Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001960.1 Kokia drynarioides strain JFW-HI SEQ_113787, 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: 5261
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:1002 original size:49 final size:49
Alignment explanation
Indices: 947--1046 Score: 159
Period size: 49 Copynumber: 2.0 Consensus size: 49
937 CGTCCAGTGA
947 GTTAGGACATAACGTTTCGAGATAC-AGAAATAACGAGT-TTTCCTTTATT
1 GTTAGGACATAACGTTTCGAGAT-CTAGAAATAACGA-TCTTTCCTTTATT
*
996 GTTAGGACATAACGTTTCGAGATCTAGAAATAACGATCTTTCCTTTGTT
1 GTTAGGACATAACGTTTCGAGATCTAGAAATAACGATCTTTCCTTTATT
1045 GT
1 GT
1047 AAACTTTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
48 2 0.04
49 46 0.96
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (49 bp):
GTTAGGACATAACGTTTCGAGATCTAGAAATAACGATCTTTCCTTTATT
Found at i:1243 original size:98 final size:97
Alignment explanation
Indices: 1074--1261 Score: 256
Period size: 98 Copynumber: 1.9 Consensus size: 97
1064 GAAAAGGATG
* * *
1074 TTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCAG
1 TTCGATTATCTCGATTTCAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAG
*
1139 AGAT-AAAGAAATATTGCCTCGATTTAAGGGTA
66 AAATAAAAG-AATATTGCCTCGATTTAAGGGTA
* *
1171 TTCGATTAT-TCCGATTTCAAGAAAAAATTGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACT
1 TTCGATTATCT-CGATTTCAAG-AAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-T
*
1235 C-GAAATAAAAGAATATTGCCTTGATTT
63 CAGAAATAAAAGAATATTGCCTCGATTT
1262 TAAAGTTTAC
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
96 1 0.01
97 18 0.22
98 55 0.69
99 6 0.08
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (97 bp):
TTCGATTATCTCGATTTCAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAG
AAATAAAAGAATATTGCCTCGATTTAAGGGTA
Found at i:1623 original size:61 final size:60
Alignment explanation
Indices: 1548--1663 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
1538 GAAAGCTCGG
1548 GGTCAAAAAAGGAATTTTTAGACA--TCTGAGGGTAAAATGGTAATTTTTTGGAAAAAATAAT
1 GGTCAAAAAAGGAATTTTTAGA-AGTTC-GAGGGTAAAATGGT-ATTTTTTGGAAAAAATAAT
* * * *
1609 GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAATTGGTATTTTTTGGAAAAA
1 GGTCAAAAAAGGAATTTTTAGAAGTTCGAGGGTAAAATGGTATTTTTTGGAAAAA
1664 TTGGAGTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 15 0.31
61 32 0.65
62 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (60 bp):
GGTCAAAAAAGGAATTTTTAGAAGTTCGAGGGTAAAATGGTATTTTTTGGAAAAAATAAT
Found at i:1688 original size:30 final size:28
Alignment explanation
Indices: 1653--1806 Score: 93
Period size: 30 Copynumber: 5.3 Consensus size: 28
1643 AATTGGTATT
1653 TTTTGGAAAAATTGGAGTCAAAAATGAAA
1 TTTTGGAAAAATTGG-GTCAAAAATGAAA
* *
1682 TTTTTGG--AAGTCCGAGTGT-AAAAAT-ATAA
1 -TTTTGGAAAAAT-TG-G-GTCAAAAATGA-AA
* * *
1711 TTTTCGAAAAATAGGGTCAAAAATGGAA
1 TTTTGGAAAAATTGGGTCAAAAATGAAA
** *
1739 TTTTGGAAAGTTTGGGGAT-AAAAATGTAA
1 TTTTGGAAAAATT-GGG-TCAAAAATGAAA
* *
1768 TCTTTGGAAAAATTAGGGTTAAAAATGGAA
1 T-TTTGGAAAAATT-GGGTCAAAAATGAAA
1798 TTTTGGAAA
1 TTTTGGAAA
1807 GTTTAGGGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
27 2 0.02
28 27 0.28
29 32 0.33
30 36 0.37
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (28 bp):
TTTTGGAAAAATTGGGTCAAAAATGAAA
Found at i:1806 original size:59 final size:57
Alignment explanation
Indices: 1593--1829 Score: 214
Period size: 59 Copynumber: 4.1 Consensus size: 57
1583 AATGGTAATT
* * * *
1593 TTTTGGAAAAAATAATGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGT-AAATTGGTATT
1 TTTTGG-AAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAAAT-GTA-A
* * * *
1653 TTTTGGAAAAATT-GGAGTCAAAAATGAAATTTTTGGAAGTCCGAGTGTAAAAATATAA
1 TTTTGGAAAAATTAGG-GTCAAAAATGGAATTTTTGGAAGTTCG-GGGTAAAAATGTAA
* *
1711 TTTTCGAAAAA-TAGGGTCAAAAATGGAA-TTTTGGAAAGTTTGGGGATAAAAATGTAA
1 TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGG-AAGTTCGGGG-TAAAAATGTAA
* ** * *
1768 TCTTTGGAAAAATTAGGGTTAAAAATGGAA-TTTTGGAAAGTTTAGGGTTAAAATATAA
1 T-TTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGG-AAGTTCGGGGTAAAAATGTAA
1826 TTTT
1 TTTT
1830 TAAACAGTTC
Statistics
Matches: 150, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
56 8 0.05
57 32 0.21
58 33 0.22
59 67 0.45
60 10 0.07
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (57 bp):
TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATGTAA
Found at i:1812 original size:29 final size:29
Alignment explanation
Indices: 1722--1903 Score: 138
Period size: 29 Copynumber: 6.2 Consensus size: 29
1712 TTTCGAAAAA
*
1722 TAGGGTCAAAAATGGAATTTTGGAAAGTT
1 TAGGGTTAAAAATGGAATTTTGGAAAGTT
* * * **
1751 TGGGGATAAAAATGTAATCTTTGGAAAAAT
1 TAGGGTTAAAAATGGAAT-TTTGGAAAGTT
1781 TAGGGTTAAAAATGGAATTTTGGAAAGTT
1 TAGGGTTAAAAATGGAATTTTGGAAAGTT
**
1810 TAGGGTTAAAATAT--AATTTTTAAACAG-T
1 TAGGGTTAAAA-ATGGAATTTTGGAA-AGTT
* * *
1838 TCGAGGTTGAAAATGGAATTTTAGAGAAGTT
1 TAG-GGTTAAAAATGGAATTTTGGA-AAGTT
* * * *
1869 CAAGGGTCAAAATAT-GATTTTTGGATAGTT
1 -TAGGGTTAAAA-ATGGAATTTTGGAAAGTT
1899 TAGGG
1 TAGGG
1904 GCCTCTAGAG
Statistics
Matches: 118, Mismatches: 25, Indels: 20
0.72 0.15 0.12
Matches are distributed among these distances:
28 13 0.11
29 47 0.40
30 39 0.33
31 16 0.14
32 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
TAGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:1820 original size:116 final size:116
Alignment explanation
Indices: 1600--1829 Score: 265
Period size: 116 Copynumber: 2.0 Consensus size: 116
1590 ATTTTTTGGA
* * * * *
1600 AAAAATAATGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAATTGGTATTTTTTGGAAAAAT
1 AAAAATAAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGATAAAATGGTAATCTTTGGAAAAAT
*
1665 TGGAGTCAAAAATGAAATTTTTGGAAGTCCGAGTGTAAAAATATAATTTTCG
66 TGGAGTCAAAAATGAAATTTTTGGAAGTCAGAGTGT-AAAATATAATTTTCG
*
1717 AAAAAT-AGGGTCAAAAATGGAA-TTTTGGAAAGTTTGGGGATAAAAAT-GTAATCTTTGGAAAA
1 AAAAATAAGGGTCAAAAATGGAATTTTTGG-AAGTTCGGGGAT-AAAATGGTAATCTTTGGAAAA
* * * *
1779 ATTAGG-GTTAAAAATGGAA-TTTTGGAAAGTTTAGGGT-TAAAATATAATTTT
64 ATT-GGAGTCAAAAATGAAATTTTTGG-AAG-TCAGAGTGTAAAATATAATTTT
1830 TAAACAGTTC
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
115 25 0.26
116 56 0.58
117 16 0.16
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (116 bp):
AAAAATAAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGATAAAATGGTAATCTTTGGAAAAAT
TGGAGTCAAAAATGAAATTTTTGGAAGTCAGAGTGTAAAATATAATTTTCG
Found at i:1829 original size:28 final size:28
Alignment explanation
Indices: 1702--1829 Score: 100
Period size: 29 Copynumber: 4.5 Consensus size: 28
1692 TCCGAGTGTA
* * *
1702 AAAATATAATTTTCGAAA-AATAGGGTC
1 AAAATATAATTTTGGAAAGATTAGGGTT
* * *
1729 AAAA-ATGGAATTTTGGAAAGTTTGGGGATA
1 AAAATAT--AATTTTGGAAAGATTAGGG-TT
* *
1759 AAAATGTAATCTTTGGAAAAATTAGGGTT
1 AAAATATAAT-TTTGGAAAGATTAGGGTT
*
1788 AAAA-ATGGAATTTTGGAAAGTTTAGGGTT
1 AAAATAT--AATTTTGGAAAGATTAGGGTT
1817 AAAATATAATTTT
1 AAAATATAATTTT
1830 TAAACAGTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.03
27 4 0.05
28 17 0.22
29 32 0.41
30 23 0.29
31 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (28 bp):
AAAATATAATTTTGGAAAGATTAGGGTT
Found at i:3668 original size:18 final size:17
Alignment explanation
Indices: 3636--3698 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 17
3626 TAAAATCATT
3636 TAAAATTAAAATAAATC
1 TAAAATTAAAATAAATC
* *
3653 TAAATTTAATAATAAATT
1 TAAAATTAA-AATAAATC
* *
3671 TAAAATCAAATTAAA-C
1 TAAAATTAAAATAAATC
* *
3687 TTAATTTAAAAT
1 TAAAATTAAAAT
3699 TAAAATTTGA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
16 8 0.23
17 13 0.37
18 14 0.40
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATTAAAATAAATC
Found at i:3668 original size:29 final size:28
Alignment explanation
Indices: 3636--3704 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
3626 TAAAATCATT
*
3636 TAAAATTAAAAT-AAATCTAAATTTAATAA
1 TAAAATTAAAATCAAAT-TAAACTTAAT-A
* *
3665 TAAATTTAAAATCAAATTAAACTTAATT
1 TAAAATTAAAATCAAATTAAACTTAATA
3693 TAAAATTAAAAT
1 TAAAATTAAAAT
3705 TTGATCCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.31
29 20 0.57
30 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAATTAAAATCAAATTAAACTTAATA
Found at i:3695 original size:11 final size:11
Alignment explanation
Indices: 3612--3701 Score: 58
Period size: 11 Copynumber: 8.0 Consensus size: 11
3602 ATTTTGTGTT
*
3612 TTTAATATTAA
1 TTTAAAATTAA
*
3623 GTTTAAAA-TCA
1 -TTTAAAATTAA
3634 TTTAAAATTAA
1 TTTAAAATTAA
**
3645 AAT-AAATCTAAA
1 TTTAAAAT-T-AA
*
3657 TTTAATAATAAA
1 TTTAA-AATTAA
*
3669 TTTAAAATCAA
1 TTTAAAATTAA
* *
3680 ATTAAACTTAA
1 TTTAAAATTAA
3691 TTTAAAATTAA
1 TTTAAAATTAA
3702 AATTTGATCC
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
10 11 0.19
11 28 0.47
12 16 0.27
13 1 0.02
14 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (11 bp):
TTTAAAATTAA
Done.