Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012597.1 Kokia drynarioides strain JFW-HI SEQ_127606, 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: 20724
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:733 original size:34 final size:34
Alignment explanation
Indices: 686--769 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
676 ATTTGTATTA
* *
686 AATTTAAATTTTAAAATAAATTTAAACTCAAAGT
1 AATTTAAAGTTTAAAATAAATTTAAACTCAAAAT
*
720 AAGTTTAAA-TTTAAAATAAATTTAAACTTAAAAT
1 AA-TTTAAAGTTTAAAATAAATTTAAACTCAAAAT
*
754 AAATTAAAGTTTAAAA
1 AATTTAAAGTTTAAAA
770 ACAATCCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 5 0.11
34 34 0.76
35 6 0.13
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AATTTAAAGTTTAAAATAAATTTAAACTCAAAAT
Found at i:767 original size:17 final size:17
Alignment explanation
Indices: 684--769 Score: 102
Period size: 17 Copynumber: 5.0 Consensus size: 17
674 TAATTTGTAT
684 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* * *
702 TAAATTTAAACTCAAAG
1 TAAATTTAAATTTAAAA
*
719 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
736 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
753 TAAA-TTAAAGTTTAAAA
1 TAAATTTAAA-TTTAAAA
770 ACAATCCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
16 5 0.09
17 42 0.74
18 10 0.18
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1583 original size:147 final size:145
Alignment explanation
Indices: 1222--1616 Score: 402
Period size: 147 Copynumber: 2.7 Consensus size: 145
1212 ACCTAAATTT
* * * *
1222 CCTTTAATGCTTCTGAGGTATAAGGTTTGTCATTGCGACTTAAACCTTTCTCTTCGTATTTTCGC
1 CCTTT-ATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGA
* * * * * *
1287 GATACTAGATTCACCATTGCGGCTTAAATCTTTTCCTTTGTCTTTGTGGTACTGGATTCATCGTT
65 GGTACTAGATTCACCATTGCGACTTAAACCTTTCCCTTTGTCTTCGTGGTACGGGATTCATCGTT
**
1352 GCGGCTTAAATCTTTC
130 GCAACTTAAATCTTTC
* * * * * * *
1368 CCTTCATG-TTTTCGCGGTACT--GGATTCGTCATTGCGGCTTAAATCTTTCCCTTTGTGTC-TC
1 CCTTTATGCTTCT-GAGGTA-TAAGG-TTCGTCATTGCGACTTAAACCTTTCCCTTCGTATCTTC
* ** * *
1429 TGAGGTACTAGGTTTGCCTTTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACGGGATTCG
63 -GAGGTACTAGATTCACCATTGCGACTTAAACCTTTCCC-TT-TGTCTTCGTGGTACGGGATTCA
1494 TCGTTGCAACTTAAATCTTTC
125 TCGTTGCAACTTAAATCTTTC
* * * * *
1515 CCTTTATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTCTCCCTTGGTATCTTCGTG
1 CCTTTATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGAG
* * * *
1580 GTACTAGATTCACCGTTGCGGCTTAAATCTTTTCCTT
66 GTACTAGATTCACCATTGCGACTTAAACCTTTCCCTT
1617 CATGCTTCTA
Statistics
Matches: 197, Mismatches: 42, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
144 7 0.04
145 65 0.33
146 10 0.05
147 109 0.55
148 6 0.03
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.41
Consensus pattern (145 bp):
CCTTTATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGAG
GTACTAGATTCACCATTGCGACTTAAACCTTTCCCTTTGTCTTCGTGGTACGGGATTCATCGTTG
CAACTTAAATCTTTC
Found at i:1599 original size:49 final size:48
Alignment explanation
Indices: 1252--1616 Score: 243
Period size: 49 Copynumber: 7.5 Consensus size: 48
1242 TAAGGTTTGT
* * * * * * *
1252 CATTGCGACTTAAACCTTTCTCTTCGTATTTTCGCGATACTAGATTCAC
1 CATTGCGACTTAAATCTTTCCCTT-GTGTCTTCGTGGTACTAGATTCGC
* * * * **
1301 CATTGCGGCTTAAATCTTTTCCTT-TGTCTTTGTGGTACTGGATTCAT
1 CATTGCGACTTAAATCTTTCCCTTGTGTCTTCGTGGTACTAGATTCGC
* * * * * * *
1348 CGTTGCGGCTTAAATCTTTCCCTTCATGTTTTCGCGGTACTGGATTCGT
1 CATTGCGACTTAAATCTTTCCCTT-GTGTCTTCGTGGTACTAGATTCGC
* * * *
1397 CATTGCGGCTTAAATCTTTCCCTTTGTGTC-TCTGAGGTACTAGGTTTGC
1 CATTGCGACTTAAATCTTTCCC-TTGTGTCTTC-GTGGTACTAGATTCGC
* * ** *
1446 CTTTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACGGGATTCGT
1 CATTGCGACTTAAATCTTTCCC-TTGTGTCTTCGTGGTACTAGATTCGC
* * * * * *
1495 CGTTGCAACTTAAATCTTTCCCTT-TATGCTCCTGAGGTA-TAAGGTTCGC
1 CATTGCGACTTAAATCTTTCCCTTGTGT-CTTC-GTGGTACT-AGATTCGC
* * * *
1544 CATTGCGACTTAAACCTCTCCCTTGGTATCTTCGTGGTACTAGATTCAC
1 CATTGCGACTTAAATCTTTCCCTT-GTGTCTTCGTGGTACTAGATTCGC
* * *
1593 CGTTGCGGCTTAAATCTTTTCCTT
1 CATTGCGACTTAAATCTTTCCCTT
1617 CATGCTTCTA
Statistics
Matches: 248, Mismatches: 57, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
47 40 0.16
48 7 0.03
49 190 0.77
50 8 0.03
51 3 0.01
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.40
Consensus pattern (48 bp):
CATTGCGACTTAAATCTTTCCCTTGTGTCTTCGTGGTACTAGATTCGC
Found at i:1622 original size:98 final size:98
Alignment explanation
Indices: 1219--1667 Score: 370
Period size: 98 Copynumber: 4.6 Consensus size: 98
1209 GTTACCTAAA
* * * * *
1219 TTTCCTTTAATGCTTCTGAGGTATAAGGTTTGTCATTGCGACTTAAACCTTTCTCTTCGTATTTT
1 TTTCCTTT-ATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTT
*
1284 CGCGATACTAGATTCACCATTGCGGCTTAAATCT
65 CGCGGTACTAGATTCACCATTGCGGCTTAAATCT
* * * ** * * * * * *
1318 TTTCCTTTGT-CT-TTGTGGTACT--GGATTCATCGTTGCGGCTTAAATCTTTCCCTTCATGTTT
1 TTTCCTTTATGCTCCTGAGGTA-TAAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCT
* **
1379 TCGCGGTACTGGATTCGTCATTGCGGCTTAAATCT
64 TCGCGGTACTAGATTCACCATTGCGGCTTAAATCT
* * * * * *
1414 TTCCCTTTGTG-TCTCTGAGGTACT-AGGTTTGCCTTTGCGACTTAAACCTTTCCCTTTGTGTCT
1 TTTCCTTTATGCTC-CTGAGGTA-TAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCT
* ** ** * **
1477 TCGTGGTACGGGATTCGTCGTTGCAACTTAAATCT
64 TCGCGGTACTAGATTCACCATTGCGGCTTAAATCT
* * *
1512 TTCCCTTTATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTCTCCCTTGGTATCTTC
1 TTTCCTTTATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTTC
* *
1577 GTGGTACTAGATTCACCGTTGCGGCTTAAATCT
66 GCGGTACTAGATTCACCATTGCGGCTTAAATCT
* * * * * * * * *
1610 TTTCCTTCATGCTTCTAACGTACAAGGTTCACCTTTGCAACTTAATCCTTTTCCCTTC
1 TTTCCTTTATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACC-TTTCCCTTC
1668 ATGTTTTGCG
Statistics
Matches: 285, Mismatches: 56, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
95 2 0.01
96 75 0.26
97 4 0.01
98 185 0.65
99 19 0.07
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (98 bp):
TTTCCTTTATGCTCCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTTC
GCGGTACTAGATTCACCATTGCGGCTTAAATCT
Found at i:13456 original size:29 final size:29
Alignment explanation
Indices: 13424--13823 Score: 125
Period size: 29 Copynumber: 13.7 Consensus size: 29
13414 ATTCGGGGGG
*
13424 TAAAATGGTAATTTTGGAAGGTTTAGGGT
1 TAAAATGGTAATTTTGGAAAGTTTAGGGT
* * * *
13453 TAAAAATGG-AATTTT-TAAACATTTGGGGG
1 T-AAAATGGTAATTTTGGAAA-GTTTAGGGT
* ** * *
13482 TAAAATTGTAATTTTCAAAAGGTTCGAGGT
1 TAAAATGGTAATTTTGGAAAGTTTAG-GGT
* * * **
13512 TAAAAAT-GAAATTTT-TAGATGTTCCGAGG-
1 T-AAAATGGTAATTTTGGA-AAGTTTAG-GGT
* **
13541 TATAATGGTAATCTTT-GAAAAATTAGGGT
1 TAAAATGGTAAT-TTTGGAAAGTTTAGGGT
* *
13570 TAGAATGG-AATTTTTGG-AAGTTTAGGGA
1 TAAAATGGTAA-TTTTGGAAAGTTTAGGGT
*****
13598 TAAAATGGTAATTTTTGGAAAAAGCGGGGT
1 TAAAATGGTAA-TTTTGGAAAGTTTAGGGT
* *
13628 TAAAAAT-GAAATTTTAGAAAGTTTGAGGGT
1 T-AAAATGGTAATTTTGGAAAGTTT-AGGGT
* *
13658 AAAAAT-GTAATTTTTAGAAAGTTTAGGGT
1 TAAAATGGTAA-TTTTGGAAAGTTTAGGGT
* *
13687 TAAAAATGG-AATTTTGGAAAATTTGGGGGT
1 T-AAAATGGTAATTTTGGAAAGTTT-AGGGT
* * **
13717 AAAAAT-GTAATTTTTAGATATTTTTA-GGT
1 TAAAATGGTAA-TTTTGGA-AAGTTTAGGGT
*
13746 TAAAAATGG-AA-TTTAGAAAGTTCGT-GGGT
1 T-AAAATGGTAATTTTGGAAAGTT--TAGGGT
* * * *
13775 AAAAAT-GTAATTTTTGGAAAGCTCAGGAT
1 TAAAATGGTAA-TTTTGGAAAGTTTAGGGT
13804 TAAAAATGG-AATTTTGGAAA
1 T-AAAATGGTAATTTTGGAAA
13824 AGTTCGAGGT
Statistics
Matches: 275, Mismatches: 62, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
27 4 0.01
28 48 0.17
29 108 0.39
30 98 0.36
31 17 0.06
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAATGGTAATTTTGGAAAGTTTAGGGT
Found at i:13513 original size:59 final size:57
Alignment explanation
Indices: 13419--13818 Score: 235
Period size: 58 Copynumber: 6.9 Consensus size: 57
13409 TGGACATTCG
*
13419 GGGGGTAAAATGGTAATTTTG-GAAGGTTTAGGGTTAAAAATGGAATTTTTAAACATTT
1 GGGGGTAAAATGGTAATTTTGAAAAGG-TTAGGGTTAAAAATGGAATTTTTAAA-ATTT
* * * * *
13477 GGGGGTAAAATTGTAATTTTCAAAAGGTTCGAGGTTAAAAATGAAATTTTT-AGATGTT
1 GGGGGTAAAATGGTAATTTTGAAAAGGTTAG-GGTTAAAAATGGAATTTTTAAAAT-TT
* * * * * * *
13535 CCGAGGTATAATGGTAATCTTTGAAAA-ATTAGGGTT-AGAATGGAATTTTTGGAAGTTT
1 -GGGGGTAAAATGGTAAT-TTTGAAAAGGTTAGGGTTAAAAATGGAATTTTT-AAAATTT
* * * ** *
13593 AGGGATAAAATGGTAATTTTTGGAAAAAG-CGGGGTTAAAAAT-GAAATTTTAGAAAGTTT
1 GGGGGTAAAATGGTAA-TTTT-GAAAAGGTTAGGGTTAAAAATGGAATTTTTA-AAA-TTT
* * * *
13652 GAGGGTAAAAAT-GTAATTTTTAGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAATTT
1 GGGGGT-AAAATGGTAATTTTGA-AAAGGTTAGGGTTAAAAATGGAATTTT-TAAAATTT
* *** ** * *
13711 GGGGGTAAAAAT-GTAATTTTTAGATATTTTTA-GGTTAAAAATGGAATTTAGAAAGTTC
1 GGGGGT-AAAATGGTAA-TTTT-GAAAAGGTTAGGGTTAAAAATGGAATTTTTAAAATTT
* * * * *
13769 GTGGGTAAAAAT-GTAATTTTTGGAAAGCTCAGGATTAAAAATGGAATTTT
1 GGGGGT-AAAATGGTAA-TTTTGAAAAGGTTAGGGTTAAAAATGGAATTTT
13819 GGAAAAGTTC
Statistics
Matches: 266, Mismatches: 55, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
57 34 0.13
58 100 0.38
59 100 0.38
60 30 0.11
61 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (57 bp):
GGGGGTAAAATGGTAATTTTGAAAAGGTTAGGGTTAAAAATGGAATTTTTAAAATTT
Found at i:13594 original size:28 final size:29
Alignment explanation
Indices: 13544--13617 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
13534 TCCGAGGTAT
* * ** * *
13544 AATGGTAATCTTTGAAAAATTAGGGTTAG
1 AATGGTAATTTTTGGAAGTTTAGGGATAA
13573 AATGG-AATTTTTGGAAGTTTAGGGATAA
1 AATGGTAATTTTTGGAAGTTTAGGGATAA
13601 AATGGTAATTTTTGGAA
1 AATGGTAATTTTTGGAA
13618 AAAGCGGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.36
Consensus pattern (29 bp):
AATGGTAATTTTTGGAAGTTTAGGGATAA
Found at i:19946 original size:11 final size:11
Alignment explanation
Indices: 19932--19999 Score: 66
Period size: 11 Copynumber: 5.8 Consensus size: 11
19922 TTAGATTGAC
*
19932 TTTAAATTTAT
1 TTTAAATTTAA
19943 TTTAAAAGTTTAAA
1 TTT-AAA-TTT-AA
19957 TTTAAATTTACA
1 TTTAAATTTA-A
19969 -TTAAATTTAAA
1 TTTAAATTT-AA
*
19980 TTTAAATTTAG
1 TTTAAATTTAA
19991 TTTAAATTT
1 TTTAAATTT
20000 GAAATGATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
11 23 0.47
12 16 0.33
13 6 0.12
14 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:19960 original size:6 final size:6
Alignment explanation
Indices: 19932--20030 Score: 73
Period size: 6 Copynumber: 16.8 Consensus size: 6
19922 TTAGATTGAC
* *
19932 TTTAAA TTT-AT TTTAAAA GTTTAAA TTTAAA TTTACA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
19980 TTTAAA TTT-AG TTTAAA TTTGAAA --TGAT TTTAAA CTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
20026 TTTAA
1 TTTAA
20031 TTTCAAAATC
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
4 1 0.01
5 13 0.18
6 47 0.66
7 7 0.10
8 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:19974 original size:17 final size:17
Alignment explanation
Indices: 19952--20004 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
19942 TTTTAAAAGT
*
19952 TTAAATTTAAATTTACA
1 TTAAATTTAAATTTAAA
19969 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
* *
19986 TTTAGTTTAAATTTGAAA
1 TTAAATTTAAATTT-AAA
20004 T
1 T
20005 GATTTTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 28 0.88
18 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:19981 original size:23 final size:23
Alignment explanation
Indices: 19932--20004 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 23
19922 TTAGATTGAC
*
19932 TTTAAATTTATTTTAAAAGTTTAAA
1 TTTAAATTTACTTT-AAA-TTTAAA
*
19957 TTTAAATTTACATTAAATTTAAA
1 TTTAAATTTACTTTAAATTTAAA
*
19980 TTTAAATTTAGTTTAAATTTGAAA
1 TTTAAATTTACTTTAAATTT-AAA
20004 T
1 T
20005 GATTTTAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 24 0.56
24 7 0.16
25 12 0.28
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTAAATTTACTTTAAATTTAAA
Done.