Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010638.1 Kokia drynarioides strain JFW-HI SEQ_125578, 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: 7199
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:456 original size:156 final size:155
Alignment explanation
Indices: 271--577 Score: 587
Period size: 156 Copynumber: 2.0 Consensus size: 155
261 CCAAAATTTT
*
271 CAATCAGGTCCTTCTCTTACTTTTTATTATTTTAAAATGCACCAGGGGCTGCCACGTGTCATTCT
1 CAATCAGGTCCTTCTCTTACTTTTAATTATTTTAAAATGCACCAGGGGCTGCCACGTGTCATTCT
336 TTAGGTTTATTTTTACGATCGATCCCTTTTCTTTTTAATTTGTTTTAATTTAATCCTTAAATCAA
66 TTAGGTTTATTTTTACGATCGATCCCTTTTCTTTTTAATTTGTTTTAATTTAATCCTTAAATCAA
401 GTTTTTTTAATTACGAAATTAGCCC
131 GTTTTTTTAATTACGAAATTAGCCC
426 NCAATCAGGTCCTTCTCTTACTTTTAATTATTTTAAAATGCACCAGGGGCTGCCACGTGTCATTC
1 -CAATCAGGTCCTTCTCTTACTTTTAATTATTTTAAAATGCACCAGGGGCTGCCACGTGTCATTC
*
491 TTTAGGTTTATTTTTACGATCGGTCCCTTTTCTTTTTAATTTGTTTTAATTTAATCCTTAAATCA
65 TTTAGGTTTATTTTTACGATCGATCCCTTTTCTTTTTAATTTGTTTTAATTTAATCCTTAAATCA
556 AGTTTTTTTAATTACGAAATTA
130 AGTTTTTTTAATTACGAAATTA
578 ACCCAAAAAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 149 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (155 bp):
CAATCAGGTCCTTCTCTTACTTTTAATTATTTTAAAATGCACCAGGGGCTGCCACGTGTCATTCT
TTAGGTTTATTTTTACGATCGATCCCTTTTCTTTTTAATTTGTTTTAATTTAATCCTTAAATCAA
GTTTTTTTAATTACGAAATTAGCCC
Found at i:735 original size:30 final size:29
Alignment explanation
Indices: 688--823 Score: 164
Period size: 29 Copynumber: 4.6 Consensus size: 29
678 CCCTAAATTG
*
688 TCCAAAAATCTCATTTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
* *
717 CCCAAAAGATCCCATTTTTACCCCCAAAACT
1 TCCAAAA-ATCCCATTTTTACCCCC-GAACT
*
748 TCCAAAAATCCCATTTTTACCCCTGAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
* ** *
777 TCCAAAAATCCTATTTTTACCTTCAAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
**
806 TTTAAAAATCCCATTTTT
1 TCCAAAAATCCCATTTTT
824 GACCTCTTAT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 49 0.54
30 32 0.35
31 10 0.11
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.33
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTACCCCCGAACT
Found at i:1289 original size:95 final size:95
Alignment explanation
Indices: 1118--1297 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 95
1108 ATTTTAAAAA
* * *
1118 AATCGAGGCAATGTTTCCTTTACTTTGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGAATT
1 AATCGAGGCAATGTTTCCTTTACTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGAACT
*
1183 TTTTTCAAATCGAAATAATCAAACACCCTT
66 TTCTTCAAATCGAAATAATCAAACACCCTT
* *
1213 AATCGAGGCAATGTTTCC-TTATCTTCGA--TTCTGAATA-TTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATGTTTCCTTTA-CTTCGAGTTTC-GAAAATTTGCGCCTTAACTCACTAGGTG-A
* *
1274 ACCTTTCTTCGAATCGAGATAATC
63 A-CTTTCTTCAAATCGAAATAATC
1298 GAATATCCTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
93 23 0.32
94 9 0.12
95 41 0.56
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (95 bp):
AATCGAGGCAATGTTTCCTTTACTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGAACT
TTCTTCAAATCGAAATAATCAAACACCCTT
Found at i:3748 original size:28 final size:27
Alignment explanation
Indices: 3716--3817 Score: 73
Period size: 28 Copynumber: 3.6 Consensus size: 27
3706 ACCCAGGGGC
*
3716 AAAATGGTAATTTTTGACACTCGAGGGT
1 AAAATGGTAATTTTTGA-AATCGAGGGT
* *
3744 AAAATGATAATTTTGGAAAAATCGA-GGT
1 AAAATGGTAATTTTTG--AAATCGAGGGT
* *
3772 CAAAAATGG-AATTTTTTGAAGTTCGGGGGT
1 --AAAATGGTAA-TTTTTGAA-ATCGAGGGT
*
3802 AAAAGGGTAATTTTTG
1 AAAATGGTAATTTTTG
3818 GAAAAATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
28 31 0.53
29 12 0.21
30 15 0.26
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.32
Consensus pattern (27 bp):
AAAATGGTAATTTTTGAAATCGAGGGT
Found at i:3805 original size:29 final size:28
Alignment explanation
Indices: 3773--4050 Score: 138
Period size: 29 Copynumber: 9.5 Consensus size: 28
3763 AATCGAGGTC
*
3773 AAAAATGGAATTTTTTGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTC-GGGGT
* * **
3802 -AAAAGGGTAATTTTTGGAAAAATT-AAGGT
1 AAAAATGG-AATTTTTGG--AAGTTCGGGGT
*
3831 AAAAAATGGAATTCTTGGAAGTTCGGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGT
** *
3860 --AAATGGTAATTTTTGGAGAAATCGAGGT
1 AAAAATGG-AATTTTTGGA-AGTTCGGGGT
* * *
3888 CAAAAAATTAGAATTTTTAGAAGTTTGGGGGT
1 --AAAAA-TGGAATTTTTGGAAG-TTCGGGGT
* * *
3920 -AAAATAGTAATTTTTGGAAAAATT-AGGGT
1 AAAAAT-GGAATTTTTGG--AAGTTCGGGGT
* *
3949 CAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGT
* * **
3978 AAAAATGTAATTTTTGAGAA-ATCAAGGT
1 AAAAATGGAATTTTTG-GAAGTTCGGGGT
*
4006 CAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAG-TTCGGGGT
*
4036 AAAAATGTAATTTTT
1 AAAAATGGAATTTTT
4051 TTATAGTTGA
Statistics
Matches: 185, Mismatches: 40, Indels: 48
0.68 0.15 0.18
Matches are distributed among these distances:
26 6 0.03
27 11 0.06
28 27 0.15
29 87 0.47
30 22 0.12
31 13 0.07
32 17 0.09
33 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:3852 original size:59 final size:59
Alignment explanation
Indices: 3740--4050 Score: 348
Period size: 58 Copynumber: 5.3 Consensus size: 59
3730 TGACACTCGA
* * * * **
3740 GGGTAAAATGATAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTTGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTTGGAAGTTTAG
* * * *
3798 GGGTAAAAGGGTAATTTTTGGAAAAATTAAGGTAAAAAATGGAATTCTTGGAAG-TTCG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTTGGAAGTTTAG
* * * * *
3856 GGGT-AAATGGTAATTTTTGGAGAAATCGAGGTCAAAAAATTAGAATTTTTAGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGT-AAAAAA-TGGAATTTTTGGAAGTTTAG
* * * *
3916 GGGTAAAATAGTAATTTTTGGAAAAATTAGGGT-CAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTTGGAAGTTTAG
* *
3974 GGGTAAAAAT-GTAATTTTT-GAGAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTTGGAAGTTTAG
4032 GGGTAAAAAT-GTAATTTTT
1 GGGT-AAAATGGTAATTTTT
4051 TTATAGTTGA
Statistics
Matches: 216, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
57 34 0.16
58 97 0.45
59 55 0.25
60 7 0.03
61 23 0.11
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTTGGAAGTTTAG
Done.