Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012673.1 Kokia drynarioides strain JFW-HI SEQ_127684, 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: 71893
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--37 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AAA
4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38 TGTTCAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1314 original size:30 final size:30
Alignment explanation
Indices: 1243--1320 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
1233 CCCCTAGTCC
* * *
1243 CAAAATCGAATTCTAGATTGTTTACCTAAA
1 CAAATTCGAATTCTAGATTATTTACCAAAA
*
1273 -AAATCCGAATTCTAGATTATTTACCAAAA
1 CAAATTCGAATTCTAGATTATTTACCAAAA
1302 CAAATTCGAATTCTAGATT
1 CAAATTCGAATTCTAGATT
1321 TCTAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (30 bp):
CAAATTCGAATTCTAGATTATTTACCAAAA
Found at i:5155 original size:12 final size:12
Alignment explanation
Indices: 5138--5221 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
5128 ATATATATAT
*
5138 AAAAGAATAAAG
1 AAAAGAAAAAAG
5150 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
5162 AAACAAAAGAAGGAAG
1 AAA-AGAA-AA--AAG
*
5178 AAAAGATATATATATAT
1 AAAAGA-A-A-A-A-AG
*
5195 AAAAGAATAAAG
1 AAAAGAAAAAAG
5207 AAAAGAAAAAAG
1 AAAAGAAAAAAG
5219 AAA
1 AAA
5222 CAAAAGAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 29 0.52
13 4 0.07
14 3 0.05
15 2 0.04
16 10 0.18
17 8 0.14
ACGTcount: A:0.74, C:0.01, G:0.15, T:0.10
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:5212 original size:57 final size:57
Alignment explanation
Indices: 5128--5240 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
5118 AAGCAGATAG
5128 ATATATATATAAAAGAATAAAGAAAAGAAAAAAGAAACAAAAGAAGGAAGAAAAGAT
1 ATATATATATAAAAGAATAAAGAAAAGAAAAAAGAAACAAAAGAAGGAAGAAAAGAT
5185 ATATATATATAAAAGAATAAAGAAAAGAAAAAAGAAACAAAAGAAGGAAGAAAAGA
1 ATATATATATAAAAGAATAAAGAAAAGAAAAAAGAAACAAAAGAAGGAAGAAAAGA
5241 AGCTCAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.12
Consensus pattern (57 bp):
ATATATATATAAAAGAATAAAGAAAAGAAAAAAGAAACAAAAGAAGGAAGAAAAGAT
Found at i:5267 original size:14 final size:15
Alignment explanation
Indices: 5250--5282 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5240 AAGCTCAAAA
5250 AAAAGGGAA-GAAAG
1 AAAAGGGAAGGAAAG
5264 AAAAGGGAAGGAAAG
1 AAAAGGGAAGGAAAG
5279 AAAA
1 AAAA
5283 AAAGGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAAGGGAAGGAAAG
Found at i:5279 original size:19 final size:18
Alignment explanation
Indices: 5252--5287 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5242 GCTCAAAAAA
*
5252 AAGGGAAGAAAGAAAAGGG
1 AAGGAAAGAAA-AAAAGGG
5271 AAGGAAAGAAAAAAAGG
1 AAGGAAAGAAAAAAAGG
5288 AGAAACTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (18 bp):
AAGGAAAGAAAAAAAGGG
Found at i:8115 original size:21 final size:22
Alignment explanation
Indices: 8091--8148 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
8081 AAATATAACA
*
8091 AAAATTAATAAAT-TTCAATAT
1 AAAATTAATAAATATCCAATAT
* *
8112 AAAAGTAATTACATATCCAATAT
1 AAAATTAA-TAAATATCCAATAT
8135 AAATATTATATAAA
1 AAA-ATTA-ATAAA
8149 ATACTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 7 0.25
22 4 0.14
23 10 0.36
24 6 0.21
25 1 0.04
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATTAATAAATATCCAATAT
Found at i:12250 original size:18 final size:18
Alignment explanation
Indices: 12227--12265 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12217 TAATATAGTT
12227 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
12245 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
12263 TTA
1 TTA
12266 GAAAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:27974 original size:29 final size:29
Alignment explanation
Indices: 27937--28008 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
27927 AAATTAATAG
* *
27937 TAATAAAATTATATTTTAATTTTTTAAAA
1 TAATAAAATTATAATTTAATTATTTAAAA
*
27966 TAATAAAATTTTAATTTAATTATTTAAAA
1 TAATAAAATTATAATTTAATTATTTAAAA
* *
27995 TTATAAAAATATAA
1 TAATAAAATTATAA
28009 ATTATTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATAAAATTATAATTTAATTATTTAAAA
Found at i:34289 original size:18 final size:19
Alignment explanation
Indices: 34260--34295 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
34250 ATTTGGACTT
34260 TACTATTATTTTATTTTAC
1 TACTATTATTTTATTTTAC
34279 TACTA-TATTTTATTTTA
1 TACTATTATTTTATTTTA
34296 ACAAGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (19 bp):
TACTATTATTTTATTTTAC
Found at i:38243 original size:21 final size:21
Alignment explanation
Indices: 38217--38256 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38207 GGAAACCCTA
*
38217 AAAATATATAATAAAAAAATC
1 AAAATAAATAATAAAAAAATC
38238 AAAATAAATAATAAAAAAA
1 AAAATAAATAATAAAAAAA
38257 GAAGTAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATAAATAATAAAAAAATC
Found at i:39935 original size:18 final size:18
Alignment explanation
Indices: 39903--39937 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39893 CACGTACCCC
**
39903 GAACATGAACTATAAAAT
1 GAACATGAAAAATAAAAT
39921 GAACATGAAAAATAAAA
1 GAACATGAAAAATAAAA
39938 AATAATAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (18 bp):
GAACATGAAAAATAAAAT
Found at i:40774 original size:20 final size:20
Alignment explanation
Indices: 40749--40787 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40739 TAATTTAATT
40749 AAAATTAAATTAAAT-TAGAG
1 AAAATT-AATTAAATATAGAG
*
40769 AAAATTTATTAAATATAGA
1 AAAATTAATTAAATATAGA
40788 TGAATGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAATTAATTAAATATAGAG
Found at i:44148 original size:3 final size:3
Alignment explanation
Indices: 44140--44177 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44130 AGAGTAATAG
44140 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44178 GAGAGTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:49994 original size:24 final size:21
Alignment explanation
Indices: 49967--50013 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
49957 ATAAATTGTG
49967 ATAATTATATATTTTAAAATAATT
1 ATAATT-TA-ATTTTAAAAT-ATT
*
49991 ATAATTTAATTTTTAAATATT
1 ATAATTTAATTTTAAAATATT
50012 AT
1 AT
50014 TTAAAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 2 0.09
24 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTTAATTTTAAAATATT
Found at i:53622 original size:17 final size:19
Alignment explanation
Indices: 53588--53624 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
53578 TGTATTTTTT
*
53588 ATATATTATATTTTAATAA
1 ATATATTATATTTAAATAA
53607 ATATATT-T-TTTAAATAA
1 ATATATTATATTTAAATAA
53624 A
1 A
53625 AATTAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTATATTTAAATAA
Found at i:54946 original size:21 final size:21
Alignment explanation
Indices: 54920--55031 Score: 70
Period size: 21 Copynumber: 5.2 Consensus size: 21
54910 TTTATATTGA
*
54920 TTTTTTTGTTGTATTTGGTTT
1 TTTTTTTGTTATATTTGGTTT
*
54941 TTTTTTTGTTGTTGATTTGATGTTAT
1 TTTTTTTGTT-AT-ATTTG--GTT-T
* *
54967 TTTTATTGTTTTTATTT--TTT
1 TTTTTTTG-TTATATTTGGTTT
* *
54987 TTTTTATGTTAT-TTTGGTTGC
1 TTTTTTTGTTATATTTGGTT-T
*
55008 TGTTTTTGTTAT-TTTGGTTT
1 TTTTTTTGTTATATTTGGTTT
55028 TTTT
1 TTTT
55032 ATGCATTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 12 0.17
21 29 0.40
22 1 0.01
23 5 0.07
25 7 0.10
26 10 0.14
27 2 0.03
ACGTcount: A:0.08, C:0.01, G:0.16, T:0.75
Consensus pattern (21 bp):
TTTTTTTGTTATATTTGGTTT
Found at i:63916 original size:23 final size:23
Alignment explanation
Indices: 63884--63930 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
63874 CTAAGAGATT
63884 ATTATGTGTTCAATTTATTTTTA
1 ATTATGTGTTCAATTTATTTTTA
* ***
63907 ATTATTTGTTTTTTTTATTTTTA
1 ATTATGTGTTCAATTTATTTTTA
63930 A
1 A
63931 ATTCATAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (23 bp):
ATTATGTGTTCAATTTATTTTTA
Found at i:64911 original size:570 final size:570
Alignment explanation
Indices: 63955--65094 Score: 2075
Period size: 570 Copynumber: 2.0 Consensus size: 570
63945 ATATGTATCG
*
63955 CTAATAGTCTGATATAGTATCAAACCATTTACCAAATTAATTAAAAACTAAAATTATGCAAGTTG
1 CTAATAGTCCGATATAGTATCAAACCATTTACCAAATTAATTAAAAACTAAAATTATGCAAGTTG
* *
64020 GAGTGAATAATTACTTTTAAAAAAATTTAAAATATTTATATAAATTTATTATATATTGTATTTTT
66 GAGTGAACAATTACTTTAAAAAAAATTTAAAATATTTATATAAATTTATTATATATTGTATTTTT
* * *
64085 TAAATTTATATTTTCTATTATTTTTAATGGTGTTCAGTTAATTTGTAATACTAACTTCTTAAAAA
131 AAAATTTATATTTTCTATTATTTTTAATGATGTTCAATTAATTTGTAATACTAACTTCTTAAAAA
*
64150 TATAAACGAAAAAAGTTATGTATCAAATTGGATAATTTCAACCATAAATAAAACAATTAAAAGGT
196 TATAAACGAAAAAAGTTATGTATCAAATTGGATAATATCAACCATAAATAAAACAATTAAAAGGT
*
64215 GTGGAATGCTTTTGTTTAAAAGTTGAAAGCTTTGGTTAGGAAGTTTGAGGATCAAATTGATAGAA
261 GTGGAATGCTTTTGTTTAAAAGTTGAAAGCTTTGATTAGGAAGTTTGAGGATCAAATTGATAGAA
64280 TATATAAATGTGAAGGGTTGAATTTATTAAATTATTTAGAGTTAGGAGCAAATTGATAAAATATG
326 TATATAAATGTGAAGGGTTGAATTTATTAAATTATTTAGAGTTAGGAGCAAATTGATAAAATATG
64345 TATGCATTGATGACTAAATGTGTTATTATACTAGTTAGAAAAATGTTTTCCGTTATCAATTTAAT
391 TATGCATTGATGACTAAATGTGTTATTATACTAGTTAGAAAAATGTTTTCCGTTATCAATTTAAT
*
64410 TGTGGGTGACCAATACAGGAATAAATTCAAACATTAGGGCCTAAATTAAAAAATTTTAAAGTTAA
456 CGTGGGTGACCAATACAGGAATAAATTCAAACATTAGGGCCTAAATTAAAAAATTTTAAAGTTAA
64475 GTGACCAAAAGAGGAACGTGAGCATTGCTGGGTGACCGTTTGTATAATTT
521 GTGACCAAAAGAGGAACGTGAGCATTGCTGGGTGACCGTTTGTATAATTT
* *
64525 CTAATAGTCCGATTTAGTATCAAACCGTTTACCAAATTAATTAAAAACTAAAATTATGCAAGTTG
1 CTAATAGTCCGATATAGTATCAAACCATTTACCAAATTAATTAAAAACTAAAATTATGCAAGTTG
* *
64590 GAGTGAACAATTA-TTTAAAAAAAATATTAAAATATTTATATAATTTTATTATATGTTGTATTTT
66 GAGTGAACAATTACTTTAAAAAAAAT-TTAAAATATTTATATAAATTTATTATATATTGTATTTT
64654 TAAAATTTATATTTTCTATTATTTTTAATGATGTTCAATTAATTTGTAATACTAACTTCTTAAAA
130 TAAAATTTATATTTTCTATTATTTTTAATGATGTTCAATTAATTTGTAATACTAACTTCTTAAAA
64719 ATATAAACGAAAAAAGTTATGTATCAAATTGGATAATATCAACCATAAATAAAACAATTAAAAGG
195 ATATAAACGAAAAAAGTTATGTATCAAATTGGATAATATCAACCATAAATAAAACAATTAAAAGG
*
64784 TGTGGAATGCTTTTGTTTAAAAGTTGAAAGTTTTGATTAGGAAGTTTGAGGATCAAATTGATAGA
260 TGTGGAATGCTTTTGTTTAAAAGTTGAAAGCTTTGATTAGGAAGTTTGAGGATCAAATTGATAGA
64849 ATATATAAATGTGAAGGGTTGAATTTATTAAATTATTTAGAGTTAGGAGCAAATTGATAAAATAT
325 ATATATAAATGTGAAGGGTTGAATTTATTAAATTATTTAGAGTTAGGAGCAAATTGATAAAATAT
64914 GTATGCATTGATGACTAAATGTGTTATTATACTAGTTAGAAAAATGTTTTCCGTTATCAATTTAA
390 GTATGCATTGATGACTAAATGTGTTATTATACTAGTTAGAAAAATGTTTTCCGTTATCAATTTAA
* * * *
64979 TCGTGGGTGACCAATACAGGAATAAATTCAAATATTAGTGCCTAAATTGAAAAATTTTAAAGTTG
455 TCGTGGGTGACCAATACAGGAATAAATTCAAACATTAGGGCCTAAATTAAAAAATTTTAAAGTTA
* * *
65044 AGTGACCAAAAGAGGAAGGTGGGCATTGCTGTGTGACCGTTTGTATAATTT
520 AGTGACCAAAAGAGGAACGTGAGCATTGCTGGGTGACCGTTTGTATAATTT
65095 ACCGTAAATT
Statistics
Matches: 548, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
569 11 0.02
570 537 0.98
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.37
Consensus pattern (570 bp):
CTAATAGTCCGATATAGTATCAAACCATTTACCAAATTAATTAAAAACTAAAATTATGCAAGTTG
GAGTGAACAATTACTTTAAAAAAAATTTAAAATATTTATATAAATTTATTATATATTGTATTTTT
AAAATTTATATTTTCTATTATTTTTAATGATGTTCAATTAATTTGTAATACTAACTTCTTAAAAA
TATAAACGAAAAAAGTTATGTATCAAATTGGATAATATCAACCATAAATAAAACAATTAAAAGGT
GTGGAATGCTTTTGTTTAAAAGTTGAAAGCTTTGATTAGGAAGTTTGAGGATCAAATTGATAGAA
TATATAAATGTGAAGGGTTGAATTTATTAAATTATTTAGAGTTAGGAGCAAATTGATAAAATATG
TATGCATTGATGACTAAATGTGTTATTATACTAGTTAGAAAAATGTTTTCCGTTATCAATTTAAT
CGTGGGTGACCAATACAGGAATAAATTCAAACATTAGGGCCTAAATTAAAAAATTTTAAAGTTAA
GTGACCAAAAGAGGAACGTGAGCATTGCTGGGTGACCGTTTGTATAATTT
Found at i:68446 original size:23 final size:21
Alignment explanation
Indices: 68397--68448 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
68387 TTAACACATG
*
68397 TTTTATAAAAATATAGTAAAA
1 TTTTAAAAAAATATAGTAAAA
* *
68418 TATTAAAAAAATGATATGTCAAA
1 TTTTAAAAAAAT-ATA-GTAAAA
68441 TTTTAAAA
1 TTTTAAAA
68449 TTACTTGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (21 bp):
TTTTAAAAAAATATAGTAAAA
Found at i:69567 original size:32 final size:32
Alignment explanation
Indices: 69471--69569 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 32
69461 ATGTATTTTT
*
69471 ATAAAATGTTTAATATGGTATTTGAATTATCA
1 ATAAAATGTTTAATATGGTATTTGAATTATTA
* * *
69503 ATATATAA--TTTATTATGGTATATGTATT-TTA
1 ATA-A-AATGTTTAATATGGTATTTGAATTATTA
*
69534 ATAAAATGTTTAATATGATATTTGAATTATTA
1 ATAAAATGTTTAATATGGTATTTGAATTATTA
69566 ATAA
1 ATAA
69570 TATATTACGG
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 21 0.39
32 27 0.50
33 1 0.02
34 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.47
Consensus pattern (32 bp):
ATAAAATGTTTAATATGGTATTTGAATTATTA
Done.