Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012025.1 Kokia drynarioides strain JFW-HI SEQ_127023, 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, 815
Length: 1359
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:289 original size:29 final size:28
Alignment explanation
Indices: 250--626 Score: 219
Period size: 30 Copynumber: 12.8 Consensus size: 28
240 GGAGGTCCTT
250 AAACTTTCCAAAAATTACCATTTTACCTCC
1 AAAC-TTCCAAAAATTACCATTTTACC-CC
* *
280 GAACTTCCAAAAA-TCCCATTTTTTACCCC
1 AAACTTCCAAAAATTACCA--TTTTACCCC
* *
309 GAACTTTCTAAAAATTACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTA-CCCC
* * ** *
339 GAACTCCCAAAAATTATTATTTTACCCTT
1 AAACTTCCAAAAATTACCATTTTACCC-C
* * * *
368 GAACTCCCAAAAA-TCCCATTTTAAACCCTA
1 AAACTTCCAAAAATTACCATTTT--ACCC-C
* *
398 AAATTTCCAAAATTTACCATTTTACCCC
1 AAACTTCCAAAAATTACCATTTTACCCC
* * *
426 TAAACTTCTAAAAA-TCCCATTTTTAACCCT
1 -AAACTTCCAAAAATTACCA-TTTT-ACCCC
*
456 AAACTTTCTAAAAATTACCATTTTACCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCC
* * *
485 AAAACTCCCAAAAA-TCCCATTTTTAACCTCG
1 -AAACTTCCAAAAATTACCA-TTTT-ACC-CC
*
516 AACCTTCCAAAAATTACCATTTTACTCCC
1 AAACTTCCAAAAATTACCATTTTAC-CCC
*
545 TAAAC-TCTCAAAAA-TCCCATTTTTAACCCC
1 -AAACTTC-CAAAAATTACCA-TTTT-ACCCC
* **
575 AAACTTTCTAAAAATTACCATTTCCCCCCC
1 AAAC-TTCCAAAAATTACCATTT-TACCCC
* *
605 GAACTTCCAAAAA-TCCCATTTT
1 AAACTTCCAAAAATTACCATTTT
627 TGATTTCGAA
Statistics
Matches: 275, Mismatches: 44, Indels: 59
0.73 0.12 0.16
Matches are distributed among these distances:
28 28 0.10
29 107 0.39
30 111 0.40
31 29 0.11
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACCATTTTACCCC
Found at i:372 original size:59 final size:59
Alignment explanation
Indices: 246--390 Score: 172
Period size: 59 Copynumber: 2.5 Consensus size: 59
236 CCCCGGAGGT
* * *
246 CCTTAAACTTTCCAAAAATTACCATTTTACCTCCGAACTTCCAAAAATCCCATTTTTTAC
1 CCTTGAACTTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT-CCATTTTTTAC
* * *
306 CC-CGAACTTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT-TATTATTTTAC
1 CCTTGAACTTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCATT-TTTTAC
* *
364 CCTTGAAC-TCCCAAAAA-TCCCATTTTA
1 CCTTGAACTTTCCAAAAATTACCATTTTA
391 AACCCTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 12 0.16
58 15 0.21
59 44 0.60
60 2 0.03
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
CCTTGAACTTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCATTTTTTAC
Found at i:408 original size:59 final size:59
Alignment explanation
Indices: 345--627 Score: 352
Period size: 59 Copynumber: 4.8 Consensus size: 59
335 CCCCGAACTC
** * * * *
345 CCAAAAATTATTATTTTACCCTTGAACTCCCAAAAATCCCATTTTAAACCCTAAAATTT
1 CCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCTAAACTTT
* * *
404 CCAAAATTTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTAACCCTAAACTTT
1 CCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCTAAACTTT
* * * *
463 CTAAAAATTACCATTTTACCCCAAAACTCCCAAAAATCCCATTTTTAA-CCTCGAACCTT
1 CCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCT-AAACTTT
* *
522 CCAAAAATTACCATTTTACTCCCTAAACTCTCAAAAATCCCATTTTTAACCCCAAACTTT
1 CCAAAAATTACCATTTTAC-CCCTAAACTCCCAAAAATCCCATTTTTAACCCTAAACTTT
* ** ** *
582 CTAAAAATTACCATTTCCCCCCCGAACTTCCAAAAATCCCATTTTT
1 CCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTT
628 GATTTCGAAC
Statistics
Matches: 192, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
58 3 0.02
59 139 0.72
60 48 0.25
61 2 0.01
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCTAAACTTT
Found at i:590 original size:119 final size:118
Alignment explanation
Indices: 369--655 Score: 382
Period size: 119 Copynumber: 2.4 Consensus size: 118
359 TTTACCCTTG
* * ** *
369 AACTCCCAAAAATCCCATTTTAAACC-CTAAAATTTCCAAAATTTACCATTTTACCCCTAAACTT
1 AACTCCCAAAAATCCCATTTTTAACCTC-GAACCTTCCAAAAATTACCATTTTACCCCTAAACTT
* *
433 CTAAAAATCCCATTTTTAACCCTAAACTTTCTAAAAATTACCATTTTACCCCAA
65 CTAAAAATCCCATTTTTAACCCCAAACTTTCTAAAAATTACCATTTCACCCCAA
487 AACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACTCCCTAAAC-T
1 AACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTAC-CCCTAAACTT
* **
551 CTCAAAAATCCCATTTTTAACCCCAAACTTTCTAAAAATTACCATTTCCCCCCCG
65 CT-AAAAATCCCATTTTTAACCCCAAACTTTCTAAAAATTACCATTTCACCCCAA
* * ** * *
606 AACTTCCAAAAATCCCATTTTTGATTTCGAACCTT-CTAAAACTACCATTT
1 AACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTT
656 CCCCCCGTGC
Statistics
Matches: 150, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
118 63 0.42
119 87 0.58
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.32
Consensus pattern (118 bp):
AACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTC
TAAAAATCCCATTTTTAACCCCAAACTTTCTAAAAATTACCATTTCACCCCAA
Found at i:643 original size:59 final size:59
Alignment explanation
Indices: 369--661 Score: 261
Period size: 59 Copynumber: 5.0 Consensus size: 59
359 TTTACCCTTG
* * * ** * * ** *
369 AACTCCCAAAAATCCCATTTTAAACC-CTAAAATTTCCAAAATTTACCATTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTAACCTC-GAACCTTCTAAAAATTACCATTTCCCCCCAA
* * * **
428 AACTTCTAAAAATCCCATTTTTAACC-CTAAACTTTCTAAAAATTACCATTTTACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCTC-GAACCTTCTAAAAATTACCATTTCCCCCCAA
* * * * *
487 AACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACTCCCTA
1 AACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCA-TTTCCCCCCAA
* * * **
547 AAC-TCTCAAAAATCCCATTTTTAACCCCAAACTTTCTAAAAATTACCATTTCCCCCCCG
1 AACTTC-CAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTCCCCCCAA
* ** *
606 AACTTCCAAAAATCCCATTTTTGATTTCGAACCTTCT-AAAACTACCATTTCCCCCC
1 AACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTCCCCCC
662 GTGCATCCAA
Statistics
Matches: 198, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
58 18 0.09
59 129 0.65
60 51 0.26
ACGTcount: A:0.35, C:0.32, G:0.01, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATTACCATTTCCCCCCAA
Found at i:833 original size:30 final size:30
Alignment explanation
Indices: 792--1117 Score: 228
Period size: 29 Copynumber: 11.1 Consensus size: 30
782 NNNNNNNNTT
*
792 TTTTA-CCCCGAACTTTCTAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
* **
821 TTTTACCCCCGAAC-TCCCAAAAATTATTA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
* * *
850 TTTTACCCTCGAACTCT-CAAAAA-TCCCA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
* * * *
878 TTTTAAACCCCAAAATTTCCAAAATTTACCA
1 TTTT-ACCCCCGAACTTTCCAAAAATTACCA
** *
909 TTTTA-CCCTAAAC-TTCCAAAAA-TCCCA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
* *** *
936 TTTTTAACCTTAAACTTTCTAAAAATTACCA
1 -TTTTACCCCCGAACTTTCCAAAAATTACCA
** * *
967 TTTTACCCCAAAAC-TCCCAAAAA-TCCCA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
* * *
995 TTTTTAACCCCGAACCTTCAAAAAATTACCA
1 -TTTTACCCCCGAACTTTCCAAAAATTACCA
* * *
1026 TTTTACTCCCTGAACTCT-CAAAAA-TCCCA
1 TTTTAC-CCCCGAACTTTCCAAAAATTACCA
* *
1055 TTTTTAACCCCGAACTTTCTAAAAATTACCA
1 -TTTTACCCCCGAACTTTCCAAAAATTACCA
*
1086 TTTTACCCCCGAAC-TTCCAAAAA-TCCCA
1 TTTTACCCCCGAACTTTCCAAAAATTACCA
1114 TTTT
1 TTTT
1118 TGATTTCGAA
Statistics
Matches: 231, Mismatches: 50, Indels: 33
0.74 0.16 0.11
Matches are distributed among these distances:
27 4 0.02
28 31 0.13
29 95 0.41
30 73 0.32
31 28 0.12
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (30 bp):
TTTTACCCCCGAACTTTCCAAAAATTACCA
Found at i:900 original size:59 final size:58
Alignment explanation
Indices: 792--1118 Score: 347
Period size: 59 Copynumber: 5.6 Consensus size: 58
782 NNNNNNNNTT
* * * * * **
792 TTTTACCCCGAACTTTCTAAAAATTACCA-TTTTACCCCCGAAC-TCCCAAAAATTATTA
1 TTTTACCCCGAACTCTC-AAAAA-TCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
* * *
850 TTTTACCCTCGAACTCTCAAAAATCCCATTTTAAACCCCAAAATTTCCAAAATTTACCA
1 TTTTACCC-CGAACTCTCAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
** ** *
909 TTTTACCCTAAACT-TCCAAAAATCCCATTTTTAACCTTAAACTTTCTAAAAATTACCA
1 TTTTACCCCGAACTCT-CAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
* * * * *
967 TTTTACCCCAAAACTCCCAAAAATCCCATTTTTAACCCCGAACCTTCAAAAAATTACCA
1 TTTTACCCC-GAACTCTCAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
* *
1026 TTTTACTCCCTGAACTCTCAAAAATCCCATTTTTAACCCCGAACTTTCTAAAAATTACCA
1 TTTTAC-CCC-GAACTCTCAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
1086 TTTTACCCCCGAACT-TCCAAAAATCCCATTTTT
1 TTTTA-CCCCGAACTCT-CAAAAATCCCATTTTT
1119 GATTTCGAAC
Statistics
Matches: 230, Mismatches: 30, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
57 5 0.02
58 72 0.31
59 96 0.42
60 56 0.24
61 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (58 bp):
TTTTACCCCGAACTCTCAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATTACCA
Found at i:1178 original size:58 final size:59
Alignment explanation
Indices: 923--1176 Score: 183
Period size: 59 Copynumber: 4.3 Consensus size: 59
913 ACCCTAAACT
* * * * * * **
923 TCCAAAAATCCCATTTTTAACCTT-AAACTTTCTAAAAATTACCATTTTACCCCAAAAC-
1 TCCAAAAATCCCATTTTTGA-TTTCGAACCTTCTAAAAACTACCATTTCACCCCCGAACA
* *** * * * *
981 TCCCAAAAATCCCATTTTTAACCCCGAACCTTCAAAAAATTACCATTTTACTCCCTGAAC-
1 T-CCAAAAATCCCATTTTTGATTTCGAACCTTCTAAAAACTACCATTTCAC-CCCCGAACA
* *** * * * *
1041 TCTCAAAAATCCCATTTTTAACCCCGAACTTTCTAAAAATTACCATTTTACCCCCGAACT
1 TC-CAAAAATCCCATTTTTGATTTCGAACCTTCTAAAAACTACCATTTCACCCCCGAACA
* **
1101 TCCAAAAATCCCATTTTTGATTTCGAACCTTCT-AAAACTACCATTTCCCCCCCGTGCA
1 TCCAAAAATCCCATTTTTGATTTCGAACCTTCTAAAAACTACCATTTCACCCCCGAACA
*
1159 TCCAAAAAGTCTCATTTT
1 TCCAAAAA-TCCCATTTT
1177 GAACTCCGAT
Statistics
Matches: 168, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
58 29 0.17
59 84 0.50
60 55 0.33
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
TCCAAAAATCCCATTTTTGATTTCGAACCTTCTAAAAACTACCATTTCACCCCCGAACA
Done.