Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_872 ID=scaffold_872-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: 4887
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.15
Warning! 2020 characters in sequence are not A, C, G, or T
Found at i:249 original size:132 final size:132
Alignment explanation
Indices: 1--1323 Score: 1397
Period size: 132 Copynumber: 10.1 Consensus size: 132
* * *
1 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGACCGAAGACGGCAAATCTTATCTTTCCAACATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* * * * * *
66 TGGGTAGCATATTTAGGTCACCAAGCATTGTCTCCCAGA-TAGCAACGGGAGTGGGTTGAAAATT
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGC-GGAGTGGGTTGAAAATT
130 GTA
130 GTA
* * * * *
133 GATCTTATCTCCCTAAGCAGTTGTGAAGCAAATCGAAGATGACAAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* *
198 TGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGGAGCGGAGTGGGTTGAAAATTG
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
263 TA
131 TA
* * * * * * * *
265 GATCTTCTCTCCCTAAACACTAGTGGAGCAGATCGAAGACGACAGATTTTATTTTTCCAACATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* * *
330 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTAAGCAACAGCGGAGTGGGTTAAAAATTG
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
395 TA
131 TA
* * * *
397 GATCTTCTCTCCCTAAACAGTAGT-GACGCAGACCGAAGACGGCAAATCTTATCTTTCCAACATA
1 GATCTTATCTCCCTAAGCAGTAGTGGA-GCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATA
* * * * * *
461 GTGGGAAGCAGATTTAAGT-AGCCATGCATAGTCTACCAGA-CAGTATCGGAGTGGGTTGAAAAT
65 GTGGGAAGCAGATTTAAGTCA-CCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAAT
524 TGTA
129 TGTA
* * * ** * *
528 GATCTTATCTCCATAAGCAGTACTGGAGCAGATCGACGATTGCAATTTTTATCTTAT-CAAGATA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTT-TCCAAGATA
* ** * * * * * * * * * * * * *
592 ATCAGAAGCAGGTCTACGTCCCCTATCCTCGTCT-GCAGCAGCAGCAGCGGTGTAGATT-AATAA
65 GTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTG-AGCAGCAGCGGAGTGGGTTGAA-AA
655 TTGTA
128 TTGTA
* * * * * * * *
660 G-TTTTCATCTCCATAAGCAGTAGTGGAGCAGATCGACGACGGTAAATTTTATATTTTCATGATA
1 GATCTT-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATA
* * * * * * * * * * * * *
724 GTGAGAATCAAATCTACA-AC-CCTAATCATCGTGT-GCAGCAGCAGCAGCGGTGTAGATTGAAA
65 GTGGGAAGCAGATTTA-AGTCACC-AAGCATTGTCTCCCTG-AGCAGCAGCGGAGTGGGTTGAAA
*
786 ATTATA
127 ATTGTA
* * * * * * * * * * * * *
792 G-TCTTTATATCCATTAGCAGTAGTGGTGCAGGTCGACGACTGTAATTTTTCTATTTTC-A-A-A
1 GATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATA
*
853 GT---AAGCAGATTTAAGTCACCAAGCCTTGTC-CCCTTGAGCAGCAGCGGAGTGGGTTGAAAAT
65 GTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCC-TGAGCAGCAGCGGAGTGGGTTGAAAAT
914 TGTA
129 TGTA
*
918 GATCTTATCTCCCTAAGGAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* * *
983 TGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
1048 TA
131 TA
* *
1050 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* * *
1115 TGAGAAGCAGATTTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTG
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
1180 TA
131 TA
* *
1182 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
* ** * *
1247 TGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATTG
66 TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
1312 TA
131 TA
1314 GATCTTATCT
1 GATCTTATCT
1324 NNNNNNNNNN
Statistics
Matches: 1009, Mismatches: 155, Indels: 54
0.83 0.13 0.04
Matches are distributed among these distances:
125 1 0.00
126 82 0.08
127 6 0.01
128 1 0.00
129 6 0.01
130 4 0.00
131 104 0.10
132 794 0.79
133 11 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (132 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
TGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG
TA
Found at i:1099 original size:44 final size:44
Alignment explanation
Indices: 919--1235 Score: 125
Period size: 44 Copynumber: 7.2 Consensus size: 44
909 AAAATTGTAG
* * *
919 ATCTTATCTCCCTAAGGAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
* * *
963 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACTAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGAC-AA
** * * * * ** * * * * *
1007 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGACAA
*
1051 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
* *
1095 ATCTTATCTTCCC-AAG-A-TAGTGAGAAGCAGATTTAAGTC-ACCAA
1 ATCTTATC-TCCCTAAGCAGTAGTG-G-AGCAGATTGAAGACGA-CAA
* * * * * ** * * * * *
1139 A-CATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTG-TAG
1 ATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGACAA
* * *
1183 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
1227 ATCTTATCT
1 ATCTTATCT
1236 TTCCAAGATA
Statistics
Matches: 187, Mismatches: 64, Indels: 44
0.63 0.22 0.15
Matches are distributed among these distances:
42 9 0.05
43 19 0.10
44 141 0.75
45 13 0.07
46 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
Found at i:3225 original size:44 final size:44
Alignment explanation
Indices: 3041--3225 Score: 99
Period size: 44 Copynumber: 4.2 Consensus size: 44
3031 AAAATTGTAG
*
3041 ATCTTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAA
* * ** **
3085 ATCTTATCTTTCC-AAG-A-TAATGGGAAGCAGATTTAAG-TCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGAT-GGCAA
** * * * * ** * * * * * *
3129 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAA
* *
3173 ATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAA
3217 ATCTTATCT
1 ATCTTATCT
3226 TTCCAAGATA
Statistics
Matches: 94, Mismatches: 39, Indels: 16
0.63 0.26 0.11
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
44 77 0.82
45 7 0.07
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAA
Found at i:3241 original size:132 final size:132
Alignment explanation
Indices: 3001--3738 Score: 1181
Period size: 132 Copynumber: 5.6 Consensus size: 132
2991 NNNNNNNNNN
* * * * *
3001 TGTCTCCCTGAGTAGCAGCGGGGGGGGTTTAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGC
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* *
3066 AGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
3131 CT
131 CT
*
3133 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCATATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
3198 AGCAGATCGAAGATGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
3263 CT
131 CT
* * * *
3265 TGTCTCCCTGAGAAGCAACGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAATAGTGT
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
3330 AGCAGATCGAAGACGGCAAATCTTCTCTTTCCAAAATAGTGGGAAACAGATTTAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
3395 CT
131 CT
* *
3397 TGTCTCCCTGAGCAGCAGTGGAGTGGGTTGCAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
3462 AGCAGATCGATGACGG-AAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACTAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
3526 CT
131 CT
* *
3528 TGTCTCCTTGAGCAGCAGCGGAGTGGGTTGACAAATTGTAGATCTTATCTCCCTAAGGAGTAGTG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGA-AAATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* * *
3593 GAGCAGATCGGAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
65 GAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAG
3658 CCT
130 CCT
* * *
3661 TGTCTCCCTTAGAAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGGAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
3726 AGCAGATCGAAGA
66 AGCAGATCGAAGA
3739 NNNNNNNNNN
Statistics
Matches: 560, Mismatches: 44, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 75 0.13
132 410 0.73
133 75 0.13
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
CT
Found at i:4334 original size:132 final size:132
Alignment explanation
Indices: 4082--4883 Score: 1351
Period size: 132 Copynumber: 6.1 Consensus size: 132
4072 NNNNNNNNNN
4082 GGGTTGAAAAATTGTAGATCTTATCTTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATC
1 GGGTTG-AAAATTGTAGATCTTATC-TCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATC
4147 TTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCT-CCTGAGCAGCAGC
64 TTATCTTTCC-AAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGC
4211 GGAGT
128 GGAGT
*
4216 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTAAATCTT
1 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
* *
4281 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGA-CAGCAACGGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
4345 G-
131 GT
4346 GGAGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCT
1 GG-GTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCT
4411 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
65 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
4476 AGT
130 AGT
4479 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
1 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
* * *
4544 ATATTTCCAAGATAGTGGGAAGGAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
4609 GT
131 GT
* * * * *
4611 GGGTTGAAAATTATAGATCTTATCTCCCTAAGCAATAGTAGTGCAGATCGAAGACGGTAAATCTT
1 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
* *
4676 ATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCAGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
4741 GT
131 GT
* * * *
4743 GGGTTGAAAATTGTAGACCTTATCTCCCTAAGCAGTAGTGGAGGAGATCGATGACGGTAAATCTT
1 GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
* * * *
4808 ATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGCGGT
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
4873 GT
131 GT
4875 GGG-TGAAAA
1 GGGTTGAAAA
4884 GTGG
Statistics
Matches: 634, Mismatches: 30, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
130 2 0.00
131 170 0.27
132 436 0.69
133 20 0.03
134 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (132 bp):
GGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTT
ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
GT
Done.