Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007291.1 Kokia drynarioides strain JFW-HI SEQ_121907, whole genome shotgun sequence
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: 2142
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:881 original size:470 final size:470
Alignment explanation
Indices: 1--2141 Score: 3771
Period size: 470 Copynumber: 4.6 Consensus size: 470
* * *
1 CGCTTAGGGGAATCAGAATACTTCTACATATAGTAACTCATACAACAACAGAGTTCAACAACCTT
1 CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
* * *
66 AGGGGAATCAGAATGCTTCCATATATAGATATGGAAATTCCTCAACTCAAGGGAGTTATAATAAC
66 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
131 CATAAACTA-CAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTAC
131 CATAAAC-AGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTAC
*
195 ATAGCCAGATGCAACCACAGATTCGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGA
195 ATAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGA
* *
260 CAGCATCAGCAACAGTAGCAATTTTCTCAACAAGGGTCAGATCCTATGGCTGCGCTTGAAGCATT
260 CAACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATT
* * *
325 GATGTCAGAGCATATCATGAGAACTGAAGCGATAGTGTACGGTAATTCTTCTTCTATCCGAGCAT
325 GATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCAT
* *
390 TGGAAGCCCATCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACTAGGTGCTCTACCTAGT
390 TGGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTGCTCTACCTAGT
455 GATACTGAGAACCCAA
455 GATACTGAGAACCCAA
* * * *
471 CGCTTAGGGGAATTAGAATACTTACACATATGGTAACTCATACAACAACAGAGTTCAGCAACCTT
1 CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
*
536 AAGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
66 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
* *
601 CATAAAGAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGTAGGTACA
131 CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTACA
*
666 TAGCCAGATGCAACCATAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
196 TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
731 AACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
261 AACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
*
796 ATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGCAATTCTTCTTCTATCCGAGCATT
326 ATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCATT
* *
861 GAAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGCGTAAGGTCACCAGGTGCTCTACCTAGTG
391 GGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTGCTCTACCTAGTG
926 ATACTGAGAACCCAA
456 ATACTGAGAACCCAA
*
941 CGCTTAGGGGAATCAAAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
1 CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
*
1006 AGGGGAATCAGAATGCTTCCACATATAGATATGNAAATTCCTCAGCTCAAGGGAGTTACAATAAC
66 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
* *
1071 CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACATTGATCAATTGCAAGTACA
131 CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTACA
* *
1136 TAGCTAGATGCAACCACAGATACGATTGTAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
196 TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
** *
1201 AGTATCAGCAACAGTAGCAATTTTCTCAACAATGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
261 AACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
* *
1266 ATGTGAGAGCATATCATGAGAACTGAAGCTATAGTGTAAGGTAATTCTTCTTCTATCCGAGCATT
326 ATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCATT
*
1331 GGAAGCCCAGCTAGGATAATTGGCTTCTAATATGAGTGTAAGGTCACCAGGTGCTCTACCTAGTG
391 GGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTGCTCTACCTAGTG
1396 ATACTGAGAACCCAA
456 ATACTGAGAACCCAA
* *
1411 CGCTTAGGGGATTCAGAATGCTTCCACATATGGTAACTCATACAACAATAGAGTTCAACAACCTT
1 CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
* *
1476 AAGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCGAGGGAGTTACAATAAC
66 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
* * **
1541 CATAAACAGTAGAATTTTAATCATAATTTGTAGGTATATTCGCACACAAATCAATTGCAGGTACA
131 CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTACA
* * *
1606 TAGCCAGATGCAACCATAGATATGATTGCAGCCACAATAGAATGTAATGCCATATATGCAAGGAC
196 TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
* *
1671 AACATCAGCAACAGTAGTAATTTTCTCAACAAAGGTCAGATCCTATTGCTGCGCTTGAAGCATTG
261 AACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
*
1736 ATGTGAGAGCATATCATGAGAACTAAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCATT
326 ATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCATT
*
1801 GGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTTCTCTACCTAGTG
391 GGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTGCTCTACCTAGTG
1866 ATACTGAGAACCCAA
456 ATACTGAGAACCCAA
*
1881 CGCTTAGGGGAATCAGAATGCTTCCACAGATGGTAACTCATACAACAACAGAGTTCAACAACCTT
1 CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
1946 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
66 AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
* *
2011 CATAAATAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGTAGGTACA
131 CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTACA
2076 TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
196 TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
2141 A
261 A
2142 G
Statistics
Matches: 1583, Mismatches: 87, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
469 1 0.00
470 1582 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (470 bp):
CGCTTAGGGGAATCAGAATGCTTCCACATATGGTAACTCATACAACAACAGAGTTCAACAACCTT
AGGGGAATCAGAATGCTTCCACATATAGATATGGAAATTCCTCAGCTCAAGGGAGTTACAATAAC
CATAAACAGCAGAATTTTAATCAGAATTTGTAGGTATATTCGCACACTGATCAATTGCAGGTACA
TAGCCAGATGCAACCACAGATACGATTGCAGCCACAATAGAATGCAATGCCATATATGCAAGGAC
AACATCAGCAACAGTAGCAATTTTCTCAACAAAGGTCAGATCCTATGGCTGCGCTTGAAGCATTG
ATGTGAGAGCATATCATGAGAACTGAAGCGATAGTGCAAGGTAATTCTTCTTCTATCCGAGCATT
GGAAGCCCAGCTAGGATAATTGGCTTCTAATCTGAGTGTAAGGTCACCAGGTGCTCTACCTAGTG
ATACTGAGAACCCAA
Done.