Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014936.1 Kokia drynarioides strain JFW-HI SEQ_129979, 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: 436333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 808 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:400948 original size:44 final size:44
Alignment explanation
Indices: 400899--400993 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
400889 CGCGCCTAGT
400899 CACGCGCATCGATCCGATCGTGTCTCCGTCGCTGCACTTCCTCC
1 CACGCGCATCGATCCGATCGTGTCTCCGTCGCTGCACTTCCTCC
*
400943 CACGCGCATCGATCCGATCGTGTCTCCGTCGCTGCGCTTCCTCC
1 CACGCGCATCGATCCGATCGTGTCTCCGTCGCTGCACTTCCTCC
400987 CACGCGC
1 CACGCGC
400994 CTCCGTCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.11, C:0.44, G:0.22, T:0.23
Consensus pattern (44 bp):
CACGCGCATCGATCCGATCGTGTCTCCGTCGCTGCACTTCCTCC
Found at i:401310 original size:15 final size:15
Alignment explanation
Indices: 401270--401311 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
401260 TTAATTATTA
*
401270 TTATTATTAAAACAT
1 TTATTATTAATACAT
* *
401285 TTATTATTAATGCCT
1 TTATTATTAATACAT
401300 TTATTATTAATA
1 TTATTATTAATA
401312 ATAATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (15 bp):
TTATTATTAATACAT
Found at i:402053 original size:24 final size:23
Alignment explanation
Indices: 402026--402070 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
402016 GTACTTGGAC
402026 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
402050 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
402071 CAACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:402061 original size:17 final size:17
Alignment explanation
Indices: 402041--402123 Score: 87
Period size: 17 Copynumber: 4.9 Consensus size: 17
402031 AAATAAATTT
402041 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
402058 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
* *
402075 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
402092 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
402109 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
402124 TGGGCCCAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 1 0.02
17 52 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:402082 original size:34 final size:34
Alignment explanation
Indices: 402042--402123 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
402032 AATAAATTTT
* * *
402042 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
* * *
402076 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
*
402110 AAATTTAAGTTTAT
1 AAATTTAAATTTAT
402124 TGGGCCCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (34 bp):
AAATTTAAATTTATAATAAACTTAAATTTAAAAC
Found at i:406046 original size:16 final size:16
Alignment explanation
Indices: 406027--406057 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
406017 TAATTTTTAA
406027 AATAATTAATTATATT
1 AATAATTAATTATATT
*
406043 AATAATTTATTATAT
1 AATAATTAATTATAT
406058 GACTAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATTAATTATATT
Found at i:408075 original size:116 final size:116
Alignment explanation
Indices: 407931--408163 Score: 371
Period size: 116 Copynumber: 2.0 Consensus size: 116
407921 ACAAATTGAA
* ** *
407931 ATCCAAACTTAGAACACCATTAGAAAAAAAAAT-GAGACTTAGAGTAGCCATCAATCCATTAAAA
1 ATCCAAACTTAGAACACCATTAGAAAAAAAAATCCAGACTTAGAACACCCATCAATCCATTAAAA
* *
407995 AAACCAAAAACTTAACATTACAAATAAAACCCTAAAAATTAACATATCAAAC
66 AAA-CAAAAACATAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
408047 ATCCAAACTTAGAACATCCATTAG-AAAAAAAATCCAGACTTAGAACACCCATCAATCCATTAAA
1 ATCCAAACTTAGAACA-CCATTAGAAAAAAAAATCCAGACTTAGAACACCCATCAATCCATTAAA
*
408111 AAAACAAAAACATAACATCACAAATAAAACTCTAAAAATTAACATATCAAAC
65 AAAACAAAAACATAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
408163 A
1 A
408164 AAACACATCA
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
116 71 0.66
117 37 0.34
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (116 bp):
ATCCAAACTTAGAACACCATTAGAAAAAAAAATCCAGACTTAGAACACCCATCAATCCATTAAAA
AAACAAAAACATAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
Found at i:409372 original size:34 final size:36
Alignment explanation
Indices: 409302--409376 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 36
409292 ATCATTACTT
*
409302 TCCTCTATCAACGACTAAAAATCCCACAGGGACTCA
1 TCCTCTATCAACCACTAAAAATCCCACAGGGACTCA
* * *
409338 TCCT-TATCAACCACTGAAAA-CCCACGGGGGCTCA
1 TCCTCTATCAACCACTAAAAATCCCACAGGGACTCA
409372 TCCTC
1 TCCTC
409377 ATCCACCCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 16 0.47
35 14 0.41
36 4 0.12
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (36 bp):
TCCTCTATCAACCACTAAAAATCCCACAGGGACTCA
Found at i:410023 original size:25 final size:26
Alignment explanation
Indices: 409980--410032 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
409970 TTTCTCGAAG
409980 TTTTACTAGGGGTAAAATCATCAAAA
1 TTTTACTAGGGGTAAAATCATCAAAA
*
410006 TTTTACTA-GGGTAAAATCGTCAAAA
1 TTTTACTAGGGGTAAAATCATCAAAA
410031 TT
1 TT
410033 GTTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (26 bp):
TTTTACTAGGGGTAAAATCATCAAAA
Found at i:414896 original size:2 final size:2
Alignment explanation
Indices: 414889--414920 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
414879 CTTAGTCTTT
414889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414921 GTCTCTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:421622 original size:19 final size:19
Alignment explanation
Indices: 421600--421636 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
421590 TAAAATTAAT
421600 GAAAATT-TCAAAAAAAATA
1 GAAAATTCT-AAAAAAAATA
421619 GAAAATTCTAAAAAAAAT
1 GAAAATTCTAAAAAAAAT
421637 TGGTAGCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
GAAAATTCTAAAAAAAATA
Found at i:422639 original size:27 final size:27
Alignment explanation
Indices: 422574--422639 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
422564 TCTTCCGACT
* * *
422574 AATTATAAGAAAACATACAAAATCTTA
1 AATTATAATATAACATACAAAATATTA
*
422601 AATTTTAATATAACA-ACAAAATAATTA
1 AATTATAATATAACATACAAAAT-ATTA
*
422628 AATTATATTATA
1 AATTATAATATA
422640 TTAAATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (27 bp):
AATTATAATATAACATACAAAATATTA
Found at i:424561 original size:25 final size:25
Alignment explanation
Indices: 424518--424578 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
424508 AATTTCAATA
424518 AATACAAAAAAATCATAATACAAAATT
1 AATA-AAAAAAAT-ATAATACAAAATT
* **
424545 AATTAAAAAAAAT-TAATGCAATTTT
1 AA-TAAAAAAAATATAATACAAAATT
424570 AATAAAAAA
1 AATAAAAAA
424579 TGAGAGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
27 10 0.33
28 2 0.07
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAAAAAATATAATACAAAATT
Found at i:425060 original size:777 final size:759
Alignment explanation
Indices: 423286--425116 Score: 2367
Period size: 777 Copynumber: 2.4 Consensus size: 759
423276 TCTATAATTT
* * * ** * **
423286 TTTTTTATATTTTTGAGTAATTCACCCACAGATCGGTACACATCGATATAAACCGAAATTGATCA
1 TTTTTGATATTTTAGAGTAATTCACCCACAAATCCATACACAT--ATATAAATCGGTATTGATCA
* * *
423351 AAACATATCAATAAATACATATCTCGAGATAT-AAGAATGATTTTTGTTCTCTGCATTTTC-CCA
64 AAACATATCAATAAATACATATCTCGAGATATGAA-AATGATTTTTGTTATCTGTATTTTCTCAA
* *
423414 T-TATTTTTTATTGTGAAAGATGTTTCTCATCATTTCATATTGTTGAATTTGGAGTTGTATTTGG
128 TATTTTTTTTATTCTGAAAGATGTTTCTCATCATTTCATATTGTTGAATTTGG-GTTGTATTTGG
* ** ** * *
423478 TACAGTTGCTAAGAGATCTCAATGTTCATGCAATGAGGCAAATGACAAACAACCATATTGAAAAA
192 TGCAACTGCTAAGAGATCTTGATGTTCATGCAATGAGGCTAATGACAAACAACCATACTGAAAAA
* * * * *
423543 TGCTGGTTTACCATATGCATTTCATGACATGCTTTTATTTTTTTTGCTAATAAAATTTTATAGAT
257 TGCTGGTTTACCATATGTATTTCATGACATGTTTTTATTTTTTTTACGAATAAAATTATATAGAT
423608 ATATTCTCTATGATCATATTTAACAACAAAATAATTAAATTAAATATAAAAATTTATTACTATGT
322 ATATTCTCTATGATCATATTTAACAACAAAATAATTAAATTAAATATAAAAATTTATTACTATGT
* * * *
423673 GCAATTGAACGATCGAAATGTGTTTATCATCCAAACGAATTAGAAAATTTATTATTACTAATTTT
387 GCAATTGAAAGATCGAAATGTGCTTATCATCCAAACGAATTAGAAAATTTATCATTACTAATTTC
** **
423738 AATAAATACAAAAAAAATTGTAATACAAAATTAATTAAAAAACCCTAATGCAATTTTAATAAAAA
452 AATAAATACAAAAAAAATCATAATACAAAATTAATTAAAAAAAACTAATGCAATTTTAATAAAAA
* *
423803 TGAGAGTTGAAAGAAAATTGAAATTTGAGTGAGAATTAAGAGTGAAATGAAAAAGTAAGAAATTA
517 TGAGAGTTGAAAGAAAACTGAAATTTGAGTGAGAATTAAGAGAGAAATGAAAAAGTAAGAAATTA
* * *
423868 GGGGTTTAAATAGGGAAAAAAATAACCGTGGGGGGAGAGTCATTGGAATTCGACCGTTGGGAGTA
582 GGGGTTTAAATAGGAAAAAAAATAACCATGGGGGGAGAGTCATTGGAATTCGACAGTTGGGAGTA
* * * *
423933 GTCGTTGCAAGATGGCCATTAGAGAAAGTGCGTTCAACTGGAAAGTGTTTTCCTGCCAAATCCGC
647 GTCATTGCAAGATGGCCATTAGAGAAAGT-CGTCCAACTGAAAAGTGTTTTCCTACCAAATCCGC
* * **
423998 TAAAAATGCGTCCAGTTCCAAAATCGGCTTAATCAATAATTTTGTATAA
711 TAAAAACGAGTCCAGTTCCAAAATCGGCTTAATCAATAATTTTCCATAA
* * *
424047 TTTTTTATATTTTTGAGTAATTCACCCACAAATCGATACACATTGATATAAATCGGTATTGATCA
1 TTTTTGATATTTTAGAGTAATTCACCCACAAATCCATACACA-T-ATATAAATCGGTATTGATCA
* * * *
424112 AAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTGTCTGTATTTTCT-TAT
64 AAACATATCAATAAATACATATCTCGAGATATGAAAATGATTTTTGTTATCTGTATTTTCTCAAT
* * * * * *
424176 ATATATTTTTATTTTAAAATATGTTTCTCATCATTTCATAATGTTGAATTTGTAGTTGTATTTGG
129 AT-TTTTTTTATTCTGAAAGATGTTTCTCATCATTTCATATTGTTGAATTTG-GGTTGTATTTGG
* *
424241 TGCAACTGCTAAGAGATCTTGATGTTCATGCCATGAGGCTAATGATAAACAACCA-AGCTGAAAA
192 TGCAACTGCTAAGAGATCTTGATGTTCATGCAATGAGGCTAATGACAAACAACCATA-CTGAAAA
*
424305 ATGCTGGTTTACCATATGTATTTCATGACATGTTTTTA-TTTTTTTACGAATAAAATTATATATA
256 ATGCTGGTTTACCATATGTATTTCATGACATGTTTTTATTTTTTTTACGAATAAAATTATATAGA
* *
424369 TATATTTTCTATTATCATATTTTAACAACAAAATAATTCAAATAATTCAAATTTAATATAAAACA
321 TATATTCTCTATGATCATA-TTTAACAACAAAATAATT---A-AATT---A---AATAT--AA-A
* *
424434 AATTTATT-TTCATGTGCAATTGAATAG-TCGAAATGTGCTTGTCATCCAAACGAATT-GAAAAA
372 AATTTATTACT-ATGTGCAATTGAA-AGATCGAAATGTGCTTATCATCCAAACGAATTAG-AAAA
*
424496 TTTATCATTACTAATTTCAATAAATAC-AAAAAAATCATAATACAAAATTAATTAAAAAAAATTA
434 TTTATCATTACTAATTTCAATAAATACAAAAAAAATCATAATACAAAATTAATTAAAAAAAACTA
* *
424560 ATGCAATTTTAATAAAAAATGAGAGTTGAGAGAAGACTGAAATTTGAGTGAGAATTAAGAGAGAA
499 ATGCAATTTTAAT-AAAAATGAGAGTTGAAAGAAAACTGAAATTTGAGTGAGAATTAAGAGAGAA
* *
424625 TTGAAAAAGTAAGAAATTAGGGGTTTAAATAGAGAAAAAAAACTAATCATGGGGGGAGAGTCATT
563 ATGAAAAAGTAAGAAATTAGGGGTTTAAATAG-GAAAAAAAA-TAACCATGGGGGGAGAGTCATT
* * * * *
424690 GGAATTCGACAGTTGGGGGTAGTCATTGC-GGAATTGCCGTTAGAGAGAACGT-GTCCAATTGAA
626 GGAATTCGACAGTTGGGAGTAGTCATTGCAAG-ATGGCCATTAGAGA-AA-GTCGTCCAACTGAA
* * * * *
424753 AAGTGTTTTCTTACCAAATTCGCTAAAAACGAGTCTAGTTTCAAAATTGGCTTAATCAAGTAATT
688 AAGTGTTTTCCTACCAAATCCGCTAAAAACGAGTCCAGTTCCAAAATCGGCTTAATCAA-TAATT
424818 TTCCATAA
752 TTCCATAA
* * *
424826 TTTTTGATATTGTTAGA-TAATTCACCCACAGATCCATACACCA-ATATAAATTGGTATTGATAA
1 TTTTTGATATT-TTAGAGTAATTCACCCACAAATCCATACA-CATATATAAATCGGTATTGATCA
*
424889 AAACATATCAATAAATACATATCTCGAGATATGAAAATGATTTTTGTTATCCGTATTTTCTCAAT
64 AAACATATCAATAAATACATATCTCGAGATATGAAAATGATTTTTGTTATCTGTATTTTCTCAAT
* *
424954 ATTTTTTTTATTCTGAAAGATGTTTCACATCATTTTATATTGTTGAATTTAGGGTTGTATTTGGT
129 ATTTTTTTTATTCTGAAAGATGTTTCTCATCATTTCATATTGTTGAATTT-GGGTTGTATTTGGT
** * ***
425019 GCAACTATTAAGAGATGTTGATGTTCATGCAATGAGGCTAATGACAAATTGCCATACTGAAAAAT
193 GCAACTGCTAAGAGATCTTGATGTTCATGCAATGAGGCTAATGACAAACAACCATACTGAAAAAT
** *
425084 ATTGGTTTACCATAAGTATTTCATGACATGTTT
258 GCTGGTTTACCATATGTATTTCATGACATGTTT
425117 GCTAATAAAA
Statistics
Matches: 932, Mismatches: 102, Indels: 56
0.86 0.09 0.05
Matches are distributed among these distances:
761 114 0.12
762 43 0.05
763 161 0.17
766 1 0.00
767 4 0.00
770 1 0.00
773 5 0.01
775 49 0.05
776 156 0.17
777 223 0.24
778 123 0.13
779 44 0.05
780 8 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (759 bp):
TTTTTGATATTTTAGAGTAATTCACCCACAAATCCATACACATATATAAATCGGTATTGATCAAA
ACATATCAATAAATACATATCTCGAGATATGAAAATGATTTTTGTTATCTGTATTTTCTCAATAT
TTTTTTTATTCTGAAAGATGTTTCTCATCATTTCATATTGTTGAATTTGGGTTGTATTTGGTGCA
ACTGCTAAGAGATCTTGATGTTCATGCAATGAGGCTAATGACAAACAACCATACTGAAAAATGCT
GGTTTACCATATGTATTTCATGACATGTTTTTATTTTTTTTACGAATAAAATTATATAGATATAT
TCTCTATGATCATATTTAACAACAAAATAATTAAATTAAATATAAAAATTTATTACTATGTGCAA
TTGAAAGATCGAAATGTGCTTATCATCCAAACGAATTAGAAAATTTATCATTACTAATTTCAATA
AATACAAAAAAAATCATAATACAAAATTAATTAAAAAAAACTAATGCAATTTTAATAAAAATGAG
AGTTGAAAGAAAACTGAAATTTGAGTGAGAATTAAGAGAGAAATGAAAAAGTAAGAAATTAGGGG
TTTAAATAGGAAAAAAAATAACCATGGGGGGAGAGTCATTGGAATTCGACAGTTGGGAGTAGTCA
TTGCAAGATGGCCATTAGAGAAAGTCGTCCAACTGAAAAGTGTTTTCCTACCAAATCCGCTAAAA
ACGAGTCCAGTTCCAAAATCGGCTTAATCAATAATTTTCCATAA
Found at i:434906 original size:4 final size:4
Alignment explanation
Indices: 434892--434932 Score: 73
Period size: 4 Copynumber: 10.0 Consensus size: 4
434882 CGCTGCAATA
434892 TATG TTATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG
434933 CAGTGTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 32 0.89
5 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:435224 original size:18 final size:16
Alignment explanation
Indices: 435197--435232 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
435187 TACGAATTTT
435197 AAAATCTAAAAAATAAA
1 AAAATCT-AAAAATAAA
435214 AAAATTCTAAAAATAAA
1 AAAA-TCTAAAAATAAA
435231 AA
1 AA
435233 TATAATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATCTAAAAATAAA
Done.