Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2054
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: 21289
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:2143 original size:35 final size:35
Alignment explanation
Indices: 2098--2172 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
2088 TTTCCCAAGA
2098 TCTC-TTACGAAACTCCTTTGCTCCCACATCGCTT
1 TCTCTTTACGAAACTCCTTTGCTCCCACATCGCTT
2132 TCTCTTTACGAAACTCCTTTGCTCCCACATCGCTT
1 TCTCTTTACGAAACTCCTTTGCTCCCACATCGCTT
2167 TC-CTTT
1 TCTCTTT
2173 TCTCCTTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 8 0.20
35 32 0.80
ACGTcount: A:0.16, C:0.37, G:0.08, T:0.39
Consensus pattern (35 bp):
TCTCTTTACGAAACTCCTTTGCTCCCACATCGCTT
Found at i:4582 original size:38 final size:40
Alignment explanation
Indices: 4434--4683 Score: 310
Period size: 39 Copynumber: 6.5 Consensus size: 40
4424 AAGCCAAGTA
* * *
4434 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
4472 CCTTCGGGACATAGCCCGGATATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4511 CCTTCGGGACTTAGCCCGG---TA-TAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4547 CCTTC-GGACTTAGCCCGGATAT-GTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4585 CCTTC-GGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
4624 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
4665 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
4684 TTATCATCCA
Statistics
Matches: 190, Mismatches: 10, Indels: 21
0.86 0.05 0.10
Matches are distributed among these distances:
35 23 0.12
36 11 0.06
38 49 0.26
39 59 0.31
40 20 0.11
41 24 0.13
42 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:4632 original size:113 final size:115
Alignment explanation
Indices: 4434--4683 Score: 316
Period size: 113 Copynumber: 2.2 Consensus size: 115
4424 AAGCCAAGTA
* * * *
4434 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAATGCCTTCGGGACATAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATAT-G-TAACTCGCACAATGCCTTCGGGACATAGCCCGGATATAA
4497 TAACTCGCACAATGCCTTCGGGACTTAGCCCGG-TA-TAACT-CGCACAAATG
64 TAACTCGCACAATGCCTTCGGGACTTAGCCCGGATAGTAACTACGCA-AAATG
* *
4547 CCTTC-GGACTTAGCCCGGATATGTAACTCGCACAAATGCCTTC-GGACTTAGCCCGGATGTAAT
1 CCTTCGGGACTTAGCCCGGATATGTAACTCGCAC-AATGCCTTCGGGACATAGCCCGGATATAAT
*
4610 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAACTAGTCACTAGCGCAAAATG
65 AACTCGCAC-AATGCCTTCGGGACTTAGCCCGG-A-TAGTAACTA-CGCAAAATG
4665 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
4684 TTATCATCCA
Statistics
Matches: 119, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
111 1 0.01
112 40 0.34
113 45 0.38
116 2 0.02
117 4 0.03
118 10 0.08
119 17 0.14
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (115 bp):
CCTTCGGGACTTAGCCCGGATATGTAACTCGCACAATGCCTTCGGGACATAGCCCGGATATAATA
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATAGTAACTACGCAAAATG
Found at i:7358 original size:40 final size:40
Alignment explanation
Indices: 7280--7413 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
7270 ACCCAAGTAT
* *
7280 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
**
7319 CTTC-GGATCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
*
7359 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
7399 CTTCGGGACTTAGCC
1 CTTCGGGACTTAGCC
7414 TGTAACACCC
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.04
39 8 0.10
40 69 0.82
41 4 0.05
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:7590 original size:15 final size:15
Alignment explanation
Indices: 7570--7598 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7560 TCACAACTCA
7570 AAAATCAGTTTCGTG
1 AAAATCAGTTTCGTG
7585 AAAATCAGTTTCGT
1 AAAATCAGTTTCGT
7599 AATTTTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (15 bp):
AAAATCAGTTTCGTG
Found at i:8881 original size:40 final size:40
Alignment explanation
Indices: 8807--8987 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
8797 GCTACTCGTT
*
8807 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
8846 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
8886 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
8925 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
8966 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
8988 AGACATCATT
Statistics
Matches: 123, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.02
39 44 0.36
40 64 0.52
41 13 0.11
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:8950 original size:79 final size:79
Alignment explanation
Indices: 8809--8987 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 79
8799 TACTCGTTCA
* * * *
8809 AATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
*
8874 TAGTAAC-TCGCACC
66 TAGTAACTTAGCA-C
**
8888 AATGCCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* *
8951 TATGGTCACTTAGCAC
64 TATAGTAACTTAGCAC
*
8967 AAAGCCTTCGGGACTTAGCCC
1 AATGCCTTCGGG-CTTAGCCC
8988 AGACATCATT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.05
79 70 0.81
80 12 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:16908 original size:79 final size:81
Alignment explanation
Indices: 16799--16981 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
16789 TACTCGTTCA
* *
16799 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
16862 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
16879 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
16942 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
16958 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
16982 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:16981 original size:40 final size:40
Alignment explanation
Indices: 16778--16981 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
16768 CGGAATTTAA
** *
16778 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16818 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16858 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
16897 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
16937 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
16977 CCGGA
1 CCGGA
16982 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18823 original size:28 final size:27
Alignment explanation
Indices: 18760--18911 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
18750 ATATTAAGTC
* * *
18760 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
18787 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
18815 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
18842 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
18870 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
18897 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18912 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:18828 original size:55 final size:55
Alignment explanation
Indices: 18760--18911 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
18750 ATATTAAGTC
* * *
18760 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
18815 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
18870 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
18912 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Done.