Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014027.1 Kokia drynarioides strain JFW-HI SEQ_129058, 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: 10300
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.28
Warning! 388 characters in sequence are not A, C, G, or T
Found at i:770 original size:6 final size:6
Alignment explanation
Indices: 749--826 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
739 TTTAAATTGG
** ** **
749 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
798 TTTAAA TTTAAA TTT-AA -TCAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
827 GGATTTAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 41 0.77
8 4 0.08
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2735 original size:59 final size:59
Alignment explanation
Indices: 2625--2822 Score: 238
Period size: 59 Copynumber: 3.4 Consensus size: 59
2615 AGAGGTCCCT
* * **
2625 AAACTATCCAAAAATTACATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTGACCTAA
1 AAACT-TCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
* * * *
2684 AAACTTTTGAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
* * * * * *
2743 AAACTTCCAAAAATTCCATTTTTACCC-CTAAAGTTCTAAAAATTCAATTTTTAACCCCA
1 AAACTTCTAAAAATTACATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTAACCCCA
2802 AAACTTCTAAAAATTACATTT
1 AAACTTCTAAAAATTACATTT
2823 ATCATTATTT
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 29 0.24
59 90 0.76
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:2750 original size:30 final size:29
Alignment explanation
Indices: 2625--2822 Score: 195
Period size: 30 Copynumber: 6.7 Consensus size: 29
2615 AGAGGTCCCT
*
2625 AAACTATCCAAAAATTACATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCC-CG
***
2656 -AACTTCC-AAAATTCCATTTTTGACCTAA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
***
2684 AAACTTTTGAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
2714 -AACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
2743 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* * * *
2772 AAAGTTCTAAAAATTCAATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
2802 AAACTTCTAAAAATTACATTT
1 AAACTTCCAAAAATTCCATTT
2823 ATCATTATTT
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
28 13 0.09
29 60 0.43
30 67 0.48
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:3822 original size:29 final size:29
Alignment explanation
Indices: 3784--4041 Score: 209
Period size: 30 Copynumber: 8.7 Consensus size: 29
3774 GAGGTCCCTA
3784 AACTATCCAAAAATTACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCCTCG
*
3814 AACTTCC-AAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
*** *
3842 AAACTTTTGAATATTACATTTTTACCCTCG
1 -AACTTCCAAAAATTACATTTTTACCCTCG
* **
3872 AACTTCCAAAAATTCCATTTTTACCCCTAA
1 AACTTCCAAAAATTACATTTTTA-CCCTCG
*
3902 AACTTCCAAAAATTCCATTTTTACCC-CAG
1 AACTTCCAAAAATTACATTTTTACCCTC-G
* * * * **
3931 AAGTTCTAAAAATTCAAATTTTGACCCTAA
1 AACTTCCAAAAATT-ACATTTTTACCCTCG
* * *
3961 AACTTCTAAAAATTATATTTTTACCCCCG
1 AACTTCCAAAAATTACATTTTTACCCTCG
* * *
3990 AACCTCCAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
*
4019 AAACTTTCAAAAATTACCATTTT
1 -AACTTCCAAAAATTA-CATTTT
4042 GCCTTCTATT
Statistics
Matches: 181, Mismatches: 36, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
28 18 0.10
29 74 0.41
30 83 0.46
31 6 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:3893 original size:59 final size:60
Alignment explanation
Indices: 3783--4041 Score: 289
Period size: 59 Copynumber: 4.4 Consensus size: 60
3773 AGAGGTCCCT
* *
3783 AAACTATCCAAAAATTACATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTGACCTC-G
1 AAACT-TCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCTA
* * * *
3842 AAACTTTTGAATATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-ACCCCTA
1 AAACTTCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCTA
* * * * * *
3901 AAACTTCCAAAAATTCCATTTTTACCC-CAGAAGTTCTAAAAATTCAAATTTTGACC-CTA
1 AAACTTCTAAAAATTACATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCTCTA
* * * *
3960 AAACTTCTAAAAATTATATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGACCT-TG
1 AAACTTCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCTA
4019 AAACTT-TCAAAAATTACCATTTT
1 AAACTTCT-AAAAATTA-CATTTT
4042 GCCTTCTATT
Statistics
Matches: 167, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
58 34 0.20
59 124 0.74
60 9 0.05
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
AAACTTCTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCTA
Found at i:4131 original size:28 final size:28
Alignment explanation
Indices: 4099--4160 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
4089 TCAAATTTTC
*
4099 CCAAAGTTACCATTTTGCCCCCGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
* * *
4127 CCAAAATTACCATTTTTCCCTCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
4155 CCAAAA
1 CCAAAA
4161 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.31, G:0.10, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:4168 original size:28 final size:28
Alignment explanation
Indices: 4101--4170 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
4091 AAATTTTCCC
4101 AAAGTTACCATTTTGCCCCCGAGAATCCA
1 AAAG-TACCATTTTGCCCCCGAGAATCCA
* * * *
4130 AAATTACCATTTTTCCCTCGAGTATCCA
1 AAAGTACCATTTTGCCCCCGAGAATCCA
4158 AAAGT-CTCATTTT
1 AAAGTAC-CATTTT
4171 CGACTCCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.03
28 31 0.89
29 3 0.09
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (28 bp):
AAAGTACCATTTTGCCCCCGAGAATCCA
Found at i:8582 original size:22 final size:21
Alignment explanation
Indices: 8541--8583 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
8531 CCTAGACAAA
*
8541 TAGAGGAAAAATTCATGCGAT
1 TAGAGGAAAAATTCACGCGAT
8562 TAGAGGAGAAAA-TCGACGCGAT
1 TAGAGGA-AAAATTC-ACGCGAT
8584 GCAAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.19
Consensus pattern (21 bp):
TAGAGGAAAAATTCACGCGAT
Done.