Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014276.1 Kokia drynarioides strain JFW-HI SEQ_129309, 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: 5191
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.25
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1163 original size:27 final size:27
Alignment explanation
Indices: 1124--1183 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1114 AACTTTCAAC
*
1124 TAATGATTGTTTC-CTTTGATCCTCTTTT
1 TAAT-ATTGTTTCTC-TTGATCCTCTTCT
1152 TAATATTGTTTCTCTTGATCCTCTTCT
1 TAATATTGTTTCTCTTGATCCTCTTCT
1179 TAATA
1 TAATA
1184 AAATTTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (27 bp):
TAATATTGTTTCTCTTGATCCTCTTCT
Found at i:2499 original size:204 final size:206
Alignment explanation
Indices: 1672--2638 Score: 1151
Period size: 206 Copynumber: 4.7 Consensus size: 206
1662 ACAAATGACA
* ** * *
1672 CGGTCATCTT-CCTAGTGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCAAAGCGAGCAA
1 CGGTCATCTTCCCGA-TGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAA
* * * * * *
1736 AATCTTCGAACCCCAGCGTCTTGATGAGACATCGAGAAGCAGGTCGAAGCAGTAAATGGTTAGCT
65 AATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAATAAACGGTTAGCT
* * * *
1801 TCCACATGAGATACTGAGGAGTGAACCAAATTCACCTTCCTGTTGAGATACAGAGAAGCGGATTG
130 TCCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTG
*
1866 AAACAAGTGATG
195 AAACAAGCGATG
* *
1878 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAATCCCACGCTCAAAGCGAGTAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAAA
* *
1943 ATCTTCGAACCCCAGTTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAGTAAACGGTTAGCTT
66 ATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAATAAACGGTTAGCTT
*
2008 CCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCTTGATGAGATACAGAGAAGCGGATTGA
131 CCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGA
2073 AACAAGCGATG
196 AACAAGCGATG
*
2084 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAAGTGAGTAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAAA
* *
2149 ATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTT
66 ATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAATAAACGGTTAGCTT
* * *
2214 CCAGATGAGATACTGAGGAGTGAACCAAATTCGTCTCCCTGATGAGATACAGAGAAGCGGATTGA
131 CCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGA
*
2279 AACAAGCAATG
196 AACAAGCGATG
* * * * * * * *
2290 TGGTCATCTTTCTGATGAGATACTGAGGAGAAGACCAAACCAAACCCACACAC-GA-TGAGT-AA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAAA
* * ** * ** *
2352 ACCTCCGAACCCCAGCTTCCTGAAAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGATAGC-
66 ATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAAT-AAACGGTTAGCT
* * * * * * *
2416 TCTCTGATGAGATATTAAGGAGAGAACCAAATTCGTCTTCCTGATGAGATGCAGAGAAACGAATT
130 TC-CAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATT
* *
2481 GAAACAAACGACG
194 GAAACAAGCGATG
* * * * * * * * * * *
2494 TGGTCATC-TCTCTGATGAGACATTGAGGAGAAGTCCAAATTAAACCCACGCGC-GA-TGAAT-G
1 CGGTCATCTTC-CCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAA
* * * ** * * ** **
2555 AATCTTCAAACCCCAGCTTTCGGATGAGGTACTGAGAAGCAGGTTGAAGTAATAAAACGGCCATA
65 AATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAAT-AAACGGTTAGC
2620 TTCCAGATGAGATACTAAG
129 TTCCAGATGAGATACTAAG
2639 AAGAAAACCA
Statistics
Matches: 673, Mismatches: 83, Indels: 12
0.88 0.11 0.02
Matches are distributed among these distances:
203 48 0.07
204 193 0.29
205 3 0.00
206 426 0.63
207 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (206 bp):
CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGTGAGTAAA
ATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGTAATAAACGGTTAGCTT
CCAGATGAGATACTAAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGA
AACAAGCGATG
Found at i:2900 original size:6 final size:6
Alignment explanation
Indices: 2889--2958 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
2879 CTGGGCCTTT
* *
2889 TTTAAA TTTAAA TTT-AA TTTAAT TTTGAA TTTAAA -TT-AA TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
* *
2935 TTTAAA TTTAAA TTCAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
2959 AGTCCAAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 41 0.77
7 3 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:2919 original size:17 final size:17
Alignment explanation
Indices: 2889--2945 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
2879 CTGGGCCTTT
*
2889 TTTAAATTTAAATTTAA
1 TTTAATTTTAAATTTAA
*
2906 TTTAATTTTGAATTTAA
1 TTTAATTTTAAATTTAA
* *
2923 ATTAATCTTAAATTTAAA
1 TTTAATTTTAAATTT-AA
2941 TTTAA
1 TTTAA
2946 ATTCAAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 27 0.82
18 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAATTTTAAATTTAA
Found at i:2919 original size:23 final size:24
Alignment explanation
Indices: 2888--2948 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
2878 ACTGGGCCTT
2888 TTTTAAATTTAAATTTAAT-TTAA
1 TTTTAAATTTAAATTTAATCTTAA
*
2911 TTTTGAATTTAAA-TTAATCTTAA
1 TTTTAAATTTAAATTTAATCTTAA
*
2934 ATTTAAATTTAAATT
1 TTTTAAATTTAAATT
2949 CAAAGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.15
23 27 0.82
24 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTAAATTTAAATTTAATCTTAA
Found at i:3643 original size:3 final size:3
Alignment explanation
Indices: 3637--3675 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3627 AATATTTTTT
3637 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
3676 TGATTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3681 original size:12 final size:13
Alignment explanation
Indices: 3637--3685 Score: 68
Period size: 12 Copynumber: 4.0 Consensus size: 13
3627 AATATTTTTT
3637 TAATAA-TAATAA
1 TAATAATTAATAA
3649 TAATAA-TAATAA
1 TAATAATTAATAA
3661 TAATAATTAATAA
1 TAATAATTAATAA
*
3674 T-ATGATTAATAA
1 TAATAATTAATAA
3686 AAGAAAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 28 0.80
13 7 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:4950 original size:30 final size:29
Alignment explanation
Indices: 4854--5145 Score: 186
Period size: 29 Copynumber: 9.9 Consensus size: 29
4844 CCCTAAGCTG
*
4854 TCCAAAAATTCTATTTTTAGCCCCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
4883 TCCAAAAATTCCATTTTTAGCCCCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* * *
4912 T-CAAAAAATCTCGTTTTTAACCCCGAAACT
1 TCCAAAAATTC-CATTTTTAGCCCCG-AACT
* **
4942 TCCCAAAATTCCATTTTTAGCCTTGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACT
* *
4971 TCCAAAAATTCCATTTTT-GACTCTGAAACT
1 TCCAAAAATTCCATTTTTAG-CCCCG-AACT
* *
5001 TCCTAAAATTACCA-TTTTA-CCCCTGGA-T
1 TCCAAAAATT-CCATTTTTAGCCCC-GAACT
* * **
5029 GTCCAAAAACTT-CATTTTCAACTTCGAAACT
1 -TCCAAAAA-TTCCATTTTTAGCCCCG-AACT
* * * *
5060 TTCTAAAATTACCA-TTTTACCCCCGGA-T
1 TCCAAAAATT-CCATTTTTAGCCCCGAACT
* * * *
5088 GTCCAAAAACTCCATTTTCAACCTCGTAACT
1 -TCCAAAAATTCCATTTTTAGCCCCG-AACT
* *
5119 TCCTAAAATTACCATTTTTACCCCCGA
1 TCCAAAAATT-CCATTTTTAGCCCCGA
5146 GACTCCGAAA
Statistics
Matches: 201, Mismatches: 41, Indels: 41
0.71 0.14 0.14
Matches are distributed among these distances:
28 16 0.08
29 98 0.49
30 61 0.30
31 26 0.13
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTAGCCCCGAACT
Found at i:4957 original size:59 final size:59
Alignment explanation
Indices: 4857--5145 Score: 207
Period size: 59 Copynumber: 4.9 Consensus size: 59
4847 TAAGCTGTCC
* *
4857 AAAAATTCTATTTTTAGCCCCG-AACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCA
1 AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCA
* * ** *
4915 AAAAA-TCTCGTTTTTAACCCCGAAACTTCCCAAAATTCCATTTTTAGCCTTGAACTTCC
1 AAAAATTC-CATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCA
* * * * *
4974 AAAAATTCCATTTTTGACTCTGAAACTTCCTAAAATTACCA-TTTTA-CCCCTGGA-TGTCCA
1 AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATT-CCATTTTTAGCCCC-GAACT-T-CA
* * ** * * * * *
5034 AAAACTT-CATTTTCAACTTCGAAACTTTCTAAAATTACCA-TTTTACCCCCGGA-TGTCC
1 AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATT-CCATTTTTAGCCCCGAACT-TCA
* * * * * *
5092 AAAAACTCCATTTTCAACCTCGTAACTTCCTAAAATTACCATTTTTACCCCCGA
1 AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATT-CCATTTTTAGCCCCGA
5146 GACTCCGAAA
Statistics
Matches: 192, Mismatches: 29, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.01
58 25 0.13
59 138 0.72
60 27 0.14
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCA
Done.