTTCTTCAAC
* *
24543 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
24560 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
24578 TTC
1 TTC
24581 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:33037 original size:21 final size:21
Alignment explanation
Indices: 32994--33056 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
32984 TTTGAACCAT
* *
32994 TACCAATTCGTACCCAATACCA
1 TACCATTTCGTA-CCAATTCCA
33016 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
33037 TACCATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
33057 CAAATACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:41441 original size:10 final size:11
Alignment explanation
Indices: 41426--41454 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
41416 ACGGTATTGT
41426 AAAAAAATC-A
1 AAAAAAATCGA
41436 AAAAAAATCGA
1 AAAAAAATCGA
41447 AAAAAAAT
1 AAAAAAAT
41455 TTAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.79, C:0.07, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAATCGA
Found at i:44661 original size:13 final size:12
Alignment explanation
Indices: 44630--44684 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
44620 AATGAAACAG
*
44630 AAAAGAAATTGA
1 AAAAGAAGTTGA
44642 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
44654 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
44666 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
44678 AAAAGAA
1 AAAAGAA
44685 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:54159 original size:8 final size:8
Alignment explanation
Indices: 54146--54234 Score: 67
Period size: 8 Copynumber: 10.9 Consensus size: 8
54136 CCATTCTGTC
54146 TTTTTCAT
1 TTTTTCAT
*
54154 TTTTTCCT
1 TTTTTCAT
*
54162 TTTTCTACGT
1 TTTT-T-CAT
*
54172 CTTTTCAT
1 TTTTTCAT
54180 TTTCTTC-T
1 TTT-TTCAT
54188 TTTTTCAAT
1 TTTTTC-AT
* *
54197 TCTTTCCT
1 TTTTTCAT
54205 TTTTTCA-
1 TTTTTCAT
54212 TTTTTC-T
1 TTTTTCAT
54219 TCTTTTCAT
1 T-TTTTCAT
54228 TTTTTCA
1 TTTTTCA
54235 CTCTCACCTC
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
7 10 0.16
8 36 0.56
9 13 0.20
10 5 0.08
ACGTcount: A:0.09, C:0.20, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTTTCAT
Found at i:54165 original size:15 final size:15
Alignment explanation
Indices: 54145--54233 Score: 53
Period size: 15 Copynumber: 6.0 Consensus size: 15
54135 ACCATTCTGT
54145 CTTTTTCATTTTTTC
1 CTTTTTCATTTTTTC
***
54160 CTTTTTC--TACGT-
1 CTTTTTCATTTTTTC
54172 C-TTTTCATTTTCTTC
1 CTTTTTCATTTT-TTC
* *
54187 TTTTTTCAATTCTTTC
1 CTTTTTC-ATTTTTTC
54203 CTTTTTTCA-TTTTTC
1 C-TTTTTCATTTTTTC
*
54218 TTCTTTTCATTTTTTC
1 CT-TTTTCATTTTTTC
54234 ACTCTCACCT
Statistics
Matches: 54, Mismatches: 11, Indels: 17
0.66 0.13 0.21
Matches are distributed among these distances:
11 5 0.09
12 1 0.02
13 3 0.06
14 2 0.04
15 18 0.33
16 15 0.28
17 10 0.19
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.70
Consensus pattern (15 bp):
CTTTTTCATTTTTTC
Found at i:54179 original size:26 final size:24
Alignment explanation
Indices: 54147--54234 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 24
54137 CATTCTGTCT
*
54147 TTTTCATTTTTTCCTTTTTCTACGTC
1 TTTTCATTTTTTCATTTTTCTA--TC
* *
54173 TTTTCATTTTCTTCTTTTTTCAAT-
1 TTTTCATTTT-TTCATTTTTCTATC
*
54197 TCTTTCCTTTTTTCATTTTTCT-TC
1 T-TTTCATTTTTTCATTTTTCTATC
54221 TTTTCATTTTTTCA
1 TTTTCATTTTTTCA
54235 CTCTCACCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 13 0.25
24 11 0.21
25 9 0.17
26 10 0.19
27 10 0.19
ACGTcount: A:0.09, C:0.20, G:0.01, T:0.69
Consensus pattern (24 bp):
TTTTCATTTTTTCATTTTTCTATC
Found at i:54223 original size:17 final size:17
Alignment explanation
Indices: 54153--54224 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
54143 GTCTTTTTCA
* *
54153 TTTTTTCCTTTTTCTAC
1 TTTTTTCATTTTTCTTC
*
54170 GTCTTTTCA-TTTTCTTC
1 -TTTTTTCATTTTTCTTC
54187 TTTTTTCAATTCTTTC--C
1 TTTTTTC-ATT-TTTCTTC
54204 TTTTTTCATTTTTCTTC
1 TTTTTTCATTTTTCTTC
54221 TTTT
1 TTTT
54225 CATTTTTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.09
16 9 0.20
17 21 0.47
18 7 0.16
19 4 0.09
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (17 bp):
TTTTTTCATTTTTCTTC
Found at i:56511 original size:13 final size:12
Alignment explanation
Indices: 56494--56518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56484 TTTTTTTTTT
56494 ATTTTTTTTCAA
1 ATTTTTTTTCAA
56506 ATTTTTTTTCAA
1 ATTTTTTTTCAA
56518 A
1 A
56519 CGAATCTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTTTTTCAA
Found at i:60356 original size:39 final size:39
Alignment explanation
Indices: 60312--60488 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 39
60302 ACTCCTCGTT
*
60312 CAAATGCCTTCGGGACATAGCCCGGTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
60351 CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGC-
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
60389 TAAATG-CTTCGGG-C-TAG-CCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
* * * *
60425 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGTAAC-TCGCA
60466 CAAA-GCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
60489 ACATAATTCA
Statistics
Matches: 112, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
34 3 0.03
35 12 0.11
36 8 0.07
37 11 0.10
38 6 0.05
39 46 0.41
40 17 0.15
41 9 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Done.