Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_846 ID=scaffold_846-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: 3158
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Found at i:1319 original size:132 final size:132
Alignment explanation
Indices: 968--2268 Score: 1965
Period size: 132 Copynumber: 9.9 Consensus size: 132
958 CTGCCGACTG
* * *
968 GGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* *
1033 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-C
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
*
1097 TA
131 CA
**
1099 TAGAGATAGAATTACTGGCTTC-ATGT-CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCC
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-C
* *
1162 TT-GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCTACTGCTGC
65 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGC
1226 CCA
130 CCA
* * * *
1229 TGGAGATAGAATTACTGGCTTCAATATACTCCATTGTAACCTCAGGGAGGTAAAATCCGTCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
*
1294 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTGCC
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
1359 CA
131 CA
* * *
1361 GGGAGATAGAACTACTGGCTTCAATGTACTCCACTATAACCTTAGGGAGGTAAAATCCGCCATCC
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-C
* *
1426 TT-GATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGC
65 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGC
1490 CCA
130 CCA
* * * *
1493 GGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCACAGAGAGGTAAAATTCGCCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
*
1558 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
1623 CA
131 CA
* * * *
1625 AGGAGATAGAATTACTGGCTTCAATATACTCCATTGTAACCTCAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* *
1690 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCT
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
1755 CA
131 CA
* * *
1757 TGGAGATAGAATTACTAGCTTCAATGT-CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCGTCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* * * ** * *
1821 ACGATCTGCTTCGCTGTCTA-TGC--AGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGC
66 TCGATCTGC-TC-C--ACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGC
*
1883 TGTCCA
127 TGCCCA
* *
1889 GGGAAATAGAATTACT-GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATTCGCCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
*
1953 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCC
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
2018 CA
131 CA
* * *
2020 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACATCAAGGAGGTAAAATCCGCCATCT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* *
2085 TCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCC
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
2150 CA
131 CA
* * *
2152 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATAT
1 GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* ** *
2217 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTCGATCTA
66 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
2269 CTTCACGCCA
Statistics
Matches: 1065, Mismatches: 89, Indels: 31
0.90 0.08 0.03
Matches are distributed among these distances:
128 3 0.00
129 94 0.09
130 30 0.03
131 136 0.13
132 792 0.74
133 4 0.00
134 3 0.00
135 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
GGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCC
CA
Found at i:1338 original size:44 final size:44
Alignment explanation
Indices: 1165--2270 Score: 241
Period size: 44 Copynumber: 25.2 Consensus size: 44
1155 GCCATCCTTG
* * * *
1165 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * * * ***
1209 ATCTATTCTACTGCTGCCCATGGAGAT-AGAAT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * * * * *
1252 ATATACTCCATTGTAAC--CTCAGGGAGGTAAAATCCGTC-ATCTTCG
1 ATCTACTCCA--CT-ACTGCTCAGGGAGATAAGATCTG-CAATCTTCA
* *
1297 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * * ***
1341 ATCTATTCCACTGCTGCCCAGGGAGAT-AGAACTACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * * * * *
1384 ATGTACTCCACTA-TAACCTTAGGGAGGTAAAATCCGCCATCCTT-G
1 ATCTACTCCACTACT--GCTCAGGGAGATAAGATCTGCAAT-CTTCA
* * * * *
1429 ATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGAAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * ***
1473 ATCTATTCCACTGCTGCCCAGGGAGAT-AGAAT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * * * * * **
1516 ATATACTCCACTGTAAC--CACAGAGAGGTAAAAT-TCGCCATCTTTG
1 ATCTACTCCAC--T-ACTGCTCAGGGAGATAAGATCT-GCAATCTTCA
* * *
1561 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * * ***
1605 ATCTATTCCACTGCTGCCCAAGGAGAT-AGAAT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * * * * *
1648 ATATACTCCATTGTAAC--CTCAGGGAGGTAAAATCTGCCATCTTCG
1 ATCTACTCCA--CT-ACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * *
1693 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* ** * * * *
1737 ATCTATTCCACTGTTGCTCATGGAGAT-AGAAT-TACTAGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * * * ** * *
1780 ATGT-CTCCACTGTAAC--CTCAGGGAGGTAAAATCCGCCGTCTACG
1 ATCTACTCCAC--T-ACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * * * ** **
1824 ATCTGCTTCGCTGTCT-ATGCAGGAAGGCAAGATCTAAAATCTTCA
1 ATCTACTCCACT-ACTGCT-CAGGGAGATAAGATCTGCAATCTTCA
* * * * *
1869 GTCTATTCCACTGCTG-TCCAGGGAAAT-AGAAT-T--ACTGCTTCA
1 ATCTACTCCACTACTGCT-CAGGGAGATAAG-ATCTGCAAT-CTTCA
* * * * *
1911 ATGTACTCCACTGTAAC--CTCAGGGAGGTAAAAT-TCGCCATCTTCG
1 ATCTACTCCAC--T-ACTGCTCAGGGAGATAAGATCT-GCAATCTTCA
* * *
1956 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * ***
2000 ATCTATTCCACTGCTGCCCAGGGAGAT-AGAAT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * ** * * * * * *
2043 ATGTACTCCACTGCAACATCAAGGAGGTAAAATCCGCCATCTTCG
1 ATCTACTCCACTACTGC-TCAGGGAGATAAGATCTGCAATCTTCA
* *
2088 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
* * * * ***
2132 ATCTATTCCACTGCTGCCCAGGGAGAT-AGAAT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGCAATCTTCA
* * * * ** * * **
2175 ATGTACTCCACTA-TAACCTCAGGGAGGTAAAATCCACCATATTTG
1 ATCTACTCCACTACT--GCTCAGGGAGATAAGATCTGCAATCTTCA
* * ** *
2220 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTCG
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
2264 ATCTACT
1 ATCTACT
2271 TCACGCCAAT
Statistics
Matches: 714, Mismatches: 282, Indels: 132
0.63 0.25 0.12
Matches are distributed among these distances:
41 2 0.00
42 28 0.04
43 154 0.22
44 383 0.54
45 137 0.19
46 10 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGCAATCTTCA
Found at i:2103 original size:659 final size:656
Alignment explanation
Indices: 969--2268 Score: 2115
Period size: 659 Copynumber: 2.0 Consensus size: 656
959 TGCCGACTGG
969 GGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTT
*
1034 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCTA
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCTA
* *
1099 TAGAGATAGAATTACTGGCTTCATGTCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTT
131 TAGAGATAGAATTACTAGCTTCATGTCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTC
* * *
1164 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCTACTGCTGCCCA
196 GATCTGCTCCACTACTGC-TAGGAAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
* * * *
1229 TGGAGATAGAATTACTGGCTTCAATATACTCCATTGTAACCTCAGGGAGGTAAAATCCGTCATCT
260 GGGAAATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
1294 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTGCC
325 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTGCC
* * * *
1359 CAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTATAACCTTAGGGAGGTAAAATCCGCCAT
390 CAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTACAACATCAAGGAGGTAAAATCCGCCAT
* *
1424 CCTTGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
455 CCTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
* * *
1489 CCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCACAGAGAGGTAAAATTCGCC
520 CCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTATAACCACAGAGAGGTAAAATCCACC
*
1554 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGC
585 ATATTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGC
1619 TGCCCAA
650 TGCCCAA
* *
1626 GGAGATAGAATTACTGGCTTCAATATACTCCATTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTT
1691 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCTC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCT-
* *
1756 ATGGAGATAGAATTACTAGCTTCAATGTCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCGT-C
130 ATAGAGATAGAATTACTAGCTTC-ATGTCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCC
* * *
1820 TACGATCTGCTTCGCTGTCTA-TGC-AGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGC
194 T-CGATCTGC-TC-C--ACTACTGCTAGGAAGACAAGATCTAAAATCTTCAATCTATTCCACTGC
* * *
1883 TGTCCAGGGAAATAGAATTACT-GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATTCG
254 TGCCCAGGGAAATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCG
*
1947 CCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACT
319 CCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACT
* *
2012 GCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACATCAAGGAGGTAAAATC
384 GCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTACAACATCAAGGAGGTAAAATC
* *
2077 CGCCAT-CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCC
449 CGCCATCCTT-GATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCC
* * *
2141 ACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAA
513 ACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTATAACCACAGAGAGGTAAA
** *
2206 ATCCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTCGATCTA
578 ATCCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
2269 CTTCACGCCA
Statistics
Matches: 594, Mismatches: 41, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
657 126 0.21
658 26 0.04
659 380 0.64
660 55 0.09
661 1 0.00
662 3 0.01
663 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (656 bp):
GGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCTA
TAGAGATAGAATTACTAGCTTCATGTCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTC
GATCTGCTCCACTACTGCTAGGAAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAG
GGAAATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTGCCC
AGGGAGATAGAACTACTGGCTTCAATGTACTCCACTACAACATCAAGGAGGTAAAATCCGCCATC
CTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGC
CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTATAACCACAGAGAGGTAAAATCCACCA
TATTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCT
GCCCAA
Done.