Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014016.1 Kokia drynarioides strain JFW-HI SEQ_129047, 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: 10159
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:47 original size:3 final size:3
Alignment explanation
Indices: 39--130 Score: 67
Period size: 3 Copynumber: 30.3 Consensus size: 3
29 ACCTTTAGTC
* * * * * * *
39 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA TTA CTA ATG ACA TTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
87 ATA CTA ATG ACA GTA ATA ATA GTA ATAA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
131 AAAAGGAAAT
Statistics
Matches: 66, Mismatches: 22, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1228 original size:29 final size:28
Alignment explanation
Indices: 1186--1406 Score: 221
Period size: 29 Copynumber: 7.5 Consensus size: 28
1176 CTAAACTGTT
*
1186 CAAAAATTATATTTTTACCCCCGAACTTC
1 CAAAAATTACATTTTTA-CCCCGAACTTC
*
1215 CAAAAATTACATTTTTACCCTCGAACTTT
1 CAAAAATTACATTTTTACCC-CGAACTTC
* * *
1244 CAAATATTACATTTTTTACCTCAAGACTTC
1 CAAAAATTACA-TTTTTACCCCGA-ACTTC
1274 CAAAAATTACATTTTTACCCTC-AAGCTTC
1 CAAAAATTACATTTTTACCC-CGAA-CTTC
* *
1303 CAAAAA-AACCATTTTTGACCCCGAAATTTC
1 CAAAAATTA-CATTTTT-ACCCCG-AACTTC
*
1333 CAAAAATTACATTTTTACCCCAAACTTC
1 CAAAAATTACATTTTTACCCCGAACTTC
* * *
1361 CAAAAATTCCATTTTTGATCCCGAAACTTG
1 CAAAAATTACATTTTT-ACCCCG-AACTTC
1391 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
1407 GCCCCCGAGT
Statistics
Matches: 161, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
28 25 0.16
29 71 0.44
30 56 0.35
31 9 0.06
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCGAACTTC
Found at i:1273 original size:59 final size:56
Alignment explanation
Indices: 1188--1406 Score: 221
Period size: 59 Copynumber: 3.8 Consensus size: 56
1178 AAACTGTTCA
* *
1188 AAAATTATATTTTT-ACCCCCG-AACTTCCAAAAATTACATTTTTACCCTCGAACTTTC
1 AAAATTACATTTTTGA--CCCGAAACTTCCAAAAATTACATTTTTACCCTC-AACTTCC
*
1245 AAATATTACATTTTTTACCTC-AAGACTTCCAAAAATTACATTTTTACCCTCAAGCTTCC
1 AAA-ATTACATTTTTGACC-CGAA-ACTTCCAAAAATTACATTTTTACCCTCAA-CTTCC
** *
1304 AAAAAAACCATTTTTGACCCCGAAATTTCCAAAAATTACATTTTTACCC-CAAACTTCC
1 AAAATTA-CATTTTTGA-CCCGAAACTTCCAAAAATTACATTTTTACCCTC-AACTTCC
* *
1362 AAAAATTCCATTTTTGATCCCGAAACTTGCAAAAATTACCATTTT
1 -AAAATTACATTTTTGA-CCCGAAACTTCCAAAAATTA-CATTTT
1407 GCCCCCGAGT
Statistics
Matches: 138, Mismatches: 12, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
57 5 0.04
58 49 0.36
59 80 0.58
60 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (56 bp):
AAAATTACATTTTTGACCCGAAACTTCCAAAAATTACATTTTTACCCTCAACTTCC
Found at i:1414 original size:30 final size:31
Alignment explanation
Indices: 1186--1414 Score: 204
Period size: 30 Copynumber: 7.8 Consensus size: 31
1176 CTAAACTGTT
*
1186 CAAAAATTA-TATTTTT-ACCCCCG-AACTTC
1 CAAAAATTACCATTTTTGA-CCCCGAAACTTC
*
1215 CAAAAATTA-CATTTTT-ACCCTCG-AACTTT
1 CAAAAATTACCATTTTTGACCC-CGAAACTTC
* * *
1244 CAAATATTA-CATTTTTTACCTC-AAGACTTC
1 CAAAAATTACCATTTTTGACCCCGAA-ACTTC
*
1274 CAAAAATTA-CATTTTT-ACCCTC-AAGCTTC
1 CAAAAATTACCATTTTTGACCC-CGAAACTTC
* *
1303 CAAAAA-AACCATTTTTGACCCCGAAATTTC
1 CAAAAATTACCATTTTTGACCCCGAAACTTC
1333 CAAAAATTA-CATTTTT-ACCCC-AAACTTC
1 CAAAAATTACCATTTTTGACCCCGAAACTTC
* *
1361 CAAAAATT-CCATTTTTGATCCCGAAACTTG
1 CAAAAATTACCATTTTTGACCCCGAAACTTC
*
1391 CAAAAATTACCA-TTTTGCCCCCGA
1 CAAAAATTACCATTTTTGACCCCGA
1415 GTATCCAAAA
Statistics
Matches: 170, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
28 25 0.15
29 70 0.41
30 71 0.42
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (31 bp):
CAAAAATTACCATTTTTGACCCCGAAACTTC
Found at i:1764 original size:9 final size:9
Alignment explanation
Indices: 1750--1775 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1740 CCTCGTGATC
1750 AATACCTTA
1 AATACCTTA
1759 AATACCTTA
1 AATACCTTA
1768 AATACCTT
1 AATACCTT
1776 TAGTCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATACCTTA
Found at i:1789 original size:3 final size:3
Alignment explanation
Indices: 1781--1893 Score: 75
Period size: 3 Copynumber: 37.3 Consensus size: 3
1771 ACCTTTAGTC
* *
1781 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A-A ATTA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * * * * * * * *
1826 TTA TTA CTA ATG ACA TTA GTA ATA CTA ATG ATA GTA ATA ATA GTA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
1875 ATA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1894 AAGAAATCGA
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
2 2 0.02
3 79 0.93
4 4 0.05
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2101 original size:9 final size:9
Alignment explanation
Indices: 2087--2112 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2077 NNNNGTGATC
2087 AATACCTTA
1 AATACCTTA
2096 AATACCTTA
1 AATACCTTA
2105 AATACCTT
1 AATACCTT
2113 TAGTCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATACCTTA
Found at i:2126 original size:3 final size:3
Alignment explanation
Indices: 2118--2233 Score: 90
Period size: 3 Copynumber: 38.3 Consensus size: 3
2108 ACCTTTAGTC
*
2118 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA A-A ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * * * * * * * * * *
2163 TTA TTA TTA CTA ATG ACA TTA GTA ATA CTA ATG ATA GTA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2211 ATAA ATA ATA ATA ATA ATA ATA A
1 AT-A ATA ATA ATA ATA ATA ATA A
2234 AAGAAATTGA
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
2 2 0.02
3 84 0.93
4 4 0.04
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2221 original size:16 final size:16
Alignment explanation
Indices: 2200--2230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2190 CTAATGATAG
*
2200 TAATAATAGTAATAAA
1 TAATAATAATAATAAA
2216 TAATAATAATAATAA
1 TAATAATAATAATAA
2231 TAAAAGAAAT
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:3352 original size:59 final size:58
Alignment explanation
Indices: 3277--3477 Score: 224
Period size: 59 Copynumber: 3.4 Consensus size: 58
3267 AGAGGTCCTT
* *** *
3277 AAACTATCAAAAAATTACATTTTTACCGTCGAACTTTTGAAAATTCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTACATTTTTACC-TCGAACTTCCAAAAATTTCATTTTTGACCCCG
* * * *
3337 ATACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTTAGCTCG
1 AAACTTCCAAAAATTACATTTTTA-CCTCGAACTTCCAAAAATTTCATTTTTGACCCCG
* * * *
3396 AAATTTCCAAAAATTACATTTTTA-CTCCAAACTTCCAAAAATTTTATTTTTGATCCCG
1 AAACTTCCAAAAATTACATTTTTACCT-CGAACTTCCAAAAATTTCATTTTTGACCCCG
*
3454 AAACTTGCAAAAATTACCATTTTT
1 AAACTTCCAAAAATTA-CATTTTT
3478 CCCCTGAGTA
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.02
58 40 0.33
59 72 0.60
60 6 0.05
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.38
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTTACCTCGAACTTCCAAAAATTTCATTTTTGACCCCG
Found at i:3357 original size:30 final size:29
Alignment explanation
Indices: 3277--3481 Score: 175
Period size: 30 Copynumber: 7.0 Consensus size: 29
3267 AGAGGTCCTT
* *
3277 AAACTATCAAAAAATTACATTTTTACCGTCG
1 AAACT-TCCAAAAATTACATTTTTACC-CCG
*** *
3308 -AACTTTTGAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACATTTTT-ACCCCG
*
3337 ATACTTCCAAAAATTACATTTTTACCCTCG
1 AAACTTCCAAAAATTACATTTTTACCC-CG
* * *
3367 -AACTTCCAAAAATTTCATTTTTTAGCTCG
1 AAACTTCCAAAAATTACA-TTTTTACCCCG
* *
3396 AAATTTCCAAAAATTACATTTTTACTCC-
1 AAACTTCCAAAAATTACATTTTTACCCCG
** *
3424 AAACTTCCAAAAATTTTATTTTTGATCCCG
1 AAACTTCCAAAAATTACATTTTT-ACCCCG
*
3454 AAACTTGCAAAAATTACCATTTTT-CCCC
1 AAACTTCCAAAAATTA-CATTTTTACCCC
3482 TGAGTATCCA
Statistics
Matches: 138, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
28 20 0.14
29 50 0.36
30 62 0.45
31 6 0.04
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCG
Done.