Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014713.1 Kokia drynarioides strain JFW-HI SEQ_129752, 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: 4340
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:1179 original size:216 final size:216
Alignment explanation
Indices: 1--3408 Score: 3308
Period size: 216 Copynumber: 16.0 Consensus size: 216
* *
1 TTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAACAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * *** * * * *
66 TTCTGAACGTTCGATTCTTTAGAAATAGCAGCATTTGGTCTAAAGAGTTTGTCATTTTGAAAACA
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* * * **
131 AGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTG-TT-TCGCTTGGTTCTTTGACAA
131 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
* *
194 ACTTCCGAACTTATCAAACTT
196 ACTTTCGAACTTGTCAAACTT
* * * * * *
215 TTAC-ACGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAAGACGATACATTCCTTCGAGCAAC
1 TTACGA-GTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAAT
* * * * *** * * *
279 TCTCTTAACATTCTATGCTCAAAAAATTGCATCATTT-TTCTAAATTGTTTGTCATTTTTGTAAA
65 TTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA-TTTTGTAAA
* * *
343 CAAGTTTT-GTCTTTAAATTAAAAATTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGG
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT-TCTCTCTTGGTTCTTGG
* * * * *
407 ACGAACTTCCAAACTTTTCAAACCT
192 ATGAACTTTCGAACTTGTCAAACTT
* * * * * **
432 TTACGAGTTCTTTTATAAC-TCYKGTTCCTTRAAKTATTCAASAACATCCATTCCTYTC-AGCAA
1 TTACGAGTTCTTTTATATCTTC-GGTTCCTTAAAGTATTCAAGATGATCCATTCCT-TCGAGCAA
* * * * * *
495 -TTT-YGAACATTCYATTCTCGGGTAATCGCATCATTTAGTCTAAATAGTTTTTCGTTTTGTAAA
64 TTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* *** * *
558 CAAGTTTTGGTCTTTAAAGCGAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGCTGTTGGAT
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAT
* * * *
621 GAACTTCCGAACTTTTTATACTT
194 GAACTTTCGAACTTGTCAAACTT
* ** *
644 TTAC--G-TC-----TA-----GGTTCCTTACAA-TAGTCAAGATGATCCATTCCTTTTAGCTAT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTA-AAGTATTCAAGATGATCCATTCCTTCGAGCAAT
* * * *
695 TTTCTGAACATTCCATACTCGGGAAATCGCATAATTTTGTCTAAATAGTTTGTCATTTTGTGAAC
65 TTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
* * * * * * *
760 AACTTTTGGTGTTTGAATTAAATACTTATTTACGCGAGAATTGTTTCTCTTTTAGTTCTTGGACG
130 AAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATG
*
825 AACTTTCGAACTTATCAAACTT
195 AACTTTCGAACTTGTCAAACTT
* * * * *
847 TTATGAGTTCTTTTATAAT-TTCAGTTCCATAAAGCATTCAAGACGATCCATTCCTTCGAGCAAT
1 TTACGAGTTCTTTTAT-ATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAAT
* * * *
911 TTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAGA
65 TTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG-TAAA
* * * * *
976 -AGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTCGAA
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTGGTTCTTGGA
*
1040 TGAACTTTCGAACTAGTCAAACTT
193 TGAACTTTCGAACTTGTCAAACTT
* * *
1064 TTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCAAACAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * * * * * *
1129 TTCTGAACGTTCGATTCTTGAGAAATAGCAGCATTTGGTCT-AAGAGTTTGTCAATTTGAAAACG
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* * * * **
1193 AGTTTTGGTCTTTGAATCAAAAACTTATTTACGTTAGAATTG-TT-TCGCTTAGTTCTTGGACAA
131 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
*
1256 ACTTCCGAACTTGTCAAACTT
196 ACTTTCGAACTTGTCAAACTT
* * * * * * *
1277 TTACGCGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAAGACGATACATTCCTTCGAGCAACT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * **
1342 TTCTTAACGTTCTATGCTC--GAATTATCGCATCATTT-TTCTAAATTTTTTGTCATTTTGTAAA
66 TTCTGAACATTCCATTCTCGGGAA--ATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * *
1404 CAA-TTTTTGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGG
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT-TCTCTCTTGGTTCTTGG
* *
1468 ATGAACTTT-GAAACTTTTCAAACCT
192 ATGAACTTTCG-AACTTGTCAAACTT
* ** * ** *
1493 TTACGAGTTCTTTTATAACAACGGTTCCTTAAAGTATTCAATAACATCCATTCCTT-TAGCAA-T
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * *
1556 TT-TGAACATTCCTTTCTCGGGTAATTGCATCATTTAGTCTAAATAGTTTTTCCTTTTGTAAACA
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* ** * *
1620 AGTTTTGGTCTTTAAAACAAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGCTGTTGGATGA
131 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
* *
1683 AC-TTCTGAACTTTTTAAACTT
196 ACTTTC-GAACTTGTCAAACTT
*
1704 TTAC--G---------A-C-TCGGTTCCTTACAA-TATTCAAGATGATCCATTCCTTCGAGCTAT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTA-AAGTATTCAAGATGATCCATTCCTTCGAGCAAT
* * * * *
1755 TTTCTGAACATTCCATACTCGGGAAATCGCATAATTTTGTCTAAATAGCTTGTCATTTTGTGAAC
65 TTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
* * ** * * * *
1820 AACTTTTGGTCTTTGAATTAAATACTTATTTACGCAATAATTGTTTCTCTTTTAGTTATTGGATG
130 AAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATG
*
1885 AACTTCCGAACTTGTCAAACTT
195 AACTTTCGAACTTGTCAAACTT
* * * * * * *
1907 TTACAAATTCTTTTATATTTTCAGTTCCATAAAGCATTCAAGACGATCCATTCCTTCGAGCAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
** * *
1972 TTCCCAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAGA-
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG-TAAAC
* * * * *
2036 AGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGATAATTGTTTTCTCTCTTGGTTCTCGGAT
130 AAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTGGTTCTTGGAT
*
2101 GAACTTTCGAACTAGTCAAACTT
194 GAACTTTCGAACTTGTCAAACTT
* * *
2124 TTACGAGTTCTTTCATATCTTCGGTTCCTTACAGTATTCAAGATGATCCATTACTTCGAGCAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * * * *
2189 TTCTAAACATTCTATTCTTGAGAAATAGCAGCTTTTGGTCTAAAGT-GTTTGTCATTTTGAAAAC
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAA-TAGTTTGTCATTTTGTAAAC
* * *
2253 AAGTTTCGGTCTTTGAATCAAAAACTTATTTACGTGAGAATT-TTT-TCCCTTGGTTCTTGG--G
130 AAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATG
* **
2314 CAAGCTTCCGAACTTGTCACTCTT
195 -AA-CTTTCGAACTTGTCAAACTT
* * * * *
2338 TTACGAGTTCTTTTATAACTTCGGTTCCTTACAGTATTCAAGACGATACATTCCTTCGAGCAACT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * * *
2403 TTCTTAACGTTCTATGT-TC-GAAATATCGCATCCTTT-TTCTAAATTGTTTGTCATTTTGTAAA
66 TTCTGAACATTCCAT-TCTCGGGAA-ATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* *
2465 CAAGTTTT-GTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGG
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT-TCTCTCTTGGTTCTTGG
* *
2529 ATGAAC-TTCGAAACTTTTCAAACCT
192 ATGAACTTTCG-AACTTGTCAAACTT
* ** * ** *
2554 TTACGAGTTCTTTTATAACAACGGTTCCTTAAAGTATTCAATAACATCCATTCCTT-TAGCAA-T
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * *
2617 TT-TGAACATTCCTTTCTCGGGTAATTGCATCATTTAGTCTAAATAGTTTTTCGTTTTGTAAACA
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* ** * *
2681 AGTTTTGGTCTTTAAAACAAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGCTGTTGGATGA
131 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
2744 AC-TT----C-TG---AACTTT
196 ACTTTCGAACTTGTCAAAC-TT
* ** * * *
2757 TTA--A--ACTTTTWYRA-C-TMGGTTCCTTMCAA-TATTCAAGATGATCCATTCCTTCGAGCTA
1 TTACGAGTTCTTTT-ATATCTTCGGTTCCTT-AAAGTATTCAAGATGATCCATTCCTTCGAGCAA
* * * * *
2815 TTTTCTGAACATTCCATACTCGGGAAATCGCATAATTTTGTCTAAATAGCTTGTCATTTTGTGAA
64 TTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * * * *
2880 CAACTTTTGGTCTTTGAATTAAATACTTATTTACGCGAGAATTGTTTCTCTTTTAGTTCTTGGAT
129 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAT
*
2945 GAACTTCCGAACTTGTCAAACTT
194 GAACTTTCGAACTTGTCAAACTT
* * * * * **
2968 TTACGAGTTCTTTTATATTTTCAGTTCCATAAAGCATTCGAGACAATCCATTCCTTCGAGCAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * *
3033 TT-TCGAACATTCCATGCTCGGAAAATCGCATCATTCGGTCTAAATAGTTTGTCATTTTGTAAA-
66 TTCT-GAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
* * *
3096 AAGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTCGGA
130 AA-GTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTGGTTCTTGGA
* *
3161 CGAACTTTCGAACTAGTCAAACTT
193 TGAACTTTCGAACTTGTCAAACTT
* * *
3185 TTACGAGTTCTTTMATATCTTCGGTTCCTTAAAGYATTCAAGATGATCCATTCCTTCGAACAATT
1 TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
* * * * * * * *
3250 TTCTGAACGTTCGATTCTTGAGAAATAGCAGCATTTGGTCTAAAGAGTTTGTCATTTTGAAAACA
66 TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* * * **
3315 AGTTTTGGTTTTTGAATCAAAAACTTATTTACGTGAGAATTG-TT-TCGCTTGGTTCTTGGACAA
131 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
3378 ACTTTCGAACTTGTCAAACTT
196 ACTTTCGAACTTGTCAAACTT
3399 TTACGAGTTC
1 TTACGAGTTC
3409 NNNNNNNNNN
Statistics
Matches: 2614, Mismatches: 461, Indels: 238
0.79 0.14 0.07
Matches are distributed among these distances:
198 57 0.02
199 47 0.02
200 13 0.00
201 262 0.10
202 9 0.00
203 89 0.03
204 5 0.00
205 2 0.00
206 3 0.00
208 1 0.00
209 5 0.00
210 3 0.00
211 63 0.02
212 117 0.04
213 256 0.10
214 324 0.12
215 152 0.06
216 629 0.24
217 569 0.22
218 8 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (216 bp):
TTACGAGTTCTTTTATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATT
TTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
ACTTTCGAACTTGTCAAACTT
Found at i:2808 original size:845 final size:845
Alignment explanation
Indices: 22--3408 Score: 2928
Period size: 845 Copynumber: 4.0 Consensus size: 845
12 TTCATATCTT
** * * * * ***
22 CGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAACAATTTTCTGAACGTTCGATTCTTTA
1 CGGTTCCTTAAAGTATTCAA-AACATCCATTCCTTCGAGCAA-TTT-TGAACATTCCATACTCGG
* * * * * *
87 GAAATAGCAGCATTTGGTCTAAAGAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTGAATCAAA
63 GAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * ** * * *
152 AACTTATTTACGTGAGAATTGTTTCGCTTGGTTCTTTGACAAACTTCCGAACTTATCAAACTTTT
128 AACTTATTTACGTGAGAATTGTTTCTCTTGGTTATTGGATGAACTTCTGAACTTTTTAAACTTTT
* * *
217 ACACGTTCTTTTATAACTTCA-GTTCCTT-ACAGTATTCAAGACGATACATTCCTTCGAGCAACT
193 -CA---------A-ATCTT-AGGTTCCTTCA-AGTATTCAAGACGATCCATTCCTTCGAGCAATT
* * * * * * * *
280 CTCTTAACATTCTATGCTCAAAAAATTGCATCATTT-TTCTAAATTGTTTGTCATTTT-TGTAAA
245 TTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-TAAA
* * *
343 CAAGTTTT-GTCTTTAAATTAAAAATTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGG
309 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT-TCTCTCTTAGTTCTTGG
* * * * *
407 ACGAACTTCCAAACTTTTCAAACCTTTACGAGTTCTTTTATAAC-TCYKGTTCCTTRA-AKTATT
372 ACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-AGTTCCTT-ACAGTATT
* * * * * * *
470 CAASAAC-ATCCATTCCTYTC-AGCAA-TTTYGAACATTCYATTCTCGGGTAATCGCATCATTTA
435 CAA-GACGATCCATTCCT-TCGAGCAATTTTTGAACATTCTATGCTCGAGAAATCGCATCATTTG
* * * * *
532 GTCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGGTCTTTAAAGCGAAAACTTATTTACGTGAG
498 GTCTAAATAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAG
* * * * *
597 AATTG--TT-TCTCTTGGCTGTTGGATGAACTTCCGAACTTTTTATACTTTTAC--G-TC-----
563 AATTGTTTTCTCTCTTGGTTCTTGGA-GAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTA
* * ** * *
651 T-A----GGTTCCTTACAA-TAGTCAAGATGATCCATTCCTTTTAGCTATTTTCTGAACATTCCA
627 TAACTTCGGTTCCTTA-AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCTA
* * * * * *
710 TACTCGGGAA-ATCGCATAATTTTGTCTAAATAGTTTGTCATTTTGTGAACAACTTTTGGTGTTT
691 T-TTCGGAAATATCGCATCA-TTTGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTT
* * * * *
774 GAATTAAATACTTATTTACGCGAGAATTGTTTCTCT-T-TTAGTTCTTGGACGAACTTTCGAACT
754 AAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTAGTTCTTGGATGAAC-TTCGAACT
* *
837 TATCAAACTTTTATGAGTTCTTTTATAA
818 TTTCAAACTTTTACGAGTTCTTTTATAA
* * * * *
865 TTTCAGTTCCATAAAGCATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCT
1 ---CGGTTCCTTAAAGTATTCAAAAC-ATCCATTCCTTCGAGCAATTTT--GAACATTCCATACT
* * * * * *
930 AGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAGA-AGGTTTTGTTGTTTGAAT
60 CGGGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTG-TAAACAAGTTTTGGTCTTTGAAT
* * *
994 TAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTCGAATGAACTT-TCGAACTAGTC
124 TAAAAACTTATTTACGTGAGAATTG--TT-TCTCTTGGTTATTGGATGAACTTCT-GAAC---T-
** * * * * *
1058 AAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCAA
181 ----TTTTA--AACT-TTTCAAATCTTAGGTTCCTTCAAGTATTCAAGACGATCCATTCCTTCGA
* * * * * * * * *
1123 ACAATTTTCTGAACGTTCGATTCTTGAGAAATAGCAGCATTTGGTCT-AAGAGTTTGTCAATTTG
239 GCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
* * * * *
1187 -AAAACGAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTTAGAATTG-TT-TCGCTTAGTTCT
304 TTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCT
* *
1249 TGGACAAACTTCCGAACTTGTCAAACTTTTACGCGTTCTTTTATAACTTCAGTTCCTTACAGTAT
369 TGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTAT
* * *
1314 TCAAGACGATACATTCCTTCGAGCAACTTTCTT-AACGTTCTATGCTCGA-ATTATCGCATCATT
434 TCAAGACGATCCATTCCTTCGAGCAA-TTT-TTGAACATTCTATGCTCGAGA-AATCGCATCATT
* ** * * *
1377 T-TTCTAAATTTTTTGTCATTTTGTAAACAA-TTTTTGTCTTTAAATTAAAAACTTATTTACGTG
496 TGGTCTAAATAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTG
* * * *
1440 AGAATTGTTTCTCTCTCTTTGTTCTTGGATGAACTT-TGAAACTTTTCAAACCTTTACGAGTTCT
561 AGAATTGTTT-TCTCTCTTGGTTCTTGGA-GAACTTCCG-AACTTGTCAAACTTTTACGAGTTCT
** * *
1504 TTTATAACAACGGTTCCTTAAAGTATTCAATAAC-ATCCATTCCTT-TAGCAA-TTT-TGAACAT
623 TTTATAACTTCGGTTCCTTAAAGTATTCAA-GACGATCCATTCCTTCGAGCAATTTTCTGAACAT
* * *
1565 TCCT-TTCTCGGGTAAT-T-GCATCATTTAGTCTAAATAGTTTTTCCTTTTGTAAACAAGTTTTG
687 T-CTATT-TC-GGAAATATCGCATCATTT-GTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG
* * * *
1627 GTCTTTAAAACAAAAACTTATTTACGTGAGAATTG--T-T-TCTCTTGGCTGTTGGATGAACTTC
748 GTCTTTAAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTAGTTCTTGGATGAACTTC
*
1688 TGAACTTTTTAAACTTTTACGA---C-----T--
813 -GAACTTTTCAAACTTTTACGAGTTCTTTTATAA
** *
1712 CGGTTCCTTACAA-TATTCAAGATGATCCATTCCTTCGAGCTATTTTCTGAACATTCCATACTCG
1 CGGTTCCTTA-AAGTATTCAA-AACATCCATTCCTTCGAGC-AATTT-TGAACATTCCATACTCG
* * * * *
1776 GGAAATCGCATAATTTTGTCTAAATAGCTTGTCATTTTGTGAACAACTTTTGGTCTTTGAATTAA
62 GGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAA
* ** * * * * *
1841 ATACTTATTTACGCAATAATTGTTTCTCTTTTAGTTATTGGATGAACTTCCGAACTTGTCAAACT
127 AAACTTATTTACGTGAGAATTGTTTCTC--TTGGTTATTGGATGAACTTCTGAACTTTTTAAACT
* * * *
1906 TTTACAAATTCTTTTATATTTTCAGTTCCATAAAGCATTCAAGACGATCCATTCCTTCGAGCAAT
190 TTT-CAAA-TC---T-TA-----GGTTCCTTCAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
** * *
1971 TTTCCCAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAGA
244 TTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAAA
* * * * * *
2036 -AGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGATAATTGTTTTCTCTCTTGGTTCTCGGA
309 CAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTAGTTCTTGGA
* * * * * *
2100 TGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTACAGTATTCAA
373 CGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAA
* * * * * * * *
2165 GATGATCCATTACTTCGAGCAATTTTCTAAACATTCTATTCTTGAGAAATAGCAGCTTTTGGTCT
438 GACGATCCATTCCTTCGAGCAATTTT-TGAACATTCTATGCTCGAGAAATCGCATCATTTGGTCT
* *
2230 AAAGT-GTTTGTCATTTTGAAAACAAGTTTCGGTCTTTGAATCAAAAACTTATTTACGTGAGAAT
502 AAA-TAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAAT
**
2294 T-TTTTC-C-CTTGGTTCTTGG-GCAAGCTTCCGAACTTGTCACTCTTTTACGAGTTCTTTTATA
566 TGTTTTCTCTCTTGGTTCTTGGAG-AA-CTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATA
* * * * *
2355 ACTTCGGTTCCTTACAGTATTCAAGACGATACATTCCTTCGAGCAACTTTCTTAACGTTCTATGT
629 ACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCTAT-T
* * *
2420 TC-GAAATATCGCATCCTTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAAT
693 TCGGAAATATCGCATCATTTGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAAT
* *
2483 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGGATGAACTTCGAAACTTTTC
758 CAAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTAGTTCTTGGATGAACTTCG-AACTTTTC
*
2548 AAACCTTTACGAGTTCTTTTATAACAA
822 AAACTTTTACGAGTTCTTTTAT---AA
* * * *
2575 CGGTTCCTTAAAGTATTCAATAACATCCATTCCTT-TAGCAATTTTGAACATTCCTTTCTCGGGT
1 CGGTTCCTTAAAGTATTCAA-AACATCCATTCCTTCGAGCAATTTTGAACATTCCATACTCGGGA
* * * * **
2639 AATTGCATCATTTAGTCTAAATAGTTTTTCGTTTTGTAAACAAGTTTTGGTCTTTAAAACAAAAA
65 AATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA
* * **
2704 CTTATTTACGTGAGAATTGTTTCTCTTGGCTGTTGGATGAACTTCTGAACTTTTTAAACTTTTWY
130 CTTATTTACGTGAGAATTGTTTCTCTTGGTTATTGGATGAACTTCTGAACTTTTTAAACTTTTCA
* * * *
2769 RA-C-TMGGTTCCTTMCAA-TATTCAAGATGATCCATTCCTTCGAGCTATTTTCTGAACATTCCA
195 AATCTTAGGTTCCTT-CAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCA
* * * * * * *
2831 TACTCGGGAAATCGCATAATTTTGTCTAAATAGCTTGTCATTTTG-TGAACAACTTTTGGTCTTT
259 TGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAAACAAGTTTTGGTCTTT
* * * *
2895 GAATTAAATACTTATTTACGCGAGAATTGTTTCTCTTTTAGTTCTTGGATGAACTTCCGAACTTG
324 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTG
** * * * * *
2960 TCAAACTTTTACGAGTTCTTTTATATTTTCAGTTCCATAAAGCATTCGAGACAATCCATTCCTTC
389 TCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAAGACGATCCATTCCTTC
* *
3025 GAGCAATTTTTCGAACATTCCATGCTCG-GAAAATCGCATCATTCGGTCTAAATAGTTTGTCATT
454 GAGCAATTTTT-GAACATTCTATGCTCGAG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATT
* * * * *
3089 TTGTAAAA-AGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGG
517 TTG-AAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGG
* * * * *
3153 TTCTCGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTMATATCTTCGGTTCCTTAAA
581 TTCTTGGA-GAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAA
* * * * * * *
3218 GYATTCAAGATGATCCATTCCTTCGAACAATTTTCTGAACGTTCGATTCTTGAGAAATA--GCAG
645 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCTATT-TCG-GAAATATCGCAT
* * * *
3281 CATTTGGTCTAAAGAGTTTGTCATTTTGAAAACAAGTTTTGGTTTTTGAATCAAAAACTTATTTA
708 CATTT-GTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTA
* * ** *
3346 CGTGAGAATTG--T-T-TCGCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGT
772 CGTGAGAATTGTTTCTCTCTCTTAGTTCTTGGATGAAC-TTCGAACTTTTCAAACTTTTACGAGT
3407 TC
836 TC
3409 NNNNNNNNNN
Statistics
Matches: 2057, Mismatches: 347, Indels: 275
0.77 0.13 0.10
Matches are distributed among these distances:
832 3 0.00
833 5 0.00
834 2 0.00
835 3 0.00
837 1 0.00
838 1 0.00
840 1 0.00
841 4 0.00
842 2 0.00
843 94 0.05
844 354 0.17
845 372 0.18
846 206 0.10
847 285 0.14
848 93 0.05
849 244 0.12
850 44 0.02
851 1 0.00
852 3 0.00
853 1 0.00
854 1 0.00
855 2 0.00
856 5 0.00
857 37 0.02
858 37 0.02
859 80 0.04
860 104 0.05
861 11 0.01
862 31 0.02
863 30 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (845 bp):
CGGTTCCTTAAAGTATTCAAAACATCCATTCCTTCGAGCAATTTTGAACATTCCATACTCGGGAA
ATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAAC
TTATTTACGTGAGAATTGTTTCTCTTGGTTATTGGATGAACTTCTGAACTTTTTAAACTTTTCAA
ATCTTAGGTTCCTTCAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATG
CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTAAACAAGTTTTGGTCTTTGA
ATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTC
AAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAAGACGATCCATTCCTTCGA
GCAATTTTTGAACATTCTATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGA
AAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTT
GGAGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTC
AAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCTATTTCGGAAATATCGCATCATTTGTC
TAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAAT
TGTTTCTCTCTCTTAGTTCTTGGATGAACTTCGAACTTTTCAAACTTTTACGAGTTCTTTTATAA
Found at i:4170 original size:216 final size:217
Alignment explanation
Indices: 3459--4334 Score: 986
Period size: 217 Copynumber: 4.1 Consensus size: 217
3449 NNNNNNNNNN
* * * * * * * *
3459 GACGAACTTCTGAACTTATCAAACTTTTATGACTTCTTCTATAATTTCAGTTCCATAAAGCATTC
1 GACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTC
* * *
3524 AAGACGATCCATTCCTTCGTGCAATTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGT
66 AAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* * * * * *
3589 CTAAATAGTTTGTCATTTTGTTAGA-AGGTTTTGTTGTTTGAATTAAAAACTTATTTACGTGAGA
131 CTAAATAGTTTGTCATTTTG-TAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGA
*
3653 ATTGTTTTCTCTCTTGGTTCTCG
195 ATTGTTTTCTCTCTTGGTTCTTG
* * * * * * *
3676 GACGAACTTTCGAACTAGTCAAAGTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTC
1 GACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTC
* * * ** * * * *
3741 AAGATGATCCATTCCTTCGAACAATTTTCTGAACGTTAGATTCTTGAGAAATAGCAGCATTTGGT
66 AAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* *
3806 CTAAATAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAA
131 CTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAA
*
3871 TTG--TT-TCGCTTGGTTCTTG
196 TTGTTTTCTCTCTTGGTTCTTG
* * * *
3890 GACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTC
1 GACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTC
* * * * * * *
3955 AAGACGATACATTCCTTCGAGCAACTCTCTTAACATTCTATGCTCGAAAAATCGCATCATTT-TT
66 AAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
* * *
4019 CTAAATTGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAATTAAAAACTTATTTATGTGAGAA
131 CTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAA
*
4083 TTGTTTCTCTCTCTTTGTTCTTG
196 TTGTTT-TCTCTCTTGGTTCTTG
* * * * * *
4106 GACGAACTTCCAAACTTTTCAAACCTTTACGAGTTCTTTTATAACTCCGGTTCCCTGAAGTATTC
1 GACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTC
* * * * * *
4171 ATGAAC-ATCCATTCCTTTC-AGCAA-TTT-TGAACATTCCATTCTCGGGTACTCGCATCATTTA
66 AAG-ACGATCCATTCC-TTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTG
* * * *
4232 GTCTAAATAGTTTTTCATTTTGTACACAAGTTTTGGTCTTTAAAGCGAAAACTTATTTACGTGAG
129 GTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAG
* *
4297 AATTG--TT-TCTCTTGGCTGTTG
194 AATTGTTTTCTCTCTTGGTTCTTG
*
4318 GATGAACTTCCGAACTT
1 GACGAACTTCCGAACTT
4335 TTTAAA
Statistics
Matches: 554, Mismatches: 96, Indels: 23
0.82 0.14 0.03
Matches are distributed among these distances:
212 58 0.10
213 32 0.06
214 146 0.26
215 35 0.06
216 115 0.21
217 168 0.30
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (217 bp):
GACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTC
AAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGT
CTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATCAAAAACTTATTTACGTGAGAA
TTGTTTTCTCTCTTGGTTCTTG
Done.