Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009854.1 Kokia drynarioides strain JFW-HI SEQ_124584, 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: 3466
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3155 original size:29 final size:28
Alignment explanation
Indices: 3114--3368 Score: 171
Period size: 29 Copynumber: 8.8 Consensus size: 28
3104 AAAGTGGAAA
*
3114 TTCGAGGGCAAAATGGTATTTTTTGGATG
1 TTCGAGGGCAAAAT-GTAATTTTTGGATG
*
3143 TTCG-GGGCAAAAATGTAATTTTTAGATG
1 TTCGAGGGC-AAAATGTAATTTTTGGATG
* *
3171 TTAGAGGGCAAAATGGTAATTTTTGGAAAG
1 TTCGAGGGCAAAAT-GTAATTTTTGG-ATG
* ***
3201 TTCGAGGTCGAAAATGCCTTTTTTGGATG
1 TTCGAGGGC-AAAATGTAATTTTTGGATG
** *
3230 TTTAAGGGTAAAATGGTAATTTTTGGATG
1 TTCGAGGGCAAAAT-GTAATTTTTGGATG
*
3259 TTCGAGGGTAAAAATGTAATTTTTGGAAAT-
1 TTCGAGGG-CAAAATGTAATTTTTGG--ATG
* **
3289 TTTG-GGTAAAAAATGTAATTTTTAGGA-G
1 TTCGAGG-GCAAAATGTAATTTTT-GGATG
* * * *
3317 TTTGAGGGTAAAAATGTGATTTTTGGAAG
1 TTCGAGGG-CAAAATGTAATTTTTGGATG
3346 TTC-AGGG-ATATAATGTAATTTTT
1 TTCGAGGGCA-A-AATGTAATTTTT
3369 TGAAATTTAG
Statistics
Matches: 182, Mismatches: 27, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 52 0.29
29 94 0.52
30 27 0.15
31 7 0.04
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (28 bp):
TTCGAGGGCAAAATGTAATTTTTGGATG
Found at i:3244 original size:59 final size:58
Alignment explanation
Indices: 3117--3282 Score: 201
Period size: 59 Copynumber: 2.9 Consensus size: 58
3107 GTGGAAATTC
* *
3117 GAGGGCAAAATGGTATTTTTTGGATGTTCG-GGGCAAAAATGTAATTTTTAGATGTTA
1 GAGGGCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAAATGCAATTTTTAGATGTTA
* * * ** *
3174 GAGGGCAAAATGGTAATTTTTGGAAAGTTCGAGGTCGAAAATGCCTTTTTTGGATGTTTA
1 GAGGGCAAAATGGTAATTTTTGG-ATGTTCGAGGGCAAAAATGCAATTTTTAGATG-TTA
* * *
3234 -AGGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTT
1 GAGGGCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAAATGCAATTTTT
3283 GGAAATTTTG
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 22 0.24
58 26 0.29
59 39 0.43
60 3 0.03
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (58 bp):
GAGGGCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAAATGCAATTTTTAGATGTTA
Found at i:3273 original size:58 final size:58
Alignment explanation
Indices: 3118--3343 Score: 221
Period size: 58 Copynumber: 3.9 Consensus size: 58
3108 TGGAAATTCG
* * *
3118 AGGGCAAAATGGTATTTTTTGGATGTTCG-GGGCAAAAATGTAATTTTTAGATG-TTA
1 AGGGCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTTGGATGTTTA
* * ***
3174 GAGGGCAAAATGGTAATTTTTGGAAAGTTCGA-GGTCGAAAATGCCTTTTTTGGATGTTTA
1 -AGGGCAAAATGGTAATTTTTGG-ATGTTCGAGGGT-AAAAATGTAATTTTTGGATGTTTA
* **
3234 AGGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTTGGAAATTT-
1 AGGGCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTTGGATGTTTA
* * * *
3291 TGGGTAAAAAAT-GTAATTTTTAGGA-GTTTGAGGGTAAAAATGTGATTTTTGGA
1 AGGG--CAAAATGGTAATTTTT-GGATGTTCGAGGGTAAAAATGTAATTTTTGGA
3344 AGTTCAGGGA
Statistics
Matches: 141, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
57 24 0.17
58 67 0.48
59 47 0.33
60 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (58 bp):
AGGGCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTTGGATGTTTA
Found at i:3369 original size:87 final size:85
Alignment explanation
Indices: 3219--3440 Score: 241
Period size: 87 Copynumber: 2.5 Consensus size: 85
3209 CGAAAATGCC
* * * *
3219 TTTTTTGGATGTTTAAGGGT-AAAATGGTAATTTTTGGATGTTCGAGGGTAAAAATGTAATTTTT
1 TTTTTAGGA-GTTTGAGGGTAAAAAT-GTGATTTTTGGAAGTTC-AGGGTAAAAATGTAATTTTT
* *
3283 GGAAATTTTGGGTAAAAAATGTAA
63 -GAAATTTAGGGGAAAAAATGTAA
*
3307 TTTTTAGGAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCAGGG-ATATAATGTAATTTTTTG
1 TTTTTAGGAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCAGGGTA-AAAATGTAA-TTTTTG
*
3371 AAATTTAGGGGCAAAAATGTAA
64 AAATTTAGGGGAAAAAATGTAA
* * * *
3393 TATTTAAGAAGTTCGAGGGAAAAAAATGTGATTTTTGGATAGTTCAGG
1 T-TTTTAGGAGTTTGAGGG-TAAAAATGTGATTTTTGGA-AGTTCAGG
3441 TACCTTTTAG
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
85 1 0.01
86 33 0.28
87 43 0.37
88 31 0.27
89 8 0.07
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (85 bp):
TTTTTAGGAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCAGGGTAAAAATGTAATTTTTGAA
ATTTAGGGGAAAAAATGTAA
Found at i:3415 original size:29 final size:29
Alignment explanation
Indices: 3114--3437 Score: 169
Period size: 29 Copynumber: 11.1 Consensus size: 29
3104 AAAGTGGAAA
* * *
3114 TTCGAGGGC-AAAATGGTATTTTTTGGATG
1 TTCGAGGGCAAAAAT-GTAATTTTTAGAAG
*
3143 TTCG-GGGCAAAAATGTAATTTTTAGATG
1 TTCGAGGGCAAAAATGTAATTTTTAGAAG
* *
3171 TTAGAGGGC-AAAATGGTAATTTTTGGAAAG
1 TTCGAGGGCAAAAAT-GTAATTTTTAG-AAG
* * *** * *
3201 TTCGAGGTCGAAAATGCCTTTTTTGGATG
1 TTCGAGGGCAAAAATGTAATTTTTAGAAG
** * * *
3230 TTTAAGGG-TAAAATGGTAATTTTTGGATG
1 TTCGAGGGCAAAAAT-GTAATTTTTAGAAG
* * *
3259 TTCGAGGGTAAAAATGTAATTTTTGGAAAT
1 TTCGAGGGCAAAAATGTAATTTTTAG-AAG
* ** *
3289 TTTG-GGTAAAAAATGTAATTTTTAGGAG
1 TTCGAGGGCAAAAATGTAATTTTTAGAAG
* * * *
3317 TTTGAGGGTAAAAATGTGATTTTTGGAAG
1 TTCGAGGGCAAAAATGTAATTTTTAGAAG
* * *
3346 TTC-AGGG-ATATAATGTAATTTTTTGAAA
1 TTCGAGGGCA-AAAATGTAATTTTTAGAAG
* *
3374 TT-TAGGGGCAAAAATGTAATATTTAAGAAG
1 TTCGA-GGGCAAAAATGTAAT-TTTTAGAAG
* * *
3404 TTCGAGGGAAAAAAATGTGATTTTTGGATAG
1 TTCGAGGG-CAAAAATGTAATTTTTAGA-AG
3435 TTC
1 TTC
3438 AGGTACCTTT
Statistics
Matches: 230, Mismatches: 48, Indels: 32
0.74 0.15 0.10
Matches are distributed among these distances:
27 1 0.00
28 56 0.24
29 109 0.47
30 43 0.19
31 21 0.09
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
TTCGAGGGCAAAAATGTAATTTTTAGAAG
Done.