Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008791.1 Kokia drynarioides strain JFW-HI SEQ_123474, 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: 45214
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:235 original size:26 final size:26
Alignment explanation
Indices: 206--270 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
196 TCAATAAATA
206 AAAAATATATAAAATTATTAAATA-TT
1 AAAAATATATAAAATTA-TAAATATTT
*
232 -AAAATA-ATATAA-TATAAATATTT
1 AAAAATATATAAAATTATAAATATTT
*
255 AAAAAAATA-AAAATTA
1 AAAAATATATAAAATTA
271 ATATATCCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 13 0.41
25 9 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATATATAAAATTATAAATATTT
Found at i:273 original size:22 final size:23
Alignment explanation
Indices: 224--274 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
214 ATAAAATTAT
* *
224 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAAAAATATAAAA
246 TAAATATTTAAAAAAATA-AAAA
1 TAAATATTTAAAAAAATATAAAA
*
268 TTAATAT
1 TAAATAT
275 ATCCGGACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATATTTAAAAAAATATAAAA
Found at i:5139 original size:4 final size:4
Alignment explanation
Indices: 5130--5164 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5120 TATTAAAGAG
5130 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
5165 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:5181 original size:14 final size:14
Alignment explanation
Indices: 5132--5183 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5122 TTAAAGAGTG
*
5132 TATGTATGTATGTA
1 TATGTGTGTATGTA
*
5146 TGTATGTATGTATGTA
1 --TATGTGTGTATGTA
* *
5162 TGTGTGTGTGTGTA
1 TATGTGTGTATGTA
5176 TATGTGTG
1 TATGTGTG
5184 GCTCTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 18 0.56
16 14 0.44
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
TATGTGTGTATGTA
Found at i:10356 original size:146 final size:147
Alignment explanation
Indices: 9907--10562 Score: 989
Period size: 146 Copynumber: 4.5 Consensus size: 147
9897 TCTTGTCAAC
9907 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
* * * * **
9972 GCAGCCACATTGAA-CATTTTTTTCTTTTATATGTTATAATT-TTCTTA---ATTA-TAG--CTT
66 GCAGCCACATTAAATAATTTTTTTCTTTAATATGTTTTGGTTATT-TTAGCTATTAGT-GCTCTT
* * **
10029 AGTTT-ATAA-GTTACAAAACA
129 ACTTTCA-AATCTTA-GTAA-A
* * *
10049 TTGTGGCTGTAGATTAGTGGTAAGAATTCCACGTTGTGGCCGGGGAGACCTAGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
* * *
10114 GCGGCCACATTAAAT-A--TTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTTCTTTTAC
66 GCAGCCACATTAAATAATTTTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTGCTCTTAC
*
10176 TTTCAAATCTTATTAAA
131 TTTCAAATCTTAGTAAA
10193 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
10258 GCAGCCACATTAAATAATTTTTTTCTTTAATATG-TTTGGTTATTTTAGCTATTAGTGCTCTTAC
66 GCAGCCACATTAAATAATTTTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTGCTCTTAC
10322 TTTCAAATCTTAGTAAA
131 TTTCAAATCTTAGTAAA
10339 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
10404 GCAGCCACATTAAATAATATTTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTGCTCTTA
66 GCAGCCACATTAAATAAT-TTTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTGCTCTTA
10469 CTTTCAAATCTTAGTAAA
130 CTTTCAAATCTTAGTAAA
* *
10487 TTGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGCCGTGGAGACCAGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
10552 GCAGCCACATT
66 GCAGCCACATT
10563 TGTCCTTTTT
Statistics
Matches: 475, Mismatches: 24, Indels: 24
0.91 0.05 0.05
Matches are distributed among these distances:
140 22 0.05
141 2 0.00
142 75 0.16
143 4 0.01
144 78 0.16
145 11 0.02
146 131 0.28
147 31 0.07
148 121 0.25
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (147 bp):
TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
GCAGCCACATTAAATAATTTTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAGTGCTCTTAC
TTTCAAATCTTAGTAAA
Found at i:10506 original size:294 final size:286
Alignment explanation
Indices: 9907--10562 Score: 982
Period size: 294 Copynumber: 2.3 Consensus size: 286
9897 TCTTGTCAAC
9907 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
* * * *
9972 GCAGCCACATTGAACATTTTTTTCTTTTATATGTTATAATTTTCTTAATTATAGCTTAGTTTATA
66 GCAGCCACATTAAAAATTTTTTTCTTTAATATGTTATAATTTTCTTAATTATAGCTTACTTTATA
*
10037 AGTTACAAAACATTGTGGCTGTAGATTAGTGGTAAGAATTCCACGTTGTGGCCGGGGAGACCTAG
131 ACTTACAAAACATTGTGGCTGTAGATTAGTGGTAAGAATTCCACGTTGTGGCCGGGGAGACCTAG
*
10102 GCTCGAATCCCAGCGGCCACATTAAATATTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAG
196 GCTCGAATCCCAGCAGCCACATTAAATATTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAG
* * *
10167 TTCTTTTACTTTCAAATCTTATTAAA
261 TGCTCTTACTTTCAAATCTTAGTAAA
10193 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
**
10258 GCAGCCACATTAAATAATTTTTTTCTTTAATATGTT-TGGTTATT-TTAGCTATTAGT-GCTCTT
66 GCAGCCACATTAAA-AATTTTTTTCTTTAATATGTTATAATT-TTCTTA---ATTA-TAG--CTT
** * *
10320 ACTTTCA-AATCTTA-GTAA-ATTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGT
123 ACTTT-ATAA-CTTACAAAACATTGTGGCTGTAGATTAGTGGTAAGAATTCCACGTTGTGGCCGG
*
10382 GGAGACCTGGGCTCGAATCCCAGCAGCCACATTAAATAATATTTTTTCTTTAATATGTTTTGGTT
186 GGAGACCTAGGCTCGAATCCCAGCAGCCACATT--A-AATA-TTTTTCTTTAATATGTTTTGGTT
10447 ATTTTAGCTATTAGTGCTCTTACTTTCAAATCTTAGTAAA
247 ATTTTAGCTATTAGTGCTCTTACTTTCAAATCTTAGTAAA
* *
10487 TTGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGCCGTGGAGACCAGGGCTCGAATCCCA
1 TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
10552 GCAGCCACATT
66 GCAGCCACATT
10563 TGTCCTTTTT
Statistics
Matches: 338, Mismatches: 18, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
286 84 0.25
287 21 0.06
289 5 0.01
290 74 0.22
291 11 0.03
292 5 0.01
293 4 0.01
294 134 0.40
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (286 bp):
TTGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCA
GCAGCCACATTAAAAATTTTTTTCTTTAATATGTTATAATTTTCTTAATTATAGCTTACTTTATA
ACTTACAAAACATTGTGGCTGTAGATTAGTGGTAAGAATTCCACGTTGTGGCCGGGGAGACCTAG
GCTCGAATCCCAGCAGCCACATTAAATATTTTTCTTTAATATGTTTTGGTTATTTTAGCTATTAG
TGCTCTTACTTTCAAATCTTAGTAAA
Found at i:17875 original size:23 final size:22
Alignment explanation
Indices: 17834--17885 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
17824 CTACATGTTT
17834 GTTTTTTAAATTCATTTGTCAAG
1 GTTTTTTAAATTCATTTGTC-AG
*
17857 GTTTTTTAAGTTTCA-TTGTCAG
1 GTTTTTTAA-ATTCATTTGTCAG
*
17879 ATTTTTT
1 GTTTTTT
17886 TTTGGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 14 0.54
24 4 0.15
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (22 bp):
GTTTTTTAAATTCATTTGTCAG
Found at i:19553 original size:69 final size:69
Alignment explanation
Indices: 19438--19575 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
19428 CTCAATCAAT
*
19438 TTGGGTCAAGTCAGTTCGAGTTTTAAAATTGTTGACAATTGGTTGATTTTTTCAGGAGAAGTTTT
1 TTGGGTCAAGTCAGTTCGAGTTTTAAAATTGTTGACAATTGATTGATTTTTTCAGGAGAAGTTTT
19503 CTAA
66 CTAA
* *
19507 TTGGGTCAAGTTAGTTCGAGTTTTAAAATTGTTGACAATTGATTGATTTTTTCGGGAGAAGTTTT
1 TTGGGTCAAGTCAGTTCGAGTTTTAAAATTGTTGACAATTGATTGATTTTTTCAGGAGAAGTTTT
19572 CTAA
66 CTAA
19576 GTGTCTACCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (69 bp):
TTGGGTCAAGTCAGTTCGAGTTTTAAAATTGTTGACAATTGATTGATTTTTTCAGGAGAAGTTTT
CTAA
Found at i:20990 original size:31 final size:29
Alignment explanation
Indices: 20926--21017 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 29
20916 ATCAAATTTG
* **
20926 ATACATG-AACTTTGATT-TGGTGAAATT
1 ATACATGAAACTTTGATTGTGATTCAATT
*
20953 ACACATGAAAC-TTGAATTGTGATTCATATAT
1 ATACATGAAACTTTG-ATTGTGATTCA-AT-T
*
20984 ATACATGAAACTTTGATTTTGATTCAATT
1 ATACATGAAACTTTGATTGTGATTCAATT
21013 ATACA
1 ATACA
21018 CATTTAAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 9 0.17
28 6 0.11
29 10 0.19
30 4 0.08
31 21 0.40
32 3 0.06
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
ATACATGAAACTTTGATTGTGATTCAATT
Found at i:28153 original size:148 final size:149
Alignment explanation
Indices: 27635--28226 Score: 786
Period size: 148 Copynumber: 4.0 Consensus size: 149
27625 TGTTTTGCTT
* * * *
27635 AAAAATACGGATCTGAAGTTTATTAGCTAAGATTGCAAAGATTTACGTAGGAAGAACAGA-TTTA
1 AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTACGTAGGAAGAACA-ACTTTA
* * *
27699 ACTTGTTTTTAGATTCTAGTTCGAAGCTTGAA-CGGTACCGCTTTTTGAATCTTTATGTGAACTG
65 GCTTGTTTTTAGATTCTAGTTCGAAGC-TGAATC-GTACTGGTTTTTGAATCTTTATGTGAACTG
* * *
27763 TTAGCTATTTGATGAGTTATAAAA
128 ATAGCTATTTGATGA-AT-TACAA
* * * * * *
27787 AAAAATACAGAACTGAAGTTTACAAGCTAAG-TTCCTATGA-CTAGCGTAGGAAGAACAGCTTTA
1 AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTA-CGTAGGAAGAACAACTTTA
* * *
27850 GCTTGTTTTTGGATTATAGTTCGAAGCTGAATCGTACTGGTTTCTGAATCTTTATGTGAACTG-T
65 GCTTGTTTTTAGATTCTAGTTCGAAGCTGAATCGTACTGGTTTTTGAATCTTTATGTGAACTGAT
* *
27914 AGCTATTTGATGGATTGC-A
130 AGCTATTTGATGAATTACAA
* *
27933 AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTACGTAGGGAGAAAAACTTTAG
1 AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTACGTAGGAAGAACAACTTTAG
*
27998 ATTGTTTTTAGATTCTAGTTCGAAGCTGAATCGTACTGGTTTTTGAATCTTTATGTGAACTG-TA
66 CTTGTTTTTAGATTCTAGTTCGAAGCTGAATCGTACTGGTTTTTGAATCTTTATGTGAACTGATA
28062 GCTATTTGATGAATTACAA
131 GCTATTTGATGAATTACAA
*
28081 AAAAATACAGATCTGAAGTTTACGAGCTAAGTTTGCTAAGATTTACGTAGGAAGAACAACTTTAG
1 AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTACGTAGGAAGAACAACTTTAG
* * * * *
28146 CTTGTTTTTAGATCCTAGTTCGAAGCTGAATTGTA-TTGTTGCTTGAATCTTTAGGTGAACTGAT
66 CTTGTTTTTAGATTCTAGTTCGAAGCTGAATCGTACTGGTT-TTTGAATCTTTATGTGAACTGAT
*
28210 AGCTATTTGTTGAATTA
130 AGCTATTTGATGAATTA
28227 AACTTTGGCT
Statistics
Matches: 389, Mismatches: 43, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
146 30 0.08
147 104 0.27
148 117 0.30
149 30 0.08
150 33 0.08
151 48 0.12
152 27 0.07
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (149 bp):
AAAAATACAGATCTGAAGTTTACTAGCTAAGTTTGCTAAGATTTACGTAGGAAGAACAACTTTAG
CTTGTTTTTAGATTCTAGTTCGAAGCTGAATCGTACTGGTTTTTGAATCTTTATGTGAACTGATA
GCTATTTGATGAATTACAA
Found at i:33654 original size:31 final size:33
Alignment explanation
Indices: 33619--33683 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
33609 TAGAAATAAT
* *
33619 AAAAT-TACATTTTGACCCTTCAAAAT-ATGAA
1 AAAATATACATTTAGACCCTTAAAAATGATGAA
*
33650 AAAATATACATTTAGTCCCTTAAAAATGATGAA
1 AAAATATACATTTAGACCCTTAAAAATGATGAA
33683 A
1 A
33684 TTATAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 5 0.17
32 18 0.62
33 6 0.21
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.31
Consensus pattern (33 bp):
AAAATATACATTTAGACCCTTAAAAATGATGAA
Found at i:34750 original size:12 final size:12
Alignment explanation
Indices: 34733--34774 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34723 AATATATATC
*
34733 AATCAAAATCAA
1 AATCAAAACCAA
34745 AATCAAAACCAA
1 AATCAAAACCAA
*
34757 AA-CTAAAACTAA
1 AATC-AAAACCAA
34769 AATCAA
1 AATCAA
34775 TAGAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 24 0.92
13 1 0.04
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (12 bp):
AATCAAAACCAA
Found at i:39071 original size:23 final size:25
Alignment explanation
Indices: 39028--39077 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
39018 ATTAAAGAGG
39028 AAACAGAGAAGAAAATAGAAAAGAAA
1 AAACAGAG-AGAAAATAGAAAAGAAA
*
39054 AAACAGAG-GAAAAT-GAAAATAAA
1 AAACAGAGAGAAAATAGAAAAGAAA
39077 A
1 A
39078 CAGTGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
26 8 0.35
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (25 bp):
AAACAGAGAGAAAATAGAAAAGAAA
Done.