Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003321.1 Kokia drynarioides strain JFW-HI SEQ_116016, 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: 1701
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Found at i:946 original size:201 final size:201
Alignment explanation
Indices: 387--1135 Score: 1042
Period size: 201 Copynumber: 3.7 Consensus size: 201
377 CAAGCGATGT
* *
387 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAACCAACTCGAGGCTCAATGCGAGCAAAT
1 GGTCATCTTCCTGATGAGATAC--AG-AGAAGA--ATACCAACTCGAGGCTCAATGCGAGCAAAT
*
452 CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAATGGTTAGCTTC
61 CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTC
* * *
517 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTAAA
126 CTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAAAGAAGCGGATTGAA
*
582 ACAAGTAAGGT
191 ACAAGTAAGGC
* * ** * * * **
593 GGTCATCCTCTTGATGAGATATTGAGAAGAAGACCAAATCAAACCT-ACA--CGAGCAAATCTT-
1 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCA-ATGCGAGCAAATCTTC
* * * ** * * *
654 TAAACCTAGTTTCCTGATGAGATACTGAGGAGCAGGGCGAAGCAATAAAATGGTTAGCTTTCTGA
65 GAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCCTGA
719 TGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGAT-ATGATACAAAGAAGCGGATTGAAACA
130 TGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGA-GATACAAAGAAGCGGATTGAAACA
*
783 AATAAGGC
194 AGTAAGGC
791 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCG
* * *
856 AACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGCAAAGTAATAAAATGGTTAGCTTCCTGAT
66 AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCCTGAT
* * * * *
921 GAGATACTGAGAAGTGGATCAAATTTTTCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAAG
131 GAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAG
986 TAAGGC
196 TAAGGC
*
992 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCA
1 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCG
* * * * *
1057 AACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAAT-AAATAGTTAGCTTCTTGTT
66 AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCCTGAT
1121 GAGATACTGAGAAGT
131 GAGATACTGAGAAGT
1136 AGGTTGAAGC
Statistics
Matches: 481, Mismatches: 55, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
197 1 0.00
198 161 0.33
199 13 0.03
200 44 0.09
201 236 0.49
202 1 0.00
203 5 0.01
204 1 0.00
206 19 0.04
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (201 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCG
AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCCTGAT
GAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAG
TAAGGC
Found at i:1176 original size:47 final size:47
Alignment explanation
Indices: 1065--1179 Score: 167
Period size: 47 Copynumber: 2.4 Consensus size: 47
1055 CAAACCCCAA
* *
1065 CTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAATAGTTAG
1 CTTCCTGTTGAGATACTGAGAAGCAGGTCAAAGCAATAAATAGTTAG
* * **
1112 CTTCTTGTTGAGATACTGAGAAGTAGGTTGAAGCAATAAATAGTTAG
1 CTTCCTGTTGAGATACTGAGAAGCAGGTCAAAGCAATAAATAGTTAG
*
1159 CTTCCTGTTGAAATACTGAGA
1 CTTCCTGTTGAGATACTGAGA
1180 TGTGAACCGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (47 bp):
CTTCCTGTTGAGATACTGAGAAGCAGGTCAAAGCAATAAATAGTTAG
Found at i:1199 original size:399 final size:394
Alignment explanation
Indices: 388--1135 Score: 1018
Period size: 399 Copynumber: 1.9 Consensus size: 394
378 AAGCGATGTG
*
388 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAACCAACTCGAGGCTCAATGCGAGCAAATC
1 GTCATCTTCCTGATGAGATAC--AG-AGAAGA-CAAACCAACTCGAGGCTCAATGCGAGCAAATC
*
453 TTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAATGGTTAGCTTCC
62 TTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCC
518 TGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTAAAA
127 TGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTAAAA
* * **
583 CAAGTAAGGTGGTCATCCTCTTGATGAGATATTGAGAAGAAGACCAAATCAAACCTACACGAGCA
192 CAAGTAAGGCGGTCATCCTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCTACACGAGCA
* * ** * * * *
648 AATCTTTAAACCTAGTTTCCTGATGAGATACTGAGGAGCAGGGCGAAGCAATAAAATGGTTAGCT
257 AATCTTCAAACCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAATAGTTAGCT
*
713 TTCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATATGATACAAAGAAGCGGATTG
322 TTCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATATGATACAAAGAAGCAGATTG
778 AAACAAAT
387 AAACAAAT
*
786 AAGGCGGTCATCTTCCTGATGAGATACAGAGAAGA-ATACCAACTCGAGGCTCAATGCGAGCAAA
1 ------GTCATCTTCCTGATGAGATACAGAGAAGACAAACCAACTCGAGGCTCAATGCGAGCAAA
* * *
850 TCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGCAAAGTAATAAAATGGTTAGCTT
60 TCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTT
* ** * * * * *
915 CCTGATGAGATACTGAGAAGTGGATCAAATTTTTCTTCTTGATGAGATACAGAGAAGTGGATTGA
125 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTAA
* * * * **
980 AACAAGTAAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCT-CAATGC
190 AACAAGTAAGGCGGTCATCCTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCTAC-A--C
*
1044 GAGCAAATCTTCAAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAAT-AAATAG
252 GAGCAAATCTTCAAA-CCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAATAG
*
1108 TTAGC-TTCTTGTTGAGATACTGAGAAGT
316 TTAGCTTTC-TGATGAGATACTGAGAAGT
1136 AGGTTGAAGC
Statistics
Matches: 305, Mismatches: 34, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
398 1 0.00
399 195 0.64
400 3 0.01
401 48 0.16
402 37 0.12
404 21 0.07
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (394 bp):
GTCATCTTCCTGATGAGATACAGAGAAGACAAACCAACTCGAGGCTCAATGCGAGCAAATCTTCG
AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAATGGTTAGCTTCCTGAT
GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGGATTAAAACAAG
TAAGGCGGTCATCCTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCTACACGAGCAAATC
TTCAAACCCAACTTCCTGATGAGATACTAAGAAGCAGGGCAAAGCAATAAAATAGTTAGCTTTCT
GATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATATGATACAAAGAAGCAGATTGAAAC
AAAT
Found at i:1634 original size:18 final size:18
Alignment explanation
Indices: 1602--1671 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 18
1592 GGCCCAATAG
1602 AATTGAAATTT-TTTTAAA
1 AATT-AAATTTATTTTAAA
1620 AATTAAATTTATTTT-AA
1 AATTAAATTTATTTTAAA
** *
1637 GTTTAAATTTA-CTTAAA
1 AATTAAATTTATTTTAAA
* *
1654 ATTTAAATTTATTATAAA
1 AATTAAATTTATTTTAAA
1672 TTTGAGTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 29 0.67
18 12 0.28
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAAATTTATTTTAAA
Found at i:1647 original size:6 final size:6
Alignment explanation
Indices: 1622--1696 Score: 52
Period size: 6 Copynumber: 13.2 Consensus size: 6
1612 TTTTTAAAAA
* * * *
1622 TTAAAT TT-ATT TTAAGT TTAAAT TT-ACT TAAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
1666 TATAAAT TT-GAG TTAAAT TTAAAT TTAAAT T
1 T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
1697 AATGT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
4 3 0.06
5 11 0.21
6 35 0.67
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:1664 original size:17 final size:16
Alignment explanation
Indices: 1615--1674 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
1605 TGAAATTTTT
*
1615 TTAAAAATTAAATTTA
1 TTAAAATTTAAATTTA
* *
1631 TTTTAAGTTTAAATTTA
1 -TTAAAATTTAAATTTA
1648 CTTAAAATTTAAATTTA
1 -TTAAAATTTAAATTTA
1665 TTATAAATTT
1 TTA-AAATTT
1675 GAGTTAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.08
17 33 0.92
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAAATTTAAATTTA
Found at i:1698 original size:17 final size:17
Alignment explanation
Indices: 1622--1698 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
1612 TTTTTAAAAA
* * *
1622 TTAAATTTATTTTAAGT
1 TTAAATTAAATTTAAAT
* * *
1639 TTAAATTTACTTAAAAT
1 TTAAATTAAATTTAAAT
*
1656 TTAAATT-TATTATAAAT
1 TTAAATTAAATT-TAAAT
* *
1673 TTGAGTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
1690 TTAAATTAA
1 TTAAATTAA
1699 TGT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 2 0.04
17 42 0.89
18 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Done.