Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014539.1 Kokia drynarioides strain JFW-HI SEQ_129578, 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: 13064
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4030 original size:23 final size:23
Alignment explanation
Indices: 4000--4043 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3990 AGTACATCCA
4000 GAATACTTTTAACTCTATAACCC
1 GAATACTTTTAACTCTATAACCC
4023 GAATACTTTTAACTCTATAAC
1 GAATACTTTTAACTCTATAAC
4044 AGTTTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
GAATACTTTTAACTCTATAACCC
Found at i:8521 original size:17 final size:17
Alignment explanation
Indices: 8501--8555 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
8491 AATTTAAAAC
*
8501 TATTTTAAAATTAAGTT
1 TATTTTAAAATTAAATT
*
8518 TATTTTAAATTTAAATT
1 TATTTTAAAATTAAATT
8535 TA--TTAAAATTAAAATT
1 TATTTTAAAATT-AAATT
8551 TATTT
1 TATTT
8556 AAATAATGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 17 0.53
18 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATTTTAAAATTAAATT
Found at i:8543 original size:16 final size:16
Alignment explanation
Indices: 8505--8559 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
8495 TAAAACTATT
*
8505 TTAAAA-TTAAGTTTA
1 TTAAAATTTAAATTTA
*
8520 TTTTAAATTTAAATTTA
1 -TTAAAATTTAAATTTA
*
8537 TTAAAATTAAAATTTA
1 TTAAAATTTAAATTTA
*
8553 TTTAAAT
1 TTAAAAT
8560 AATGTCCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 25 0.76
17 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAAATTTAAATTTA
Found at i:9226 original size:3 final size:3
Alignment explanation
Indices: 9218--9246 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9208 TTTCTAAACA
9218 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9247 ACCGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10034 original size:58 final size:59
Alignment explanation
Indices: 9970--10418 Score: 459
Period size: 58 Copynumber: 7.7 Consensus size: 59
9960 CCATGACCCA
* * * * * *
9970 ATTTTTCC-AATATTAACATTTTACACTCGAACTTCCAAAAATTCCATTTTTGACCCCG
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
10028 ATTTTTCCAAAAATTACCATTTTACCCCCTAAATTCTAAAAATTCCATTTTTAACCAT-G
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACC-TCG
** * * *
10087 A-TTTTCCAAAAATTAAAAATTTACCCCCGAACTTCCAACAATTCCA-TTTTAACC-CTA
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTC-G
* * * * * *
10144 ATTTTTCCAAAAATTATCATTTTACCCCTCAAAATTCCAAAAATTCCATTTTTGACGTAG
1 ATTTTTCCAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
10204 ATTTTTCAAAAAATTACCATTTTACCACCGAACTTCCAAAAATTTCATTTTTAACCTCG
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
10263 A-TTTTCCAAAAATTACCATTTTACCCTCAAAATTCCAAAAATTTCA-TTTTAACCTC-
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
* ** * *
10319 AATTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTTTA-TTTTGACCTCA
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
** * * * *
10377 AAGTATCC-AAAATTATCATTTTACCCCCGAGCATCCAAAAAT
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
10419 CACATTTCTG
Statistics
Matches: 330, Mismatches: 51, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
56 1 0.00
57 100 0.30
58 115 0.35
59 83 0.25
60 31 0.09
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
ATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:10055 original size:29 final size:28
Alignment explanation
Indices: 10002--10362 Score: 204
Period size: 29 Copynumber: 12.4 Consensus size: 28
9992 ACACTCGAAC
*
10002 TTCCAAAAATTCCATTTTTGACCCCGATTT
1 TTCCAAAAATTCCA-TTTTAACCCCGA-TT
* * **
10032 TTCCAAAAATTACCATTTTACCCCCTAAA
1 TTCCAAAAATT-CCATTTTAACCCCGATT
* **
10061 TTCTAAAAATTCCATTTTTAACCATGATT
1 TTCCAAAAATTCCA-TTTTAACCCCGATT
** * * **
10090 TTCCAAAAATTAAAAATTTACCCCCGAAC
1 TTCCAAAAATT-CCATTTTAACCCCGATT
* **
10119 TTCCAACAATTCCATTTTAACCCTAATTT
1 TTCCAAAAATTCCATTTTAACCCCGA-TT
* * * **
10148 TTCCAAAAATTATCATTTTACCCCTCAAAA
1 TTCCAAAAATT-CCATTTTAACCC-CGATT
* ***
10178 TTCCAAAAATTCCATTTTTGACGTAGATTT
1 TTCCAAAAATTCCA-TTTTAACCCCGA-TT
* **
10208 TTCAAAAAATTACCATTTT-ACCACCGAAC
1 TTCCAAAAATT-CCATTTTAACC-CCGATT
* *
10237 TTCCAAAAATTTCATTTTTAACCTCGATT
1 TTCCAAAAATTCCA-TTTTAACCCCGATT
* **
10266 TTCCAAAAATTACCATTTT-ACCCTCAAAA
1 TTCCAAAAATT-CCATTTTAACCC-CGATT
* * *
10295 TTCCAAAAATTTCATTTTAACCTCAATT
1 TTCCAAAAATTCCATTTTAACCCCGATT
* **
10323 TTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATT-CCATTTTAACCCCGATT
10352 TTCCAAAAATT
1 TTCCAAAAATT
10363 TTATTTTGAC
Statistics
Matches: 244, Mismatches: 71, Indels: 33
0.70 0.20 0.09
Matches are distributed among these distances:
28 37 0.15
29 131 0.54
30 68 0.28
31 8 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTAACCCCGATT
Found at i:10313 original size:176 final size:176
Alignment explanation
Indices: 9965--10362 Score: 522
Period size: 176 Copynumber: 2.3 Consensus size: 176
9955 CAGACCCATG
* * *
9965 ACCC-AATTTTTCC-AATATTAACATTTTA-CACTCGAACTTCCAAAAATTCCATTTTTGACCCC
1 ACCCTAATTTTTCCAAAAATTAACATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACCCA
* * * *
10027 GATTTTTCCAAAAATTACCATTTTACCCCCTAAATTCTAAAAATTCCATTTTTAACCATGATTTT
66 GATTTTTCAAAAAATTACCATTTTACCACCGAAATTCCAAAAATTCCATTTTTAACCATGATTTT
* * *
10092 CCAAAAATTAAAAATTTACCCCCGAACTTCCAACAATTCCATTTTA
131 CCAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
* * * **
10138 ACCCTAATTTTTCCAAAAATTATCATTTTACCCCTCAAAATTCCAAAAATTCCATTTTTGACGTA
1 ACCCTAATTTTTCCAAAAATTAACATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACCCA
* *
10203 GATTTTTCAAAAAATTACCATTTTACCACCGAACTTCCAAAAATTTCATTTTTAACC-TCGATTT
66 GATTTTTCAAAAAATTACCATTTTACCACCGAAATTCCAAAAATTCCATTTTTAACCAT-GATTT
** * * *
10267 TCCAAAAATTACCATTTTACCCTCAAAATTCCAAAAATTTCATTTTA
130 TCCAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
*
10314 A-CCTCAA-TTTTCCAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATT
1 ACCCT-AATTTTTCCAAAAATTAACATTTTACCCCTCGAACTTCCAAAAATT
10363 TTATTTTGAC
Statistics
Matches: 195, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
173 4 0.02
174 23 0.12
175 42 0.22
176 126 0.65
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (176 bp):
ACCCTAATTTTTCCAAAAATTAACATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACCCA
GATTTTTCAAAAAATTACCATTTTACCACCGAAATTCCAAAAATTCCATTTTTAACCATGATTTT
CCAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
Found at i:10369 original size:28 final size:29
Alignment explanation
Indices: 9981--10418 Score: 197
Period size: 29 Copynumber: 15.1 Consensus size: 29
9971 TTTTTCCAAT
* *
9981 ATTAACATTTTACACTCGAACTTCCAAAA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
* **
10010 ATT-CCATTTTTGACCC-CGATTTTTCCAAAA
1 ATTATCA-TTTT-ACCCTCGA-ACTTCCAAAA
* * * * *
10040 ATTACCATTTTACCCCCTAAATTCTAAAA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
* * **
10069 ATT-CCATTTTTAACCAT-GATTTTCCAAAA
1 ATTATCA-TTTT-ACCCTCGAACTTCCAAAA
** * * *
10098 ATTAAAAATTTACCCCCGAACTTCCAACA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
* *
10127 ATT-CCATTTTAACCCT--AATTTTTCCAAAA
1 ATTATCATTTT-ACCCTCGAA--CTTCCAAAA
* *
10156 ATTATCATTTTACCCCTCAAAATTCCAAAA
1 ATTATCATTTTA-CCCTCGAACTTCCAAAA
* * * ** *
10186 ATT-CCATTTTTGA-CGTAGATTTTTCAAAAA
1 ATTATCA-TTTT-ACCCTCGA-ACTTCCAAAA
*
10216 ATTACCATTTTACCAC-CGAACTTCCAAAA
1 ATTATCATTTTACC-CTCGAACTTCCAAAA
* **
10245 ATT-TCATTTTTAACCTCGATTTTCCAAAA
1 ATTATCA-TTTTACCCTCGAACTTCCAAAA
* * *
10274 ATTACCATTTTACCCTCAAAATTCCAAAA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
* *
10303 ATT-TCATTTTAACCTC-AATTTTCCAAAA
1 ATTATCATTTTACCCTCGAA-CTTCCAAAA
* *
10331 ATTACCATTTTACCCCCGAACTTCCAAAA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
* * *
10360 ATT-TTATTTTGA-CCTCAAAGTATCC-AAA
1 ATTATCATTTT-ACCCTCGAACT-TCCAAAA
* * *
10388 ATTATCATTTTACCCCCGAGCATCCAAAA
1 ATTATCATTTTACCCTCGAACTTCCAAAA
10417 AT
1 AT
10419 CACATTTCTG
Statistics
Matches: 307, Mismatches: 69, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.01
28 58 0.19
29 166 0.54
30 70 0.23
31 7 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
ATTATCATTTTACCCTCGAACTTCCAAAA
Found at i:10766 original size:29 final size:28
Alignment explanation
Indices: 10671--11030 Score: 176
Period size: 29 Copynumber: 12.4 Consensus size: 28
10661 ATCCTCGAAC
* **
10671 TTCCAAAAATTCCATTTTTGACTTTGATTT
1 TTCCAAAAATTCCA-TTTTAACCCTGA-TT
* **
10701 TTCCAAAAATTACCATTTTACCCCCT-AAA
1 TTCCAAAAATT-CCATTTTA-ACCCTGATT
* *
10730 TTCTAAAAATTCAATTTTTAACCCTGATT
1 TTCCAAAAATTCCA-TTTTAACCCTGATT
** * * * **
10759 TTCCAAAAATTAAAAATTTACCCCCGAAC
1 TTCCAAAAATT-CCATTTTAACCCTGATT
* *
10788 TTCCAACAATTCCATTTTAACCCTAATTT
1 TTCCAAAAATTCCATTTTAACCCTGA-TT
* * **
10817 TTCC-AAAATTACCATTTTACCCCTCAAAA
1 TTCCAAAAATT-CCATTTTAACCCT-GATT
* *
10846 TTCCAAAAATTCCATTTTTGA-CGTAGATTT
1 TTCCAAAAATTCCA-TTTTAACCCT-GA-TT
* **
10876 TTCCAAAAATTACCATTTT-ACCACCGAAC
1 TTCCAAAAATT-CCATTTTAACC-CTGATT
10905 TTCCAAAAA-TCTCATTTTTAA-CCTCGATT
1 TTCCAAAAATTC-CA-TTTTAACCCT-GATT
* **
10934 TTCCAAAAATTACCATTTT-ACCCTTAAAA
1 TTCCAAAAATT-CCATTTTAACCC-TGATT
* *
10963 TTCCAAAAATTCCATTTTAACCTTAATT
1 TTCCAAAAATTCCATTTTAACCCTGATT
* * **
10991 TTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATT-CCATTTTAACCCTGATT
11020 TTCCAAAAATT
1 TTCCAAAAATT
11031 TTATTTTGAC
Statistics
Matches: 249, Mismatches: 57, Indels: 49
0.70 0.16 0.14
Matches are distributed among these distances:
27 1 0.00
28 46 0.18
29 140 0.56
30 53 0.21
31 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTAACCCTGATT
Found at i:10781 original size:58 final size:59
Alignment explanation
Indices: 10639--11030 Score: 426
Period size: 58 Copynumber: 6.7 Consensus size: 59
10629 CCATGACCCA
* * * * * * **
10639 ATTTTTCC-AATATTAACATTTTATCCTCGAACTTCCAAAAATTCCATTTTTGACTTTG
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTCCATTTTTAACCCTG
* * *
10697 ATTTTTCCAAAAATTACCATTTTACCCCCTAAATTCTAAAAATTCAATTTTTAACCCTG
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTCCATTTTTAACCCTG
** * * * *
10756 A-TTTTCCAAAAATTAAAAATTTACCCCCGAACTTCCAACAATTCCA-TTTTAACCCTA
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTCCATTTTTAACCCTG
* * *
10813 ATTTTTCC-AAAATTACCATTTTACCCCTCAAAATTCCAAAAATTCCATTTTTGA-CGTAG
1 ATTTTTCCAAAAATTACCATTTTACCCC-CGAAATTCCAAAAATTCCATTTTTAACCCT-G
* *
10872 ATTTTTCCAAAAATTACCATTTTACCACCGAACTTCCAAAAA-TCTCATTTTTAA-CCTCG
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTC-CATTTTTAACCCT-G
*** *
10931 A-TTTTCCAAAAATTACCATTTTACCCTTAAAATTCCAAAAATTCCA-TTTTAA-CCTT
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTCCATTTTTAACCCTG
* *
10987 AATTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT
1 ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATT
11031 TTATTTTGAC
Statistics
Matches: 280, Mismatches: 45, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
56 1 0.00
57 74 0.26
58 108 0.39
59 79 0.28
60 18 0.06
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (59 bp):
ATTTTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTCCATTTTTAACCCTG
Found at i:10936 original size:175 final size:175
Alignment explanation
Indices: 10634--11030 Score: 545
Period size: 175 Copynumber: 2.3 Consensus size: 175
10624 CAGACCCATG
* * * * *
10634 ACCC-AATTTTTCCAATATTAACATTTTA-TCCTCGAACTTCCAAAAATTCCATTTTTGACTTTG
1 ACCCTAATTTTTCCAAAATTACCATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACGTAG
* * *
10697 ATTTTTCCAAAAATTACCATTTTACCCCCTAAATTCTAAAAATTCAATTTTTAACCCTGATTTTC
66 ATTTTTCCAAAAATTACCATTTTACCACCGAAATTCCAAAAATTCAATTTTTAACCCTGATTTTC
* * *
10762 CAAAAATTAAAAATTTACCCCCGAACTTCCAACAATTCCATTTTA
131 CAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
* *
10807 ACCCTAATTTTTCCAAAATTACCATTTTACCCCTCAAAATTCCAAAAATTCCATTTTTGACGTAG
1 ACCCTAATTTTTCCAAAATTACCATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACGTAG
*
10872 ATTTTTCCAAAAATTACCATTTTACCACCGAACTTCCAAAAATCTC-ATTTTTAA-CCTCGATTT
66 ATTTTTCCAAAAATTACCATTTTACCACCGAAATTCCAAAAAT-TCAATTTTTAACCCT-GATTT
** * **
10935 TCCAAAAATTACCATTTTACCCTTAAAATTCCAAAAATTCCATTTTA
129 TCCAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
*
10982 ACCTTAA-TTTTCCAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATT
1 ACCCTAATTTTTCC-AAAATTACCATTTTACCCCTCGAACTTCCAAAAATT
11031 TTATTTTGAC
Statistics
Matches: 197, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
173 4 0.02
174 45 0.23
175 146 0.74
176 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (175 bp):
ACCCTAATTTTTCCAAAATTACCATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACGTAG
ATTTTTCCAAAAATTACCATTTTACCACCGAAATTCCAAAAATTCAATTTTTAACCCTGATTTTC
CAAAAATTAAAAATTTACCCCCAAAATTCCAAAAATTCCATTTTA
Found at i:11086 original size:29 final size:29
Alignment explanation
Indices: 10992--11086 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
10982 ACCTTAATTT
* *
10992 TCCAAAAATTACCATTTTACCCCCGAA-CT
1 TCCAAAAATTATCATTTTACCCCC-AAGCA
* * * *
11021 TCCAAAAATT-TTATTTTGACCTCAAAGTA
1 TCCAAAAATTATCATTTT-ACCCCCAAGCA
*
11050 TCC-AAAATTATCGTTTTACCCCCAAGCA
1 TCCAAAAATTATCATTTTACCCCCAAGCA
11078 TCCAAAAAT
1 TCCAAAAAT
11087 CACATTTCTG
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 24 0.47
29 27 0.53
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTACCCCCAAGCA
Done.