Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011020.1 Kokia drynarioides strain JFW-HI SEQ_125991, 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: 5484
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1425 original size:29 final size:30
Alignment explanation
Indices: 1395--1730 Score: 193
Period size: 30 Copynumber: 11.4 Consensus size: 30
1385 TTTGCCCTCG
*
1395 AACTTTTAAAAATCTCATTTTCAACCCCGA
1 AACTTCTAAAAATCTCATTTTCAACCCCGA
1425 AACTTCTAAAAAT-TACCATTTT--ACCCCG-
1 AACTTCTAAAAATCT--CATTTTCAACCCCGA
* *
1453 AACTT-TCAAAAATCCCATTTTCAACCCTGA
1 AACTTCT-AAAAATCTCATTTTCAACCCCGA
*
1483 AACTTCTAAAAAT-TACCATTTT--ACCCCTA
1 AACTTCTAAAAATCT--CATTTTCAACCCCGA
* * * * *
1512 AGCTTCCAAAAAT-TCCATTTTTAACTCTGA
1 AACTTCTAAAAATCT-CATTTTCAACCCCGA
*
1542 AACTTCTAAAAAT-TACCATTTT--ACCCCTA
1 AACTTCTAAAAATCT--CATTTTCAACCCCGA
* * *
1571 AACTTCCAAAAATCTCATTTTTAAACCCGA
1 AACTTCTAAAAATCTCATTTTCAACCCCGA
* ** *
1601 AACTTCTAAAAATCCCATTTTTGA-CCCTA
1 AACTTCTAAAAATCTCATTTTCAACCCCGA
* * * **
1630 GAACTTCCAAAATTC-CATTTTTAACCCTAA
1 -AACTTCTAAAAATCTCATTTTCAACCCCGA
* *
1660 AACTTCTAAAAAT-TCCATTTTTAGCCCC-A
1 AACTTCTAAAAATCT-CATTTTCAACCCCGA
* ** *
1689 AACTTCTCAAAAT-TCCATTTTTGACTCCGA
1 AACTTCTAAAAATCT-CATTTTCAACCCCGA
1719 AACTTCCTAAAA
1 AACTT-CTAAAA
1731 TTACCATTTT
Statistics
Matches: 247, Mismatches: 37, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
27 7 0.03
28 24 0.10
29 93 0.38
30 98 0.40
31 25 0.10
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (30 bp):
AACTTCTAAAAATCTCATTTTCAACCCCGA
Found at i:1551 original size:59 final size:59
Alignment explanation
Indices: 1363--1744 Score: 415
Period size: 59 Copynumber: 6.5 Consensus size: 59
1353 GGAGGTCCCT
** * ** *
1363 AAACTATCTAAAAATTACCATTTTTGCCCTCGAACTTTTAAAAA-TCTCATTTTCAACCCCG
1 AAACT-TCTAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATTC-CATTTTTAACCCCG
* * * * *
1424 AAACTTCTAAAAATTACCATTTTACCCC-GAACTTTCAAAAATCCCATTTTCAACCCTG
1 AAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
1482 AAACTTCTAAAAATTACCATTTTACCCCTAAGCTTCCAAAAATTCCATTTTTAACTCTG
1 AAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCCG
*
1541 AAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAA-TCTCATTTTTAAACCCG
1 AAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTC-CATTTTTAACCCCG
* **
1600 AAACTTCTAAAAA-TCCCATTTTTGA-CCCTAGAACTTCC-AAAATTCCATTTTTAACCCTA
1 AAACTTCTAAAAATTACCA-TTTT-ACCCCTA-AACTTCCAAAAATTCCATTTTTAACCCCG
* *
1659 AAACTTCTAAAAATT-CCATTTTTAGCCCC-AAACTTCTC-AAAATTCCATTTTTGACTCCG
1 AAACTTCTAAAAATTACCA-TTTTA-CCCCTAAACTTC-CAAAAATTCCATTTTTAACCCCG
1718 AAACTTCCT-AAAATTACCATTTTACCC
1 AAACTT-CTAAAAATTACCATTTTACCC
1745 TCGGATGTCC
Statistics
Matches: 285, Mismatches: 23, Indels: 29
0.85 0.07 0.09
Matches are distributed among these distances:
58 69 0.24
59 171 0.60
60 40 0.14
61 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:3140 original size:16 final size:17
Alignment explanation
Indices: 3092--3134 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
3082 CTTTCAAATT
*
3092 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
3109 T-AATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
3125 TAAATTTAAA
1 TAAATTTAAA
3135 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:4003 original size:30 final size:30
Alignment explanation
Indices: 3898--4112 Score: 144
Period size: 30 Copynumber: 7.3 Consensus size: 30
3888 CATTAAAATC
* *
3898 GGGTCAAATTTAAATTTTTGAAAAG-TTAA
1 GGGTCAAATTTGAATTTTTGAAAAGTTTGA
* *
3927 TGGTCAAATTGGAATTTTTAGAAAA-TTT-A
1 GGGTCAAATTTGAATTTTT-GAAAAGTTTGA
** * * *
3956 GGGGTTGACTTGGAATTTTTAAAAAGTTTGA
1 -GGGTCAAATTTGAATTTTTGAAAAGTTTGA
** *
3987 GGGTCAAATTCAAATTTTTGGAAAGTTTTG-
1 GGGTCAAATTTGAATTTTTGAAAAG-TTTGA
4017 GGG--AAATTT-AATTTTTTGGAAAA-TTT-A
1 GGGTCAAATTTGAA-TTTTT-GAAAAGTTTGA
* * *
4044 GGGGTAAAATTTGGATTTTTGGAAAA-TTTAA
1 -GGGTCAAATTTGAATTTTT-GAAAAGTTTGA
*
4075 GGGTCAAATTCGAATTTTTGAAAAGTTTGA
1 GGGTCAAATTTGAATTTTTGAAAAGTTTGA
*
4105 GAGTCAAA
1 GGGTCAAA
4113 ACATAATTTC
Statistics
Matches: 148, Mismatches: 23, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.03
28 13 0.09
29 30 0.20
30 93 0.63
31 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGAAAAGTTTGA
Found at i:4063 original size:88 final size:88
Alignment explanation
Indices: 3898--4102 Score: 236
Period size: 88 Copynumber: 2.3 Consensus size: 88
3888 CATTAAAATC
* * * **
3898 GGGTCAAATTTAAATTTTTGAAAAGTTAATGGTCAAATTGGAATTTTTAGAAAATTTAGGGGTTG
1 GGGTCAAATTCAAATTTTTGAAAAGTT-TTGGGCAAATTGGAATTTTTAGAAAATTTAGGGGTAA
*
3963 ACTTGGAATTTTT-AAAAAGTTTGA
65 ACTTGGAATTTTTGAAAAA-TTTAA
* * * *
3987 GGGTCAAATTCAAATTTTTGGAAAGTTTTGGGGAAATT-TAATTTTTTGGAAAATTTAGGGGTAA
1 GGGTCAAATTCAAATTTTTGAAAAGTTTTGGGCAAATTGGAA-TTTTTAGAAAATTTAGGGGT-A
* *
4051 AATTTGG-ATTTTTGGAAAATTTAA
64 AACTTGGAATTTTTGAAAAATTTAA
*
4075 GGGTCAAATTCGAATTTTTGAAAAGTTT
1 GGGTCAAATTCAAATTTTTGAAAAGTTT
4103 GAGAGTCAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 2 0.02
88 63 0.64
89 34 0.34
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (88 bp):
GGGTCAAATTCAAATTTTTGAAAAGTTTTGGGCAAATTGGAATTTTTAGAAAATTTAGGGGTAAA
CTTGGAATTTTTGAAAAATTTAA
Done.