Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005874.1 Kokia drynarioides strain JFW-HI SEQ_120202, 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, 856
Length: 1427
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Found at i:1066 original size:347 final size:348
Alignment explanation
Indices: 1--1427 Score: 2231
Period size: 348 Copynumber: 4.1 Consensus size: 348
* *
1 GAGGCACGAATGGGATGAAAGGTAGCGTTTATGTAAATAGATTGCGCAGAACATAATGGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * * *
66 TCAT-TCATGCAGTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGTGTGCTTGGGCTAGAG
66 TCATACCA-GCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAG
130 TAGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTG-TTTTTTTTC
130 TAGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTC
**
194 TTTTTGTATTATTTTATTTATTGTAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATAC
195 TTTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATAC
259 ATTGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTAT
260 ATTGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTAT
*
324 TTGGGTATACTTCCATTCAAATTC
325 TTGGGTATACTTACATTCAAATTC
* * * * *
348 AAGGCACGAATGGGATGAAAGCTAGCGTTTATGTAAATAGATTGCACATAACATAATGGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * * * * *
413 TCATTCCAACAGTAATGGACTGGATCCCAACAGAACTCCGCAGTTAAGTGTGCTTGGGCGAGAGT
66 TCATACCAGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
*
478 AGTACTAGGATGGGTGACCTCCTTGGAAATCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTCT
131 AGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTCT
*
543 TTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAATAAAGCTTCATGGGATACA
196 TTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATACA
* *
608 TTGACATTATTAGTGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCTCGAGCATTATT
261 TTGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTATT
*
673 CGGGTATACTTACATTCAAATTC
326 TGGGTATACTTACATTCAAATTC
* * *
696 GAGGCATGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGTAAAACATAATTGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * *
761 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGGGAGT
66 TCATACCAGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
*
826 AGTACCAGGATGGGTGACCTCC-TGGAAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTC
131 AGTACTAGGATGGGTGACCTCCTTGG-AAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTC
* *
890 -TTTTGTACTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAACGCTT-ATGGGATAC
195 TTTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATAC
* * * * *
953 ATGGAAATTATTAGCGTCTTTTTTATTTTATTTTTATCCACCAAAATACGTGTTCCCGAGCATTA
260 ATTGACATTATTAGCGT-GTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTA
*
1018 TTTGGGTATACTTCCATTCAAATTC
324 TTTGGGTATACTTACATTCAAATTC
*
1043 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAAAAGATTGCGCAAAACATAATGGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * * * *
1108 TCATACCAGCACTAATGCAACGGAT-CCATTCAAAACTCCGCAGTTAAGCGTGCTTAGGCGTGAG
66 TCATACCAGCACTAATGCACCGGATCCCA-ACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAG
* * * *
1172 TAGTACTAGGTTGGTTGACCTCCTAGGAAGTCCTCGTGTTGCACCCCTTTTTTTGTTTTTTTTT-
130 TAGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTC
* *
1236 TCTTTTGTATTATTTTATTTATCTTAAGTTTGTAATTTTGCGAAATAGTAAAGCTTCATAGGG-T
195 T-TTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCAT-GGGAT
* * *
1300 ACATAGACATTATTAGCGTGTTTTTATTTTCTTTTTATCCGCGAAAATACGTCTTCCCGAGCATT
258 ACATTGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATT
* *
1365 ATTTAGGTATATTTACATTCAAATTC
323 ATTTGGGTATACTTACATTCAAATTC
1391 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAA
Statistics
Matches: 994, Mismatches: 76, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
346 26 0.03
347 463 0.47
348 482 0.48
349 20 0.02
350 3 0.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (348 bp):
GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
TCATACCAGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
AGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTTCT
TTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATACA
TTGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTATT
TGGGTATACTTACATTCAAATTC
Found at i:1337 original size:695 final size:695
Alignment explanation
Indices: 1--1427 Score: 2249
Period size: 695 Copynumber: 2.1 Consensus size: 695
* *
1 GAGGCACGAATGGGATGAAAGGTAGCGTTTATGTAAATAGATTGCGCAGAACATAATGGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * * *
66 TCATTCATGCAGTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGTGTGCTTGGGCTAGAGT
66 TCATCCATGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
*
131 AGTACTAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTCTT
131 AGTACCAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTCTT
* **
196 TTTGTATTATTTTATTTATTGTAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATACAT
196 TTTGTACTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATACAT
* * *
261 TGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAAATACGTCTTCCCGAGCATTATTT
261 GGAAATTATTAGCGTGTTTTTATTTTATTTTTATCCACCAAAATACGTCTTCCCGAGCATTATTT
* *
326 GGGTATACTTCCATTCAAATTCAAGGCACGAATGGGATGAAAGCTAGCGTTTATGTAAATAGATT
326 GGGTATACTTCCATTCAAATTCAAGGCACGAATGGGATGAAAGCTAGCCTTTATGTAAAAAGATT
* * * * *
391 GCACATAACATAATGGGTGCGATCATTCCAACAGTAATGGACTGGATCCCAACAGAACTCCGCAG
391 GCACAAAACATAATGGGTGCGATCATACCAACACTAATGAACTGGATCCCAACAAAACTCCGCAG
* * *
456 TTAAGTGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTTGGAAATCCTCGTGTTGCAC
456 TTAAGCGTGCTTAGGCGAGAGTAGTACTAGGATGGGTGACCTCCTAGGAAATCCTCGTGTTGCAC
521 CCCTCTTTTTGTTTTTTTTTCTTTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAA
521 CCCTCTTTTTGTTTTTTTTTCTTTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAA
* *
586 TAATAAAGCTTCATGGGATACATTGACATTATTAGTGTGTTTTTATTTTATTTTTATCCACGAAA
586 TAATAAAGCTTCATGGGATACATAGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAA
* *
651 ATACGTCTTCTCGAGCATTATTCGGGTATACTTACATTCAAATTC
651 ATACGTCTTCCCGAGCATTATTCAGGTATACTTACATTCAAATTC
* * *
696 GAGGCATGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGTAAAACATAATTGGTGCGA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
* * *
761 TCATACCA-GCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGGGAG
66 TCAT-CCATGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAG
825 TAGTACCAGGATGGGTGACCTCC-TGGAAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTT-
130 TAGTACCAGGATGGGTGACCTCCTTGG-AAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTC
*
888 TCTTTTGTACTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAACGCTT-ATGGGATA
194 T-TTTTGTACTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATA
* *
952 CATGGAAATTATTAGCGTCTTTTTTATTTTATTTTTATCCACCAAAATACGTGTTCCCGAGCATT
258 CATGGAAATTATTAGCGT-GTTTTTATTTTATTTTTATCCACCAAAATACGTCTTCCCGAGCATT
* *
1017 ATTTGGGTATACTTCCATTCAAATTCGAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAAAA
322 ATTTGGGTATACTTCCATTCAAATTCAAGGCACGAATGGGATGAAAGCTAGCCTTTATGTAAAAA
* * *
1082 GATTGCGCAAAACATAATGGGTGCGATCATACCAGCACTAATGCAAC-GGAT-CCATTCAAAACT
387 GATTGCACAAAACATAATGGGTGCGATCATACCAACACTAATG-AACTGGATCCCA-ACAAAACT
* * * *
1145 CCGCAGTTAAGCGTGCTTAGGCGTGAGTAGTACTAGGTTGGTTGACCTCCTAGGAAGTCCTCGTG
450 CCGCAGTTAAGCGTGCTTAGGCGAGAGTAGTACTAGGATGGGTGACCTCCTAGGAAATCCTCGTG
* * *
1210 TTGCACCCCTTTTTTTGTTTTTTTTT-TCTTTTGTATTATTTTATTTATCTTAAGTTTGTAATTT
515 TTGCACCCCTCTTTTTGTTTTTTTTTCT-TTTTGTATTATTTTATTTATCATAAGTTTGCAATTT
* *
1274 TGCGAAATAGTAAAGCTTCATAGGG-TACATAGACATTATTAGCGTGTTTTTATTTTCTTTTTAT
579 TGCGAAATAATAAAGCTTCAT-GGGATACATAGACATTATTAGCGTGTTTTTATTTTATTTTTAT
* * *
1338 CCGCGAAAATACGTCTTCCCGAGCATTATTTAGGTATATTTACATTCAAATTC
643 CCACGAAAATACGTCTTCCCGAGCATTATTCAGGTATACTTACATTCAAATTC
1391 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAA
1 GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAA
Statistics
Matches: 670, Mismatches: 54, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
694 32 0.05
695 631 0.94
696 7 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (695 bp):
GAGGCACGAATGGGATGAAAGGTAGCCTTTATGTAAATAGATTGCGCAAAACATAATGGGTGCGA
TCATCCATGCACTAATGCACCGGATCCCAACAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
AGTACCAGGATGGGTGACCTCCTTGGAAGTCCTCGTGTTGCACCCCTCTTTTTGTTTTTTTTCTT
TTTGTACTATTTTATTTATCATAAGTTTGCAATTTTGCGAAATAGTAAAGCTTCATGGGATACAT
GGAAATTATTAGCGTGTTTTTATTTTATTTTTATCCACCAAAATACGTCTTCCCGAGCATTATTT
GGGTATACTTCCATTCAAATTCAAGGCACGAATGGGATGAAAGCTAGCCTTTATGTAAAAAGATT
GCACAAAACATAATGGGTGCGATCATACCAACACTAATGAACTGGATCCCAACAAAACTCCGCAG
TTAAGCGTGCTTAGGCGAGAGTAGTACTAGGATGGGTGACCTCCTAGGAAATCCTCGTGTTGCAC
CCCTCTTTTTGTTTTTTTTTCTTTTTGTATTATTTTATTTATCATAAGTTTGCAATTTTGCGAAA
TAATAAAGCTTCATGGGATACATAGACATTATTAGCGTGTTTTTATTTTATTTTTATCCACGAAA
ATACGTCTTCCCGAGCATTATTCAGGTATACTTACATTCAAATTC
Done.