Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004507.1 Kokia drynarioides strain JFW-HI SEQ_117950, 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: 11131
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:1353 original size:435 final size:434
Alignment explanation
Indices: 524--1394 Score: 1253
Period size: 435 Copynumber: 2.0 Consensus size: 434
514 AATCTATCTT
* * * *
524 AGAGTATTCCCTTAATGAGTAGTACTTCTTCAAGAATCTATATTGGTGGAGGATAATGAAGAGTG
1 AGAGTATTCCCTCAATGAATAGTACTTCTTCAAGAATCTATATTAGTGGAGGATAATAAAGAGTG
* * *
589 CTACGAATCTTTATGCTCGCTATTTTCTTTGGCGAGGATTTGAAGGATCAAGTAGTTTTTTTTAT
66 CTACGAATCCTTATGCTCGCTATTTTCTTTGGCAAGGATTTGAAGGATCAACTAGTTTTTTTTAT
* * * * *
654 CTAGATGAACTAACTTGAAAAATGTTCAGATGGTTACCTTTGAGCCAGATTGGGGGTCCACATGT
131 CCAGATAAACTAACCTGAAAAATGTACAGATGGTTACCTTTGAGCCAGATTGAGGGTCCACATGT
* * * ** * *
719 GGTGCATTGATAGACTTATTGAAGATTATTAATTGTTTGGAATATGAGCATAATTTCGTGCATCG
196 GGTGCATTGATAGACTTATGGAAAACTATTAATTGCCTGGAATATGAGCATAATTTCGTGCAACA
* * * *
784 AAAATTGGGTAGATCTTTAAGTTATCAAGAGCTCCATATGCAAAATTTAACTACCAAAATATAGG
261 AAAATTGGGCAGATCTTTAAGATATCAAGAGCTCCATATGCAAAATTTAACTACCAAAAGATAAG
* * * * *
849 TCTTAAAGAAATTAGTTGCTAAAGCTTCCTAAAGGGTAGCCATTTTATAGGAAAAACGGTAGTCA
326 TCTTAAAGAAATTAGTCGCTAAAGCTTCCTAAAGGGTAACCACTTTATAGGAAAAAAGGTAGCCA
*
914 TTTTATATGTTTCTGATGGTTCAATTACTCATATTCTATCACAA
391 TTTTATATGTTTCTAATGGTTCAATTACTCATATTCTATCACAA
* * *
958 AGAGTGTTCCCTCAATGAATAGTACTTCTTCAAGAATTTATCTTAGTGGAGGATAATAAAGAGTG
1 AGAGTATTCCCTCAATGAATAGTACTTCTTCAAGAATCTATATTAGTGGAGGATAATAAAGAGTG
*
1023 CTACGAATCCTTATGCTCTCTATTTTCTTTGGCAAGGATTTGTAA-GATCAACTAGTTTTTTTTC
66 CTACGAATCCTTATGCTCGCTATTTTCTTTGGCAAGGATTTG-AAGGATCAACTAGTTTTTTTT-
* * * * * * *
1087 ATCCCGATAAAGTAACCTGAAAGATGTACGGATGGTTTCCTTTGAGTCAGATTGAGGGTCCACTT
129 ATCCAGATAAACTAACCTGAAAAATGTACAGATGGTTACCTTTGAGCCAGATTGAGGGTCCACAT
* *
1152 GTGGTGCATTGATAGACTTATGGAAAACTATTAATTGCCTGGAATATTAGCATAATTTTGTGCAA
194 GTGGTGCATTGATAGACTTATGGAAAACTATTAATTGCCTGGAATATGAGCATAATTTCGTGCAA
* * *
1217 CAAAAATTGGGCATG-TCTTTAAGATATCAAGAGCTCCATTTGCAAAGTTTAACTATCAAAAGAT
259 CAAAAATTGGGCA-GATCTTTAAGATATCAAGAGCTCCATATGCAAAATTTAACTACCAAAAGAT
* *
1281 AATTCTTAAAGAAATTCA-TCGCTAAAGCTTCCTCAAGGGTAACCACTTTATAGGAAAAAAGGTA
323 AAGTCTTAAAGAAATT-AGTCGCTAAAGCTTCCTAAAGGGTAACCACTTTATAGGAAAAAAGGTA
*
1345 GCCATTTTATATGTTTCTAATGGTTCAATTACTCATATTTTATCACAA
387 GCCATTTTATATGTTTCTAATGGTTCAATTACTCATATTCTATCACAA
1393 AG
1 AG
1395 TTGAAGCTCT
Statistics
Matches: 385, Mismatches: 48, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
434 114 0.30
435 269 0.70
436 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (434 bp):
AGAGTATTCCCTCAATGAATAGTACTTCTTCAAGAATCTATATTAGTGGAGGATAATAAAGAGTG
CTACGAATCCTTATGCTCGCTATTTTCTTTGGCAAGGATTTGAAGGATCAACTAGTTTTTTTTAT
CCAGATAAACTAACCTGAAAAATGTACAGATGGTTACCTTTGAGCCAGATTGAGGGTCCACATGT
GGTGCATTGATAGACTTATGGAAAACTATTAATTGCCTGGAATATGAGCATAATTTCGTGCAACA
AAAATTGGGCAGATCTTTAAGATATCAAGAGCTCCATATGCAAAATTTAACTACCAAAAGATAAG
TCTTAAAGAAATTAGTCGCTAAAGCTTCCTAAAGGGTAACCACTTTATAGGAAAAAAGGTAGCCA
TTTTATATGTTTCTAATGGTTCAATTACTCATATTCTATCACAA
Found at i:9254 original size:7 final size:7
Alignment explanation
Indices: 9244--9270 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9234 CTTTTGGGGT
9244 TTGGGAA
1 TTGGGAA
9251 TTGGGAA
1 TTGGGAA
9258 TTGGGAA
1 TTGGGAA
9265 TTGGGA
1 TTGGGA
9271 CAAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (7 bp):
TTGGGAA
Done.