Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008296.1 Kokia drynarioides strain JFW-HI SEQ_122961, 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: 25320
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 380 characters in sequence are not A, C, G, or T
Found at i:2672 original size:52 final size:51
Alignment explanation
Indices: 2438--2678 Score: 209
Period size: 52 Copynumber: 4.7 Consensus size: 51
2428 TCACTTCATT
* ** * * * *
2438 CATATACTCATGATGA-ACATAGCCACCAGACCTTATAATCCGCAAGGGATC
1 CATATACTCACGATGACACATAATCATCGGACCTT-TAATCCGTAAAGGATC
* *
2489 CGTATACTCACGATGACACA-AAGTCATCGGACCTCTTAATACGTAAAGGATC
1 CATATACTCACGATGACACATAA-TCATCGGACCT-TTAATCCGTAAAGGATC
* * * * *
2541 CATATACTCACTATGACACTTAGTCATCGGACCGTTTAATCCGTAACGGATT
1 CATATACTCACGATGACACATAATCATCGGACC-TTTAATCCGTAAAGGATC
* * * * * *
2593 CAGACACTCACGATGACACTTAGTCATC-TAGCCATTTAATCCGTAAAGGATT
1 CATATACTCACGATGACACATAATCATCGGA-CC-TTTAATCCGTAAAGGATC
* *
2645 CATATACTCACGATGACTCATAATCATCAGACCT
1 CATATACTCACGATGACACATAATCATCGGACCT
2679 CTTCGTTTAT
Statistics
Matches: 155, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
51 17 0.11
52 134 0.86
53 4 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (51 bp):
CATATACTCACGATGACACATAATCATCGGACCTTTAATCCGTAAAGGATC
Found at i:6490 original size:11 final size:11
Alignment explanation
Indices: 6476--6516 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
6466 TTATTTTTTC
*
6476 ACTATTTTGCT
1 ACTATTTTACT
6487 ACTATTTTACT
1 ACTATTTTACT
* *
6498 ATTATATTACT
1 ACTATTTTACT
6509 ACTATTTT
1 ACTATTTT
6517 GTTGTTATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (11 bp):
ACTATTTTACT
Found at i:10471 original size:18 final size:19
Alignment explanation
Indices: 10435--10471 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10425 ATATATTATT
10435 AAAAATTTGTATTTCTTAA
1 AAAAATTTGTATTTCTTAA
10454 AAAACATTT-TATTT-TTAA
1 AAAA-ATTTGTATTTCTTAA
10472 TAATGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
AAAAATTTGTATTTCTTAA
Found at i:13792 original size:72 final size:71
Alignment explanation
Indices: 13646--13792 Score: 240
Period size: 72 Copynumber: 2.1 Consensus size: 71
13636 AAACACGAGT
* * *
13646 AATGTGGATGTGCTACTCTCAAATGTTCATTTGAAAAATTAAGAGGTAATTTAAAATAAATAAAT
1 AATGTAGATGTGCTACTCTCAAATGTTCATTTGAAAAAATAAAAGGTAATTTAAAATAAATAAAT
13711 AAAAAG
66 AAAAAG
* *
13717 AATGTAGATGTGCTGCTCTCAAATGTTCATTTGAAACAAATAAAAGGTAATTTAAAATAACTAAA
1 AATGTAGATGTGCTACTCTCAAATGTTCATTTGAAA-AAATAAAAGGTAATTTAAAATAAATAAA
13782 TAAAAAG
65 TAAAAAG
13789 AATG
1 AATG
13793 GGCAAAAACA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 34 0.49
72 36 0.51
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (71 bp):
AATGTAGATGTGCTACTCTCAAATGTTCATTTGAAAAAATAAAAGGTAATTTAAAATAAATAAAT
AAAAAG
Found at i:14295 original size:23 final size:24
Alignment explanation
Indices: 14267--14311 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
14257 CCATCATTTG
14267 AAAATTA-AAAAT-ATATATAATCT
1 AAAATTATAAAATAATA-ATAATCT
14290 AAAATTATAAAATAATAATAAT
1 AAAATTATAAAATAATAATAAT
14312 AATTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 10 0.50
25 3 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATTATAAAATAATAATAATCT
Found at i:15771 original size:101 final size:101
Alignment explanation
Indices: 15662--15862 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
15652 TTTTATTTTA
*
15662 TTTTTTTTCAATTTGATCACTAAATTTGGTTTCTGTTAAGTGTGATGATCTAACACTTCAAATTT
1 TTTTTTTTCAATTTGATCACTAAATTTGGTTTCTATTAAGTGTGATGATCTAACACTTCAAATTT
15727 GTAACACTTCATCATTTGAAAATTAATATATATATT
66 GTAACACTTCATCATTTGAAAATTAATATATATATT
15763 TTTTTTTTCAATTTGATCACTAAATTTGGTTTCTATTAAGTGTGATGATCTAACACTTCAAATTT
1 TTTTTTTTCAATTTGATCACTAAATTTGGTTTCTATTAAGTGTGATGATCTAACACTTCAAATTT
15828 GTAACACTTCATCATTTGAAAATTAATATATATAT
66 GTAACACTTCATCATTTGAAAATTAATATATATAT
15863 AATATCTAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (101 bp):
TTTTTTTTCAATTTGATCACTAAATTTGGTTTCTATTAAGTGTGATGATCTAACACTTCAAATTT
GTAACACTTCATCATTTGAAAATTAATATATATATT
Found at i:16661 original size:22 final size:21
Alignment explanation
Indices: 16618--16662 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16608 ATAATAATAA
* * *
16618 TATAAAAATTCATTTATAATT
1 TATAAAAATTAAATTAAAATT
16639 TATAAAAATTAAATTAAATATT
1 TATAAAAATTAAATTAAA-ATT
16661 TA
1 TA
16663 AACTAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAAAAATTAAATTAAAATT
Found at i:16922 original size:23 final size:25
Alignment explanation
Indices: 16896--16944 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
16886 AATCATCATG
*
16896 TTATGTTTA-TTTATTAAT-TATTT
1 TTATGTTTAGTTTAATAATATATTT
*
16919 TTATTTTTAGTTTAATAATATATTT
1 TTATGTTTAGTTTAATAATATATTT
16944 T
1 T
16945 AAAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 8 0.36
25 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATGTTTAGTTTAATAATATATTT
Found at i:17877 original size:132 final size:133
Alignment explanation
Indices: 17640--17995 Score: 480
Period size: 132 Copynumber: 2.7 Consensus size: 133
17630 AATAAGAAAG
**
17640 AAAAATCTAGAATACCCACAAAGATATTATGGGTAAACAAGCCGATTCAAATCAGAAAAATCGGA
1 AAAAATCTAGAATACCCACAAAGGGATTATGGGTAAACAAGCCGATTCAAATCAGAAAAATCGGA
* *
17705 TTGAGAAATCAATTATTCAAGAACCTGGAGTACCCACAAAGGTAAATCAACACAAAATCAACAAT
66 TTGAGAAATCAATTATTCAAGAACTTGGAATACCCACAAAGGTAAATCAACACAAAATCAACAAT
17770 -AA
131 AAA
* * * *
17772 AAAAATCTAAAATACCCACAAAGGGATTGTGGGTAAACAAGTCGATTCAGATCAGAAAAATCGGA
1 AAAAATCTAGAATACCCACAAAGGGATTATGGGTAAACAAGCCGATTCAAATCAGAAAAATCGGA
* * * *
17837 TTGAGAAGTCAATTATTCAAGAACTTGGAATACCCACAAAGGTAAATCAGCACAAAATCAGCAGT
66 TTGAGAAATCAATTATTCAAGAACTTGGAATACCCACAAAGGTAAATCAACACAAAATCAACAAT
17902 AAA
131 AAA
* * * *** * * * *
17905 AAAAACCTGGAATACCCACAAAGGGATTTTGAACAAACAAGCCGGTTCATATCAGAAAAAATTGA
1 AAAAATCTAGAATACCCACAAAGGGATTATGGGTAAACAAGCCGATTCAAATCAG-AAAAATCGG
* *
17970 ATTCAGAAACCAATTATTCAAGAACT
65 ATTGAGAAATCAATTATTCAAGAACT
17996 GAGAAAGAAC
Statistics
Matches: 195, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
132 118 0.61
133 47 0.24
134 30 0.15
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (133 bp):
AAAAATCTAGAATACCCACAAAGGGATTATGGGTAAACAAGCCGATTCAAATCAGAAAAATCGGA
TTGAGAAATCAATTATTCAAGAACTTGGAATACCCACAAAGGTAAATCAACACAAAATCAACAAT
AAA
Found at i:21231 original size:23 final size:23
Alignment explanation
Indices: 21201--21249 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
21191 AGGCGACGAT
*
21201 CACCATCGCCAACAATTGGTGGC
1 CACCATCGCCAACAATCGGTGGC
21224 CACCATCGCCAACAATCGGTGGC
1 CACCATCGCCAACAATCGGTGGC
21247 CAC
1 CAC
21250 GGTTACGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.39, G:0.20, T:0.14
Consensus pattern (23 bp):
CACCATCGCCAACAATCGGTGGC
Found at i:22115 original size:21 final size:21
Alignment explanation
Indices: 22089--22132 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
22079 GCACTTGGTG
22089 TTATTTT-T-ATTCATTTGTTTA
1 TTATTTTGTCATTC-TTT-TTTA
22110 TTATTTTGTCATTCTTTTTTA
1 TTATTTTGTCATTCTTTTTTA
22131 TT
1 TT
22133 GTAAATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (21 bp):
TTATTTTGTCATTCTTTTTTA
Found at i:24048 original size:6 final size:6
Alignment explanation
Indices: 24037--24097 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
24027 ATTTGTTTAA
* * *
24037 AAATTT AAATTT -ATTTT TAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
24083 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
24098 ATTGCTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 13 0.30
6 27 0.61
7 4 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:24058 original size:17 final size:17
Alignment explanation
Indices: 24038--24097 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
24028 TTTGTTTAAA
24038 AATTTAAATTTATTTTT
1 AATTTAAATTTATTTTT
*
24055 AATTTAAATTTA-ATTT
1 AATTTAAATTTATTTTT
*
24071 AAGTTTAAATTTATTTTCA
1 AA-TTTAAATTTATTTT-T
24090 AATTTAAA
1 AATTTAAA
24098 ATTGCTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.14
17 22 0.59
18 8 0.22
19 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATTTTT
Done.