Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013929.1 Kokia drynarioides strain JFW-HI SEQ_128959, 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: 2215
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.23
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:1346 original size:139 final size:140
Alignment explanation
Indices: 939--1428 Score: 795
Period size: 139 Copynumber: 3.5 Consensus size: 140
929 NNNNNNNNNN
*
939 AAGTGAACCAGATTCGTATTCATTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
1 AAGTGAACCAGATTCGTATTCACTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
*
1004 TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAACTCTTCCTGATG
66 TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATG
1069 AGATACGAAG
131 AGATACGAAG
*
1079 AAGTGAACCAGATTCGTATTCATTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
1 AAGTGAACCAGATTCGTATTCACTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
*
1144 TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTTCTGATG
66 TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATG
1209 AGATACGAAG
131 AGATACGAAG
* * * * *
1219 AAGTGAACTAGATTCGTATTC-CTGATAAGATACAGAGAAACGGATCGAAGCAGTGATGGGATCA
1 AAGTGAACCAGATTCGTATTCACTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
* * *
1283 TCTTCTTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAGTCTTCCTGATG
66 TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATG
*
1348 AGATACGGAG
131 AGATACGAAG
* * * ** *
1358 AAGTGAACCAGATTCGTCTTC-CTGATGAGATACAGAGAAATGGGTCGAAACAGCGATGGGATCA
1 AAGTGAACCAGATTCGTATTCACTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
1422 TCTTCCT
66 TCTTCCT
1429 NNNNNNNNNN
Statistics
Matches: 329, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
139 171 0.52
140 158 0.48
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (140 bp):
AAGTGAACCAGATTCGTATTCACTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCA
TCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATG
AGATACGAAG
Found at i:1349 original size:279 final size:267
Alignment explanation
Indices: 820--1428 Score: 842
Period size: 279 Copynumber: 2.2 Consensus size: 267
810 ATCCACAAAG
*
820 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACATTGATGGGATCATCTTCCTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
**********
885 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAANNNNNNNNNNAAGTGAACCAG
66 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAAGATACGAAGAAGTGAACCAG
* *
950 ATTCGTATTCATTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCATCTTCCTGATG
131 ATTCGTATTCACTGATAAGATACAAAGAAACGAATCGAAACAGTGATGGGATCATCTTCCTGATG
1015 AGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAACTCTTCCTGATGAGATACGAAGA
196 AGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAACTCTTCCTGATGAGATACGAAGA
1080 AGTGAAC
261 AGTGAAC
* * * *
1087 CAGATTCGTATTCATTGATGAGATACAAAGAAACGAATCGAAACAGTGATGGGATCATCTTCCTG
1 CAGATTCGTCTTC-CTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTG
1152 ATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTTCTGATGAGATACGA
65 ATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGC--A--------A--AGATACGA
* * * *
1217 AGAAGTGAACTAGATTCGTATTC-CTGATAAGATACAGAGAAACGGATCGAAGCAGTGATGGGAT
118 AGAAGTGAACCAGATTCGTATTCACTGATAAGATACAAAGAAACGAATCGAAACAGTGATGGGAT
* * *
1281 CATCTTCTTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAGTCTTCCTGA
183 CATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAACTCTTCCTGA
*
1346 TGAGATACGGAGAAGTGAAC
248 TGAGATACGAAGAAGTGAAC
* * *
1366 CAGATTCGTCTTCCTGATGAGATACAGAGAAATGGGTCGAAACAGCGATGGGATCATCTTCCT
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCT
1429 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 32, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
267 12 0.04
268 90 0.30
270 1 0.00
278 45 0.15
279 129 0.43
280 20 0.07
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (267 bp):
CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAAGATACGAAGAAGTGAACCAG
ATTCGTATTCACTGATAAGATACAAAGAAACGAATCGAAACAGTGATGGGATCATCTTCCTGATG
AGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAACTCTTCCTGATGAGATACGAAGA
AGTGAAC
Found at i:2197 original size:17 final size:17
Alignment explanation
Indices: 2175--2215 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2165 TTGGAAATTG
* *
2175 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTTGA
2192 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
2209 AATTTAA
1 AATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Done.