Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3190
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: 45598
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:5382 original size:27 final size:27
Alignment explanation
Indices: 5365--5542 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
5355 ATATTAAGTC
5365 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
5392 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
5419 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
5447 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
5474 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
5501 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
5528 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
5543 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:5504 original size:82 final size:81
Alignment explanation
Indices: 5386--5541 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5376 TGCTATATAA
* *
5386 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
5451 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
5468 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
5532 CACTTAGTGC
65 CACTTAGTGC
5542 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:5525 original size:54 final size:54
Alignment explanation
Indices: 5365--5541 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
5355 ATATTAAGTC
* * * *
5365 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
5419 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
5474 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
5528 CGCACACTTAGTGC
1 CGCACACTTAGTGC
5542 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:9259 original size:246 final size:247
Alignment explanation
Indices: 8822--9307 Score: 812
Period size: 246 Copynumber: 2.0 Consensus size: 247
8812 AGTTCATGGT
8822 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
1 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
* **
8887 ATTTATGGACTATGATAAGAGTGTGTGGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
66 ATTTATGGACTATGATAACAGTGTACGGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
* *
8952 TAGCTCTTTAGAGGGAGTAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
131 TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
* *
9017 AAGCGCACTGAGTGTGAGAGGAGAGACCAAGAGAGAGG-TCAAGTTTCTGCA
196 AAGCACACTGAATGTGAGAGGAGAGACCAAGAGAGAGGTTCAAGTTTCTGCA
* * *
9068 GAGATAATTTTAGCCATGTATGATGCCAAGTTTTTGAGATTGAGCAGATATACTTGTGCTTTGGT
1 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
* * *
9133 ATTTATGGACTATGATAACAGTGTACGGTTTGAAGAAGGTTTGTGTTATAATCTATGGGTTTTGA
66 ATTTATGGACTATGATAACAGTGTACGGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
* * *
9198 TAGCTCTTCAGAGGGAGCGAGTGTTTGTAGCCTTGGTTGACAAGGCAAAGATAGTGAAAGAAGTG
131 TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
*
9263 AAGCATACTGAATGTGAGAGGAGAGACCAAGAGAGAGGTTCAAGT
196 AAGCACACTGAATGTGAGAGGAGAGACCAAGAGAGAGGTTCAAGT
9308 AAGATTAAGA
Statistics
Matches: 222, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
246 216 0.97
247 6 0.03
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.30
Consensus pattern (247 bp):
GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
ATTTATGGACTATGATAACAGTGTACGGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
AAGCACACTGAATGTGAGAGGAGAGACCAAGAGAGAGGTTCAAGTTTCTGCA
Found at i:12768 original size:46 final size:46
Alignment explanation
Indices: 12715--12845 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 46
12705 GGGTTATTGT
* *
12715 GAGCTAGTGTAAGACTTGTCTGGGACATGCATCGGCCACATTATG-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTAAGAA
12761 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG--CATTAAGACAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATTAAG--AA
* *
12809 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
12846 TCGAGATGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
45 6 0.08
46 21 0.28
47 26 0.35
48 21 0.28
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAAGAA
Found at i:12887 original size:46 final size:46
Alignment explanation
Indices: 12717--12942 Score: 163
Period size: 50 Copynumber: 4.8 Consensus size: 46
12707 GTTATTGTGA
* * ** ** *
12717 GCTAGTGTAAGACTTGTCTGGGACATGCATCGGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACAGGCATCGG-CACTAAGACAAGT
*
12763 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAAGACAAGT
1 GCTAGTGTAAGA-CATGTCTGGGACA-GGCATCGGCACTAAGACAAGT
* * * * *
12811 GCTAGTGTAAGACATGTTTGGGACATGCATCGGC-CT-CGAGATGT
1 GCTAGTGTAAGACATGTCTGGGACAGGCATCGGCACTAAGACAAGT
* * * * *
12855 GTTAGTGTAAGACTATCTCTGGGACACGGCATCGACAC-AGATATGCTAGT
1 GCTAGTGTAAGAC-ATGTCTGGGACA-GGCATCGGCACTA-AGA--CAAGT
*
12905 GCTTGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
1 GCTAGTGTAAGA-CATGTCTGGGACA-GGCATCGGCAC
12943 CTTACCCCAT
Statistics
Matches: 140, Mismatches: 29, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
44 17 0.12
45 11 0.08
46 27 0.19
47 27 0.19
48 24 0.17
50 33 0.24
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACAGGCATCGGCACTAAGACAAGT
Found at i:12905 original size:44 final size:42
Alignment explanation
Indices: 12717--12905 Score: 117
Period size: 47 Copynumber: 4.2 Consensus size: 42
12707 GTTATTGTGA
* * * * *
12717 GCTAGTGTAAGACTTGTCTGGGACATGCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACAGGCATC-GACACA-GAT-A-T
* * *
12763 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAAGACAAGT
1 GCTAGTGTAAGA-CATGTCTGGGACA-GGCATCGACA--CAGA-TA-T
* * * * *
12811 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATGT
1 GCTAGTGTAAGACATGTCTGGGACAGGCATC-GACAC-AGATAT
* *
12855 GTTAGTGTAAGACTATCTCTGGGACACGGCATCGACACAGATAT
1 GCTAGTGTAAGAC-ATGTCTGGGACA-GGCATCGACACAGATAT
12899 GCTAGTG
1 GCTAGTG
12906 CTTGTGTAAG
Statistics
Matches: 112, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
44 24 0.21
45 13 0.12
46 25 0.22
47 29 0.26
48 20 0.18
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (42 bp):
GCTAGTGTAAGACATGTCTGGGACAGGCATCGACACAGATAT
Found at i:12906 original size:94 final size:93
Alignment explanation
Indices: 12717--12940 Score: 238
Period size: 94 Copynumber: 2.4 Consensus size: 93
12707 GTTATTGTGA
* * *
12717 GCTAGTGTAAGACTTGTCTGGGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGAT-AGAGCTAGTGTAAGACCATCTC
* * *
12782 TGGGACATGGCATCGGCATTAAGACAAGT
65 TGGGACACGGCATCGACAATAAGACAAGT
* * * * *
12811 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCGA-GAT-GTGTTAGTGTAAGACTATCTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATAGAGCTAGTGTAAGACCATCTC
* *
12874 TGGGACACGGCATCGACACAGATATG-CTAGT
65 TGGGACACGGCATCG--ACA-ATAAGACAAGT
*
12905 GCTTGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
12941 ACCTTACCCC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
92 31 0.28
94 53 0.49
95 17 0.16
96 8 0.07
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATAGAGCTAGTGTAAGACCATCTCT
GGGACACGGCATCGACAATAAGACAAGT
Found at i:19016 original size:3 final size:3
Alignment explanation
Indices: 19008--19068 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
18998 GTTAGCTTTC
19008 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
19056 CTT CTT CTC CTT C
1 CTT CTT CTT CTT C
19069 CTTTTGTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:23665 original size:40 final size:40
Alignment explanation
Indices: 23593--23774 Score: 231
Period size: 40 Copynumber: 4.6 Consensus size: 40
23583 AAACCAAGTA
* * * * *
23593 CCTTCGGGATTTAG-CCGGATATCGCAATTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
23632 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
23672 CCTTCGGGTCTTAGCTCGGAAATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
23712 CCTTCGGGTCTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
23752 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
23775 CATCCGAATA
Statistics
Matches: 123, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 12 0.10
40 111 0.90
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:31915 original size:40 final size:40
Alignment explanation
Indices: 31846--32027 Score: 249
Period size: 40 Copynumber: 4.6 Consensus size: 40
31836 GAACCAAGTA
* * *
31846 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
31885 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * * *
31925 CCTTCAGGTCTTAGCCCGGAAATAGTCACTAGCACTAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
31965 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
32005 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
32028 CATCCGAATA
Statistics
Matches: 123, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 12 0.10
40 111 0.90
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45220 original size:28 final size:27
Alignment explanation
Indices: 45155--45227 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
45145 ATAATAAGCC
* *
45155 CGCACACTTAGTGCT-TAATAGTCGACT
1 CGCACACTTAGTGCTAT-ATAATCAACT
*
45182 CGTACACTTAGTGCTATATAATCAACCT
1 CGCACACTTAGTGCTATATAATCAA-CT
45210 CGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
45228 CAATTTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Done.