Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005107.1 Kokia drynarioides strain JFW-HI SEQ_118930, 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: 8876
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:3572 original size:25 final size:25
Alignment explanation
Indices: 3508--3572 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
3498 AAAAGCACAT
* **
3508 AAATATTTAAACATAATTTTTTTCA
1 AAATATTTAAACATAATTCTTTAAA
*
3533 ATA-ATTTAAACATAATTCTTTAAA
1 AAATATTTAAACATAATTCTTTAAA
*
3557 AAATATTTAAATATAA
1 AAATATTTAAACATAA
3573 AACATATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATATTTAAACATAATTCTTTAAA
Found at i:6147 original size:154 final size:155
Alignment explanation
Indices: 5633--6379 Score: 668
Period size: 159 Copynumber: 4.8 Consensus size: 155
5623 AACAACATAG
* ** * * * *
5633 TACTCGATAAAACAGAATGATC-AGAATAACTTGATCATGAATTATATCTAATATTGATGCAAAT
1 TACTCAATAAAACAGAACCATCTAG-ATAGCTTGATCATGAATTAAATCAAATATTCATGCAAAT
* * * * ** *
5697 AGATAACAATGAAGAAGGT-AAATCCTACTTCAAGCCCTCAAGGAAGTTTATCTTCTATCTTATG
65 AGATGACAATGAAGAAGATAAAATCCTATTTCAAGTCCTCAAACAAGTTTATCTTCTATCTTAAG
* **
5761 TGGACCCACGATTCAGGTACGCGTTTC
130 TGGACCCATGATT-AGGTACATGTTTC
* * *
5788 TACTCAATAAAAC-GAACCATCTAGATAGCTTGATGATGAATTAAAT-ATAATAGTCATGCAAAG
1 TACTCAATAAAACAGAACCATCTAGATAGCTTGATCATGAATTAAATCA-AATATTCATGCAAAT
* * *
5851 AGATGGCAATGAAGAAGGA-AAAAGCCTATTTCAAGTCCTGAAACAAGTTTATCTTCTTCTATCT
65 AGATGACAATGAAGAA-GATAAAATCCTATTTCAAGTCCTCAAACAAGTTTA---TCTTCTATCT
* * *
5915 TAAGTGGACTCATGATTAGGATACATGATTG
126 TAAGTGGACCCATGATTAGG-TACATGTTTC
* * * * * *
5946 TACTCAATTAAACAAAATCATC-CGACTAGCTTGATCATTAATAAAATCAAATATTCATGCAAAT
1 TACTCAATAAAACAGAACCATCTAGA-TAGCTTGATCATGAATTAAATCAAATATTCATGCAAAT
* * * * * *
6010 AGGTGACGATAAAGAAGATAAAATCCCATTTCAAGCCCTCAAACAAGTTTATC-T-TATCTTATG
65 AGATGACAATGAAGAAGATAAAATCCTATTTCAAGTCCTCAAACAAGTTTATCTTCTATCTTAAG
* * *
6073 TGGACCCATGATTCAAGTCCGTGTTTC
130 TGGACCCATGATT-AGGTACATGTTTC
* * * * * * *
6100 TACTCAATAAAACAGAACCATCTGGATAGCTTGGTAATGAATTAAATCTAATAGTCATGCGAAGA
1 TACTCAATAAAACAGAACCATCTAGATAGCTTGATCATGAATTAAATCAAATATTCATGCAAATA
*
6165 GATGACAATGAAGAAGGA-AAAAGCCTATTTCAAGTCCTCAAACAAGTTTATCTTCTTCTATCTT
66 GATGACAATGAAGAA-GATAAAATCCTATTTCAAGTCCTCAAACAAGTTTA---TCTTCTATCTT
*** **
6229 AAGTGGACTTGTGATTAGGGTACATGTTAG
127 AAGTGGACCCATGATTA-GGTACATGTTTC
* * * * * * * *
6259 TATTCGATAAAACGGAACCATCCAAATAGCTAGATCATGAATAAAAGCAAATATTCATGCAAATA
1 TACTCAATAAAACAGAACCATCTAGATAGCTTGATCATGAATTAAATCAAATATTCATGCAAATA
* ** * * *
6324 GGTGATGATGAAGAAGGT-AAATCCCCATTTCATGTCCTCAAACAAGTTTATCTTCT
66 GATGACAATGAAGAAGATAAAAT-CCTATTTCAAGTCCTCAAACAAGTTTATCTTCT
6380 TATATCTTAC
Statistics
Matches: 470, Mismatches: 99, Indels: 45
0.77 0.16 0.07
Matches are distributed among these distances:
154 168 0.36
155 47 0.10
156 8 0.02
157 5 0.01
158 52 0.11
159 189 0.40
160 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (155 bp):
TACTCAATAAAACAGAACCATCTAGATAGCTTGATCATGAATTAAATCAAATATTCATGCAAATA
GATGACAATGAAGAAGATAAAATCCTATTTCAAGTCCTCAAACAAGTTTATCTTCTATCTTAAGT
GGACCCATGATTAGGTACATGTTTC
Found at i:6230 original size:313 final size:311
Alignment explanation
Indices: 5630--6377 Score: 1005
Period size: 313 Copynumber: 2.4 Consensus size: 311
5620 TCCAACAACA
* * ** * * * * *
5630 TAGTACTCGATAAAACAGAATGAT-CAGAATAACTTGATCATGAATTATATCTAATATTGATGCA
1 TAGTACTCAATAAAACAAAACCATCCA-AATAGCTTGATCATGAATAAAATCAAATATTCATGCA
* * * * * **
5694 AATAGATAACAATGAAGAAGGTAAATCCTACTTCAAGCCCTCAAGGAAGTTTATCTTCTATCTTA
65 AATAGGTGACGATGAAGAAGGTAAATCCCATTTCAAGCCCTCAAACAAGTTTATC-T-TATCTTA
* *
5759 TGTGGACCCACGATTCAGGTACGCGTTTCTACTCAATAAAACGAACCATCTAGATAGCTTGATGA
128 TGTGGACCCACGATTCAAGTACGCGTTTCTACTCAATAAAACGAACCATCTAGATAGCTTGATAA
*
5824 TGAATTAAATATAATAGTCATGCAAAGAGATGGCAATGAAGAAGGAAAAAGCCTATTTCAAGTCC
193 TGAATTAAATATAATAGTCATGCAAAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCC
*
5889 TGAAACAAGTTTATCTTCTTCTATCTTAAGTGGACTCATGATTAGGATACATGAT
258 TCAAACAAGTTTATCTTCTTCTATCTTAAGTGGACTCATGATTAGGATACATG-T
* * * * *
5944 T-GTACTCAATTAAACAAAATCATCCGACTAGCTTGATCATTAATAAAATCAAATATTCATGCAA
1 TAGTACTCAATAAAACAAAACCATCCAAATAGCTTGATCATGAATAAAATCAAATATTCATGCAA
* *
6008 ATAGGTGACGATAAAGAAGATAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATG
66 ATAGGTGACGATGAAGAAGGT-AAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATG
* * * * *
6073 TGGACCCATGATTCAAGTCCGTGTTTCTACTCAATAAAACAGAACCATCTGGATAGCTTGGTAAT
130 TGGACCCACGATTCAAGTACGCGTTTCTACTCAATAAAAC-GAACCATCTAGATAGCTTGATAAT
* *
6138 GAATTAAATCTAATAGTCATGCGAAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCT
194 GAATTAAATATAATAGTCATGCAAAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCT
** *
6203 CAAACAAGTTTATCTTCTTCTATCTTAAGTGGACTTGTGATTAGGGTACATGT
259 CAAACAAGTTTATCTTCTTCTATCTTAAGTGGACTCATGATTAGGATACATGT
* * ** * *
6256 TAGTATTCGATAAAACGGAACCATCCAAATAGCTAGATCATGAATAAAAGCAAATATTCATGCAA
1 TAGTACTCAATAAAACAAAACCATCCAAATAGCTTGATCATGAATAAAATCAAATATTCATGCAA
* * *
6321 ATAGGTGATGATGAAGAAGGTAAATCCCCATTTCATGTCCTCAAACAAGTTTATCTT
66 ATAGGTGACGATGAAGAAGGTAAAT-CCCATTTCAAGCCCTCAAACAAGTTTATCTT
6378 CTTATATCTT
Statistics
Matches: 378, Mismatches: 51, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
312 51 0.13
313 296 0.78
314 31 0.08
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (311 bp):
TAGTACTCAATAAAACAAAACCATCCAAATAGCTTGATCATGAATAAAATCAAATATTCATGCAA
ATAGGTGACGATGAAGAAGGTAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGT
GGACCCACGATTCAAGTACGCGTTTCTACTCAATAAAACGAACCATCTAGATAGCTTGATAATGA
ATTAAATATAATAGTCATGCAAAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCA
AACAAGTTTATCTTCTTCTATCTTAAGTGGACTCATGATTAGGATACATGT
Done.