Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011736.1 Kokia drynarioides strain JFW-HI SEQ_126730, 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: 20923
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:137 original size:38 final size:38
Alignment explanation
Indices: 95--207 Score: 102
Period size: 41 Copynumber: 2.9 Consensus size: 38
85 TCTACCCTCT
*
95 GATTAGGGTAAGAGATTGGATACTTCAATCTGCCTTCA
1 GATTAGGGTAAAAGATTGGATACTTCAATCTGCCTTCA
* * * * *
133 GATTAAGGTAAAAGCTTTGGTGTGTCTTCAATCTGCCCTT-T
1 GATTAGGGTAAAAG-ATTGG-AT-ACTTCAATCTG-CCTTCA
* **
174 GATTAGTGTAAAAGATTGGATGTTTCAATCTGCC
1 GATTAGGGTAAAAGATTGGATACTTCAATCTGCC
208 CCATGATCGG
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
37 2 0.03
38 21 0.36
39 5 0.08
40 5 0.08
41 22 0.37
42 4 0.07
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (38 bp):
GATTAGGGTAAAAGATTGGATACTTCAATCTGCCTTCA
Found at i:222 original size:79 final size:78
Alignment explanation
Indices: 1--230 Score: 225
Period size: 79 Copynumber: 2.9 Consensus size: 78
* * *
1 TTCAATCTACCC-CATGA-TCGAGGTAAGAGATTGGATGGTCCTCAATCTG-CCCATGATCGGGA
1 TTCAATCTACCCTC-TGATTAG-GGTAAGAGATTGGAT-GT-TTCAATCTGCCCCATGATCGGGG
*
63 TAAGAGATTGGTGTGTC
62 TAAAAGATTGGTGTGTC
* ** * ***
80 TTTAATCTACCCTCTGATTAGGGTAAGAGATTGGATACTTCAATCTGCCTTCA-GATTAAGGTAA
1 TTCAATCTACCCTCTGATTAGGGTAAGAGATTGGATGTTTCAATCTGCC-CCATGATCGGGGTAA
*
144 AAGCTTTGGTGTGTC
65 AAG-ATTGGTGTGTC
* * * * *
159 TTCAATCTGCCCTTTGATTAGTGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCGGGGTAAG
1 TTCAATCTACCCTCTGATTAGGGTAAGAGATTGGATGTTTCAATCTGCCCCATGATCGGGGTAAA
224 AGATTGG
66 AGATTGG
231 GTGACAGCTT
Statistics
Matches: 120, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
77 8 0.07
78 16 0.13
79 93 0.77
80 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (78 bp):
TTCAATCTACCCTCTGATTAGGGTAAGAGATTGGATGTTTCAATCTGCCCCATGATCGGGGTAAA
AGATTGGTGTGTC
Found at i:228 original size:38 final size:39
Alignment explanation
Indices: 1--230 Score: 168
Period size: 38 Copynumber: 5.9 Consensus size: 39
*
1 TTCAATCTACCCCATGATC-GAGGTAAGAGATTGGATGGTC
1 TTCAATCTGCCCCATGATCAG-GGTAAGAGATTGGAT-GTC
* *
41 CTCAATCTG-CCCATGATC-GGGATAAGAGATTGGTGTGTC
1 TTCAATCTGCCCCATGATCAGGG-TAAGAGATTGG-ATGTC
* * * *
80 TTTAATCTACCCTC-TGATTAGGGTAAGAGATTGGAT-AC
1 TTCAATCTGCCC-CATGATCAGGGTAAGAGATTGGATGTC
* * * * * *
118 TTCAATCTGCCTTCA-GATTAAGGTAAAAGCTTTGGTGTGTC
1 TTCAATCTGCC-CCATGATCAGGGTAAGAG-ATTGG-ATGTC
** * * *
159 TTCAATCTGCCCTTTGATTAGTGTAAAAGATTGGATGT-
1 TTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGTC
*
197 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
1 TTCAATCTGCCCCATGATCAGGGTAAGAGATTGG
231 GTGACAGCTT
Statistics
Matches: 149, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
38 53 0.36
39 38 0.26
40 30 0.20
41 28 0.19
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (39 bp):
TTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGTC
Found at i:561 original size:49 final size:49
Alignment explanation
Indices: 449--1081 Score: 285
Period size: 49 Copynumber: 12.9 Consensus size: 49
439 TGTTTTTTCT
* * * * * **
449 CATCTTCAAGGTATAAGATTCGCCGTTGCGACCTCAATCTTTTCCTTTTA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAA-CCTTTCCCTCCA
* * *
499 CACCTTTAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* * * **
548 CATCTTTAAGGTATAAGATTCGTCATTGCAGCTTCAGTCTTTCCCAT-CA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCCA
* * * * * * ** *
597 AATATTTATGGTATAAGGTTCGTCGGTGCGATTTCAACCTTTCCCTCAA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* ** * * * * * *
646 TATCTCCATGGTACAAGATTCACCGTTGTGGCTTTAATCTTTCCCAT-CA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCCA
* * * * * * ** * *
695 -TTTTTCTAAAGTATAAGGTTCACCATTGTAGCCTCAACCTTTCCCACCA
1 CATCTT-TAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* ** * * * **
744 TATCTCCATGGTACAAGATTCGTCGTTGCGGCTTCAGTCTTTCCCAT-CA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCCA
* * *
793 CAT-TTCTATGGTATAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCA
1 CATCTT-TAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* * * * * **
842 TATCTTCAAGGTATAAGATTCGTCGTTGTGACTTCAATATTT--C-CCA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* * * *
888 TCATATTTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCA
1 -CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* ** * * * * * * *
938 TATCTCCATGGTACAAGATTAGCTGTTACAGCTTCAATCTTTCCCAT-CA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCC-TCCA
** * * * * * ** *
987 TGTCTCTAAGATACAAGGTTTGCCGTTGCAACTTTAACCTTTCCCTCCA
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
* * * * ** * * *
1036 TATCTTTAGGGTGTTAGATTTTCCATTGCAGCTTCAATCTTTCCCT
1 CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCT
1082 TCAAACCTGT
Statistics
Matches: 425, Mismatches: 142, Indels: 33
0.71 0.24 0.05
Matches are distributed among these distances:
46 3 0.01
47 32 0.08
48 6 0.01
49 343 0.81
50 41 0.10
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (49 bp):
CATCTTTAAGGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCA
Found at i:637 original size:98 final size:99
Alignment explanation
Indices: 503--1040 Score: 524
Period size: 98 Copynumber: 5.5 Consensus size: 99
493 CTTTTACACC
* ** * *
503 TTTAAGGTATAAGGTTCACCGTTGCG-GCTTCAACCTTTCCCTCCACATCTTTAAGGTATAAGAT
1 TTTAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
* *
567 TCGTCATTGCAGCTTCAGTCTTTCCCATCAAATA
66 TCGTCGTTGCAGCTTCAATCTTTCCCATCAAATA
* ** * * *
601 TTTATGGTATAAGGTTCGTCGGTGCGA-TTTCAACCTTTCCCTCAATATCTCCATGGTACAAGAT
1 TTTAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
** ** * * *
665 TCACCGTTGTGGCTTTAATCTTTCCCATC-ATTT
66 TCGTCGTTGCAGCTTCAATCTTTCCCATCAAATA
* * * * *
698 TTCTAAAGTATAAGGTTCACCATTG-TAGCCTCAACCTTTCCCACCATATCTCCATGGTACAAGA
1 TT-TAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
* * *
762 TTCGTCGTTGCGGCTTCAGTCTTTCCCATCACAT-
65 TTCGTCGTTGCAGCTTCAATCTTTCCCATCAAATA
* * * * * *
796 TTCTATGGTATAAGGTTCGCCATTGCG-GCTTCAACCTTTCCCTCCATATCTTCAAGGTATAAGA
1 TT-TAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
* *
860 TTCGTCGTTG-TGACTTCAATATTTCCCATC--ATA
65 TTCGTCGTTGCAG-CTTCAATCTTTCCCATCAAATA
893 TTTAAGGTATAAGGTTCACCGTTGC-AGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
1 TTTAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
* * ** *
957 TAG-CTGTTACAGCTTCAATCTTTCCCATCATGTC
66 TCGTC-GTTGCAGCTTCAATCTTTCCCATCAAATA
* * * ** * *
991 TCTAAGATACAAGGTTTGCCGTTGC-AACTTTAACCTTTCCCTCCATATCT
1 TTTAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCT
1041 TTAGGGTGTT
Statistics
Matches: 359, Mismatches: 69, Indels: 24
0.79 0.15 0.05
Matches are distributed among these distances:
95 1 0.00
96 78 0.22
97 9 0.03
98 270 0.75
99 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (99 bp):
TTTAAGGTATAAGGTTCACCGTTGCGAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
TCGTCGTTGCAGCTTCAATCTTTCCCATCAAATA
Found at i:862 original size:196 final size:194
Alignment explanation
Indices: 503--1041 Score: 650
Period size: 196 Copynumber: 2.8 Consensus size: 194
493 CTTTTACACC
* * * ** * *
503 TTTAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCACATCTTTAAGGTATAAGATT
1 TTTAAAGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATT
* * * *
568 CGTCATTGCAGCTTCAGTCTTTCCCATCAAATATT-TATGGTATAAGGTTCGTCGGTGCGATTTC
66 CGTCGTTGCAGCTTCAGTCTTTCCCATCAAAT-TTCTATGGTATAAGGTTCGCCGTTGCGACTTC
* * * * * *
632 AACCTTTCCCTCAATATCTCCATGGTACAAGATTCACCGTTGTGGCTTTAATCTTTCCCATCATT
130 AACCTTTCCCTCCATATCTTCAAGGTACAAGATTCACCGTTGTGACTTCAATATTTCCCATCA-T
*
697 T
194 A
* * * *
698 TTCTAAAGTATAAGGTTCACCATTGTAGCCTCAACCTTTCCCACCATATCTCCATGGTACAAGAT
1 TT-TAAAGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGAT
* * * *
763 TCGTCGTTGCGGCTTCAGTCTTTCCCATCACATTTCTATGGTATAAGGTTCGCCATTGCGGCTTC
65 TCGTCGTTGCAGCTTCAGTCTTTCCCATCAAATTTCTATGGTATAAGGTTCGCCGTTGCGACTTC
* **
828 AACCTTTCCCTCCATATCTTCAAGGTATAAGATTCGTCGTTGTGACTTCAATATTTCCCATCATA
130 AACCTTTCCCTCCATATCTTCAAGGTACAAGATTCACCGTTGTGACTTCAATATTTCCCATCATA
*
893 TTTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATT
1 TTTAAAGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATT
* * * ** * * * * * * *
958 AG-CTGTTACAGCTTCAATCTTTCCCATCATGTCTCTAAGATACAAGGTTTGCCGTTGCAACTTT
66 CGTC-GTTGCAGCTTCAGTCTTTCCCATCAAATTTCTATGGTATAAGGTTCGCCGTTGCGACTTC
1022 AACCTTTCCCTCCATATCTT
130 AACCTTTCCCTCCATATCTT
1042 TAGGGTGTTA
Statistics
Matches: 292, Mismatches: 49, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
193 1 0.00
194 125 0.43
195 7 0.02
196 159 0.54
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (194 bp):
TTTAAAGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATT
CGTCGTTGCAGCTTCAGTCTTTCCCATCAAATTTCTATGGTATAAGGTTCGCCGTTGCGACTTCA
ACCTTTCCCTCCATATCTTCAAGGTACAAGATTCACCGTTGTGACTTCAATATTTCCCATCATA
Found at i:1678 original size:112 final size:112
Alignment explanation
Indices: 1489--1691 Score: 255
Period size: 112 Copynumber: 1.8 Consensus size: 112
1479 ACTAATCATC
* * * *
1489 ATTTCAATGCAAAAATGCTTGCACAGGGTTGTAAGATGGATAAAATTGAATTTTATTAGAGGCAA
1 ATTTCAATACAAAAATGCTTGAACAAGGTTGTAAGATGGATAAAATTAAATTTTATTAGAGGCAA
** *
1554 AGCTCGTGTGAATTAAAAGAATAAAAATCATTAGTCCACTAACTGTT
66 AGCTCGCATGAATGAAAAGAATAAAAATCATTAGTCCACTAACTGTT
** * **
1601 ATTTCAATACAAACGTGCTTGAACAAGGTTGTAA-AGTGGATAAAATTAAATTTTATTGGAGGTG
1 ATTTCAATACAAAAATGCTTGAACAAGGTTGTAAGA-TGGATAAAATTAAATTTTATTAGAGGCA
* * *
1665 AATCTTGCATGAATGAAAAGATTAAAA
65 AAGCTCGCATGAATGAAAAGAATAAAA
1692 TGACAAACAT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
111 1 0.01
112 74 0.99
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (112 bp):
ATTTCAATACAAAAATGCTTGAACAAGGTTGTAAGATGGATAAAATTAAATTTTATTAGAGGCAA
AGCTCGCATGAATGAAAAGAATAAAAATCATTAGTCCACTAACTGTT
Found at i:2848 original size:5 final size:5
Alignment explanation
Indices: 2838--2877 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
2828 TTTTCTTCCT
2838 TTTTC TTTTC TTCTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTT
2878 TTTAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:8422 original size:18 final size:18
Alignment explanation
Indices: 8399--8435 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8389 CGAAATAAGG
*
8399 AAATAAAAAAAATATATA
1 AAATAAAAAAAATAAATA
*
8417 AAATAAAATAAATAAATA
1 AAATAAAAAAAATAAATA
8435 A
1 A
8436 CTATATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAAAAAAATAAATA
Found at i:8426 original size:14 final size:13
Alignment explanation
Indices: 8399--8432 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
8389 CGAAATAAGG
8399 AAATAAAAAAAAT
1 AAATAAAAAAAAT
*
8412 ATATAAAATAAAAT
1 AAATAAAA-AAAAT
8426 AAATAAA
1 AAATAAA
8433 TAACTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:19540 original size:26 final size:26
Alignment explanation
Indices: 19509--19708 Score: 193
Period size: 26 Copynumber: 7.7 Consensus size: 26
19499 TAACACAGTA
* *
19509 CCTGCTAAATATTCACCAGCTCGAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
* * * * *
19535 CTTGCTAAATGATCATCGGCTTGAGG
1 CCTGCTAAATAATCACCGGCTCGAAG
* * * *
19561 CTTGCTAAATAATCACTGGATCAAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
* *
19587 CCTGCTAAATAATCACTGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
* **
19613 CTTGCTAAATAATCACTAGCTCGAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
* *
19639 CCTACTAAATAACCACCGGCTCGAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
* * *
19665 CCAGCTAAATAATCATCGGCTTGAAG
1 CCTGCTAAATAATCACCGGCTCGAAG
*
19691 ACTGCTAAAATAATCACC
1 CCTGCT-AAATAATCACC
19709 TCACATTTTC
Statistics
Matches: 141, Mismatches: 32, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
26 131 0.93
27 10 0.07
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (26 bp):
CCTGCTAAATAATCACCGGCTCGAAG
Found at i:19830 original size:3 final size:3
Alignment explanation
Indices: 19822--19872 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19812 ATAAACACAG
19822 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19870 ATA
1 ATA
19873 TGAACTTACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.