Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_754 ID=scaffold_754-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: 4036
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:3221 original size:339 final size:335
Alignment explanation
Indices: 2743--3862 Score: 1138
Period size: 339 Copynumber: 3.3 Consensus size: 335
2733 GCGGACCAGC
* ** * * * * *
2743 GGACTCGCAGAGCTTTTTAGAC-CAGAAAATCGGACTCAGCGGGTCATTTCCAAG-GGGACTTGC
1 GGACTCGCGGAGCTTTTCGGACTC-GAAAATCGCACTCAGCGAGTCAATTCCAAGCGAG-CTTAC
** * * * *
2806 CCGGATTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCG-AAATTTCACTCCATGGT-ACCCC
64 TTGGTTTCAGCCCGATCGGCGAACTTTCGATTTCGACCCCGAAAATTT-AGTCCAT-GTAACCCC
* * * * *
2869 TGTCGATTTTTCTCGATTATGGA-GGAGAAAAAAAAGTTCGAGCTGAGTGTCGGATCTTACATAG
127 TGTCGATTTTTCTCGATT-TGGACTGAGAAAAAAAAGTTCGAGTTCAGT-TC-GATCCTACGTAG
* * *
2933 TTGGAGGCGTAGAATCGCTTCCGCACGCTCTTGACTCTCGGCGAGGC-TCTCTGAGCCGAGAAAC
189 TTGGAGGCGTAGAATCGATTCCGCACGGTCTTGACTCTCTGCGAGGCTTC-CTGAGCCGAGAAAC
* * *
2997 AGTCAGAAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTGGAGCATTTTC
253 AGTCA-AAAC-GGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTC
3062 AGCAGATAGCTGTAAGCGAG
316 AGCAGATAGCTGTAAGCGAG
* *
3082 GGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCAAAGCGAGCTTACTT
1 GGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGAGCTTACTT
** * *
3147 GGTTTTTGCCCGATGGGCGAACTTTCGATTTCGA-CCCGAAAAATTTAGTCCATGTAACCCATGT
66 GGTTTCAGCCCGATCGGCGAACTTTCGATTTCGACCCCG-AAAATTTAGTCCATGTAACCCCTGT
* * * *
3211 C-AGTTTTTCTCCAGTTTGGACTGAG-AAAAAACGTTTGAAATTTCAGTT-GCATCCTACGTAGT
130 CGA-TTTTTCTCGA-TTTGGACTGAGAAAAAAAAGTTCG--AGTTCAGTTCG-ATCCTACGTAGT
** *
3273 TGGAGGCGTAGAATCGATTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGAGCCGAG-AA-A-
190 TGGAGGCGTAGAATCGATTCCGCACGGTCTTGACTCTCTGCGAGGCTTCCTGAGCCGAGAAACAG
* * *
3335 -C---A--GTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCA
255 TCAAAACGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCA
*
3394 GATAGCTCTAAGCGAG
320 GATAGCTGTAAGCGAG
* *
3410 GGACTCGCGGAGC-TTTCGGACTCGAAAATCGCACTCAGCGGGTCAATTCCAAGCG-GCCTAACT
1 GGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGAG-CTTACT
* * * * * * * *
3473 TGCTTTCGGCTCGATCGGCGAACTATCGATTTTGA-CGCTAAAAGTTTAGTTCATGTAACCCCTG
65 TGGTTTCAGCCCGATCGGCGAACTTTCGATTTCGACCCCGAAAA-TTTAGTCCATGTAACCCCTG
* *
3537 TCGATTTTTCTCGATTTGGGACTGA-AAAAAAAAATTCGAGATTTCAGTCTC-ATCCTACGCAGT
129 TCGATTTTTCTCGATTT-GGACTGAGAAAAAAAAGTTCGAG--TTCAGT-TCGATCCTACGTAGT
* * ** ** * *
3600 TGGAAGCGTAGAATCGATTCCGCACGGTCTTGGCGGTCTGAAAGGCTTCCTCAGCCGAAAAACAG
190 TGGAGGCGTAGAATCGATTCCGCACGGTCTTGACTCTCTGCGAGGCTTCCTGAGCCGAGAAACAG
* * ** *
3665 TCAAAAACAGGTCAAAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCTAGAGCGTTTTCAG
255 TC-AAAAC-GGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAG
* * *
3730 CGGACAGCCCG-AAGCGAG
318 CAGATAG-CTGTAAGCGAG
* * * * * * *
3748 GGACTCGCGGAGCTTTTCAGACTGGAGAATCGCACTTAGCGTGTCAATTCCAAGCGAGCTTCCTC
1 GGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGAGCTTACTT
*
3813 GGTTTCAGCCTGATCGGCGAACTTTCGATTTCGACCCCGAAAATTTAGTC
66 GGTTTCAGCCCGATCGGCGAACTTTCGATTTCGACCCCGAAAATTTAGTC
3863 GATTAAAGAA
Statistics
Matches: 642, Mismatches: 103, Indels: 72
0.79 0.13 0.09
Matches are distributed among these distances:
325 1 0.00
326 8 0.01
327 185 0.29
328 82 0.13
329 1 0.00
331 2 0.00
335 2 0.00
337 1 0.00
338 82 0.13
339 249 0.39
340 24 0.04
341 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (335 bp):
GGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGAGCTTACTT
GGTTTCAGCCCGATCGGCGAACTTTCGATTTCGACCCCGAAAATTTAGTCCATGTAACCCCTGTC
GATTTTTCTCGATTTGGACTGAGAAAAAAAAGTTCGAGTTCAGTTCGATCCTACGTAGTTGGAGG
CGTAGAATCGATTCCGCACGGTCTTGACTCTCTGCGAGGCTTCCTGAGCCGAGAAACAGTCAAAA
CGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCAGATAGC
TGTAAGCGAG
Found at i:3547 original size:327 final size:330
Alignment explanation
Indices: 3003--3862 Score: 966
Period size: 327 Copynumber: 2.6 Consensus size: 330
2993 AAACAGTCAG
* * * * *
3003 AAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTGGAGCATTTTCAGCAGA
1 AAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTC-AGAGCGTTTTCAGCAGA
* * *
3068 TAGCTGTAAGCGAGGGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCA
65 TAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCC
* * ** * *
3133 AAGCGAGCTTACTTGGTTTTTGCCCGATGGGCGAACTTTCGATTTCGACCCGAAAAATTTAGTCC
130 AAGCGAGCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCC
* ** *
3198 ATGTAACCCATGTCAGTTTTTCTCCAGTTT-GGACTGAGAAAAAACGTTTGAAATTTCAGT-TGC
195 ATGTAACCCATGTCAGTTTTTCTCCA-TTTGGGACTGAAAAAAAAAATTCGAAATTTCAGTCT-C
* * * ** *
3261 ATCCTACGTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGA
258 ATCCTACGCAGTTGGAAGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGAAAGACTTCCTCA
3326 GCCG-AG-
323 GCCGAAGA
* *
3332 AAACA-GTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGA
1 AAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAG-AGCGTTTTCAGCAGA
*
3396 TAGCTCTAAGCGAGGGACTCGCGGAGC-TTTCGGACTCGAAAATCGCACTCAGCGGGTCAATTCC
65 TAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCC
* * * * * *
3460 AAGCG-GCCTAACTTGCTTTCGGCTCGATCGGCGAACTATCGATTTTGACGCTAAAAGTTTAGTT
130 AAGCGAG-CTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTC
* * *
3524 CATGTAACCCCTGTC-GATTTTTCTCGATTTGGGACTGAAAAAAAAAATTCGAGATTTCAGTCTC
194 CATGTAACCCATGTCAG-TTTTTCTCCATTTGGGACTGAAAAAAAAAATTCGAAATTTCAGTCTC
** * * *
3588 ATCCTACGCAGTTGGAAGCGTAGAATCGATTCCGCACGGTCTTGGCGGTCTGAAAGGCTTCCTCA
258 ATCCTACGCAGTTGGAAGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGAAAGACTTCCTCA
3653 GCCGAAAAACAGTCAA
323 GCCG----A-AG---A
* * *
3669 AAACAGGTCAAAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCT-AGAGCGTTTTCAGCGG
1 AAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTT--CTCAGAGCGTTTTCAGCAG
* * * * * * * *
3733 ACAGCCCGAAGCGAGGGACTCGCGGAGCTTTTCAGACTGGAGAATCGCACTTAGCGTGTCAATTC
64 ATAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTC
** * * * * *
3798 CAAGCGAGCTTCCTCGGTTTCAGCCTGATCGGCGAACTTTCGATTTCGACCCCG-AAAATTTAGT
129 CAAGCGAGCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTCGA-CCCGAAAAATTTAGT
3862 C
193 C
3863 GATTAAAGAA
Statistics
Matches: 444, Mismatches: 66, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
326 5 0.01
327 193 0.43
328 78 0.18
329 4 0.01
333 2 0.00
337 5 0.01
338 73 0.16
339 79 0.18
340 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (330 bp):
AAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAGAGCGTTTTCAGCAGAT
AGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCA
AGCGAGCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCA
TGTAACCCATGTCAGTTTTTCTCCATTTGGGACTGAAAAAAAAAATTCGAAATTTCAGTCTCATC
CTACGCAGTTGGAAGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGAAAGACTTCCTCAGCC
GAAGA
Done.