Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004845.1 Kokia drynarioides strain JFW-HI SEQ_118497, 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: 26394
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:47 original size:9 final size:9
Alignment explanation
Indices: 35--101 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
25 AAACACATTA
35 CCTTTCTTT
1 CCTTTCTTT
44 CC-TTC-TT
1 CCTTTCTTT
51 -CTTTCTTT
1 CCTTTCTTT
*
59 CCTCTCCTTCT
1 CCT-TTCTT-T
*
70 TCTTTCTTT
1 CCTTTCTTT
*
79 CCTCTCTTT
1 CCTTTCTTT
88 CCTTT-TTT
1 CCTTTCTTT
*
96 TCTTTC
1 CCTTTC
102 CCGTTTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.02
7 5 0.11
8 12 0.27
9 16 0.36
10 8 0.18
11 3 0.07
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:68 original size:20 final size:20
Alignment explanation
Indices: 43--84 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
33 TACCTTTCTT
43 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
63 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
83 TC
1 TC
85 TTTCCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:1492 original size:31 final size:31
Alignment explanation
Indices: 1457--1518 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1447 TAAGACTCAA
1457 TCGTTAACTAATAAAGATATTTGATTTAAAC
1 TCGTTAACTAATAAAGATATTTGATTTAAAC
1488 TCGTTAACTAATAAAGATATTTGATTTAAAC
1 TCGTTAACTAATAAAGATATTTGATTTAAAC
1519 CTGACCGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
TCGTTAACTAATAAAGATATTTGATTTAAAC
Found at i:3330 original size:150 final size:149
Alignment explanation
Indices: 3076--3349 Score: 345
Period size: 150 Copynumber: 1.8 Consensus size: 149
3066 TATAAATTTA
* * * * *
3076 GTATTCTTGTAATTTTCGAATTGATCAATTTTAATCTATATATTTTAGTAGATGTTAAATCAGTG
1 GTATTCTTGTAATTTTCAAATTGATCAATATTAATCTATATACTTTAATAGATGTTAAATAAGTG
** * * *
3141 TACTTTGTATAAATTGTGAATTCAGTATTTTGATAATTTTTGAATTGATCAATTTTAGTGTATTC
66 TACTCGGCATAAATTGTGAATTCAGTATTCTGATAATTTTTGAATTGATCAAATTTAGTGTATTC
3206 AACGTAATTTGTGAAAATC
131 AACGTAATTTGTGAAAATC
* * * *
3225 GTATTCTTGTATTTTTCAAATTGATCAAATATTAGT-TCGTATACTTTAATAGTTGTTAAATAAG
1 GTATTCTTGTAATTTTCAAATTGATC-AATATTAATCT-ATATACTTTAATAGATGTTAAATAAG
* * * *
3289 TGTACTCGGCCTAAGTTGTGAATTTAGTATTCCT-ATCATTTTTGAATTGATCAAATTTAGT
64 TGTACTCGGCATAAATTGTGAATTCAGTATT-CTGATAATTTTTGAATTGATCAAATTTAGT
3350 TCGTATGCTT
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
149 25 0.24
150 78 0.75
151 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (149 bp):
GTATTCTTGTAATTTTCAAATTGATCAATATTAATCTATATACTTTAATAGATGTTAAATAAGTG
TACTCGGCATAAATTGTGAATTCAGTATTCTGATAATTTTTGAATTGATCAAATTTAGTGTATTC
AACGTAATTTGTGAAAATC
Found at i:4182 original size:11 final size:11
Alignment explanation
Indices: 4163--4201 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4153 TTTTAAAATG
4163 TTAATATTTTT
1 TTAATATTTTT
*
4174 TTAA-AATTTT
1 TTAATATTTTT
*
4184 TTATTATTTTT
1 TTAATATTTTT
4195 TTAATAT
1 TTAATAT
4202 AATAATATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:4193 original size:19 final size:20
Alignment explanation
Indices: 4151--4194 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4141 GCAAGATTTG
4151 ATTTTTAAAATGTTAATATT
1 ATTTTTAAAATGTTAATATT
**
4171 -TTTTTAAAAT-TTTTTATT
1 ATTTTTAAAATGTTAATATT
4189 ATTTTT
1 ATTTTT
4195 TTAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTAAAATGTTAATATT
Found at i:7739 original size:57 final size:58
Alignment explanation
Indices: 7678--7857 Score: 219
Period size: 57 Copynumber: 3.1 Consensus size: 58
7668 GTAAAACGGT
* *
7678 AATTTTT-GACATTTCGGGGGTAAAATAGTAATTTTGG-AGGTTCGAGGTCAAAAATGG
1 AATTTTTAGACA-TTCGGGGGTAAAATGGTAATTTTGGAAGATTCGAGGTCAAAAATGG
* * *
7735 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGAAAATTCG-GGATCAAAAATGA
1 AATTTTTAGACATTCGGGGGTAAAATGGTAATTTTGGAAGATTCGAGG-TCAAAAATGG
*
7793 AATTTTTAGACATTC-GAGGTAAAATGGTAATTTTTGGAAGATTCGAGGGT--AAAATGG
1 AATTTTTAGACATTCGGGGGTAAAATGGTAA-TTTTGGAAGATTCGA-GGTCAAAAATGG
7850 TAATTTTT
1 -AATTTTT
7858 GGAAAATTTG
Statistics
Matches: 108, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
57 53 0.49
58 52 0.48
59 1 0.01
60 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (58 bp):
AATTTTTAGACATTCGGGGGTAAAATGGTAATTTTGGAAGATTCGAGGTCAAAAATGG
Found at i:7846 original size:30 final size:30
Alignment explanation
Indices: 7663--7966 Score: 212
Period size: 29 Copynumber: 10.4 Consensus size: 30
7653 TTTAGATACC
* *
7663 CGAGGGTAAAACGGTAATTTTT-GACA-TTT
1 CGAGGGTAAAATGGTAATTTTTGGA-AGATT
* * *
7692 CGGGGGTAAAATAGTAA-TTTTGG-AGGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAGATT
*
7720 CGA-GGTCAAAAATGG-AATTTTTGG-ACATT
1 CGAGGGT--AAAATGGTAATTTTTGGAAGATT
* *
7749 CGGGGGTAAAATGGTAA-TTTTGGAAAATT
1 CGAGGGTAAAATGGTAATTTTTGGAAGATT
* * * *
7778 CG-GGATCAAAAAT-GAAATTTTTAG-ACATT
1 CGAGGGT--AAAATGGTAATTTTTGGAAGATT
7807 CGA-GGTAAAATGGTAATTTTTGGAAGATT
1 CGAGGGTAAAATGGTAATTTTTGGAAGATT
*
7836 CGAGGGTAAAATGGTAATTTTTGGAAAATT
1 CGAGGGTAAAATGGTAATTTTTGGAAGATT
* *
7866 TG-GGGTCAAAAATGG-AATTTTTGGAAGTTT
1 CGAGGGT--AAAATGGTAATTTTTGGAAGATT
* *
7896 AG-GGGTAAAATGTTAATTTTTGGAA-AGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAGA-TT
** *
7925 CGAAGGCCAAAAT-GAAATTTTTGGAAG-TT
1 CG-AGGGTAAAATGGTAATTTTTGGAAGATT
7954 CGAGGGTGAAAAT
1 CGAGGGT-AAAAT
7967 AAATTTTTAG
Statistics
Matches: 220, Mismatches: 32, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
27 9 0.04
28 44 0.20
29 85 0.39
30 68 0.31
31 14 0.06
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (30 bp):
CGAGGGTAAAATGGTAATTTTTGGAAGATT
Found at i:7855 original size:58 final size:59
Alignment explanation
Indices: 7663--7966 Score: 242
Period size: 58 Copynumber: 5.2 Consensus size: 59
7653 TTTAGATACC
* * *
7663 CGAGGGT-AAAACGGTAATTTTT-GACATTTCGGGGGTAAAATAGTAA-TTTTGG-AGGTT
1 CGAGGGTAAAAATGGTAATTTTTGGACA-TTC-GGGGTAAAATGGTAATTTTTGGAAGATT
*
7720 CGA-GGTCAAAAATGG-AATTTTTGGACATTCGGGGGTAAAATGGTAA-TTTTGGAAAATT
1 CGAGGGT-AAAAATGGTAATTTTTGGACATTC-GGGGTAAAATGGTAATTTTTGGAAGATT
* * * *
7778 CG-GGATCAAAAAT-GAAATTTTTAGACATTCGAGGTAAAATGGTAATTTTTGGAAGATT
1 CGAGGGT-AAAAATGGTAATTTTTGGACATTCGGGGTAAAATGGTAATTTTTGGAAGATT
* * *
7836 CGAGGGT-AAAATGGTAATTTTTGGAAAATTTGGGGTCAAAAATGG-AATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGTAATTTTTGG-ACATTCGGGGT--AAAATGGTAATTTTTGGAAGATT
* * * ** *
7896 AG-GGGT-AAAATGTTAATTTTTGGAAAGTTCGAAGGCCAAAAT-GAAATTTTTGGAAG-TT
1 CGAGGGTAAAAATGGTAATTTTTGGACA-TTCG--GGGTAAAATGGTAATTTTTGGAAGATT
*
7954 CGAGGGTGAAAAT
1 CGAGGGTAAAAAT
7967 AAATTTTTAG
Statistics
Matches: 208, Mismatches: 21, Indels: 33
0.79 0.08 0.13
Matches are distributed among these distances:
56 3 0.01
57 54 0.26
58 67 0.32
59 55 0.26
60 20 0.10
61 9 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (59 bp):
CGAGGGTAAAAATGGTAATTTTTGGACATTCGGGGTAAAATGGTAATTTTTGGAAGATT
Found at i:7913 original size:59 final size:60
Alignment explanation
Indices: 7813--7966 Score: 179
Period size: 59 Copynumber: 2.6 Consensus size: 60
7803 CATTCGAGGT
* * * *
7813 AAAATGGTAATTTTTGGAAGATTCGAGGGTAAAATGGTAATTTTTGGAAAATTTG-GGGTCA
1 AAAATGG-AATTTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAAGG-CA
* * *
7874 AAAATGGAATTTTTGGAAGTTTAG-GGGTAAAATGTTAATTTTTGGAAAGTTCGAAGGCC
1 AAAATGGAATTTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAAGGCA
* *
7933 AAAATGAAATTTTTGGAAG-TTCGAGGGTGAAAAT
1 AAAATGGAATTTTTGGAAGTTTAGAGGGT-AAAAT
7967 AAATTTTTAG
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.04
59 49 0.60
60 22 0.27
61 7 0.09
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAAGGCA
Found at i:7944 original size:89 final size:88
Alignment explanation
Indices: 7728--7950 Score: 233
Period size: 89 Copynumber: 2.6 Consensus size: 88
7718 TTCGAGGTCA
* * ** *
7728 AAAATGG-AATTTTTGG-ACATTCGGGGGTAAAATGGTAA-TTTTGGAAAATTCGGGATCAAAAA
1 AAAATGGTAATTTTTGGAAGATTCGAGGCCAAAATGGAAATTTTTGGAAAATTCGGGATCAAAAA
*
7790 TGAAATTTTTAGACATTCGAGGT
66 TGAAATTTTTAGACATTAGAGGT
** * * *
7813 AAAATGGTAATTTTTGGAAGATTCGAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCAAAAA
1 AAAATGGTAATTTTTGGAAGATTCGAGGCCAAAATGGAAATTTTTGGAAAATTCGGGATCAAAAA
* * *
7878 TGGAATTTTTGGA-AGTTTAGGGGT
66 TGAAATTTTTAGACA--TTAGAGGT
*
7902 AAAATGTTAATTTTTGGAA-AGTTCGAAGGCCAAAAT-GAAATTTTTGGAA
1 AAAATGGTAATTTTTGGAAGA-TTCG-AGGCCAAAATGGAAATTTTTGGAA
7951 GTTCGAGGGT
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
85 7 0.06
86 9 0.08
87 21 0.18
88 34 0.29
89 40 0.34
90 8 0.07
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (88 bp):
AAAATGGTAATTTTTGGAAGATTCGAGGCCAAAATGGAAATTTTTGGAAAATTCGGGATCAAAAA
TGAAATTTTTAGACATTAGAGGT
Found at i:7945 original size:29 final size:29
Alignment explanation
Indices: 7910--7996 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
7900 GTAAAATGTT
7910 AATTTTTGGAAAGTTCGAAGGCCAAAATGA
1 AATTTTTGGAAAGTTCGAAGGCCAAAAT-A
* **
7940 AATTTTTGG-AAGTTCGAGGGTGAAAATA
1 AATTTTTGGAAAGTTCGAAGGCCAAAATA
* *
7968 AATTTTTAGAAAGTTCGGAGGCCAAAATA
1 AATTTTTGGAAAGTTCGAAGGCCAAAATA
7997 TGATTTCTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 9 0.19
29 30 0.62
30 9 0.19
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (29 bp):
AATTTTTGGAAAGTTCGAAGGCCAAAATA
Found at i:9824 original size:11 final size:11
Alignment explanation
Indices: 9808--9866 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
9798 TGAGACTTTT
9808 AATAAATTTAA
1 AATAAATTTAA
9819 AATAAATTTAA
1 AATAAATTTAA
*
9830 ATTTAGAA--TAA
1 A-ATA-AATTTAA
*
9841 ATTTAAATTTAAA
1 A-ATAAATTT-AA
9854 AATAAATTTAA
1 AATAAATTTAA
9865 AA
1 AA
9867 GGGTTTGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.05
11 24 0.59
12 10 0.24
13 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:9830 original size:6 final size:6
Alignment explanation
Indices: 9810--9865 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
9800 AGACTTTTAA
* **
9810 TAAATT TAAA-A TAAATT TAAATT TAGAA-- TAAATT TAAATT TAAAAA
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT
9856 TAAATT TAAA
1 TAAATT TAAA
9866 AGGGTTTGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 30 0.75
7 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:9832 original size:17 final size:17
Alignment explanation
Indices: 9810--9865 Score: 94
Period size: 17 Copynumber: 3.2 Consensus size: 17
9800 AGACTTTTAA
9810 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
*
9827 TAAATTTAGAATAAATT
1 TAAATTTAAAATAAATT
9844 TAAATTTAAAAATAAATT
1 TAAATTT-AAAATAAATT
9862 TAAA
1 TAAA
9866 AGGGTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 23 0.64
18 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:15103 original size:37 final size:37
Alignment explanation
Indices: 15056--15131 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
15046 TGCATGCCTA
*
15056 TATTTAGAACTTACCTTGGCTATGAATTCTAAAGATT
1 TATTTAGAACTTACCTTGGCTATGAATTATAAAGATT
15093 TATTTAGAACTTACCTTGGCTATGAATTATAAAGATT
1 TATTTAGAACTTACCTTGGCTATGAATTATAAAGATT
15130 TA
1 TA
15132 AGTAGTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
TATTTAGAACTTACCTTGGCTATGAATTATAAAGATT
Found at i:16212 original size:61 final size:57
Alignment explanation
Indices: 16098--16229 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 57
16088 CACACTAGTA
**
16098 GTCACCCAACTATTAGTAAATTTTTTTGGTCATCCAACTTTGAAAAGTTACAAAATG
1 GTCACCCAACTATTAGTAAATTTTTTTGGTCATCCAACCATGAAAAGTTACAAAATG
* *
16155 GTCACCCAACTATTTGTAAATTTCTTTTTTTGGTCA-CCTAACCATGACAAGTTACAAAATG
1 GTCACCCAACTATTAGTAAA----TTTTTTTGGTCATCC-AACCATGAAAAGTTACAAAATG
**
16216 GTCACTAAACTATT
1 GTCACCCAACTATT
16230 CAATTTCATC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 19 0.30
60 2 0.03
61 43 0.67
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (57 bp):
GTCACCCAACTATTAGTAAATTTTTTTGGTCATCCAACCATGAAAAGTTACAAAATG
Found at i:16541 original size:61 final size:61
Alignment explanation
Indices: 16406--16530 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 61
16396 GACAAAATTG
* * * * * *
16406 AATAATTGGGTAACGATTTTGTTACTTTTCATAGTTAGGTGACTAAAAAAAGGAATTTACT
1 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTAGATGACTAAAAAAAGGAATTCACT
*
16467 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTAGATGACT-AGAAAA-GAAGTTCACT
1 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTAGATGACTAAAAAAAGGAA-TTCACT
16527 AATA
1 AATA
16531 GTTTAGGTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 3 0.05
60 14 0.25
61 39 0.70
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (61 bp):
AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTAGATGACTAAAAAAAGGAATTCACT
Found at i:21455 original size:4 final size:4
Alignment explanation
Indices: 21446--21471 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21436 TAGGTCTAAA
21446 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
21472 AAATTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Done.