Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011851.1 Kokia drynarioides strain JFW-HI SEQ_126847, 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: 4528
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Found at i:723 original size:217 final size:217
Alignment explanation
Indices: 24--4509 Score: 4300
Period size: 216 Copynumber: 20.7 Consensus size: 217
14 GCTTTTTTTA
* * * ** **
24 GTCTAAATAGTTTGTCATTTTGAAAACCAAGTTTTT-CTCTTCAAATTAAAAACTTATTTACATG
1 GTCTAAATAGTTTGTCATTTTGTAAA-CAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* * * * * * * *
88 AGAA-TAGTTTCAC-CTTTGGTTCTTAGATGGACTTCTGAACTAGTCAAGCTTTTACGAGTTCTT
65 AGAATTA-TTTCTCTC-TTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTT
* * * * * * * * *
151 TTATAACTTTGGTTCCTTACAGTATTCAAGACGATCTATTCCTTCGATCAGTATTCCGATCATTC
128 TTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTC
* * *
216 CATGCTCGGGAAGTAGCATCACTT-G
193 CATGCTCGAGAAATCGCATCA-TTCG
*
241 GTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCTTTGAATTAAAAA-TATATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACT-TATTTATGTG
* * * * * * *
305 AGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTTT
65 AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTT
* * * * * * *
370 ATTATCACTTCGGTTCCTTAAAGTACTCAAAATGATCCATTGCTTCAAGAAATATTCC-ATCATT
130 A-TA--ACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATT
*
434 CCATGCTCGAGAAATCTCATCATTCG
192 CCATGCTCGAGAAATCGCATCATTCG
* * * * *
460 GTCAAAATAGTTTGCCATTTTGTAGAAAAAC-TTTTGGTCGTTGAATTAAATACTTATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTA-AACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* ** * *
524 TA-AATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAGGAAAACTTTTACTATTTCTGT
65 -AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTT
* * * *
588 TATAAGTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTTGAGCAATTTTACGAATATTCC
129 TATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCC
* * *
653 ATGCTCGGGAAGTAGCATCATTCG
194 ATGCTCGAGAAATCGCATCATTCG
*
677 GTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCTTTGAATTAAAAA-TATATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACT-TATTTATGTG
* * * * * *
741 AGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAGA-TTTTACTATTTCTTT
65 AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAA-ACTTTTACTAGTTCTTT
* * * * * *
805 TATTATCACTTCGGTTCCTTAAAGTACTCAAAATGATCCATTGCTTCAAGCAATATTCCGATCAT
129 TA-TA--ACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACAT
*
870 TCCATGCTCGAGAAATCTCATCATTCG
191 TCCATGCTCGAGAAATCGCATCATTCG
* * * * *
897 GTCAAAATAGTTTGCCATTTTGTAGAAAAAC-TTTTGGTCGTTGAATTAAATACTTATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTA-AACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* ** * *
961 TA-AATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTAGGAAAACTTTTACTATTTCTGT
65 -AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTT
* * * *
1025 TATAAGTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTTGAGCAATTTTACGAATATTCC
129 TATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCC
*
1090 ATGCTCGAGAAATTGCATCACTT-G
194 ATGCTCGAGAAATCGCATCA-TTCG
* * *
1114 GTCTAAATTGTTTGTCATTTTGCAAACAACTTTTTGGTCTTTGAATTAATAA-TATATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACT-TATTTATGTG
* * * * ** * *
1178 AGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAACTTGTC-AAGTTTTACTATTTCTTTT
65 AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTT
* * * * *
1242 ATAACTTCAGTTCCTTAAAGTATGCAAGATGATCCATTCCTTCGAGCAGTATTCCGAACATTCCA
130 ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCCA
*
1307 TGCTCGAGAAATCCCATCATTCG
195 TGCTCGAGAAATCGCATCATTCG
* *
1330 GTCAAAATAGTTTGTCATTTTGTAAACAAC-TATTGGTCTTTGAATTAAAAACTTATTTATGTG-
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * ** * * *
1393 GAAATTGTTTCTCTCTTGGTTCTTGGACGAACTACCGAACTCCTAAAACTTTTACGAGTTATTTT
66 G-AATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTT
* * ** * **
1458 ATAACATCGATTCCTTAAAGTATTCAAGACCATCCATTTCTACGAGCAATTTTCAAAACATTCCA
130 ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCCA
* ** **
1523 TGCTCGAGAAAAT-GCTTTTTTTA
195 TGCTCGAG-AAATCGCATCATTCG
* * * ** **
1546 GTCTAAATAGTTTGTCATTTTGAAAACCAAGTTTTT-CTCTTCAAATTAAAAACTTATTTACATG
1 GTCTAAATAGTTTGTCATTTTGTAAA-CAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* * * * * * * *
1610 AGAA-TAGTTTCAC-CTTTGGTTCTTAGATGGACTTCTGAACTAGTCAAGCTTTTACGAGTTCTT
65 AGAATTA-TTTCTCTC-TTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTT
* * * * * * * * *
1673 TTATAACTTTGGTTCCTTACAGTATTCAAGACGATCTATTCCTTCGATCAGTATTCCGATCATTC
128 TTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTC
* * *
1738 CATGCTCGGGAAGTAGCATCATTCG
193 CATGCTCGAGAAATCGCATCATTCG
*
1763 GTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCTTTGAATTAAAAA-TATATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACT-TATTTATGTG
* * * * * * *
1827 AGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTTT
65 AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTT
* * * * *
1892 ATTATCACTTCTGTTCCTTAAAGTACTCAAGATGATCCATTGCTTCAAGCAATATTCC-AATCAT
130 A-TA--ACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAA-CAT
*
1956 TCCATGCTCGAGAAATCTCATCATTCG
191 TCCATGCTCGAGAAATCGCATCATTCG
* * * * *
1983 GTCAAAATAGTTTGCCATTTTGTAGAAAAAC-TTTTGGTCGTTGAATTAAATACTTATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTA-AACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* * * ** * **
2047 TA-AATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTAGAAAAACTTTTACTATTTCTGA
65 -AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTT
* * * * *
2111 TATAACTTCGGTTCCTAAAAGTTTTCAAGATGATCTATTTCTTCAAGCAATTTTACGAACATTCC
129 TATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCC
* *
2176 ATGCTCGAGAAATTGCATTA-TCTG
194 ATGCTCGAGAAATCGCATCATTC-G
* * * *
2200 GTCTAAATA--TTGTCATTTTGTAACCAAC-TTTTGGTCTTTGAATTAAAAACTTAATGACGTG-
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * * *
2261 GAAATTGTTTCTCTTTTAGTTCTTGGATGAACTTTCGAACTAGTCAAACTTTTA-TGAGTTCTTT
66 G-AATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACT-AGTTCTTT
* * * * * **
2325 TATAACTTAGGTTCCTTAAAGTATTC-TG-TGTTATCCATTCCTTCTAGAAATTTTTTGAACATT
129 TATAACTTCGGTTCCTTAAAGTATTCAAGATG--ATCCATTTCTTCGAGCAATTTTCCGAACATT
* * * * **
2388 GCATGTTCAAAAAATCGCATCATTTT
192 CCATGCTCGAGAAATCGCATCATTCG
** * *
2414 ACCTAAATAGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTGAATTAAAATCATATTTATGTGA
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * ** * *
2478 G-ATTATTTCTCTCTTGATTCTTAGACAAACTTCTAAACTTGTCAAGCTTTTACTATTTCTTTTA
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
** * * * *
2542 TAACTTCAATTCCTTAAAGTATTCAAGACGATCCA-TTCTTTCGAGCTATATTCCAAACATTCCA
131 TAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTC-TTCGAGCAATTTTCCGAACATTCCA
2606 TGCTCGAGAAATCGCATCATTCG
195 TGCTCGAGAAATCGCATCATTCG
* * * * **
2629 ATCTAAATATTTTGTCATTTTGTAAACAA-ATTTTGGTCTTTCAATTAAAAACTTATTTACATGA
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * *
2693 GAATTGTTTCTCTCTTAGTTCTTGGATGAACTTCCAAACTTGTCAAACTTTTA-TGAGCTCTTTT
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACT-AGTTCTTTT
* * * * * * * * *
2757 ATAACTTAGGTTCCTTAAAGCATTCTATG-CGATCCATTCCTTCTA-CAAATTTTTCGAACTTTT
130 ATAACTTCGGTTCCTTAAAGTATTC-AAGATGATCCATTTCTTCGAGC-AATTTTCCGAACATTC
* * * *
2820 AATGGTCG-GAAAATCGCATCTTTTG
193 CATGCTCGAG-AAATCGCATCATTCG
* ** * * * *
2845 ATCTAAA-A-ACTGTCATTTTGTAAACAAC-TTTTGGTCTTTGAGTTAAAAACTTATTGACGTGG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * * *
2907 GATTTGTCTCTCTCTTGGTTCTTGGACGAACCTCTGAACTTGTCAAACTTTTACAAGTTCTTTTA
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
* ** * * * *
2972 AAACTTTTGTTCCTTGAAGTATT-ATAAATGATCCACTTCATCGAGCAATTTT-CGAACATTCCA
131 TAACTTCGGTTCCTTAAAGTATTCA-AGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCCA
* * * * * *
3035 TTCTTC-AAAAATTGAATCTTTTG
195 TGC-TCGAGAAATCGCATCATTCG
* * * *
3058 GTTTAAATAGTGTGTCATTTTGTAAACAA-ATTTTGGTCTTTGAATTAAAAACTTATATATGTGA
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * *
3122 GAATTGTTTCTCTCTTGGTTCTTGGACGAACTACCGAACTTGTAAAACTTTTACGAGTTATTTTA
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
* * * * * * *
3187 CAACTTTGGTTCCATAAAGTATTCAAGATCATCCATTTCTACGACCAATTTTCCAAACATTCCAT
131 TAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCCAT
* * * *
3252 GCTCTAGAAATTGCATCTTTTG
196 GCTCGAGAAATCGCATCATTCG
* * ** * * *
3274 GTCTAAATAGTTTGTCATTTTGAAAACCAA-GTTTTGGTCTTCAAATTAAAAACATATTTACGTC
1 GTCTAAATAGTTTGTCATTTTGTAAA-CAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTG
* * * * ** * *
3338 AGAATTTTTTCTC-CTTTGTTCTTAGATGAACTTATGAACTAGTCAAGCTTTTA-TGAGTTCTTT
65 AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACT-AGTTCTTT
* * * * *
3401 TATAACTTTGGTTCCTTATAA-TATTCAAGACGATCCATTCCTTCGATCAATATTCCGAACATTC
129 TATAACTTCGGTTCCTTA-AAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTC
* * **
3465 CATGCTCGGGAAATAGCATCATTTT
193 CATGCTCGAGAAATCGCATCATTCG
* *
3490 GTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCTTTCAATTAAAAA-TATATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACT-TATTTATGTG
* * * * * *
3554 AGAATTATTTCTCTTTTGATTCTTAGG-CAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTT
65 AGAATTATTTCTCTCTTGGTTCTT-GGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTC-TT
* * * *
3618 TATAATAACTTTGGTTCCTTAAAGTATTCAGGATGATCCATTCCTTCGAGCAATTTTCCAAACAT
128 T-T-ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACAT
* * * *
3683 TCCATGCTCGGGAAATCGTACCGTTCG
191 TCCATGCTCGAGAAATCGCATCATTCG
* * * * *
3710 GTCAAAATAGCTTGTCATTTTGTGAACAACTTTTT-GT-TAATGAATTAAATACTTATTTATGTG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCT-TTGAATTAAAAACTTATTTATGTG
* * * * ** * **
3773 TA-AATTGTTTCTCCCTTGGTTCTTGGACGAACTTTCGAACTAGGAAAACTTTTACTATTTCTGA
65 -AGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTT
* * * * *
3837 TATAACTTTGGTTCCTTAAAGTTTTCAAGATGATCTATTTCTTCGACCAATTTTGCGAACATTCC
129 TATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCC
* *
3902 ATGCTCGAGAAATTGCATCATTTG
194 ATGCTCGAGAAATCGCATCATTCG
* *
3926 GTCTAAATAGTTTGTCATTTTGTAAACATC-TTTTGTTCTTTGAATTAAAAACTTATTTATGTGA
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * * * *
3990 GAATTGTTTTTCTCTTGGTTCTTAGACGAACTT-CTATACTTTTCAAGCTTTTACGAGTTCTTTT
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGA-ACTTGTCAAACTTTTACTAGTTCTTTT
* * * * * *
4054 ACAACTTTGGTTCCTTAAAGTATTCAAGACGATCCA-TTCTTTCGAGCTATATTCCAAACATTCC
130 ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTC-TTCGAGCAATTTTCCGAACATTCC
*
4118 ATGCTCGAGAAATTGCATCATTCG
194 ATGCTCGAGAAATCGCATCATTCG
* * *
4142 GTCTAAATATTTTGTCATTTTGTAAACAAATTTTT-GTCTTTGAATTAAAAACTTATTTACGTGA
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * *
4206 GAATTGTTTCTCTCTTTGTTCTTGGATGAACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTA
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
* * * * * *
4271 TAA-TTGAGGTTCCTTAAAGCATTCTATG-CGATCC-TTTCCTTCTA-CAAATTTTTCGAACATT
131 TAACTT-CGGTTCCTTAAAGTATTC-AAGATGATCCATTT-CTTCGAGC-AATTTTCCGAACATT
* * * *
4332 CAATGGTCG-GAAAATCGCATCTTTTG
192 CCATGCTCGAG-AAATCGCATCATTCG
* * * * * *
4358 ATCTAAATACTTTGTCATTTTGTAAAGAA-TTTTTGGTCTTTGAATTAAAAACTTATTGACGTGG
1 GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
* * * * *
4422 GAATTGTTTCTCTCTTGGTTTTTGGACGAACCTCCGAACTTGTCAAACTTTTACAAGTTCTTTCA
66 GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
* * *
4487 AAACCTCGGTTCCTTGAAGTATT
131 TAACTTCGGTTCCTTAAAGTATT
4510 ATAAATGAAC
Statistics
Matches: 3519, Mismatches: 635, Indels: 231
0.80 0.14 0.05
Matches are distributed among these distances:
212 3 0.00
213 29 0.01
214 297 0.08
215 414 0.12
216 1237 0.35
217 791 0.22
218 32 0.01
219 204 0.06
220 498 0.14
221 14 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (217 bp):
GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATTAAAAACTTATTTATGTGA
GAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTA
TAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAATTTTCCGAACATTCCAT
GCTCGAGAAATCGCATCATTCG
Done.