Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011341.1 Kokia drynarioides strain JFW-HI SEQ_126321, 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: 4510
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1558 original size:26 final size:25
Alignment explanation
Indices: 1507--1557 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1497 ATAAAAGTAC
*
1507 TAAAAAATGAACAAAATAAAATAAAA
1 TAAAAAAT-AACAAAACAAAATAAAA
*
1533 TAAAAAATAACAGAACAAAATAAAA
1 TAAAAAATAACAAAACAAAATAAAA
1558 ACAAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (25 bp):
TAAAAAATAACAAAACAAAATAAAA
Found at i:2872 original size:19 final size:19
Alignment explanation
Indices: 2848--2895 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2838 GGTATTGGGC
* **
2848 TATTTGTAATTGTTTTTTT
1 TATTTGTAATTGTGTAATT
2867 TATTTGTAA-TGTGTAATT
1 TATTTGTAATTGTGTAATT
2885 TATTTGTAATT
1 TATTTGTAATT
2896 TGGACTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (19 bp):
TATTTGTAATTGTGTAATT
Found at i:3756 original size:18 final size:19
Alignment explanation
Indices: 3733--3779 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3723 GGTATTGGGC
**
3733 TATTTGTAATTGT-TTTTT
1 TATTTGTAATTGTGTAATT
3751 TATTTGTAA-TGTGTAATT
1 TATTTGTAATTGTGTAATT
3769 TATTTGTAATT
1 TATTTGTAATT
3780 TGGACTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (19 bp):
TATTTGTAATTGTGTAATT
Found at i:3803 original size:884 final size:834
Alignment explanation
Indices: 2258--3972 Score: 2714
Period size: 884 Copynumber: 2.0 Consensus size: 834
2248 CAAAATTCCA
2258 AAAATCTTAGCCAAAACCTCCAAAAATAAGAAACCCTTTCGATTTCTTCGAAAAGAAAAAACAAA
1 AAAATCTTAGCCAAAACCTCCAAAAATAAGAAACCCTTTCGATTTCTTCGAAAAGAAAAAACAAA
*
2323 ACTCCCCTCTGACGAAACCTATGCAACCAAAAGGAGGCCAGGGGTCACTCGCGCACAAAGGAAGG
66 ACTCCCCTCTGACAAAACCTATGCAACCAAAAGGAGGCCAGGGGTCACTCGCGCACAAAGGAAGG
2388 GGTCATCCTTCATCAGGGACGGCATCCTCGTTTGCCTATGGTGGCGGAAGACGAACGATCAAGTA
131 GGTCATCCTTCATCAGGGACGGCATCCTCGTTTGCCTATGGTGGCGGAAGACGAACGATCAAGTA
2453 AAAAATAACTAAACCTATACTTTATAGATTTTTTAGTTTTGAAATAAAATGTAAAAACAAAAATT
196 AAAAATAACTAAACCTATACTTTATAGATTTTTTAGTTTTGAAATAAAATGTAAAAACAAAAATT
2518 TATACCTTAAAAATTGCTTTTCGATTTCAATATGCATGTGTAAAAAATTTACAATTATTCATATG
261 TATACCTTAAAAATTGCTTTTCGATTTCAATATGCATGTGTAAAAAATTTACAATTATTCATATG
2583 GCTTTTATAGCCAGAATACATTTTGTTTTTGTATATTTTCTTTTCATTTTTAGTTTTCTTTCTAT
326 GCTTTTATAGCCAGAATACATTTTGTTTTTGTATATTTTCTTTTCATTTTTAGTTTTCTTTCTAT
2648 TTTGCACGTACGACAAGATCTATAAGGTGTCCTTGTGTCCGGACGTCGCGAAGGCGACTAATGTG
391 TTTGCACGTACGACAAGATCTATAAGGTGTCCTTGTGTCCGGACGTCGCGAAGGCGACTAATGTG
2713 GCGAGAGCTACGACTGTTAGAGTTTAGGGGTCTAGGGTTTCTATGAAAAGTCTAGTTAGTGGGCT
456 GCGAGAGCTACGACTGTTAGAGTTTAGGGGTCTAGGGTTTCTATGAAAAGTCTAGTTAGTGGGCT
*
2778 AGGTTTTGCATTTGGGCTTTAGTCGGCTTTGGGATAGATTTAATTTGGCTTTAGGTATTGGGTAT
521 AGGTTTTGCATTTGGGCTTTAGTCGCCTTTGGGATAGATTTAATTTGGCTTTAGGTATTGGGTAT
2843 TGGGCTATTTGTAATTGTTTTTTTTATTTGTAATGTGTAATTTATTTGTAATTTGGACTAATGGA
586 TGGGCTATTTGTAATTGTTTTTTTTATTTGTAATGTGTAATTTATTTGTAATTTGGACTAATGGA
2908 CTTGTCGACCCAATTTCTCTCATCTTGTCAGCTTTGTTTCTCTGTTGCTCTGCTTTTGTTTCAAC
651 CTTGTCGACCCAATTTCTCTCATCTTGTCAGCTTTGTTTCTCTGTTGCTCTGCTTTTGTTTCAAC
*
2973 ACACAAACTCAAAGTTGGTAATGTCGAAAACAAATTATATTTATCTTCTTCTTCTTCCTCCTCTT
716 ACACAAACTCAAAGTTGGTAATGTCGAAAACAAACTATATTTATCTTCTTCTTCTTCCTCCTCTT
3038 TTTCTAGATTGCTTACATTGTATATATATGAAAATGAAATCAATTGCAAAAGAT
781 TTTCTAGATTGCTTACATTGTATATATATGAAAATGAAATCAATTGCAAAAGAT
************ *
3092 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAATCTTAGCCAAA
1 --------------------------------------AAAATCTTAGCCAAAA-CCT--CC-A-
*
3157 ACCTCCAAAAATAAGAAACCCTTTCGGTTTCTTCGAAAAGAAAAAACAAAACTCCCCTCTGACAA
23 -------AAAATAAGAAACCCTTTCGATTTCTTCGAAAAGAAAAAACAAAACTCCCCTCTGACAA
* *
3222 AACCTATGCAACCAAAAGGAGGCCAGGGGTCACTCGCGCACAAAGGAAGGGGTCGTCCTTCATCG
81 AACCTATGCAACCAAAAGGAGGCCAGGGGTCACTCGCGCACAAAGGAAGGGGTCATCCTTCATCA
* *
3287 GGGACGGCATCCTCGTTTGCCTATGGTGGCGGAAGACGAATGATGAAGTAAAAAA-AACATAAAC
146 GGGACGGCATCCTCGTTTGCCTATGGTGGCGGAAGACGAACGATCAAGTAAAAAATAAC-TAAAC
3351 CTATACTTTATAGATTTTTTAGTTTTGAAATAAAATGTAAAAACAAAAATTTATACCTTAAAAAT
210 CTATACTTTATAGATTTTTTAGTTTTGAAATAAAATGTAAAAACAAAAATTTATACCTTAAAAAT
*
3416 TGCTTTTCGATTTCAATATGCATGTGTAAAAAATTTACAATTATTCATATGGCTTTTATAGCGAG
275 TGCTTTTCGATTTCAATATGCATGTGTAAAAAATTTACAATTATTCATATGGCTTTTATAGCCAG
3481 AATACATTTTGTTTTTGTATATTTTCTTTTCATTTTTAGTTTTCTTTCTATTTTGCACGTACGAC
340 AATACATTTTGTTTTTGTATATTTTCTTTTCATTTTTAGTTTTCTTTCTATTTTGCACGTACGAC
* * *
3546 AAGATCTATAAGTTGTCCTTGTGTCCGGACGTGGCGAAGGCGACTAATGTGGCGAGAGCTATGAC
405 AAGATCTATAAGGTGTCCTTGTGTCCGGACGTCGCGAAGGCGACTAATGTGGCGAGAGCTACGAC
*
3611 TGTTGGAGTTTAGGGGTCTAGGGTTTCTATGAAAAGTCTAGTTAGTGGGCTAGGTTTTGCATTTG
470 TGTTAGAGTTTAGGGGTCTAGGGTTTCTATGAAAAGTCTAGTTAGTGGGCTAGGTTTTGCATTTG
3676 GGCTTTAGTCGCCTTTGGGTATAGATTTAATTTGGCTTTAGGTATTGGGTATTGGGCTATTTGTA
535 GGCTTTAGTCGCCTTTGGG-ATAGATTTAATTTGGCTTTAGGTATTGGGTATTGGGCTATTTGTA
3741 ATTG-TTTTTTTATTTGTAATGTGTAATTTATTTGTAATTTGGACTAATGGACTTGTCGACCCAA
599 ATTGTTTTTTTTATTTGTAATGTGTAATTTATTTGTAATTTGGACTAATGGACTTGTCGACCCAA
3805 TTTCTCTCATCTTGTCAGCTTTGTTTCTCTGTTGCTCTGCTTTTGTTTCAACACACAAACTCAAA
664 TTTCTCTCATCTTGTCAGCTTTGTTTCTCTGTTGCTCTGCTTTTGTTTCAACACACAAACTCAAA
3870 GTTGGTAATGTCGAAAACAAACTATATTTATCTTCTTCTTCTTCCTCCTCTTTTTCTAGATTGCT
729 GTTGGTAATGTCGAAAACAAACTATATTTATCTTCTTCTTCTTCCTCCTCTTTTTCTAGATTGCT
3935 TACATTGTATATATATGAAAATGAAATCAATTGCAAAA
794 TACATTGTATATATATGAAAATGAAATCAATTGCAAAA
3973 AATGAGAGGG
Statistics
Matches: 803, Mismatches: 26, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
872 4 0.00
873 2 0.00
875 2 0.00
876 1 0.00
883 3 0.00
884 742 0.92
885 49 0.06
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.35
Consensus pattern (834 bp):
AAAATCTTAGCCAAAACCTCCAAAAATAAGAAACCCTTTCGATTTCTTCGAAAAGAAAAAACAAA
ACTCCCCTCTGACAAAACCTATGCAACCAAAAGGAGGCCAGGGGTCACTCGCGCACAAAGGAAGG
GGTCATCCTTCATCAGGGACGGCATCCTCGTTTGCCTATGGTGGCGGAAGACGAACGATCAAGTA
AAAAATAACTAAACCTATACTTTATAGATTTTTTAGTTTTGAAATAAAATGTAAAAACAAAAATT
TATACCTTAAAAATTGCTTTTCGATTTCAATATGCATGTGTAAAAAATTTACAATTATTCATATG
GCTTTTATAGCCAGAATACATTTTGTTTTTGTATATTTTCTTTTCATTTTTAGTTTTCTTTCTAT
TTTGCACGTACGACAAGATCTATAAGGTGTCCTTGTGTCCGGACGTCGCGAAGGCGACTAATGTG
GCGAGAGCTACGACTGTTAGAGTTTAGGGGTCTAGGGTTTCTATGAAAAGTCTAGTTAGTGGGCT
AGGTTTTGCATTTGGGCTTTAGTCGCCTTTGGGATAGATTTAATTTGGCTTTAGGTATTGGGTAT
TGGGCTATTTGTAATTGTTTTTTTTATTTGTAATGTGTAATTTATTTGTAATTTGGACTAATGGA
CTTGTCGACCCAATTTCTCTCATCTTGTCAGCTTTGTTTCTCTGTTGCTCTGCTTTTGTTTCAAC
ACACAAACTCAAAGTTGGTAATGTCGAAAACAAACTATATTTATCTTCTTCTTCTTCCTCCTCTT
TTTCTAGATTGCTTACATTGTATATATATGAAAATGAAATCAATTGCAAAAGAT
Found at i:4298 original size:2 final size:2
Alignment explanation
Indices: 4291--4319 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4281 TAAATGCGCT
4291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4320 GAATAACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.