Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014917.1 Kokia drynarioides strain JFW-HI SEQ_129960, 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: 341305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 345 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:313151 original size:117 final size:116
Alignment explanation
Indices: 313005--313233 Score: 282
Period size: 117 Copynumber: 2.0 Consensus size: 116
312995 TATTAGTCTA
*** * *
313005 GTAGTGTTTACAATGTCACTACTGCTTCAGTATAGCATTACGGTGTTTA-TAGTGTCACCATC-A
1 GTAGTGTTTACAATGTCACTACCAATTCAGTATAACATTACAGTGTTTACT-GTGTCACCATCGA
* *
313068 GTTCAGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAGTTCAATATATCATT
65 -TTCAGTATAACATTG-AGTGTTTACAGTGTCACTACCAGTTCAATATATCATT
* * ** * **
313122 GTAGTGTTTACAGTGTCACTGCCAATTCAGTATAATGTTGCAGTGTTTACTGTGTCACTGTCGAT
1 GTAGTGTTTACAATGTCACTACCAATTCAGTATAACATTACAGTGTTTACTGTGTCACCATCGAT
*
313187 TCAGTATAACATTGAGTGTTTACAGTGTCACTACCGGTTCAATATAT
66 TCAGTATAACATTGAGTGTTTACAGTGTCACTACCAGTTCAATATAT
313234 TTTTGACGTG
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
116 31 0.33
117 62 0.65
118 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (116 bp):
GTAGTGTTTACAATGTCACTACCAATTCAGTATAACATTACAGTGTTTACTGTGTCACCATCGAT
TCAGTATAACATTGAGTGTTTACAGTGTCACTACCAGTTCAATATATCATT
Found at i:314837 original size:21 final size:21
Alignment explanation
Indices: 314799--314838 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
314789 TACCCTGTAC
* *
314799 TTCTACCGATACATGTAAGAG
1 TTCTACCGAAACAAGTAAGAG
*
314820 TTCTACTGAAACAAGTAAG
1 TTCTACCGAAACAAGTAAG
314839 CAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAGTAAGAG
Found at i:315243 original size:7 final size:7
Alignment explanation
Indices: 315213--315357 Score: 74
Period size: 7 Copynumber: 21.9 Consensus size: 7
315203 CTCTCCCTCA
315213 TTTC-CC
1 TTTCTCC
*
315219 TTTCCCC
1 TTTCTCC
* *
315226 TTCCTCT
1 TTTCTCC
315233 TTTCTCC
1 TTTCTCC
315240 TTTC-CC
1 TTTCTCC
* *
315246 TTCCCCC
1 TTTCTCC
* *
315253 TTCCCCC
1 TTTCTCC
*
315260 TTCCTCC
1 TTTCTCC
315267 TTTCTCC
1 TTTCTCC
*
315274 TTCCTCC
1 TTTCTCC
315281 -TTC-CC
1 TTTCTCC
*
315286 -TTCCCC
1 TTTCTCC
* * *
315292 CTCCCCC
1 TTTCTCC
* *
315299 TTCCCCC
1 TTTCTCC
315306 TTTCTCC
1 TTTCTCC
315313 TTTCTCC
1 TTTCTCC
315320 TTTC-CC
1 TTTCTCC
315326 TTTC-CC
1 TTTCTCC
*
315332 TTTCCCC
1 TTTCTCC
315339 TTTCT-C
1 TTTCTCC
315345 TATTC-CC
1 T-TTCTCC
315352 TTTCTC
1 TTTCTC
315358 GTTTTCAATT
Statistics
Matches: 116, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.04
6 30 0.26
7 81 0.70
ACGTcount: A:0.01, C:0.54, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTCTCC
Found at i:315306 original size:46 final size:46
Alignment explanation
Indices: 315217--315339 Score: 167
Period size: 46 Copynumber: 2.6 Consensus size: 46
315207 CCCTCATTTC
* *
315217 CCTTTCCCCTTCCTCTTTTCTCCTTTCCCTTCCCCCTTCCCCCTTCCT
1 CCTTTCTCCTTCCTC-TTTC-CCTTTCCCCTCCCCCTTCCCCCTTCCT
* * *
315265 CCTTTCTCCTTCCTCCTTCCCTTCCCCCTCCCCCTTCCCCCTTTCT
1 CCTTTCTCCTTCCTCTTTCCCTTTCCCCTCCCCCTTCCCCCTTCCT
315311 CCTTTCTCCTTTCC-CTTTCCCTTTCCCCT
1 CCTTTCTCC-TTCCTCTTTCCCTTTCCCCT
315340 TTCTCTATTC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 46 0.69
47 7 0.10
48 14 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (46 bp):
CCTTTCTCCTTCCTCTTTCCCTTTCCCCTCCCCCTTCCCCCTTCCT
Found at i:315340 original size:26 final size:26
Alignment explanation
Indices: 315303--315355 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
315293 TCCCCCTTCC
*
315303 CCCTTTCTCCTTTCTCCT-TTCCCTTT
1 CCCTTTCCCCTTTCT-CTATTCCCTTT
315329 CCCTTTCCCCTTTCTCTATTCCCTTT
1 CCCTTTCCCCTTTCTCTATTCCCTTT
315355 C
1 C
315356 TCGTTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (26 bp):
CCCTTTCCCCTTTCTCTATTCCCTTT
Found at i:315354 original size:39 final size:39
Alignment explanation
Indices: 315233--315357 Score: 146
Period size: 39 Copynumber: 3.2 Consensus size: 39
315223 CCCTTCCTCT
315233 TTTCTCCTTTCCCTTCCCCCTTCCCCCTTCCTCCTTTCTCC
1 TTTCTCCTTTCCCTT-CCCCTTCCCCCTTCCT-CTTTCTCC
* * *
315274 TTCCTCC-TTCCCTTCCCCCTCCCCCTTCCCCCTTTCTCC
1 TTTCTCCTTTCCCTTCCCCTTCCCCCTT-CCTCTTTCTCC
* * *
315313 TTTCTCCTTTCCCTTTCCCTTTCCCCTTTCTCTATTC-CC
1 TTTCTCCTTTCCCTTCCCCTTCCCCCTTCCTCT-TTCTCC
315352 TTTCTC
1 TTTCTC
315358 GTTTTCAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
39 37 0.51
40 29 0.40
41 6 0.08
ACGTcount: A:0.01, C:0.54, G:0.00, T:0.45
Consensus pattern (39 bp):
TTTCTCCTTTCCCTTCCCCTTCCCCCTTCCTCTTTCTCC
Found at i:318196 original size:24 final size:24
Alignment explanation
Indices: 318129--318187 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
318119 TTAAACTCTA
318129 TCTGGGCTCGTAAGAGCTAACTAT
1 TCTGGGCTCGTAAGAGCTAACTAT
318153 TCTGGGCTCGTAAGAGCTAA-TCAT
1 TCTGGGCTCGTAAGAGCTAACT-AT
318177 TCTGGGCTCGT
1 TCTGGGCTCGT
318188 GTGGGCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACTAT
Found at i:318807 original size:24 final size:24
Alignment explanation
Indices: 318775--318832 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
318765 ACTTGGGTTC
318775 TATCGGTAGTTTATGGTATTGATG
1 TATCGGTAGTTTATGGTATTGATG
318799 TATCGGTAGTTTATGGTATTGATG
1 TATCGGTAGTTTATGGTATTGATG
318823 TATCGGTAGT
1 TATCGGTAGT
318833 AAGAATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (24 bp):
TATCGGTAGTTTATGGTATTGATG
Found at i:320447 original size:109 final size:109
Alignment explanation
Indices: 320256--320471 Score: 432
Period size: 109 Copynumber: 2.0 Consensus size: 109
320246 ACAAGCATTA
320256 AAGAACAAAGAGAGAGAGTAACTCAACATGTATGGTCTTGTTTAGTGATAAATAATATGCTTTTT
1 AAGAACAAAGAGAGAGAGTAACTCAACATGTATGGTCTTGTTTAGTGATAAATAATATGCTTTTT
320321 TGAAATAACCTCAGGGAATAAGAATGATTTCTATATGTTAATTT
66 TGAAATAACCTCAGGGAATAAGAATGATTTCTATATGTTAATTT
320365 AAGAACAAAGAGAGAGAGTAACTCAACATGTATGGTCTTGTTTAGTGATAAATAATATGCTTTTT
1 AAGAACAAAGAGAGAGAGTAACTCAACATGTATGGTCTTGTTTAGTGATAAATAATATGCTTTTT
320430 TGAAATAACCTCAGGGAATAAGAATGATTTCTATATGTTAAT
66 TGAAATAACCTCAGGGAATAAGAATGATTTCTATATGTTAAT
320472 GCTTCATATT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (109 bp):
AAGAACAAAGAGAGAGAGTAACTCAACATGTATGGTCTTGTTTAGTGATAAATAATATGCTTTTT
TGAAATAACCTCAGGGAATAAGAATGATTTCTATATGTTAATTT
Found at i:320660 original size:22 final size:22
Alignment explanation
Indices: 320629--320677 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
320619 AAGTACTAAG
*
320629 CATCAGCTAACTAGGTATGATT
1 CATCAACTAACTAGGTATGATT
*
320651 CATCAACTAATTAGGTATGATT
1 CATCAACTAACTAGGTATGATT
320673 -ATCAA
1 CATCAA
320678 TATATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
CATCAACTAACTAGGTATGATT
Found at i:324366 original size:17 final size:17
Alignment explanation
Indices: 324327--324366 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
324317 TTTTAAACCG
* *
324327 AATAATTAATTGAATTA
1 AATAATTAATCGAAATA
*
324344 ATTAATTAATCGAAATA
1 AATAATTAATCGAAATA
324361 AATAAT
1 AATAAT
324367 ATATATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (17 bp):
AATAATTAATCGAAATA
Found at i:324505 original size:16 final size:16
Alignment explanation
Indices: 324486--324525 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
324476 TTTGAAAATC
*
324486 ATAATTTTTAAAAAAA
1 ATAATTATTAAAAAAA
*
324502 ATAATTATTATAAAAA
1 ATAATTATTAAAAAAA
*
324518 ATATTTAT
1 ATAATTAT
324526 AATTTGAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTATTAAAAAAA
Found at i:339869 original size:486 final size:485
Alignment explanation
Indices: 339053--340095 Score: 1694
Period size: 486 Copynumber: 2.1 Consensus size: 485
339043 AGCCTCTGCA
*
339053 GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCCACTTCCTGCATCA-TTAAGTTTTTGA
1 GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCTACTTCCTGCATCATTTAAG-TTTT-A
*
339117 CCTCAGTTAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTT
64 CCTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTT
* * *
339182 TTGTCCTTCTGCGAAGATAATCTAGCAAGGACAACCGGGTCAGATGCAAAACAAAATTGAGCTGA
129 TTGCCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGA
* *
339247 ATGTGAAGTTTTAGATTCATGGTAGCAAGAACCATTATCATAACTTGGACCCAGAGAAAGTAAGA
194 ATGTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGA
* * * * *
339312 AGCAACAAACCTGCAAACTATTCAACTTTACTTCCAGCTCATAATTATAGTTTTTGCAGCGTCCA
259 AGAAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCA
*
339377 ATTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCTTCAACATCTGGAC
324 ATTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGAC
*
339442 TTCATTTGAAAGTAACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATT
389 TTCATTTGAAAGTAACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCACCTTCTCAATT
*
339507 CTTCAACAAATCTATTCTTGTCAGCTTCAG-TG
454 CTTCAACAAATCTATTCTTATCAGCTTC-GCTG
* *
339539 GTCCGCAGCTTTTCAGCAAGATCATACTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTCAC
1 GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTT-AC
339604 CTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTT
65 CTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTT
* *
339669 TGCCCTTCTGCGAGGATAATCTAGCAAGGACAACCAGGTCAGATGCCAAACAAAATTGAACTGAA
130 TGCCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAA
*
339734 TGTGAAGTTTTAGATTCTTGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAA
195 TGTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAA
* * * * *
339799 GAAACAAACCTGCAAACTATTCAGCTTCATTTTCAGCTCATCATTATAGATCTTACAGCGTCCGA
260 GAAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCAA
* * * * *
339864 TTTCCTGTTCCTTCTCCTGTTTCTCTCTTTTGATCTGCTTGAGTTCTTGCCTCAACCTCTGGACT
325 TTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGACT
* *
339929 TCATTTGAAAGTGACTGTTGTTCTGCTTTTTGAGCTTCAACTTCTGAAGTGCACCTTCTCAATTC
390 TCATTTGAAAGTAACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCACCTTCTCAATTC
** *
339994 TTCAATGAATCTGTTCTTATCAGCTTCGCTG
455 TTCAACAAATCTATTCTTATCAGCTTCGCTG
* * *
340025 GTCCTCAGCTTTTTAGCAAGACCATTCTTCTCTTGAACTACTTCCTGCATCATTTAAGTTTTACC
1 GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTACC
340090 TCAGTA
66 TCAGTA
340096 CGATAAACAA
Statistics
Matches: 514, Mismatches: 41, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
485 10 0.02
486 499 0.97
487 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (485 bp):
GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTACC
TCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTTT
GCCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAAT
GTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAAG
AAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCAAT
TTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGACTT
CATTTGAAAGTAACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCACCTTCTCAATTCT
TCAACAAATCTATTCTTATCAGCTTCGCTG
Done.