Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009801.1 Kokia drynarioides strain JFW-HI SEQ_124522, 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: 2333
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Found at i:688 original size:13 final size:14
Alignment explanation
Indices: 670--698 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
660 GATTTTCTTT
670 AAAAAAAAAAG-GA
1 AAAAAAAAAAGAGA
683 AAAAAAAAAAGAGA
1 AAAAAAAAAAGAGA
697 AA
1 AA
699 GTGTAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAGA
Found at i:1039 original size:146 final size:148
Alignment explanation
Indices: 735--1264 Score: 676
Period size: 148 Copynumber: 3.6 Consensus size: 148
725 GTTTTTTTAG
* * * * *
735 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAATTATTTCGAAATAAAATTTTAAATTT
1 AAAAATTTAAATTTTTAAACAAAGTTTTTATTTTTTTAACTATTTCGAAATAAAAATTTAGATTT
* * *
800 TTAAGAAAG-TAGTGATTTTCATTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGT
66 TAAAGTAAGATAGTGATTTTCATTAAAAAAA-ATAAAGTTTATATTTTTAAAAATAAAAATCTGT
*
864 TTTTTAGTTATTTTAAAGC
130 TTTTTAGTTATTTTAAAGA
* * * * * *
883 AAAACTTTAAATTTTTAAATAAATTTTTTATTTTTCTAACTATTTCGAAATAAAAGTTTGGATTT
1 AAAAATTTAAATTTTTAAACAAAGTTTTTATTTTTTTAACTATTTCGAAATAAAAATTTAGATTT
* * * *
948 TTAAGTAAGATAGTGA-TTTCATT-AAAAAAATAAAGTTTATATTTTTGAAGATAAAAATATGTT
66 TAAAGTAAGATAGTGATTTTCATTAAAAAAAATAAAGTTTATATTTTTAAAAATAAAAATCTGTT
1011 TTTTAGTTATTTTAAAGA
131 TTTTAGTTATTTTAAAGA
* * * *
1029 AAAAAATTAAA-TTTTAAATAAAGTGTTAATTTTTTTAACTATTTCGAAATAAAAATTTAGATTT
1 AAAAATTTAAATTTTTAAACAAAGTTTTTATTTTTTTAACTATTTCGAAATAAAAATTTAGATTT
* **
1093 TAAAGTAA-AGTAGTGATTTTCATTAAAAAAAATAAAGTTTAGATTTAAAAAAAATAAAAAATCT
66 TAAAGTAAGA-TAGTGATTTTCATTAAAAAAAATAAAGTTTATATTT-TTAAAAAT-AAAAATCT
1157 GTTTTTTTA-TTGATTTTAAAGA
128 G-TTTTTTAGTT-ATTTTAAAGA
* * * *
1179 AAAAGGTTTAAAATTTTAAACAAAATTTTTATTTTTTTAACTATTTCGAAATAAAAATTTTGATT
1 AAAA-ATTTAAATTTTTAAACAAAGTTTTTATTTTTTTAACTATTTCGAAATAAAAATTTAGATT
*
1244 TTAAAGTAAAATAGTGATTTT
65 TTAAAGTAAGATAGTGATTTT
1265 GTTTTAATCA
Statistics
Matches: 334, Mismatches: 37, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
144 1 0.00
145 60 0.18
146 63 0.19
147 26 0.08
148 75 0.22
149 16 0.05
150 21 0.06
151 5 0.01
152 66 0.20
153 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (148 bp):
AAAAATTTAAATTTTTAAACAAAGTTTTTATTTTTTTAACTATTTCGAAATAAAAATTTAGATTT
TAAAGTAAGATAGTGATTTTCATTAAAAAAAATAAAGTTTATATTTTTAAAAATAAAAATCTGTT
TTTTAGTTATTTTAAAGA
Found at i:1208 original size:145 final size:144
Alignment explanation
Indices: 764--1264 Score: 533
Period size: 152 Copynumber: 3.4 Consensus size: 144
754 CAAAGTTTTG
* * * *
764 ATTTTTTTAATTATTTCGAAATAAAATTTTAAATTTTTAAG-AAAGTAGTGATTTTCATTAAAAA
1 ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAGTAGTGATTTTCATT-AAAA
* * ** * * **
828 AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGCAAAACTTTAA
65 AA-ATAAAGTTTAGATTTAAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAAATTAA
* *
893 ATTTTTAAATAAATTTTTT
129 A-TTTTAAATAAA--ATAT
* * * *
912 ATTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGT-AAGATAGTGA-TTTCATTAAAA
1 ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAG-TAGTGATTTTCATTAAAA
* *** *
975 AAATAAAGTTTATATTTTTGAAGATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAAATTAAA
65 AAATAAAGTTTAGATTTAAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAAATTAAA
* *
1040 TTTTAAATAAAGTGTT
130 TTTTAAATAAAAT-AT
1056 AATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAGTAGTGATTTTCATTAAAA
1 -ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAGTAGTGATTTTCATT-AAA
* *
1121 AAAATAAAGTTTAGATTTAAAAAAAATAAAAAATCTGTTTTTTTA-TTGATTTTAAAGAAAAAGG
64 AAAATAAAGTTTAGATTT-AAAAAAAT-AAAAATATG-TTTTTTAGTT-ATTTTAAAGAAAAA-A
* * *
1185 TTTAAAATTTTAAACAAAATTTTT
124 ATT-AAATTTTAAATAAAA--TAT
* *
1209 ATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTAAAGTAAAATAGTGATTTT
1 ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAGTAGTGATTTT
1265 GTTTTAATCA
Statistics
Matches: 309, Mismatches: 29, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
143 1 0.00
144 2 0.01
145 55 0.18
146 66 0.21
147 26 0.08
148 50 0.16
149 16 0.05
150 21 0.07
151 2 0.01
152 67 0.22
153 2 0.01
154 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (144 bp):
ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTAAAGTAAAGTAGTGATTTTCATTAAAAA
AATAAAGTTTAGATTTAAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAAATTAAAT
TTTAAATAAAATAT
Done.