Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010284.1 Kokia drynarioides strain JFW-HI SEQ_125133, 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, 768
Length: 1281
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.30
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:186 original size:29 final size:29
Alignment explanation
Indices: 153--343 Score: 179
Period size: 29 Copynumber: 6.5 Consensus size: 29
143 CTAAACTGTT
*
153 CAAAAATTATATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
*
182 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
1 CAAAAATTACATTTTT-ACCCTCG-AACTTC
* * ** *
212 TAAAAATTACATTTTTACACTTAAATTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* ***
241 CAAAAATTCCATTTTTGACCCAAAAACTTC
1 CAAAAATTACATTTTT-ACCCTCGAACTTC
* *
271 CAAAAATCACATTTTT-CCCCCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* *
299 CAAAAAATCATATTTTTACCCTCGAACTTC
1 C-AAAAATTACATTTTTACCCTCGAACTTC
* *
329 AAAAAATTCCATTTT
1 CAAAAATTACATTTT
344 AACNNNNNNN
Statistics
Matches: 131, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
28 10 0.08
29 64 0.49
30 57 0.44
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:217 original size:30 final size:28
Alignment explanation
Indices: 153--343 Score: 161
Period size: 30 Copynumber: 6.5 Consensus size: 28
143 CTAAACTGTT
**
153 CAAAAATTATATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTA-CCTCGAACTTC
182 CAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTT-ACCTCG-AACTTC
* * ** *
212 TAAAAATTACATTTTTACACTTAAATTTC
1 CAAAAATTCCATTTTTAC-CTCGAACTTC
*
241 CAAAAATTCCATTTTTGACC-CAAAAACTTC
1 CAAAAATTCCATTTTT-ACCTC--GAACTTC
* *
271 CAAAAA-TCACATTTTTCCCCCGAACTTC
1 CAAAAATTC-CATTTTTACCTCGAACTTC
* *
299 CAAAAAATCATATTTTTACCCTCGAACTTC
1 CAAAAATTC-CATTTTTA-CCTCGAACTTC
*
329 AAAAAATTCCATTTT
1 CAAAAATTCCATTTT
344 AACNNNNNNN
Statistics
Matches: 133, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.09
29 59 0.44
30 62 0.47
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCTCGAACTTC
Found at i:305 original size:59 final size:59
Alignment explanation
Indices: 153--343 Score: 201
Period size: 59 Copynumber: 3.3 Consensus size: 59
143 CTAAACTGTT
* *
153 CAAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTC
* * ** *
212 TAAAAATTACATTTTTACACTTAAATTTCCAAAAATTCCATTTTTGACC-CAAAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTC-AAAACTTC
* * * * *
271 CAAAAATCACATTTTT-CCCCCGAACTTCCAAAAAAT-CATATTTTTACCCTC-GAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCAT-TTTTGA-CCTCAAAACTTC
* *
329 AAAAAATTCCATTTT
1 CAAAAATTACATTTT
344 AACNNNNNNN
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
57 3 0.03
58 38 0.35
59 66 0.61
60 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTC
Found at i:487 original size:59 final size:60
Alignment explanation
Indices: 395--646 Score: 238
Period size: 59 Copynumber: 4.3 Consensus size: 60
385 NNNNNNTTCA
* *
395 AAAAATTCCA-TTTTAACCCTAAAACTTCC-AAAAATCACATTTTTACCCTC-AAATTTTC
1 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATC-CATTTTTACCCTCGAAATTTCC
* * *
453 AAAAATCCCATTTTTGACCCCAAAACTT-CAAAAAATTCCATTTTTGA-CCTCGAAACTTCC
1 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAA-TCCATTTTT-ACCCTCGAAATTTCC
* * * *
513 AAAAATTACATTTTT-ACCCTC-GAACTTCCAAAAAATCACA-TTTTACCC-CTAAATATCC
1 AAAAATTCCATTTTTAACCC-CAAAACTTCCAAAAAATC-CATTTTTACCCTCGAAATTTCC
* * * *
571 AAAAATTTCATCTTTAACCCCAAAACTTCCAAAAAATCCATTTTTGA-TCTTGAAACTTT-C
1 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATCCATTTTT-ACCCTCGAAA-TTTCC
*
631 AAAAATTTCATTTTTA
1 AAAAATTCCATTTTTA
647 CCTCCGAACT
Statistics
Matches: 160, Mismatches: 19, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
58 34 0.21
59 72 0.45
60 52 0.32
61 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATCCATTTTTACCCTCGAAATTTCC
Found at i:557 original size:118 final size:118
Alignment explanation
Indices: 395--722 Score: 335
Period size: 118 Copynumber: 2.8 Consensus size: 118
385 NNNNNNTTCA
* * ** * *
395 AAAAATTCCATTTTAACCCTAAAACTTCCAAAAATCACATTTTTA-CCCTCAAATTTTCAAAAAT
1 AAAAATTACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCCCT-AAATATCCAAAAAT
* *
459 CCCATTTTTGACCCCAAAACTT-CAAAAAATTCCATTTTTGACCTCGAAACTTCC
65 CCCATCTTTAACCCCAAAACTTCCAAAAAA-TCCATTTTTGACCTCGAAACTTCC
513 AAAAATTACATTTTTACCCTCGAACTTCCAAAAAATCACA-TTTTACCCCTAAATATCCAAAAAT
1 AAAAATTACATTTTTACCCTCGAACTTCC-AAAAATCACATTTTTACCCCTAAATATCCAAAAAT
** * * *
577 TTCATCTTTAACCCCAAAACTTCCAAAAAATCCATTTTTGATCTTGAAACTTTC
65 CCCATCTTTAACCCCAAAACTTCCAAAAAATCCATTTTTGACCTCGAAACTTCC
* * * * * **
631 AAAAATTTCATTTTTA-CCTCCGAAC-TCTTAAAAATTACACTTTT-CCCCTGAACCTCCAAAAA
1 AAAAATTACATTTTTACCCT-CGAACTTC-CAAAAATCACATTTTTACCCCTAAATATCCAAAAA
** * * * *
693 TTTCATATTTAACCTCGAAACTTTCAAAAA
64 TCCCATCTTTAACCCCAAAACTTCCAAAAA
723 TTACTATTTC
Statistics
Matches: 181, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
117 55 0.30
118 105 0.58
119 21 0.12
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (118 bp):
AAAAATTACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCCCTAAATATCCAAAAATC
CCATCTTTAACCCCAAAACTTCCAAAAAATCCATTTTTGACCTCGAAACTTCC
Found at i:656 original size:29 final size:28
Alignment explanation
Indices: 417--761 Score: 169
Period size: 30 Copynumber: 11.8 Consensus size: 28
407 TTAACCCTAA
** *
417 AACTTCCAAAAATCACATTTTTACCCTCA
1 AACTTCCAAAAATTTCATTTTTACCC-CG
* * ** *
446 AATTTTCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTTCATTTTT-ACCCC-G
* * *
476 AACTTCAAAAAATTCCATTTTTGACCTCG
1 AACTTCCAAAAATTTCATTTTT-ACCCCG
*
505 AAACTTCCAAAAATTACATTTTTACCCTCG
1 -AACTTCCAAAAATTTCATTTTTACCC-CG
* * *
535 AACTTCCAAAAA-ATCACATTTTACCCCT
1 AACTTCCAAAAATTTCA-TTTTTACCCCG
* * *
563 AAATATCCAAAAATTTCATCTTTAACCCCAA
1 AACT-TCCAAAAATTTCAT-TTTTACCCC-G
* * * **
594 AACTTCCAAAAAATCCATTTTTGATCTTG
1 AACTTCCAAAAATTTCATTTTT-ACCCCG
*
623 AAACTTTCAAAAATTTCATTTTTACCTCCG
1 -AACTTCCAAAAATTTCATTTTTACC-CCG
* * *
653 AAC-TCTTAAAAATTACACTTTT-CCCCTG
1 AACTTC-CAAAAATTTCATTTTTACCCC-G
* * *
681 AACCTCCAAAAATTTCATATTTAACCTCG
1 AACTTCCAAAAATTTCAT-TTTTACCCCG
* * *
710 AAACTTTCAAAAATTAC-TATTTCACCCCCG
1 -AACTTCCAAAAATTTCAT-TTTTA-CCCCG
*
740 AA-TGTCCAAAAATTCCATTTTT
1 AACT-TCCAAAAATTTCATTTTT
762 GATCCTGATT
Statistics
Matches: 243, Mismatches: 52, Indels: 42
0.72 0.15 0.12
Matches are distributed among these distances:
27 2 0.01
28 23 0.09
29 99 0.41
30 116 0.48
31 3 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTTCATTTTTACCCCG
Found at i:698 original size:57 final size:58
Alignment explanation
Indices: 630--761 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 58
620 TTGAAACTTT
* *
630 CAAAAATTTCATTTTTACCTCCG-AACTCTT-AAAAATTAC-ACTTT-TCCCCTGAACCTC
1 CAAAAATTTCATTTTTACCT-CGAAACT-TTCAAAAATTACTA-TTTCACCCCCGAACCTC
* **
687 CAAAAATTTCATATTTAACCTCGAAACTTTCAAAAATTACTATTTCACCCCCGAATGTC
1 CAAAAATTTCAT-TTTTACCTCGAAACTTTCAAAAATTACTATTTCACCCCCGAACCTC
*
746 CAAAAATTCCATTTTT
1 CAAAAATTTCATTTTT
762 GATCCTGATT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 16 0.25
58 26 0.41
59 21 0.33
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
CAAAAATTTCATTTTTACCTCGAAACTTTCAAAAATTACTATTTCACCCCCGAACCTC
Found at i:722 original size:58 final size:57
Alignment explanation
Indices: 510--760 Score: 161
Period size: 59 Copynumber: 4.3 Consensus size: 57
500 CCTCGAAACT
* * * *
510 TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAAAT-CACATTTTACCCCTAAATA
1 TCCAAAAATTTCA-TTTTAACCTCGAACTTCCAAAAAATACAC-TTTTACCCCTGAACA
* * * * * * *
568 TCCAAAAATTTCATCTTTAACCCCAAAACTTCCAAAAAATCCATTTTTGA-TCTTGAAACT
1 TCCAAAAATTTCAT-TTTAACCTC-GAACTTCCAAAAAATACACTTTT-ACCCCTG-AACA
* * * * *
628 TTCAAAAATTTCATTTTTACCTCCGAAC-TCTTAAAAATTACACTTTT-CCCCTGAACC
1 TCCAAAAATTTCATTTTAACCT-CGAACTTC-CAAAAAATACACTTTTACCCCTGAACA
* * * * **
685 TCCAAAAATTTCATATTTAACCTCGAAACTTTCAAAAATTACTA-TTTCACCCCCGAATG
1 TCCAAAAATTTCAT-TTTAACCTCG-AACTTCCAAAAAATAC-ACTTTTACCCCTGAACA
*
744 TCCAAAAATTCCATTTT
1 TCCAAAAATTTCATTTT
761 TGATCCTGAT
Statistics
Matches: 150, Mismatches: 30, Indels: 26
0.73 0.15 0.13
Matches are distributed among these distances:
57 19 0.13
58 49 0.33
59 63 0.42
60 19 0.13
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (57 bp):
TCCAAAAATTTCATTTTAACCTCGAACTTCCAAAAAATACACTTTTACCCCTGAACA
Found at i:723 original size:30 final size:30
Alignment explanation
Indices: 395--724 Score: 209
Period size: 30 Copynumber: 11.2 Consensus size: 30
385 NNNNNNTTCA
*
395 AAAAATTCCA-TTTTAACC-CTAAAACTTCC
1 AAAAATTCCATTTTTAACCTC-GAAACTTCC
* * *
424 AAAAA-TCACATTTTTACCCTC-AAATTTTC
1 AAAAATTC-CATTTTTAACCTCGAAACTTCC
* * * * *
453 AAAAATCCCATTTTTGACCCCAAAACTTCA
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
*
483 AAAAATTCCATTTTTGACCTCGAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
513 AAAAATTACATTTTTACCCTCG-AACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * *
542 AAAAAATCACA-TTTT-ACCCCTAAA-TATCC
1 AAAAATTC-CATTTTTAACCTCGAAACT-TCC
* * * *
571 AAAAATTTCATCTTTAACCCCAAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * * * *
601 AAAAAATCCATTTTTGATCTTGAAACTTTC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
631 AAAAATTTCATTTTT-ACCTCCG-AAC-TCTT
1 AAAAATTCCATTTTTAACCT-CGAAACTTC-C
* * ** *
660 AAAAATTACACTTTTCCCCT-G-AACCTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * *
688 AAAAATTTCATATTTAACCTCGAAACTTTC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
718 AAAAATT
1 AAAAATT
725 ACTATTTCAC
Statistics
Matches: 232, Mismatches: 52, Indels: 33
0.73 0.16 0.10
Matches are distributed among these distances:
28 28 0.12
29 81 0.35
30 121 0.52
31 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCC
Done.