Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013356.1 Kokia drynarioides strain JFW-HI SEQ_128379, 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: 36804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:3206 original size:31 final size:31
Alignment explanation
Indices: 3159--3247 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 31
3149 GCTAGAAGGT
*
3159 CTCTAAA-TTTTCCAAAAAATCATATTTTAAC
1 CTCTAAACTTTT-CAAAAAATCACATTTTAAC
* *
3190 C-CTAAAACTTTTC-AAAAATTACATTTTGAC
1 CTCT-AAACTTTTCAAAAAATCACATTTTAAC
* *
3220 CTCTAACCTTTTCAAAAAATTACATTTT
1 CTCTAAACTTTTCAAAAAATCACATTTT
3248 GCCCTCGAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
30 25 0.50
31 21 0.42
32 4 0.08
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.39
Consensus pattern (31 bp):
CTCTAAACTTTTCAAAAAATCACATTTTAAC
Found at i:3248 original size:31 final size:30
Alignment explanation
Indices: 3159--3480 Score: 120
Period size: 29 Copynumber: 10.9 Consensus size: 30
3149 GCTAGAAGGT
* * * *
3159 CTCTAAATTTTCCAAAAAATCATATTTTAAC
1 CTCTAACTTTT-CAAAAAATTACATTTTGAC
3190 C-CTAAAACTTTTC-AAAAATTACATTTTGAC
1 CTCT--AACTTTTCAAAAAATTACATTTTGAC
*
3220 CTCTAACCTTTTCAAAAAATTACATTTTGCC
1 CTCTAA-CTTTTCAAAAAATTACATTTTGAC
* * * *
3251 CTCGAAC-TTCCAATAAATTACAATTTTGCC
1 CTCTAACTTTTCAAAAAATTAC-ATTTTGAC
* * * * *
3281 CCCAAAC--TTCCAAAAATTATATTTTTACC
1 CTCTAACTTTTCAAAAAATTACATTTTGA-C
* * *
3310 CTCTAAC--TTCCAAAAATCACATTTTTACC
1 CTCTAACTTTTCAAAAAATTACATTTTGA-C
* * * *
3339 CCCAAACTTCTC-AAAAATTACATTTTTGCC
1 CTCTAACTTTTCAAAAAATTACA-TTTTGAC
* * * *
3369 CTCGAAC--ATCCAAAAACTACAGTTTT-AC
1 CTCTAACTTTTCAAAAAATTACA-TTTTGAC
* *
3397 CTCTGAAC--TTCCAAAAATTACATTTTTAC
1 CTCT-AACTTTTCAAAAAATTACATTTTGAC
* * * * *
3426 CCCTTAGCTTGTC-AAAAGTTACATTTTTAC
1 CTC-TAACTTTTCAAAAAATTACATTTTGAC
*
3456 C-CTGAAC--TTCCAAAAATTACATTTT
1 CTCT-AACTTTTCAAAAAATTACATTTT
3481 TACCCTCGTA
Statistics
Matches: 231, Mismatches: 42, Indels: 39
0.74 0.13 0.12
Matches are distributed among these distances:
27 2 0.01
28 29 0.13
29 91 0.39
30 70 0.30
31 33 0.14
32 6 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
CTCTAACTTTTCAAAAAATTACATTTTGAC
Found at i:3297 original size:29 final size:29
Alignment explanation
Indices: 3202--3658 Score: 389
Period size: 29 Copynumber: 15.7 Consensus size: 29
3192 TAAAACTTTT
* *
3202 CAAAAATTACATTTTGA-CCTCTAACCTTTTC
1 CAAAAATTACATTTTTACCCTCGAA-C--TTC
* *
3233 AAAAAATTACA-TTTTGCCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * * *
3261 CAATAAATTACAATTTTGCCCCCAAACTTC
1 CAA-AAATTACATTTTTACCCTCGAACTTC
* *
3291 CAAAAATTATATTTTTACCCTCTAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * *
3320 CAAAAATCACATTTTTACCCCCAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* *
3349 TCAAAAATTACATTTTTGCCCTCGAACATC
1 -CAAAAATTACATTTTTACCCTCGAACTTC
* *
3379 CAAAAACTACAGTTTTA-CCTCTGAACTTC
1 CAAAAATTACATTTTTACCCTC-GAACTTC
* * *
3408 CAAAAATTACATTTTTACCC-CTTAGCTTGT
1 CAAAAATTACATTTTTACCCTC-GAACTT-C
*
3438 CAAAAGTTACATTTTTACCCT-GAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
*
3466 CAAAAATTACATTTTTACCCTCGTACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * * *
3495 CAAAAATCACATTATTT-CCCT-TAGTCTTT
1 CAAAAATTACATT-TTTACCCTCGA-ACTTC
* *
3524 CAAAAATTACA-TTTTATCCCTCAAACTAC
1 CAAAAATTACATTTTTA-CCCTCGAACTTC
* *
3553 CAAAAATCACATTTTT-GCCTCGAACTTCC
1 CAAAAATTACATTTTTACCCTCGAACTT-C
* *
3582 CAAAAATCACATTTTT-GCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
*
3610 TCAAAAATCACATTTTTACCC-CGAACTCTC
1 -CAAAAATTACATTTTTACCCTCGAACT-TC
* *
3640 CCAAAATGAC-TTTTTACCC
1 CAAAAATTACATTTTTACCC
3659 CTAACTCTTC
Statistics
Matches: 354, Mismatches: 53, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
27 3 0.01
28 48 0.14
29 208 0.59
30 79 0.22
31 16 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:4769 original size:17 final size:16
Alignment explanation
Indices: 4747--4789 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4737 ATAAAAATAT
4747 AAATTAAATTGACAAAA
1 AAATTAAATTGA-AAAA
* *
4764 AAATTATATTTAAAAA
1 AAATTAAATTGAAAAA
*
4780 AAAGTAAATT
1 AAATTAAATT
4790 TATTATTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (16 bp):
AAATTAAATTGAAAAA
Found at i:9450 original size:12 final size:10
Alignment explanation
Indices: 9423--9449 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9413 AAATTATAAC
9423 AAATATAAAA
1 AAATATAAAA
9433 AAATATAAAA
1 AAATATAAAA
9443 AAATATA
1 AAATATA
9450 TTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAATATAAAA
Found at i:9518 original size:19 final size:19
Alignment explanation
Indices: 9486--9540 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
9476 TTAGAAAAAC
* * *
9486 TAAAAAATAGAAAATTATT
1 TAAAATATAAAAAATTATA
9505 TAAAATATAAAAAA--ATA
1 TAAAATATAAAAAATTATA
9522 TAAAATATGGAAAAAATTA
1 TAAAATAT--AAAAAATTA
9541 CAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.34
19 18 0.62
21 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
TAAAATATAAAAAATTATA
Found at i:9713 original size:19 final size:19
Alignment explanation
Indices: 9633--9729 Score: 71
Period size: 19 Copynumber: 5.3 Consensus size: 19
9623 AAAGTCAATA
9633 AAAAATA-TGAAAAATTAT
1 AAAAATATTGAAAAATTAT
* *
9651 AAAAA-A-TGTAGAAAGTAT
1 AAAAATATTG-AAAAATTAT
* *
9669 --AAAGATTAAAAAATTAT
1 AAAAATATTGAAAAATTAT
9686 AAAAATATTGAAAAA-TAT
1 AAAAATATTGAAAAATTAT
* *
9704 AGAAAATATTTAAAATTTATT
1 A-AAAATATTGAAAAATTA-T
9725 AAAAA
1 AAAAA
9730 AGTTATAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.05
17 11 0.18
18 17 0.27
19 23 0.37
20 6 0.10
21 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAATATTGAAAAATTAT
Found at i:9907 original size:1 final size:1
Alignment explanation
Indices: 9903--9928 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9893 NNNNNNNNNN
9903 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
9929 CCCTTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19619 original size:24 final size:24
Alignment explanation
Indices: 19589--19642 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
19579 CTGTGGAGAT
* *
19589 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
19613 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
19637 TGATGA
1 TGATGA
19643 ACATGAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:29645 original size:27 final size:26
Alignment explanation
Indices: 29598--29654 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
29588 TTGATATTAT
*
29598 TTTTATAATATTTAATATTTTATAACA
1 TTTTATAAAATTTAATATTTTATAA-A
* *
29625 TTTTCTAAAATTT-ATATTTTTCTAAA
1 TTTTATAAAATTTAATA-TTTTATAAA
29651 TTTT
1 TTTT
29655 TCATGCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATAAAATTTAATATTTTATAAA
Found at i:29715 original size:31 final size:31
Alignment explanation
Indices: 29677--29735 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
29667 AATAGTTTTT
29677 AAATAATTAAAAAATAAATTAAACCATCATA
1 AAATAATTAAAAAATAAATTAAACCATCATA
* *
29708 AAATAATTAAAAAATCAATTAAGCCATC
1 AAATAATTAAAAAATAAATTAAACCATC
29736 CACATTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (31 bp):
AAATAATTAAAAAATAAATTAAACCATCATA
Found at i:29724 original size:19 final size:20
Alignment explanation
Indices: 29687--29724 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
29677 AAATAATTAA
**
29687 AAAATAAATTAAACCATCAT
1 AAAATAAATTAAAAAATCAT
29707 AAAAT-AATTAAAAAATCA
1 AAAATAAATTAAAAAATCA
29725 ATTAAGCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAATTAAAAAATCAT
Found at i:36640 original size:669 final size:669
Alignment explanation
Indices: 35360--36804 Score: 2581
Period size: 669 Copynumber: 2.2 Consensus size: 669
35350 NNNNNNNNNN
*
35360 GTCATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTAAT
1 GTCATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
*
35425 GAGTTGGC-ATTTGTTCCTTACTATGGAGCTGATCACACTTTAGAGACTCTTTATACTTCTCCTG
66 GAGTTGGCGA-TTGTTCCTTTCTATGGAGCTGATCACACTTTAGAGACTCTTTATACTTCTCCTG
*
35489 ACTGTTTCTTGAGGAATGAACGGATGGCCTAAGAAGGTGTGGCTGGTATCAGGGAGCAATGAGCA
130 ACTGTTTCTTGAGGAATGAACGGATGGCCTAAGAAGGTGTGGCTGATATCAGGGAGCAATGAGCA
35554 AATAAGTGAGGAGCTGCGGAAGATTCAAGCTGGAGGAGAAACAACAACTCCAGGAGGCCTTACTG
195 AATAAGTGAGGAGCTGCGGAAGATTCAAGCTGGAGGAGAAACAACAACTCCAGGAGGCCTTACTG
* *
35619 AGCGGGATATTGAGGTTAAGGATTTAAGCCTGCAGCTTCAAAATATGTGCCAGTGCTTAGAGAAT
260 AACGGGATATTGAGGTTAAGGATTTAAGCCTGCAGCTTCAAAATATGTGCCAGTGCTTAGAGAAG
* * * *
35684 GAACAAAAAAGGCTGGAGGAGGTCCAAGTGATTGTTCTTACCATTGTTGTGGATGGTGTTATACT
325 GAACAAAAAAGGCTGGAGGAAGTCCAAGTGATTGTTCCTACCATTGCTGTGGATGGGGTTATACT
*
35749 AGCTATGCAAGTAGCTTTTGGTCCTATTCATACATATGGGATGGACTTCAGGATATTTTTTGATG
390 AGCTATGCAAGTAGCTTTTGGTCCTATTCAAACATATGGGATGGACTTCAGGATATTTTTTGATG
35814 TAATTAGATGTGGTCAGTTTATTGGACTTTGACATTAGTAGCCTCTTAGGGATTTGCCAGTAAAT
455 TAATTAGATGTGGTCAGTTTATTGGACTTTGACATTAGTAGCCTCTTAGGGATTTGCCAGTAAAT
* *
35879 GCGACCGTTTGTTTTATTGGGACTCTTCAGGAAAGAACTCTTTGGAAGATGAGACTTAGAGGTCG
520 GCGACCGTTTGTTTTATTGGAACTCTTCAGGAAAGAACTCTTTGAAAGATGAGACTTAGAGGTCG
35944 ATAGCTTATCTGGAGGAGCTGGAAAAGGATGGAATCCTTTGTAACCAAAAGGGTACAAAGGTAAA
585 ATAGCTTATCTGGAGGAGCTGGAAAAGGATGGAATCCTTTGTAACCAAAAGGGTACAAAGGTAAA
*
36009 TCTTTGCAGGTATTGTTTAT
650 TCTTTGCAGGTATCGTTTAT
*
36029 GTTATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
1 GTCATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
* * *
36094 GAGTTGGCGATTATTCCTTTCTATGGAGTTGATCACACTTTAGAGACTCTTTATACTTCTCTTGA
66 GAGTTGGCGATTGTTCCTTTCTATGGAGCTGATCACACTTTAGAGACTCTTTATACTTCTCCTGA
36159 CTGTTTCTTGAGGAATGAACGGATGGCCTAAGAAGGTGTGGCTGATATCAGGGAGCAATGAGCAA
131 CTGTTTCTTGAGGAATGAACGGATGGCCTAAGAAGGTGTGGCTGATATCAGGGAGCAATGAGCAA
36224 ATAAGTGAGGAGCTGCGGAAGATTCAAGCTGGAGGAGAAACAACAACTCCAGGAGGCCTTACTGA
196 ATAAGTGAGGAGCTGCGGAAGATTCAAGCTGGAGGAGAAACAACAACTCCAGGAGGCCTTACTGA
* *
36289 ACGGGATATTGAGGTTAAGGATTTACGCCTGCAGCTTTAAAATATGTGCCAGT-CTTTAGAGAAG
261 ACGGGATATTGAGGTTAAGGATTTAAGCCTGCAGCTTCAAAATATGTGCCAGTGC-TTAGAGAAG
36353 GAACAAAAAAGGCTGGAGGAAGTCCAAGTGATTGTTCCTACCATTGCTGTGGATGGGGTTATACT
325 GAACAAAAAAGGCTGGAGGAAGTCCAAGTGATTGTTCCTACCATTGCTGTGGATGGGGTTATACT
* * *
36418 AGCTATTCAAGTAGCTTTTGGT-TTCATTCAAACATATGGGATGGACTTTAGGATATTTTTTGAT
390 AGCTATGCAAGTAGCTTTTGGTCCT-ATTCAAACATATGGGATGGACTTCAGGATATTTTTTGAT
* *
36482 GTAATTAGATGTGGTCAGTTTCTTGGACTTTGACATTAGTAGCCTCTTAGGGATTTGCTAGTAAA
454 GTAATTAGATGTGGTCAGTTTATTGGACTTTGACATTAGTAGCCTCTTAGGGATTTGCCAGTAAA
*
36547 TGCGACCTTTTGTTTTATTGGAACTCTTCAGGAAAGAACTCTTTGAAAGATGAGACTTAGAGGTC
519 TGCGACCGTTTGTTTTATTGGAACTCTTCAGGAAAGAACTCTTTGAAAGATGAGACTTAGAGGTC
36612 GATAGCTTATCTGGAGGAGCTGGAAAAGGATGGAATCCTTTGTAACCAAAAGGGTACAAAGGTAA
584 GATAGCTTATCTGGAGGAGCTGGAAAAGGATGGAATCCTTTGTAACCAAAAGGGTACAAAGGTAA
*
36677 ATCTTTGTAGGTATCGTTTAT
649 ATCTTTGCAGGTATCGTTTAT
*
36698 GTCATTACTACTGTTGGTTATCTCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
1 GTCATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
* *
36763 GAGTTGGCGATTGTTCCTTTTTATGGAGCTGATCACAGTTTA
66 GAGTTGGCGATTGTTCCTTTCTATGGAGCTGATCACACTTTA
Statistics
Matches: 741, Mismatches: 32, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
668 2 0.00
669 738 1.00
670 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (669 bp):
GTCATTACTACTGTTGGTTATCCCGGATCTTGTTTTCACTTAACTATCTGCTTGTAACAGGTACT
GAGTTGGCGATTGTTCCTTTCTATGGAGCTGATCACACTTTAGAGACTCTTTATACTTCTCCTGA
CTGTTTCTTGAGGAATGAACGGATGGCCTAAGAAGGTGTGGCTGATATCAGGGAGCAATGAGCAA
ATAAGTGAGGAGCTGCGGAAGATTCAAGCTGGAGGAGAAACAACAACTCCAGGAGGCCTTACTGA
ACGGGATATTGAGGTTAAGGATTTAAGCCTGCAGCTTCAAAATATGTGCCAGTGCTTAGAGAAGG
AACAAAAAAGGCTGGAGGAAGTCCAAGTGATTGTTCCTACCATTGCTGTGGATGGGGTTATACTA
GCTATGCAAGTAGCTTTTGGTCCTATTCAAACATATGGGATGGACTTCAGGATATTTTTTGATGT
AATTAGATGTGGTCAGTTTATTGGACTTTGACATTAGTAGCCTCTTAGGGATTTGCCAGTAAATG
CGACCGTTTGTTTTATTGGAACTCTTCAGGAAAGAACTCTTTGAAAGATGAGACTTAGAGGTCGA
TAGCTTATCTGGAGGAGCTGGAAAAGGATGGAATCCTTTGTAACCAAAAGGGTACAAAGGTAAAT
CTTTGCAGGTATCGTTTAT
Done.