Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_742 ID=scaffold_742-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: 4228
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:154 original size:88 final size:88
Alignment explanation
Indices: 1--647 Score: 853
Period size: 88 Copynumber: 7.5 Consensus size: 88
*
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAAGG-AAGATCTTTTGTCTTCAACCAGCTTCAT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGG-AAGGCAAGATCTTTTGTCTTCAACCAGCTCCAT
65 CACAACCGAGAGAGGCAAGGTTTG
65 CACAACCGAGAGAGGCAAGGTTTG
* * *
89 TGTCTTCGACCTGCTTCACTGTCAATGCAGGAATGCAAGATCTTTTGTTTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
*
154 ACCACCGAGAGAGGCAAGGTTTG
66 ACAACCGAGAGAGGCAAGGTTTG
* * *
177 TGTCTTTGACCTACTTCACTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
*
242 ACAACCGAGAGAGGCAAGATTTG
66 ACAACCGAGAGAGGCAAGGTTTG
265 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
*
330 ACAACCGAGAGAGGCAAGGTTTA
66 ACAACCGAGAGAGGCAAGGTTTG
* * * * *
353 TGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC---TG-CTCCATCACAAC-CGA-
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAAC-CAGCTCCAT
* * * *** * *
412 GAGAA--G-CA-AGG-TTTGTGTC
65 CACAACCGAGAGAGGCAAGGTTTG
* * * *
431 T-TCAATCTG--CTTC-GC--TGTCAATACAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA
1 TGTC-TTC-GACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA
490 TCACAACCGAGAGAGGCAAGGTTTG
64 TCACAACCGAGAGAGGCAAGGTTTG
* *
515 TGTCTTCGACCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
580 ACAACCGAGAGAGGCAAGGTTTG
66 ACAACCGAGAGAGGCAAGGTTTG
* *
603 TGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGACCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
648 AACTTCGTTG
Statistics
Matches: 482, Mismatches: 56, Indels: 42
0.83 0.10 0.07
Matches are distributed among these distances:
74 22 0.05
76 1 0.00
77 10 0.02
78 12 0.02
79 7 0.01
80 1 0.00
81 2 0.00
82 1 0.00
83 7 0.01
84 13 0.03
85 10 0.02
86 1 0.00
87 3 0.01
88 392 0.81
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (88 bp):
TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
ACAACCGAGAGAGGCAAGGTTTG
Found at i:213 original size:44 final size:44
Alignment explanation
Indices: 1--393 Score: 163
Period size: 44 Copynumber: 8.9 Consensus size: 44
* * *
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAAGG-AAGATCTTT
1 TGTCTTCGACCTACTTCACTGTCAATGCAGG-AAGGCAAGAT-TTG
* ** * *
46 TGTCTTCAACC-AGCTTCA-TCACAA--CCGAGAGAGGCAAGGTTTG
1 TGTCTTCGACCTA-CTTCACTGTCAATGCAG-GA-AGGCAAGATTTG
* * *
89 TGTCTTCGACCTGCTTCACTGTCAATGCAGGAATGCAAGATCTTT
1 TGTCTTCGACCTACTTCACTGTCAATGCAGGAAGGCAAGAT-TTG
* * * *** * *
134 TGTTTTCAACC-AGC-TC-C-ATCACCACCGAGAGAGGCAAGGTTTG
1 TGTCTTCGACCTA-CTTCACTGTCAATGCAG-GA-AGGCAAGATTTG
* *
177 TGTCTTTGACCTACTTCACTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTACTTCACTGTCAATGCAGGAAGGCAAGAT-TTG
* * ** *
222 TGTCTTCAACC-AGCTCCA-TCACAA--CCGAGAGAGGCAAGATTTG
1 TGTCTTCGACCTA-CTTCACTGTCAATGCAG-GA-AGGCAAGATTTG
* * *
265 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTACTTCACTGTCAATGCAGGAAGGCAAGAT-TTG
* * ** * * *
310 TGTCTTCAACC-AGCTCCA-TCACAA--CCGAGAGAGGCAAGGTTTA
1 TGTCTTCGACCTA-CTTCACTGTCAATGCAG-GA-AGGCAAGATTTG
* * *
353 TGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
1 TGTCTTCGACCTACTTCACTGTCAATGCAGGAAGGCAAGAT
394 CTGCTCCATC
Statistics
Matches: 246, Mismatches: 70, Indels: 65
0.65 0.18 0.17
Matches are distributed among these distances:
42 12 0.05
43 68 0.28
44 90 0.37
45 65 0.26
46 11 0.04
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
TGTCTTCGACCTACTTCACTGTCAATGCAGGAAGGCAAGATTTG
Found at i:320 original size:176 final size:176
Alignment explanation
Indices: 1--647 Score: 1009
Period size: 176 Copynumber: 3.8 Consensus size: 176
*
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAAGG-AAGATCTTTTGTCTTCAACCAGCTTCAT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGG-AAGGCAAGATCTTTTGTCTTCAACCAGCTCCAT
* *
65 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAATGCAAGAT
65 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
* *
130 CTTTTGTTTTCAACCAGCTCCATCACCACCGAGAGAGGCAAGGTTTG
130 CTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTG
* * *
177 TGTCTTTGACCTACTTCACTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
*
242 ACAACCGAGAGAGGCAAGATTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
66 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
*
307 TTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTA
131 TTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTG
*
353 TGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGA-------TC-T------GCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
* * * *
404 ACAACCGAGAGAAGCAAGGTTTGTGTCTTCAATCTGCTTCGCTGTCAATACAGGAAGGCAAGATC
66 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
469 TTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTG
131 TTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTG
* *
515 TGTCTTCGACCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
* *
580 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGACC
66 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
645 TTT
131 TTT
648 AACTTCGTTG
Statistics
Matches: 430, Mismatches: 26, Indels: 30
0.88 0.05 0.06
Matches are distributed among these distances:
162 151 0.35
168 1 0.00
169 4 0.01
170 1 0.00
175 4 0.01
176 269 0.63
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (176 bp):
TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC
ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
TTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTG
Found at i:443 original size:74 final size:74
Alignment explanation
Indices: 322--469 Score: 242
Period size: 74 Copynumber: 2.0 Consensus size: 74
312 TCTTCAACCA
* ** *
322 GCTCCATCACAACCGAGAGAGGCAAGGTTTATGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAAGCAAGGTTTATGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
387 GCAAGATCT
66 GCAAGATCT
* *
396 GCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAATCTGCTTCGCTGTCAATACAGGAAG
1 GCTCCATCACAACCGAGAGAAGCAAGGTTTATGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
461 GCAAGATCT
66 GCAAGATCT
470 TTTGTCTTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (74 bp):
GCTCCATCACAACCGAGAGAAGCAAGGTTTATGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
GCAAGATCT
Found at i:478 original size:45 final size:45
Alignment explanation
Indices: 427--647 Score: 147
Period size: 44 Copynumber: 5.0 Consensus size: 45
417 GCAAGGTTTG
*
427 TGTCTTCAATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTT
1 TGTCTTCAACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTT
* * * * *
472 TGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGGT-TTG
1 TGTCTTCAACCTGCTTCGCTGTCA-ATACAG-GA-AGGCAAGATCTTT
* * * *
515 TGTCTTCGACCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGT
1 TGTCTTCAACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTT
* * * * *
560 TGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGGT-TTG
1 TGTCTTCAACCTGCTTCGCTGTCA-ATACAG-GA-AGGCAAGATCTTT
* * * *
603 TGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGACCTTT
1 TGTCTTCAACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTT
648 AACTTCGTTG
Statistics
Matches: 127, Mismatches: 33, Indels: 32
0.66 0.17 0.17
Matches are distributed among these distances:
42 10 0.08
43 34 0.27
44 39 0.31
45 35 0.28
46 9 0.07
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (45 bp):
TGTCTTCAACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTT
Found at i:501 original size:162 final size:162
Alignment explanation
Indices: 234--558 Score: 578
Period size: 162 Copynumber: 2.0 Consensus size: 162
224 TCTTCAACCA
* * *
234 GCTCCATCACAACCGAGAGAGGCAAGATTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAAGCAAGATTTGTGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
*
299 GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTATGTCTTTGACC
66 GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTATGTCTTCGACC
364 TGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
131 TGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* *
396 GCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAATCTGCTTCGCTGTCAATACAGGAAG
1 GCTCCATCACAACCGAGAGAAGCAAGATTTGTGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
*
461 GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACC
66 GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTATGTCTTCGACC
*
526 TGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
131 TGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
558 G
1 G
559 TTGTCTTCAA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 155 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (162 bp):
GCTCCATCACAACCGAGAGAAGCAAGATTTGTGTCTTCAACCTGCTTCGCTGTCAATACAGGAAG
GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTATGTCTTCGACC
TGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
Found at i:587 original size:250 final size:252
Alignment explanation
Indices: 145--642 Score: 856
Period size: 250 Copynumber: 2.0 Consensus size: 252
135 GTTTTCAACC
* * ** *
145 AGCTCCATCACCACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTACTTCACTGTCAATGCAGGAA
1 AGCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAACCTACTTCACTGTCAATACAGGAA
210 GGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGATTTGTGTCTTCGAC
66 GGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGATTTGTGTCTTCGAC
275 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
131 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
* *
340 GAGGCAAGGTTTATGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC-T
196 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
* * *
396 -GCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAATCTGCTTCGCTGTCAATACAGGAA
1 AGCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAACCTACTTCACTGTCAATACAGGAA
*
460 GGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGAC
66 GGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGATTTGTGTCTTCGAC
* *
525 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGA
131 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
590 GAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGA
196 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGA
643 CCTTTAACTT
Statistics
Matches: 233, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
250 233 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (252 bp):
AGCTCCATCACAACCGAGAGAAGCAAGGTTTGTGTCTTCAACCTACTTCACTGTCAATACAGGAA
GGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGATTTGTGTCTTCGAC
CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
Found at i:1894 original size:11 final size:9
Alignment explanation
Indices: 1861--1893 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
1851 CCATTTTTAC
1861 TTTTTCATT
1 TTTTTCATT
1870 TTTTTCATT
1 TTTTTCATT
1879 TTTTTCATCT
1 TTTTTCAT-T
1889 TTTTT
1 TTTTT
1894 TTTGACTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCATT
Found at i:2495 original size:18 final size:19
Alignment explanation
Indices: 2472--2510 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2462 TAAAAAAAAA
2472 TTTTGA-CTTTGATTTTTT
1 TTTTGATCTTTGATTTTTT
*
2490 TTTTGATTTTTTGATTTTTT
1 TTTTGA-TCTTTGATTTTTT
2510 T
1 T
2511 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (19 bp):
TTTTGATCTTTGATTTTTT
Found at i:2501 original size:9 final size:9
Alignment explanation
Indices: 2487--2519 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2477 ACTTTGATTT
2487 TTTTTTTGA
1 TTTTTTTGA
2496 -TTTTTTGA
1 TTTTTTTGA
*
2504 TTTTTTTAA
1 TTTTTTTGA
2513 TTTTTTT
1 TTTTTTT
2520 TTGAATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:2519 original size:20 final size:19
Alignment explanation
Indices: 2479--2523 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2469 AAATTTTGAC
2479 TTTGATTTTTTTTTTGATTT
1 TTTGATTTTTTTTTT-ATTT
2499 TTTGATTTTTTTAATTT-TTT
1 TTTGATTTTTTT--TTTATTT
2519 TTTGA
1 TTTGA
2524 ATCTAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 20 0.87
22 3 0.13
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (19 bp):
TTTGATTTTTTTTTTATTT
Done.