Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013727.1 Kokia drynarioides strain JFW-HI SEQ_128755, 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: 29764
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:111 original size:39 final size:38
Alignment explanation
Indices: 68--167 Score: 155
Period size: 39 Copynumber: 2.6 Consensus size: 38
58 TTAATTTGTC
* *
68 TCAAACTTAGACACCTTCAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATT-AAAACAACTATTAAATATGTA
*
107 TCAAAATAAGACACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATT-AAAACAACTATTAAATATGTA
146 TCAAACTAAGACACATTAAAAC
1 TCAAACTAAGACACATTAAAAC
168 CCTATTTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 5 0.09
39 51 0.91
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (38 bp):
TCAAACTAAGACACATTAAAACAACTATTAAATATGTA
Found at i:1303 original size:196 final size:194
Alignment explanation
Indices: 955--1339 Score: 447
Period size: 196 Copynumber: 2.0 Consensus size: 194
945 AATTAAAAAC
*
955 TTATTTAGGTGAGAATTGTTTCTATATTCGTTCTCAGCCGAACTTCTGAACTTGACAAACTTTTA
1 TTATTTAGGTGAGAATTGTTTCTATATTCGTTCTCAGCCGAACTTCCGAACTTGACAAACTTTTA
* ** *
1020 CGAGTTCTTTTTTAACTTCTGTTCCTTAAAGAATTCAAGACAATCCATTCCTTCAAGCAATTTTT
66 CGAGTTCTTTTATAACTTCTGTTCAATAAAGAATTCAAGACAATCCATTCCTTCAAGCAATTTTC
** * * * *
1085 TGAACATTTCATGCTCGGGAAATCGCATCACTT-GTTCTAAATAGACTGTCATTTTGTTAAAAAA
131 CCAACAGTCCATGCTCGGGAAATCACATCA-TTAGGTCTAAATAG-CTGTCATTTT-TTAAAAAA
1149 TG
193 TG
* * * **
1151 TTATTTATGTTAGAATTGTTTCT-TACTTTGTTCTCAGTTGAACTTCCGAACTTGACAAAC-TTT
1 TTATTTAGGTGAGAATTGTTTCTATA-TTCGTTCTCAGCCGAACTTCCGAACTTGACAAACTTTT
* * * * * * *
1214 AGTGAGTTCTTTTATAACTTTTGTTCAAT-AAGTTATTCAGGACGATCCATTCTTTCGAGCAA-T
65 A-CGAGTTCTTTTATAACTTCTGTTCAATAAAG-AATTCAAGACAATCCATTCCTTCAAGCAATT
* *
1277 TTCCCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATTTTTTAAA
128 TTCCCA-ACAGTCCATGCTCGGGAAATCACATCATTAGGTCTAAATAGCTGTCATTTTTTAAA
1340 CTACTTTTGG
Statistics
Matches: 159, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
194 5 0.03
195 24 0.15
196 130 0.82
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (194 bp):
TTATTTAGGTGAGAATTGTTTCTATATTCGTTCTCAGCCGAACTTCCGAACTTGACAAACTTTTA
CGAGTTCTTTTATAACTTCTGTTCAATAAAGAATTCAAGACAATCCATTCCTTCAAGCAATTTTC
CCAACAGTCCATGCTCGGGAAATCACATCATTAGGTCTAAATAGCTGTCATTTTTTAAAAAATG
Found at i:1964 original size:214 final size:213
Alignment explanation
Indices: 1199--3965 Score: 2325
Period size: 215 Copynumber: 13.1 Consensus size: 213
1189 TGAACTTCCG
* ** *
1199 AACTTGACAAAC-TTTAGTGAGTTCTTTTATAACTTTTGTTCAAT-AAGTTATTCAGGACGATCC
1 AACTTGACAAACTTTTA-CGAGTTCTTTTATAACTTTTGTTCCTTAAAG-TATTCAAGACGATCC
* * ** * *
1262 ATTCTTTCGAGCAA-TTTCCCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGT
64 ATTCCTTCAAGCAATTTTCTGA-ACATTCCATGCTT-GGAAATCACATCATTTGGTCTAAATAGT
* * *
1326 TGTCATTTTTTAAACTACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCCCT
127 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
* * *
1391 TTTGGTTCTCGGTCGAACTTTTG
192 CTTGGTTCTCGGCCGAAC-TTTA
* * *
1414 AACTTGAAAAACTTTTACGAGTTCTTTTATAAC-TTTGATTCCTTAAACTATTCAAGACGATTCA
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTG-TTCCTTAAAGTATTCAAGACGATCCA
* ** * *
1478 TTCCTTCGAGCAATTTTAAGAACATTCCATGCTCTAGAAATCACATCATTTAGTCTAAATAGTTG
65 TTCCTTCAAGCAATTTTCTGAACATTCCATGCT-TGGAAATCACATCATTTGGTCTAAATAGTTG
* * * *
1543 CCATTATGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCTCT
129 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
* * **
1608 TGGTTCTAGGCAGAACATCCA
194 TGGTTCTCGGCCGAAC-TTTA
* * * *
1629 AAGTTGACAAA-TTGTTACGAGTTCTTTTATAACTTTCGTTCCTTGAAGTATTCAAGACGAACCA
1 AACTTGACAAACTT-TTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCA
* * * *
1693 TTCCTTCAAGCAATTTTTTGAACATTCCAAGCTTAGGAAATCTCATCTTTTGGTCTAAATAGTTG
65 TTCCTTCAAGCAATTTTCTGAACATTCCATGCTT-GGAAATCACATCATTTGGTCTAAATAGTTG
* * * *
1758 TCATTTTGTAAACAACTTTTGATCTTTGAATTAAAAA-ATACTTTATGTGAGAATTGTTTCTTTC
129 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA-TTTAGGTGAGAATTGTTTCTCTC
*
1822 TTGGTTCTCGGCCGAACCTTA
193 TTGGTTCTCGGCCGAACTTTA
* * *
1843 AACTTGACAAACTTTTACAAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACAATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* * *
1908 TCCTTCAAGCAATTTTCTGTACAGTCCATGCTTGGAAAATCACATCATTAGGTCTAAATAGTTGT
66 TCCTTCAAGCAATTTTCTGAACATTCCATGCTTGG-AAATCACATCATTTGGTCTAAATAGTTGT
* * * * *
1973 CATTTTGTAAACTACTTTTGGT-TTTCCAATTAAAAACTTATTTAGGTGAGAATTATTTCCCTTT
130 CATTTTGTAAACAACTTTTGGTCTTT-GAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
**
2037 TGGTTCTCGATCGAAC-TTA
194 TGGTTCTCGGCCGAACTTTA
* * * *
2056 CGAACCTGAAAAACTTTTACGAGTTCTTTCATAAC-TTCGATTCCTTAAAGTATTCAAG-CGATC
1 --AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTG-TTCCTTAAAGTATTCAAGACGATC
** ** * ** *
2119 CATTCCTTTGAGCAATTTTCCAAACATTCCATGCTCTAGAAATTGCATAATTTGGTCTAAATAGT
63 CATTCCTTCAAGCAATTTTCTGAACATTCCATGCT-TGGAAATCACATCATTTGGTCTAAATAGT
* *
2184 TGTAATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAGTTTCTCT
127 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
* * *
2249 CTTGGTTCTAGGCTGAACTTTCG
192 CTTGGTTCTCGGCCGAACTTT-A
* * * **
2272 AAGTTAACAAACTTTTACGACTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCC--
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* * *
2335 T--TT-GAGCAATTTTCTGAACATTCCAAGCTCAGGAAATCACATCATTTGGTCTAAATAGTTGT
66 TCCTTCAAGCAATTTTCTGAACATTCCATGCT-TGGAAATCACATCATTTGGTCTAAATAGTTGT
* * * *
2397 CATTTTATAAAAAAACTTTTGGTCTTTGAATTAAAAAACTTATTTATAGGTGATAATAGTTTCTC
130 CATTTTGT-AAACAACTTTTGGTCTTTGAATT-AAAAACTTA-TT-TAGGTGAGAATTGTTTCTC
* * *
2462 TCTAGGTTCTAGGCCGAACTTTCG
191 TCTTGGTTCTCGGCCGAACTTT-A
* * * * * ** *
2486 AACTTAAAAAACCTTTACGATTTCTTTTTTAACTTCGGTTCCTTAAATTATTCAAG--GA---AT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* * * * * * * *
2546 T-TTTCAAAC-A--TTC----CATT-C-T--TAGAAAATCCCATCAATTGTTCCAAATAGATTGT
66 TCCTTCAAGCAATTTTCTGAACATTCCATGCTTGGAAATCACATCATTTGGTCTAAATAG-TTGT
* * * *
2599 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTAAGAATTGTTTCTTTCTA
130 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTT
*
2664 GGTTCTCGGCCGAACTTCCA
195 GGTTCTCGGCCGAACTT-TA
* *
2684 AACTTGACAAACTTTTATGAGTTCTTTTATAACTTTTATTCCTTAAAGTATTCAAGACGATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* ** * * * *
2749 TCCTCCCGGCCATTTT-TCAAACAATCCATGCTCTGGAAATCATATCATTTGGT-TCAAATAGTT
66 TCCTTCAAGCAATTTTCT-GAACATTCCATGCT-TGGAAATCACATCATTTGGTCT-AAATAGTT
* * * * * * * *
2812 GTAATTTTATAAACAGCTTTAGGTCTTTGAATTAAAAACTTATTTAGGCGATAATAGTTCCTCTC
128 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTC
* * * *
2877 TAGGTTCTCGACAGAACTTTTG
193 TTGGTTCTCGGCCGAAC-TTTA
* * * * * * *
2899 AACTTGACAAACATTTAAGAGTTCTTTGT-TGAC-TTCGATTTCTTAAAGTATTCAAAATGATCC
1 AACTTGACAAACTTTTACGAGTTCTTT-TATAACTTTTG-TTCCTTAAAGTATTCAAGACGATCC
* * * *
2962 ATTCTTTCGAA-CAATTTTTTGAACATTCCATGCTTTGGAAATCATATCATTTGTTCTAAATAGA
64 ATTCCTTC-AAGCAATTTTCTGAACATTCCATGC-TTGGAAATCACATCATTTGGTCTAAATAG-
* * * * * **
3026 TTGGT-ATTTTGTAAACAACTTTTGGTCTTTAAATTTAAAAGTTATTTATGTGAG--TCG-AACT
126 TT-GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCT
** * * *
3087 -T-TT-GAACT-TGACAAACTGTTA
190 CTCTTGGTTCTCGGCCGAACT-TTA
* * ** * * * ** * ***
3108 CGAGTTGTTTTATAACTTTT---A-TTC-CTTA-AA---GTATTCAATACAATTCATTC-CTTCG
1 -AACTTG--ACA-AACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTA-AAGT-ATTCAAGACG
* * * * *
3163 AGCCATT-TTTCGAA-C-A--GTC----CA-TGC-T--TGGGAAATCACATCATTAT-GTCTAAA
60 ATCCATTCCTTC-AAGCAATTTTCTGAACATTCCATGCTTGGAAATCACATCATT-TGGTCTAAA
* * * *
3214 TAGTTGCCATTTTGTAAACTACTTTTGGTATTTGAATTAAAAACTTATTTAGGTGTGAATTGTTT
123 TAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTT
* ** * *
3279 CTTTCTTGGTTCTCGATCAAACTTTCG
188 CTCTCTTGGTTCTCGGCCGAACTTT-A
** * * *
3306 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAACTATTTAAGATGATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* **
3371 TCCTTCAAGCAATTTT-TCGAACATTCCATGCTAGAGAAATTGCATCATTTGGTCTAAATAGTTG
66 TCCTTCAAGCAATTTTCT-GAACATTCCATGCTTG-GAAATCACATCATTTGGTCTAAATAGTTG
**
3435 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTCTCT
129 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
* **
3500 TGGTTCAT-GGTCGAACTTCCG
194 TGGTTC-TCGGCCGAACTT-TA
* * * * * * * *
3521 AAGTTGACAAACTTTTATGGGTT-TTTTTTAACATTGGTTCCATAAATTATTCAAGACGATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* * * * * *
3585 TCCTTCGAGCAATTTTCTGAGCATTCCATGCTAAGAAAATCGCATCATCTGGTCTAAATAGTTGT
66 TCCTTCAAGCAATTTTCTGAACATTCCATGCT-TGGAAATCACATCATTTGGTCTAAATAGTTGT
* * * * * * *
3650 CATTTTATAAACAACATTCGATCTTTGAATTAAAAGCTTATTTAGGTGATAATAGTTTCTCTCTT
130 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTT
* * **
3715 GGTTCTTGGTCGAACTTCCG
195 GGTTCTCGGCCGAACTT-TA
* * * * **
3735 AAGTTGACAAACTGTTAGGAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
* ** * * * *
3800 TACTTCGTGCAATTTT-TCGAACATTCCATGTCTGGGAAATCACATCAATTGTTCTAAACAGATT
66 TCCTTCAAGCAATTTTCT-GAACATTCCATG-CTTGGAAATCACATCATTTGGTCTAAATAG-TT
* * * * ** * *
3864 GTCATTTTGTAAAAAACTTATGTTCTTTAAATTAAAATGTTATTTATGTGAGAATTGTTT-TTTC
128 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTC
* *
3928 TTGGTTCTCGGTCGAACTTTCG
193 TTGGTTCTCGGCCGAACTTT-A
3950 AACTTGACAAACTTTT
1 AACTTGACAAACTTTT
3966 GTTCCATAAA
Statistics
Matches: 2072, Mismatches: 365, Indels: 230
0.78 0.14 0.09
Matches are distributed among these distances:
190 1 0.00
191 44 0.02
192 24 0.01
193 3 0.00
194 9 0.00
195 3 0.00
196 4 0.00
197 12 0.01
198 89 0.04
199 5 0.00
200 13 0.01
201 49 0.02
202 24 0.01
203 13 0.01
204 16 0.01
205 12 0.01
206 9 0.00
207 4 0.00
208 2 0.00
209 8 0.00
210 70 0.03
211 31 0.01
212 18 0.01
213 23 0.01
214 636 0.31
215 813 0.39
216 135 0.07
217 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (213 bp):
AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGATCCAT
TCCTTCAAGCAATTTTCTGAACATTCCATGCTTGGAAATCACATCATTTGGTCTAAATAGTTGTC
ATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTG
GTTCTCGGCCGAACTTTA
Found at i:2006 original size:429 final size:428
Alignment explanation
Indices: 1190--4677 Score: 3336
Period size: 429 Copynumber: 8.3 Consensus size: 428
1180 GTTCTCAGTT
* * * **
1190 GAACTTCCGAACTTGACAAAC-TTTAGTGAGTTCTTTTATAACTTTTGTTCAAT-AAGTTATTCA
1 GAACTTTCGAACTTGACAAACTTTTA-CGAGTTCTTTTATAAC-TTCGTTCCTTAAAG-TATTCA
* * * * * * * * *
1253 GGACGATCCATTCTTTCGAGCAA-TTTCCCATACAGTCCATGCTTGGGAAATCACATCATTAGGT
63 AGACGATCCATTCCTTCAAGCAATTTTTCGA-ACATTCCATGCTTAGGAAATCTCATCATTTGGT
* * *
1317 CTAAATAGTTGTCATTTTTTAAACTACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAAT
127 CTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
* * *
1382 TGTTTCCCTT-TTGGTTCTCGGTCGAACTTTTGAACTTGAAAAACTTTTACGAGTTCTTTTATAA
192 TGTTT-CTTTCTTGGTTCTCGGTCGAAC-TTCGAACTTGACAAACTTTTACGAGTTCTTTTATAA
* * * **
1446 C-TTTGATTCCTTAAACTATTCAAGACGATTCATTCCTTCGAGCAATTTTAAGAACATTCCATGC
255 CTTTTG-TTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGC
* * * * *
1510 TCTAGAAATCACATCATTTA-GTCTAAATAGTTGCCATTATGTAAACAACTTTTGGTCTTTAAAT
319 TCTGGAAATCACATCA-TTAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAAT
*
1574 TAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGCA
383 TAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCGGCA
* * * * *
1620 GAACATCCAAAGTTGACAAA-TTGTTACGAGTTCTTTTATAACTTTCGTTCCTTGAAGTATTCAA
1 GAACTTTCGAACTTGACAAACTT-TTACGAGTTCTTTTATAAC-TTCGTTCCTTAAAGTATTCAA
* * * *
1684 GACGAACCATTCCTTCAAGCAATTTTTTGAACATTCCAAGCTTAGGAAATCTCATCTTTTGGTCT
64 GACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTTAGGAAATCTCATCATTTGGTCT
* *
1749 AAATAGTTGTCATTTTGTAAACAACTTTTGATCTTTGAATTAAAAA-ATACTTTATGTGAGAATT
129 AAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA-TTTATGTGAGAATT
* * *
1813 GTTTCTTTCTTGGTTCTCGGCCGAACCTT-AAACTTGACAAACTTTTACAAGTTCTTTTATAACT
193 GTTTCTTTCTTGGTTCTCGGTCGAA-CTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
* * * *
1877 TTTGTTCATTAAAGTATTCAAGACAATCCATTCCTTCAAGCAA-TTTTCTGTACAGTCCATGCT-
257 TTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTC
* * *
1940 TGGAAAATCACATCATTAGGTCTAAATAGTTGTCATTTTGTAAACTACTTTTGGT-TTTCCAATT
321 TGG-AAATCACATCATTAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTT-GAATT
* * *
2004 AAAAACTTATTTAGGTGAGAATTA-TTTCCCTTTTGGTTCTCGATC-
384 AAAAACTTATTTAGGTGAGAA-TAGTTTCTCTCTTGGTTCTCG-GCA
* * * *
2049 GAACTTACGAACCTGAAAAACTTTTACGAGTTCTTTCATAACTTCGATTCCTTAAAGTATTCAAG
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTCG-TTCCTTAAAGTATTCAAG
** * * *
2114 -CGATCCATTCCTTTGAGCAATTTTCCAAACATTCCATGCTCTA-GAAAT-TGCATAATTTGGTC
65 ACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCT-TAGGAAATCT-CATCATTTGGTC
* * *
2176 TAAATAGTTGTAATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATA
128 TAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
* * * * *
2241 GTTTCTCTCTTGGTTCTAGG-CTGAACTTTCGAAGTTAACAAACTTTTACGACTTCTTTTATAAC
193 GTTTCTTTCTTGGTTCTCGGTC-GAAC-TTCGAACTTGACAAACTTTTACGAGTTCTTTTATAAC
** * *
2305 TTCGGTTCCTTAAAGTATTCAAGACGATCC--T--TT-GAGCAA-TTTTCTGAACATTCCAAGCT
256 TTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCT
* * *
2364 CAGGAAATCACATCATTTGGTCTAAATAGTTGTCATTTTATAAAAAAACTTTTGGTCTTTGAATT
320 CTGGAAATCACATCATTAGGTCTAAATAGTTGTCATTTTAT-AAACAACTTTTGGTCTTTGAATT
* * * *
2429 AAAAAACTTATTTATAGGTGATAATAGTTTCTCTCTAGGTTCTAGGCC
384 -AAAAACTTA-TT-TAGGTGAGAATAGTTTCTCTCTTGGTTCTCGGCA
* * * * *
2477 GAACTTTCGAACTTAAAAAACCTTTACGATTTCTTTTTTAACTTCGGTTCCTT-AA--A-T----
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCTTAAAGTATTCAAG
* * * * * * * *
2534 ----T--A----TTCAAGGAATTTTTCAAACATTCCATTCTTAGAAAATCCCATCAATTGTTCCA
65 ACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTTAGGAAATCTCATCATTTGGTCTA
*
2589 AATAGATTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTAAGAATTG
130 AATAG-TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTG
* * * *
2654 TTTCTTTCTAGGTTCTCGGCCGAACTTCCAAACTTGACAAACTTTTATGAGTTCTTTTATAACTT
194 TTTCTTTCTTGGTTCTCGGTCGAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
* * * * * *
2719 TTATTCCTTAAAGTATTCAAGACGATCCATTCCTCCCG-GCCATTTTTCAAACAATCCATGCTCT
258 TTGTTCATTAAAGTATTCAAGACGATCCATTCCT-TCGAGCAATTTTTCGAACATTCCATGCTCT
* * * * *
2783 GGAAATCATATCATTTGGT-TCAAATAGTTGTAATTTTATAAACAGCTTTAGGTCTTTGAATTAA
322 GGAAATCACATCATTAGGTCT-AAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATTAA
* * * * *
2847 AAACTTATTTAGGCGATAATAGTTCCTCTCTAGGTTCTCGACA
386 AAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCGGCA
* * * * *
2890 GAACTTTTGAACTTGACAAACATTTAAGAGTTCTTTGT-TGACTTCGATTTCTTAAAGTATTCAA
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTT-TATAACTTCG-TTCCTTAAAGTATTCAA
* * * * * *
2954 AATGATCCATTCTTTCGAA-CAATTTTTTGAACATTCCATGCTTTGGAAATCAT-ATCATTTGTT
64 GACGATCCATTCCTTC-AAGCAATTTTTCGAACATTCCATGCTTAGGAAATC-TCATCATTTGGT
* * *
3017 CTAAATAGATTGGT-ATTTTGTAAACAACTTTTGGTCTTTAAATTTAAAAGTTATTTATGT--G-
127 CTAAATAG-TT-GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
** * *
3078 A--G------TC---GAACT---T-----TT-GAACTTGACAAACTGTTACGAGTTGTTTTATAA
190 ATTGTTTCTTTCTTGGTTCTCGGTCGAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAA
* * * * * * *
3123 CTTTTATTCCTTAAAGTATTCAATACAATTCATTCCTTCGAGCCATTTTTCGAACAGTCCATGCT
255 CTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCT
* * * * *
3188 -TGGGAAATCACATCATTATGTCTAAATAGTTGCCATTTTGTAAACTACTTTTGGTATTTGAATT
320 CT-GGAAATCACATCATTAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATT
* * * *
3252 AAAAACTTATTTAGGTGTGAATTGTTTCTTTCTTGGTTCTCGATCA
384 AAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCG-GCA
* *
3298 -AACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAACTATTTAAG
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCTTAAAGTATTCAAG
*
3362 ATGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGC-TAGAGAAAT-TGCATCATTTGGTC
65 ACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTTAG-GAAATCT-CATCATTTGGTC
* *
3425 TAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATA
128 TAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
* * * * * *
3490 ATTTCTCTCTTGGTTCAT-GGTCGAACTTCCGAAGTTGACAAACTTTTATGGGTT-TTTTTTAAC
193 GTTTCTTTCTTGGTTC-TCGGTCGAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAAC
* * * *
3553 ATTGGTTCCA-TAAATTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCTGAGCATTCCATGC
256 TTTTGTT-CATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGC
** * * * * *
3616 TAAGAAAATCGCATCATCT-GGTCTAAATAGTTGTCATTTTATAAACAACATTCGATCTTTGAAT
319 TCTGGAAATCACATCAT-TAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAAT
* * *
3680 TAAAAGCTTATTTAGGTGATAATAGTTTCTCTCTTGGTTCTTGGTC-
383 TAAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCGG-CA
* * * * *
3726 GAACTTCCGAAGTTGACAAACTGTTAGGAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAG
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCTTAAAGTATTCAAG
* ** * * * *
3791 ACGATCCATTACTTCGTGCAATTTTTCGAACATTCCATG-TCTGGGAAATCACATCAATTGTTCT
65 ACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCT-TAGGAAATCTCATCATTTGGTCT
* * * * * **
3855 AAACAGATTGTCATTTTGTAAAAAACTTATGTTCTTTAAATTAAAATGTTATTTATGTGAGAATT
129 AAATAG-TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
3920 GTTT-TTTCTTGGTTCTCGGTCGAACTTTCGAACTTGACAAACTTTT----G------T-T--C-
193 GTTTCTTTCTTGGTTCTCGGTCGAAC-TTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
*
3970 ------CA-TAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCT-T
257 TTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCT
* * *
4027 GGGAAATCGA-ATCATTTGGTCTAAATATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
322 -GGAAATC-ACATCATTAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATTA
* * * * *
4091 AAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGCT
385 AAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCGGCA
* * * *
4135 GAA-ATTCAAACTTGACAAACTTTTACTAGTTC-TTTATAACTTTTGTTCCTTAAAGTATTCAAG
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAAC-TTCGTTCCTTAAAGTATTCAAG
* * * * ** *
4198 GCGATCCATTTCTTCAAGCAA-TTTTCAGAATAGTCCATGCTCGGGAAATCGCATCATTTGGTCT
65 ACGATCCATTCCTTCAAGCAATTTTTC-GAACATTCCATGCTTAGGAAATCTCATCATTTGGTCT
* *
4262 AAATAGTTGTCATTTTATAAA-ATACTTTTGGTCTTTGAATTAAAAATTTATTTA-GCTGAGAAT
129 AAATAGTTGTCATTTTGTAAACA-ACTTTTGGTCTTTGAATTAAAAACTTATTTATG-TGAGAAT
* * * * * *
4325 AGTTTCTCTCTTGGTTCTCAGTCAAACTTCCGAACTTGACAAACTTTTACGAGCTCTTCTATAAC
192 TGTTTCTTTCTTGGTTCTCGGTCGAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAAC
* ** * * * * *
4390 ATCAGTTCATTAAAGTATTTAAGAGGATCCATTCTTTC-ACACAATTTTTCGAACATTCCACGCT
256 TTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGA-GCAATTTTTCGAACATTCCATGCT
* ** *
4454 CAGGAAATTGCATCA-TATGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGCATT
320 CTGGAAATCACATCATTA-GGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATT
* * * * *
4518 AAAAACATATTTAAGTGATAATAGTTCCTCTCTTGGTTCTCAGCCA
384 AAAAACTTATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTC-GGCA
* * * * * *
4564 -AACTTTCGAAGTTAACAAACTTTTACGAGTTCTTTTTTAACTTGGGTTCCATAAAGTATTCAAC
1 GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT-CGTTCCTTAAAGTATTCAAG
* * * *
4628 ACTATCCATTCCTTCGAGCAATTTTTCAAACATTCTATGCTT-GAGAAATC
65 ACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTTAG-GAAATC
4678 GCAAAATCGA
Statistics
Matches: 2538, Mismatches: 363, Indels: 314
0.79 0.11 0.10
Matches are distributed among these distances:
405 5 0.00
406 110 0.04
407 392 0.15
408 32 0.01
409 143 0.06
410 7 0.00
411 46 0.02
412 133 0.05
413 71 0.03
414 6 0.00
415 10 0.00
416 23 0.01
417 59 0.02
418 7 0.00
419 1 0.00
420 6 0.00
421 1 0.00
423 1 0.00
424 58 0.02
425 23 0.01
426 13 0.01
427 16 0.01
428 354 0.14
429 593 0.23
430 317 0.12
431 107 0.04
432 4 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (428 bp):
GAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTCGTTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTTAGGAAATCTCATCATTTGGTCTAA
ATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTT
TCTTTCTTGGTTCTCGGTCGAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTG
TTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCTGGAA
ATCACATCATTAGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATTAAAAACT
TATTTAGGTGAGAATAGTTTCTCTCTTGGTTCTCGGCA
Found at i:2728 original size:198 final size:200
Alignment explanation
Indices: 2368--2739 Score: 498
Period size: 198 Copynumber: 1.9 Consensus size: 200
2358 CAAGCTCAGG
* *
2368 AAATCACATCATTTGGTCTAAATAGTTGTCATTTTATAAAAAAACTTTTGGTCTTTGAATTAAAA
1 AAATCACATCAATTGGTCCAAATAGTTGTCATTTTATAAAAAAACTTTTGGTCTTTGAATTAAAA
* * * *
2433 AACTTATTTATAGGTGATAATAGTTTCTCTCTAGGTTCTAGGCCGAACTTTCGAACTTAAAAAAC
66 AACTTATTTATA-GTAAGAATAGTTTCTCTCTAGGTTCTAGGCCGAACTTCCAAACTTAAAAAAC
* * * *
2498 CTTTACGATTTCTTTTTTAACTTCGGTTCCTTAAATTATTCAAGGAATTTTTCAAACATTCCATT
130 CTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGAATTTTTCAAACATTCCATT
2563 CTTAGA
195 CTTAGA
* * * *
2569 AAATCCCATCAATTGTTCCAAATAGATTGTCATTTTGT-AAACAACTTTTGGTCTTTGAATT-AA
1 AAATCACATCAATTGGTCCAAATAG-TTGTCATTTTATAAAAAAACTTTTGGTCTTTGAATTAAA
* * * * *
2632 AAACTTATTTAT-GTAAGAATTGTTTCTTTCTAGGTTCTCGGCCGAACTTCCAAACTTGACAAAC
65 AAACTTATTTATAGTAAGAATAGTTTCTCTCTAGGTTCTAGGCCGAACTTCCAAACTTAAAAAAC
* * **
2696 TTTTATGAGTTCTTTTATAACTTTTATTCCTTAAAGTATTCAAG
130 CTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAG
2740 ACGATCCATT
Statistics
Matches: 147, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
198 79 0.54
200 14 0.10
201 43 0.29
202 11 0.07
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (200 bp):
AAATCACATCAATTGGTCCAAATAGTTGTCATTTTATAAAAAAACTTTTGGTCTTTGAATTAAAA
AACTTATTTATAGTAAGAATAGTTTCTCTCTAGGTTCTAGGCCGAACTTCCAAACTTAAAAAACC
TTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGAATTTTTCAAACATTCCATTC
TTAGA
Found at i:4124 original size:194 final size:193
Alignment explanation
Indices: 3772--4372 Score: 645
Period size: 213 Copynumber: 3.0 Consensus size: 193
3762 TTTAACTTCG
*
3772 GTTCCTTAAAGTATTCAAGACGATCCATTACTTCGTGCAATTTTTCGAACATTCCATG-TCTGGG
1 GTTCCTTAAAGTATTCAAGACGATCCATTACTTCGAGCAATTTTTCGAACATTCCATGCT-TGGG
* * * * * *
3836 AAATC-ACATCAATTGTTCTAAACAGATTGTCATTTTGTAAAAAACTTATGTTCTTTAAATTAAA
65 AAATCGA-ATCATTTGGTCTAAATA-ATTGTCATTTTGT-AAAAACTTTTGGTCTTTGAATTAAA
** * *
3900 ATGTTATTTATGTGAGAATTGTTT-TTTCTTGGTTCTCGGTCGAACTTTCGAACTTGACAAACTT
127 AAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGTCAAACTTACGAACTTGACAAACTT
3964 TT
192 TT
* * *
3966 GTTCCATAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTACTTCGAGCAATTTTTCGAACATTCCATGCTTGGGA
*
4031 AATCGAATCATTTGGTCTAAATATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAA
66 AATCGAATCATTTGGTCTAAATAATTGTCATTTTGTAAA-AACTTTTGGTCTTTGAATTAAAAAA
*
4096 TTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGCTGAAATTCAAACTTGACAAACTTTTAC
130 TTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTC-G--G----TCAAACTT-ACGAAC---T--
*
4161 TAGTTCTTTATAACTTTT
182 T-G-AC---A-AACTTTT
* * * * * *
4179 GTTCCTTAAAGTATTCAAGGCGATCCATTTCTTCAAGCAA-TTTTCAGAATAGTCCATGCTCGGG
1 GTTCCTTAAAGTATTCAAGACGATCCATTACTTCGAGCAATTTTTC-GAACATTCCATGCTTGGG
* * *
4243 AAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAAATACTTTTGGTCTTTGAATTAAAAA
65 AAATCGAATCATTTGGTCTAAATAATTGTCATTTTGTAAAA-ACTTTTGGTCTTTGAATTAAAAA
* * * * *
4308 TTTATTTA-GCTGAGAATAGTTTCTCTCTTGGTTCTCAGTCAAACTTCCGAACTTGACAAACTTT
129 ATTATTTATG-TGAGAATTGTTTCTTTCTTGGTTCTCGGTCAAACTTACGAACTTGACAAACTTT
4372 T
193 T
4373 ACGAGCTCTT
Statistics
Matches: 346, Mismatches: 35, Indels: 52
0.80 0.08 0.12
Matches are distributed among these distances:
192 3 0.01
193 53 0.15
194 97 0.28
195 4 0.01
197 1 0.00
198 1 0.00
199 1 0.00
200 1 0.00
201 7 0.02
202 5 0.01
205 5 0.01
206 8 0.02
207 1 0.00
208 1 0.00
209 1 0.00
210 1 0.00
212 8 0.02
213 148 0.43
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (193 bp):
GTTCCTTAAAGTATTCAAGACGATCCATTACTTCGAGCAATTTTTCGAACATTCCATGCTTGGGA
AATCGAATCATTTGGTCTAAATAATTGTCATTTTGTAAAAACTTTTGGTCTTTGAATTAAAAAAT
TATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGTCAAACTTACGAACTTGACAAACTTTT
Found at i:4339 original size:213 final size:213
Alignment explanation
Indices: 3959--4680 Score: 884
Period size: 215 Copynumber: 3.4 Consensus size: 213
3949 GAACTTGACA
* *
3959 AACTTTTGTTCCATAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATG
1 AACTTTTGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATG
* * * *
4024 CTTGGGAAATCGAATCATTTGGTCTAAATATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAT
66 CTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAAT
* * * * *
4089 TAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGCTGAAA-TTCAAACTTGACAA
131 TAAAAAATTATTTA-GTGAGAATAGTTTCTCTCTTGGTTCTCAGCTCAAACTTCGAACTTGACAA
*
4153 ACTTTTACTAGTTCTTTAT
195 ACTTTTACGAGTTCTTTAT
* * * * *
4172 AACTTTTGTTCCTTAAAGTATTCAAGGCGATCCATTTCTTCAAGCAA-TTTTCAGAATAGTCCAT
1 AACTTTTGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTC-GAACATTCCAT
4236 GCTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAA-ATACTTTTGGTCTTTGA
65 GCTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAACA-ACTTTTGGTCTTTGA
*
4300 ATTAAAAATTTATTTAGCTGAGAATAGTTTCTCTCTTGGTTCTCAG-TCAAACTTCCGAACTTGA
129 ATTAAAAAATTATTTAG-TGAGAATAGTTTCTCTCTTGGTTCTCAGCTCAAACTT-CGAACTTGA
*
4364 CAAACTTTTACGAGCTCTTCTAT
192 CAAACTTTTACGAGTTCTT-TAT
* ** * * *
4387 AACATCAGTT-CATTAAAGTATTTAAGAGGATCCATTCTTTCACA-CAATTTTTCGAACATTCCA
1 AACTTTTGTTCCA-TAAAGTATTCAAGACGATCCATTCCTTCA-AGCAATTTTTCGAACATTCCA
* * * * *
4450 CGCTCAGGAAATTGCATCATATGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGC
64 TGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGA
* * * *
4515 ATTAAAAACA-TATTTAAGTGATAATAGTTCCTCTCTTGGTTCTCAGC-CAAACTTTCGAAGTTA
129 ATTAAAAA-ATTATTT-AGTGAGAATAGTTTCTCTCTTGGTTCTCAGCTCAAAC-TTCGAACTTG
*
4578 ACAAACTTTTACGAGTTCTTTTTT
191 ACAAACTTTTACGAGTTC-TTTAT
** * * * * *
4602 AACTTGGGTTCCATAAAGTATTCAACACTATCCATTCCTTCGAGCAATTTTTCAAACATTCTATG
1 AACTTTTGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATG
* *
4667 CTTGAGAAATCGCA
66 CTCGGGAAATCGCA
4681 AAATCGATGC
Statistics
Matches: 434, Mismatches: 58, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
212 11 0.03
213 151 0.35
214 27 0.06
215 230 0.53
216 15 0.03
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (213 bp):
AACTTTTGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATG
CTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAAT
TAAAAAATTATTTAGTGAGAATAGTTTCTCTCTTGGTTCTCAGCTCAAACTTCGAACTTGACAAA
CTTTTACGAGTTCTTTAT
Found at i:4437 original size:622 final size:623
Alignment explanation
Indices: 3343--4587 Score: 1590
Period size: 622 Copynumber: 2.0 Consensus size: 623
3333 TATAACTTCG
* * *
3343 GTTCCTTAAACTATTTAAGATGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTAGAGA
1 GTTCCATAAACTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTAGAGA
* * *
3408 AATTGCATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAC
66 AATCGAATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAA
* * *
3473 TTATTTAGGTGAGAATAATTTCTCTCTTGGTTCATGGTCGAACTTCCGAAGTTGACAAACTTTTA
131 TTATTTAGGTGAGAATAATTTCTCTCTTGGTTCATGGTCGAAATTCCAAACTTGACAAACTTTTA
* * * * * *
3538 TGGGTTTTTTTTAACATTGGTTCCATAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT
196 TGAGTTCTTTATAACATTGGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTCA
* *
3603 GAGCATTCCATGCTAAGAAAATCGCATCATCTGGTCTAAATAGTTGTCATTTTATAAACAACATT
261 GAACAGTCCATGCTAAGAAAATCGCATCATCTGGTCTAAATAGTTGTCATTTTATAAACAACATT
* * * ** *
3668 CGATCTTTGAATTAAAAGCTTATTTAGGTGATAATAGTTTCTCTCTTGGTTCTTGGTCGAACTTC
326 CGATCTTTGAATTAAAAACTTATTTAGCTGAGAATAGTTTCTCTCTTGGTTCTCAGTCAAACTTC
* * * * * * * *
3733 CGAAGTTGACAAACTGTTAGGAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAGACGATCC
391 CGAACTTGACAAACTGTTACGAGCTCTTCTATAACATCAGTTCATTAAAGTATTCAAGACGATCC
*** * * *
3798 ATTACTTCGTGCAATTTTTCGAACATTCCATG-TCTGGGAAATCACATCA-ATTGTTCTAAACAG
456 ATTACTTCACACAATTTTTCGAACATTCCACGCTC-AGGAAATCACATCATA-TGGTCTAAACAG
* * *** * * *
3861 ATTGTCATTTTGTAAAAAACTTATGTTCTTTAAATTAAAATGTTATTTATGTGAGAATTGTT-TT
519 -TTGTCATTTTATAAAAAACTTATGGTCTTTAAATTAAAAACATATTTAAGTGAGAATAGTTCCT
* * * * *
3925 TTCTTGGTTCTCGGTCGAACTTTCGAACTTGACAAACTTTT
583 CTCTTGGTTCTCAGCCAAACTTTCGAACTTAACAAACTTTT
* * * *
3966 GTTCCATAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTTGGGA
1 GTTCCATAAACTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTAGAGA
*
4031 AATCGAATCATTTGGTCTAAATATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAA
66 AATCGAATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAA
* ** *
4096 TTATTTATGTGAGAATTGTTTCTTTCTTGGTTC-TCGG-CTGAAATT-CAAACTTGACAAACTTT
131 TTATTTAGGTGAGAATAATTTCTCTCTTGGTTCAT-GGTC-GAAATTCCAAACTTGACAAACTTT
* * * * *
4158 TACT-AGTTCTTTATAACTTTTGTTCCTTAAAGTATTCAAGGCGATCCATTTCTTCAAGCAATTT
194 TA-TGAGTTCTTTATAACATTGGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
* ** * *
4222 TCAGAATAGTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTGTCATTTTATAAA-ATA
258 TCAGAACAGTCCATGCTAAGAAAATCGCATCATCTGGTCTAAATAGTTGTCATTTTATAAACA-A
* * * *
4286 CTTTTGGTCTTTGAATTAAAAATTTATTTAGCTGAGAATAGTTTCTCTCTTGGTTCTCAGTCAAA
322 CATTCGATCTTTGAATTAAAAACTTATTTAGCTGAGAATAGTTTCTCTCTTGGTTCTCAGTCAAA
* * *
4351 CTTCCGAACTTGACAAACTTTTACGAGCTCTTCTATAACATCAGTTCATTAAAGTATTTAAGAGG
387 CTTCCGAACTTGACAAACTGTTACGAGCTCTTCTATAACATCAGTTCATTAAAGTATTCAAGACG
**
4416 ATCCATT-CTTTCACACAATTTTTCGAACATTCCACGCTCAGGAAATTGCATCATATGGTCTAAA
452 ATCCATTAC-TTCACACAATTTTTCGAACATTCCACGCTCAGGAAATCACATCATATGGTCTAAA
* * * ** *
4480 TAGTTGTCATTTTATAAACAACTTTTGGTCTTTGCATTAAAAACATATTTAAGTGATAATAGTTC
516 CAGTTGTCATTTTATAAAAAACTTATGGTCTTTAAATTAAAAACATATTTAAGTGAGAATAGTTC
*
4545 CTCTCTTGGTTCTCAGCCAAACTTTCGAAGTTAACAAACTTTT
581 CTCTCTTGGTTCTCAGCCAAACTTTCGAACTTAACAAACTTTT
4588 ACGAGTTCTT
Statistics
Matches: 529, Mismatches: 85, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
621 51 0.10
622 319 0.60
623 159 0.30
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (623 bp):
GTTCCATAAACTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTAGAGA
AATCGAATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAA
TTATTTAGGTGAGAATAATTTCTCTCTTGGTTCATGGTCGAAATTCCAAACTTGACAAACTTTTA
TGAGTTCTTTATAACATTGGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTCA
GAACAGTCCATGCTAAGAAAATCGCATCATCTGGTCTAAATAGTTGTCATTTTATAAACAACATT
CGATCTTTGAATTAAAAACTTATTTAGCTGAGAATAGTTTCTCTCTTGGTTCTCAGTCAAACTTC
CGAACTTGACAAACTGTTACGAGCTCTTCTATAACATCAGTTCATTAAAGTATTCAAGACGATCC
ATTACTTCACACAATTTTTCGAACATTCCACGCTCAGGAAATCACATCATATGGTCTAAACAGTT
GTCATTTTATAAAAAACTTATGGTCTTTAAATTAAAAACATATTTAAGTGAGAATAGTTCCTCTC
TTGGTTCTCAGCCAAACTTTCGAACTTAACAAACTTTT
Found at i:21550 original size:15 final size:16
Alignment explanation
Indices: 21532--21569 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21522 ACCCTAAACC
21532 AACTAACCTAA-CCCA
1 AACTAACCTAAGCCCA
*
21547 AACTCACCTAAGCCCA
1 AACTAACCTAAGCCCA
21563 AGACTAA
1 A-ACTAA
21570 AATAGGCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 5 0.26
17 4 0.21
ACGTcount: A:0.45, C:0.37, G:0.05, T:0.13
Consensus pattern (16 bp):
AACTAACCTAAGCCCA
Found at i:22172 original size:34 final size:34
Alignment explanation
Indices: 22129--22198 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
22119 ATTTTTTAAG
22129 TATGTTTCAATGTCTACACATAAGTATGCTGAAA
1 TATGTTTCAATGTCTACACATAAGTATGCTGAAA
22163 TATGTTTCAATGTCTACACATAAGTATGCTGAAA
1 TATGTTTCAATGTCTACACATAAGTATGCTGAAA
22197 TA
1 TA
22199 AAATGATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (34 bp):
TATGTTTCAATGTCTACACATAAGTATGCTGAAA
Found at i:24844 original size:26 final size:26
Alignment explanation
Indices: 24808--24863 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
24798 GGTTTAATTG
24808 CATTAGATATCAATTGCATCTAGTTA
1 CATTAGATATCAATTGCATCTAGTTA
24834 CATTAGATATCAATTGCATCTAGTTA
1 CATTAGATATCAATTGCATCTAGTTA
24860 CATT
1 CATT
24864 TATTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (26 bp):
CATTAGATATCAATTGCATCTAGTTA
Done.