Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005166.1 Kokia drynarioides strain JFW-HI SEQ_119014, 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: 2087
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Found at i:697 original size:39 final size:39
Alignment explanation
Indices: 632--867 Score: 132
Period size: 39 Copynumber: 6.1 Consensus size: 39
622 GATAACTGCA
* * * * *
632 ATCTACCCCAGACTCGGGGTAGGAGATTGGTTGAT-GATG
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAG-TG
*
671 ATTTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
* * * ** ** * * **
710 ATCTGCCTCAGGCTTGAGGTAAAAGACCGAATGGTTGCA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
* * * *
749 ATCTGCCCCAGGCTCGGGGTAGGAGATTGGCTAATGGTG
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
* * * * ** * * **
788 ATCTACCCTAAGCTCGGGGTAAGAGATTGAATGGTTGCA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
* * * * *
827 ATCTACCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
866 AT
1 AT
868 GTAACTTCAC
Statistics
Matches: 146, Mismatches: 50, Indels: 2
0.74 0.25 0.01
Matches are distributed among these distances:
39 145 0.99
40 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTG
Found at i:809 original size:78 final size:78
Alignment explanation
Indices: 674--867 Score: 246
Period size: 78 Copynumber: 2.5 Consensus size: 78
664 GATGATGATT
* * * * *
674 TGCCCCAGGCTCGAGGTAAGAGATTGGCTGATAGTGATCTGCCTCAGGCTTGAGGTAAAAGACCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTCCCTCAAGCTCGAGGTAAAAGACCG
739 AATGGTTGCAATC
66 AATGGTTGCAATC
* * * * **
752 TGCCCCAGGCTCGGGGTAGGAGATTGGCTAATGGTGATCTACCCT-AAGCTCGGGGTAAGAGATT
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT-CCCTCAAGCTCGAGGTAAAAGACC
816 GAATGGTTGCAATC
65 GAATGGTTGCAATC
* * *
830 TACCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGAT
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGAT
868 GTAACTTCAC
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
78 96 0.97
79 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (78 bp):
TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTCCCTCAAGCTCGAGGTAAAAGACCG
AATGGTTGCAATC
Found at i:848 original size:117 final size:117
Alignment explanation
Indices: 628--848 Score: 253
Period size: 117 Copynumber: 1.9 Consensus size: 117
618 TTTAGATAAC
* * * * *
628 TGCAATCTACCCCAGACTCGGGGTAGGAGATTGGTTGATGATGATTTGCCCCAGGCTCGAGGTAA
1 TGCAATCTACCCCAGACTCGGGGTAGGAGATTGGCTAATGATGATCTACCCCAAGCTCGAGGTAA
** ** * * * *
693 GAGATTGGCTGATAGTGATCTGCCTCAGGCTTGAGGTAAAAGACCGAATGGT
66 GAGATTGAATGATAGCAATCTACCCCAAGCTCGAGGTAAAAGACCGAATGGT
* * * * *
745 TGCAATCTGCCCCAGGCTCGGGGTAGGAGATTGGCTAATGGTGATCTACCCTAAGCTCGGGGTAA
1 TGCAATCTACCCCAGACTCGGGGTAGGAGATTGGCTAATGATGATCTACCCCAAGCTCGAGGTAA
* * *
810 GAGATTGAATGGTTGCAATCTACCCCAAGCTCGGGGTAA
66 GAGATTGAATGATAGCAATCTACCCCAAGCTCGAGGTAA
849 GAGATTGGTT
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
117 83 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (117 bp):
TGCAATCTACCCCAGACTCGGGGTAGGAGATTGGCTAATGATGATCTACCCCAAGCTCGAGGTAA
GAGATTGAATGATAGCAATCTACCCCAAGCTCGAGGTAAAAGACCGAATGGT
Found at i:1216 original size:49 final size:50
Alignment explanation
Indices: 1163--1308 Score: 138
Period size: 49 Copynumber: 3.0 Consensus size: 50
1153 TATTGGATTA
1163 GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTC-GAGGTACAAGGTCC
1 GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTCTGAGGTACAAGGTCC
* * * ** * * * *
1212 GCCGTTGCGACTTAAA-CATTTCCCTTTTAT-ATCCCTGTGGTACTAGATTC
1 GCCGTTGCGGCTTAAATC-TTTCCC-TTCATGCTTTCTGAGGTACAAGGTCC
* **
1262 GTCGTTGCGGCTTAAATCTTTCTTTTCATGC-TTCTGAGGTACAAGGT
1 GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTCTGAGGTACAAGGT
1309 TTGCCATTGT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
48 1 0.01
49 38 0.53
50 32 0.44
51 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (50 bp):
GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTCTGAGGTACAAGGTCC
Found at i:1282 original size:99 final size:98
Alignment explanation
Indices: 1132--1404 Score: 298
Period size: 99 Copynumber: 2.8 Consensus size: 98
1122 AGTTGTAACC
* * * * *
1132 TTTCCCTTCATAT-CTTCGTGGTATTGGATTAGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
1 TTTCCCTTCATATCCCT-GTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
*
1196 -TCGAGGTACAAGGTCCGCCGTTGCGACTTAAACA
65 CT-GAGGTACAAGGTCCGCCATTGCGACTTAAACA
* **
1230 TTTCCCTTTTATATCCCTGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCTTTTCATGCTT
1 TTTCCC-TTCATATCCCTGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
** * *
1295 CTGAGGTACAAGGTTTGCCATTGTGACTTAAACC
65 CTGAGGTACAAGGTCCGCCATTGCGACTTAAACA
* * * * * * * ** *
1329 TTTCTCTTCATATCCTTGTGGTATTGGATTTGTCGTAGTGGCTTAAATCTCCCCCTTCATGGTTC
1 TTTCCCTTCATATCCCTGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTC
1394 TGAGGTACAAG
66 TGAGGTACAAG
1405 ATTCGTCGTT
Statistics
Matches: 146, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
98 64 0.44
99 79 0.54
100 3 0.02
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (98 bp):
TTTCCCTTCATATCCCTGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTC
TGAGGTACAAGGTCCGCCATTGCGACTTAAACA
Found at i:1388 original size:98 final size:98
Alignment explanation
Indices: 1128--1439 Score: 360
Period size: 98 Copynumber: 3.2 Consensus size: 98
1118 TTACAGTTGT
*
1128 AACCTTTCCCTTCATAT-CTTCGTGGTATTGGATTAGCCGTTGCGGCTTAAATCTTTCCCTTCAT
1 AACCTTTCCCTTCATATCCTT-GTGGTATTGGATTAGTCGTTGCGGCTTAAATCTTTCCCTTCAT
* *
1192 GCTT-TCGAGGTACAAGGTCCGCCGTTGCGACTTA
65 GCTTCT-GAGGTACAAGGTTCGCCGTTGTGACTTA
* * * * * * **
1226 AACATTTCCCTTTTATATCCCTGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCTTTTCAT
1 AACCTTTCCC-TTCATATCCTTGTGGTATTGGATTAGTCGTTGCGGCTTAAATCTTTCCCTTCAT
* *
1291 GCTTCTGAGGTACAAGGTTTGCCATTGTGACTTA
65 GCTTCTGAGGTACAAGGTTCGCCGTTGTGACTTA
* * * * **
1325 AACCTTTCTCTTCATATCCTTGTGGTATTGGATTTGTCGTAGTGGCTTAAATCTCCCCCTTCATG
1 AACCTTTCCCTTCATATCCTTGTGGTATTGGATTAGTCGTTGCGGCTTAAATCTTTCCCTTCATG
* * *
1390 GTTCTGAGGTACAAGATTCGTCGTTGTGAGC-TA
66 CTTCTGAGGTACAAGGTTCGCCGTTGTGA-CTTA
*
1423 AACCTTTCCCTCCATAT
1 AACCTTTCCCTTCATAT
1440 GGCTTAAACC
Statistics
Matches: 177, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
98 94 0.53
99 80 0.45
100 3 0.02
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (98 bp):
AACCTTTCCCTTCATATCCTTGTGGTATTGGATTAGTCGTTGCGGCTTAAATCTTTCCCTTCATG
CTTCTGAGGTACAAGGTTCGCCGTTGTGACTTA
Found at i:1535 original size:121 final size:121
Alignment explanation
Indices: 1321--1554 Score: 283
Period size: 121 Copynumber: 1.9 Consensus size: 121
1311 GCCATTGTGA
* * ** * *
1321 CTTAAACCTTTCTCTTCATATCCTTGTGGTATTGGATTTGTCGTAGTGGCTTAAATCTCCCCCTT
1 CTTAAACCTTTCCCTTCAAATCCTTGTGGTACCGGATTCGCCGTAGTGGCTTAAATCTCCCCCTT
* * * *
1386 CATGGTTCTGAGGTACAAGATTCGTCGTTGTGAGC-TAAACCTTTCCCTCCATATGG
66 CATGCTTCTGAGGTAAAAGATTCATCGTTGCGA-CTTAAACCTTTCCCTCCATATGG
* **
1442 CTTAAACCTTTCCCTTCAAAT-CTTCGTGGTACCGGATTCGCCGTTGTGGCTTAAATCTTTCCCT
1 CTTAAACCTTTCCCTTCAAATCCTT-GTGGTACCGGATTCGCCGTAGTGGCTTAAATCTCCCCCT
* * * *
1506 TTATGCTTCTGAGGTAAAAGGTTTATCGTTGCGACTTAAACTTTTCCCT
65 TCATGCTTCTGAGGTAAAAGATTCATCGTTGCGACTTAAACCTTTCCCT
1555 TCAAATCTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
120 4 0.04
121 90 0.96
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (121 bp):
CTTAAACCTTTCCCTTCAAATCCTTGTGGTACCGGATTCGCCGTAGTGGCTTAAATCTCCCCCTT
CATGCTTCTGAGGTAAAAGATTCATCGTTGCGACTTAAACCTTTCCCTCCATATGG
Found at i:1585 original size:49 final size:48
Alignment explanation
Indices: 1442--1604 Score: 154
Period size: 49 Copynumber: 3.3 Consensus size: 48
1432 CTCCATATGG
* * *
1442 CTTAAACCTTTCCCTTCAAATCTTCGTGGTACCGGATTCGCCGTTGTGG
1 CTTAAATCTTTCCCTTCAAATCTTC-TGGTACCGGATTCGCCGTTGCGA
* ** ***
1491 CTTAAATCTTTCCCTT--TATGCTTCTGAGGTAAAAGG-TTTATCGTTGCGA
1 CTTAAATCTTTCCCTTCAAAT-CTTCT--GGT-ACCGGATTCGCCGTTGCGA
1540 CTTAAA-CTTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGA
1 CTTAAATC-TTTCCCTTCAAATCTTC-TGGTACCGGATTCGCCGTTGCGA
1589 CTTAAATCTTTCCCTT
1 CTTAAATCTTTCCCTT
1605 TATGCTTCTG
Statistics
Matches: 89, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
47 3 0.03
48 8 0.09
49 67 0.75
50 8 0.09
51 3 0.03
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (48 bp):
CTTAAATCTTTCCCTTCAAATCTTCTGGTACCGGATTCGCCGTTGCGA
Found at i:1611 original size:98 final size:98
Alignment explanation
Indices: 1442--1652 Score: 350
Period size: 98 Copynumber: 2.2 Consensus size: 98
1432 CTCCATATGG
* * *
1442 CTTAAACCTTTCCCTTCAAATCTTCGTGGTACCGGATTCGCCGTTGTGGCTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGACTTAAATCTTTCCCTT
* *
1507 TATGCTTCTGAGGTAAAAGGTTTATCGTTGCGA
66 TATGCTTCTGAGGTAAAAGGTTCATCATTGCGA
*
1540 CTTAAACTTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGACTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGACTTAAATCTTTCCCTT
* *
1605 TATGCTTCTGAGGTACAAGGTTCGTCATTGCGA
66 TATGCTTCTGAGGTAAAAGGTTCATCATTGCGA
1638 CTTAAACCTTTCCCT
1 CTTAAACCTTTCCCT
1653 CTATATCTCC
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (98 bp):
CTTAAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGACTTAAATCTTTCCCTT
TATGCTTCTGAGGTAAAAGGTTCATCATTGCGA
Found at i:1620 original size:49 final size:48
Alignment explanation
Indices: 1469--1652 Score: 160
Period size: 49 Copynumber: 3.8 Consensus size: 48
1459 AAATCTTCGT
* * *
1469 GGTACCGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTTATGCTTCTGA
1 GGTACAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCTGA
* *** *
1518 GGTAAAAGGTTTATCGTTGCGACTTAAA-CTTTTCCCTTCAAAT-CTTC--A
1 GGT-ACAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTT--TATGCTTCTGA
*
1566 TGGTACCGGATTCGCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCTGA
1 -GGTACAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCTGA
* * *
1616 GGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
1 GGTAC-AGGTTCGCCGTTGCGACTTAAATCTTTCCCT
1653 CTATATCTCC
Statistics
Matches: 106, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
47 2 0.02
48 9 0.08
49 82 0.77
50 11 0.10
51 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (48 bp):
GGTACAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCTGA
Found at i:1646 original size:219 final size:219
Alignment explanation
Indices: 1248--1658 Score: 513
Period size: 219 Copynumber: 1.9 Consensus size: 219
1238 TTATATCCCT
* * * * *
1248 GTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCTTTTCATGCTTCTGAGGTACAAGGTTTGC
1 GTGGTACCAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTAAAAGGTTTAC
* * * * ** * * * *
1313 CATTGTGACTTAAACCTTTCTCTTCATATCCTTGTGGTATTGGATTTGTCGTAGTGGCTTAAATC
66 CATTGCGACTTAAACCTTTCCCTTCAAATCCTTATGGTACCGGATTCGCCGTAGCGACTTAAATC
* * *
1378 TCCCCCTTCATGGTTCTGAGGTACAAGATTCGTCGTTGTGAGCTAAACCTTTCCCTCCATATGGC
131 TCCCCCTTCATGCTTCTGAGGTACAAGATTCGTCATTGCGAGCTAAACCTTTCCCTCCATATGGC
1443 TTAAACCTTTCCCTTCAAATCTTC
196 TTAAACCTTTCCCTTCAAATCTTC
* *
1467 GTGGTACCGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTT-ATGCTTCTGAGGTAAAAGGTTTA
1 GTGGTACCAGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCATGCTTCTGAGGTAAAAGGTTTA
* * * *
1531 TCGTTGCGACTTAAACTTTTCCCTTCAAAT-CTTCATGGTACCGGATTCGCCGTTGCGACTTAAA
65 CCATTGCGACTTAAACCTTTCCCTTCAAATCCTT-ATGGTACCGGATTCGCCGTAGCGACTTAAA
** * * *
1595 TCTTTCCCTTTATGCTTCTGAGGTACAAGGTTCGTCATTGCGA-CTTAAACCTTTCCCTCTATAT
129 TCTCCCCCTTCATGCTTCTGAGGTACAAGATTCGTCATTGCGAGC-TAAACCTTTCCCTCCATAT
1659 CTCCATGATA
Statistics
Matches: 160, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
218 4 0.03
219 152 0.95
220 4 0.03
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (219 bp):
GTGGTACCAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTAAAAGGTTTAC
CATTGCGACTTAAACCTTTCCCTTCAAATCCTTATGGTACCGGATTCGCCGTAGCGACTTAAATC
TCCCCCTTCATGCTTCTGAGGTACAAGATTCGTCATTGCGAGCTAAACCTTTCCCTCCATATGGC
TTAAACCTTTCCCTTCAAATCTTC
Done.