Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012546.1 Kokia drynarioides strain JFW-HI SEQ_127555, 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: 3970
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:3011 original size:204 final size:204
Alignment explanation
Indices: 2650--3723 Score: 1347
Period size: 204 Copynumber: 5.3 Consensus size: 204
2640 GATTATCCAC
*
2650 AAAC-AACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * ** *
2714 GATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* *
2779 ACGGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATCCGTC-TCCTTGATGAGATACAAA
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCC-TGATGAGATACAAA
2843 GAAGCGATTG
195 GAAGCGATTG
* * * *
2853 AAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACACATGTTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
2918 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* *
2983 ACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
3048 AAGCAGATTG
196 AAGC-GATTG
*
3058 AAACAAACGACGCGGTCATCTTCTTGATGAGATACT--G-AGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
3120 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * * **********
3185 ATGGTAAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATNNNNNNNNNNN
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT-GAGATACAAA
**********
3250 NNNNNNNNNN
195 GAAGCGATTG
*
3260 AAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
3325 GATGTGAGCAAATCTTCGAATCTCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * *
3390 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAT
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
3455 AAGCGGATTG
196 AAGC-GATTG
* *
3465 AAACAAACGACGCGATTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * * * * * * *
3530 GA--TGAACAAATCTTCGAA-CCCTAGCTTCATGATGAGATACTGAGAAGCGGGTCAAAGTAATA
66 GATGTGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAAT-
* * * * * * * * * *
3592 AAACGGTTAGCTTCCTAATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGAAACACAG
129 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAA
* **
3657 AGAAGTGGATCA
194 AGAAG-CGATTG
** *** * *
3669 AAACAAGTGATATGGTCATCTT-CTAGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 AAACAAACGACGCGGTCATCTTCCT-GATGAGATACTGAGAAGAAGACCAAATCAA
3724 TGAAACCAGA
Statistics
Matches: 751, Mismatches: 108, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
202 172 0.23
203 54 0.07
204 279 0.37
205 246 0.33
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.21
Consensus pattern (204 bp):
AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAG
AAGCGATTG
Found at i:3388 original size:205 final size:204
Alignment explanation
Indices: 2650--3647 Score: 1186
Period size: 205 Copynumber: 4.9 Consensus size: 204
2640 GATTATCCAC
*
2650 AAAC-AACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * ** *
2714 GATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * * * *
2779 ACGGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATCCGTC-TCCTTGATGAGATACAAA
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCC-TGAT-AAAAAAAAA
* *
2843 GAAGC-GATTG
194 AAAACAGATTG
* * * *
2853 AAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACACATGTTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
2918 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * * * * *
2983 ACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT-AAAAAAAAAA
*
3048 AAGCAGATTG
195 AAACAGATTG
*
3058 AAACAAACGACGCGGTCATCTTCTTGATGAGATACT--G-AGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
3120 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * * **********
3185 ATGGTAAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATNNNNNNNNNNN
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT-AAAAAAAAAA
**********
3250 NNNNNNNNNN
195 AAACAGATTG
*
3260 AAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
3325 GATGTGAGCAAATCTTCGAATCTCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
* * * * * *
3390 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAT
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT-AAAAAAAAAA
* *
3455 AAGCGGATTG
195 AAACAGATTG
* *
3465 AAACAAACGACGCGATTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * * * * * * *
3530 GA--TGAACAAATCTTCGAA-CCCTAGCTTCATGATGAGATACTGAGAAGCGGGTCAAAGTAATA
66 GATGTGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAAT-
* * * * * * *
3592 AAACGGTTAGCTTCCTAATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGAT
129 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT
3648 GAAACACAGA
Statistics
Matches: 693, Mismatches: 94, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
202 172 0.25
203 52 0.08
204 223 0.32
205 246 0.35
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.21
Consensus pattern (204 bp):
AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAA
ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAAAAAAAAAA
AACAGATTG
Found at i:3443 original size:407 final size:407
Alignment explanation
Indices: 2650--3723 Score: 1370
Period size: 407 Copynumber: 2.6 Consensus size: 407
2640 GATTATCCAC
*
2650 AAAC-AACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACT-AGAAGAAGACCAAATCAAACCCACGCTC
* *
2714 GATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
65 GATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
* *
2779 ACGGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATCCGTC-TCCTTGATGAGATACAAA
129 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCC-TGATGAGATACAAA
2843 GAAGCGATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
193 GAAGCGATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
* *
2908 ACACATGTTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATC
258 ACACACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATC
2973 GAAGCAATAAACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATG
323 GAAGCAATAAACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATG
*
3038 AGATACAGAGAAGCAGATTG
388 AGATACAAAGAAGCAGATTG
*
3058 AAACAAACGACGCGGTCATCTTCTTGATGAGATACT-G-AGAAGACCAAATCAAACCCACGCTCG
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTAGAAGAAGACCAAATCAAACCCACGCTCG
* *
3121 ATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCGAAGCAATAAA
66 ATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
* * * ***********
3186 TGGTAAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATNNNNNNNNNNNN
130 CGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGAT-GAGATACAAAG
********* **
3251 NNNNNNNNNAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
194 AAGCGATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
* * *
3316 CCCACGCTCGATGTGAGCAAATCTTCGAATCTCAGCTTCCTGATGAGACACTAAGAAGCAGATCG
259 CACACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATCG
** *
3381 AAGCAATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
324 AAGCAATAAACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
* *
3446 GATACAAATAAGCGGATTG
389 GATACAAAGAAGCAGATTG
* *
3465 AAACAAACGACGCGATTATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACT-AGAAGAAGACCAAATCAAACCCACGCTC
* * * * * *
3530 GA--TGAACAAATCTTCGAACCCTAGCTTCATGATGAGATACTGAGAAGCGGGTCAAAGTAATAA
65 GATGTGAGCAAATCTTCGAACCC-AGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-A
* * * * * * * * * *
3593 AACGGTTAGCTTCCTAATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGAAACACAGA
128 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAA
* ** ** * * * *
3658 GAAGTGGATCAAAACAAGTGATATGGTCATCTT-CTAGATGAGATACTGAGAAGAAGGCCAAGTC
193 GAAG-CGATTGAAACAAACGACACGGTCATCTTCCT-GATGAGATACTGAGAAGAAGACCAAATC
3722 AA
256 AA
3724 TGAAACCAGA
Statistics
Matches: 564, Mismatches: 92, Indels: 19
0.84 0.14 0.03
Matches are distributed among these distances:
406 130 0.23
407 232 0.41
408 53 0.09
409 122 0.22
410 27 0.05
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.21
Consensus pattern (407 bp):
AAACAAACGACGCGGTCATCTTCCTGATGAGATACTAGAAGAAGACCAAATCAAACCCACGCTCG
ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAC
GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAA
GCGATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACA
CACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTAAGAAGCAAATCGAA
GCAATAAACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
TACAAAGAAGCAGATTG
Done.