Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_801 ID=scaffold_801-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: 5482
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.20
Warning! 1887 characters in sequence are not A, C, G, or T
Found at i:242 original size:132 final size:132
Alignment explanation
Indices: 1--1277 Score: 1807
Period size: 132 Copynumber: 9.7 Consensus size: 132
* * * *
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTTGTCTTCGATCTGTTCTACTACTGCTAA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * * * *
66 GGGAGATAACATCAACAATTTTAAACCCACTCTGCAGCTGCTCAGGGAGACAATGCTTGGTGACC
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
*
131 GA
131 TA
* * * * * ** *
133 AATTTGCTTCCCATTATCTTGTAAAAATAAAATTTACCGTCTTCGATCTACTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
198 GGGAGATAAGATCTACAATTTTCAACCCATTCCGCTCCTGCTCAGGGAGACAATGCTTGGTTACT
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
263 TA
131 TA
** * * * *
265 AATCTGCTTCCCACTAAGTTGGAAAGATAAAATTTGTCTTCTTCGATCCGCTCCACTAGTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * * *
330 GGGAGAGAAGATCTACAATTTTCAACCCACTCCGCTCCTGCTCAGAGGAGACAAGGCATGGTGGC
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAG-GGAGACAATGCTTGGTGAC
395 TTA
130 TTA
* * *
398 AATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCATCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
*
463 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGTTGACT
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
528 TA
131 TA
* *
530 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCGTCGATCAGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
595 GAGGAGATAAGATCTACAATTTTCAACGCACTCTGCTACTGCTCAGGGAGACAAGGCTTGGTGAC
66 G-GGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGAC
660 TTA
130 TTA
* ** * * *
663 AATCTGCTTCCCACTATCTTGGAAAGATATGATTTGTTATCTTCGATCTGTTCTACTACTGCTAA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
728 GGGAGATAACATCAACAATTTTCAACCCACTCAGCAGCTGCTCAGGGAGACAATGCTTGGTGACT
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
793 TA
131 TA
** * * * *
795 AATCTGCTTCCCACTAAGTTGGAAAGATAAAATTTGTCTTCTTCGATCTGCTCCACTAGTGCTCA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
860 GGGAGAGAAGATCTACAATTTTCAACCCACTCCGCTCCTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
925 TA
131 TA
* * *
927 AATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTATTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
992 GGGAGATAAGATCTACAATTTTCAACTCACTCCGCTGCTGTTCAGGGAGACAATGCTTGGTGACA
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
1057 TA
131 TA
* * *
1059 AATCTGCTTCCCACTATCTTGGAAATATAAGATTTGTCGTCTTTGATCTGCTCCACAACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* *
1124 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGTTGCTCAGGGAGACAATGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
1189 TA
131 TA
* ** ** * *
1191 AATCTGCTTCCCACTATCCTGGAAAGAGCAGATTTACCGTCTTCGATCTACTCTACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1256 GGGAGATAAGATCTACAATTTT
66 GGGAGATAAGATCTACAATTTT
1278 NNNNNNNNNN
Statistics
Matches: 1010, Mismatches: 133, Indels: 4
0.88 0.12 0.00
Matches are distributed among these distances:
132 773 0.77
133 237 0.23
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACT
TA
Found at i:3308 original size:132 final size:132
Alignment explanation
Indices: 3065--5478 Score: 2164
Period size: 132 Copynumber: 17.8 Consensus size: 132
3055 NNNNNNNNNN
* *
3065 GAAATATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGAAAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * *
3130 TCAACCTACT-CTGCTCCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATA
66 TCAACCCACTAC-GCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
3194 TTG
130 TTG
* * * *
3197 GAAAGATAAGATTTTCCATCTTCGATCTGCTGCACTACTGCTTAGGGAGATAAGATCGATAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * *
3262 TCAACCCACTACGCTGCTCCTCAGGGAGACAAGGCTTGATGGCTTAAATATGCTTCCCTACTAAT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCC-ACT-AT
*
3327 CTTG
129 TTTG
*
3331 GAAAGATAAGATTTGCCATCTTTCGATCTGCTCCCACTACTGCTTAAGGAGATAAGATCTACAAT
1 GAAAGATAAGATTTGCCATC-TTCGATCTGCT-CCACTACTGCTTAGGGAGATAAGATCTACAAT
* * * *
3396 TTTCAAGCAAC-ACCGCTGCTGCTCAGGGAGACAATGTTTGGTGACTTTAAATCTGCTTCCCACT
64 TTTCAACCCACTA-CGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC-TTAAATCTGCTTCCCACT
3460 ATTTTG
127 ATTTTG
* * * *
3466 GAAAGATAAGATTTTACCGTCATCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACAATT
1 GAAAGATAAGA-TTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATT
* *
3531 TCCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
65 TTCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
3596 TTG
130 TTG
* * * * *
3599 GAAAGATAAGATTTGCCGTCTTCGATCTGCACTACTATTGCTTAGGGAGATAAGATCTATAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * * * * * *
3664 TTAACCCACTCCGCTGCTGCTCAGGGAGGCAATGTTTGGTGGCTTAAATCTGTTTCCCACTATGT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
3729 TG
131 TG
*** * * ***************************
3731 GTGTTGA-AAAATTTGCCGTCTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 G-AAAGATAAGATTTGCCATCTTC--------------GATCTGCTCCACTACTGCTTAGGGAGA
***************************************************************
3795 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCTTG
51 TAAGATCTACAATTTTCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAAT-
* * **
3860 GTGACTTAAATCTGCTTTGGATTGTCTTG
115 CTG-C-T---TC-CCACT--A-T-T-TTG
* *
3889 GAAAGATAAGATTTGCCATCTTCGATCTGTTGCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* *
3954 TCAACCCAC-ACCGCTGCTGCTCAGGGAGACAATGTTTGGTGACTTAAATCTGCTTCCCACTATT
66 TCAACCCACTA-CGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
4018 TTG
130 TTG
* ** * *
4021 GTAAGATAAGATTTATCATCTTTGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* *
4086 TCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTTCCACTATTT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
4151 TG
131 TG
* *
4153 GAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * * *
4218 TCAACCCACT-CTTCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTGAAATCTCCTTCCCACTATC
66 TCAACCCACTAC-GCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
4282 TTG
130 TTG
* * * *
4285 GAAATATAAGATTTGCCGTCTTCGATCCGCTCCACTACTGCCTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA-TT
* *
4350 TTCAACCCACTTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTAT
65 TTCAACCCAC-TACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTAT
*
4415 ATTAG
129 -TTTG
* *
4420 GAAAGATAAGATTTGCCCATCTTTCGATCTGCTGCACTACTGCTTTAGGGAGATAAGGATCTAAT
1 GAAAGATAAGATTTG-CCATC-TTCGATCTGCTCCACTACTGC-TTAGGGAGATAA-GATCT-AC
* * *
4485 AATTTTTCAACCCACTCCGCTTGCTGCTTCAGGGAGAACAAATGTTTGGGTGACTTTAAATCTGC
61 AA-TTTTCAACCCACTACGC-TGCTGC-TCAGGGAG-AC-AAGGCTT-GGTGAC-TTAAATCTGC
*
4550 TTTCTCCCACTATCTATG
119 --T-TCCCACTAT-TTTG
* * *
4568 GAACAGA-AAGGATTTGATCGTCTTTCGATTTCTGCTTCCACTATTGCTTAGAGGAAGAATAAAG
1 GAA-AGATAA-GATTTG-CCATC-TTCGA--TCTGC-TCCACTACTGCTTAG-GG-AG-AT-AAG
* * * * *
4632 AATCCAACAAATTTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAATGTTTGTTGACTTAAATC
55 -AT-CTAC-AA-TTTTCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATC
*
4697 TGCTTCCCACTATTTTC
116 TGCTTCCCACTATTTTG
* * *
4714 GAAAGATAAGATTTACCGTCATCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * * *
4779 TCAACCCACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCTCATTATCT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
4844 TG
131 TG
*
4846 GAAAGATAAGATTTGCCATCTTCGATCTGCTGCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
*
4911 CCAACCCAC-ACCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
66 TCAACCCACTA-CGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATT
4975 TTG
130 TTG
* * * *
4978 GTAAGATAAGATTTACCATCTTCGCTCTTCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* *
5043 TCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTTCCACTATTT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
5108 TG
131 TG
* * * *
5110 GAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTATTGCTTTGGGAGATAAGATCTATAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * **
5175 TCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCA
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
5240 TG
131 TG
* *
5242 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * * * *
5307 TCAACCCACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGACTTAAATTTGTTTCCCACTATGT
66 TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
5372 TG
131 TG
* * *
5374 GAAAGATAAAATTTACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
1 GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
* * *
5439 TTAACCTACTCTAC-C-GCTGCTCAGGGAGACAAAGCTTGGT
66 TCAACC--CACTACGCTGCTGCTCAGGGAGACAAGGCTTGGT
5479 TACT
Statistics
Matches: 1838, Mismatches: 369, Indels: 150
0.78 0.16 0.06
Matches are distributed among these distances:
131 1 0.00
132 1168 0.64
133 56 0.03
134 147 0.08
135 58 0.03
136 81 0.04
137 37 0.02
138 15 0.01
139 12 0.01
140 36 0.02
141 14 0.01
142 3 0.00
143 11 0.01
144 11 0.01
145 18 0.01
146 8 0.00
147 12 0.01
148 16 0.01
149 19 0.01
150 10 0.01
151 14 0.01
152 20 0.01
153 6 0.00
154 11 0.01
155 12 0.01
156 22 0.01
157 2 0.00
158 18 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.30
Consensus pattern (132 bp):
GAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
TCAACCCACTACGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATTT
TG
Done.