Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002887.1 Kokia drynarioides strain JFW-HI SEQ_115300, 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: 14923
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1254 original size:215 final size:215
Alignment explanation
Indices: 1--2247 Score: 2556
Period size: 215 Copynumber: 10.5 Consensus size: 215
* * *
1 AAGTATTCAAGACGAACCAATCCTTCGAGCAATTTTTTGAACATTACATGCTCGGGAAGTCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
66 CATTTGGTCTAAAT-GTTTTTCATTTTGTAGACAAGTTTTGGCCTTTGAATTTAAAACTTATTTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * * *
130 CTTGAGAATTGATTCTCTATTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTC
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTT-
*
195 CTTTTTAAATCTGGTTCCTTA
195 CTTTTTAAATCTAGTTCCTTA
* * * * * * * * * *
216 AAGTGTTCAAGACGATCCATTACTTCGAGTAATTTTACAAACATTCCATGCGAGGGAAATCGTAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
281 CATTTGATCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA-TTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * ** *
345 CGTGAGAATTG-TGCTCTCTTGGTTATTGGACGAACTTTCGAACTTGTTGAACTTTTACGAGTTC
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTTC
* *
409 TTTTCTAGCATC-AATTCCTTA
196 TTTT-TA-AATCTAGTTCCTTA
* * * *
430 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTCCGAACATTACATGCTCGGGAGGTCGCAC
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
495 CATTTGGTCTAAA-AGTTTGTCATTTTGTAAACATGTTTTGGCCTTTGAATTAAAAACTTATTTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTA-TT-
* * * *
559 TACGTGAGAATTGATTTTCTCTTGGTTGTTGGATGAACTTAT-GAAATTGTCAAACTTTTAAGAT
129 TACGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTT-TCGAACTTGTCAAACTTTTAAGAG
623 TTCTTTTTTAAAT-TCAGTTCCTTA
193 TTC-TTTTTAAATCT-AGTTCCTTA
* * * * * * * * * * **
647 AAGTGTTCAAGACGATCCATTACTTCGAGTAATTTTCCAAACATTCCAGGCGAGGGAAATTTCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
712 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACATGTTTTGATCATTGAATTAAAAACTTA-TTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * * *
776 AGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCGAAA-TTTTACGAGTT
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTC-AAACTTTTAAGAGTT
*
840 C--TTT-AA--TAG--CTTTA
195 CTTTTTAAATCTAGTTCCTTA
* * * * *
854 AAGTATACAAGACGATCCAATCTTTCTAGCAATTTTCCGAACATTACATGCTCGGGAAGTCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
919 CATTTGGTCTAAA-CGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * *
983 CGTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTAT-GAAATTGTCAAACTTTTAAGAATT
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTT-TCGAACTTGTCAAACTTTTAAGAGTT
*
1047 CCTTTTTAAATCTGGTTCCTTA
195 -CTTTTTAAATCTAGTTCCTTA
* * * ** * * *
1069 AAGTGTTCAAGATGATCCATTCCTTCGAGTTATTTTTCGAACATTCCATGCGAGGGAAATCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * * *
1134 CATTTGATCTAAATAGTTTTTCGTTTTGTAAACAGGTTTTGATCTTTGAATTAAAAAACTTA-TT
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATT-AAAAACTTATTT
* * **
1198 ACGTGAGAATTG-TGCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTTGAACTTTTACA-AGT
130 ACGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTA-AGAGT
** * *
1261 TCTTTTCTAGCT-TCGATTCCATA
194 TCTTTT-TAAATCTAG-TTCCTTA
* * *
1284 AAGTATTCAAGATGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* *
1349 CATTTGGTCTAAA-AGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * *
1413 CGTGAGAATTGATTCTCTCTTGGTTGTTGGATGAACTTACGAAATTGTCAAACTTTTAAGAGTTC
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTTC
* *
1478 ATTTTTAAACCTGGTTCCTTA
196 -TTTTTAAATCTAGTTCCTTA
* * * * * * * * *
1499 AAGTGTCCAAGACGATCCATTACTTCGAGTAATTTTCCGAACATTCCATGCGAGGGAAATCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* ** *
1564 CGTTTGGTCTAAATAGTTTTTCATTTTGTAAACATCTTTTGATCTTTGAATTAAAAACTTA-TTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* * * * *
1628 TGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAATTTCGAGCTTGTCAAACTTTTACA-AGTT
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTA-AGAGTT
*
1692 C-TTTT--A--TAG--CTTTA
195 CTTTTTAAATCTAGTTCCTTA
* * ** * * *
1706 AAGTATGCAAGACGATCCAATCCTTAGAGCAATTTTTCGAACATTATGTGCTTGAGATGTCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
*
1771 CATTTGGTCTAAA-AGGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
66 CATTTGGTCTAAATA-GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* * * * **
1835 GCGTGAGAATTGTTTCTCTCTTAGTTGTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTT
130 ACGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTT
*
1900 CTTTTTTAAATCCAGTTCCTTA
195 C-TTTTTAAATCTAGTTCCTTA
* * * * *
1922 AAGTGTTCAAGACGATCCATTCCTTCGAG-AATTTTTCGAACATTACATGCGAGGGAAATTGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* *
1986 CATTTAGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA-TTA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
* ** *
2050 CGTGAGAATTG--TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTTGAACTTTTACGAGTTC
131 CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTTC
* * *
2113 -TTTTATAGCTTCGGTTCCTTA
196 TTTTTAAATC-T-AGTTCCTTA
*** * * * *
2134 AAGTATTCAAGATTTTTCAATCCTTTGAGCAATTTTTCGAACATTACATGATCGGGAAGTCGCAT
1 AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
* * *
2199 CATTTGGTATAAA-AGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAA
66 CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAA
2248 ACATGCAGAT
Statistics
Matches: 1699, Mismatches: 280, Indels: 109
0.81 0.13 0.05
Matches are distributed among these distances:
206 45 0.03
207 229 0.13
208 60 0.04
209 4 0.00
210 15 0.01
211 5 0.00
212 113 0.07
213 103 0.06
214 187 0.11
215 579 0.34
216 186 0.11
217 125 0.07
218 48 0.03
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (215 bp):
AAGTATTCAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTAGGGAAGTCGCAT
CATTTGGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
CGTGAGAATTGATTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCAAACTTTTAAGAGTTC
TTTTTAAATCTAGTTCCTTA
Found at i:1749 original size:852 final size:853
Alignment explanation
Indices: 1--2247 Score: 3662
Period size: 853 Copynumber: 2.6 Consensus size: 853
* * *
1 AAGTATTCAAGACGAACCAATCCTTCGAGCAATTTTTTGAACATTACATGCTCGGGAAGTCGCAT
1 AAGTATACAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTCGGGAAGTCGCAT
* * * *
66 CATTTGGTCTAAATGTTTTTCATTTTGTAGACAAGTTTTGGCCTTTGAATTTAAAACTTATTTAC
66 CATTTGGTCTAAACGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTAC
* *
131 TTGAGAATTGATTCTCTATTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTCC
131 GTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTCC
* * *
196 TTTTTAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTACTTCGAGTAATTTTACAAACATT
196 TTTTTAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTTCGAACATT
*
261 CCATGCGAGGGAAATCGTATCATTTGATCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGATCT
261 CCATGCGAGGGAAATCGCATCATTTGATCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGATCT
*
326 TTGAATTAAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTATTGGACGAACTTTCGAACTTG
326 TTGAATTAAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTCTTGGACGAACTTTCGAACTTG
* * *
391 TTGAACTTTTACGAGTTCTTTTCTAGCATCAATTCCTTAAAGTATTCAAGACGATCCAATCCTTC
391 TTGAACTTTTACGAGTTCTTTTCTAGCTTCGATTCCTTAAAGTATTCAAGATGATCCAATCCTTC
* *
456 GAGCAATTTTCCGAACATTACATGCTCGGGAGGTCGCACCATTTGGTCTAAAAGTTTGTCATTTT
456 GAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCATCATTTGGTCTAAAAGTTTGTCATTTT
* *
521 GTAAACATGTTTTGGCCTTTGAATTAAAAACTTATTTATACGTGAGAATTGATTTTCTCTTGGTT
521 GTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTATACGTGAGAATTGATTCTCTCTTGGTT
* * * *
586 GTTGGATGAACTTATGAAATTGTCAAACTTTTAAGATTTCTTTTTTAAATTCAGTTCCTTAAAGT
586 GTTGGATGAACTTACGAAATTGTCAAACTTTTAAGAGTTCATTTTTAAACTCAGTTCCTTAAAGT
* **
651 GTTCAAGACGATCCATTACTTCGAGTAATTTTCCAAACATTCCAGGCGAGGGAAATTTCATCATT
651 GTCCAAGACGATCCATTACTTCGAGTAATTTTCCAAACATTCCAGGCGAGGGAAATCGCATCATT
*
716 TGGTCTAAATAGTTTTTCATTTTGTAAACATGTTTTGATCATTGAATTAAAAACTTATTAAGTGA
716 TGGTCTAAATAGTTTTTCATTTTGTAAACATCTTTTGATCATTGAATTAAAAACTTATTAAGTGA
* *
781 GAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCGAAATTTTACGAGTTCTTTAA
781 GAATTGTTTCTCTCTTGGTTCTTGGACGAAATTCCGAACTTGTCGAAATTTTACAAGTTCTTTAA
846 TAGCTTTA
846 TAGCTTTA
* * *
854 AAGTATACAAGACGATCCAATCTTTCTAGCAATTTTCCGAACATTACATGCTCGGGAAGTCGCAT
1 AAGTATACAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTCGGGAAGTCGCAT
919 CATTTGGTCTAAACGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTAC
66 CATTTGGTCTAAACGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTAC
* *
984 GTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTATGAAATTGTCAAACTTTTAAGAATTCC
131 GTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTCC
* *
1049 TTTTTAAATCTGGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTTATTTTTCGAACATT
196 TTTTTAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTTCGAACATT
*
1114 CCATGCGAGGGAAATCGCATCATTTGATCTAAATAGTTTTTCGTTTTGTAAACAGGTTTTGATCT
261 CCATGCGAGGGAAATCGCATCATTTGATCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGATCT
1179 TTGAATTAAAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTCTTGGACGAACTTTCGAACTT
326 TTGAATT-AAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTCTTGGACGAACTTTCGAACTT
* *
1244 GTTGAACTTTTACAAGTTCTTTTCTAGCTTCGATTCCATAAAGTATTCAAGATGATCCAATCCTT
390 GTTGAACTTTTACGAGTTCTTTTCTAGCTTCGATTCCTTAAAGTATTCAAGATGATCCAATCCTT
1309 CGAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCATCATTTGGTCTAAAAGTTTGTCATTT
455 CGAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCATCATTTGGTCTAAAAGTTTGTCATTT
1374 TGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTA-TT-TACGTGAGAATTGATTCTCTCTTGGT
520 TGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTATACGTGAGAATTGATTCTCTCTTGGT
*
1437 TGTTGGATGAACTTACGAAATTGTCAAACTTTTAAGAGTTCATTTTTAAAC-CTGGTTCCTTAAA
585 TGTTGGATGAACTTACGAAATTGTCAAACTTTTAAGAGTTCATTTTTAAACTC-AGTTCCTTAAA
* * *
1501 GTGTCCAAGACGATCCATTACTTCGAGTAATTTTCCGAACATTCCATGCGAGGGAAATCGCATCG
649 GTGTCCAAGACGATCCATTACTTCGAGTAATTTTCCAAACATTCCAGGCGAGGGAAATCGCATCA
* *
1566 TTTGGTCTAAATAGTTTTTCATTTTGTAAACATCTTTTGATCTTTGAATTAAAAACTTATTATGT
714 TTTGGTCTAAATAGTTTTTCATTTTGTAAACATCTTTTGATCATTGAATTAAAAACTTATTAAGT
* *
1631 GAGAATTGTTTCTCTCTTGGTTCTTGGACGAAATTTCGAGCTTGTC-AAACTTTTACAAGTTCTT
779 GAGAATTGTTTCTCTCTTGGTTCTTGGACGAAATTCCGAACTTGTCGAAA-TTTTACAAGTTCTT
*
1695 TTATAGCTTTA
843 TAATAGCTTTA
* * ** * * *
1706 AAGTATGCAAGACGATCCAATCCTTAGAGCAATTTTTCGAACATTATGTGCTTGAGATGTCGCAT
1 AAGTATACAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTCGGGAAGTCGCAT
* * *
1771 CATTTGGTCTAAAAGGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTG
66 CATTTGGTCT-AAACGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTA
* * * * * **
1836 CGTGAGAATTGTTTCTCTCTTAGTTGTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTC
130 CGTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTC
* **
1901 TTTTTTAAATCCAGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAG-AATTTTTCGAACAT
195 CTTTTTAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTTCGAACAT
* * *
1965 TACATGCGAGGGAAATTGCATCATTT-AGTCTAAATAGTTTTTCATTTTGTAAACAAGTTTTGAT
260 TCCATGCGAGGGAAATCGCATCATTTGA-TCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGAT
2029 CTTTGAATTAAAAACTTATTACGTGAGAATTGT-CTCTCTTGGTTCTTGGACGAACTTTCGAACT
324 CTTTGAATTAAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTCTTGGACGAACTTTCGAACT
* * ** *
2093 TGTTGAACTTTTACGAGTTCTTTTATAGCTTCGGTTCCTTAAAGTATTCAAGATTTTTCAATCCT
389 TGTTGAACTTTTACGAGTTCTTTTCTAGCTTCGATTCCTTAAAGTATTCAAGATGATCCAATCCT
* * * *
2158 TTGAGCAATTTTTCGAACATTACATGATCGGGAAGTCGCATCATTTGGTATAAAAGTTTGTCATT
454 TCGAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCATCATTTGGTCTAAAAGTTTGTCATT
2223 TTGTAAACAAGTTTTGGCCTTTGAA
519 TTGTAAACAAGTTTTGGCCTTTGAA
2248 ACATGCAGAT
Statistics
Matches: 1297, Mismatches: 92, Indels: 13
0.93 0.07 0.01
Matches are distributed among these distances:
850 175 0.13
851 29 0.02
852 414 0.32
853 466 0.36
854 213 0.16
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (853 bp):
AAGTATACAAGACGATCCAATCCTTCGAGCAATTTTTCGAACATTACATGCTCGGGAAGTCGCAT
CATTTGGTCTAAACGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTAC
GTGAGAATTGATTCTCTCTTGGTTGTTGGAAGAACTTACGAAATTGTCAAACTTTTAAGAGTTCC
TTTTTAAATCTGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTTCGAACATT
CCATGCGAGGGAAATCGCATCATTTGATCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGATCT
TTGAATTAAAAACTTATTACGTGAGAATTGTGCTCTCTTGGTTCTTGGACGAACTTTCGAACTTG
TTGAACTTTTACGAGTTCTTTTCTAGCTTCGATTCCTTAAAGTATTCAAGATGATCCAATCCTTC
GAGCAATTTTTCGAACATTACATGCTCGGGAGGTCGCATCATTTGGTCTAAAAGTTTGTCATTTT
GTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTATACGTGAGAATTGATTCTCTCTTGGTT
GTTGGATGAACTTACGAAATTGTCAAACTTTTAAGAGTTCATTTTTAAACTCAGTTCCTTAAAGT
GTCCAAGACGATCCATTACTTCGAGTAATTTTCCAAACATTCCAGGCGAGGGAAATCGCATCATT
TGGTCTAAATAGTTTTTCATTTTGTAAACATCTTTTGATCATTGAATTAAAAACTTATTAAGTGA
GAATTGTTTCTCTCTTGGTTCTTGGACGAAATTCCGAACTTGTCGAAATTTTACAAGTTCTTTAA
TAGCTTTA
Found at i:2223 original size:20 final size:20
Alignment explanation
Indices: 2198--2236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2188 GGAAGTCGCA
2198 TCATTTGGTATAA-AAGTTTG
1 TCATTTGGTA-AACAAGTTTG
*
2218 TCATTTTGTAAACAAGTTT
1 TCATTTGGTAAACAAGTTT
2237 TGGCCTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (20 bp):
TCATTTGGTAAACAAGTTTG
Found at i:9694 original size:43 final size:43
Alignment explanation
Indices: 9638--9771 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
9628 ATCTGTTAAT
* *
9638 TTTAGCGGCATTTGTTAGAAAAGAGCCGTTGAAA-ACCATGTTA
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCT-AAAGACCATGTTA
* *
9681 TTTAGCGGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
* * * * * * * *
9724 TTTAGTGGCGTTTATGGGAAAAGCGTCGCTAAAGACCTTGTTC
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
9767 TTTAG
1 TTTAG
9772 TGGCGTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 3 0.04
43 76 0.96
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
Found at i:10427 original size:17 final size:17
Alignment explanation
Indices: 10413--10452 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
10403 ATTATTCATA
10413 TGGTAAGTGTATTCACT
1 TGGTAAGTGTATTCACT
10430 TGGTAAGTGTATTCACT
1 TGGTAAGTGTATTCACT
10447 TGGTAA
1 TGGTAA
10453 TTTAATCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (17 bp):
TGGTAAGTGTATTCACT
Done.