Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011021.1 Kokia drynarioides strain JFW-HI SEQ_125992, 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: 30266
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:612 original size:12 final size:11
Alignment explanation
Indices: 567--608 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
557 ATTTATTTTA
*
567 AAATAATTAAT
1 AAATAAATAAT
578 AAATATAATAAT
1 AAATA-AATAAT
590 -AAT-AATAAT
1 AAATAAATAAT
599 AAATAAATAA
1 AAATAAATAA
609 ATAAGGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 6 0.22
10 3 0.11
11 13 0.48
12 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:1697 original size:29 final size:29
Alignment explanation
Indices: 1632--1856 Score: 147
Period size: 28 Copynumber: 7.9 Consensus size: 29
1622 CGAAATTTGC
* *
1632 AAAAATTACATTTTGACCCTCAAACTT-TT
1 AAAAATTACATTTTAACCCT-AAACTTCTA
* * * *
1661 TAATATTACATTTTAACCTTGAACTTCTA
1 AAAAATTACATTTTAACCCTAAACTTCTA
* *
1690 AAAAATTACATTTTTACCCAAAACTTC-A
1 AAAAATTACATTTTAACCCTAAACTTCTA
* * * *
1718 AAAAATCACATTTTTACCCTTAAACTTTTC
1 AAAAATTACATTTTAACCC-TAAACTTCTA
* ** *
1748 AAAAATTACATTTTTACCCCGAACTTCTC
1 AAAAATTACATTTTAACCCTAAACTTCTA
* ** *
1777 AAAAATCT-CATTTT-ACCCCAAGTTTC-C
1 AAAAAT-TACATTTTAACCCTAAACTTCTA
* * *
1804 CAAAATTACATTTTATCCCTAAACTT-TC
1 AAAAATTACATTTTAACCCTAAACTTCTA
* * *
1832 CAAAATTACGTTTTAACCCAAAACT
1 AAAAATTACATTTTAACCCTAAACT
1857 CTTCAAAACT
Statistics
Matches: 158, Mismatches: 31, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
26 1 0.01
27 12 0.08
28 63 0.40
29 63 0.40
30 19 0.12
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTAAACTTCTA
Found at i:1791 original size:58 final size:57
Alignment explanation
Indices: 1632--1794 Score: 164
Period size: 58 Copynumber: 2.8 Consensus size: 57
1622 CGAAATTTGC
* * *** * * * *
1632 AAAAATTACATTTTGACCCTCAAACTTTTTAATATTACATTTTAACCTTGAACTTCTA
1 AAAAATTACATTTTTACCC-AAAACTTCAAAAAATCACATTTTACCCTTAAACTTCTA
* *
1690 AAAAATTACATTTTTACCCAAAACTTCAAAAAATCACATTTTTACCCTTAAACTTTTC
1 AAAAATTACATTTTTACCCAAAACTTCAAAAAATCACA-TTTTACCCTTAAACTTCTA
** * *
1748 AAAAATTACATTTTTACCCCGAACTTCTCAAAAATCTCATTTTACCC
1 AAAAATTACATTTTTACCCAAAACTTC-AAAAAATCACATTTTACCC
1795 CAAGTTTCCC
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 13 0.15
58 66 0.75
59 9 0.10
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCAAAACTTCAAAAAATCACATTTTACCCTTAAACTTCTA
Found at i:1795 original size:28 final size:29
Alignment explanation
Indices: 1632--1797 Score: 142
Period size: 29 Copynumber: 5.8 Consensus size: 29
1622 CGAAATTTGC
* *
1632 AAAAATTACATTTTGACCCTCAAACTT-TT
1 AAAAATTACATTTTTACCC-CAAACTTCTA
* * * ***
1661 TAATATTACATTTTAACCTTGAACTTCTA
1 AAAAATTACATTTTTACCCCAAACTTCTA
*
1690 AAAAATTACATTTTTACCCAAAACTTC-A
1 AAAAATTACATTTTTACCCCAAACTTCTA
* * * *
1718 AAAAATCACATTTTTACCCTTAAACTTTTC
1 AAAAATTACATTTTTACCC-CAAACTTCTA
* *
1748 AAAAATTACATTTTTACCCCGAACTTCTC
1 AAAAATTACATTTTTACCCCAAACTTCTA
1777 AAAAATCT-CA-TTTTACCCCAA
1 AAAAAT-TACATTTTTACCCCAA
1798 GTTTCCCAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
28 34 0.31
29 58 0.52
30 19 0.17
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCAAACTTCTA
Found at i:1834 original size:28 final size:28
Alignment explanation
Indices: 1631--1873 Score: 135
Period size: 29 Copynumber: 8.5 Consensus size: 28
1621 TCGAAATTTG
1631 CAAAAATTACATTTTGA-CCCTCAAACTTT
1 CAAAAATTACATTTT-ATCCCT-AAACTTT
** * * * *
1660 TTAATATTACATTTTAACCTTGAACTTCT
1 CAAAAATTACATTTTATCCCTAAACTT-T
* *
1689 AAAAAATTACATTTT-TACCCAAAAC-TT
1 CAAAAATTACATTTTAT-CCCTAAACTTT
*
1716 CAAAAAATCACATTTT-TACCCTTAAACTTTT
1 C-AAAAATTACATTTTAT-CCC-TAAAC-TTT
**
1747 CAAAAATTACATTTT-TACCCCGAACTTCT
1 CAAAAATTACATTTTAT-CCCTAAACTT-T
* *
1776 CAAAAATCT-CATTTTA-CCC-CAAGTTT
1 CAAAAAT-TACATTTTATCCCTAAACTTT
*
1802 CCCAAAATTACATTTTATCCCTAAACTTT
1 -CAAAAATTACATTTTATCCCTAAACTTT
* * * *
1831 CCAAAATTACGTTTTAACCCAAAACTCTT
1 CAAAAATTACATTTTATCCCTAAACT-TT
*
1860 CAAAACTT-CATTTT
1 CAAAAATTACATTTT
1874 CAACCCCGAT
Statistics
Matches: 170, Mismatches: 29, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
26 2 0.01
27 18 0.11
28 61 0.36
29 67 0.39
30 19 0.11
31 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (28 bp):
CAAAAATTACATTTTATCCCTAAACTTT
Found at i:2589 original size:18 final size:18
Alignment explanation
Indices: 2566--2603 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2556 CTGGATTTCG
2566 AAGACCAAAATGTTTTTA
1 AAGACCAAAATGTTTTTA
2584 AAGACCAAAATGTTTTTA
1 AAGACCAAAATGTTTTTA
2602 AA
1 AA
2604 ACAGACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
AAGACCAAAATGTTTTTA
Found at i:4127 original size:195 final size:194
Alignment explanation
Indices: 3733--4173 Score: 510
Period size: 195 Copynumber: 2.3 Consensus size: 194
3723 TACCAGTACT
* * * * * * * * *
3733 CGATGCTACTTACACGAGCTGTTGAGGACTCGCAACGTATGCGGTTCCCCAGCCATCGGTACGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACAATCGATACGGT
* * * * *
3798 GTCTGTCTGTACTATAAACTATTCCCTAACGATGCTGCTCATATGAGTTGTCGAGAGTATGCATA
66 ATCTG-CTGCACTATAAACTATTCCCTAACGATGCTGCTCACATGAGCTGTCGAGAATATGCATA
* * *
3863 AAGCATAGTCCCAGCCATCGTAGGGTCTATAATCCATTTAGGATCCATATCTCTTTCCCGAGGCA
130 AAGCATAATCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCGACGCA
* *
3928 CGATGCTGCTCACATGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACAATCGATACGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACAATCGATACGGT
* *
3993 ATCTG-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACATGAGCTGTCGAGAATATGCACTT
66 ATCTGCTGCACTATAAACTATTCCCTAACGATGCTGCTCACATGAGCTGTCGAGAATATGCA-TA
* * * * * * * * * *
4055 ATGCATAAATCTCAGTCATCGTAGGGCCTGTAATCCATTCTTGGATTCTTTTTTCATTTCTCGAC
130 AAGCAT-AATCCCAGCCATCGTAGGGCCTATAATCCATT-TAGGATCCATATCTC-TTTCCCGAC
*
4120 TCA
192 GCA
* *
4123 CGATGCTGCTCACACGAGTTGTCGAGGACTCGCAACATATGCGATACCTCA
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCA
4174 GCCATCGCGC
Statistics
Matches: 206, Mismatches: 36, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
191 43 0.21
192 9 0.04
193 30 0.15
194 10 0.05
195 114 0.55
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (194 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACAATCGATACGGT
ATCTGCTGCACTATAAACTATTCCCTAACGATGCTGCTCACATGAGCTGTCGAGAATATGCATAA
AGCATAATCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCGACGCA
Found at i:13801 original size:89 final size:89
Alignment explanation
Indices: 13650--13830 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
13640 GCTTTGAAAT
*
13650 TCTCCCCTCAACCAGACTGAACTTCTTTAATCTTAGCATCAAACTGCAGCTTAACATGCTTTTTA
1 TCTCCCCCCAACCAGACTGAACTTCTTTAATCTTAGCATCAAACTGCAGCTTAACATGCTTTTTA
13715 AACGGAGAAAACGCAGTAATAACA
66 AACGGAGAAAACGCAGTAATAACA
*
13739 TCTCCCCCCAACCAGACTGAACTTCTTTAATCTTAGCATCTAACTGCAGCTTAACATGCTTTTTA
1 TCTCCCCCCAACCAGACTGAACTTCTTTAATCTTAGCATCAAACTGCAGCTTAACATGCTTTTTA
* *
13804 AACTGAGAAAATGCAGTAATAACA
66 AACGGAGAAAACGCAGTAATAACA
13828 TCT
1 TCT
13831 GACTTGTACT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (89 bp):
TCTCCCCCCAACCAGACTGAACTTCTTTAATCTTAGCATCAAACTGCAGCTTAACATGCTTTTTA
AACGGAGAAAACGCAGTAATAACA
Found at i:24749 original size:55 final size:57
Alignment explanation
Indices: 24682--24787 Score: 139
Period size: 55 Copynumber: 1.9 Consensus size: 57
24672 AATTGGTGTC
*
24682 GGTCATTGCATGGATGACACC-CTCTTTTTTATCAGA-C-AAAAAATTTTTTATTGTT
1 GGTCATTGCATGGATGACACCACT-TTTATTATCAGACCAAAAAAATTTTTTATTGTT
* *
24737 GGTCA-TGCCATGGTTGACACCACTTTTATTATCTGACCAAAAAAATTTTTT
1 GGTCATTG-CATGGATGACACCACTTTTATTATCAGACCAAAAAAATTTTTT
24788 TGGTATTGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
54 2 0.05
55 27 0.61
56 3 0.07
57 12 0.27
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (57 bp):
GGTCATTGCATGGATGACACCACTTTTATTATCAGACCAAAAAAATTTTTTATTGTT
Found at i:24847 original size:61 final size:61
Alignment explanation
Indices: 24779--24909 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 61
24769 CTGACCAAAA
* * * *
24779 AAATTTTTTTGGTATTGACCATTCCATGGTC-GACACCCCCTTTTTGTCAGATAAAAAATTC
1 AAATTTTTTTGGTATTGACCATGCAATGGCCAG-CACCCCCTTTTTGTCAGATAAAAAAATC
* * * * **
24840 AAA-TTTTTGGGTGTTGGCCATGCAATGGCCAGCACCCTCTTTTTGTTTGATAAAAAAATC
1 AAATTTTTTTGGTATTGACCATGCAATGGCCAGCACCCCCTTTTTGTCAGATAAAAAAATC
24900 AAATTTTTTT
1 AAATTTTTTT
24910 ATGTCGGCCA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
60 48 0.84
61 9 0.16
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (61 bp):
AAATTTTTTTGGTATTGACCATGCAATGGCCAGCACCCCCTTTTTGTCAGATAAAAAAATC
Found at i:25069 original size:62 final size:62
Alignment explanation
Indices: 24943--25080 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 62
24933 AAAAATCAAA
* * *
24943 TTTTTTTGTGTTGATCATCCATGGTTGACACCTCCTTTTTATCAGATAAAAAATTTGAATTT
1 TTTTTTTGTGTTGATCATCCATGATTGAAACCTCCTTTTTATCAGATAAAAAATATGAATTT
*
25005 TTTTTTTGTGTTGGTCATGCCATGATTGAAACC-CCTTTTTTTTATCTAG-TAAAAAA-AT-AAT
1 TTTTTTTGTGTTGATCAT-CCATGATTGAAACCTCC---TTTTTATC-AGATAAAAAATATGAAT
25066 TT
61 TT
*
25068 TTTTTTGGTGTTG
1 TTTTTTTGTGTTG
25081 CCATGCAATG
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
62 19 0.29
63 29 0.44
64 1 0.02
65 15 0.23
66 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (62 bp):
TTTTTTTGTGTTGATCATCCATGATTGAAACCTCCTTTTTATCAGATAAAAAATATGAATTT
Found at i:29220 original size:86 final size:84
Alignment explanation
Indices: 29115--29329 Score: 324
Period size: 86 Copynumber: 2.5 Consensus size: 84
29105 AATTTAGCAT
* *
29115 TATTTAAATAAAAAAATTATTATTATATTTCAATTTACATTAAATAATGTGTTGATTTGACAATA
1 TATTTAAATAAAAAAATTATTATTATATTTAAATTT-CATCAAATAATGTGTTGATTTGACAATA
*
29180 CATTATTTATCAAATTTTAA
65 CATTATTTACCAAATTTTAA
*
29200 TATTTAAATAAAAAAGATTATTATTATATTATAAATTTTATCAAATAATGTGTTGATTTGACAAT
1 TATTTAAATAAAAAA-ATTATTATTATATT-TAAATTTCATCAAATAATGTGTTGATTTGACAAT
29265 ACATTATTTACCAAATTTTAA
64 ACATTATTTACCAAATTTTAA
* * *
29286 TATTTAAAT-TAAAAATTATTATTATATTTTAATTTTTATCAAAT
1 TATTTAAATAAAAAAATTATTATTATA-TTTAAATTTCATCAAAT
29330 TTTAAATTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
84 26 0.21
85 21 0.17
86 68 0.56
87 6 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (84 bp):
TATTTAAATAAAAAAATTATTATTATATTTAAATTTCATCAAATAATGTGTTGATTTGACAATAC
ATTATTTACCAAATTTTAA
Found at i:29450 original size:22 final size:22
Alignment explanation
Indices: 29422--29478 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
29412 TGGACCACCC
*
29422 AAATTCCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCG
29444 AAATTCCAGCTCACCAAAACCG
1 AAATTCCAGCTCACCAAAACCG
29466 AAATTCCAGCTCA
1 AAATTCCAGCTCA
29479 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.18
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Done.