Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_874 ID=scaffold_874-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: 2961
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:238 original size:132 final size:132
Alignment explanation
Indices: 1--1850 Score: 2761
Period size: 132 Copynumber: 14.1 Consensus size: 132
* * *
1 GGCTTAAATCTGCTTCTCCACTTTATTTGGAAGATAAGATTCACAATCTTCGATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* *
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTAATGCTTAAGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
131 AT
131 AT
* * * * *
133 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA-ACAAATTTATCATATTCGATCTACTCCACT
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATA-AGATTCACCATCTTCGATCTGCTCCACT
* * * * ** *
197 ACTGTTTAGGGTGACAGAATCTATC-ATCTTTAACCTACTCCACTACTCCTTAGGCAGATAGGTC
65 ACTGCTTAGGGTGACAGAATCT-GCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGAC
261 TAAT
129 TAAT
* * * *
265 GGCTTAAATCTGCTTCTCTACTGTGTTAGGAAGATAAGATTCACCATCTTCGATCTACTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * *
330 CTGCTTAGGGTGACAGAATCTGTAATCTTCAACCGAGTCCACTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
395 AT
131 AT
*
397 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCAATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
462 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
527 AT
131 AT
* * * *
529 GGCATAAATCTGCTTCTCCACTGTATTGGGAAGATAGGATTCACCATCGTCGATCTGCTCTACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * * * *
594 CTGCTTAGGGTGATAGAATATGCAACCTTTAACCTACTCCACTACTGCTTTGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
659 AT
131 AT
* * *
661 GGCTTAAATCTGCTTCTCCACTGTATTGGGAA-AGTAAGATTCATCATATTCGATCTGCTTCACT
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA-TAAGATTCACCATCTTCGATCTGCTCCACT
* * * * *
725 ACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCAATTGCACTA-TGGCTTAGGGAGATAGGAC
65 ACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGAC
*
789 AAAT
129 TAAT
* * *
793 GGCTTAAATTTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTACTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * *
858 CAGCTCAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
923 AT
131 AT
*
925 GGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* *
990 -TAGCTTAGGGTGACAGAATTTGCAATCTTCAACCTACTCTACTACTGCTTAGGGTGATAGGACT
66 CT-GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACT
1054 AAT
130 AAT
* * *
1057 GGCTTAAATTTGCTTCTCCACTGTATTAGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * * *
1122 CT-CTTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCCCTACTGCTTAGAGTGGTAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1186 AT
131 AT
* *
1188 GGCTTAAATCTTCTTCTCCACTGTATTGGGAATATAAGATTCACCATCTTCGATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * * * *
1253 CTGATTAGGGTGACAGAATCAGCAATCTTCGACCTACTCTAATACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1318 AT
131 AT
* *
1320 GGCTTAAATCTGCTTCCCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGTTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * * * *
1385 CTGATTAGGG-GACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGAGTGGTAGGACAA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1449 AT
131 AT
* * * * *
1451 GGCTTACATCTTCTTCTCCACTGTATTGGGAATATAAGATTCACCATGTTCGATC--C-GC-CTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * * *
1512 CTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCTATTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1577 AT
131 AT
*
1579 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGTTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * *
1644 CTGATTAGGGTGACAGAATCTGTAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1709 AT
131 AT
*
1711 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTCCGATCTGCTCCACTA
1 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
* * *
1776 CTGCTTAGGGTGACAGAAT-TGTAATCTTCAACCGAGTCCACTACTGCTTAGGGTGATAGGACTA
66 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
1840 AT
131 AT
1842 GGCTTAAAT
1 GGCTTAAAT
1851 NNNNNNNNNN
Statistics
Matches: 1550, Mismatches: 152, Indels: 33
0.89 0.09 0.02
Matches are distributed among these distances:
127 13 0.01
128 103 0.07
131 277 0.18
132 1152 0.74
133 5 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTA
CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTA
AT
Found at i:358 original size:44 final size:43
Alignment explanation
Indices: 310--518 Score: 145
Period size: 44 Copynumber: 4.8 Consensus size: 43
300 AAGATTCACC
* *
310 ATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGTGACAGAATC-GCA
* * * * * *
354 ATCTTCAACCGAGTCCACTACTGCTTAGGGTGATAGGA-C-TA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGTGACAGAATCGCA
* * * * * * * * * * *
395 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTCACC
1 AT--CTTCAATCTACTCCACTACTGCT-TAGGG-TGA-CAGAATCGCA
*
442 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGTGACAGAATC-GCA
*
486 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGTGA
519 TAGGACTAAT
Statistics
Matches: 123, Mismatches: 33, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
41 4 0.03
42 1 0.01
43 23 0.19
44 68 0.55
45 23 0.19
46 2 0.02
47 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
ATCTTCAATCTACTCCACTACTGCTTAGGGTGACAGAATCGCA
Found at i:1283 original size:44 final size:43
Alignment explanation
Indices: 1228--1435 Score: 120
Period size: 43 Copynumber: 4.8 Consensus size: 43
1218 AATATAAGAT
*
1228 TCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAA
1 TCACAATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAA
* * * * * * *
1271 TCAGCAATCTTCGACCTACTCTAATACTGCTTAGGGTGATAGGA
1 TCA-CAATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAA
* ** * * * *
1315 -C-TAATGGCTTAAATCTGCTTCC-CCACTGTATT-GGGAAGATAAGAT
1 TCACAAT--CTTCGATCTGC-TCCACTACTG-ATTAGGG-TGA-CAGAA
* *
1360 TCACCATCTTCGATCTGTTCCACTACTGATTAGGG-GACAGAA
1 TCACAATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAA
* * * *
1402 TCTGCAATCTTCGACCTACTCCACTACTGCTTAG
1 TC-ACAATCTTCGATCTGCTCCACTACTGATTAG
1436 AGTGGTAGGA
Statistics
Matches: 118, Mismatches: 35, Indels: 24
0.67 0.20 0.14
Matches are distributed among these distances:
41 3 0.03
42 5 0.04
43 45 0.38
44 44 0.37
45 18 0.15
46 1 0.01
47 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
TCACAATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAA
Found at i:2293 original size:132 final size:132
Alignment explanation
Indices: 1951--2957 Score: 1358
Period size: 132 Copynumber: 7.6 Consensus size: 132
1941 NNNNNNNNNN
* * *
1951 AAGATAAGATTCGCCATCTCCGATCTGCAT-CACTACTAG-TTAGGGTGACAGAATCTGCAATCC
1 AAGATAAGATTCACCATATTCGATCTGC-TCCACTACT-GCTTAGGGTGACAGAATCTGCAAT-C
*
2014 TTCAACCTACTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCCTGCTTCTCCACTGT
63 TTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAAT-CTGCTTCTCCACTGT
2079 ATTGGG
127 ATTGGG
* * **
2085 AAGATAAGATTCACCATCTTACGATCTGCTCCACTACTGCTTAGGGTGACAAAATCTAAAATCTT
1 AAGATAAGATTCACCATATT-CGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
* *
2150 CAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCCTTCTCCACTGTATT
65 CAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATT
*
2215 TGG
130 GGG
* * *
2218 AAGATAAGATTCGCCATCTTCGATCTGCAT-CACTACTGGTTAGGGTGACAGAATCTGCAATCTT
1 AAGATAAGATTCACCATATTCGATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
* * * *
2282 CAACCGACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTATCCACTATATT
65 CAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATT
2347 GGG
130 GGG
* * *
2350 AAGATAAGATTTATCATATTCGATCTGCTCTACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
1 AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
* * *
2415 AACCTATTCAAGTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
66 AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
2480 GG
131 GG
* * * * * **
2482 AATATCAGATTTATCATATTCGATCTGCTCCACTACTGTTTAGGGTGACAGAATCTATAATCTTC
1 AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
* * * * *
2547 AACCTACTCCACTACTCCTTAGAGAGATAGGTCTAATGGCTTAAATCTGCTTCTCTACTGTATTG
66 AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
2612 GG
131 GG
* * * *
2614 AAGTTAAGATTCACCATATTCGATCTACTCCACTACTGTTTAGGGTGACAAAATCTGCAATCTTC
1 AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
* * * * *
2679 AACCTATTCGACTACTGCTGAGGGAGATAGGACTAATGGCTTAAATCTTCTTCTCCACTGTATTG
66 AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
2744 GG
131 GG
* * * * * *
2746 AAGATAAGATTTATCATATTCGATCTACTCCACTACTGTTTAAGGTGACAGAATCTGTAATCTTC
1 AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
* * * * * *
2811 AACCTACTCCACTACTGCTTA-GGTAGATTGGACAAATGGCTTACATCTGCTGCTCCACTATTTT
66 AACCTACTCCACTACTGCTTAGGGT-GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATT
*
2875 GAG
130 GGG
* * * *
2878 AAGATATGATTCACCAT-TTCGATCCGCTCCACTACTGCTTAGGGCGATAGAATCTGCAATCTTC
1 AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
2942 AACCTACTCCACTACT
66 AACCTACTCCACTACT
2958 ACTT
Statistics
Matches: 775, Mismatches: 92, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
131 59 0.08
132 575 0.74
133 39 0.05
134 68 0.09
135 34 0.04
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (132 bp):
AAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
GG
Done.