Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_522 ID=scaffold_522-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: 6111
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Found at i:780 original size:332 final size:331
Alignment explanation
Indices: 216--1066 Score: 1603
Period size: 332 Copynumber: 2.6 Consensus size: 331
206 AAGACCGTGC
216 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
1 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
*
281 CATAATCGAGAAAAATCGACAGGGGTACCATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
66 CAAAATCGAGAAAAATCGACAGGGGTA-CATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
*
346 CCGATCGGGCTGAATCCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
130 CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
411 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCG
195 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCG
*
476 AAACGGTCAAAAATACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
260 AAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
541 ACCAATG
325 ACCAATG
548 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
1 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
* *
613 CAAAATCGAGAAAAATCGACAGGGGAAGAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
66 CAAAATCGAGAAAAATCGACAGGGGTA-CATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
678 CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
130 CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
743 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCG
195 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCG
*
808 AAACGGTCAAAAACAGTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
260 AAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
873 ACCAATG
325 ACCAATG
880 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
1 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
945 CAAAATCGAGAAAAATCGACAGGGGTACATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTC
66 CAAAATCGAGAAAAATCGACAGGGGTACATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTC
* * *
1010 CGTTCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTGCAATTTTC
131 CGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTC
1067 CAGTCGGTAT
Statistics
Matches: 507, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
331 91 0.18
332 416 0.82
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24
Consensus pattern (331 bp):
GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
CAAAATCGAGAAAAATCGACAGGGGTACATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTC
CGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTAA
AAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGA
AACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGGA
CCAATG
Found at i:4010 original size:339 final size:338
Alignment explanation
Indices: 3390--4425 Score: 1286
Period size: 339 Copynumber: 3.1 Consensus size: 338
3380 TTTGGATCTG
* * * * *
3390 AGCTCGCATGGAATTGACCCGCTGTGTTCGATTTTCGAGTTGGAAAAGCTCCGCGAGTCCCTAGC
1 AGCTCGCTTGGAATTGACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTAGC
* * *
3455 TTCGAGCTATCCGCTGAAAACGCTTCAGAGAAACAG-GCAAAAAGTGGTCAGAAAAGCTCCTTTT
66 TTCGAGCTATCCGCTGAAAACGC-TCCGAGAAAAAGAGCAAAAAGTGGTCAGAAAAGCT-CGTTT
* * * * * *
3519 TGACCAGCTTTTGACTGTTTC-TCGACTC-GGGAAGCCTCGCCGAGTGTCGGGAGCGTGCGGAAC
129 TGACCAGTTTTTGACTGTTTCTTAG-CTCAGGG-AGCCTCGCCAAATGTCGGGACCGTGCGGAAT
** * ** *
3582 CGATTCTACGCCACCGACTATATAGGATGCGACTGAAATCTTGAAATTTTTTTCTCAGTCCCAAA
192 CGATTCTACGCCTTCAACTACGTAGGATGCGACTGAAATCTCGAAATTTTTTTCTCAGTCCCAAA
* *
3647 TCGAGAAAAATCGACAGGGGTTACATGGACTAAATTATTAGCGTCAAAATCGATAGTTCGCCGAT
257 TCGAGAAAAATCGACAGGGGTTACATGGACTAAATTTTTAGCGTCAAAATCGAAAGTTCGCCGAT
3712 CGGGTCGGAACCAAGTA
322 CGGGTCGGAACCAAGTA
* * ** *
3729 AGCTCGCTTGGAATTGACCCGCTGAGTGGGATTTTCCAGTCGGAAACGCTCCTTGAGTCCCTCGC
1 AGCTCGCTTGGAATTGACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTAGC
* *
3794 TACGAGTTATCCGCTGAAAACGCTCCGA-AAAAAGAGACAAAAAGTGGTCAGAAACA-CTCGTTT
66 TTCGAGCTATCCGCTGAAAACGCTCCGAGAAAAAGAG-CAAAAAGTGGTCAGAAA-AGCTCGTTT
* * *
3857 TGAACCAATTTTTGACTGATTCTTAGCTCAGGGAGCCTCGCCAAATGTTGGGACCGTGCGGAATC
129 TG-ACCAGTTTTTGACTGTTTCTTAGCTCAGGGAGCCTCGCCAAATGTCGGGACCGTGCGGAATC
* *
3922 GATTCTTCGCCTTCAACTACGTAGGATGCGACTGAAATCTCGAAATTTTTTTCTCAGTCCCAAAC
193 GATTCTACGCCTTCAACTACGTAGGATGCGACTGAAATCTCGAAATTTTTTTCTCAGTCCCAAAT
* *
3987 CGAGAAAAATCGACAGGGGTTACATGGACTAAATTTTTAGCGTCAAAATCTAAAGTTCGCTGATC
258 CGAGAAAAATCGACAGGGGTTACATGGACTAAATTTTTAGCGTCAAAATCGAAAGTTCGCCGATC
* *
4052 GGG-CCGAATTCAAGTA
323 GGGTCGGAA-CCAAGTA
* * * * *
4068 AGCTCGCTTGGAATTGACCCGCCGAGTGCAATTTTTCAGTC-GAAATAGCTCCGCAAGTCCCTTG
1 AGCTCGCTTGGAATTGACCCGCTGAGTGCGATTTTCCAGTCGGAAA-AGCTCCGCGAGTCCCTAG
* * *
4132 CTTCGAGCTAGCCGCTGAAAACGCT-CTAGAGAAAGAGTCAAAAAGTGGTCAGAAAAGCTCGTTT
65 CTTCGAGCTATCCGCTGAAAACGCTCCGAGAAAAAGAG-CAAAAAGTGGTCAGAAAAGCTCG-TT
** * * *
4196 TTGACCAGTTTCTT-ACTGTTTCTCGGCTCAGGAAGCCTCCCCGAGA-GTCGGGACCGTGCGGAA
128 TTGACCAGTTT-TTGACTGTTTCTTAGCTCAGGGAGCCTCGCC-AAATGTCGGGACCGTGCGGAA
* * * * *
4259 TCGATTCTACG-CTTCCAGCAACGTAGGATGCGACTGAAATCTCG-AATATTTTTCTCCGTCTCA
191 TCGATTCTACGCCTT-CAACTACGTAGGATGCGACTGAAATCTCGAAATTTTTTTCTCAGTCCCA
* * * * * * *
4322 AATCGAGAAAAATCGACACGGATAACATGGACTAAATTTTTCGGGTCAAAATGGAAATTTCGCCG
255 AATCGAGAAAAATCGACAGGGGTTACATGGACTAAATTTTTAGCGTCAAAATCGAAAGTTCGCCG
*
4387 ATAGGGTCGGAACCAAGTA
320 ATCGGGTCGGAACCAAGTA
4406 AGCTCGCTTGGAATTGACCC
1 AGCTCGCTTGGAATTGACCC
4426 TTGACCGATT
Statistics
Matches: 602, Mismatches: 80, Indels: 31
0.84 0.11 0.04
Matches are distributed among these distances:
337 5 0.01
338 127 0.21
339 455 0.76
340 15 0.02
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (338 bp):
AGCTCGCTTGGAATTGACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTAGC
TTCGAGCTATCCGCTGAAAACGCTCCGAGAAAAAGAGCAAAAAGTGGTCAGAAAAGCTCGTTTTG
ACCAGTTTTTGACTGTTTCTTAGCTCAGGGAGCCTCGCCAAATGTCGGGACCGTGCGGAATCGAT
TCTACGCCTTCAACTACGTAGGATGCGACTGAAATCTCGAAATTTTTTTCTCAGTCCCAAATCGA
GAAAAATCGACAGGGGTTACATGGACTAAATTTTTAGCGTCAAAATCGAAAGTTCGCCGATCGGG
TCGGAACCAAGTA
Found at i:5104 original size:109 final size:109
Alignment explanation
Indices: 4902--5112 Score: 368
Period size: 109 Copynumber: 1.9 Consensus size: 109
4892 TTAACTGAAA
* *
4902 AATTCGTCTTCAGCTGCGTCTGCGGCAATTGTTGTTACGAATATGTTGTGCGTGCTGGTTTCAGG
1 AATTCGCCTTCAGCTGCGTCTGCAGCAATTGTTGTTACGAATATGTTGTGCGTGCTGGTTTCAGG
*
4967 TCATTACATACACGAATCTCTGACGGCGTTTTATGTGCGAGAGC
66 TCATTACATACACGAATCTCTGAAGGCGTTTTATGTGCGAGAGC
5011 AATTCGCCTTCAGCTGCGTCTGCAGCAATTGTTGTTACGAATATGTTGTGCGTGCTGGTTTCAGG
1 AATTCGCCTTCAGCTGCGTCTGCAGCAATTGTTGTTACGAATATGTTGTGCGTGCTGGTTTCAGG
* * *
5076 TCATTACATACTCGACTCTGTGAAGGCGTTTTATGTG
66 TCATTACATACACGAATCTCTGAAGGCGTTTTATGTG
5113 ATCAAGTGGC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 96 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (109 bp):
AATTCGCCTTCAGCTGCGTCTGCAGCAATTGTTGTTACGAATATGTTGTGCGTGCTGGTTTCAGG
TCATTACATACACGAATCTCTGAAGGCGTTTTATGTGCGAGAGC
Done.