Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007875.1 Kokia drynarioides strain JFW-HI SEQ_122516, 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: 6871
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2324 original size:60 final size:58
Alignment explanation
Indices: 2094--2363 Score: 248
Period size: 60 Copynumber: 4.6 Consensus size: 58
2084 AAATTTGGGC
* **
2094 ATGGCCGACACCCTTTTTTGTCAGAT--AAAAAA-TACAATTTGTT-GTGTTGGCCATACA
1 ATGGGCGACACCCCCTTTT-TCAGATAAAAAAAATTA-AATTT-TTGGTGTTGGCCATACA
* * **
2151 ATGGCCGACA-CCCCTATTTATCTA-AT-AAAAAAATCAAATTTTTGGATGTTGGCCATGTA
1 ATGGGCGACACCCCCT-TTT-TC-AGATAAAAAAAATTAAATTTTTGG-TGTTGGCCATACA
* ** *
2210 ATGGGCGACACCCCCTTTTTCAAATAAAAAATTTTCAAAATTTTTTGGTGTTGGCCATGCA
1 ATGGGCGACACCCCCTTTTTCAGATAAAAAAAATT--AAA-TTTTTGGTGTTGGCCATACA
*
2271 ATGGGCGACACCCCCTTTTCTCAGATAAAAAAAATTACATTTTTGAGTGTTGGCCATACA
1 ATGGGCGACACCCCCTTTT-TCAGATAAAAAAAATTAAATTTTTG-GTGTTGGCCATACA
* *
2331 ATGGTCGACACCCCCTTTTTTCGGATAAAAAAA
1 ATGGGCGACACCCCC-TTTTTCAGATAAAAAAA
2364 TTGTATTTTT
Statistics
Matches: 180, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
56 3 0.02
57 20 0.11
58 17 0.09
59 36 0.20
60 46 0.26
61 38 0.21
62 20 0.11
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (58 bp):
ATGGGCGACACCCCCTTTTTCAGATAAAAAAAATTAAATTTTTGGTGTTGGCCATACA
Found at i:2361 original size:121 final size:119
Alignment explanation
Indices: 2129--2350 Score: 297
Period size: 121 Copynumber: 1.8 Consensus size: 119
2119 TAAAAAATAC
2129 AATTTGTTGTGTTGGCCATACAATGGCCGACACCCCTATTTATCTAATAAAAAAATCAAATTTTT
1 AATTTGTTGTGTTGGCCATACAATGGCCGACACCCCTATTTATCTAATAAAAAAATCAAATTTTT
**
2194 GGATGTTGGCCATGTAATGGGCGACACCCCCTTTTTCAAATAAAAAATTTTCAA
66 GGATGTTGGCCATACAATGGGCGACACCCCCTTTTTCAAATAAAAAATTTTCAA
* * * * * *
2248 AATTTTTTGGTGTTGGCCATGCAATGGGCGACACCCC-CTTT-TCTCAGATAAAAAAAATTACAT
1 AATTTGTT-GTGTTGGCCATACAATGGCCGACACCCCTATTTATCT-A-AT-AAAAAAATCAAAT
*
2311 TTTT-GAGTGTTGGCCATACAATGGTCGACACCCCCTTTTT
62 TTTTGGA-TGTTGGCCATACAATGGGCGACACCCCCTTTTT
2351 TCGGATAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
118 3 0.03
119 11 0.12
120 30 0.34
121 45 0.51
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (119 bp):
AATTTGTTGTGTTGGCCATACAATGGCCGACACCCCTATTTATCTAATAAAAAAATCAAATTTTT
GGATGTTGGCCATACAATGGGCGACACCCCCTTTTTCAAATAAAAAATTTTCAA
Found at i:2372 original size:59 final size:58
Alignment explanation
Indices: 2137--2374 Score: 237
Period size: 59 Copynumber: 4.0 Consensus size: 58
2127 ACAATTTGTT
* * * * *
2137 GTGTTGGCCATACAATGGCCGACA-CCCCTATTTATCTAATAAAAAAATCAAATTTTTG
1 GTGTTGGCCATACAATGGGCGACACCCCCT-TTTTTCAAATAAAAAAATTATATTTTTG
** * *
2195 GATGTTGGCCATGTAATGGGCGACACCCCC-TTTTTCAAATAAAAAATTTTCAAAATTTTTTG
1 G-TGTTGGCCATACAATGGGCGACACCCCCTTTTTTCAAATAAAAAA-ATT--ATA-TTTTTG
* * * *
2257 GTGTTGGCCATGCAATGGGCGACACCCCCTTTTCTCAGATAAAAAAAATTACATTTTTG
1 GTGTTGGCCATACAATGGGCGACACCCCCTTTTTTCAAAT-AAAAAAATTATATTTTTG
* ** *
2316 AGTGTTGGCCATACAATGGTCGACACCCCCTTTTTTCGGATAAAAAAATTGTATTTTTG
1 -GTGTTGGCCATACAATGGGCGACACCCCCTTTTTTCAAATAAAAAAATTATATTTTTG
2375 CATGGCCGAC
Statistics
Matches: 153, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
58 15 0.10
59 43 0.28
60 42 0.27
61 30 0.20
62 17 0.11
63 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (58 bp):
GTGTTGGCCATACAATGGGCGACACCCCCTTTTTTCAAATAAAAAAATTATATTTTTG
Found at i:2427 original size:106 final size:106
Alignment explanation
Indices: 2271--2472 Score: 273
Period size: 106 Copynumber: 1.9 Consensus size: 106
2261 TGGCCATGCA
* * *
2271 ATGGGCGACACCCCCTTTTCTCAGATAAAAAAAATTACATTTTTGAGTGTTGGCCATACAATGGT
1 ATGGCCGACACCCCCTTTTCTCAGATAAAAAAAATTAAATTTTTGAGTGTTGGCCATACAATGGC
*
2336 CGACA-CCCCCTTTTTTCGGATAAAAAAATTGTATTTTTGC
66 CGACACCCCCCTTTTATCGGATAAAAAAATTGTATTTTTGC
* * ** * *
2376 ATGGCCGACACCCTCTTTT-TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATG
1 ATGGCCGACACCCCCTTTTCTCAGATAAAAAAAATT--AAATTTTTGAGTGTTGGCCATACAATG
*
2440 GCCGACACCCCCCTTTTATCGGATAAACAAATT
64 GCCGACACCCCCCTTTTATCGGATAAAAAAATT
2473 TTTTTTTNNN
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 15 0.18
105 17 0.20
106 28 0.34
107 23 0.28
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (106 bp):
ATGGCCGACACCCCCTTTTCTCAGATAAAAAAAATTAAATTTTTGAGTGTTGGCCATACAATGGC
CGACACCCCCCTTTTATCGGATAAAAAAATTGTATTTTTGC
Found at i:2585 original size:61 final size:60
Alignment explanation
Indices: 2506--2710 Score: 270
Period size: 61 Copynumber: 3.4 Consensus size: 60
2496 ACAAATTTTT
* * *
2506 TTTTTTTTTGTGTTGGCCATGCTATGACCGACACCCCATTTTTCTGATAAAAAATTTTCAA
1 TTTTTTTTTATGTTGGCCATGCAATGACCGACACCCCATTTTTCAGATAAAAAA-TTTCAA
* *
2567 TTTTTTTTTATGTTGGCCATGCAATGACCGACATCCCTTTTTTCAGATAAAAAATTTCAA
1 TTTTTTTTTATGTTGGCCATGCAATGACCGACACCCCATTTTTCAGATAAAAAATTTCAA
* * * *
2627 --ATTTTTGAGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTTCAA
1 TTTTTTTTTA-TGTTGGCCATGCAATGACCGACACCCCATTTTTCAGAT-AAAAAATTTCAA
* *
2687 ATTTTTTTTGTGTTGGCCATGCAA
1 TTTTTTTTTATGTTGGCCATGCAA
2711 AGTTTTTTTA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
58 6 0.05
59 35 0.28
60 18 0.14
61 63 0.50
62 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (60 bp):
TTTTTTTTTATGTTGGCCATGCAATGACCGACACCCCATTTTTCAGATAAAAAATTTCAA
Found at i:6416 original size:12 final size:12
Alignment explanation
Indices: 6399--6448 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
6389 TATTTGTGTA
6399 AAAATTAATTTG
1 AAAATTAATTTG
6411 AAAATTAATTTAAGTTG
1 AAAATTAA--T---TTG
6428 AAAATTAATTTG
1 AAAATTAATTTG
6440 AAAATTAAT
1 AAAATTAAT
6449 GAACATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 20 0.61
14 1 0.03
15 1 0.03
17 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:6428 original size:17 final size:17
Alignment explanation
Indices: 6403--6438 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6393 TGTGTAAAAA
*
6403 TTAATTTGAAAATTAAT
1 TTAAGTTGAAAATTAAT
6420 TTAAGTTGAAAATTAAT
1 TTAAGTTGAAAATTAAT
6437 TT
1 TT
6439 GAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TTAAGTTGAAAATTAAT
Found at i:6786 original size:86 final size:85
Alignment explanation
Indices: 6549--6871 Score: 429
Period size: 86 Copynumber: 3.8 Consensus size: 85
6539 TACATATAAA
* * *
6549 ATTAATTTAACATTATTTAAATAGAAAA-GATTATTATTATATTACAATTTATATCAAATATTGT
1 ATTAATTTAA-A-TATTTAAATA-AAAATTATTATTATTATATTACAATTTTTATCAAATAATGT
*
6613 GTTAATTTGACAATACATTATTT
63 GTTGATTTGACAATACATTATTT
* ** * * *
6636 ATCAAATTTTCATATTTAAAGT-ACAA--ATTATTATTATAGTACAATTTTTATCAAATAATATG
1 AT-TAATTTAAATATTTAAA-TAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTG
*
6698 TTGATTTGACAATATATTATTT
64 TTGATTTGACAATACATTATTT
*
6720 AATTAATTTAAATATTTAAATAAAAATTATTATTATTATATTTCAATTTTTATCAAATAATGTGT
1 -ATTAATTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
6785 TGCTTTGACAATACATTATTT
65 TGATTTGACAATACATTATTT
*
6806 ATTAATTTTATATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAA-TTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
6871 T
65 T
Statistics
Matches: 208, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
83 1 0.00
84 69 0.33
85 10 0.05
86 119 0.57
87 4 0.02
88 5 0.02
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (85 bp):
ATTAATTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTT
GATTTGACAATACATTATTT
Done.