Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009660.1 Kokia drynarioides strain JFW-HI SEQ_124378, 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: 7074
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:2164 original size:29 final size:28
Alignment explanation
Indices: 2116--2185 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
2106 CCGTTTTACA
*
2116 AATTTTATAGTTATGCCACTATTTTTCAT
1 AATTTTATAGTTATGCCACTAGTTTTC-T
*
2145 AATTTTATAGCTT-TGTCACTAGTTTTCT
1 AATTTTATAG-TTATGCCACTAGTTTTCT
*
2173 ATATTTTACAGTT
1 A-ATTTTATAGTT
2186 CTGGTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 30 0.83
30 2 0.06
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (28 bp):
AATTTTATAGTTATGCCACTAGTTTTCT
Found at i:2381 original size:27 final size:27
Alignment explanation
Indices: 2351--2411 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
2341 GGTTTTTTAA
2351 ACTATTTTCAAAATTTACAATTTTGCC
1 ACTATTTTCAAAATTTACAATTTTGCC
* * * *
2378 ACTATTTTTTAGATTTTACGATTTTGCC
1 ACTA-TTTTCAAAATTTACAATTTTGCC
2406 ACTATT
1 ACTATT
2412 CTTAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (27 bp):
ACTATTTTCAAAATTTACAATTTTGCC
Found at i:3331 original size:29 final size:29
Alignment explanation
Indices: 3247--3499 Score: 147
Period size: 29 Copynumber: 8.7 Consensus size: 29
3237 CGACTGTGTA
* * *
3247 CCACTA-TTTTACAAATTTTATAGTTATG
1 CCACTAGTTTTCCAAATTTTACAGTTTTG
* * *
3275 CCA-TTG-TTTCCAGAATTTTATAGCTTTG
1 CCACTAGTTTTCCA-AATTTTACAGTTTTG
* *
3303 TCACTAGTTTTCCATATTTTACAGTTTTG
1 CCACTAGTTTTCCAAATTTTACAGTTTTG
* * * * *
3332 CTAGTATTTTTTTTTCAAATTTTATAGTTTTG
1 CCACTA---GTTTTCCAAATTTTACAGTTTTG
* * * * *
3364 CCACTGGTTTTCTAGATTTTACAGTTCTA
1 CCACTAGTTTTCCAAATTTTACAGTTTTG
*
3393 CCATTA-TTTTCCAAAATTTTACAGTTTTG
1 CCACTAGTTTTCC-AAATTTTACAGTTTTG
* * * *
3422 CCACTAGCTTTCCAGATTTTACAATTCTG
1 CCACTAGTTTTCCAAATTTTACAGTTTTG
* * * *
3451 CCATTA-TTTTTCAGATTTTATAGTTTTG
1 CCACTAGTTTTCCAAATTTTACAGTTTTG
* * *
3479 CCATTGGTTTTTCAAAATTTT
1 CCACTAG-TTTTCCAAATTTT
3500 CAACTCTGCC
Statistics
Matches: 167, Mismatches: 47, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
27 6 0.04
28 45 0.27
29 73 0.44
30 21 0.13
32 22 0.13
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (29 bp):
CCACTAGTTTTCCAAATTTTACAGTTTTG
Found at i:3439 original size:58 final size:57
Alignment explanation
Indices: 3247--3481 Score: 213
Period size: 58 Copynumber: 4.1 Consensus size: 57
3237 CGACTGTGTA
* * * * * * *
3247 CCACTA-TTTTACAAATTTTATAGTTATGCCATT-GTTTCCAGAATTTTATAGCTTTG
1 CCACTAGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCA-AATTTTATAGTTTTG
* * ** * *
3303 TCACTAGTTTTCCATATTTTACAGTTTTGCTAGTATTTTTTTTTCAAATTTTATAGTTTTG
1 CCACTAGTTTTCCAGATTTTACAG--TT-CTACCA-TTATTTTCCAAATTTTATAGTTTTG
* * *
3364 CCACTGGTTTTCTAGATTTTACAGTTCTACCATTATTTTCCAAAATTTTACAGTTTTG
1 CCACTAGTTTTCCAGATTTTACAGTTCTACCATTATTTTCC-AAATTTTATAGTTTTG
* * * * *
3422 CCACTAGCTTTCCAGATTTTACAATTCTGCCATTATTTTTCAGATTTTATAGTTTTG
1 CCACTAGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCAAATTTTATAGTTTTG
3479 CCA
1 CCA
3482 TTGGTTTTTC
Statistics
Matches: 144, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
56 5 0.03
57 38 0.26
58 54 0.38
59 4 0.03
60 2 0.01
61 36 0.25
62 5 0.03
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (57 bp):
CCACTAGTTTTCCAGATTTTACAGTTCTACCATTATTTTCCAAATTTTATAGTTTTG
Found at i:3499 original size:58 final size:58
Alignment explanation
Indices: 3342--3537 Score: 191
Period size: 58 Copynumber: 3.4 Consensus size: 58
3332 CTAGTATTTT
* * * *
3342 TTTTTC-AAATTTTATAGTTTTGCCACTGGTTTTCTAGATTTTACAGTTCTACCATTA
1 TTTTTCAAAATTTTACAGTTTTGCCACTGGTTTTCAAGATTTTACAATTCTGCCATTA
* * * *
3399 TTTTCCAAAATTTTACAGTTTTGCCACTAGCTTTCCAGATTTTACAATTCTGCCATTA
1 TTTTTCAAAATTTTACAGTTTTGCCACTGGTTTTCAAGATTTTACAATTCTGCCATTA
* * * * * **
3457 TTTTTC-AGATTTTATAGTTTTGCCATTGGTTTTTCAAAATTTT-CAACTCTGCCGCTA
1 TTTTTCAAAATTTTACAGTTTTGCCACTGG-TTTTCAAGATTTTACAATTCTGCCATTA
* * * *
3514 TTTTTCTAGACTTTACAATTTTGC
1 TTTTTCAAAATTTTACAGTTTTGC
3538 TACTATTTCT
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
57 41 0.36
58 74 0.64
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (58 bp):
TTTTTCAAAATTTTACAGTTTTGCCACTGGTTTTCAAGATTTTACAATTCTGCCATTA
Found at i:3563 original size:27 final size:28
Alignment explanation
Indices: 3516--3572 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3506 TGCCGCTATT
3516 TTTCTAGACTTTACAATTTTGCT-ACTA
1 TTTCTAGACTTTACAATTTTGCTCACTA
* *
3543 TTTCTGAGATTTTACAA-TTTGTTCACTA
1 TTTCT-AGACTTTACAATTTTGCTCACTA
3571 TT
1 TT
3573 CTTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTCTAGACTTTACAATTTTGCTCACTA
Found at i:5035 original size:3 final size:3
Alignment explanation
Indices: 5027--5069 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
5017 AGCAATTTAT
*
5027 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TT- TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5070 AGAACCGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.