Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009428.1 Kokia drynarioides strain JFW-HI SEQ_124135, 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: 6081
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Found at i:965 original size:15 final size:17
Alignment explanation
Indices: 945--977 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
935 GCAACCCTAG
945 CTCAAGC-TCTCC-TTT
1 CTCAAGCATCTCCGTTT
960 CTCAAGCATCTCCGTTT
1 CTCAAGCATCTCCGTTT
977 C
1 C
978 AATAGCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.36
Consensus pattern (17 bp):
CTCAAGCATCTCCGTTT
Found at i:1335 original size:382 final size:383
Alignment explanation
Indices: 612--1379 Score: 1288
Period size: 382 Copynumber: 2.0 Consensus size: 383
602 TCCCATATTG
612 ATGACTAAAACTCTTTACAACCAGTCTTGCCTTCAGTCTGTTGAGTGAACCATCGAGATTGAGTT
1 ATGACTAAAACTCTTTACAACCAGTCTTGCCTTCAGTCTGTTGAGTGAACCATCGAGATTGAGTT
* *
677 TGGTTTTGAACACCCATTTGAAGCTAATAACCCTTTTGTGTGATGGCCTATCACCAAGTTCACAT
66 TGGTTTTGAACACCCATTTGAAGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCACAC
*
742 ATCTGGTTCTTGCAAATCATATTTAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTC
131 ATCTGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTC
* ** *
807 AGCTTCTTCGGAGTTCACAGATTTAACAGTTGCTACCTCTACTCTTTGGTAAATTTTAACAATTT
196 AGCTTCTTCGGAGTTCACAGATTTAACAGTTGCTACCTCTAATCTTCAGTAAATTTTAACAATTG
* * *
872 TTCGCGTACCCCTAAATGGTATATCATTGAAGTCTTCTTCTTTAACTTGATTATCCCCAAGTTGC
261 GTCGCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGC
* *
937 AACCCTAGCTCAAGCTCTCCTTTCTCAAGCATCTCCGTTTCAATAGCATCCCATTTCC
326 AACCCTAGCTCAAGCTCTCCTTTCTCAAGCATCTCAGTTTCAACAGCATCCCATTTCC
* *
995 ATGACTAAAACTCTTTACAACCAGTCTTGCCTTCGGTGTGTTGAGTGAACCATCGACG-TTGAGT
1 ATGACTAAAACTCTTTACAACCAGTCTTGCCTTCAGTCTGTTGAGTGAACCATCGA-GATTGAGT
* *
1059 TTGGTTTTGAACACCCATTTGATGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCCCA
65 TTGGTTTTGAACACCCATTTGAAGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCACA
*
1124 CATCTGGTTCTTGCAAATCATATTCAACTC-GCTTGCATAGCTTCTTTTAAGCCTTTTGTTGCTT
130 CATCTGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTT
* * *
1188 CAGCTTCTTCGGAGTTCACAGGTTTAAGAGTTGCTACCTTTAATCTTCAGTAAATTTTAACAATT
195 CAGCTTCTTCGGAGTTCACAGATTTAACAGTTGCTACCTCTAATCTTCAGTAAATTTTAACAATT
*
1253 GGTCGCGTACCCCTAAATGGCATGTCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTG
260 GGTCGCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTG
* * * *
1318 TAACCTTATCTCAAGCTCTCCTTTCTCAAGCATCTCAGTTTCAACAGCATCCTATTTCC
325 CAACCCTAGCTCAAGCTCTCCTTTCTCAAGCATCTCAGTTTCAACAGCATCCCATTTCC
1377 ATG
1 ATG
1380 TTTTTTCTTC
Statistics
Matches: 359, Mismatches: 25, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
382 208 0.58
383 150 0.42
384 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (383 bp):
ATGACTAAAACTCTTTACAACCAGTCTTGCCTTCAGTCTGTTGAGTGAACCATCGAGATTGAGTT
TGGTTTTGAACACCCATTTGAAGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCACAC
ATCTGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTC
AGCTTCTTCGGAGTTCACAGATTTAACAGTTGCTACCTCTAATCTTCAGTAAATTTTAACAATTG
GTCGCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGC
AACCCTAGCTCAAGCTCTCCTTTCTCAAGCATCTCAGTTTCAACAGCATCCCATTTCC
Found at i:1346 original size:15 final size:17
Alignment explanation
Indices: 1321--1353 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1311 CAAGTTGTAA
1321 CCTTATCTCAAGC-TCT
1 CCTTATCTCAAGCATCT
1337 CCTT-TCTCAAGCATCT
1 CCTTATCTCAAGCATCT
1353 C
1 C
1354 AGTTTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.39, G:0.06, T:0.36
Consensus pattern (17 bp):
CCTTATCTCAAGCATCT
Found at i:2617 original size:24 final size:24
Alignment explanation
Indices: 2590--2640 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2580 AATTTCACTC
* * *
2590 AAACAACTAATCAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
2614 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
2638 AAA
1 AAA
2641 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:4605 original size:24 final size:24
Alignment explanation
Indices: 4578--4652 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
4568 AATTTAACTC
*
4578 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
4602 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
4626 AAATAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
4650 AAA
1 AAA
4653 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Done.