Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008945.1 Kokia drynarioides strain JFW-HI SEQ_123639, 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: 43256
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:4587 original size:21 final size:21
Alignment explanation
Indices: 4529--4588 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
4519 AACAGTGCAG
* *
4529 ACTTCTACCGATAAC-TGTGAC
1 ACTTCTACCGA-AACAAGTGAA
* **
4550 AGTTCTACCGATTCAAGTGAA
1 ACTTCTACCGAAACAAGTGAA
4571 ACTTCTACCGAAACAAGT
1 ACTTCTACCGAAACAAGT
4589 CATGCTTCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTGAA
Found at i:23444 original size:167 final size:167
Alignment explanation
Indices: 23168--23498 Score: 644
Period size: 167 Copynumber: 2.0 Consensus size: 167
23158 AGGTGGGGGT
*
23168 AATTTTTCGCTGATTTCTACCATGACATGAGACTCAATGGCCAAGGACAATCCTCTCTATTGCCA
1 AATTTTTCGCTGATTTCTACCATGACATGAGACTCAATGGCCAAGGACAATCCCCTCTATTGCCA
23233 TGAAGTGACATTTCTCTCAATTCAGAACCAAGTTTGTTTCCTCGCATCTTCTCAAAACAGTTGAC
66 TGAAGTGACATTTCTCTCAATTCAGAACCAAGTTTGTTTCCTCGCATCTTCTCAAAACAGTTGAC
23298 AAGTTGTCGGTGCATTGGTCGAAACTCTGTCCATGAC
131 AAGTTGTCGGTGCATTGGTCGAAACTCTGTCCATGAC
*
23335 AATTTTTCGCTGATTTCTACCATGACATGAGACTCAATGGCCAAGGACAATCCCCTTTATTGCCA
1 AATTTTTCGCTGATTTCTACCATGACATGAGACTCAATGGCCAAGGACAATCCCCTCTATTGCCA
23400 TGAAGTGACATTTCTCTCAATTCAGAACCAAGTTTGTTTCCTCGCATCTTCTCAAAACAGTTGAC
66 TGAAGTGACATTTCTCTCAATTCAGAACCAAGTTTGTTTCCTCGCATCTTCTCAAAACAGTTGAC
23465 AAGTTGTCGGTGCATTGGTCGAAACTCTGTCCAT
131 AAGTTGTCGGTGCATTGGTCGAAACTCTGTCCAT
23499 AGATTGCAAA
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 162 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (167 bp):
AATTTTTCGCTGATTTCTACCATGACATGAGACTCAATGGCCAAGGACAATCCCCTCTATTGCCA
TGAAGTGACATTTCTCTCAATTCAGAACCAAGTTTGTTTCCTCGCATCTTCTCAAAACAGTTGAC
AAGTTGTCGGTGCATTGGTCGAAACTCTGTCCATGAC
Found at i:29588 original size:99 final size:99
Alignment explanation
Indices: 29418--29759 Score: 341
Period size: 99 Copynumber: 3.4 Consensus size: 99
29408 CTACAGTTCA
* * *
29418 TTTTAATCTACCCCTCTGTAAC-TTAGAGGTATAGGATTTGGTGTTATAACTTCACTCCATTCCA
1 TTTTAATCTACCCCTCTATAACTTTAGAGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCA
* *
29482 CTGTAACTTTAGGGAGATTGAGATCTGCTATAGT
66 CTATAACTTTAGGGAGATTAAGATCTGCTATAGT
* *
29516 TTTTAATCTACCCTTCTATAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCA
1 TTTTAATCTACCCCTCTATAACTTTAGAGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCA
* * *
29581 CTATAACTTCAGGGAGATTAAGATTTGCTATGGTT
66 CTATAACTTTAGGGAGATTAAGATCTGCTATAG-T
* ** * * * * * *
29616 AGTTTTAATCTGCCCCTCCGTAACTTTAGAGATATAGGATTTGATTTTGTAGCTTTAATCT-TGC
1 --TTTTAATCTACCCCTCTATAACTTTAGAGGTATAGGATTTGGTGTTGTAACTTCACTCTAT--
* * * *
29680 TCTACTACATCTTTAGAGAGA-TAAGATCTGCTTCTATAG-
62 TCCACTATAACTTTAGGGAGATTAAGATCTG---CTATAGT
* * * *
29719 CTTTAATTTACCCCTCTACAACTTTAGGGGTATAGGATTTG
1 TTTTAATCTACCCCTCTATAACTTTAGAGGTATAGGATTTG
29760 ATTTTGTAGC
Statistics
Matches: 199, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
98 20 0.10
99 67 0.34
100 1 0.01
101 34 0.17
102 56 0.28
103 16 0.08
105 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (99 bp):
TTTTAATCTACCCCTCTATAACTTTAGAGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCA
CTATAACTTTAGGGAGATTAAGATCTGCTATAGT
Found at i:29673 original size:50 final size:49
Alignment explanation
Indices: 29619--29777 Score: 142
Period size: 50 Copynumber: 3.2 Consensus size: 49
29609 TATGGTTAGT
29619 TTTAATCTGCCCCTCCGTAACTTTAGAGATATAGGATTTGATTTTGTAGC
1 TTTAATCTGCCCCTCC-TAACTTTAGAGATATAGGATTTGATTTTGTAGC
* * * * * * * *
29669 TTTAATCTTG-CTCTACTACATCTTTAGAGAGATAAGATCTGCTTCTATAGC
1 TTTAATC-TGCCCCTCCTA-A-CTTTAGAGATATAGGATTTGATTTTGTAGC
* * * *
29720 TTTAATTTACCCCT-CTACAACTTTAGGGGTATAGGATTTGATTTTGTAGC
1 TTTAATCTGCCCCTCCT--AACTTTAGAGATATAGGATTTGATTTTGTAGC
29770 TTTAATCT
1 TTTAATCT
29778 TGCTCTACTG
Statistics
Matches: 83, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
49 2 0.02
50 44 0.53
51 36 0.43
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (49 bp):
TTTAATCTGCCCCTCCTAACTTTAGAGATATAGGATTTGATTTTGTAGC
Found at i:29696 original size:51 final size:51
Alignment explanation
Indices: 29639--29827 Score: 186
Period size: 51 Copynumber: 3.7 Consensus size: 51
29629 CCCTCCGTAA
* * *
29639 CTTTAGAGATATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTACAT
1 CTTTAGAGAGATAAGATTTGATTCTGTAGCTTTAATCTTGCTCTACTACAT
* * * * * *
29690 CTTTAGAGAGATAAGATCTGCTTCTATAGCTTTAAT-TTACCCCT-CTACAA
1 CTTTAGAGAGATAAGATTTGATTCTGTAGCTTTAATCTT-GCTCTACTACAT
* * * *
29740 CTTTAG-GGGTATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTGCAT
1 CTTTAGAGAG-ATAAGATTTGATTCTGTAGCTTTAATCTTGCTCTACTACAT
* * * *
29791 CTTCAGAGAGATAAAATTTGCTTCTGTAGCTCTAATC
1 CTTTAGAGAGATAAGATTTGATTCTGTAGCTTTAATC
29828 CTCACCTCTG
Statistics
Matches: 107, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
49 2 0.02
50 37 0.35
51 66 0.62
52 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (51 bp):
CTTTAGAGAGATAAGATTTGATTCTGTAGCTTTAATCTTGCTCTACTACAT
Found at i:29753 original size:101 final size:101
Alignment explanation
Indices: 29637--29856 Score: 316
Period size: 101 Copynumber: 2.2 Consensus size: 101
29627 GCCCCTCCGT
* * *
29637 AACTTTAGAGATATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTACATCTTTAGAGAGAT
1 AACTTTAGGGGTATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTACATCTTCAGAGAGAT
* * * *
29702 AAGATCTGCTTCTATAGCTTTAAT-TTACCCCTCTAC
66 AAAATCTGCTTCTATAGCTCTAATCCT-CACCTCTAC
*
29738 AACTTTAGGGGTATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTGCATCTTCAGAGAGAT
1 AACTTTAGGGGTATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTACATCTTCAGAGAGAT
* * **
29803 AAAATTTGCTTCTGTAGCTCTAATCCTCACCTCTGT
66 AAAATCTGCTTCTATAGCTCTAATCCTCACCTCTAC
29839 AACTTTAGGGGTATAGGA
1 AACTTTAGGGGTATAGGA
29857 GTTGGTGATA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 105 0.99
102 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (101 bp):
AACTTTAGGGGTATAGGATTTGATTTTGTAGCTTTAATCTTGCTCTACTACATCTTCAGAGAGAT
AAAATCTGCTTCTATAGCTCTAATCCTCACCTCTAC
Found at i:30457 original size:20 final size:19
Alignment explanation
Indices: 30411--30457 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
30401 TTAAAAATAT
* *
30411 CAAACATTGGTCAAAATGT
1 CAAACATTGATCAAAATGG
*
30430 CTAACATTGATCAAAGATGG
1 CAAACATTGATCAAA-ATGG
30450 CAAACATT
1 CAAACATT
30458 AAACAATGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (19 bp):
CAAACATTGATCAAAATGG
Found at i:30494 original size:20 final size:20
Alignment explanation
Indices: 30471--30524 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
30461 CAATGGCCAC
30471 AAATTGCAAACATTGGTAAA
1 AAATTGCAAACATTGGTAAA
**
30491 AAA-TGACAAATGTTGGTAAA
1 AAATTG-CAAACATTGGTAAA
* *
30511 AAGTAGCAAACATT
1 AAATTGCAAACATT
30525 AATCAAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (20 bp):
AAATTGCAAACATTGGTAAA
Found at i:35373 original size:6 final size:6
Alignment explanation
Indices: 35359--35388 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35349 GAGAGAGAAT
*
35359 GGGGAA GGGGTA GGGGTA GGGGTA GGGGTA
1 GGGGTA GGGGTA GGGGTA GGGGTA GGGGTA
35389 TGGGAATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.67, T:0.13
Consensus pattern (6 bp):
GGGGTA
Done.