Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012612.1 Kokia drynarioides strain JFW-HI SEQ_127621, 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: 15575
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:36 original size:9 final size:9
Alignment explanation
Indices: 22--54 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12 AACGTTTTTT
22 AAAAAAGGA
1 AAAAAAGGA
31 AAAAAAGG-
1 AAAAAAGGA
39 AAAAAAGGA
1 AAAAAAGGA
*
48 AAGAAAG
1 AAAAAAG
55 AGGGTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAAAGGA
Found at i:44 original size:17 final size:17
Alignment explanation
Indices: 22--54 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12 AACGTTTTTT
22 AAAAAAGGAAAAAAAGG
1 AAAAAAGGAAAAAAAGG
*
39 AAAAAAGGAAAGAAAG
1 AAAAAAGGAAAAAAAG
55 AGGGTACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAAAAGG
Found at i:855 original size:29 final size:29
Alignment explanation
Indices: 806--1179 Score: 255
Period size: 29 Copynumber: 12.8 Consensus size: 29
796 GAAGGTCTCT
**
806 AAACTGTCCAAAAATTTTATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* * * * * * *
836 GAACTTCAAAAAATACTATTTATGACCTCG
1 AAACTTCCAAAAATTCCATTT-TTACCCCC
* *
866 AAACTTCCAAAAATCCCATTTTTGA-CCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
895 AAACTTCCAAAAATTCCATTTTTAGCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
924 AAACTTCCAAAATTTTCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
954 AAACCATT--AAAAATTACCA-TTTTA-CCTC
1 AAA-C-TTCCAAAAATT-CCATTTTTACCCCC
* * *
982 GAACTTCCAAAAA-TCACATTTTCAACCCCA
1 AAACTTCCAAAAATTC-CATTTT-TACCCCC
* *
1012 AAACTTCAAAAAATTCCATTTTTAGCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
1041 AAACTTCCAAAATTTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
1071 AAACCTCCAAAAATTACCA--TTTATCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCC
* **
1099 GAACTTCCAAAAA-TCTCATTTTTAACCCTG
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
*
1129 AAACTTCCAAAAATTCTA-TTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
1157 AAACTTCTAAAAATGCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
1180 GATCCTACAA
Statistics
Matches: 263, Mismatches: 59, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.02
27 7 0.03
28 45 0.17
29 102 0.39
30 93 0.35
31 10 0.04
32 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:945 original size:58 final size:57
Alignment explanation
Indices: 866--1179 Score: 312
Period size: 58 Copynumber: 5.4 Consensus size: 57
856 TATGACCTCG
* *
866 AAACTTCCAAAAATCCCATTTTTGACCCAAAACTTCCAAAAATTCCATTTTTAGCCTC
1 AAACTTCCAAAAATCCCATTTTTAACCCAAAACTTCCAAAAATTCCA-TTTTAGCCCC
* ** * *
924 AAACTTCCAAAATTTTCATTTTTAACCTCGAAACCATT--AAAAATTACCATTTTA-CCTC
1 AAACTTCCAAAAATCCCATTTTTAACC-C-AAAAC-TTCCAAAAATT-CCATTTTAGCCCC
* * * *
982 GAACTTCCAAAAATCACATTTTCAACCCCAAAACTTCAAAAAATTCCATTTTTAGCCCC
1 AAACTTCCAAAAATCCCATTTTTAA-CCCAAAACTTCCAAAAATTCCA-TTTTAGCCCC
* * * *
1041 AAACTTCCAAAATTTCCATTTTTAACCTCAAAACCTCCAAAAATTACCA-TTTATCCCC
1 AAACTTCCAAAAATCCCATTTTTAACC-CAAAACTTCCAAAAATT-CCATTTTAGCCCC
* * * * *
1099 GAACTTCCAAAAATCTCATTTTTAACCCTGAAACTTCCAAAAATTCTATTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTAACCC-AAAACTTCCAAAAATTCCATTTTAGCCCC
* *
1157 AAACTTCTAAAAATGCCATTTTT
1 AAACTTCCAAAAATCCCATTTTT
1180 GATCCTACAA
Statistics
Matches: 211, Mismatches: 32, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.01
57 10 0.05
58 134 0.64
59 53 0.25
60 10 0.05
61 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATCCCATTTTTAACCCAAAACTTCCAAAAATTCCATTTTAGCCCC
Found at i:1013 original size:117 final size:116
Alignment explanation
Indices: 860--1179 Score: 430
Period size: 117 Copynumber: 2.8 Consensus size: 116
850 ACTATTTATG
* * *
860 ACCTCGAAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCAAAAATTCCATTTTTAGCCTC
1 ACCTCG-AACTTCCAAAAATCACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAGCCCC
* * *
924 AAACTTCCAAAATTTTCATTTTTAACCTCGAAACCAT-TAAAAATTACCATTTT
65 AAACTTCCAAAATTTCCATTTTTAACCTCAAAACC-TCCAAAAATTACCA-TTT
* *
977 ACCTCGAACTTCCAAAAATCACATTTTCAACCCCAAAACTTCAAAAAATTCCATTTTTAGCCCCA
1 ACCTCGAACTTCCAAAAATCACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAGCCCCA
1042 AACTTCCAAAATTTCCATTTTTAACCTCAAAACCTCCAAAAATTACCATTT
66 AACTTCCAAAATTTCCATTTTTAACCTCAAAACCTCCAAAAATTACCATTT
* * ** * *
1093 ATCCCCGAACTTCCAAAAATCTCATTTTTAACCCTGAAACTTCCAAAAATTCTA-TTTTACCCCC
1 A-CCTCGAACTTCCAAAAATCACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAGCCCC
* * *
1157 AAACTTCTAAAAATGCCATTTTT
65 AAACTTCCAAAATTTCCATTTTT
1180 GATCCTACAA
Statistics
Matches: 181, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
116 55 0.30
117 126 0.70
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (116 bp):
ACCTCGAACTTCCAAAAATCACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAGCCCCA
AACTTCCAAAATTTCCATTTTTAACCTCAAAACCTCCAAAAATTACCATTT
Found at i:13376 original size:206 final size:205
Alignment explanation
Indices: 13019--13987 Score: 1202
Period size: 206 Copynumber: 4.8 Consensus size: 205
13009 TGCGATATCC
*
13019 ACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
1 ACAAGCGATGAG-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
* * *
13084 AGCGAGCAAAATCTTTAAACCCCAGCTTCCTAATGAAACACCGAGAAGCAGGTCGAAGCAATAAA
65 AGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAATAAA
* * * *
13149 CGGTTAGCTTCTAGGTGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATAAGATACAGAGA
130 CGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
13214 AGCAGATTGAA
195 AGCAGATTGAA
* * * *
13225 ATAAGCGATGATGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAAACTCACGCTCAA
1 ACAAGCGATGA-GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
* *
13290 AGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAAGTCGAAGCAATAAA
65 AGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAATAAA
13355 CGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
130 CGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
13420 AGCAGATTGAA
195 AGCAGATTGAA
*
13431 ACAAGCGATGCAGTCATCTTCCTGATGAGATACT-----G-AG-----ATCAAACCCAAGCTCAA
1 ACAAGCGATG-AGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
* * * *
13485 AGCGAGTAAAATCTTTGAACCTCAACTTCCTAATGAGACACCGAGAAGTAGGTCGAAGTAATAAA
65 AGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAATAAA
* * *
13550 TGGTTAGCTTCTAGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
130 CGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
*
13615 AGCCGATTGAA
195 AGCAGATTGAA
*
13626 ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG--C--
1 ACAAGCGATG-AGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
* * * * * * *
13687 A-TGATGAATAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATA
65 AGCGA-GCA-AAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAAT-
* * * *
13751 AAACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTAATGAGATACAG
127 AAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAG
*
13816 AGAAGCGGATTGAA
192 AGAAGCAGATTGAA
* * * * * * * * *
13830 ACAAACGACGCGATCATCTTCCTAATGAGATACTGAGGAGAATACTAAATCAAACCCACGCGC-G
1 ACAAGCGATGAG-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
* * * ** * ** * *
13894 A-TGAAC-GAATCTTCAAACCTCAGCTTCCGGATGAGATACTGAGAAGCAGGTCGAAGTAATAAA
65 AGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAAT-AA
* * *
13957 ACGGTCATCTTCCGGATGAGATACTGAGAAG
129 ACGGTTAGCTTCCAGATGAGATACTGAGAAG
13988 AAGGCCAAGT
Statistics
Matches: 678, Mismatches: 65, Indels: 42
0.86 0.08 0.05
Matches are distributed among these distances:
195 179 0.26
200 3 0.00
201 5 0.01
202 3 0.00
203 47 0.07
204 201 0.30
206 234 0.35
207 6 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
ACAAGCGATGAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAA
GCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAGCAGGTCGAAGTAATAAAC
GGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCAGATTGAA
Found at i:13605 original size:195 final size:195
Alignment explanation
Indices: 13067--13866 Score: 998
Period size: 195 Copynumber: 4.0 Consensus size: 195
13057 AGAAGACCAA
* * *
13067 ATCAAACCCACGCTCAAAGCGAGCAAAATCTTTAAACCCCAGCTTCCTAATGAAACACCGAGAAG
1 ATCAAACCCAAGCTCAAAGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAG
* *
13132 CAGGTCGAAGCAATAAACGGTTAGCTTCTAGGTGAGATACTGAGAAGTGAACCAAACTCGTCTTC
66 CAGGTCGAAGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTC
* * *
13197 CTGATAAGATACAGAGAAGCAGATTGAAATAAGCGATG-ATGTCATCTTCTTGATGAGATACTAA
131 CTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCA-GTCATCTTCCTGATGAGATACT--
13261 GAAGAAG
193 ---G-AG
* *
13268 ACCAAATCAAACTCACGCTCAAAGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCG
1 -----ATCAAACCCAAGCTCAAAGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCG
* *
13333 AGAAGCAAGTCGAAGCAATAAACGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTCG
61 AGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGAAGTGAACCAAATTCG
13398 TCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATA
126 TCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATA
13463 CTGAG
191 CTGAG
* * *
13468 ATCAAACCCAAGCTCAAAGCGAGTAAAATCTTTGAACCTCAACTTCCTAATGAGACACCGAGAAG
1 ATCAAACCCAAGCTCAAAGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAG
* * * *
13533 TAGGTCGAAGTAATAAATGGTTAGCTTCTAGATGAGATATTGAGAAGTGAACCAAATTCGTCTTC
66 CAGGTCGAAGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTC
* *
13598 CTGATGAGATACAGAGAAGCCGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAG
131 CTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATACTGAG
** * * * * *
13663 AAGAAGA-CCAA-ATCAAACCCACGCATGATGAATAAATCTTCGAACCCTAGCTTCCTGATGAGA
1 ATCAA-ACCCAAGCTC-AA---A-GC--GA-GCA-AAATCTTTGAACCCCAGCTTCCTAATGAGA
* * * * *
13726 TACTGAGAAGCAGGTCGAAGTAATAAAACGGATAGCTTCCT-GATGAGATACTGAGGAGTGAACC
56 CACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTT-CTAGATGAGATACTGAGAAGTGAACC
* * * * *
13790 AAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAAACGACGC-GATCATCTTCCTA
119 AAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCAG-TCATCTTCCTG
13854 ATGAGATACTGAG
183 ATGAGATACTGAG
13867 GAGAATACTA
Statistics
Matches: 536, Mismatches: 44, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
194 2 0.00
195 191 0.36
196 1 0.00
198 1 0.00
199 2 0.00
200 2 0.00
201 3 0.01
202 2 0.00
203 47 0.09
204 102 0.19
205 2 0.00
206 180 0.34
207 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (195 bp):
ATCAAACCCAAGCTCAAAGCGAGCAAAATCTTTGAACCCCAGCTTCCTAATGAGACACCGAGAAG
CAGGTCGAAGCAATAAACGGTTAGCTTCTAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTC
CTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCAGTCATCTTCCTGATGAGATACTGAG
Found at i:14356 original size:17 final size:17
Alignment explanation
Indices: 14331--14378 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
14321 GAATTTGTTT
* *
14331 TAAAATTAAGTTTATT-
1 TAAATTTAAATTTATTA
14347 TGAAATTTAAATTTATTA
1 T-AAATTTAAATTTATTA
14365 TAAATTTAAATTTA
1 TAAATTTAAATTTA
14379 AAATGTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:14434 original size:15 final size:15
Alignment explanation
Indices: 14416--14471 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
14406 GTACAAATCT
*
14416 AAATGGCACAATTAC
1 AAATGGCCCAATTAC
14431 AAATGGCCCAATTAC
1 AAATGGCCCAATTAC
*
14446 AAATGACCCAATTAC
1 AAATGGCCCAATTAC
14461 AAATGGCCCAA
1 AAATGGCCCAA
14472 GATTCCAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (15 bp):
AAATGGCCCAATTAC
Found at i:15003 original size:3 final size:3
Alignment explanation
Indices: 14997--15024 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14987 ATAATTGTTT
14997 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15025 GAACATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15327 original size:17 final size:17
Alignment explanation
Indices: 15305--15345 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
15295 AGCGTTTTTT
*
15305 AAAAAAGGAATAAAGGA
1 AAAAAAGGAAAAAAGGA
15322 AAAAAAGGAAAAAAGGA
1 AAAAAAGGAAAAAAGGA
15339 AAGAAAA
1 AA-AAAA
15346 AGGGTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAAAAGGAAAAAAGGA
Found at i:15330 original size:9 final size:8
Alignment explanation
Indices: 15305--15340 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
15295 AGCGTTTTTT
15305 AAAAAAGG
1 AAAAAAGG
*
15313 AATAAAGG
1 AAAAAAGG
15321 AAAAAAAGG
1 -AAAAAAGG
15330 AAAAAAGG
1 AAAAAAGG
15338 AAA
1 AAA
15341 GAAAAAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (8 bp):
AAAAAAGG
Done.