Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010955.1 Kokia drynarioides strain JFW-HI SEQ_125923, 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: 9280
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:491 original size:29 final size:29
Alignment explanation
Indices: 419--677 Score: 238
Period size: 29 Copynumber: 8.8 Consensus size: 29
409 TCTTCGAACA
* *
419 TTCGAGGGT-AAAAGGGTATTTTTTGGAAG
1 TTCGAGGGTAAAAATGG-AATTTTTGGAAG
* * * *
448 TTTTGAGGTTAAAAATGGGATTATTGGAAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAG
* *
478 CTCGAGGGTAAAAACGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
** * * *
507 TTTTAGGGTCAAAATGGTATTATTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
536 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
* * *
565 TTTC-ATGGTCAAAAATGGGATTTTTGGAAA
1 -TTCGAGGGT-AAAAATGGAATTTTTGGAAG
*
595 TT-TAGGGGTAAAAATGGAATTTTTGGATAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGA-AG
* * * *
625 TT-TAGGGGTCAAAATGGGATTATTGGAAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGAAG
654 TTCGAGGGTAAAAATGGAATTTTT
1 TTCGAGGGTAAAAATGGAATTTTT
678 AGATAGTTTA
Statistics
Matches: 185, Mismatches: 37, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
29 113 0.61
30 66 0.36
31 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAG
Found at i:544 original size:58 final size:58
Alignment explanation
Indices: 419--690 Score: 336
Period size: 59 Copynumber: 4.6 Consensus size: 58
409 TCTTCGAACA
* * * *
419 TTCGAGGGT-AAAAGGGTATTTTTTGGAAGTTTTGAGGTTAAAAATGGGATTATTGGAAG
1 TTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTT-AGGGTCAAAATGGGATTATTGGAAG
* * *
478 CTCGAGGGTAAAAACGGAATTTTTGGAAGTTTTAGGGTCAAAATGGTATTATTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAATGGGATTATTGGAAG
* * * *
536 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCATGGTCAAAAATGGGATTTTTGGAAA
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC-AAAATGGGATTATTGGAAG
*
595 TT-TAGGGGTAAAAATGGAATTTTTGGATAG-TTTAGGGGTCAAAATGGGATTATTGGAAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGA-AGTTTTA-GGGTCAAAATGGGATTATTGGAAG
*
654 TTCGAGGGTAAAAATGGAATTTTTAGATAG-TTTAGGG
1 TTCGAGGGTAAAAATGGAATTTTTGGA-AGTTTTAGGG
691 ACCTCTGGGG
Statistics
Matches: 187, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
58 61 0.33
59 113 0.60
60 13 0.07
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAATGGGATTATTGGAAG
Found at i:1850 original size:3 final size:3
Alignment explanation
Indices: 1807--1832 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1797 TCATTAATGC
1807 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1833 AAACAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2510 original size:17 final size:16
Alignment explanation
Indices: 2484--2524 Score: 73
Period size: 17 Copynumber: 2.5 Consensus size: 16
2474 TTTAATTTTG
2484 AAATTAAATTTAAAAT
1 AAATTAAATTTAAAAT
2500 AAATCTAAATTTAAAAT
1 AAAT-TAAATTTAAAAT
2517 AAATTAAA
1 AAATTAAA
2525 AAGGGGACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTAAATTTAAAAT
Found at i:2971 original size:23 final size:22
Alignment explanation
Indices: 2941--2987 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
2931 TTTCCCTATA
*
2941 TTTCATCAGGAAGCTAACCTGTT
1 TTTCATCAAGAAGCTAACC-GTT
2964 TTTCATCAAGAAGCTAACCGTT
1 TTTCATCAAGAAGCTAACCGTT
2986 TT
1 TT
2988 ATTACTTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (22 bp):
TTTCATCAAGAAGCTAACCGTT
Found at i:3347 original size:206 final size:207
Alignment explanation
Indices: 2966--3471 Score: 651
Period size: 206 Copynumber: 2.4 Consensus size: 207
2956 AACCTGTTTT
* * *
2966 TCATCAAGAAGCTAACCGTTTTATTACTTGCTTCGACCAGCTTCTCGGTGTCTTATCAGGAAGCT
1 TCATCAGGAAGCTAACCG--TT-TTA-TTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCT
** ** * * * * *
3031 AAGGTTCGAAGATTACGCTTGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTTATC
62 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTCTGATTTGGTCTTCTTCTCAATACCTCATA
* * * * * * *
3096 AGGAAGATGACCGCATCTCTTGTTTCAATCCGCTTCTTTGTATCTCATCAGG-AGAATGAATTTG
127 AAGAAGATGACCGCATCGCCTATTTCAATCCGCTTCTCTGTATCTCACCAGGAAG-ACGAATTTG
3160 GTTCACTTCTCAGTATC
191 GTTCACTTCTCAGTATC
*
3177 TCATCAGGAAGCTAACCG-TTTATTGCTTCGACCTGCTTCTCGGTGCCTCATCAGGAAGCTGGGG
1 TCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGG
*
3241 TTC-AGAGATTTTGCTCGCTTTGAGCGTGGGTCTGATTTGGTCTTCTTCTCAATATCTCATAAAG
66 TTCGA-AGATTTTGCTCGCTTTGAGCGTGGGTCTGATTTGGTCTTCTTCTCAATACCTCATAAAG
* **
3305 AAGATGACTGCATCGCCTATTTCAATTTGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTTC
130 AAGATGACCGCATCGCCTATTTCAATCCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTTC
*
3370 ACTTCTTAGTATC
195 ACTTCTCAGTATC
* * * *
3383 TCATCAGGAAGCTAACCGTTTTATTGCTTCGATCTGCTTCTCGGTATCTCTTCAGGAAGCTGGGA
1 TCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGG
**
3448 TTCGAAGA-TTTGCTCATTTTGAGC
66 TTCGAAGATTTTGCTCGCTTTGAGC
3472 CTCGTTTGGG
Statistics
Matches: 259, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
205 1 0.00
206 187 0.72
207 52 0.20
208 2 0.01
211 17 0.07
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (207 bp):
TCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGG
TTCGAAGATTTTGCTCGCTTTGAGCGTGGGTCTGATTTGGTCTTCTTCTCAATACCTCATAAAGA
AGATGACCGCATCGCCTATTTCAATCCGCTTCTCTGTATCTCACCAGGAAGACGAATTTGGTTCA
CTTCTCAGTATC
Found at i:3533 original size:152 final size:152
Alignment explanation
Indices: 3334--3661 Score: 584
Period size: 152 Copynumber: 2.2 Consensus size: 152
3324 TTTCAATTTG
* * *
3334 CTTCTCTGTATCTCACCAGGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAAC
1 CTTCTCAGTGTCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
* *
3399 CGTTTTATTGCTTCGATCTGCTTCTCGGTATCTCTTCAGGAAGCTGGGATTCGAAGATTTGCTCA
66 CGTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCA
3464 TTTTGAGCCTCGTTTGGGTCTT
131 TTTTGAGCCTCGTTTGGGTCTT
3486 CTTCTCAGTGTCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCAGTGTCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
**
3551 CGTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTTG
66 CGTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCA
3616 TTTTGAGCCTCGTTTGGGTCTT
131 TTTTGAGCCTCGTTTGGGTCTT
*
3638 CTTCTCAGTGTCTCACCAAGAAGA
1 CTTCTCAGTGTCTCACCAGGAAGA
3662 TGATCACATC
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
152 168 1.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (152 bp):
CTTCTCAGTGTCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
CGTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCA
TTTTGAGCCTCGTTTGGGTCTT
Found at i:4180 original size:23 final size:23
Alignment explanation
Indices: 4154--4200 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4144 AGAATTCTAT
*
4154 TAAAAAAGGATCAAAGGAAACAA
1 TAAAAAAGGATCAAAGAAAACAA
*
4177 TAAAAGAGGATCAAAGAAAACAA
1 TAAAAAAGGATCAAAGAAAACAA
4200 T
1 T
4201 CACTAGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.17, T:0.11
Consensus pattern (23 bp):
TAAAAAAGGATCAAAGAAAACAA
Done.