Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_45 ID=scaffold_45-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: 27539
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.31
Warning! 2619 characters in sequence are not A, C, G, or T
Found at i:2437 original size:71 final size:72
Alignment explanation
Indices: 2356--2488 Score: 180
Period size: 71 Copynumber: 1.9 Consensus size: 72
2346 CTTGTTGGTC
* * **
2356 GATAATACTGACT-ATAGATGTGCCCTGCACTGGTCGGATACTCCAACAATGTTTTACGCCCAAA
1 GATAATACTGA-TGATAGATGTGCCCTACACTGGTCAGATAAACCAACAATGTTTTACGCCCAAA
2420 GCTAGTTG
65 GCTAGTTG
* * *
2428 GATAA-ACTGATGATAGATGTGCCCTACACTTGTCAGATAAACCGACAATGTTTTGCGCCCA
1 GATAATACTGATGATAGATGTGCCCTACACTGGTCAGATAAACCAACAATGTTTTACGCCCA
2489 GCGTTGATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
70 1 0.02
71 47 0.89
72 5 0.09
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (72 bp):
GATAATACTGATGATAGATGTGCCCTACACTGGTCAGATAAACCAACAATGTTTTACGCCCAAAG
CTAGTTG
Found at i:6110 original size:12 final size:12
Alignment explanation
Indices: 6095--6145 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
6085 AATTATAATT
6095 AATATTTAGGTA
1 AATATTTAGGTA
6107 AATA--TA-GTA
1 AATATTTAGGTA
*
6116 TAAAATTTAGGTA
1 -AATATTTAGGTA
6129 AATATTTAGGTA
1 AATATTTAGGTA
6141 AATAT
1 AATAT
6146 AGTACAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 3 0.09
10 5 0.15
12 22 0.67
13 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (12 bp):
AATATTTAGGTA
Found at i:11887 original size:18 final size:17
Alignment explanation
Indices: 11861--11899 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
11851 TCATTATTTA
11861 AAAATT-AAAAAATATAT
1 AAAATTAAAAAAATAT-T
11878 AAAATCTAAAAAAATATT
1 AAAAT-TAAAAAAATATT
11896 AAAA
1 AAAA
11900 AGAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAAAAAATATT
Found at i:19712 original size:13 final size:13
Alignment explanation
Indices: 19696--19738 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
19686 ACTTTTTTAT
19696 ATATACTTTTAGA
1 ATATACTTTTAGA
* *
19709 ATAT-TTTTTATAA
1 ATATACTTTTA-GA
19722 ATATACTTTTAGA
1 ATATACTTTTAGA
19735 ATAT
1 ATAT
19739 TTATAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (13 bp):
ATATACTTTTAGA
Found at i:19717 original size:26 final size:26
Alignment explanation
Indices: 19688--19740 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
19678 AAATTTTAAC
19688 TTTTTTAT--ATATACTTTTAGAATA
1 TTTTTTATAAATATACTTTTAGAATA
19712 TTTTTTATAAATATACTTTTAGAATA
1 TTTTTTATAAATATACTTTTAGAATA
19738 TTT
1 TTT
19741 ATAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 8 0.30
26 19 0.70
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTTATAAATATACTTTTAGAATA
Found at i:19752 original size:26 final size:26
Alignment explanation
Indices: 19696--19746 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19686 ACTTTTTTAT
* *
19696 ATATACTTTTAGAATATTTTTTATAA
1 ATATACTTTTAGAATATTTATAATAA
19722 ATATACTTTTAGAATATTTATAATA
1 ATATACTTTTAGAATATTTATAATA
19747 TTTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
ATATACTTTTAGAATATTTATAATAA
Found at i:22191 original size:14 final size:15
Alignment explanation
Indices: 22165--22197 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
22155 TGTCAAACTG
*
22165 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
22180 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
22194 GGAA
1 GGAA
22198 AAGTGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:23239 original size:44 final size:45
Alignment explanation
Indices: 23184--23406 Score: 139
Period size: 44 Copynumber: 4.8 Consensus size: 45
23174 ATGGCAGATT
*
23184 TTATCTTCCTGAAGTTGCAATGAAGCAGATTAAAGCCA-CCAGCC
1 TTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGCCAGCCAGCC
** * * * **
23228 TTATCTCCCTGAAGTTGCAGCGAAGCAGACTAAAGACAGCAAATC
1 TTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGCCAGCCAGCC
* ** * * *
23273 TTATTTCCCTGGCGTTGCAGTGGAA-CAGATTAAAGCTACAAGTTATGGCAGATC
1 TTATCTCCCTGAAGTTGCAAT-GAAGCAGATTAAAGC--C-----A-GCCAG-CC
* * * *
23327 TTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGTCA-CCAGCC
1 TTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGCCAGCCAGCC
**
23371 TTATCTCCCTGAAGTTGCAGCGGAA-CAGATTAAAGC
1 TTATCTCCCTGAAGTTGCA-ATGAAGCAGATTAAAGC
23407 TACAAGTTAT
Statistics
Matches: 133, Mismatches: 33, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
44 61 0.46
45 34 0.26
46 3 0.02
47 2 0.02
52 2 0.02
53 4 0.03
54 27 0.20
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGCCAGCCAGCC
Found at i:23356 original size:54 final size:54
Alignment explanation
Indices: 23286--23460 Score: 165
Period size: 54 Copynumber: 3.4 Consensus size: 54
23276 TTTCCCTGGC
*
23286 GTTGCAGTGGAACAGATTAAAGCTACAAGTTATGGCAGATCTTATCTTCCTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAGTTATGACAGATCTTATCTTCCTGAA
* * * * * *
23340 GTTGCAATGGAGCAGATT---G----AAGTCA--CCAG-CCTTATCTCCCTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAGTTATGACAGATCTTATCTTCCTGAA
* * * *
23384 GTTGCAGCGGAACAGATTAAAGCTACAAGTTATGATAGATCTTATCTTTCTAAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAGTTATGACAGATCTTATCTTCCTGAA
23438 GTTGCAGT-GAAGCAGATTAAAGC
1 GTTGCAGTGGAA-CAGATTAAAGC
23461 CACCAACCTT
Statistics
Matches: 93, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
44 28 0.30
45 3 0.03
47 6 0.06
51 6 0.06
53 5 0.05
54 45 0.48
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (54 bp):
GTTGCAGTGGAACAGATTAAAGCTACAAGTTATGACAGATCTTATCTTCCTGAA
Found at i:23398 original size:98 final size:98
Alignment explanation
Indices: 23227--23490 Score: 312
Period size: 98 Copynumber: 2.7 Consensus size: 98
23217 AGCCACCAGC
* * ** * * * * * **
23227 CTTATCTCCCTGAAGTTGCAGCGAAGCAGACTAAAGACAGCAAATCTTATTTCCCTGGCGTTGCA
1 CTTATCTTCCTAAAGTTGCAATGAAGCAGATTAAAGCCA-CCAACCTTATCTCCCTGAAGTTGCA
* *
23292 GTGGAACAGATTAAAGCTACAAGTTATGGCAGAT
65 GCGGAACAGATTAAAGCTACAAGTTATGACAGAT
* * * * *
23326 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGTCACCAGCCTTATCTCCCTGAAGTTGCAG
1 CTTATCTTCCTAAAGTTGCAATGAAGCAGATTAAAGCCACCAACCTTATCTCCCTGAAGTTGCAG
*
23391 CGGAACAGATTAAAGCTACAAGTTATGATAGAT
66 CGGAACAGATTAAAGCTACAAGTTATGACAGAT
* * * *
23424 CTTATCTTTCTAAAGTTGCAGTGAAGCAGATTAAAGCCACCAACCTTATCTCTCTGAAGTTACAG
1 CTTATCTTCCTAAAGTTGCAATGAAGCAGATTAAAGCCACCAACCTTATCTCCCTGAAGTTGCAG
23489 CG
66 CG
23491 AAGCAGACTG
Statistics
Matches: 140, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 108 0.77
99 32 0.23
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (98 bp):
CTTATCTTCCTAAAGTTGCAATGAAGCAGATTAAAGCCACCAACCTTATCTCCCTGAAGTTGCAG
CGGAACAGATTAAAGCTACAAGTTATGACAGAT
Found at i:23517 original size:143 final size:143
Alignment explanation
Indices: 23326--24029 Score: 742
Period size: 143 Copynumber: 4.9 Consensus size: 143
23316 TATGGCAGAT
* ** * * * ** * *
23326 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGTCA-CCAGCCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGAAGTTGTA
* * *
23390 GCGGAACAGATTAAAGCTACAAGTTATGATAGATCTTATCTTTCTAAAGTTGCAGTGAAGCAGAT
66 GTGGAACAGATTAAAGCTACAAGTTATGATAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAGAT
* *
23455 TAAAGCCACCAAC
131 TGAAGCCACCAGC
* * * ** *
23468 CTTATCTCTCTGAAGTTACAGCGAAGCAGACTGAAGACAATGAATCTTATTTCCCTAGCA-TTGT
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCT-GAAGTTGT
* *
23532 AGTGGAACAAGATTGAAGCTACAAGTTATGACAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAG
65 AGTGGAAC-AGATTAAAGCTACAAGTTATGATAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAG
*
23597 ATTGAAGCTACCAGC
129 ATTGAAGCCACCAGC
* * * *
23612 CTTATCTCCCTGAAGTTGCAACGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGACGTTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGAAGTTGTA
* ** * * *
23677 GTGGAACAGATTAAAGCTACAAATTAT-AGCGAATCTTATCTTCCTGGAGTTGCAGTGGAGCATA
66 GTGGAACAGATTAAAGCTACAAGTTATGATAG-ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGA
*
23741 TTGAAGCCACTAGC
130 TTGAAGCCACCAGC
* * **
23755 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACGGC-AGATCTTATATT-CCTGGCGTTG
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGA-ATCTTAT-TTCCCTGAAGTTG
* * * * *
23818 TAGTGGAACAGATTAAAGCTACAAATTATGGTGGATCTTATCTTACTGAAGTTGCAGTGGAGCAG
64 TAGTGGAACAGATTAAAGCTACAAGTTATGATAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAG
*
23883 ATTGAAGCCATCAGC
129 ATTGAAGCCACCAGC
* * * * * *
23898 CCTATCTTCCTAAAGTTGCAGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTAAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGAAGTTGTA
*** * * * * * * *
23963 GCAAAATAGATTGAAGCTACAAG-T-TGCA-A-ACCTTATATCCCTGAAGTTGCAGTGGAGCAGG
66 GTGGAACAGATTAAAGCTACAAGTTATG-ATAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAGA
24024 TTGAAG
130 TTGAAG
24030 TTACCAATTC
Statistics
Matches: 475, Mismatches: 76, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
140 33 0.07
141 2 0.00
142 37 0.08
143 273 0.57
144 130 0.27
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (143 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGAAGTTGTA
GTGGAACAGATTAAAGCTACAAGTTATGATAGATCTTATCTTCCTGAAGTTGCAGTGAAGCAGAT
TGAAGCCACCAGC
Found at i:23617 original size:44 final size:44
Alignment explanation
Indices: 23568--23933 Score: 189
Period size: 44 Copynumber: 7.8 Consensus size: 44
23558 TATGACAGAT
* *
23568 CTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCTACCAGC
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAGC
* ** * * * **
23612 CTTATCTCCCTGAAGTTGCAACGGAGCAGACTGAAGATAGCGAAT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CTAGC
* * *
23657 CTTAT-TTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATAGC
1 CTTATCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC------TAGC
* * *
23707 GAATCTTATCTTCCTGGAGTTGCAGTGGAGCATATTGAAGCCACTAGC
1 ----CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAGC
* * ** *
23755 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACGGC-AGAT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAG-CTACTAG-C
* ** * * * *
23800 CTTATATTCCTGGCGTTGTAGTGGAACAGATTAAAGCTACAAATTATGGTGGAT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC----TA-----G-C
* *
23854 CTTATCTTACTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TCAGC
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT-AGC
* * *
23898 CCTATCTTCCTAAAGTTGCAGTGGAGCAGACTGAAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
23934 ACAGCAAATC
Statistics
Matches: 240, Mismatches: 56, Indels: 52
0.69 0.16 0.15
Matches are distributed among these distances:
44 103 0.43
45 62 0.26
48 4 0.02
49 2 0.01
50 2 0.01
54 65 0.27
55 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAGC
Found at i:24152 original size:44 final size:44
Alignment explanation
Indices: 23993--24194 Score: 158
Period size: 44 Copynumber: 4.5 Consensus size: 44
23983 AAGTTGCAAA
* * * *
23993 CCTTATATCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTA-CAAT
* * * * *
24038 TCTTATCTCCTTAAAGTT-CTAGCGGAGTAGATCGAAGCTACAAAT
1 CCTTATCTCCCTGAAGTTGC-AGTGGAGCAGATCGAAGCTAC-AAT
* * * * *
24083 -CTCT-TCTCCTTGAAATTACATTGGAGCAGATCGAAGCCACAAT
1 CCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAT
* * ** *
24126 CCTTATTTCCCTGAAGTTGCAGTGGAGCAGGATAAGAATATACAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCA-GAT-CGAAGCTACAAT
24172 CCTTATCTCCCTGAAGTTGCAGT
1 CCTTATCTCCCTGAAGTTGCAGT
24195 AGAGTGGATT
Statistics
Matches: 123, Mismatches: 26, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
43 4 0.03
44 53 0.43
45 37 0.30
46 29 0.24
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAT
Found at i:24887 original size:41 final size:40
Alignment explanation
Indices: 24795--24887 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
24785 TTTTTCTATT
* * *
24795 TATTTATTTAT-TTTTCTTTATTTTCCTCCTTCAAAAATA
1 TATTTATATATATTTTCTTTATTTTACTCCTTCAAAAAAA
* ** * *
24834 TATATACCTATATTTTCTTTATTTTACTTCTTTAAAAAAA
1 TATTTATATATATTTTCTTTATTTTACTCCTTCAAAAAAA
24874 TAGTTTATATATAT
1 TA-TTTATATATAT
24888 ACAAATATAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
39 8 0.19
40 26 0.62
41 8 0.19
ACGTcount: A:0.31, C:0.12, G:0.01, T:0.56
Consensus pattern (40 bp):
TATTTATATATATTTTCTTTATTTTACTCCTTCAAAAAAA
Done.