Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011345.1 Kokia drynarioides strain JFW-HI SEQ_126325, 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: 4061
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:383 original size:216 final size:215
Alignment explanation
Indices: 4--897 Score: 882
Period size: 216 Copynumber: 4.2 Consensus size: 215
1 TTT
* * *
4 CTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTCCAAACATTCAATGCTCGGGAGATC
1 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCAATGCTCAGGAAATC
* * * ***
69 ACATCTTTTGGTGTAAATAGTTTTTCATTTTGTAAACAACTTTTTATCTTTGAATTAAAGACTTA
66 ACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTAGGTCTTTGAATTAAA-ACTTA
* * * *
134 TTTTCGTGACAATTATTTCTCTCTTTG-TTCTTGGCCGAACTTCCAAACTTGTCAAACTTTTACG
130 TTTTCGTGAGAATTGTTTCTCTC-TTGATTCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACA
*
198 AGTTGTTTTTA-AACTTTTGTTC
194 AGTT-TTTTTATAACTTTGGTTC
* ** * ** * * *
220 CTTAAAGTATTCAAGGCGATCCATTCCTTTTACCAATTTTCTGAACATTCCATGCTTAGTAAATC
1 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCAATGCTCAGGAAATC
*
285 ACATCATTTGGTCTAAATAGTTTGTCATTTTGTACACAACTTTAGGTCTTTGAATTTAAAACTTA
66 ACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTAGGTCTTTGAA-TTAAAACTTA
* * * * * * *
350 TTTACGTGAGAATTGTTTCTCTATTGATTCTTGGCCTAACTTTCGAACATGTCAAACTTATACAA
130 TTTTCGTGAGAATTGTTTCTCTCTTGATTCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACAA
* **
415 G-TTTTTTATAATTTTTTTTC
195 GTTTTTTTATAACTTTGGTTC
* * * * * *
435 CTAAAAGTATTCAAGACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCAAGAAATC
1 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCAATGCTCAGGAAATC
* * * ** * *
500 GCATCATTAGGTCTAAAAAGGCTATCATTTTGTCGAA-AAC---A----TTTG--TT-----TTA
66 ACATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTTAGGTCTTTGAATTAAAACTTA
** *
550 ---T-GTGAGAATTGTTTCTCTCTTGGA-TCTTGGCCAAACTTCCAATTTTTTCAAACTTTTACA
130 TTTTCGTGAGAATTGTTTCTCTCTT-GATTCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACA
610 AGTTTTTTTTATAACTTTGGTTC
194 AG-TTTTTTTATAACTTTGGTTC
* * * * *
633 CTTAAAGTATTCAAGACAATACATTCCTTCGAGCAATTTCCCAAACATT-AACTACTCGGGAAAT
1 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCAA-TGCTCAGGAAAT
* * * * * *
697 CACATCTTTTGGTCTACATAGTTTGTCATTTTATAAACAACTTTTGGTCTTTTAATTAAAAACTG
65 CACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTAGGTCTTTGAATT-AAAACTT
* * * * * * *
762 ATTTTCGTGAGAATTCTTTCTCTCTTGGTTCTTGGCCAAACTTTCGATCTTTTCAAACCTTTACA
129 ATTTTCGTGAGAATTGTTTCTCTCTTGATTCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACA
*
827 AGTTATTTTATAACTTTGGTTC
194 AGTTTTTTTATAACTTTGGTTC
* * * *
849 CTTATAGTATTCAAGAAGATCCATTCCTTCGAGTAATTTTCAAAACATT
1 CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATT
898 TCATGCGTAA
Statistics
Matches: 548, Mismatches: 101, Indels: 58
0.78 0.14 0.08
Matches are distributed among these distances:
196 49 0.09
197 5 0.01
198 95 0.17
200 3 0.01
205 5 0.01
207 2 0.00
208 4 0.01
212 1 0.00
213 2 0.00
214 6 0.01
215 97 0.18
216 221 0.40
217 58 0.11
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (215 bp):
CTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCAATGCTCAGGAAATC
ACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTAGGTCTTTGAATTAAAACTTAT
TTTCGTGAGAATTGTTTCTCTCTTGATTCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACAAG
TTTTTTTATAACTTTGGTTC
Found at i:970 original size:74 final size:74
Alignment explanation
Indices: 836--976 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 74
826 AAGTTATTTT
* * * * * *
836 ATAACTTTGGTTCCTTATAGTATTCAAGAAGATCCATTCCTTCGAGTAATTTTCAAAACATTTCA
1 ATAACTTCGGTTCCTAAAAGTATTCAAGAAGATCAATTCCTTCGAGCAATTTTCAAAACATTCCA
901 TGCGTAAGA
66 TGCGTAAGA
* ***
910 ATAACTTCGGTTCCTAAAAGGT-TTCAAGATGATCAATTCCTTCGAGCAATTTTTTGAACATTCC
1 ATAACTTCGGTTCCTAAAA-GTATTCAAGAAGATCAATTCCTTCGAGCAATTTTCAAAACATTCC
974 ATG
65 ATG
977 GTCGAGAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 54 0.96
75 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (74 bp):
ATAACTTCGGTTCCTAAAAGTATTCAAGAAGATCAATTCCTTCGAGCAATTTTCAAAACATTCCA
TGCGTAAGA
Found at i:1733 original size:213 final size:216
Alignment explanation
Indices: 910--1960 Score: 1098
Period size: 215 Copynumber: 4.9 Consensus size: 216
900 ATGCGTAAGA
* * * * * * *
910 ATAACTTCGGTTCCTAAAAGGT-TTCAAGATGATCAATTCCTTCGAGCAATTTTTTGAACATTCC
1 ATAACTTTGATTCCTTAAA-GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCA
* ** *
974 ATGGTC-GAGAAATCGTATCATTT-GATCTAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCT
65 ATGCTCAG-GAAATCACATCATTTAG-TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * * *
1037 TTGAATTAAAAACTTATTTTCGTGAGAATTGTTTCTGTCTTGGTTCTTGGTCGAACTTTCGAATT
128 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACT
* *
1102 TGTCAAACTTTTACGAGTTGTTTT
193 TGTCAAACTTTTACAAGTTCTTTT
* * *
1126 TTAACGTTTG-TTCCTTAAAGTATTC-A-ACG--CAATTCATTC---C------T-GAACATTTC
1 ATAAC-TTTGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACA-TTC
* * *
1176 -ATGCTCAGGAAATTACATCATTTAGTCTAAATAGTTTGTCATTTTGTATACAACTTTAGGTCTT
64 AATGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * *
1240 TGAACTAAAAACTTATTTACGTGAAAATTGATTCTCTCTTGGTTCTTGGCCAAACATCCAAACTT
129 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACTT
* *
1305 GTAAAACTTTTACTAGTT-TTTT
194 GTCAAACTTTTACAAGTTCTTTT
* * * * * * *
1327 ATAACTTTGTTTCGTAAAAGTATTCAAGATGATCCATTCCTTTGAG-AAATTTTCTGAACATTCC
1 ATAACTTTGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCA
* * * * *
1391 ATTCTCTGAAAATCGCATCATTT-GTTCTAAATAGTTTGTCATTTTGTGAACAACTTTTGGTCTT
65 ATGCTCAGGAAATCACATCATTTAG-TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * *
1455 TGAATTAAATACTTATTTACATGAGAATTTTTTCTCTCTTGGTTCATGGCCAAACTTTCGAACTT
129 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACTT
1520 GTCAAACTTTTACAAGTTCTTTT
194 GTCAAACTTTTACAAGTTCTTTT
* * * *
1543 ACAAC-TTCAGTTCCTTAGAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTCA
1 ATAACTTTGA-TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCA
* * *
1607 ATGCT-AGGAAATCACATCTTTTGGTCTAGATAGTTTGTCATTTTGTAAACAAC-TTT-GTCTTT
65 ATGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTT
* * * *
1669 AAATTAAAAACTTATTTACGTGACAATTGTTTCTCTCTTGGTTCTTGGTCGAGA-TTTCGAACTT
130 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGG-CCAAACTTTCGAACTT
* * *
1733 GCCAAACTTTTACGAGTACTTTT
194 GTCAAACTTTTACAAGTTCTTTT
* * * *
1756 ATAACTTTGATTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTCCAAACATTCAA
1 ATAACTTTGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCAA
* * * * * *
1821 TGCTC-GAGATATCAAATCATTTAGTCTAAACAGTTTATCATTGTGTAAAAAACTTTTGGTCTTT
66 TGCTCAG-GAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTT
* * * * * *
1885 GAATTAAAAACTTATTTTCGTTAGAATTGTTTCTCTCTTGGATCTTGGCCGAACTTT-AAAATCT
130 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACT-T
1949 GTCAAACTTTTA
194 GTCAAACTTTTA
1961 TGATACGAGA
Statistics
Matches: 691, Mismatches: 109, Indels: 70
0.79 0.13 0.08
Matches are distributed among these distances:
200 4 0.01
201 21 0.03
202 129 0.19
203 8 0.01
205 7 0.01
209 1 0.00
212 9 0.01
213 137 0.20
214 52 0.08
215 183 0.26
216 130 0.19
217 10 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (216 bp):
ATAACTTTGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCAA
TGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACTTGT
CAAACTTTTACAAGTTCTTTT
Found at i:1880 original size:429 final size:430
Alignment explanation
Indices: 1167--1960 Score: 1046
Period size: 429 Copynumber: 1.8 Consensus size: 430
1157 ATTCATTCCT
* *
1167 GAACATTTCATGCTCAGGAAATTACATCATTTAGTCTAAATAGTTTGTCATTTTGTATACAACTT
1 GAACATTTCATGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTT
*
1232 TAGGTCTTTGAACTAAAAACTTATTTACGTGAAAATTGATTCTCTCTTGGTTCTTGGCCAAACAT
66 TA-GTCTTTAAACTAAAAACTTATTTACGTGAAAATTGATTCTCTCTTGGTTCTTGGCCAAACAT
* * * * * *
1297 CCAAACTTGTAAAACTTTTACTAGTTTTTTATAACTTTGTTTCGTAAAAGTATTCAAGATGATCC
130 CCAAACTTGCAAAACTTTTACGAGTCTTTTATAACTTTGTTCCATAAAAGTATTCAAGACGATCC
** ** * * ** *
1362 ATTCCTTTGAGAAATTTTCTGAACATTCCATTCTCTGAAAATCGCATCATTTGTTCTAAATAGTT
195 ATTCCTTCAAGAAATTTTCCAAACATTCAATGCTCTGAAAATCAAATCATTTGTTCTAAACAGTT
* * * * * *
1427 TGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAAATACTTATTTACATGAGAATTTTTTCTCT
260 TATCATTGTGTAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCT
* **
1492 CTTGGTTCATGGCCAAACTTTCGAA-CTTGTCAAACTTTTACAAGTTCTTTTACAACTTCAGTTC
325 CTTGGATCATGGCCAAACTTTAAAATC-TGTCAAACTTTTACAAGTTCTTTTACAACTTCAGTTC
1556 CTTAGAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTC
389 CTTAGAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTC
* * *
1598 GAACA-TTCAATGCT-AGGAAATCACATCTTTTGGTCTAGATAGTTTGTCATTTTGTAAACAACT
1 GAACATTTC-ATGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACT
* * * * * *
1661 TT-GTCTTTAAATTAAAAACTTATTTACGTGACAATTGTTTCTCTCTTGGTTCTTGGTCGAGA-T
65 TTAGTCTTTAAACTAAAAACTTATTTACGTGAAAATTGATTCTCTCTTGGTTCTTGG-CCAAACA
* * *
1724 TTCGAACTTGCCAAACTTTTACGAGTACTTTTATAACTTTGATTCCAT-AAAGTATTCAAGACGA
129 TCCAAACTTGCAAAACTTTTACGAGT-CTTTTATAACTTTG-TTCCATAAAAGTATTCAAGACGA
* *
1788 TCCATTCCTTCAAGCAATTTTCCAAACATTCAATGCTC-GAGATATCAAATCATTTAG-TCTAAA
192 TCCATTCCTTCAAGAAATTTTCCAAACATTCAATGCTCTGA-AAATCAAATCATTT-GTTCTAAA
* * *
1851 CAGTTTATCATTGTGTAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTTCGTTAGAATTGTT
255 CAGTTTATCATTGTGTAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTT
* *
1916 TCTCTCTTGGATCTTGGCCGAACTTTAAAATCTGTCAAACTTTTA
320 TCTCTCTTGGATCATGGCCAAACTTTAAAATCTGTCAAACTTTTA
1961 TGATACGAGA
Statistics
Matches: 310, Mismatches: 46, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
428 73 0.24
429 172 0.55
430 55 0.18
431 10 0.03
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (430 bp):
GAACATTTCATGCTCAGGAAATCACATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTT
TAGTCTTTAAACTAAAAACTTATTTACGTGAAAATTGATTCTCTCTTGGTTCTTGGCCAAACATC
CAAACTTGCAAAACTTTTACGAGTCTTTTATAACTTTGTTCCATAAAAGTATTCAAGACGATCCA
TTCCTTCAAGAAATTTTCCAAACATTCAATGCTCTGAAAATCAAATCATTTGTTCTAAACAGTTT
ATCATTGTGTAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTC
TTGGATCATGGCCAAACTTTAAAATCTGTCAAACTTTTACAAGTTCTTTTACAACTTCAGTTCCT
TAGAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTC
Done.