Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012490.1 Kokia drynarioides strain JFW-HI SEQ_127494, 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: 4152
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.24
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:3157 original size:139 final size:139
Alignment explanation
Indices: 2783--3469 Score: 1128
Period size: 139 Copynumber: 5.0 Consensus size: 139
2773 ATCCACAAAA
* *
2783 CAGATTCGTATTCCTGATGAGATATAGAGAAACGGATCGAAATAATGATGGGATCATCTTCCTGA
1 CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
* *
2848 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAATGAGCAAATCTTCCTGATAAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
*
2913 GAAGTGAGC
131 GAAGTGAAC
2922 CAGATTCGTATTCCTGAT--GATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
1 CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
* * *
2985 TGAGACACGGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATATTCTTGATGAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
*
3050 AAAGTGAAC
131 GAAGTGAAC
* * *
3059 CAGATTCGTATTCCTGATGAGATACAGAGAAACAGATTGAAACAATAATGGGATCATCTTCCTGA
1 CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
3124 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
3189 GAAGTGAAC
131 GAAGTGAAC
* * *
3198 CAGATTCGTATTCTTGATGAGATATAGAGAAACGGATCGAAACAATGATGAGATCATCTTCCTGA
1 CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
*
3263 TGAGACAATGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
3328 GAAGTGAAC
131 GAAGTGAAC
** *
3337 CAGATTCGTATTCCTGATGAGATACAGAGAAACAGG-TCGAAACAGCGATGGGATTATCTTCCTG
1 CAGATTCGTATTCCTGATGAGATACAGAGAAAC-GGATCGAAACAATGATGGGATCATCTTCCTG
* * * * *
3401 GTGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCTTGATAAGATACAG
65 ATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGG
3466 AGAA
130 AGAA
3470 ACGGATCGAA
Statistics
Matches: 510, Mismatches: 35, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
137 128 0.25
139 380 0.75
140 2 0.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (139 bp):
CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGA
TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
GAAGTGAAC
Found at i:3451 original size:54 final size:54
Alignment explanation
Indices: 3392--3562 Score: 149
Period size: 54 Copynumber: 3.3 Consensus size: 54
3382 CGATGGGATT
*
3392 ATCTTCCTGGTGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
* * * * ** * * * *** *
3446 ATCTTCTTGATAAGATACAGAGAA-ACGGATCGAAAC-A--AT-GATGGGATC--
1 ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACGAGGCTCGAAACGAGCAA
*
3494 ATCTTCTTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
3548 ATCTTCCTGATGAGA
1 ATCTTCCTGATGAGA
3563 TACGAAGAAG
Statistics
Matches: 82, Mismatches: 27, Indels: 16
0.66 0.22 0.13
Matches are distributed among these distances:
48 27 0.33
49 2 0.02
50 5 0.06
51 2 0.02
52 5 0.06
53 2 0.02
54 39 0.48
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (54 bp):
ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
Found at i:3507 original size:241 final size:241
Alignment explanation
Indices: 3208--3710 Score: 835
Period size: 241 Copynumber: 2.1 Consensus size: 241
3198 CAGATTCGTA
*
3208 TTCTTGATGAGATATAGAGAAACGGATCGAAACAATGATGAGATCATCTTCCTGATGAGACAATG
1 TTCTTGATGAGATACAGAGAAACGGATCGAAACAATGATGAGATCATCTTCCTGATGAGACAATG
*
3273 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAAGAAGTGAACC
* * *
3338 AGATTCGTATTCCTGATGAGATACAGAGAAACAGGTCGAAACAGCGATGGGATTATCTTCCTGGT
131 AGATTCGTATTCCTGATGAGATACAGAGAAACAGGTCGAAACAGCGATAGGATCATCTTCCTGAT
*
3403 GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
196 GAGACACTGAGAAGAAAACCCAAACGAAGCTCGAAACGAGCAAATC
* * * *
3449 TTCTTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCTTGATGAGACACTG
1 TTCTTGATGAGATACAGAGAAACGGATCGAAACAATGATGAGATCATCTTCCTGATGAGACAATG
*
3514 AGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAAGAAGTGAACC
* *
3579 AGATTCGTATTCCTGATGAGATATAGAGAAACGGGTCGAAACAGCGATAGGATCATCTTCCTGAT
131 AGATTCGTATTCCTGATGAGATACAGAGAAACAGGTCGAAACAGCGATAGGATCATCTTCCTGAT
* * *
3644 GAGATACTGAGAAGAAAACCCAAATGAAGCTCGAAGCGAGCAAATC
196 GAGACACTGAGAAGAAAACCCAAACGAAGCTCGAAACGAGCAAATC
** *
3690 TTCCCGATGAGATACTGAGAA
1 TTCTTGATGAGATACAGAGAA
3711 GTGAACCAAA
Statistics
Matches: 242, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
241 242 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (241 bp):
TTCTTGATGAGATACAGAGAAACGGATCGAAACAATGATGAGATCATCTTCCTGATGAGACAATG
AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAAGAAGTGAACC
AGATTCGTATTCCTGATGAGATACAGAGAAACAGGTCGAAACAGCGATAGGATCATCTTCCTGAT
GAGACACTGAGAAGAAAACCCAAACGAAGCTCGAAACGAGCAAATC
Found at i:3532 original size:102 final size:102
Alignment explanation
Indices: 3347--3565 Score: 359
Period size: 102 Copynumber: 2.1 Consensus size: 102
3337 CAGATTCGTA
* * *
3347 TTCCTGATGAGATACAGAGAAACAGGTCGAAACAGCGATGGGATTATCTTCCTGGTGAGACACTG
1 TTCCTGATGAGATACAGAGAAACAGGTCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
3412 AGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
66 AGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
* * * *
3449 TTCTTGATAAGATACAGAGAAAC-GGATCGAAACAATGATGGGATCATCTTCTTGATGAGACACT
1 TTCCTGATGAGATACAGAGAAACAGG-TCGAAACAACGATGGGATCATCTTCCTGATGAGACACT
3513 GAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
65 GAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
3551 TTCCTGATGAGATAC
1 TTCCTGATGAGATAC
3566 GAAGAAGTGA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 2 0.02
102 105 0.98
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (102 bp):
TTCCTGATGAGATACAGAGAAACAGGTCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
Found at i:3711 original size:139 final size:139
Alignment explanation
Indices: 3453--3723 Score: 409
Period size: 139 Copynumber: 1.9 Consensus size: 139
3443 CAAATCTTCT
* * *
3453 TGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCTTGATGAGACACTGAGAA
1 TGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTGAGAA
* * *
3518 GAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAAGAAGTGAACCAGAT
66 GAAAACCCAAACGAAGCTCGAAACGAGCAAATCTTCCCGATGAGATACGAAGAAGTGAACCAAAT
3583 TCGTATTCC
131 TCGTATTCC
* * * * *
3592 TGATGAGATATAGAGAAACGGGTCGAAACAGCGATAGGATCATCTTCCTGATGAGATACTGAGAA
1 TGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTGAGAA
* *
3657 GAAAACCCAAATGAAGCTCGAAGCGAGCAAATCTTCCCGATGAGATACTG-AGAAGTGAACCAAA
66 GAAAACCCAAACGAAGCTCGAAACGAGCAAATCTTCCCGATGAGATAC-GAAGAAGTGAACCAAA
3721 TTC
130 TTC
3724 ATAAGCAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
139 117 0.99
140 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (139 bp):
TGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTGAGAA
GAAAACCCAAACGAAGCTCGAAACGAGCAAATCTTCCCGATGAGATACGAAGAAGTGAACCAAAT
TCGTATTCC
Done.