Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011835.1 Kokia drynarioides strain JFW-HI SEQ_126831, 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: 15079
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:1360 original size:29 final size:29
Alignment explanation
Indices: 1327--1510 Score: 83
Period size: 29 Copynumber: 6.4 Consensus size: 29
1317 TCAAATATGC
1327 AATTTTTGGATGCCCGAGGGCAAAATGAT
1 AATTTTTGGATGCCCGAGGGCAAAATGAT
* * **
1356 AATTTTTGAAAGTTCG-GGGCAAAAATGCAT
1 AATTTTTGGATGCCCGAGGGC-AAAATG-AT
* * * *
1386 --TTTTTAGATACCCGGGGGTAAAA-GAGT
1 AATTTTTGGATGCCCGAGGGCAAAATGA-T
* *** *
1413 AATTTTGGGACATCCGAGGGTAAAATGAT
1 AATTTTTGGATGCCCGAGGGCAAAATGAT
* ** **
1442 AATTTTTGGA--CACTTGGAGCAAAATGGC
1 AATTTTTGGATGCCCGAGG-GCAAAATGAT
** * * *
1470 AATTTTTGGATGTTCAAGGGTAAAATGGT
1 AATTTTTGGATGCCCGAGGGCAAAATGAT
1499 AATTTTTGGATG
1 AATTTTTGGATG
1511 TTCGGGGGTA
Statistics
Matches: 115, Mismatches: 30, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
26 1 0.01
27 5 0.04
28 33 0.29
29 69 0.60
30 7 0.06
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (29 bp):
AATTTTTGGATGCCCGAGGGCAAAATGAT
Found at i:1511 original size:29 final size:29
Alignment explanation
Indices: 1401--1769 Score: 189
Period size: 29 Copynumber: 12.8 Consensus size: 29
1391 AGATACCCGG
* ** *
1401 GGGTAAAA-GAGTAATTTTGGGACATCCGA
1 GGGTAAAATG-GTAATTTTTGGATGTTCGA
* **
1430 GGGTAAAATGATAATTTTTGGACACTT-G-
1 GGGTAAAATGGTAATTTTTGGA-TGTTCGA
* * * *
1458 GAGCAAAATGGCAATTTTTGGATGTTCAA
1 GGGTAAAATGGTAATTTTTGGATGTTCGA
*
1487 GGGTAAAATGGTAATTTTTGGATGTTCGG
1 GGGTAAAATGGTAATTTTTGGATGTTCGA
* * * *
1516 GGGTAAAACGGTAGTTTTTGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGATGTTCGA
* * * * * *
1545 GGGCAAAATTGTGATTTTTAGATATTCGG
1 GGGTAAAATGGTAATTTTTGGATGTTCGA
* *
1574 GGGTAAAATGGTAATTTTTGGAAAGTT-TA
1 GGGTAAAATGGTAATTTTTGG-ATGTTCGA
** *
1603 GGGTTAAAAAT-GTAATTTTTGGACATCCG-
1 GGG-T-AAAATGGTAATTTTTGGATGTTCGA
* * *
1632 GGATAAAATGGTAA-TTTTGGAAAGTTCAA
1 GGGTAAAATGGTAATTTTTGG-ATGTTCGA
* * ** * *
1661 GGTTAAAAAT-TTAATTTTTGGACATCCGG
1 GGGT-AAAATGGTAATTTTTGGATGTTCGA
* * *
1690 GGGTAAAATAGTAATTTTTAGATGTTTTG-
1 GGGTAAAATGGTAATTTTTGGATG-TTCGA
* ** *
1719 GGCTAAAATGGTAATTTTTGGACATCCGA
1 GGGTAAAATGGTAATTTTTGGATGTTCGA
***
1748 GGGTAAAACAATAATTTTTGGA
1 GGGTAAAATGGTAATTTTTGGA
1770 CACCGGGGGC
Statistics
Matches: 250, Mismatches: 74, Indels: 32
0.70 0.21 0.09
Matches are distributed among these distances:
27 13 0.05
28 33 0.13
29 169 0.68
30 30 0.12
31 5 0.02
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGATGTTCGA
Found at i:1553 original size:58 final size:57
Alignment explanation
Indices: 1355--1708 Score: 218
Period size: 58 Copynumber: 6.1 Consensus size: 57
1345 GGCAAAATGA
* * * * **
1355 TAATTTTTGAAAGTTC-GGGGCAAAAATGCATTTTTTAGATACCCGGGGGTAAAA-GAG
1 TAATTTTTGAAAGTTCAAGGG-AAAAATGTAATTTTTGGATATTCGGGGGTAAAACG-G
* * * * * * * * *
1412 TAATTTTGGGACA-TCCGAGGGTAAAATGATAATTTTTGGACACTT--GGAGCAAAATGG
1 TAATTTT-TGAAAGTTCAAGGGAAAAATG-TAATTTTTGGATA-TTCGGGGGTAAAACGG
* * * * *
1469 CAATTTTTGGATGTTCAAGGGTAAAATGGTAATTTTTGGATGTTCGGGGGTAAAACGG
1 TAATTTTTGAAAGTTCAAGGGAAAAAT-GTAATTTTTGGATATTCGGGGGTAAAACGG
* * * * * *
1527 TAGTTTTTGAAAGTTCGAGGGCAAAATTGTGATTTTTAGATATTCGGGGGTAAAATGG
1 TAATTTTTGAAAGTTCAAGGG-AAAAATGTAATTTTTGGATATTCGGGGGTAAAACGG
* * * * *
1585 TAATTTTTGGAAAGTT-TAGGGTTAAAAATGTAATTTTTGGACA-TCCGGGATAAAATGG
1 TAATTTTT-GAAAGTTCAAGGG--AAAAATGTAATTTTTGGATATTCGGGGGTAAAACGG
* * * * * **
1643 TAATTTTGGAAAGTTCAAGGTTAAAAATTTAATTTTTGGACATCCGGGGGTAAAATAG
1 TAATTTTTGAAAGTTCAAGG-GAAAAATGTAATTTTTGGATATTCGGGGGTAAAACGG
1701 TAATTTTT
1 TAATTTTT
1709 AGATGTTTTG
Statistics
Matches: 228, Mismatches: 54, Indels: 29
0.73 0.17 0.09
Matches are distributed among these distances:
56 3 0.01
57 78 0.34
58 120 0.53
59 27 0.12
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.34
Consensus pattern (57 bp):
TAATTTTTGAAAGTTCAAGGGAAAAATGTAATTTTTGGATATTCGGGGGTAAAACGG
Found at i:1726 original size:58 final size:59
Alignment explanation
Indices: 1491--1769 Score: 255
Period size: 58 Copynumber: 4.8 Consensus size: 59
1481 GTTCAAGGGT
** * ** * * *
1491 AAAATGGTAATTTTTGGATGTTCGGGGGTAAAACGGTAGTTTTT-GAAAGTTCGAGGG-CA
1 AAAAT-GTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGAAAGTT-TAGGGTTA
* * * * * *
1550 AAATTGTGATTTTTAGATATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTA
1 AAAATGTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTTA
* * * *
1609 AAAATGTAATTTTTGGACATCC-GGGATAAAATGGTAA-TTTTGGAAAGTTCAAGGTTA
1 AAAATGTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTTA
* * * * *
1666 AAAATTTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTAG-ATGTTTTGGGCT-
1 AAAATGTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTTA
* * *
1723 AAAATGGTAATTTTTGGACATCCGAGGGTAAAACAATAATTTTTGGA
1 AAAAT-GTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGA
1770 CACCGGGGGC
Statistics
Matches: 184, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
57 44 0.24
58 106 0.58
59 34 0.18
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTTGGACATCCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTTA
Found at i:1829 original size:29 final size:28
Alignment explanation
Indices: 1784--1953 Score: 107
Period size: 28 Copynumber: 6.0 Consensus size: 28
1774 GGGGGCAAAG
*
1784 GGCAAAAATATAATTTTTGAAAGTTTAA
1 GGCAAAAATGTAATTTTTGAAAGTTTAA
*
1812 GGCAAAAATGTAATTTTTTAGAAGTTT--
1 GGCAAAAATGTAATTTTTGA-AAGTTTAA
* * ***
1839 GG-ATATAATGGTAAATTTTGGAAAGTTCGGG
1 GGCA-AAAAT-GT-AATTTTTGAAAGTT-TAA
* **
1870 GGC-AAAATGTAATTTTTGGAAGTTCGA
1 GGCAAAAATGTAATTTTTGAAAGTTTAA
* * *
1897 GGTAAAAATTTAATTTTTGAGAAGTTTAG
1 GGCAAAAATGTAATTTTTGA-AAGTTTAA
*
1926 GGTC-AAAATGTAATTTTTAGAGAGTTTA
1 GG-CAAAAATGTAATTTTT-GAAAGTTTA
1954 GGGACCTTCT
Statistics
Matches: 110, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
26 1 0.01
27 9 0.08
28 51 0.46
29 41 0.37
30 6 0.05
31 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (28 bp):
GGCAAAAATGTAATTTTTGAAAGTTTAA
Found at i:3033 original size:19 final size:19
Alignment explanation
Indices: 2996--3042 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2986 TACCTTTTTA
*
2996 TTATTT-TTTAATATATAT
1 TTATTTATTAAATATATAT
*
3014 TTATTTATTAAATTTATAT
1 TTATTTATTAAATATATAT
*
3033 TTATTAATTA
1 TTATTTATTA
3043 TTATTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATTAAATATATAT
Found at i:3182 original size:73 final size:73
Alignment explanation
Indices: 3098--3272 Score: 282
Period size: 73 Copynumber: 2.4 Consensus size: 73
3088 ATAAATAATA
* *
3098 ATATAATAAATATGTTAATACATATATATACAAAACTTCCCGAATATTAAAGGAAATAATAAATG
1 ATATAATAAATATATTAATACATATATATACAAAACATCCCGAATATTAAAGGAAATAATAAATG
3163 TATTAAAT
66 TATTAAAT
*
3171 ATATAATAAATATATTAATACATATATATACACAACATCCCGAATATTAAAGGAAATAATAAATG
1 ATATAATAAATATATTAATACATATATATACAAAACATCCCGAATATTAAAGGAAATAATAAATG
3236 TATTAAAT
66 TATTAAAT
* *
3244 ATATAATTAATATCA--AATAAATATATATA
1 ATATAATAAATAT-ATTAATACATATATATA
3273 TTATTATATA
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
72 13 0.14
73 82 0.85
74 1 0.01
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (73 bp):
ATATAATAAATATATTAATACATATATATACAAAACATCCCGAATATTAAAGGAAATAATAAATG
TATTAAAT
Found at i:3262 original size:34 final size:34
Alignment explanation
Indices: 3224--3290 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3214 ATATTAAAGG
*
3224 AAAT-AATAAATGTATTAAATATATAATTAATATC
1 AAATAAATAAATATATT-AATATATAATTAATATC
* * *
3258 AAATAAATATATATATTATTATATATTTAATAT
1 AAATAAATAAATATATTAATATATAATTAATAT
3291 TTATAGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (34 bp):
AAATAAATAAATATATTAATATATAATTAATATC
Found at i:3883 original size:17 final size:17
Alignment explanation
Indices: 3863--3984 Score: 163
Period size: 17 Copynumber: 7.1 Consensus size: 17
3853 ACATTATTAA
*
3863 TTAAATTTAAAATAATT
1 TTAAATTTAAAATAAAT
3880 TTAAATTTATAAATAAAT
1 TTAAATTTA-AAATAAAT
* *
3898 TTAAACTTAAATTAAAT
1 TTAAATTTAAAATAAAT
*
3915 TTAAATTTAAAATAATT
1 TTAAATTTAAAATAAAT
*
3932 TTAAACTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
3949 TTAAATTTAAAATAAAC
1 TTAAATTTAAAATAAAT
**
3966 TTAACCTTAAAATAAAT
1 TTAAATTTAAAATAAAT
3983 TT
1 TT
3985 TAAAAAATGA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
17 76 0.84
18 15 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:3888 original size:6 final size:6
Alignment explanation
Indices: 3863--3959 Score: 78
Period size: 6 Copynumber: 16.8 Consensus size: 6
3853 ACATTATTAA
* * * *
3863 TTAAAT TTAAA- ATAATT TTAAAT TTATAA- ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT
* * * *
3909 TTAAAT TTAAAT TTAAA- ATAATT TTAAAC TTAAA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
3955 TTAAA
1 TTAAA
3960 ATAAACTTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
5 17 0.24
6 52 0.73
7 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:3921 original size:52 final size:51
Alignment explanation
Indices: 3863--3988 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 51
3853 ACATTATTAA
* * *
3863 TTAAATTTAAAATAATTTTAAATTTATAAATAAATTTAAACTTAAATTAAAT
1 TTAAATTTAAAATAATTTTAAACTTA-AAATAAATTTAAACTTAAAATAAAC
*
3915 TTAAATTTAAAATAATTTTAAACTTAAAATAAATTTAAATTTAAAATAAAC
1 TTAAATTTAAAATAATTTTAAACTTAAAATAAATTTAAACTTAAAATAAAC
**
3966 TTAACCTTAAAATAAATTTTAAA
1 TTAAATTTAAAAT-AATTTTAAA
3989 AAATGAGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 33 0.49
52 34 0.51
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (51 bp):
TTAAATTTAAAATAATTTTAAACTTAAAATAAATTTAAACTTAAAATAAAC
Found at i:4095 original size:20 final size:21
Alignment explanation
Indices: 4070--4109 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4060 GAGTGTGTTC
*
4070 TAATAAGA-TAAAAAAAATAT
1 TAATAAAATTAAAAAAAATAT
*
4090 TAATAAAATTTAAAAAAATA
1 TAATAAAATTAAAAAAAATA
4110 ATACATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
TAATAAAATTAAAAAAAATAT
Found at i:5677 original size:19 final size:19
Alignment explanation
Indices: 5653--5694 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5643 TATGATTTGA
5653 AAAAGGAATACATTTAATT
1 AAAAGGAATACATTTAATT
** *
5672 AAAAGGGCTTCATTTAATT
1 AAAAGGAATACATTTAATT
5691 AAAA
1 AAAA
5695 TAAGGAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (19 bp):
AAAAGGAATACATTTAATT
Found at i:7252 original size:42 final size:42
Alignment explanation
Indices: 7193--7276 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
7183 AAAGGGATAG
7193 TACCTTCAATGAGATTAATATAATAGTGCGCCACCTCCGAGC
1 TACCTTCAATGAGATTAATATAATAGTGCGCCACCTCCGAGC
7235 TACCTTCAATGAGATTAATATAATAGTGCGCCACCTCCGAGC
1 TACCTTCAATGAGATTAATATAATAGTGCGCCACCTCCGAGC
7277 CAAGAATGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
TACCTTCAATGAGATTAATATAATAGTGCGCCACCTCCGAGC
Found at i:8594 original size:18 final size:18
Alignment explanation
Indices: 8571--8606 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
8561 GTTTCCATTA
8571 GAAAAATTACAAAGAGTT
1 GAAAAATTACAAAGAGTT
8589 GAAAAATTACAAAGAGTT
1 GAAAAATTACAAAGAGTT
8607 TAATTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (18 bp):
GAAAAATTACAAAGAGTT
Found at i:9959 original size:22 final size:22
Alignment explanation
Indices: 9931--9974 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9921 CGAAAAACAG
*
9931 GAAACGTGCTACAAAGCAGAGA
1 GAAACGTGCTACAAAACAGAGA
*
9953 GAAACGTGTTACAAAACAGAGA
1 GAAACGTGCTACAAAACAGAGA
9975 TTTTATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.16, G:0.25, T:0.11
Consensus pattern (22 bp):
GAAACGTGCTACAAAACAGAGA
Done.