Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013810.1 Kokia drynarioides strain JFW-HI SEQ_128838, 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: 4142
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Found at i:2408 original size:205 final size:205
Alignment explanation
Indices: 2027--2834 Score: 1003
Period size: 205 Copynumber: 3.9 Consensus size: 205
2017 GCGATTATCC
* * * * *
2027 ACAAACAACGCGGTCAT-TTACCTGATGAGATATTGAGAAAAAGA-CAAAGACAAAC-CTACGCT
1 ACAAACGACGCAGTCATCTT-CCTGATGAAATATTGAGAAGAAGACCAAA-TCAAACTC-ACGCT
* * * *
2089 CGATGTGAACAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATA
63 CGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATA
* * *
2154 AAAGGTTAACTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGA
128 AAAGGTTAACTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGA
*
2219 GTAGCGGATTGAA
193 GTAACGGATTGAA
* *
2232 ACAAACGATGCAGTCATCTTCCTAATGAAATATTGAGAAGAAGACCAAATCAAACTCACGCTCGA
1 ACAAACGACGCAGTCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACTCACGCTCGA
* *
2297 TGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTTAGAAGTAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* *
2362 GGTTAACTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGTA
131 GGTTAACTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGTA
2427 ACGGATTGAA
196 ACGGATTGAA
* *
2437 ACAAACGACACAGTCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCAGTCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACTCACGCTCGA
* * *
2502 TGTGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAA
66 TGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
2567 CGGTTAGCTTCCTGACTATCTTTCTGATAAGATACGGAGAAGTGGACCAAATCCGTTTTCCTGAT
131 -GGTTA--------ACT-TC---CTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGAT
* * * *
2632 GAGATACAAAGAAATGAATTGAA
183 GAGATACAGAGTAACGGATTGAA
* * * *
2655 ACAAACGACGTAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGA
1 ACAAACGACGCAGTCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACTCACGCTCGA
* * ***
2720 TGTGAGCGAATCTTCGAACTC-TAGCTTCCTGATGAGACGTTGAGAAGCAGGTCGAAGCAATGAA
66 TGTGAGCAAATCTTCGAAC-CACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AA
** * * * * *
2784 GTGGTTAGCTCCCTGATGAGATACAGAGAAGTGAATCAAATCCGTCTTCCT
129 AAGGTTAACTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCT
2835 AACGAAACAC
Statistics
Matches: 531, Mismatches: 54, Indels: 35
0.86 0.09 0.06
Matches are distributed among these distances:
205 301 0.57
206 46 0.09
209 1 0.00
210 2 0.00
214 3 0.01
215 2 0.00
218 173 0.33
219 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (205 bp):
ACAAACGACGCAGTCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACTCACGCTCGA
TGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
GGTTAACTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGTA
ACGGATTGAA
Found at i:2766 original size:218 final size:218
Alignment explanation
Indices: 2385--2799 Score: 616
Period size: 218 Copynumber: 1.9 Consensus size: 218
2375 ATGAGATATT
* * * *
2385 GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGTAACGGATTGAAACAAACGACACAG
1 GAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAACGAATTGAAACAAACGACACAG
* *
2450 TCATCTTCCTGATGAAATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCT
66 TCATCTTCCCGATGAAATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCT
* * *
2515 TCGAACCATAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCCT
131 TCGAACCATAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAACGGTTAGCTCCCT
2580 GACTATCTTTCTGATAAGATACG
196 GACTATCTTTCTGATAAGATACG
* * **
2603 GAGAAGTGGACCAAATCCGTTTTCCTGATGAGATACAAAGAAATGAATTGAAACAAACGACGTAG
1 GAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAACGAATTGAAACAAACGACACAG
* * *
2668 TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGTGAGCGAATCT
66 TCATCTTCCCGATGAAATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCT
** * * **
2733 TCGAACTC-TAGCTTCCTGATGAGACGTTGAGAAGCAGGTCGAAGCAATGAAGTGGTTAGCTCCC
131 TCGAAC-CATAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAACGGTTAGCTCCC
2797 TGA
195 TGA
2800 TGAGATACAG
Statistics
Matches: 174, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
218 173 0.99
219 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (218 bp):
GAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAACGAATTGAAACAAACGACACAG
TCATCTTCCCGATGAAATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCT
TCGAACCATAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAACGGTTAGCTCCCT
GACTATCTTTCTGATAAGATACG
Found at i:3250 original size:17 final size:17
Alignment explanation
Indices: 3224--3306 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
3214 TCTGGGCCTA
3224 ATAAACTTAAATTTATT
1 ATAAACTTAAATTTATT
* * *
3241 TTAAAATTAAGTTTATT
1 ATAAACTTAAATTTATT
* *
3258 CTAAACTTAAATTTAACT
1 ATAAACTTAAATTT-ATT
* *
3276 GT-AATTTAAATTTATT
1 ATAAACTTAAATTTATT
*
3292 ATAAATTTAAATTTA
1 ATAAACTTAAATTTA
3307 AAATTTATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
16 3 0.06
17 47 0.89
18 3 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAAACTTAAATTTATT
Found at i:3290 original size:34 final size:35
Alignment explanation
Indices: 3224--3307 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 35
3214 TCTGGGCCTA
* * *
3224 ATAAACTTAAATTT-ATTTTAAAATTAAGTTTATT
1 ATAAACTTAAATTTAACTGTAAAATTAAATTTATT
* *
3258 CTAAACTTAAATTTAACTGT-AATTTAAATTTATT
1 ATAAACTTAAATTTAACTGTAAAATTAAATTTATT
*
3292 ATAAATTTAAATTTAA
1 ATAAACTTAAATTTAA
3308 AATTTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 39 0.93
35 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (35 bp):
ATAAACTTAAATTTAACTGTAAAATTAAATTTATT
Found at i:3988 original size:3 final size:3
Alignment explanation
Indices: 3975--4019 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
3965 AATTTATTAT
3975 TAA TAA GTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4020 TCATTAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Done.