Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1523
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: 33980
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:292 original size:28 final size:28
Alignment explanation
Indices: 260--623 Score: 340
Period size: 28 Copynumber: 12.6 Consensus size: 28
250 CAATACGATG
* *
260 CTTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
288 CTTTTCAAAGCCAACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
317 C-TTTCAAAGCCCACAAGTCAGTGGAATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
345 CTTCTCAAAGCCCACAAGTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
374 CATGTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
403 C-TTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
*
433 CTCTCTCAAAGCCCACAAGTCAGTGGCAC
1 CT-TTTCAAAGCCCACAAGTCAGTGGCAC
*
462 CCTTTCAAAGCCCACATAAGTCAGTGGCAAC
1 CTTTTCAAAGCCCAC--AAGTCAGTGGC-AC
* * *
493 CTCTCTCAAAGTCCACAAGTTAGTGGCAAC
1 CT-TTTCAAAGCCCACAAGTCAGTGGC-AC
* * *
523 C-ATTCAAAGCTCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
550 CCTTTCGAAGCCCACAAATCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
**
579 CTTTT-AAAGCCCACAAGTTGGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
607 CTTCTCTAAAGCCCACA
1 CTTTTC-AAAGCCCACA
624 CAAGTTGGTG
Statistics
Matches: 282, Mismatches: 38, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
27 3 0.01
28 131 0.46
29 61 0.22
30 63 0.22
31 6 0.02
32 18 0.06
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:456 original size:60 final size:59
Alignment explanation
Indices: 264--623 Score: 389
Period size: 60 Copynumber: 6.2 Consensus size: 59
254 ACGATGCTTT
* * *
264 TCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCA-ACAAGTCAGTGGCATCCT-T-
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
* * * * * *
320 TCAAAGCCCACAAGTCAGTGGAATCCTTCTCAAAGCC-CACAAGTTAGTAGCATCC-ATG
1 TCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCACACAAGTCAGTGGCAACCTCTC
*
378 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCACACAAGTCAGTGGCAACCTCTC
* *
438 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACATAAGTCAGTGGCAACCTCTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCACACAAGTCAGTGGCAACCTCTC
* * * * * * *
498 TCAAAGTCCACAAGTTAGTGGCAACCATTCAAAG-CTCACAAGTTAGTGGC-ACC-CTT
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
* * * * **
554 TCGAAGCCCACAAATCAGTGGCACCCTTTTAAAGCC-CACAAGTTGGTGGCAACCT-TC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
611 TCTAAAGCCCACA
1 TC-AAAGCCCACA
624 CAAGTTGGTG
Statistics
Matches: 260, Mismatches: 33, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
56 67 0.26
57 40 0.15
58 51 0.20
59 14 0.05
60 88 0.34
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (59 bp):
TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
Found at i:1691 original size:20 final size:20
Alignment explanation
Indices: 1614--1691 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
1604 TTTTTACCAA
** *
1614 AATGTATCGATGTATTTTTC
1 AATGTATCGATACATTCTTC
* *
1634 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
*
1654 AATGTGTCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1674 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
1692 ATCTTTTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:15128 original size:30 final size:28
Alignment explanation
Indices: 14909--15385 Score: 490
Period size: 28 Copynumber: 16.5 Consensus size: 28
14899 ATATGACCCT
* *
14909 TTTCAAAGCCTAC-AGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
14936 TTTCAAAGCCCATAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
14964 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
14992 TTCTCAAAGGCCACAAGTCAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* *
15021 TCTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
15049 TTTTCAAAGCCCACACAAATCGGTGGTAACCTC
1 -TTTCAAAG-CC-CACAAGTCAGTGG-CATC-C
*
15082 TTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
15110 TTTCAAAGCCTACACAAGTCGGTGGCAACC
1 TTTCAAAGCC--CACAAGTCAGTGGCATCC
15140 TCTCTCAAAGCCCACAAGTCAGTGGCATCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
*
15170 TTTCAAAGCCCACATAAGTCAGTGGCAACC
1 TTTCAAAGCCCAC--AAGTCAGTGGCATCC
* *
15200 TCTCTCAAAGCCTACAAGTCAGTGGCACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
* * *
15230 TTTCAAAGCCCACAAGTTAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
15258 TTTCGAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
15286 TTTCGAAGCCCACAAGTTAGCGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
15314 GTTT-GAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
15342 TTTTAAAGCACACAAGTTAGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
15370 TTCTTCAAAGCCCACA
1 -T-TTCAAAGCCCACA
15386 CAAGTTGGTG
Statistics
Matches: 389, Mismatches: 42, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
27 14 0.04
28 205 0.53
29 41 0.11
30 86 0.22
31 14 0.04
32 28 0.07
33 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:15140 original size:60 final size:58
Alignment explanation
Indices: 14909--15385 Score: 517
Period size: 60 Copynumber: 8.2 Consensus size: 58
14899 ATATGACCCT
* * * *
14909 TTTCAAAGCCTAC-AGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGC-ATC-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTC
* *
14964 TTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGGCCACAAGTCAGTGGCATCCTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCAACCTC
* * * *
15023 --TCAAAGCCCACAAGTTAGTGGCATCCTTTTCAAAGCCCACACAAATCGGTGGTAACCTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAG-CC-CACAAGTCAGTGGCAACCTC
* *
15082 TTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCTACACAAGTCGGTGGCAACCTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC--CACAAGTCAGTGGCAACCTC
*
15142 TCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACATAAGTCAGTGGCAACCTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC--AAGTCAGTGGCAACCTC
* * * * *
15202 TCTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGG-TACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTC
* * * * * * *
15258 TTTCGAAGCCCACAAGTTAGTGGCACCCTTTCGAAGCCCACAAGTTAGCGAC-ACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTC
* * * * *
15314 GTTT-GAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCACACAAGTTAGTGGCAACCT-
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTC
15371 TCTTCAAAGCCCACA
1 T-TTCAAAGCCCACA
15386 CAAGTTGGTG
Statistics
Matches: 367, Mismatches: 37, Indels: 33
0.84 0.08 0.08
Matches are distributed among these distances:
55 12 0.03
56 107 0.29
57 62 0.17
58 25 0.07
59 19 0.05
60 118 0.32
61 24 0.07
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (58 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTC
Found at i:16403 original size:20 final size:20
Alignment explanation
Indices: 16374--16515 Score: 104
Period size: 20 Copynumber: 6.6 Consensus size: 20
16364 TACCCAGATA
16374 TATCGATACATTTTTTAATG
1 TATCGATACATTTTTTAATG
*
16394 TATTGATACATTTTTTAATG
1 TATCGATACATTTTTTAATG
16414 TATCGATACATTCTGTCTTTTACTCAGATG
1 TATCGATACA-----T-TTTT--T-A-ATG
* * *
16444 TATCGTTACATTTATCAATG
1 TATCGATACATTTTTTAATG
* * * *
16464 TATTGATACATGTATGAATG
1 TATCGATACATTTTTTAATG
* *
16484 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTTAATG
16504 TATCGATACATT
1 TATCGATACATT
16516 CTGTCTTTTT
Statistics
Matches: 98, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
20 74 0.76
21 1 0.01
24 3 0.03
25 2 0.02
26 4 0.04
28 1 0.01
29 1 0.01
30 12 0.12
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (20 bp):
TATCGATACATTTTTTAATG
Found at i:16474 original size:70 final size:70
Alignment explanation
Indices: 16361--16497 Score: 202
Period size: 70 Copynumber: 2.0 Consensus size: 70
16351 AAAGTCATAT
* * * * *
16361 TTTTACCCAGATATATCGATACATTTTTTAATGTATTGATACATTTTTTAATGTATCGATACATT
1 TTTTACCCAGATATATCGATACATTTATCAATGTATTGATACATGTATGAATGTATCGATACATT
16426 CTGTC
66 CTGTC
* * *
16431 TTTTACTCAGATGTATCGTTACATTTATCAATGTATTGATACATGTATGAATGTATCGATACATT
1 TTTTACCCAGATATATCGATACATTTATCAATGTATTGATACATGTATGAATGTATCGATACATT
16496 CT
66 CT
16498 TCAATGTATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (70 bp):
TTTTACCCAGATATATCGATACATTTATCAATGTATTGATACATGTATGAATGTATCGATACATT
CTGTC
Found at i:29192 original size:30 final size:31
Alignment explanation
Indices: 29156--29226 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
29146 TCATTTTATC
29156 AATACATTCTGGG-TTTGACCCAAATGTATT
1 AATACATTCTGGGTTTTGACCCAAATGTATT
29186 AATACATTCTGGGTTTTGACCCAAATGTATT
1 AATACATTCTGGGTTTTGACCCAAATGTATT
*
29217 GATACATTCT
1 AATACATTCT
29227 TCAATGTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (31 bp):
AATACATTCTGGGTTTTGACCCAAATGTATT
Done.