Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012788.1 Kokia drynarioides strain JFW-HI SEQ_127801, 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: 25203
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:654 original size:30 final size:30
Alignment explanation
Indices: 584--966 Score: 462
Period size: 30 Copynumber: 12.9 Consensus size: 30
574 GGAGGTCCCT
584 AAACTGTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTGACCC-CG
615 -AACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
644 AAAATTCCAAAAATTCCATTTTT-ACCCACG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* * *
674 -AACTTCCAAAGATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
703 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* **
733 AAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
**
763 AAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
793 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * *
822 AAACTTCCAAAAATCCCATTTTCGA-CCTG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
851 AAACTTCCAAAAATTCTATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* * *
881 -AACTTCCAAAAATCCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
910 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
940 AAACTTCCAAAAATTACC-TTTTT-ACCC
1 AAACTTCCAAAAATT-CCATTTTTGACCC
967 TCGGATGTCC
Statistics
Matches: 314, Mismatches: 27, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.00
29 118 0.38
30 193 0.61
31 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:682 original size:59 final size:59
Alignment explanation
Indices: 584--1079 Score: 467
Period size: 59 Copynumber: 8.4 Consensus size: 59
574 GGAGGTCCCT
584 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
* * * * *
644 AAAATTCCAAAAATTCCATTTTTACCCACGAACTTCCAAAGATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
* * * **
703 AAACTTCCAAAAATCCCATTTTTGACCC-CAAAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTGACCCCG
** *
763 AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
* * *
822 AAACTTCCAAAAATCCCATTTTCGA-CCT-GAAACTTCCAAAAATTCTATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCTCG-AACTTCCAAAAATTCCATTTTTGACCC-CG
* * * *
881 -AACTTCCAAAAATCCCATTTTCGA-CCTCGAAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCCG
* * * * * *
940 AAACTTCCAAAAATTACC-TTTTTACCCTCGGA-TGTCCGAAGACTCCATTTTTTACCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACCCCG
* * * * *
999 AAAC-TCTC-AAAATTACCCTTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AAACTTC-CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACCCCG
** *
1058 AATTTTCCCAAAATTACCATTT
1 AAACTTCCAAAAATT-CCATTT
1080 CACCCCCAGA
Statistics
Matches: 377, Mismatches: 43, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
58 67 0.18
59 187 0.50
60 121 0.32
61 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:969 original size:30 final size:30
Alignment explanation
Indices: 584--1079 Score: 458
Period size: 30 Copynumber: 16.7 Consensus size: 30
574 GGAGGTCCCT
584 AAACTGTCCAAAAATTCCATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCG
615 -AACTTCCAAAAATTCCATTTTTGACCC-CG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
644 AAAATTCCAAAAATTCCATTTTTACCCACG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
* *
674 -AACTTCCAAAGATCCCATTTTTGA-CCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
703 AAACTTCCAAAAATCCCATTTTTGACCC-CA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
733 AAACTTCCAAAAATCCCATTTTTGACCCT-A
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
*
763 AAACTTCCAAAAATTCCATTTTTGACCCT-A
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
*
793 AAACTTCCAAAAATTCCATTTTTACCC-CC
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
* *
822 AAACTTCCAAAAATCCCATTTTCGA-CCT-G
1 AAACTTCCAAAAATTCCATTTT-TACCCTCG
*
851 AAACTTCCAAAAATTCTATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
* *
881 -AACTTCCAAAAATCCCATTTTCGA-CCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCTCG
*
910 AAACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
940 AAACTTCCAAAAATTACC-TTTTTACCCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCG
* * * *
970 -GA-TGTCCGAAGACTCCATTTTTTA-CCTCG
1 AAACT-TCCAAAAATTCCA-TTTTTACCCTCG
* *
999 AAAC-TCTC-AAAATTACCCTTTTTACCCCCG
1 AAACTTC-CAAAAATT-CCATTTTTACCCTCG
* *
1029 -AA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCG
** *
1058 AATTTTCCCAAAATTACCATTT
1 AAACTTCCAAAAATT-CCATTT
1080 CACCCCCAGA
Statistics
Matches: 398, Mismatches: 36, Indels: 62
0.80 0.07 0.12
Matches are distributed among these distances:
28 4 0.01
29 161 0.40
30 222 0.56
31 11 0.03
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:15535 original size:95 final size:97
Alignment explanation
Indices: 15426--15611 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 97
15416 TTAAGGGCGG
* ** * *
15426 TGAGATACGATACAGTGCGATGTATTTAA-TT-TATTTTTTGTCTCACGTTATACTATTTAATTT
1 TGAGATACGATACAGTGCAATACATTTAACTTATATTTTTTGTCTCACGCTATAATATTTAATTT
** *
15489 AA-TCGTTATTTTTGTTTTTACACTAATTGTGA
66 AACT-GTTATCGTTATTTTTACACTAATTGTGA
* * *
15521 TGAGATGCGGTACAGTGCAATACATTTAACTTATTTTTTTTGTCTCACGCTATAATATTTAATTT
1 TGAGATACGATACAGTGCAATACATTTAACTTATATTTTTTGTCTCACGCTATAATATTTAATTT
15586 AACTGTTATCGTTATTTTTACACTAA
66 AACTGTTATCGTTATTTTTACACTAA
15612 CTGTAAATAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 24 0.31
96 2 0.03
97 50 0.65
98 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.47
Consensus pattern (97 bp):
TGAGATACGATACAGTGCAATACATTTAACTTATATTTTTTGTCTCACGCTATAATATTTAATTT
AACTGTTATCGTTATTTTTACACTAATTGTGA
Found at i:16697 original size:39 final size:39
Alignment explanation
Indices: 16622--16695 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
16612 TGTTTTACTC
*
16622 TAAATTATATTAATACTCACTCAAGTATTGATTTTTAGA
1 TAAATTATATTAATAATCACTCAAGTATTGATTTTTAGA
* * *
16661 TAAATTATATTAGTAATCATTCAATTA-TGATTTTT
1 TAAATTATATTAATAATCACTCAAGTATTGATTTTT
16696 TATCACCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 8 0.26
39 23 0.74
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (39 bp):
TAAATTATATTAATAATCACTCAAGTATTGATTTTTAGA
Found at i:19969 original size:16 final size:16
Alignment explanation
Indices: 19945--20024 Score: 79
Period size: 16 Copynumber: 5.0 Consensus size: 16
19935 TTAATTTTTT
*
19945 TAAAATTTTAAAAATA
1 TAAATTTTTAAAAATA
* * *
19961 TAAATTTTTTATAATT
1 TAAATTTTTAAAAATA
*
19977 TTAATTTTTAAAAATA
1 TAAATTTTTAAAAATA
* * *
19993 TAAATTTTTTATAATT
1 TAAATTTTTAAAAATA
*
20009 TTAATTTTTAAAAATA
1 TAAATTTTTAAAAATA
20025 ATTTTTTATA
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTTTAAAAATA
Found at i:19976 original size:25 final size:26
Alignment explanation
Indices: 19937--20012 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 26
19927 ACATTTAATT
*
19937 AATTTTTTTAAAATTTTAAAAATATA
1 AATTTTTTTATAATTTTAAAAATATA
19963 AATTTTTTATAATTTTAATTTTTAAAAATATA
1 AATTTTTT-T-A---TAA-TTTTAAAAATATA
19995 AA-TTTTTTATAATTTTAA
1 AATTTTTTTATAATTTTAA
20013 TTTTTAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
25 6 0.14
26 11 0.26
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 7 0.16
32 15 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTTTTTATAATTTTAAAAATATA
Found at i:20047 original size:8 final size:9
Alignment explanation
Indices: 20025--20056 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20015 TTTAAAAATA
20025 ATTTTTTAT
1 ATTTTTTAT
20034 ATTTTTTAT
1 ATTTTTTAT
*
20043 ATTTTTTAA
1 ATTTTTTAT
20052 ATTTT
1 ATTTT
20057 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:20052 original size:32 final size:32
Alignment explanation
Indices: 19950--20048 Score: 150
Period size: 32 Copynumber: 3.1 Consensus size: 32
19940 TTTTTTAAAA
19950 TTTTAAAAATATAAATTTTTTATAATTTTAAT
1 TTTTAAAAATATAAATTTTTTATAATTTTAAT
19982 TTTTAAAAATATAAATTTTTTATAATTTTAAT
1 TTTTAAAAATATAAATTTTTTATAATTTTAAT
*
20014 TTTT-AAAA-AT-AATTTTTTATATTTTTTATAT
1 TTTTAAAAATATAAATTTTTTATA-ATTTTA-AT
20045 TTTT
1 TTTT
20049 TAAATTTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
29 11 0.17
30 7 0.11
31 10 0.16
32 36 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTAAAAATATAAATTTTTTATAATTTTAAT
Found at i:20056 original size:16 final size:16
Alignment explanation
Indices: 19963--20058 Score: 83
Period size: 16 Copynumber: 6.1 Consensus size: 16
19953 TAAAAATATA
19963 AATTTTTTATAATTTT
1 AATTTTTTATAATTTT
* * * *
19979 AATTTTTAAAAATATA
1 AATTTTTTATAATTTT
19995 AATTTTTTATAATTTT
1 AATTTTTTATAATTTT
**
20011 AA-TTTTTA-AA-AAT
1 AATTTTTTATAATTTT
*
20024 AATTTTTTATATTTTTT
1 AATTTTTTATA-ATTTT
20041 ATATTTTTTA-AATTTT
1 A-ATTTTTTATAATTTT
20057 AA
1 AA
20059 AAATTAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
13 3 0.05
14 8 0.13
15 8 0.13
16 31 0.51
17 3 0.05
18 8 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTTTATAATTTT
Found at i:22100 original size:28 final size:28
Alignment explanation
Indices: 22028--22106 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 28
22018 ATAACAATAA
* * *
22028 AAATAAAATTTTATTA-TTTTAATAGTTT
1 AAATTAAA-TTTATTATTTTTAAAAGATT
* * *
22056 ATA-TAAATATATAATTTTTAAAAGATT
1 AAATTAAATTTATTATTTTTAAAAGATT
22083 AAATTAAATTTATTATTTTTAAAA
1 AAATTAAATTTATTATTTTTAAAA
22107 AGTTAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 5 0.12
27 15 0.38
28 20 0.50
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (28 bp):
AAATTAAATTTATTATTTTTAAAAGATT
Found at i:23516 original size:21 final size:21
Alignment explanation
Indices: 23502--23552 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
23492 AAAATTTAAA
23502 AAAATTTTGATAAAAAGAAAT
1 AAAATTTTGATAAAAAGAAAT
23523 AAAATTTTGATAAAAAGAAAT
1 AAAATTTTGATAAAAAGAAAT
23544 AAAATTTTG
1 AAAATTTTG
23553 TTTTCAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATTTTGATAAAAAGAAAT
Found at i:23615 original size:5 final size:5
Alignment explanation
Indices: 23605--23631 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
23595 TTCTCTAACA
23605 TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TA
23632 CATTTATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:24218 original size:18 final size:18
Alignment explanation
Indices: 24195--24237 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24185 AAATAGATTT
24195 TTAATTAAACAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
24213 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
24231 TTAATTA
1 TTAATTA
24238 CCCATTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Done.