Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012274.1 Kokia drynarioides strain JFW-HI SEQ_127275, 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: 15679
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Found at i:3926 original size:31 final size:31
Alignment explanation
Indices: 3891--4030 Score: 108
Period size: 31 Copynumber: 4.5 Consensus size: 31
3881 TTATTATAAT
* *
3891 ATTTGGTATTTAAACTTGACATTTTTTCTTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
* ** *
3922 ATTTGGTACCTAAACTT---TTTTTTTGGTTCA
1 ATTTGGTACTTAAACTTGACACTTTTT-CTT-A
* * * *
3952 ATTTAGTACTCAAACGTGACACTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
* *
3983 ATTTGATACCTAAACTTGACAACTTTTT-TTA
1 ATTTGGTACTTAAACTTGAC-ACTTTTTCTTA
*
4014 AGTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
4031 TTTGGGGTCC
Statistics
Matches: 82, Mismatches: 21, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
28 6 0.07
29 2 0.02
30 14 0.17
31 47 0.57
32 8 0.10
33 5 0.06
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTTTTCTTA
Found at i:4370 original size:60 final size:59
Alignment explanation
Indices: 4255--4407 Score: 166
Period size: 57 Copynumber: 2.6 Consensus size: 59
4245 ATTGAATCTT
* * ** * * **
4255 TAAAAAAAAAAGCTTAGGTACCAAATTAG-GAAATGTCAAGTTCAGGTTCCCAATTGGG
1 TAAAAAAAAAAGTTTAGGTACCAAATTAGAAAAATGTCAAGTTCAAATACCAAATTGAA
** *
4313 T-CTAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAGTGTCAAGTTCAAATACCAAATTGAA
1 TAAAAAAAAAAGTTTAGGTACCAAATT-AGAAAAA-TGTCAAGTTCAAATACCAAATTGAA
4373 TAAAAAAAAAAGGTTTAGGTACCAAATTAGAAAAA
1 TAAAAAAAAAA-GTTTAGGTACCAAATTAGAAAAA
4408 AAATTTCAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
57 21 0.28
58 3 0.04
59 3 0.04
60 20 0.26
61 14 0.18
62 15 0.20
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAAAAAAAAAGTTTAGGTACCAAATTAGAAAAATGTCAAGTTCAAATACCAAATTGAA
Found at i:4421 original size:32 final size:31
Alignment explanation
Indices: 4321--4431 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
4311 GGTCTAAAAA
* * *
4321 AAGTTTAGGTGCCAAATTA-AGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAAAT-TC
* ** **
4352 AAGTTCAAATACCAAATT-GAATAAAAAA-AA
1 AAGTTTAGGTACCAAATTAGAA-AAAAAATTC
4382 AAGGTTTAGGTACCAAATTAGAAAAAAAATTTC
1 AA-GTTTAGGTACCAAATTAGAAAAAAAA-TTC
*
4415 AAGTTTAGGTTCCAAAT
1 AAGTTTAGGTACCAAAT
4432 ATTATATTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
30 2 0.03
31 34 0.57
32 22 0.37
33 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGAAAAAAAATTC
Found at i:5196 original size:17 final size:18
Alignment explanation
Indices: 5171--5213 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5161 TTATATTTTG
*
5171 AAATTTAATAAAAG-AAA
1 AAATATAATAAAAGAAAA
*
5188 AAATATAATAATAGTAAAA
1 AAATATAATAAAAG-AAAA
5207 AAATATA
1 AAATATA
5214 TAATTAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAATATAATAAAAGAAAA
Found at i:5240 original size:16 final size:17
Alignment explanation
Indices: 5185--5241 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
5175 TTAATAAAAG
*
5185 AAAAAATATAATAATAGT
1 AAAAAATATTATAATA-T
5203 AAAAAA-ATATATAAT-T
1 AAAAAATAT-TATAATAT
*
5219 AGAAAATATTA-AATAT
1 AAAAAATATTATAATAT
5235 AAAAAAT
1 AAAAAAT
5242 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 3 0.09
16 15 0.45
17 4 0.12
18 11 0.33
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAAATATTATAATAT
Found at i:9287 original size:42 final size:40
Alignment explanation
Indices: 9206--9289 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 40
9196 AAAAGGAGTT
* *
9206 GTTTATGAGTGTTATTAGAATAAAATTATATTTGAGTTTA
1 GTTTATGAGTGTTATTAAAATAAAATTAAATTTGAGTTTA
* * *
9246 GTTTATGAGTGTTTTTTAAAAATGAAATTAAATTTGGGTTTA
1 GTTTATGAGTG-TTATT-AAAATAAAATTAAATTTGAGTTTA
9288 GT
1 GT
9290 CTGTTGATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.30
41 4 0.11
42 22 0.59
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (40 bp):
GTTTATGAGTGTTATTAAAATAAAATTAAATTTGAGTTTA
Found at i:9890 original size:29 final size:29
Alignment explanation
Indices: 9855--9917 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
9845 AAAATATGTC
* *
9855 AAGTTCAGTTACCAAATCGAGTCCAAAAA
1 AAGTTCAGGTACCAAATCGAGTCAAAAAA
* * *
9884 AAGTTCAGGTATCAAATTGGGTCAAAAAA
1 AAGTTCAGGTACCAAATCGAGTCAAAAAA
9913 AAGTT
1 AAGTT
9918 TAAGTATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (29 bp):
AAGTTCAGGTACCAAATCGAGTCAAAAAA
Found at i:9938 original size:28 final size:29
Alignment explanation
Indices: 9879--9938 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
9869 AATCGAGTCC
* * **
9879 AAAAAAAGTTCAGGTATCAAATTGGGTCA
1 AAAAAAAGTTCAAGTATCAAATTGAGAAA
*
9908 AAAAAAAGTTTAAGTATCAAATT-AGAAA
1 AAAAAAAGTTCAAGTATCAAATTGAGAAA
9936 AAA
1 AAA
9939 GTGTTAAGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (29 bp):
AAAAAAAGTTCAAGTATCAAATTGAGAAA
Found at i:10242 original size:317 final size:316
Alignment explanation
Indices: 9660--10256 Score: 780
Period size: 317 Copynumber: 1.9 Consensus size: 316
9650 CTAATATTTT
** *
9660 TAATATTAATTCGTTAAGGATAGCTTAAAATCTATTTTTAACATAAAATTTCTCTAAAACTGACA
1 TAATATTAATTCGTTAAACATAGCTCAAAATCTATTTTTAACATAAAATTTCTCTAAAACTGACA
* *
9725 ATATTTTTGTAGCATAACAAAAAAAAAAATTCAACACAGTTATTGTTGTGTAATTTTTATAATAT
66 ATATTTTTATAGCATAAC-AAAAAAAAAATTCAACACAGTTATTGTTGCGTAATTTTTATAATAT
* * * * *
9790 TTAATAAATTTAAGTATCAAGTTGAATCTTAAAAAAGCTTAGGTACCAAACTAGGAAAATATGTC
130 TTAATAAATTTAAGTATCAAATTGAATCTTAAAAAAACTTAGATACCAAACTAAGAAAATATATC
** * *
9855 AAGTTCAGTTACCAAATCGAGTCCAAAAAAAGTTCAGGTATCAAATTGGGTCAAAAAAAAGTTTA
195 AAACTCAGTTACCAAATCGAGTCCAAAAAAAGTTCAGGTATCAAATTAGG-CAAAAAAAAGTTCA
9920 AGTATCAAATTAGA-AAAAAGTGTTAAGTCAAGTACTAAATATTATATTAAGCCTTTA
259 AGTATCAAATTAGATAAAAAGTGTTAAGTCAAGTACTAAATATTATATTAAGCCTTTA
* * *
9977 TAATATTAATTCGTTAAACATAGCTCAATATCTATTTTTAACATGAATTTTCTCTAAAACTGACA
1 TAATATTAATTCGTTAAACATAGCTCAAAATCTATTTTTAACATAAAATTTCTCTAAAACTGACA
*
10042 ATATTTTTATAGCATAAC-AAAAAAAAA-TCAATATC-GTTATTGTTTTGCGTAATTTTTATAAT
66 ATATTTTTATAGCATAACAAAAAAAAAATTCAACA-CAGTTATTG--TTGCGTAATTTTTATAAT
* *
10104 ATTTAATAAATTT-AGATATCAAATTGAATCTTAAAAAAAAACTTTGATACCAAATTAAGAAAAT
128 ATTTAATAAATTTAAG-TATCAAATTGAATCTT--AAAAAAACTTAGATACCAAACTAAGAAAAT
* * * *
10168 ATATCAAACTCAG-TACCAAATTGGGTCC-AAAAAA-TTTAGGTATTAAATTAGG-AAAAAGTGT
190 ATATCAAACTCAGTTACCAAATCGAGTCCAAAAAAAGTTCAGGTATCAAATTAGGCAAAAA----
* * *
10229 CAAGTTCAAGTATCGAATTGGATAAAAA
251 AAAGTTCAAGTATCAAATTAGATAAAAA
10257 AAGTTTAAGT
Statistics
Matches: 242, Mismatches: 27, Indels: 21
0.83 0.09 0.07
Matches are distributed among these distances:
313 5 0.02
314 12 0.05
315 27 0.11
316 51 0.21
317 107 0.44
318 40 0.17
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (316 bp):
TAATATTAATTCGTTAAACATAGCTCAAAATCTATTTTTAACATAAAATTTCTCTAAAACTGACA
ATATTTTTATAGCATAACAAAAAAAAAATTCAACACAGTTATTGTTGCGTAATTTTTATAATATT
TAATAAATTTAAGTATCAAATTGAATCTTAAAAAAACTTAGATACCAAACTAAGAAAATATATCA
AACTCAGTTACCAAATCGAGTCCAAAAAAAGTTCAGGTATCAAATTAGGCAAAAAAAAGTTCAAG
TATCAAATTAGATAAAAAGTGTTAAGTCAAGTACTAAATATTATATTAAGCCTTTA
Found at i:10831 original size:22 final size:23
Alignment explanation
Indices: 10789--10831 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10779 ATTTATAAAA
*
10789 GTTCAAATAAATGTTAAAAATAT
1 GTTCAAATAAATGCTAAAAATAT
*
10812 GTTCAAA-ATATGCTAAAAAT
1 GTTCAAATAAATGCTAAAAAT
10832 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
GTTCAAATAAATGCTAAAAATAT
Found at i:10931 original size:23 final size:23
Alignment explanation
Indices: 10900--10978 Score: 140
Period size: 23 Copynumber: 3.4 Consensus size: 23
10890 TTATTTTTAA
*
10900 AATTGTATTAAAGTAAAATTTTG
1 AATTTTATTAAAGTAAAATTTTG
10923 AATTTTATTAAAGTAAAATTTTG
1 AATTTTATTAAAGTAAAATTTTG
*
10946 AATTTTATTAAAGTAAAATTTTT
1 AATTTTATTAAAGTAAAATTTTG
10969 AATTTTATTA
1 AATTTTATTA
10979 CAGTTACTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
AATTTTATTAAAGTAAAATTTTG
Done.