Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011211.1 Kokia drynarioides strain JFW-HI SEQ_126189, 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: 3397
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:754 original size:17 final size:17
Alignment explanation
Indices: 733--815 Score: 112
Period size: 17 Copynumber: 4.8 Consensus size: 17
723 TTTTAGCTGT
*
733 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
750 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
768 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
785 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
802 ATTTAAATTTAAAA
1 ATTTAAATTTAAAA
816 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 42 0.75
18 14 0.25
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:779 original size:6 final size:6
Alignment explanation
Indices: 733--814 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
723 TTTTAGCTGT
* * *
733 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
780 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
815 ANNNNNNNNN
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 1 0.02
5 13 0.22
6 41 0.68
7 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:790 original size:11 final size:11
Alignment explanation
Indices: 752--810 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
742 TATAATAATT
752 TTAAATTTGAAA
1 TTAAATTT-AAA
*
764 ATAAATTTAAA
1 TTAAATTTAAA
775 CTTAAA-TTAAA
1 -TTAAATTTAAA
*
786 TTTAAATTCAAA
1 -TTAAATTTAAA
*
798 ATAAATTTAAA
1 TTAAATTTAAA
809 TT
1 TT
811 TAAAANNNNN
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 23 0.61
12 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:879 original size:6 final size:6
Alignment explanation
Indices: 868--948 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
858 NNNNNNNNAA
* * * *
868 TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAAA ATAAAT TTAAAATT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAA-T
* * *
917 TTAAA- -CAAAT TTAATT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
949 GGGAATTTGG
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
4 3 0.05
5 7 0.13
6 36 0.65
7 6 0.11
8 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:905 original size:18 final size:17
Alignment explanation
Indices: 869--948 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
859 NNNNNNNAAT
*
869 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
886 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
*
904 TAAATTTAAAATTTTAAA
1 TAAATTT-AAATTTAAAA
* *
922 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
939 TAAATTTAAA
1 TAAATTTAAA
949 GGGAATTTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
17 28 0.52
18 20 0.37
19 6 0.11
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:933 original size:35 final size:36
Alignment explanation
Indices: 869--948 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 36
859 NNNNNNNAAT
*
869 TAAATTT-AAATTCAAAATAAATTTAAATTTAAAAA
1 TAAATTTAAAATTCAAAACAAATTTAAATTTAAAAA
** *
904 TAAATTTAAAATTTTAAACAAATTT-AATTTTAAAA
1 TAAATTTAAAATTCAAAACAAATTTAAATTTAAAAA
939 TAAATTTAAA
1 TAAATTTAAA
949 GGGAATTTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 26 0.65
36 14 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (36 bp):
TAAATTTAAAATTCAAAACAAATTTAAATTTAAAAA
Found at i:934 original size:16 final size:17
Alignment explanation
Indices: 870--947 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
860 NNNNNNAATT
* * *
870 AAATTTAAATTCAAAAT
1 AAATTTAATTTTAAAAC
* *
887 AAATTTAAATTTAAAAAT
1 AAATTT-AATTTTAAAAC
905 AAATTTAAAATTTT-AAAC
1 AAATTT--AATTTTAAAAC
*
923 AAATTTAATTTTAAAAT
1 AAATTTAATTTTAAAAC
940 AAATTTAA
1 AAATTTAA
948 AGGGAATTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
16 6 0.11
17 17 0.32
18 24 0.45
19 6 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTTAATTTTAAAAC
Found at i:1749 original size:198 final size:198
Alignment explanation
Indices: 1185--2220 Score: 1375
Period size: 198 Copynumber: 5.2 Consensus size: 198
1175 GTTTTATTGA
* ** * * * ** *
1185 TTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATTGCATCGTTTGTTTCAATTTGCTTCTTT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
* * *
1250 ATACCTCATCAGGAATAC-GAGTTTGGT-TCACTTCTCAGTATCTCATCAGGAAGCTAACCTTGT
66 ATATCTCATCAGGAAGACGGA-TTTGGTCT-ACTTCTCCGTATCTCATCAGGAAGCTAA---T-T
* * * * * * * * *
1313 ATTGTTTTGAC-CTGCTTTTCAGTATCTTCTTTAGGAAGCTGGGGGTTCAAAGATTTTG-T-TTG
125 A---CTTCGACAC-GCTTCTCAGTATC-TCATCAGGGAGCT-GTGGTTCGAAGA-TTTGCTCATG
* * ***
1375 CTTTGAGCGTGGGTTCAA
183 --TCGAGCATGGGTTTGG
* * * ** * *
1393 TTTGGTCTTCCTCTCAATATCTCATTTAGGAAGATGACCGCGTCATTTGTTT-TATCCGCTTCTC
1 TTTGGTCTTCTTCTCAGTATCTCA-TCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTC
*
1457 TGTATCTCATCAGGAAGACGGATTTGGTCTA------C---T-TCATCAGGAAGCTAATTACTTC
65 TATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTC
1512 GACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGT
130 GACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGT
1577 TTGG
195 TTGG
* *
1581 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCATTTCAATCTGCTTCTCT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
*
1646 ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTTCTTCG
66 ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCG
* * *
1711 ACTCGCTTCTCAGTATCTCATCAAGGAGCTGTGGTTCGAAGATTTGCTCATGTCTAGCATGGGTT
131 ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
1776 TGG
196 TGG
** *
1779 TTTCTTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
*
1844 ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTAGTTCG
66 ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCG
1909 ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
131 ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
1974 TGG
196 TGG
*
1977 TTTGGTCTTCTTCTCAGTATTTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
* * * *
2042 GTATCTCATCTGGAAGACGGATTTGGTCTACTTCTCCTTATCTCATCAGAAAGCTAATTACTTCG
66 ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCG
2107 ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
131 ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
2172 TGG
196 TGG
2175 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTT
2221 TTGTGGGTAT
Statistics
Matches: 747, Mismatches: 64, Indels: 44
0.87 0.07 0.05
Matches are distributed among these distances:
187 22 0.03
188 77 0.10
189 11 0.01
190 12 0.02
191 17 0.02
192 1 0.00
194 3 0.00
195 1 0.00
197 1 0.00
198 524 0.70
199 1 0.00
208 52 0.07
209 25 0.03
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (198 bp):
TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCT
ATATCTCATCAGGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCG
ACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTT
TGG
Found at i:3103 original size:21 final size:21
Alignment explanation
Indices: 3077--3118 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3067 CCGAGTCTAA
3077 ATTGACGGGGTTGTACAGCTC
1 ATTGACGGGGTTGTACAGCTC
3098 ATTGACGGGGTTGTACAGCTC
1 ATTGACGGGGTTGTACAGCTC
3119 CTTGCCGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (21 bp):
ATTGACGGGGTTGTACAGCTC
Done.