Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_382 ID=scaffold_382-JGI_221_v2.0
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: 7659
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:74 original size:19 final size:21
Alignment explanation
Indices: 36--74 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
26 CCTTTTTTAA
*
36 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
57 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
75 AGAAAACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:280 original size:23 final size:22
Alignment explanation
Indices: 237--294 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
227 AAAGGGTATC
* *
237 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
258 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
281 TACATATCATATCT
1 TACAAATCATATCT
295 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:297 original size:19 final size:19
Alignment explanation
Indices: 250--347 Score: 106
Period size: 19 Copynumber: 4.8 Consensus size: 19
240 AAATTAAATC
*
250 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
270 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
292 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
313 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
332 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
348 CTCGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
19 33 0.48
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:310 original size:21 final size:21
Alignment explanation
Indices: 284--346 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
274 CTAAGATTAC
284 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
305 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
324 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
345 AT
1 AT
347 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:812 original size:128 final size:129
Alignment explanation
Indices: 632--883 Score: 303
Period size: 128 Copynumber: 2.0 Consensus size: 129
622 AGATGAATTT
* * * *
632 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
697 ACTTTAAGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTACAACTTCAGGAAGATAAGACT
66 ACTTCAAGGAGATAGGATTATCG--GATTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACT
760 A
129 A
* ** * * * *
761 GATGCGTTCTGCTCT-CTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * * *
825 ACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
66 ACTTCAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAGGAAGATAA
884 AATTTGCCAT
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 87 0.84
129 15 0.15
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTA
Found at i:827 original size:44 final size:44
Alignment explanation
Indices: 776--883 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
766 GTTCTGCTCT
* * *
776 CTGCAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCGCTTCA
1 CTGCAACTTCAGGGAGATAAGAT-CATAGGCTTTAATCCGCTCCA
* * * *
820 CTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCA
864 CTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAGGGAGATAA
884 AATTTGCCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 1 0.02
44 54 0.98
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCA
Found at i:1244 original size:44 final size:43
Alignment explanation
Indices: 1190--1609 Score: 485
Period size: 44 Copynumber: 9.7 Consensus size: 43
1180 GCTATTTTTC
* ** * *
1190 ACCTACTCCACTGCTGCTCAGGGAGATAGGGCTCACGATCTCCA
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGATTCACAATCTTCA
* *
1234 ACCTATTCCACTGCTGACTAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
* * *
1278 ATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGCC-AGGGAGATAGGATTCACAATCTTCA
* *
1322 ACCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGCC-AGGGAGATAGGATTCACAATCTTCA
* *
1366 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
1410 ACCTATTCCACTGCTGTCCAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * *
1448 ATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGCC-AGGGAGATAGGATTCACAATCTTCA
* *
1492 ACCTATTCCACTGCTGACCAGAGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * * *
1536 ACTTATTTCACTGTTGTCCAAGGAGATAGGATTCACAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
1580 ACCTATTCCACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTG-CCAGGGAGATAGG
1610 GCTGGGGTCA
Statistics
Matches: 326, Mismatches: 37, Indels: 26
0.84 0.10 0.07
Matches are distributed among these distances:
37 2 0.01
38 29 0.09
39 2 0.01
40 2 0.01
42 2 0.01
43 4 0.01
44 280 0.86
45 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGATTCACAATCTTCA
Found at i:1496 original size:170 final size:171
Alignment explanation
Indices: 1190--1609 Score: 585
Period size: 170 Copynumber: 2.4 Consensus size: 171
1180 GCTATTTTTC
* ** * * *
1190 ACCTACTCCACTGCTGCTCAGGGAGATAGGGCTCACGATCTCCAACCTATTCCACTGCTGACTAG
1 ACCTATTCCACTGCTGCT-AGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
1255 GGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTT
65 GGAGATAGGA-CT---ATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTT
* *
1320 CAACCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCA
126 CAACCTATTCCACTGCTGACC-AGAGAGATAGAATTCACAATCTTCA
* *
1366 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTGCTG-CTAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
*
1431 GGAGATAGGA-T-TCTTTAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAAC
65 GGAGATAGGACTATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAAC
* *
1494 CTATTCCACTGCTGACCAGAGAGATAGGATTCACAATCTTTA
130 CTATTCCACTGCTGACCAGAGAGATAGAATTCACAATCTTCA
* * * * *
1536 ACTTATTTCACTGTTGTCCAAGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTG-CTAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
1601 GGAGATAGG
65 GGAGATAGG
1610 GCTGGGGTCA
Statistics
Matches: 221, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
170 152 0.69
171 2 0.01
174 1 0.00
176 64 0.29
177 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (171 bp):
ACCTATTCCACTGCTGCTAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGG
GAGATAGGACTATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACC
TATTCCACTGCTGACCAGAGAGATAGAATTCACAATCTTCA
Found at i:1523 original size:126 final size:129
Alignment explanation
Indices: 1190--1608 Score: 537
Period size: 132 Copynumber: 3.2 Consensus size: 129
1180 GCTATTTTTC
* *** * * *
1190 ACCTACTCCACTGCTG-CTCAGGGAGATAGGGCTCACGATCTCCAACCTATTCCACTGCTGACTA
1 ACCTATTCCACTGCTGCCT-AGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACTA
* * * *
1254 GGGAGATAGGA-CCTACAATCTTCAATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAAT
65 GGGAGATAGGATTC-ACAATCTTTAACCTATTCCACTGCTGTCC-AGGGAGATAGGA-T-TC-AT
1317 CTTCA
125 CTTCA
1322 ACCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACTAG
1 ACCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACTAG
1387 GGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTC-T-TT-A
66 GGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCATCTTCA
* *
1448 ATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACTAG
* * * * *
1513 AGAGATAGGATTCACAATCTTTAACTTATTTCACTGTTGTCCAAGGAGATAGGATTCACAATCTT
66 GGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATT--C-ATCTT
1578 CA
128 CA
1580 ACCTATTCCACTGCTGACC-AGGGAGATAG
1 ACCTATTCCACTGCTG-CCTAGGGAGATAG
1609 GGCTGGGGTC
Statistics
Matches: 258, Mismatches: 19, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
126 115 0.45
127 2 0.01
128 2 0.01
130 3 0.01
131 3 0.01
132 126 0.49
133 7 0.03
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (129 bp):
ACCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACTAG
GGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCATCTTCA
Found at i:1671 original size:88 final size:88
Alignment explanation
Indices: 1609--2098 Score: 739
Period size: 88 Copynumber: 5.6 Consensus size: 88
1599 AGGGAGATAG
* * * * * * *
1609 GGCTGGGGTCATCAATCTGCTTTGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1674 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
1697 GGCTGGTGTCTTCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
1762 TCCGCTGTAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
1785 GACTGGTGTCTTCGATCTACTTCACTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1850 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
1873 GGCTGGTGACTTCGATCTACTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1938 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
1961 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
2026 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
2049 GGCTGGTGACTTCGATCTGCTTCACT-TCCAGTACAGGAAGACAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGT-CGGTGCAGGAAGGCAAGATCTG
2099 TTATCTTCTC
Statistics
Matches: 367, Mismatches: 34, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
87 1 0.00
88 366 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:1739 original size:44 final size:44
Alignment explanation
Indices: 1686--2001 Score: 134
Period size: 44 Copynumber: 7.2 Consensus size: 44
1676 CGCTGCAACC
* *
1686 CAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * * * ** * * **
1730 CAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGT-AACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * * * * * *
1774 CAGGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTATCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * * * * ** * * **
1818 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * * * * *
1862 CAGGGAGGCAAGGCTGGTGACTTCGATCTACTTCGTTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * * * * ** * * **
1906 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
* * *
1950 CAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGATG
1 CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
1994 CAGGAAGG
1 CAGGAAGG
2002 TAAGATCTGC
Statistics
Matches: 172, Mismatches: 94, Indels: 12
0.62 0.34 0.04
Matches are distributed among these distances:
43 46 0.27
44 78 0.45
45 48 0.28
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTGTCGATG
Found at i:3363 original size:6 final size:6
Alignment explanation
Indices: 3352--3379 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3342 GGCCTCTCCA
3352 TTTTCC TTTTCC TTTTCC TTTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTT
3380 TATCACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCC
Done.