Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4186
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: 15664
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Found at i:1792 original size:49 final size:49
Alignment explanation
Indices: 1614--2374 Score: 1323
Period size: 49 Copynumber: 15.8 Consensus size: 49
1604 CCCTTCGGGA
* * * * *
1614 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1661 CCTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1708 CTTATCACATA-A-ATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1755 CTTATCACATATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1803 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1852 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1899 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1948 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1997 CTTATCAC--ATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2044 CTTATCACATATATATATAGACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2095 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2144 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2193 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2242 CTTATCACATATATATACAATTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2291 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2338 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATATACACTTTCACATTCATCACAT
2375 AGAATCCTAA
Statistics
Matches: 684, Mismatches: 15, Indels: 28
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.00
47 229 0.33
48 50 0.07
49 359 0.52
51 45 0.07
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5981 original size:40 final size:40
Alignment explanation
Indices: 5919--6376 Score: 659
Period size: 40 Copynumber: 11.4 Consensus size: 40
5909 TCTTCGGAAC
* * * * **
5919 TAGCCCGGATATAACACCAGCATGAATGCTCTTCGAGGTT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
* * * *
5959 TAGCACGGATATATTACTAGCATGAATGCTCTTC-AGAACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAG-ACT
5999 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
*
6039 TAGCCTGGATACATCACTAGCACGAATGCTCTTCGAGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
6079 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
*
6119 TAGCCCGGATACATCACTAGCATGAATGCTCTTCGAGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
** * *
6159 TAGCAGGGATACATCACTAGCAAGAATGCTCTTCGGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
*
6199 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGAGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
6239 TAGCCCGGATACATCACTAGCACGAATGCTCTTC-AGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGA-GACT
* * *
6279 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
* * * *
6319 TAGCCCGGATATATCACTAGCATGAATGCTCCTCGGGACT
1 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
*
6359 TAGCCCGGATATATCACT
1 TAGCCCGGATACATCACT
6377 CTCAATTCTC
Statistics
Matches: 387, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
39 3 0.01
40 382 0.99
41 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACT
Found at i:7658 original size:37 final size:37
Alignment explanation
Indices: 7585--7662 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
7575 TTATTACGAA
* * * * * *
7585 GTCTTACCCGGACATAATCTCCGCGCGAAGTTATCGG
1 GTCTCACCCGGACAAAATCCCCACACGAAGTCATCGG
*
7622 GTCTCACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTCACCCGGACAAAATCCCCACACGAAGTCATCGG
7659 GTCT
1 GTCT
7663 TTAGAGCTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (37 bp):
GTCTCACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:7912 original size:49 final size:47
Alignment explanation
Indices: 7782--8631 Score: 1425
Period size: 49 Copynumber: 17.7 Consensus size: 47
7772 CCCTTCGGGA
* * * * * *
7782 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7829 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7876 CTTAATCACATATATACACTTTTCACATTCATCACATCGGCCATTAGGC
1 CTT-ATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGC
7925 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7973 CTTATCACATGTATATCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGC
8021 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8069 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8118 CTTATCACATATATTACACTTTCACATTCATCTCATCGGCCATTAGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
8166 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8213 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8262 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8308 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8357 CTTATCACATATATACACTTTCACATTCATCGCATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8403 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8452 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8501 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8550 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8597 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
8632 AGAATCCTAA
Statistics
Matches: 772, Mismatches: 16, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
46 41 0.05
47 217 0.28
48 232 0.30
49 282 0.37
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8053 original size:144 final size:143
Alignment explanation
Indices: 7782--8631 Score: 1462
Period size: 144 Copynumber: 5.9 Consensus size: 143
7772 CCCTTCGGGA
* * * * * * *
7782 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
7845 ACTTTCACATTCATCACATCGGCCATTAGGCCTTAATCACATATATACACTTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTT-ATCACATATATACAC-TTTCACATTCATCA
7910 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
*
7925 CTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-
7989 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATACACTTTCACATTCATCA
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCA
8054 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
8069 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA-TA
*
8134 CACTTTCACATTCATCTCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
8199 ATCGGCCATTAGGC
130 ATCGGCCATTAGGC
8213 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
8278 ACTTTCACATTCA-CACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
8342 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
*
8357 CTTATCAC--ATATATACACTTTCACATTCATCGCATCGG-CATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
8419 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
8484 CACATCGGCCATTAGGC
127 CACATCGGCCATTAGGC
8501 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
8566 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
8631 T
131 T
8632 AGAATCCTAA
Statistics
Matches: 680, Mismatches: 13, Indels: 28
0.94 0.02 0.04
Matches are distributed among these distances:
141 16 0.02
142 54 0.08
143 73 0.11
144 307 0.45
145 183 0.27
146 31 0.05
147 16 0.02
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:8125 original size:193 final size:191
Alignment explanation
Indices: 7782--8631 Score: 1478
Period size: 193 Copynumber: 4.4 Consensus size: 191
7772 CCCTTCGGGA
* * * * * * * *
7782 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATACA
7846 CTTTCACATTCATCACATCGGCCATTAGGCCTTAATCACATATATACACTTTTCACATTCATCAC
66 CTTTCACATTCATCACATCGGCCATTAGGCCTT-ATCACATATATACAC-TTTCACATTCATCAC
7911 ATCGGCCATTAGGCCTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 ATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7973 CTTATCACATGTATATCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATAC
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATAC
8038 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
*
8103 CATCGGCCATTAGGCCTTATCACATATAT-TACACTTTCACATTCATCTCATCGGCCATTAGGC
128 CATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8166 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-TATATATAC
8231 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCA-CACA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
8295 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
130 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8357 CTTATCACATATATACACTTTCACATTCATCGCATCGG-CATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-TATATATAC
8421 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
8486 CATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
128 CATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8550 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATACA
8614 CTTTCACATTCATCACAT
66 CTTTCACATTCATCACAT
8632 AGAATCCTAA
Statistics
Matches: 635, Mismatches: 13, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
190 96 0.15
191 105 0.17
192 126 0.20
193 277 0.44
194 31 0.05
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (191 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACTATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.