Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011147.1 Kokia drynarioides strain JFW-HI SEQ_126121, 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: 3196
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.40
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:533 original size:216 final size:215
Alignment explanation
Indices: 154--962 Score: 1005
Period size: 215 Copynumber: 3.8 Consensus size: 215
144 GCTCATATCA
* * *
154 GAACTTGTCAAACATTT-TTGAGTTCTTTTATAACTTTGGTT-TCTGAGAGTATTCAAGATGATC
1 GAACTTGTCAAACATTTACT-AGTTCTTTTATAACTTCGGTTCT-TGATAGTATTCAAGATGATC
* * * *
217 CATTCTTTCGACCAATTTTT-GAACATTCCAT-CTCGGGAAATCACGTCATTTGGTCTAAAA-AA
64 CATTCCTTCGACC-ATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAG
* *
279 TTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGTTTAT
128 TTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCT
*
344 CTCTCGGTTCTTGGACGAAGTGTC
193 CTCTCAGTTCTTGGACGAAGT-TC
* * *
368 GAACTTGTCAAACATATACTAGTTCTTTTATAACTTCAGTTCTTGATAGTATTAAAGATGATCCA
1 GAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCTTGATAGTATTCAAGATGATCCA
* * * *
433 TTCCTTCGACCGATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTTTAAAAT-GTT
66 TTCCTTCGACC-ATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTT
*
497 TGTCATTTTGTAAACAACTTTTGATCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
130 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
* *
562 CTCAGTTCTTGGATGAGGTTCC
195 CTCAGTTCTTGGACGAAGTT-C
* * * * * *
584 TAACTT-TCAAACATTTACTAGTTCTTTGATAACTTCGATTCCTAATAGTAGTCAAGATGATCCA
1 GAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCTTGATAGTATTCAAGATGATCCA
* * *
648 TTCCTTCGACTAATTTTTCGAACATTCCATGATCGAGAAATCGCATCATTTGGTC-AAAATAGTT
66 TTCCTTCGAC-CATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTT
* * * *
712 TGTCATTTTGTAAACAACTTTT-GTGCTTTGAATTAAACACTTTTTTATGAGAGAATTGTTTCCC
130 TGTCATTTTGTAAACAACTTTTGGT-CTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
* * * *
776 TTTTAGTTCTTGGACGAACATAC
194 TCTCAGTTCTTGGACGAA-GTTC
* * * * * *
799 AAACTAGT-AAAAATTTTACAAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACGATC
1 GAACTTGTCAAACA-TTTACTAGTTCTTTTATAACTTCGGTT-CTTGATAGTATTCAAGATGATC
* * * *
862 CAATCCTTTGAGCATTTTTCGAACATTCTATGCT-GAGAAATCACATCATTTGGTCT-AAATAGT
64 CATTCCTTCGACCATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGT
925 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
129 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
963 NNNNNNNNNN
Statistics
Matches: 520, Mismatches: 60, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
214 139 0.27
215 217 0.42
216 162 0.31
217 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (215 bp):
GAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCTTGATAGTATTCAAGATGATCCA
TTCCTTCGACCATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTTT
GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
TCAGTTCTTGGACGAAGTTC
Found at i:1025 original size:48 final size:48
Alignment explanation
Indices: 973--1127 Score: 238
Period size: 48 Copynumber: 3.2 Consensus size: 48
963 NNNNNNNNNN
* * * * *
973 AAATGCATCTTTGTTTAATAATCTGCATCATTAAGTGTTTTGTTTGTT
1 AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTT
* * *
1021 AAATGCATCTTTGTTTAGTAATTTGTATTATTAATTGTTTGGTTTGTT
1 AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTT
1069 AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTT
1 AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTT
1117 AAATGCATCTT
1 AAATGCATCTT
1128 CGTTAAATGC
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (48 bp):
AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTT
Found at i:1143 original size:96 final size:96
Alignment explanation
Indices: 973--1146 Score: 249
Period size: 96 Copynumber: 1.8 Consensus size: 96
963 NNNNNNNNNN
* * * *
973 AAATGCATCTTTGTTTAATAATCTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA
1 AAATGCATCTTTGTTTAATAATATGCATCATTAACTGTTTTGTTTGTTAAATGCATCTTCGTTAA
* *
1038 GTAATTTGTATTATTAATTGTTTGGTTTGTT
66 ATAACTTGTATTATTAATTGTTTGGTTTGTT
* * *
1069 AAATGCATCTTTGTTTAGTAATATGTATTATTAACTGTTTTGTTTGTTAAATGCATCTTCGTTAA
1 AAATGCATCTTTGTTTAATAATATGCATCATTAACTGTTTTGTTTGTTAAATGCATCTTCGTTAA
**
1134 ATGCCTTGTATTA
66 ATAACTTGTATTA
1147 ATGCATCAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (96 bp):
AAATGCATCTTTGTTTAATAATATGCATCATTAACTGTTTTGTTTGTTAAATGCATCTTCGTTAA
ATAACTTGTATTATTAATTGTTTGGTTTGTT
Found at i:2128 original size:214 final size:215
Alignment explanation
Indices: 1325--3196 Score: 1334
Period size: 215 Copynumber: 8.6 Consensus size: 215
1315 GCTCATATCA
* *** * * * *
1325 GAACTTGTCAAACATTTTTGAGTTCTTTTATAACTTTGGTTTCTGAGAGTATTCAAGATGATCCA
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
* * * * *
1390 TT-CTTTCGACCAATTTTTGAACATTCCAT-CTCGGGAAATCACGTCATTTGGTCTAAAAAATTT
66 TTCCTTT-GACCAATTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* *
1453 GTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGTTTATCTC
130 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
* * *
1518 TCGGTTCTTGGACGAA-GTGTC
195 TTGGTTCTTGGACGAACAT-AC
* * * * * *
1539 GAACTTGTCAAACATATACTAGTTCTTTTATAACTTCAGTT-CTTGATAGTATTAAAGATGATCC
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGATGATCC
* * * *
1603 ATTCCTTCGACCGATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTTTAAA-ATGT
65 ATTCCTTTGACC-AATTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA-GT
*
1667 TTGTCATTTTGTAAACAACTTTTGATCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
128 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
** * *** *
1732 TCTCAGTTCTTGGATGAGGTTCC
193 TCTTGGTTCTTGGACGAACATAC
* * * * * *
1755 TAACT-TTCAAACATTTACTAGTTCTTTGATAACTTCGATTCC-TAATAGTAGTCAAGATGATCC
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAA-AGTATTCAAGATGATCC
* * * *
1818 ATTCCTTCGACTAATTTTTCGAACATTCCATGATCGAGAAATCGCATCATTTGGTCAAAATAGTT
65 ATTCCTTTGACCAATTTTT-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTT
* * * *
1883 TGTCATTTTGTAAACAACTTTT-GTGCTTTGAATTAAACACTTTTTTATGAGAGAATTGTTTCCC
129 TGTCATTTTGTAAACAACTTTTGGT-CTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
* *
1947 TTTTAGTTCTTGGACGAACATAC
193 TCTTGGTTCTTGGACGAACATAC
* * *
1970 AAACTAGT-AAAAATTTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCC
1 GAACTAGTCAAACA-TTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCC
* * * *
2034 AATCCTTTGAGC-ATTTTTCGAACATTCTATGCT-GAGAAATCACATCATTTGGTCTAAATAGTT
65 ATTCCTTTGACCAATTTTT-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTT
*
2097 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAC-TTTTTACATGAGAATTGTTTCTCT
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
* * ** * *
2161 ATTGGTTCTTAGAATAACTTCC
194 CTTGGTTCTTGGACGAACATAC
* * ** * *
2183 GAACTCGTCAAACATTTACGAGTTCTTTTATAACTTCAATTCC-TAAGAGTATTAAAGATGGTCC
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAA-AGTATTCAAGATGATCC
** ** * * * * *
2247 ATTCCTTCAAAAAAATTTTGAACATTCTATGCTCAAGAAATTGCATCATTTGATCTAAATAGTTT
65 ATTCCTTTGACCAATTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
** * **
2312 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAATGCTTATTTACGTGAGAATTGTAACTCTC
130 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
* *
2377 TTGGTTATTGGATGAACATAC
195 TTGGTTCTTGGACGAACATAC
* * * * *
2398 GAACTAGTCAAACTTTTACAAGTCCTTTTATAACTTCGGTT-CTT-GAGAATT-AAGACGATCCA
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
* * * * * * * *
2460 TTCCTTTGACTTATTTTTTGATCCATTTC-T--TCGACCAATTTTTCG-AACATTCCATGATCGG
66 TTCCTTTGAC-CAATTTTTGA-ACATTCCATGCTCGA-GAA---ATCGCATCATT---TGGTC--
* * ** * * *
2521 GAAATCG--CATCATTTGGTCAAA-ATA-ATTT-GTCATTT---TGTAAACTACTTTTGGTCTTT
120 TAAATAGTTTGTCATTTTGT-AAACA-ACTTTTGGTC-TTTGAAT-TAAA-AAC--TT--T-TTT
** * * * * * * * * *
2578 GAATTAAAAACTTTTTTACATAAGATTTTTTTGTCTCTTGGCTCTTTGATGAAATTTC
175 -ACGTGAGAA-TTGTTT-C------TCTCTTGGT-TCTTGG-AC---GA--ACA-TAC
* ** * * ** *
2636 GAACCTA-TCAAACTTTTATGAGTTCTTTTATAACTTTGATTCCTTTAAAGTATTCAAGACAACC
1 GAA-CTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCC-TTAAAGTATTCAAGATGATC
* ** * ** * * *
2700 CCTTCCTTCAAGC-ATTCTTTCGAACATTCCATGCTTCG-GGTATCACATCATTT-GTTTAAAAA
64 CATTCCTTTGACCAATT-TTT-GAACATTCCATGC-TCGAGAAATCGCATCATTTGGTCTAAATA
* * * * **
2762 GTTTGTCATTTCGTAAAGAACTTTTGGTCTTTAAATTAAAAACTTGTTTACGTGAGAGCTGTTTC
126 GTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTC
** * *
2827 TCTCTTTCTTCTTGGATGAA-ATTC
191 TCTCTTGGTTCTTGGACGAACATAC
* * * * * * *
2851 TGAACTTGTCAAAAATTTACGAGTTCCTCTATAACATT-TGTTCCTGT-GAGTATTCAAGATGAT
1 -GAACTAGTCAAACATTTACAAGTTCTTTTATAAC-TTCGGTTCCT-TAAAGTATTCAAGATGAT
** * * *
2914 CCATTCCTTCAACCAATTTCTCGTAA-ATTCCATGATCGAGAAATCGCATCATTTGGTCTTAATA
63 CCATTCCTTTGACCAATTT-TTG-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * *
2978 GTTTGTCATTTTGGAAACAACTTTTGGTCTTTCAATTAAAAACTTTTTTACGTGTGAATTGTTTC
126 GTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTC
* * * * *
3043 TCCCTT-ATTCTTAGACGAACTTCC
191 TCTCTTGGTTCTTGGACGAACATAC
* ** * * * * *
3067 GAACTTGTCAAATTTTTACGAGTACTTTTATAACTTTGGTTCCTGAGAGTATTCAAGATGATCCA
1 GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
** * * *
3132 TTCCTTCAACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGACTAAAAAGTTT
66 TTCCTTTGACCAA-TTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
Statistics
Matches: 1313, Mismatches: 252, Indels: 185
0.75 0.14 0.11
Matches are distributed among these distances:
211 3 0.00
212 21 0.02
213 117 0.09
214 222 0.17
215 464 0.35
216 275 0.21
217 27 0.02
218 6 0.00
219 7 0.01
221 3 0.00
222 5 0.00
223 9 0.01
224 7 0.01
230 7 0.01
231 9 0.01
232 4 0.00
233 3 0.00
235 6 0.00
236 6 0.00
237 18 0.01
238 40 0.03
239 8 0.01
240 7 0.01
241 18 0.01
242 18 0.01
245 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (215 bp):
GAACTAGTCAAACATTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
TTCCTTTGACCAATTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCT
TGGTTCTTGGACGAACATAC
Found at i:2500 original size:25 final size:25
Alignment explanation
Indices: 2454--2502 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2444 GAATTAAGAC
* **
2454 GATCCATTCCTTTGACTTATTTTTT
1 GATCCATTCCTTCGACCAATTTTTT
*
2479 GATCCATTTCTTCGACCAATTTTT
1 GATCCATTCCTTCGACCAATTTTT
2503 CGAACATTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.51
Consensus pattern (25 bp):
GATCCATTCCTTCGACCAATTTTTT
Found at i:2983 original size:216 final size:215
Alignment explanation
Indices: 2478--3184 Score: 791
Period size: 216 Copynumber: 3.3 Consensus size: 215
2468 ACTTATTTTT
* * **
2478 TGATCCATTTCTTCGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCAAA
1 TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTTA
* * * * * * *
2543 ATAATTTGTCATTTTGTAAACTACTTTTGGTCTTTGAATTAAAAACTTTTTTACATAAGATTTTT
66 ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGT
* * * * * * *
2608 TTGTCTCTTGGC-TCTTTGATGAAATT-TCGAACCTATCAAACTTTTATGAGTTCTTTTATAACT
131 TTCTCTCTT-TCTTCTTAGATGAAATTCT-GAACTTGTCAAAATTTTACGAGTTCTTTTATAACT
* *
2671 TTGATTCCTTTAAAGTATTCAAGA
194 TTG-TTCCTGT-GAGTATTCAAGA
** * * * * * *
2695 CAACCCCTTCCTTCAAGC-ATTCTTTCGAACATTCCATGCTTCGGG-TATCACATCATTT-GT-T
1 TGATCCATTCCTTCAACCAATT-TTTCGAACATTCCATG-ATCGGGAAATCGCATCATTTGGTCT
* * * * **
2756 TAAAAAGTTTGTCATTTCGTAAAGAACTTTTGGTCTTTAAATTAAAAACTTGTTTACGTGAGAGC
64 T-AATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAAT
* * * *
2821 TGTTTCTCTCTTTCTTCTTGGATGAAATTCTGAACTTGTCAAAAATTTACGAGTTCCTCTATAAC
128 TGTTTCTCTCTTTCTTCTTAGATGAAATTCTGAACTTGTCAAAATTTTACGAGTTCTTTTATAAC
2886 ATTTGTTCCTGTGAGTATTCAAGA
193 -TTTGTTCCTGTGAGTATTCAAGA
* *
2910 TGATCCATTCCTTCAACCAATTTCTCGTAA-ATTCCATGATCGAGAAATCGCATCATTTGGTCTT
1 TGATCCATTCCTTCAACCAATTTTTCG-AACATTCCATGATCGGGAAATCGCATCATTTGGTCTT
* * *
2974 AATAGTTTGTCATTTTGGAAACAACTTTTGGTCTTTCAATTAAAAACTTTTTTACGTGTGAATTG
65 AATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTG
* * * * * * *
3039 TTTCTC-CCTTATTCTTAGACGAACTTCCGAACTTGTCAAATTTTTACGAGTACTTTTATAACTT
130 TTTCTCTCTTTCTTCTTAGATGAAATTCTGAACTTGTCAAAATTTTACGAGTTCTTTTATAACTT
*
3103 TGGTTCCTGAGAGTATTCAAGA
195 T-GTTCCTGTGAGTATTCAAGA
* *
3125 TGATCCATTCCTTCAACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGG
1 TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGG
3185 ACTAAAAAGT
Statistics
Matches: 406, Mismatches: 71, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
214 9 0.02
215 165 0.41
216 182 0.45
217 45 0.11
218 5 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (215 bp):
TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTTA
ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGT
TTCTCTCTTTCTTCTTAGATGAAATTCTGAACTTGTCAAAATTTTACGAGTTCTTTTATAACTTT
GTTCCTGTGAGTATTCAAGA
Done.