Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_569 ID=scaffold_569-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: 6070
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.24
Warning! 449 characters in sequence are not A, C, G, or T
Found at i:2828 original size:327 final size:331
Alignment explanation
Indices: 2213--3125 Score: 920
Period size: 327 Copynumber: 2.7 Consensus size: 331
2203 TTCGGGGTCG
* ** * * *
2213 AAATCGAAAGTTCGCCGATC-AGGCTGAAACCGAGGAAGCTCGCTTGGAATTGACACGCTAAGTG
1 AAATCGAAAGTTCGCCCATCGA-GCAAAAACCAAGTAAGCTCGCTTGGAATTGACACGCTGAGTG
* * * * * * *
2277 CGATTCTCCAGTCTGAAAAGCTCCGCGAGTCCCTCGCTTCGGGCTGTCCGCTGAAAACGCTCTGG
65 CGATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCTGCTGAAAACGCTC-GG
* * *
2342 CCAAAA-AGTCAAAAATTGGTCAGAAAAGCTCGTTTTTGACCTGTTTTTGACTGTTTTTCGGCTA
129 -AAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACCTG-TTTT-AC-----TTCGGCTA
* * *
2406 AGGAAGCCTCGCAGAGCGCCAAGACCGTGCGGAATCGATTCTACGCCTCCAACTGCGTAGGATGA
186 AGGAAGCCTCGCAGAGAGCCAAGACCGTGCGGAATCGATTCTACGCCGCCAACTACGTAGGATGA
** ** *
2471 GACTGGTATCTCGAAATTTTTTTTTCAGTCCCAAA-TCGAGAAAAA-TCGACAGGGGTTACATGG
251 GACTGAAATCTCGAAAGGTTTTTCTCAGT-CCAAACTCGAGAAAAACT-GACAGGGGTTACATGG
2534 ACTAAACTTTTAGCGTCA
314 ACTAAACTTTTAGCGTCA
* * *** * * *
2552 AAATCGATAGTTCGCCGATCGAGCCGGAAGCAAGTTAGGC-CGCTTGGAATTGACCCGCTGAGTG
1 AAATCGAAAGTTCGCCCATCGAGCAAAAACCAAG-TAAGCTCGCTTGGAATTGACACGCTGAGTG
*
2616 CGATTTTCGAGTCCG-AAAGCCCCGCGAGTCCCTCGCTTAGAGCTATCTGCTGAAAACGCTACGG
65 CGATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCTGCTGAAAACGCT-CGG
* * * *
2680 AGAAAGAGTCAAAAAGTGTTCAGAAATGCTCGTTTTTGA-CTG-TTT-C-TCGGCTCAGGAAGTC
129 AAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACCTGTTTTACTTCGGCTAAGGAAGCC
* **
2741 TCGCAGAGAGTCGGGACCGTGCGGAATCGATTCTACGCCGCCAACTACGTAGGATGCA-ACTGAA
194 TCGCAGAGAGCCAAGACCGTGCGGAATCGATTCTACGCCGCCAACTACGTAGGATG-AGACTGAA
* * * *
2805 ATTTC-AAACGGTTTTTCTCAGTCCAAACTGGAGAAAAACTGACATGGGTTACATGGACTAAATT
258 ATCTCGAAA-GGTTTTTCTCAGTCCAAACTCGAGAAAAACTGACAGGGGTTACATGGACTAAACT
* * *
2869 TTTCGGGTCG
322 TTTAGCGTCA
* * * * *
2879 ATATCGAAAGTTCGCCCATCGGGCAAAAACCAAGTAAGCTCGATTTGAATTGACTCGCTGAGTGC
1 AAATCGAAAGTTCGCCCATCGAGCAAAAACCAAGTAAGCTCGCTTGGAATTGACACGCTGAGTGC
* * *
2944 GATTTTCGAGTCCGAAAAGCTCCGC-ATGTCCCTCGCTTACAGCTATCTGCTG-AAATGCTCCTG
66 GATTTTCGAGTCCGAAAAGCTCCGCGA-GTCCCTCGCTTAGAGCTATCTGCTGAAAACGCT-CGG
* * * *
3007 AAAAAGAGTCCAAAAGTGGTCAGAAATGCTCGTTTTCGACCAGTTTCTGACTGCTTCTCGGCTCA
129 AAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACCTGTTT-T-A---C-T-TCGGCTAA
* * * *
3072 -GAGAGCCTCGCCGAGAGTCAAGAGCGTGCGGAATCGATTCTACGCCTCCAACTA
187 GGA-AGCCTCGCAGAGAGCCAAGACCGTGCGGAATCGATTCTACGCCGCCAACTA
3126 TGTAAGATCC
Statistics
Matches: 481, Mismatches: 70, Indels: 47
0.80 0.12 0.08
Matches are distributed among these distances:
326 12 0.02
327 225 0.47
328 37 0.08
329 2 0.00
330 1 0.00
333 1 0.00
335 4 0.01
337 8 0.02
338 125 0.26
339 62 0.13
340 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (331 bp):
AAATCGAAAGTTCGCCCATCGAGCAAAAACCAAGTAAGCTCGCTTGGAATTGACACGCTGAGTGC
GATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCTGCTGAAAACGCTCGGAA
AAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACCTGTTTTACTTCGGCTAAGGAAGCCTC
GCAGAGAGCCAAGACCGTGCGGAATCGATTCTACGCCGCCAACTACGTAGGATGAGACTGAAATC
TCGAAAGGTTTTTCTCAGTCCAAACTCGAGAAAAACTGACAGGGGTTACATGGACTAAACTTTTA
GCGTCA
Found at i:3229 original size:338 final size:333
Alignment explanation
Indices: 2194--3312 Score: 1077
Period size: 338 Copynumber: 3.3 Consensus size: 333
2184 TTCTTTAATC
* * * * *
2194 GACTAAATTTTCGGGGTCGAAATCGAAAGTTCGCCGATCAGGCTGAAACCGAGGAAGCTCGCTTG
1 GACTAAATTTTCGGGGTCAAAATCGAAAGTTCGCCGATCGGGCAGAAACCAAGTAAGCTCGCTTG
* * * * * *
2259 GAATTGACACGCTAAGTGCGATTCTCCAGTCTGAAAAGCTCCGCGAGTCCCTCGCTT-CGGGCTG
66 GAATTGACACGCTGAGTGCGATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAC-AGCTA
* * * *
2323 TCCGCTGAAAACGCTCTGGCCAAAA-AGTCAAAAATTGGTCAGAAAAGCTCGTTTTTGACCTGTT
130 TCTGCTGAAAACGCTCT-G-AAAAAGAGTCAAAAAGTGGTCAGAAATGCTCG-TTTTGACC-G-T
* * * *
2387 TTTGACTGTTTTTCGGCTAAGGAAGCCTCGCAGAGCGCCAAGACCGTGCGGAATCGATTCTACGC
190 TTTGACTGTTTCTCGGCTCAGGAAGCCTCGCAGAGAGTCAAGACCGTGCGGAATCGATTCTACGC
* * *
2452 CTCCAACTGCGTAGGAT-GAGACTGGTATCTCGAAATTTTTTTT-TCAGTCCCAAATCGAGAAAA
255 CTCCAACTACGTAGGATCGA-ACT-GAATCTCGAACTTTTTTTTCTCAGT-CCAAATCGAGAAAA
2515 ATCGACAGGGGTTACATG
317 ATCGACAGGGG-TACATG
* * * * * * * *
2533 GACTAAACTTTT-AGCGTCAAAATCGATAGTTCGCCGATCGAGCCGGAAGCAAGTTAGGC-CGCT
1 GACTAAA-TTTTCGGGGTCAAAATCGAAAGTTCGCCGATCGGGCAGAAACCAAG-TAAGCTCGCT
* * *
2596 TGGAATTGACCCGCTGAGTGCGATTTTCGAGTCCG-AAAGCCCCGCGAGTCCCTCGCTTAGAGCT
64 TGGAATTGACACGCTGAGTGCGATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTACAGCT
* * *
2660 ATCTGCTGAAAACGCTACGGAGAAAGAGTCAAAAAGTGTTCAGAAATGCTCG---T-----TTTT
129 ATCTGCTGAAAACGCT-CTGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTGACCGTTTT
* ** *
2717 GACTGTTTCTCGGCTCAGGAAGTCTCGCAGAGAGTCGGGACCGTGCGGAATCGATTCTACGCCGC
193 GACTGTTTCTCGGCTCAGGAAGCCTCGCAGAGAGTCAAGACCGTGCGGAATCGATTCTACGCCTC
* * ** *
2782 CAACTACGTAGGAT-GCAACTGAAATTTCAAAC-GGTTTTTCTCAGTCCAAACTGGAGAAAAA-C
258 CAACTACGTAGGATCG-AACTG-AATCTCGAACTTTTTTTTCTCAGTCCAAA-TCGAGAAAAATC
*
2844 TGACATGGGTTACATG
320 -GACA-GGGGTACATG
* * * * *
2860 GACTAAATTTTTC-GGGTCGATATCGAAAGTTCGCCCATCGGGCAAAAACCAAGTAAGCTCGATT
1 GACTAAA-TTTTCGGGGTCAAAATCGAAAGTTCGCCGATCGGGCAGAAACCAAGTAAGCTCGCTT
* *
2924 TGAATTGACTCGCTGAGTGCGATTTTCGAGTCCGAAAAGCTCCGC-ATGTCCCTCGCTTACAGCT
65 GGAATTGACACGCTGAGTGCGATTTTCGAGTCCGAAAAGCTCCGCGA-GTCCCTCGCTTACAGCT
* *
2988 ATCTGCTG-AAATGCTCCTGAAAAAGAGTCCAAAAGTGGTCAGAAATGCTCGTTTTCGACCAGTT
129 ATCTGCTGAAAACGCT-CTGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTT-GACC-GTT
* * *
3052 TCTGACTGCTTCTCGGCTCA-GAGAGCCTCGCCGAGAGTCAAGAGCGTGCGGAATCGATTCTACG
191 T-TGACTGTTTCTCGGCTCAGGA-AGCCTCGCAGAGAGTCAAGACCGTGCGGAATCGATTCTACG
* * * * *
3116 CCTCCAACTATGTAAGATCCGACACT-CAGCTCGAACTTTTTTTTCTC-CTCCATAATCGAGAAA
254 CCTCCAACTACGTAGGAT-CGA-ACTGAATCTCGAACTTTTTTTTCTCAGTCCA-AATCGAGAAA
3179 AATCGACAGGGGTACCATG
316 AATCGACAGGGGTA-CATG
* * * ** * *
3198 GAGTGAAA-TTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACCGGGCAAG-TCCCCT
1 GACT-AAATTTTCGGGGTCAAAATCGAAAGTTCGCCGATCGGGCAGAAACCAAGTAAGCT-CGCT
* * * ** *
3261 TGGAAATGACCCGCTGAGTCCGATTTTCTG-GTCTAAAAAGCTCTGCGAGTCC
64 TGGAATTGACACGCTGAGTGCGATTTTC-GAGTCCGAAAAGCTCCGCGAGTCC
3313 GCTGGTCCGC
Statistics
Matches: 636, Mismatches: 105, Indels: 79
0.78 0.13 0.10
Matches are distributed among these distances:
326 16 0.03
327 223 0.35
328 37 0.06
330 1 0.00
334 1 0.00
337 18 0.03
338 239 0.38
339 90 0.14
340 11 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (333 bp):
GACTAAATTTTCGGGGTCAAAATCGAAAGTTCGCCGATCGGGCAGAAACCAAGTAAGCTCGCTTG
GAATTGACACGCTGAGTGCGATTTTCGAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTACAGCTAT
CTGCTGAAAACGCTCTGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTGACCGTTTTGAC
TGTTTCTCGGCTCAGGAAGCCTCGCAGAGAGTCAAGACCGTGCGGAATCGATTCTACGCCTCCAA
CTACGTAGGATCGAACTGAATCTCGAACTTTTTTTTCTCAGTCCAAATCGAGAAAAATCGACAGG
GGTACATG
Found at i:4750 original size:327 final size:331
Alignment explanation
Indices: 4166--4780 Score: 753
Period size: 327 Copynumber: 1.8 Consensus size: 331
4156 GAAGCTCGCT
* * *
4166 TGGAATTGACACGCTAAGTGCGATTCTCCAGTCTGAAAAGCTCCGCGAGTCCCTCGCTTCGGGCT
1 TGGAATTGACACGCTAAGTGCGATTCTCCAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCT
* * *
4231 GTCCGCTGAAAACGCTCTAGCCAAAGAGTCAAAAATTGGTCAGAAAAGCTCGTTTTTGACCTGTT
66 ATCCGCTGAAAACGCTCGAG-CAAAGAGTCAAAAAGTGGTCAGAAAAGCTCGTTTTTGACCTG-T
*
4296 TTTGACTGTTTTTCGGCTAAGGAAGCCTCGCACAGCGCCAAGACCGTGCGGAATCGATTCGAAGC
129 TTT-AC-----TTCGGCTAAGGAAGCCTCGCACAGAGCCAAGACCGTGCGGAATCGATTCGAAGC
* * ** *
4361 CTCCAACTGCGTAGGATGAGACTGAAATCCCGAATTTTTTTTTTCAGTCCCAAATCGAGAAAAA-
188 CTCCAACTACGTAGGATGAGACTGAAATCCCAAACGTTTTTTCTCAGTCCCAAATCGAGAAAAAC
4425 TCGAAAGGGGTTACATGGACTAAACTTTTAGCGTCAAAATCGATAGTTCGCCGATCGAGCCGAAA
253 T-GAAAGGGGTTACATGGACTAAACTTTTAGCGTCAAAATCGATAGTTCGCCGATCGAGCCGAAA
4490 GCAAGTTAGGCCGCC
317 GCAAGTTAGGCCGCC
* * * *
4505 TGGAATTGACCCGCTGAGTGCGATTTTCGAGTCCG-AAAGCTCCGCGAGTCCCTCGCTTAGAGCT
1 TGGAATTGACACGCTAAGTGCGATTCTCCAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCT
* * *
4569 ATCTGCTGAAAACGCTACGGAG-AAAGAGTCAAAAAGTGTTCAGAAATGCTCGTTTTTGA-CTG-
66 ATCCGCTGAAAACGCT-C-GAGCAAAGAGTCAAAAAGTGGTCAGAAAAGCTCGTTTTTGACCTGT
* * * * ** * *
4631 TTT-C-TCGGCTCAGGAAGTCTCGCAGAGAGTCGGGACCGTGCGGAATCGATTCTACGCCTCCAA
129 TTTACTTCGGCTAAGGAAGCCTCGCACAGAGCCAAGACCGTGCGGAATCGATTCGAAGCCTCCAA
** * *
4694 CTACGTAGGATGCA-ACTGAAATTTCAAACGTTTTTTCTCAGT-CCAAACTGGAGAAAAACTGAC
194 CTACGTAGGATG-AGACTGAAATCCCAAACGTTTTTTCTCAGTCCCAAA-TCGAGAAAAACTGAA
* *
4757 ATGGGTTACATGGACTAAATTTTT
257 AGGGGTTACATGGACTAAACTTTT
4781 CGGGTCGANN
Statistics
Matches: 238, Mismatches: 33, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
326 5 0.02
327 116 0.49
328 2 0.01
333 1 0.00
335 3 0.01
337 3 0.01
338 75 0.32
339 31 0.13
340 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (331 bp):
TGGAATTGACACGCTAAGTGCGATTCTCCAGTCCGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCT
ATCCGCTGAAAACGCTCGAGCAAAGAGTCAAAAAGTGGTCAGAAAAGCTCGTTTTTGACCTGTTT
TACTTCGGCTAAGGAAGCCTCGCACAGAGCCAAGACCGTGCGGAATCGATTCGAAGCCTCCAACT
ACGTAGGATGAGACTGAAATCCCAAACGTTTTTTCTCAGTCCCAAATCGAGAAAAACTGAAAGGG
GTTACATGGACTAAACTTTTAGCGTCAAAATCGATAGTTCGCCGATCGAGCCGAAAGCAAGTTAG
GCCGCC
Done.