Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_487 ID=scaffold_487-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: 6695
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.26
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:692 original size:339 final size:326
Alignment explanation
Indices: 10--751 Score: 755
Period size: 339 Copynumber: 2.2 Consensus size: 326
1 ACTTTTAGC
* * ** * *
10 GTCAAAATCGATAGTTCGCCGATCGAGCCGAAAGCAAGTTAGGCCGCTTGGAATTGACCCGCTGA
1 GTCAAAATCGAAAGTTCGCCGATCGGGCAAAAACCAAGTTAAGCCGCTTGGAATTGACCCGCTGA
* *
75 GTGCGATTTTCGAGTCCGAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCTGCTGAAAACGCTAC
66 GTGCGATTTTCGAGTCCGAAAGCTCCGCAAGTCCCTCGCTTACAGCTATCTGCTGAAAACGCTAC
* * * * *
140 GGAGAAAGAGTCAAAAAGTGTTCAGAAATGCTCGTTTTTGACTGTTTCTCGGCTCAGGAAGTCTC
131 AGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACTGTTTCTCGGCTAAGAAAGTCTC
* * * * ** **
205 GCAGAGAGTCGGGACCGTGCGGAATCGATTCTACGCCTCCAACTACGTAGGATGCAACTGAAATT
196 GCAGAGACTCGGGACCATGCGGAATCGATTCTACGCCTCCAACTACGTAAGATCCAACACAAAGC
* * ** *
270 TCAAACGTTTTTTCTCAGTCCAAACTGGAGAAAAAGTGACATGGGTTACATGGACTAAATTTTTC
261 TCAAACGTTTTTTCTCACTCCAAACTCGAGAAAAAGTGACATGGGGAAAATGGACTAAA-TTTTC
335 GG
325 GG
** * * *
337 GTTGAAATCGAAAGTTCGCCCATCGGGCAAAAACCAAG-TAAGCTCGCTTTGAATTGACTCGCTG
1 GTCAAAATCGAAAGTTCGCCGATCGGGCAAAAACCAAGTTAAGC-CGCTTGGAATTGACCCGCTG
*
401 AGTGCGATTTTCGAGTCCGAAAAGCTCCGCAAGTCCCTCGCTTACAGCTATCTGCTGAAAATGCT
65 AGTGCGATTTTCGAGTCCG-AAAGCTCCGCAAGTCCCTCGCTTACAGCTATCTGCTGAAAACGCT
* *
466 CCAGAAAAAGAGTCAAAAAGTGGTCGGAAATGCTCGTTTTTGACTAGTTTTTGACCGTTTCTCGG
129 ACAGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGAC-------T----GTTTCTCGG
* * *
531 CTAAGAAAG-CTCCGCCGAGCCTCGGGACCAATG-GGAATCGATTCTACGCCTCCAACTATGTAA
183 CTAAGAAAGTCT-CGCAGAGACTCGGGACC-ATGCGGAATCGATTCTACGCCTCCAACTACGTAA
** * *
594 GATCCAACACTCAGCTCGAACTTTTTTTTCTC-CTCCATAA-TCGAGAAAAA-TCGACA-GGGGA
246 GATCCAACACAAAGCTCAAAC-GTTTTTTCTCACTCCA-AACTCGAGAAAAAGT-GACATGGGGA
*
655 AGAATGGAGTGAAA-TTTCGGG
308 A-AATGGACT-AAATTTTC-GG
* ** * ** * *
676 GTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACC-GGGCAAGTCCCCTTGGAAATGACCCGCTG
1 GTCAAAATCGAAAGTTCGCCGATCGGGCAAAAACCAAGTTAAG-CCGCTTGGAATTGACCCGCTG
*
740 AGTCCGATTTTC
65 AGTGCGATTTTC
752 TGGTCTAAAA
Statistics
Matches: 337, Mismatches: 55, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
326 4 0.01
327 67 0.20
328 81 0.24
335 1 0.00
338 12 0.04
339 155 0.46
340 17 0.05
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (326 bp):
GTCAAAATCGAAAGTTCGCCGATCGGGCAAAAACCAAGTTAAGCCGCTTGGAATTGACCCGCTGA
GTGCGATTTTCGAGTCCGAAAGCTCCGCAAGTCCCTCGCTTACAGCTATCTGCTGAAAACGCTAC
AGAAAAAGAGTCAAAAAGTGGTCAGAAATGCTCGTTTTTGACTGTTTCTCGGCTAAGAAAGTCTC
GCAGAGACTCGGGACCATGCGGAATCGATTCTACGCCTCCAACTACGTAAGATCCAACACAAAGC
TCAAACGTTTTTTCTCACTCCAAACTCGAGAAAAAGTGACATGGGGAAAATGGACTAAATTTTCG
G
Found at i:2864 original size:332 final size:332
Alignment explanation
Indices: 2474--3134 Score: 1236
Period size: 332 Copynumber: 2.0 Consensus size: 332
2464 AAGACCGTGC
2474 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
1 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
*
2539 CAAAATCAAGATAAATCGACA-GGGTGAGAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTC
66 CAAAATCAAGATAAATCGACAGGGGT-ACAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTC
2603 TCCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCT
130 TCCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCT
2668 AAAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGGT-GAACTTTCG
195 AAAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTC-GTCGAACTTTCG
2732 CGAAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCG
259 CGAAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCG
2797 GGACCACGG
324 GGACCACGG
2806 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
1 GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
* * * *
2871 CAAAATCGAGATTAATCGACAGGGGTACCATGGAGTGAAATTTCGGGGTCGAAATCGAAAGTTCT
66 CAAAATCAAGATAAATCGACAGGGGTACAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
*
2936 CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCTGCTGAGTCCGATTTTCTGGTCTA
131 CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
3001 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGTCGAACTTTCGCG
196 AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGTCGAACTTTCGCG
3066 AAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
261 AAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
3131 ACCA
326 ACCA
3135 ATCGGAAAGC
Statistics
Matches: 321, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
331 2 0.01
332 315 0.98
333 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (332 bp):
GGAATCGATTCTACGCCTCCAACTATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTC
CAAAATCAAGATAAATCGACAGGGGTACAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCT
CCGATCGGGCTGAAACCGGGCAAGTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTA
AAAAGCTCTGCGAGTCCGCTGGTCCGCTGGATCGGCGAAAAACGCGCGGTCGTCGAACTTTCGCG
AAACGGTCAAAAACACTGGAGTTTTTGACCGTTTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGG
ACCACGG
Found at i:4235 original size:332 final size:330
Alignment explanation
Indices: 3624--4506 Score: 1453
Period size: 332 Copynumber: 2.7 Consensus size: 330
3614 TTCTGACTGC
* ** * *
3624 TTCTAGGCTAAGAAAGCTCCGCCGAGAGTCAAGA-C-CGTGCGGAATCGATTCTACGCCTCCAAC
1 TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGAGACCACG-GGGGAATCGATTCTACGCCTCCAAC
*
3687 TATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCAAGATAAATCGACAGG
65 TATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGATAAATCGACAGG
*
3752 GTGAGAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAATCGGGCAA
130 GT---AATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACCGGGCAA
*
3817 GTCCCCTTGGAAATGACCCGCTGAATCCGATTTTCTGGTCTAAAAAGCTCTGCGAGTCCGCTGGT
192 GTCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTAAAAAGCTCTGCGAGTCCGCTGGT
*
3882 CCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGAAACGGTCAAAAACAGTGGAGTT
257 CCGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGAAACGGTCAAAAACACTGGAGTT
3947 TTTGACCGT
322 TTTGACCGT
*
3956 TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGGGACCACGGGGGAATCGATTCTACGCCTCCAACT
1 TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGAGACCACGGGGGAATCGATTCTACGCCTCCAACT
*
4021 ATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGATTAATCGACAGGG
66 ATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGATAAATCGACA-GG
*
4086 GTACCATGGAGTGAAATTTCGGGGTCGAAATCG-AAGTTCTCCGATCGGGCTGAAACCGGGCAAG
130 GTA--ATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACCGGGCAAG
4150 TCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTAAAAAGCTCTGCGAGTCCGCTGGTC
193 TCCCCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTAAAAAGCTCTGCGAGTCCGCTGGTC
4215 CGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGAAACGGTCAAAAACACTGGAGTTT
258 CGCTGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGAAACGGTCAAAAACACTGGAGTTT
4280 TTGACCGT
323 TTGACCGT
** *
4288 TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGAGACCA-ATGAGAATCGATTCTACGCCTCCAACT
1 TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGAGACCACGGGGGAATCGATTCTACGCCTCCAACT
* *
4352 ATGCAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGAAAAATCGACA--G
66 ATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGATAAATCGACAGGG
*
4415 ----GGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTTCGATCGGGCTGAAACCGGGCAAGTCC
131 TAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACCGGGCAAGTCC
* *
4476 CCTTGGAAATGACCCGCTGAGTGCAATTTTC
196 CCTTGGAAATGACCCGCTGAGTCCGATTTTC
4507 CAGTCGGAAT
Statistics
Matches: 522, Mismatches: 23, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
322 25 0.05
323 62 0.12
328 1 0.00
331 84 0.16
332 231 0.44
333 113 0.22
334 6 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (330 bp):
TTCTCGGCTAAGAAAGCTCCGCCGAGCCTCGAGACCACGGGGGAATCGATTCTACGCCTCCAACT
ATGTAAGATCCGACACTCAGCTCGAAATTTTTTTTCTCCTCCAAAATCGAGATAAATCGACAGGG
TAATGGAGTGAAATTTCGGGGTCAAAATCGAAAGTTCTCCGATCGGGCTGAAACCGGGCAAGTCC
CCTTGGAAATGACCCGCTGAGTCCGATTTTCTGGTCTAAAAAGCTCTGCGAGTCCGCTGGTCCGC
TGGATCGGCGAAAAACGCGCGGTCGGTGAACTTTCGCGAAACGGTCAAAAACACTGGAGTTTTTG
ACCGT
Done.