Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008707.1 Kokia drynarioides strain JFW-HI SEQ_123389, 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: 10757
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1518 original size:24 final size:21
Alignment explanation
Indices: 1469--1524 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
1459 ATATATTACC
*
1469 AATTCGTTTAATTTTTTTGTT
1 AATTCGATTAATTTTTTTGTT
1490 AATTCGATTAATTTTAATTTGGTT
1 AATTCGATTAATTTT--TTT-GTT
*
1514 AATTCGGTTAA
1 AATTCGATTAA
1525 ATGAACATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 14 0.47
23 3 0.10
24 13 0.43
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.55
Consensus pattern (21 bp):
AATTCGATTAATTTTTTTGTT
Found at i:4749 original size:3 final size:3
Alignment explanation
Indices: 4741--4769 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4731 TCCTTAATCC
4741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4770 CAAAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4965 original size:21 final size:21
Alignment explanation
Indices: 4941--4998 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4931 AGAATTGGGA
4941 GTTCTA-CAGATACAACTTAGG
1 GTTCTACCAG-TACAACTTAGG
**
4962 GTTCTACCAGTACAACTTAAA
1 GTTCTACCAGTACAACTTAGG
* *
4983 CTTCTACCGGTACAAC
1 GTTCTACCAGTACAAC
4999 AAACTCTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (21 bp):
GTTCTACCAGTACAACTTAGG
Found at i:5176 original size:21 final size:21
Alignment explanation
Indices: 5146--5221 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
5136 TCCCTTATAT
5146 TTCTACCGATACTCT-ACTGGG
1 TTCTACCGATACTCTGA-TGGG
*
5167 TTCTATCGATACTCTGATGGG
1 TTCTACCGATACTCTGATGGG
*
5188 TTTTACCGATACTCTGATGGG
1 TTCTACCGATACTCTGATGGG
*
5209 TTCTACCAATACT
1 TTCTACCGATACT
5222 AAAAATAACC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 48 0.98
22 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (21 bp):
TTCTACCGATACTCTGATGGG
Found at i:6360 original size:20 final size:20
Alignment explanation
Indices: 6335--6373 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6325 TACTGAATTG
6335 AATACACAACAT-ATTTCATC
1 AATACACAA-ATAATTTCATC
6355 AATACACAAATAATTTCAT
1 AATACACAAATAATTTCAT
6374 TCTAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
AATACACAAATAATTTCATC
Found at i:9390 original size:216 final size:214
Alignment explanation
Indices: 9005--10757 Score: 1661
Period size: 216 Copynumber: 8.2 Consensus size: 214
8995 GTAATTAGTA
* * * * *
9005 CTTGGTT-TTCGGACGAACTTTCGAACATGTCAAACTCTTATTGGTTCTTTTATAACTTTGGTTC
1 CTTGGTTCTT-GGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTC
* * ** * *
9069 CTTGAAGTATTCATGATGATCCATTCCTTCGAGCAATTTTCTGAACATTCCCTGCTCGAGAAATC
65 CTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAATC
* * ** * * * * *
9134 TTATCATGTAATCTAAATAGGTTGTCAATTTGTAAACAACTTTTGGTGTTTGAATTAAAAACCTA
129 GTATCATTTGGTCTAAATA-GTTTTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA
* *
9199 GTCACGTGAGAATTGTTTCTTT
193 TTCACGTGAGAATTGTTTCTCT
* * *
9221 CATGGTTCTTTGACGAACTTCCGAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
1 CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
* * * * ** *
9286 TTAAAGTATTCATGGCGATCCATTCCTTTGAGTAATTTCCTAAACACACCATGCTCGGGAAATAG
66 TTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTT-CTGAACATTCCATGCTCGGGAAATCG
* * * *
9351 TATTATTCGGTCTAAATAATTTGTTATTTTGTAAACAAC---T--T-TTTGTATTAAAAACTTAT
130 TATCATTTGGTCTAAATAGTTT-TTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
* *
9410 TCACGGGATAA-TGTTTTCTCT
194 TCACGTGAGAATTG-TTTCTCT
* * * *
9431 CTTGGTTCTTAGACAAACTTCCAAACTTGTCAAACTCTTATTGGTTATTTTATAACTTCGGTTCC
1 CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
* * * * * *
9496 TTAAAGTATTCAAGGTGATCCATTCCTTCGAACAATTTTTTGAACATTCCATACTCAGGAAATCT
66 TTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAATCG
* * * * * *
9561 TATAATTTAGTCTAAATAGTTTGTCATTCTGTAAACAACTATTGGTCTTTGAATTAAAAATTTAT
130 TATCATTTGGTCTAAATAGTTT-TTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAT
*
9626 TCACGTCAGAATTGTTTCTCT
194 TCACGTGAGAATTGTTTCTCT
* ** * * * *
9647 CTTGGTTCTTGGATGAACTTTAAAACTTGTCAAATTTTTATTGGTTCTTTAATAACTTTGGTTCT
1 CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
* * * * * *
9712 TTAAAGTATTCAAGGCGAT-CAGTTCCTTTGAGAAATTTTTCGAACATTCCATGTTCGAGAAATA
66 TTAAAGTATTCAAGGCGATCCA-TTCCTTCGAGCAATTTCT-GAACATTCCATGCTCGGGAAATC
* * *** *
9776 ATTTCATTTGGTCTAAATAGTTTTTCATTTTGTAAACAACTTTCCATCTTTGAATTAAAAGCTTA
129 GTATCATTTGGTCTAAATAGTTTTT-ATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA
*
9841 TTTACGTGAGAATTGTTTCTCT
193 TTCACGTGAGAATTGTTTCTCT
* *
9863 CTTGGTT-TTGGGATGAACTTCCAAACTTGTCAAACTCTTT-TTGGTTCTTTTATAACTTCGATT
1 CTTGGTTCTT-GGACGAACTTCCAAACTTGTCAAACT-TTTATTGGTTCTTTTATAACTTCGGTT
* *
9926 CCTTAAAGTACTT-AA-GCTGATCCGTTCCTTCGAGCAATTT-TAAGAACATTCCTTGCTCGGGA
64 CCTTAAAGTA-TTCAAGGC-GATCCATTCCTTCGAGCAATTTCT--GAACATTCCATGCTCGGGA
* * *
9988 AATCGTATCATTTGGTTTAAATTGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAA
125 AATCGTATCATTTGGTCTAAATAGTTT-TTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAA
10053 CTTATTCACGTGAGAATTGTTTCTCT
189 CTTATTCACGTGAGAATTGTTTCTCT
* * * * *
10079 CTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTCTTATTGGTTCTTTTCTAACTTCTGTTCC
1 CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
* * * * * * *
10144 TTAAAGTATTCATGGTGATCCGTTCCTTTGAGCAATTTTCTGGACATTCGATGCTCGGGAAATTG
66 TTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGGGAAATCG
* *
10209 TATCATTTGGTC-AAA-A-----TA----GT-TACAACTTTTGGTCTTTGAATTAAAAAGTTATT
130 TATCATTTGGTCTAAATAGTTTTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATT
* * *
10262 TACATAAGAATTGTTTCTCT
195 CACGTGAGAATTGTTTCTCT
*** * *
10282 CTTGGTTCTT-G-CTGAACTTCCAAACTTGTCAAACTTTTACAAGTTATTTTATCACTT-GAGTT
1 CTTGGTTCTTGGAC-GAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCG-GTT
* * *** * * *
10344 CCTAAAAGCATTCAAAATGATCCATTCCTTCAAGAAATTTTTCGAACATTCCATGCTCGGGAAAT
64 CCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTCT-GAACATTCCATGCTCGGGAAAT
** * * * * * *
10409 CACATAATATGGTGTCAATAGTTTTTCATATTGTAAACAACTTTT-GTCTTTTAATTAAAAACTT
128 CGTATCATTTGGTCTAAATAGTTTTT-ATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTT
* * * ** *
10473 ATTTATGTGAGAACTAATTCTTT
192 ATTCACGTGAGAATTGTTTCTCT
* * * *** * **
10496 ACAT-GTTCTT-GACCGAAGTTTCAAAACTTGTCAAACTTTTACAAGTTCTTTAATAACTTTAGT
1 -CTTGGTTCTTGGA-CGAA-CTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGT
*** * *
10559 TTAATAAAGTATTCAAGGCGATCCCTTCCTTCGAGCAATTT-T--ACGATCTCCATGCTCGAGAA
63 TCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTCTGAAC-AT-TCCATGCTCGGGAA
* * *
10621 ATCGAATCATTTGGTCTTAATAGTTTTTCATTTTGGAAACAGA-TTTTGGTCTTTGAATTAAAAA
126 ATCGTATCATTTGGTCTAAATAGTTTTT-ATTTTGTAAACA-ACTTTTGGTCTTTGAATTAAAAA
* *
10685 CTTATTCACGTGAGAATTATTTCTAT
189 CTTATTCACGTGAGAATTGTTTCTCT
* *
10711 CTTGGTTCTTGGACGAACTTCCAAACTTTTCAAACTCTTATTGGTTC
1 CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTC
Statistics
Matches: 1258, Mismatches: 224, Indels: 112
0.79 0.14 0.07
Matches are distributed among these distances:
201 5 0.00
202 95 0.08
203 60 0.05
204 3 0.00
208 1 0.00
209 3 0.00
210 171 0.14
211 4 0.00
212 2 0.00
213 4 0.00
214 117 0.09
215 88 0.07
216 687 0.55
217 17 0.01
218 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (214 bp):
CTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTATTGGTTCTTTTATAACTTCGGTTCC
TTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTCTGAACATTCCATGCTCGGGAAATCGT
ATCATTTGGTCTAAATAGTTTTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTC
ACGTGAGAATTGTTTCTCT
Done.