Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_969 ID=scaffold_969-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: 6076
ACGTcount: A:0.08, C:0.07, G:0.06, T:0.09
Warning! 4267 characters in sequence are not A, C, G, or T
Found at i:238 original size:132 final size:132
Alignment explanation
Indices: 7--713 Score: 1200
Period size: 132 Copynumber: 5.4 Consensus size: 132
1 TTGTCG
* *
7 TCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACAATCTTCAACATTCTCCGCTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
* * * * *
72 ACTCAGGGTGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGT
66 GCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
137 CA
131 CA
* *
139 TCTTTGATCTGCTCCACTACTGCTTAGGGATATAAGATCTACAATCTTCATCCTTCTCCGCTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
*
204 ACTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
66 GCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
269 CA
131 CA
271 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
*
336 GCTCAGAGAGACAAGGCTTTATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
66 GCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
401 CA
131 CA
403 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
* *
468 GCTAAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGT
66 GCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
*
533 CG
131 CA
* * *
535 TCTTTGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTACAATCTTCAACATTCTCCACTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
* * *
600 GCTCAGAGAGACAAGGCTTTTTGGCTTAAATCAT-CTTTCCACTATCTTGGAAAGATAAGATTTA
66 GCTCAGAGAGACAAGGCTTTGTGGCTTAAATC-TGCTTCCCACTATCTTGGAAAGATAAGATTTG
664 CCA
130 CCA
* *
667 TCTTTAATCTGCTCCACTACTGCTTAGGGGGATAAGATCTACAATCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
714 NNNNNNNNNN
Statistics
Matches: 546, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
132 545 1.00
133 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (132 bp):
TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCT
GCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGC
CA
Found at i:304 original size:44 final size:44
Alignment explanation
Indices: 124--704 Score: 151
Period size: 44 Copynumber: 13.2 Consensus size: 44
114 TATCTTGGAA
* *
124 AGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * * *
168 ATATAAGATCTACAATC-TTCATCCTTCTCCGCTGCTACTCAGAG
1 AGATAAGATTTGCCATCTTTAAT-CTGCTCCACTACTGCTTAGGG
* * *** * *
212 AGACAAGGCTTTG-TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
256 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
300 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGAG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * *
344 AGACAAGGCTTT---ATGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCAT--CTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
388 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
432 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * *** * *
476 AGACAAGGCTTTG-TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
520 AGATAAGATTTGTCGTCTTTGATCTGCTCCACTAGTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
564 AGATAAGATCTACAATCTTCAA-CATTCTCCACTGCTGCTCAGAG
1 AGATAAGATTTGCCATCTTTAATC-TGCTCCACTACTGCTTAGGG
* * **** * *
608 AGACAAGGCTTT-TTGGCTTAAATCAT-CTTTCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCATCTTTAATC-TGC--TCCACTACTGCTTAGG-G
*
652 AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
*
696 GGATAAGAT
1 AGATAAGAT
705 CTACAATCTN
Statistics
Matches: 367, Mismatches: 129, Indels: 82
0.63 0.22 0.14
Matches are distributed among these distances:
42 27 0.07
43 35 0.10
44 252 0.69
45 33 0.09
46 20 0.05
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:1179 original size:132 final size:131
Alignment explanation
Indices: 938--1350 Score: 682
Period size: 132 Copynumber: 3.1 Consensus size: 131
928 NNNNNNNNNN
* *
938 CTGCTACACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGAG
1 CTGCTCCACTACTGCTTA-GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
** * * * * *
1003 AGACAAGGCTTTTTGGCTTAAATCTGCTTTCCACTATCTAGGAAAGATAAGATTTACCATCTTTA
65 AGACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTG
1068 AT
130 AT
* * *
1070 CTGCTTCAGTACTGTTTACGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1 CTGCTCCACTACTGCTTA-GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1135 AGACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTG
65 AGACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTG
1200 AT
130 AT
*
1202 CTGCTCCACTACAGCTTAGTGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1 CTGCTCCACTACTGCTTAG-GAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1267 AGACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTG
65 AGACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTG
1332 AT
130 AT
1334 CTGCTCCACTACTGCTT
1 CTGCTCCACTACTGCTT
1351 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 262 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGA
GACAAGGCTTCGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGA
T
Found at i:5633 original size:132 final size:132
Alignment explanation
Indices: 5394--6074 Score: 976
Period size: 132 Copynumber: 5.2 Consensus size: 132
5384 NNNNNNNNNN
* *
5394 TTGGAAAGATAAGATTTGTCGTCTCTTGATCTGCTCC-CATCACCGACTTAGGGAGATAAGATCT
1 TTGGAAAGATAAGATTTGTCATCT-TTGATCTGCTCCAC-T-ACTG-CTTAGGGAGATAAGATCT
*
5458 ACAATC-TCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCC
62 ACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCC
5522 ACTATC
127 ACTATC
* *
5528 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTACAA
1 TTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
** * *
5593 TCTTCAACCTACTTTGCTACTGCTCAGGGAGAAAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
66 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
5658 TC
131 TC
* * *
5660 ATGGAAAGATAAGATTTGTAATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACAA
1 TTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * * * *
5725 TTTTCAACCTTCTCTGCTGCTGCTTAGAGAGACAAAGCTTTGTGGCTTAAATCTGCTTCCCACTA
66 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
*
5790 AC
131 TC
** * *
5792 TTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAGAAGATCAACAA
1 TTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* *
5857 TC-TCAACCTACTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTA
66 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
5921 TC
131 TC
*
5923 TTAGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * * * * *
5988 TATTCAACATTCTGCGCTGCTACTCAGAGAGACAAGGCTTTGTGGCTTAAATTTGCTTCCCACTA
66 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
6053 TC
131 TC
6055 -TGGAAAGATAAGA-TTGTCAT
1 TTGGAAAGATAAGATTTGTCAT
6075 GT
Statistics
Matches: 490, Mismatches: 54, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
130 7 0.01
131 152 0.31
132 293 0.60
133 13 0.03
134 25 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (132 bp):
TTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
TC
Found at i:5850 original size:44 final size:44
Alignment explanation
Indices: 5798--5981 Score: 122
Period size: 44 Copynumber: 4.2 Consensus size: 44
5788 TAACTTGGAA
*
5798 AGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * * * *
5842 AGAGAAGATCAACAATC-TCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * ***** * **
5885 AGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTTAGAA
1 AGATAAGATTTACCATCTTTAATCTGC-T-CCACTACTGCTTAGGG
** *
5929 AGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
5973 AGATAAGAT
1 AGATAAGAT
5982 CTACAATATT
Statistics
Matches: 99, Mismatches: 36, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
42 6 0.06
43 30 0.30
44 56 0.57
45 2 0.02
46 5 0.05
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:5932 original size:263 final size:263
Alignment explanation
Indices: 5397--6069 Score: 987
Period size: 263 Copynumber: 2.5 Consensus size: 263
5387 NNNNNNNTTG
* *
5397 GAAAGATAAGATTTGTCGTCTCTTGATCTGCTCC-CATCACCGACTTAGGGAGATAAGATCTACA
1 GAAAGATAAGATTTGTCATCT-TTGATCTGCTCCAC-T-ACTG-CTTAGGGAGATAAGATCTACA
* * *
5461 A-TCTCAACCTACTCCGCTGCTGCTCA-AGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCAC
62 ATTTTCAACCTTCT-CGCTGCTGCTCAGA-GAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCAC
** * * * *
5524 TATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCT
125 TATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAGAAGATCA
***
5589 ACAATCTTCAACCTACTTTGCTACTGCTCAGGGAGAAAAGGCTTGGTGGCTTAAATCTGCTTCCC
190 ACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAAAAGGCTTGGTGGCTTAAATCTGCTTCCC
*
5654 ACTATCATG
255 ACTATCATA
* *
5663 GAAAGATAAGATTTGTAATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * *
5728 TCAACCTTCTCTGCTGCTGCTTAGAGAGACAAAGCTTTGTGGCTTAAATCTGCTTCCCACTAACT
66 TCAACCTTCTC-GCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCT
5793 TGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAGAAGATCAACAAT
130 TGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAGAAGATCAACAAT
* * *
5858 C-TCAACCTACTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTAT
195 CTTCAACCTACTCCACTACTGCTCAGGGAGAAAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
5922 CTTA
260 CATA
*
5926 GAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATAT
1 GAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * *
5991 TCAACATTCTGCGCTGCTACTCAGAGAGACAAGGCTTTGTGGCTTAAATTTGCTTCCCACTATC-
66 TCAACCTTCT-CGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCT
6055 TGGAAAGATAAGATT
130 TGGAAAGATAAGATT
6070 GTCATGT
Statistics
Matches: 369, Mismatches: 33, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
262 15 0.04
263 200 0.54
264 120 0.33
265 14 0.04
266 20 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (263 bp):
GAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
TCAACCTTCTCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTT
GGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAGAAGATCAACAATC
TTCAACCTACTCCACTACTGCTCAGGGAGAAAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATC
ATA
Done.