Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007648.1 Kokia drynarioides strain JFW-HI SEQ_122279, 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: 4609
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Found at i:1692 original size:35 final size:30
Alignment explanation
Indices: 1621--1678 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1611 AACAGTTCAT
1621 AATACACCCACATTGGAGTGTCTTTTATAC
1 AATACACCCACATTGGAGTGTCTTTTATAC
*
1651 AATACACGCACATTGGAGTGTCTTTTAT
1 AATACACCCACATTGGAGTGTCTTTTAT
1679 TTATAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (30 bp):
AATACACCCACATTGGAGTGTCTTTTATAC
Found at i:1831 original size:41 final size:41
Alignment explanation
Indices: 1784--2192 Score: 467
Period size: 41 Copynumber: 10.0 Consensus size: 41
1774 TTTCCATAAA
* * *
1784 CGCCGCTAAAGGTCAAAGCATTAGCAGTGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * *
1825 CACCGCTAAAGGTCAGAGAATTAGCGCCGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * * *
1866 TGCCACTAAAGGTCAGAGCATTAGCGACATTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* *
1907 CTCCGCTAAAGGTTAGAGCATTAGCGGCGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * *
1948 CGCCACTAAAGGTCAGAGCATTAACGGCTTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * * * *
1989 CACCGTTAAATGTTAGAGAATTAGCGGCGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* *
2030 TGTCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* ** *
2071 CACCGCTAAAGGTCAGAGCATTAGCAACGTTTATAAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * * * * * *
2112 TGCCACTAAAGGTCAGAGTAATAGCGGCATTTATGAAAAAA
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * * * * *
2153 TGTCACTAAAGGTCAGAGCATTAGCGACATTTATGGGAAA
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAA
2193 AATGCCGTTA
Statistics
Matches: 307, Mismatches: 61, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 307 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
Found at i:4263 original size:3 final size:3
Alignment explanation
Indices: 4255--4283 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4245 GGATAAAATA
4255 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4284 ATTACATTAA
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:4362 original size:30 final size:30
Alignment explanation
Indices: 4299--4441 Score: 110
Period size: 30 Copynumber: 4.8 Consensus size: 30
4289 ATTAAAATCA
* * * * * *
4299 GGTCAAATTTGAAATTTTGGGAACTTCAGG
1 GGTCAAATTAGAATTTTTAGAAAATTCAAG
* *
4329 GGTCAAATCATAATTTTTAGAAAATTCAAG
1 GGTCAAATTAGAATTTTTAGAAAATTCAAG
* * *
4359 GGTCAAATTGGAATTTTTGGAAAATT--TG
1 GGTCAAATTAGAATTTTTAGAAAATTCAAG
***
4387 GAGTCAAATTAGAATTTTTAGAAAATTTTGGG
1 G-GTCAAATTAGAATTTTTAGAAAA-TTCAAG
* *
4419 GGTCAAATTAAAATTTTTGGAAA
1 GGTCAAATTAGAATTTTTAGAAA
4442 GTTTTGGGGT
Statistics
Matches: 91, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.02
29 21 0.23
30 46 0.51
31 20 0.22
32 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (30 bp):
GGTCAAATTAGAATTTTTAGAAAATTCAAG
Found at i:4393 original size:29 final size:31
Alignment explanation
Indices: 4360--4449 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
4350 AAATTCAAGG
*
4360 GTCAAATTGGAATTTTTGGAAAA-TTT-GGA
1 GTCAAATTAGAATTTTTGGAAAATTTTGGGA
* *
4389 GTCAAATTAGAATTTTTAGAAAATTTTGGGG
1 GTCAAATTAGAATTTTTGGAAAATTTTGGGA
* *
4420 GTCAAATTAAAATTTTTGGAAAGTTTTGGG
1 GTCAAATTAGAATTTTTGGAAAATTTTGGG
4450 GTTAAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.40
30 3 0.06
31 29 0.55
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.39
Consensus pattern (31 bp):
GTCAAATTAGAATTTTTGGAAAATTTTGGGA
Found at i:4427 original size:31 final size:30
Alignment explanation
Indices: 4327--4451 Score: 126
Period size: 30 Copynumber: 4.2 Consensus size: 30
4317 GGGAACTTCA
* * **
4327 GGGGTCAAATCATAATTTTTAGAAAATTCA
1 GGGGTCAAATTAGAATTTTTAGAAAATTTG
* * *
4357 AGGGTCAAATTGGAATTTTTGGAAAATTT-
1 GGGGTCAAATTAGAATTTTTAGAAAATTTG
*
4386 GGAGTCAAATTAGAATTTTTAGAAAATTTTG
1 GGGGTCAAATTAGAATTTTTAGAAAA-TTTG
* * * *
4417 GGGGTCAAATTAAAATTTTTGGAAAGTTTT
1 GGGGTCAAATTAGAATTTTTAGAAAATTTG
4447 GGGGT
1 GGGGT
4452 TAAAAAATAA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
29 22 0.28
30 34 0.44
31 22 0.28
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGTCAAATTAGAATTTTTAGAAAATTTG
Found at i:4465 original size:30 final size:31
Alignment explanation
Indices: 4327--4450 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 31
4317 GGGAACTTCA
* * **
4327 GGGGTCAAATCATAATTTTTAGAAAA-TTCA
1 GGGGTCAAATAAAAATTTTTAGAAAATTTTG
* *** *
4357 AGGGTCAAATTGGAATTTTTGGAAAA-TTT-
1 GGGGTCAAATAAAAATTTTTAGAAAATTTTG
* * *
4386 GGAGTCAAATTAGAATTTTTAGAAAATTTTG
1 GGGGTCAAATAAAAATTTTTAGAAAATTTTG
* * *
4417 GGGGTCAAATTAAAATTTTTGGAAAGTTTTG
1 GGGGTCAAATAAAAATTTTTAGAAAATTTTG
4448 GGG
1 GGG
4451 TTAAAAAATA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.28
30 26 0.33
31 30 0.38
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (31 bp):
GGGGTCAAATAAAAATTTTTAGAAAATTTTG
Done.