Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003870.1 Kokia drynarioides strain JFW-HI SEQ_116904, 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: 1972
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Found at i:661 original size:156 final size:154
Alignment explanation
Indices: 368--684 Score: 481
Period size: 156 Copynumber: 2.0 Consensus size: 154
358 GATGGAAAGA
*
368 ACTGAAGGGTTCTTCAAGACATTGGCAACATTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTA
1 ACTGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTA
* * * *
433 GTTAACACAAATATTTTTCGTTTTAATTGTCGTAGCAAATATTAGGCGATCACTAATTGCCCTTT
66 GTTAACACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCCC--T
498 GTGTTTTTTTCTTGTACAAACCAATC
129 GTGTTTTTTTCTTGTACAAACCAATC
* * * * * *
524 ATTGAAGAGTTCTTCAAGGCGTTGGGAACATTGTCAATGAATGAGCCGCAGCACAAGGGAAGGTA
1 ACTGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTA
* * *
589 GTTAAGACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGTAATCACTAATTGCTCTGT
66 GTTAACACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCCCTGT
*
654 GTTTTTTTCTTGTAGAAACCAATC
131 GTTTTTTTCTTGTACAAACCAATC
678 ACTGAAG
1 ACTGAAG
685 GGGATGTTGT
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
154 32 0.22
156 113 0.78
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (154 bp):
ACTGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTA
GTTAACACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCCCTGT
GTTTTTTTCTTGTACAAACCAATC
Found at i:1047 original size:291 final size:290
Alignment explanation
Indices: 527--1838 Score: 1537
Period size: 291 Copynumber: 4.6 Consensus size: 290
517 ACCAATCATT
* * * * * *
527 GAAGAGTTCTTCAAGGCGTTGGGAACATTGTCAATGAATGAGCCGCAGCACAAGGGAAGGTAG--
1 GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
* * *
590 T---T-AAGACAAAAATGTTTCGTTTTAATT-GTAGTAGCAAATATTAGGTAATCACTAATTGCT
66 TCAGTAAACACAAAAATGTTTCTTTTTAATTAG-AGTAGCAAATATTAGGCAATCACTAATTGCT
* * * * *
650 C-T-GTGTTTTTTTCTTGTAGAAACCAATCACTGAAGGGGATGTTGTGGTTGGACGAGCAGTGAA
130 CTTGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGTTGTGGTTGCACAAGCAGTGAA
** *
713 AGGAGCTCAAAGGAAGCAAGTTGACAGGCCAATTTTATACTTTCTTTGTTTTCAAGAGGAGTGAA
195 AGGAGC-CAAAGGAAGCAAGTTGACAAACCAATTTTATACTTTCTTTGTTTTCAGGAGGAGTGAA
778 GCAGAAAAATGCAATAGCAGATGGAAGGAACC
259 GCAGAAAAATGCAATAGCAGATGGAAGGAACC
* * * *
810 GAAAAGTTCTTCAGGACATTGGTAACTTTGTCAATGAACGAGCAGCAGCACAAGGTAAGGTAGTT
1 GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
*
875 TCAGTAAACACAAAAATGTTTCTTTTTAATTAGAGTAGCAAATATTAGGCAATCACTAATTGTTC
66 TCAGTAAACACAAAAATGTTTCTTTTTAATTAGAGTAGCAAATATTAGGCAATCACTAATTGCTC
* *
940 TTGGT-TATTTTTGCTTGTAGAAACCAATCTCCGAAGGGGCTGTTGTGGTTGCACAAGCTGTGAA
131 TTGGTGT-TTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGTTGTGGTTGCACAAGCAGTGAA
*
1004 AGGAGCTCAAAGGAAGCAAGTTGACAAACCATTTTTATACTTTCTTTGTTTTTCAGGA-GATGTG
195 AGGAGC-CAAAGGAAGCAAGTTGACAAACCAATTTTATACTTTCTTTG-TTTTCAGGAGGA-GTG
*
1068 AAGCA-AAAAATGCAATTGCAGATGGAAGGAACC
257 AAGCAGAAAAATGCAATAGCAGATGGAAGGAACC
*
1101 GAAGAGTTCTTCAAGACATTGGTAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
1 GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
* * * *
1166 CCAGCAAACAC-AAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGCAATCACTAATTGCTC
66 TCAGTAAACACAAAAATGTTTCTTTTTAATTAGAGTAGCAAATATTAGGCAATCACTAATTGCTC
* * * * * * * * *
1230 TTGGTGTTTTTTGCTTTTAAAAACCAATCACTGTAGGGACAGTTGTGG-TGCGCAAGCTGTAAAA
131 TTGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGTTGTGGTTGCACAAGCAGTGAAA
* * * * * *
1294 GGAGCCCAA--ATG-AAGTTGGCAAACCAATTTTATATTTTCTTTTTTTTTTCAGGAGGATTGAA
196 GGAGCCAAAGGAAGCAAGTTGACAAACCAATTTTATACTTTC--TTTGTTTTCAGGAGGAGTGAA
* * * *
1356 GCAGAGAAATGCAACAGTAGATGGAAAGAACC
259 GCAGAAAAATGCAATAGCAGATGGAAGGAACC
* * * * * *
1388 GAATAGTTCGTCAAGACTTTGGCAACTTAGTCAATGAACGAGCAGCAACGCAAGGGAAGGTA-TT
1 GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
* * * *
1452 TCCAGTAAACACAAAATTGTTACTTTTTCATTATG-GTCGCAAATATTAGGCAATCACTAATTGC
66 T-CAGTAAACACAAAAATGTTTCTTTTTAATTA-GAGTAGCAAATATTAGGCAATCACTAATTGC
* * * * * *
1516 ACTTTGTGTTTTTTGCTTGTAGAATCCAATCACCGAAGGGGTTGTTGTGGTTGGACAAGCAATGA
129 TCTTGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGTTGTGGTTGCACAAGCAGTGA
* * * *
1581 AAGGAGCCTAAAGGAAGCAAGTTGACAAATCATTTTTATACTTTCCTTGTTTAT-AGGAGAAGTG
194 AAGGAGCC-AAAGGAAGCAAGTTGACAAACCAATTTTATACTTTCTTTGTTT-TCAGGAGGAGTG
**
1645 AAGCAGAAAAATGCAATAGCAGATGGAAGGAAGT
257 AAGCAGAAAAATGCAATAGCAGATGGAAGGAACC
* * * * * **
1679 GAAGGGTTCTTCAAGACATTTGCAACATTGTGAATGAAAGAGCAGTGGCACAAGGGAAGGTAG--
1 GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
* * *
1742 T---T-AACACAAAAATGTTTCGTTCTAATT-GTAGTAGCAAATATTAGGCGATCACTAATTGCT
66 TCAGTAAACACAAAAATGTTTCTTTTTAATTAG-AGTAGCAAATATTAGGCAATCACTAATTGCT
* * *
1802 CTTTGTGTCTTTTT-CTTGTACAAACCAATCACTGAAG
130 CTTGGTGT-TTTTTGCTTGTAGAAACCAATCACCGAAG
1839 AGTTCTTCAA
Statistics
Matches: 877, Mismatches: 122, Indels: 58
0.83 0.12 0.05
Matches are distributed among these distances:
283 55 0.06
285 100 0.11
286 26 0.03
287 92 0.10
288 90 0.10
289 89 0.10
290 95 0.11
291 288 0.33
292 19 0.02
293 23 0.03
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (290 bp):
GAAGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
TCAGTAAACACAAAAATGTTTCTTTTTAATTAGAGTAGCAAATATTAGGCAATCACTAATTGCTC
TTGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGTTGTGGTTGCACAAGCAGTGAAA
GGAGCCAAAGGAAGCAAGTTGACAAACCAATTTTATACTTTCTTTGTTTTCAGGAGGAGTGAAGC
AGAAAAATGCAATAGCAGATGGAAGGAACC
Found at i:1433 original size:578 final size:573
Alignment explanation
Indices: 527--1838 Score: 1721
Period size: 578 Copynumber: 2.3 Consensus size: 573
517 ACCAATCATT
* * * * *
527 GAAGAGTTCTTCAAGGCGTTGGGAACATTGTCAATGAATGAGCCGCAGCACAAGGGAAGGTAGTT
1 GAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAGCAGCAGCACAAGGGAAGGTAGTT
* *
592 AAGACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGTAATCACTAATTGCTC-TGTGT
66 AAAACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCTCTTGTG-
* * * *
656 TTTTTTCTTGTAGAAACCAATCACTGAAGGGGATGTTGTGGTTGGACGAGCAGTGAAAGGAGCTC
130 TTTTTTCTTGTAAAAACCAATCACTGAAGGGGAAGTTGTGGTTGGACAAGCAGTAAAAGGAGCTC
**
721 AAAGGAAGCAAGTTGACAGGCCAATTTTATACTTTCTTTGTTTTCAAGAGGAGTGAAGCAGAAAA
195 AAA-GAAGCAAGTTGACAAACCAATTTTATACTTTCTTTGTTTTCAAGAGGAGTGAAGCAGAAAA
* * * * * *
786 ATGCAATAGCAGATGGAAGGAACCGAAAAGTTCTTCAGGACATTGGTAACTTTGTCAATGAACGA
259 ATGCAACAGCAGATGGAAAGAACCGAAAAGTTCGTCAAGACATTGGCAACTTAGTCAATGAACGA
* * *
851 GCAGCAGCACAAGGTAAGGTAGTTT-CAGTAAACACAAAAATGTTTCTTTTTAATTA-GAGTAGC
324 GCAGCAACACAAGGGAAGGTA-TTTCCAGTAAACACAAAAATGTTACTTTTTAATTATG-GTAGC
** *
914 AAATATTAGGCAATCACTAATTGTTCTTGGT-TATTTTTGCTTGTAGAAACCAATCTCCGAAGGG
387 AAATATTAGGCAATCACTAATTGCACTTGGTGT-TTTTTGCTTGTAGAAACCAATCACCGAAGGG
**
978 GCTGTTGTGGTTGCACAAGCTGTGAAAGGAG-CTCAAAGGAAGCAAGTTGACAAACCATTTTTAT
451 GCTGTTGTGGTTGCACAAGCAATGAAAGGAGCCT-AAAGGAAGCAAGTTGACAAACCATTTTTAT
* * * *
1042 ACTTTCTTTGTTTTTCAGGAGATGTGAAGCA-AAAAATGCAATTGCAGATGGAAGGAACC
515 ACTTTCCTTGTTTAT-AGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACC
* * *
1101 GAAGAGTTCTTCAAGACATTGGTAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTT
1 GAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAGCAGCAGCACAAGGGAAGGTAGTT
* * *
1166 CCAGCAAACACAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGCAATCACTAATTGCTCT
66 --A--AAACA-AAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCTCT
* * *
1231 TGGTGTTTTTTGCTTTTAAAAACCAATCACTGTA-GGGACAGTTGTGG-TGCG-CAAGCTGTAAA
126 T-GTGTTTTTT-CTTGTAAAAACCAATCACTGAAGGGGA-AGTTGTGGTTG-GACAAGCAGTAAA
* * * * * * *
1293 AGGAGC-CCAA-ATG-AAGTTGGCAAACCAATTTTATATTTTCTTTTTTTTTTCAGGAGGATTGA
187 AGGAGCTCAAAGAAGCAAGTTGACAAACCAATTTTATACTTTC--TTTGTTTTCAAGAGGAGTGA
* * * *
1355 AGCAGAGAAATGCAACAGTAGATGGAAAGAACCGAATAGTTCGTCAAGACTTTGGCAACTTAGTC
250 AGCAGAAAAATGCAACAGCAGATGGAAAGAACCGAAAAGTTCGTCAAGACATTGGCAACTTAGTC
* * *
1420 AATGAACGAGCAGCAACGCAAGGGAAGGTATTTCCAGTAAACACAAAATTGTTACTTTTTCATTA
315 AATGAACGAGCAGCAACACAAGGGAAGGTATTTCCAGTAAACACAAAAATGTTACTTTTTAATTA
* * *
1485 TGGTCGCAAATATTAGGCAATCACTAATTGCACTTTGTGTTTTTTGCTTGTAGAATCCAATCACC
380 TGGTAGCAAATATTAGGCAATCACTAATTGCACTTGGTGTTTTTTGCTTGTAGAAACCAATCACC
* * *
1550 GAAGGGGTTGTTGTGGTTGGACAAGCAATGAAAGGAGCCTAAAGGAAGCAAGTTGACAAATCATT
445 GAAGGGGCTGTTGTGGTTGCACAAGCAATGAAAGGAGCCTAAAGGAAGCAAGTTGACAAACCATT
**
1615 TTTATACTTTCCTTGTTTATAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAAGT
510 TTTATACTTTCCTTGTTTATAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACC
* * * **
1679 GAAGGGTTCTTCAAGACATTTGCAACATTGTGAATGAAAGAGCAGTGGCACAAGGGAAGGTAGTT
1 GAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAGCAGCAGCACAAGGGAAGGTAGTT
* * *
1744 AACACAAAAATGTTTCGTTCTAATTGTAGTAGCAAATATTAGGCGATCACTAATTGCTCTTTGTG
66 AAAACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCTC-TTGTG
*
1809 TCTTTTTCTTGTACAAACCAATCACTGAAG
130 T-TTTTTCTTGTAAAAACCAATCACTGAAG
1839 AGTTCTTCAA
Statistics
Matches: 641, Mismatches: 77, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
573 71 0.11
574 70 0.11
576 25 0.04
577 19 0.03
578 343 0.54
579 56 0.09
580 27 0.04
581 30 0.05
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (573 bp):
GAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAGCAGCAGCACAAGGGAAGGTAGTT
AAAACAAAAATGTTTCGTTTTAATTGTAGTAGCAAATATTAGGCAATCACTAATTGCTCTTGTGT
TTTTTCTTGTAAAAACCAATCACTGAAGGGGAAGTTGTGGTTGGACAAGCAGTAAAAGGAGCTCA
AAGAAGCAAGTTGACAAACCAATTTTATACTTTCTTTGTTTTCAAGAGGAGTGAAGCAGAAAAAT
GCAACAGCAGATGGAAAGAACCGAAAAGTTCGTCAAGACATTGGCAACTTAGTCAATGAACGAGC
AGCAACACAAGGGAAGGTATTTCCAGTAAACACAAAAATGTTACTTTTTAATTATGGTAGCAAAT
ATTAGGCAATCACTAATTGCACTTGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGT
TGTGGTTGCACAAGCAATGAAAGGAGCCTAAAGGAAGCAAGTTGACAAACCATTTTTATACTTTC
CTTGTTTATAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACC
Found at i:1962 original size:156 final size:156
Alignment explanation
Indices: 1678--1972 Score: 446
Period size: 156 Copynumber: 1.9 Consensus size: 156
1668 TGGAAGGAAG
* * * * ** *
1678 TGAAGGGTTCTTCAAGACATTTGCAACATTGTGAATGAAAGAGCAGTGGCACAAGGGAAGGTAGT
1 TGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAACAGCAGCACAAAGGAAGGTAGT
* * *
1743 TAACACAAAAATGTTTCGTTCTAATTGTAGTAGCAAATATTAGGCGATCACTAATTGCTCTTTGT
66 TAACAAAAAAATGTTTCGTTCTAATTGTAGTAACAAATATTAGGCAATCACTAATTGCTCTTTGT
1808 GTCTTTTTCTTGTACAAACCAATCAC
131 GTCTTTTTCTTGTACAAACCAATCAC
* * *
1834 TGAAGAGTTCTTCAAGGCATTGGCGACATTGTCAATGAACGAACAGCAGCACAAAGGAAGGTAGT
1 TGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAACAGCAGCACAAAGGAAGGTAGT
* *
1899 TAACAAAAAAATGTTTCGTTTTAATTGTAGTAACAAATATTAGGCAATCTCTAATTGCTCTTTGT
66 TAACAAAAAAATGTTTCGTTCTAATTGTAGTAACAAATATTAGGCAATCACTAATTGCTCTTTGT
*
1964 GTTTTTTTC
131 GTCTTTTTC
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
156 123 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (156 bp):
TGAAGAGTTCTTCAAGACATTGGCAACATTGTCAATGAAAGAACAGCAGCACAAAGGAAGGTAGT
TAACAAAAAAATGTTTCGTTCTAATTGTAGTAACAAATATTAGGCAATCACTAATTGCTCTTTGT
GTCTTTTTCTTGTACAAACCAATCAC
Done.