Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010818.1 Kokia drynarioides strain JFW-HI SEQ_125785, 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: 4341
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.39
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:381 original size:216 final size:215
Alignment explanation
Indices: 5--2609 Score: 1724
Period size: 216 Copynumber: 11.9 Consensus size: 215
1 AACG
* *
5 ACTTTTGGTCTTTGAATGAAAAACTTATTTATGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* * * * *
70 ACTTCTGAACTTGGAACACTTTTACCAGTTCATCTCTAACTTTCGTTCCTTTAAA-TATTCATGA
66 ACTTCTGAACTT-GAAAACTTTTACCAGTTCTTCTATAAC-TTCGTTTCATTAAAGTATTCATGA
* * * *
134 CAATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGGGAAGTCACATCATTTGGTCTAA
129 CAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * *
199 ATACTTTGTCATTTTCTAAACG
194 ATAGTTTGTCATTTTGTAAACA
* * *
221 ACTTTTGGTCTTTGAGTGAAAAACTCATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* *
286 ACTTCTGAACATGGAAAACTTTTACCAGTTCATCTATAACTTTC-TTTCATTAAAGTATTCATGA
66 ACTTCTGAAC-TTGAAAACTTTTACCAGTTCTTCTATAAC-TTCGTTTCATTAAAGTATTCATGA
* ** * *
350 CAATCCATTCCTTCAAGCAATTTTCCGAACATTCCTTGCTCGGGAAATCGCATCATTTAGTCTAA
129 CAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * *
415 ATAGTTTGCCTTTTTATAAACA
194 ATAGTTTGTCATTTTGTAAACA
* * * * * *
437 ACTTTTGGTCTTTAAATTACAAAGTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* * * * * * * *
502 ACTTAC-GTACTTGATGAAGTTTTGCAAGTTCTTTTAAAACTTCAG-TTCCTTAAAGTATTCATG
66 ACTT-CTGAACTTGA-AAACTTTTACCAGTTCTTCTATAACTTC-GTTTCATTAAAGTATTCATG
* * ** * * * * *
565 ACTATCCATTCCATCGAGCAATTTTCCGAGCATTCCATGCACAGCAAATCGCATCATTTTGTCTA
128 ACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
*
630 AATAGTTTGTCATTTGGTAAACA
193 AATAGTTTGTCATTTTGTAAACA
* * * * *
653 ACTTTTGGCCTTTGAATTAAAAACCTATTTACGTGAGAGTTGTCTT-TCTCTTGGTTTTTAGATG
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGT-TTCTCTCTTGGTTCTTGGACG
** * ** * * *
717 AACTTCCAAACTTGACGAACTTTTAGGAGTTCTTCAATAACTTCGGTTTC-TTAAAGTATTTAGG
65 AACTTCTGAACTTGA-AAACTTTTACCAGTTCTTCTATAACTTC-GTTTCATTAAAGTATTCATG
* * * * *
781 ACAA-CCAATT-CTTAGAGCAATTTTTTGAACATTACATACTCGAGAAATCACATCATTTGG---
128 ACAATCC-ATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * *
841 -AATACTTTGTCATTTTCTAAACT
192 AAATAGTTTGTCATTTTGTAAACA
* *
864 ACTTTTGGTCTTTGAATGAAAAACTT-TCTTACGTGAGAGTTGTTTCTATCTTGGTTCTTGGACG
1 ACTTTTGGTCTTTGAATTAAAAACTTAT-TTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACG
* * * * * * * *
928 AACTTCCGAACGTGGCAAGCTTTTACGAGTTCTTTTATAACTTCAG-TTCAATAAAG---TGATG
65 AACTTCTGAAC-TTGAAAACTTTTACCAGTTCTTCTATAACTTC-GTTTCATTAAAGTATTCATG
* * * ** * **
989 ---ATTCATTCCTTCGAGAAATTTTTTGAAAATTTAATGCTTGGGAAATCGCATCATTTTTTTCT
128 ACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCT
* *
1051 AAACTA-TTTGTCATTTGGTAAGCA
192 AAA-TAGTTTGTCATTTTGTAAACA
** * * * * *
1075 ACTTTTGGGGTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGATATTGGATGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* * * * * * * *
1140 ACTTCTAAACTTGATAACTTTGACGACTTCTTCTATAACTTC-TGTTCTTTAAAGTTTTCATTAC
66 ACTTCTGAACTTGAAAACTTTTACCAGTTCTTCTATAACTTCGT-TTCATTAAAGTATTCATGAC
* * * * * **
1204 GATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTAGGGAAATCACATCATTTTGTCTACT
130 AATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
* *
1269 TAGTTTGTCATTTGGTATACA
195 TAGTTTGTCATTTTGTAAACA
* * * *
1290 ACTTTTGGTCATTT-AATTAAAAACTTATTTACGTGAGAATT-TATTATCTCTTGGATCATGGAC
1 ACTTTTGGTC-TTTGAATTAAAAACTTATTTACGTGAGAGTTGT-TTCTCTCTTGGTTCTTGGAC
* * * * * * * *
1353 AAACTTCCT-AACTTCACAAACTTTTGCCAGTTGTTCTCTAACTTTGGTTCATTAAAGTATTTAT
64 GAACTT-CTGAACTTGA-AAACTTTTACCAGTTCTTCTATAACTTCGTTTCATTAAAGTATTCAT
* * * *
1417 GACAATCCACTCCTTCGAGTAATTTTTTGAACATTCTATGCTCGGGAAATTGCATCATTTGGTCT
127 GACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* *
1482 AAATAGTTTGCCATTTTGTTAACA
192 AAATAGTTTGTCATTTTGTAAACA
* * * * *
1506 ACTTTTGGT-TTATAAATTAAAAAGTGATTTATGTGAGAGTTTTTTCTCTCTTTGG-TCTTGGAC
1 ACTTTTGGTCTT-TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTC-TTGGTTCTTGGAC
**********************************
1569 GAACTT-TCGAACTTGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
64 GAACTTCT-GAACTTGA--------------AAACTTTTACCAGTTCTTCTATAACTTCGTTTCA
*** * * ** * **** * * * * *
1633 NNNAAGTTTTACGA-GTTCTTTTAAAAC-TTCAATTCCTTAAAGTATTCATGAAGA-TCCATTCC
114 TTAAAGTATT-C-ATG-AC----AATCCATTC-CTTCGAGCAATTTTTT--GAACATTCCA-TGC
* * *
1695 TTC-GAACAATTTTCCCAACATTCCAAGCACGGGAAATCGCATCATTATGTCTAAATAGTTTGTC
168 -TCGGGA-AA---T--C-GC----------------AT--CAT--TT-GGTCTAAATAGTTTGTC
* *
1759 ATTTTCTAAATA
204 ATTTTGTAAACA
* * * * * * * *
1771 AATTTTGGTCCTTGAATTTAAAACCTATTTATGTGAGAGTTGTTTCTCTTTTGGCTCTTAGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
** * * * *
1836 ACTTCCAAACTAGAAATACTTTTACGAGTTCTTCTATAACTTTGATTTC-TTAAAGTATTCAAGA
66 ACTTCTGAACTTGAAA-ACTTTTACCAGTTCTTCTATAACTTCG-TTTCATTAAAGTATTCATGA
* * *
1900 CAATCCATTCCTTAGAGCAATTTTTGGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAA
129 CAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * *
1965 ATACTTTGTCATTTTCTAAACG
194 ATAGTTTGTCATTTTGTAAACA
** * *
1987 ACTTTTGGTCTTTGAATGCAATACTTATTTGCGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* * *
2052 ACTTCTGAACTTGGAAAACTTTTACCAGTTCATATATAACTTTCG-TTCCTTAAAGTATTCATGA
66 ACTTCTGAACTT-GAAAACTTTTACCAGTTCTTCTATAAC-TTCGTTTCATTAAAGTATTCATGA
* * *
2116 CAATACATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
129 CAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
*
2181 ATAGTTTGCCATTTTGTAAACA
194 ATAGTTTGTCATTTTGTAAACA
* * * * *
2203 ACTTTTGGTCTTTAAATTAAAATCTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGA
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
* * * * * * * *
2268 ACTT-TCAAACTTGATGAAGTTTTGCAAGTTCTTTTAAAACTTCAG-TTCCTTAAAGTATTCATG
66 ACTTCT-GAACTTGA-AAACTTTTACCAGTTCTTCTATAACTTC-GTTTCATTAAAGTATTCATG
* * * * * * * * * **
2331 ACGATCCATTCCTTCGTGCAATTGTGTGAGCATTCCATGCACAGGTAATCACATCATTTCTTCTA
128 ACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
* *
2396 AATAGTTAGTCATTTTCTAAACA
193 AATAGTTTGTCATTTTGTAAACA
* * *
2419 ACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAGGTT-TTT-TCTCTTGGCTCTTAGACG
1 ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA-GTTGTTTCTCTCTTGGTTCTTGGACG
** * * * * * * *
2482 AACTTCCAAACTTTATATACTTTTACGAGTTCTACTATTACTTCGATTTCA-TAAGGTATTCAAG
65 AACTTCTGAACTTGA-AAACTTTTACCAGTTCTTCTATAACTTCG-TTTCATTAAAGTATTCATG
* * * * *
2546 ATAATCCATTCCTTAGAGTAATTTTTTGAACATTTCATGCTCGGGAAATCGCATCTTTTGGTCT
128 ACAATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
2610 TTGAATGAAA
Statistics
Matches: 1833, Mismatches: 441, Indels: 231
0.73 0.18 0.09
Matches are distributed among these distances:
205 4 0.00
206 37 0.02
207 3 0.00
208 3 0.00
210 39 0.02
211 188 0.10
212 5 0.00
213 3 0.00
214 7 0.00
215 255 0.14
216 1087 0.59
217 23 0.01
219 3 0.00
221 2 0.00
229 6 0.00
230 1 0.00
231 2 0.00
234 2 0.00
235 11 0.01
236 3 0.00
237 9 0.00
238 5 0.00
240 1 0.00
241 1 0.00
243 4 0.00
244 8 0.00
245 4 0.00
246 10 0.01
247 3 0.00
250 2 0.00
251 2 0.00
252 6 0.00
260 2 0.00
262 3 0.00
264 6 0.00
265 82 0.04
266 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.39
Consensus pattern (215 bp):
ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGA
ACTTCTGAACTTGAAAACTTTTACCAGTTCTTCTATAACTTCGTTTCATTAAAGTATTCATGACA
ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
AGTTTGTCATTTTGTAAACA
Found at i:2735 original size:181 final size:180
Alignment explanation
Indices: 2420--2790 Score: 464
Period size: 181 Copynumber: 2.1 Consensus size: 180
2410 TTCTAAACAA
* *
2420 CTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAGGTTTTTTCTCTTGGCTCTTAGACGAAC
1 CTTTTGGTCTTTGAATGAAAAACCTATTTACGTGAGAGGTTTTTTCTCCTGGCTCTTAGACGAAC
* * * * * *
2485 TTCCAAACTTTATATACTTTTACGAGTTCTACTATTACTTCGATTTCATAAGGTATTCAAGATAA
66 TTCCAAACTTTATAAACTTTTACCAGTTCTACTATAACTTCGATTCCATAAAGTATTCAAGACAA
* * *
2550 TCCATTCCTT-AGAGTAATTTTTTGAACATTTCATGCTCGGGAAATCGCAT
131 TCCATTCCTTCA-AGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCAT
* * *
2600 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGA-GTTATTTCTCTCCTGGTTCTTGGACGA
1 CTTTTGGTCTTTGAATGAAAAACCTATTTACGTGAGAGGTT-TTT-TCTCCTGGCTCTTAGACGA
** * *
2664 ACTTCTGAACTTGTA-AAACTTTTACCAGTTC-ATCTATAACTTTCG-TTCCTTAAAGTATTCAT
64 ACTTCCAAACTT-TATAAACTTTTACCAGTTCTA-CTATAAC-TTCGATTCCATAAAGTATTCAA
* *
2726 GACAATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGTAT
126 GACAATCCATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCAT
*
2781 CATTTGGTCT
1 CTTTTGGTCT
2791 AAATAGTTTG
Statistics
Matches: 164, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
179 3 0.02
180 39 0.24
181 115 0.70
182 7 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (180 bp):
CTTTTGGTCTTTGAATGAAAAACCTATTTACGTGAGAGGTTTTTTCTCCTGGCTCTTAGACGAAC
TTCCAAACTTTATAAACTTTTACCAGTTCTACTATAACTTCGATTCCATAAAGTATTCAAGACAA
TCCATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCAT
Found at i:3663 original size:421 final size:423
Alignment explanation
Indices: 3166--4340 Score: 1311
Period size: 429 Copynumber: 2.8 Consensus size: 423
3156 CAATTTTTTG
* * *
3166 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATACTTTGTCATTTTCTAAACGACTTT
1 AACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATA-TTTGTCA-TTTCTAAACAACTTT
* * * * *
3231 TGGTATTTGAATGAAAAACTTATTTACGTGGGAGTTATTTCTCTCCTGGTTCTTGGACGAACTTC
64 TGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGATGAACTTC
* * *
3296 TGAACTTGTA-AAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACAATC
129 TAAACTTG-ACAAACTTTTACGAGTTCTTCTATAACTTTCGTTCCTTAAAGTATTCATGACAATC
* *
3360 CATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGT
193 CATTCCTTCAAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGT
3425 TTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTG-TT-TC
258 TTGTCATTTTGTAAACAACTTTTGGTCTTT-AATTAAAATCTTATTTACTT-AGAATTGTTTATC
** *
3488 -T-CTCTT-TGAACTTTCGAACTTGATTAA-GTTT-CGCATGTTCTTTTA-AACCTTCAGTTCCA
321 TTGCTCTTGTGAACTTTCGAACTTGACAAACATTTACG-A-GTTCTTTTATAA-CTTCAGTTCCA
*
3547 TAAAGTATTAATAACGATCAATTCCTTCTAGCAATTTTCCA
383 TAAAGTATTAATAACGATCAATTCCTTCGAGCAATTTTCCA
* *
3588 AACATTGCATGCACGGGAAATCGCATCATTTTGTCTAAATAGTTTGTCATTTCTAAACAACTTTT
1 AACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATA-TTTGTCATTTCTAAACAACTTTT
* * * * * *
3653 AGTCTTTGAATTAAAAACCTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTAGATGAACTTCC
65 GGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGATGAACTTCT
* * * * * * * *
3718 AAACTTGACGAACTTCTATGAGTTCTTCAATAACTTTGGTTTCTTATAGTATTCAGGACAATCCA
130 AAACTTGACAAACTTTTACGAGTTCTTCTATAACTTTCGTTCCTTAAAGTATTCATGACAATCCA
* * * *
3783 TTCATT-ATAGCAGTTTTTTGAACATTCCATGCTCGGGAAGGT-GCATCATTTGGTCTAAATACT
195 TTCCTTCA-AGCAATTTTTTGAACATTCCATGCTCGGGAA-ATCGCATCATTTGGTCTAAATAGT
* * * * * * *
3846 TTATCATTTTCTAAACTACTTTTGGTCTGTGAA-TGAAATACTTTTTTA-TTAGAGTTGTTTTTA
258 TTGTCATTTTGTAAACAACTTTTGGTCT-TTAATTAAAAT-CTTATTTACTTAGAATTG--TTTA
* * *
3909 TCTTGGTTCTTGGATGAACTTTCGAACTTGGCAAACATTTACGAGTTCTTTTATAACTTTAGTTC
319 TCTT-GCTCTT-G-TGAACTTTCGAACTTGACAAACATTTACGAGTTCTTTTATAACTTCAGTTC
* * * ***
3974 CATAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTTG
381 CATAAAGTATTAATAACGATCAATTCCTTCGAGCAATTTTCCA
* ** * * *
4017 AACATTTCATGCTTTGGAAATCGCATAATTTTTTCTAAACTATTTGTCATTTGGTAAACAACTTT
1 AACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAA-TATTTGTCATTT-CTAAACAACTTT
* * ***
4082 TGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGAAATTGGATGAACTTC
64 TGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGATGAACTTC
* * *
4147 TAAACTTGACAAACTTTAACGAGTTCTTCTATAAC-TTCGATTCTTTAAAGTATTCAT-ACGATC
129 TAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTTCG-TTCCTTAAAGTATTCATGACAATC
* * * * * * * *
4210 CATTCCTTCGAGTAATTTTTTGAACTTTCCATGCTTGGGAAATCACACCATTTTGTCTACATAGT
193 CATTCCTTCAAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGT
* * * *
4275 TTGTCATTTGGTATACAACTTTTGGTCATTTAATTAAAAACTTATTTACGTGAGAATT-TATTAT
258 TTGTCATTTTGTAAACAACTTTTGGTC-TTTAATTAAAATCTTATTTAC-TTAGAATTGT-TTAT
4339 CT
320 CT
4341 C
Statistics
Matches: 619, Mismatches: 106, Indels: 49
0.80 0.14 0.06
Matches are distributed among these distances:
419 6 0.01
420 9 0.01
421 208 0.34
422 48 0.08
423 2 0.00
424 1 0.00
426 4 0.01
428 2 0.00
429 210 0.34
430 121 0.20
431 8 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (423 bp):
AACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATATTTGTCATTTCTAAACAACTTTTG
GTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGATGAACTTCTA
AACTTGACAAACTTTTACGAGTTCTTCTATAACTTTCGTTCCTTAAAGTATTCATGACAATCCAT
TCCTTCAAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTGTAAACAACTTTTGGTCTTTAATTAAAATCTTATTTACTTAGAATTGTTTATCTTGCT
CTTGTGAACTTTCGAACTTGACAAACATTTACGAGTTCTTTTATAACTTCAGTTCCATAAAGTAT
TAATAACGATCAATTCCTTCGAGCAATTTTCCA
Found at i:3841 original size:215 final size:215
Alignment explanation
Indices: 2600--4329 Score: 1280
Period size: 206 Copynumber: 8.2 Consensus size: 215
2590 GAAATCGCAT
* * * *
2600 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTATTTCTCTCCTGGTTCTTGGACGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* * * *
2665 CTTCTGAACTTGTA-AAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGAC
66 CTTCCGAACTTG-ACAAAC-TTTACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGAC
* * * * *
2729 AATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGTATCATTTGGTCTAAA
129 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
* *
2794 TAGTTTGCCATTTTGTAAACAA
194 TAGTTTGTCATTTTCTAAACAA
* * * * * *
2816 CTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTG--TTTCTC-----TCTT---TGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
** * * * * *
2871 CTTCCGAACTTGATTAAGTTT-CGCAAGTTCTTTTA-AACCTTCAGTTCCATAAAGTATTCATAA
66 CTTCCGAACTTGACAAACTTTACG--AGTTCTTCTATAA-CTTTAGTTCCTTAAAGTATTCATGA
* * *** * * *
2934 CGATCAATTCCTTCTAGCAATTTTCCAAACATTCCATGCACGGGAAATCGAATCATTTTGTCTAA
128 CGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
*
2999 ATAGTTTGTCA-TTTCTATACAA
193 ATAGTTTGTCATTTTCTAAACAA
* * *
3021 CTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTAGATGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* **************************************************
3086 CTTCCAAACTTGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
66 CTTCCGAACTTGACAAACTTTACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGACGA
*
3151 T--A-------GAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
131 TCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATA
* *
3207 CTTTGTCATTTTCTAAACGA
196 GTTTGTCATTTTCTAAACAA
* * * * * *
3227 CTTTTGGTATTTGAATGAAAAACTTATTTACGTGGGAGTTATTTCTCTCCTGGTTCTTGGACGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* * * *
3292 CTTCTGAACTTGTA-AAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGAC
66 CTTCCGAACTTG-ACAAAC-TTTACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGAC
* * * *
3356 AATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
129 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
*
3421 TAGTTTGTCATTTTGTAAACAA
194 TAGTTTGTCATTTTCTAAACAA
* * * * * *
3443 CTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTG--TTTCTC-----TCTT---TGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* ** * * * * * *
3498 CTTTCGAACTTGATTAAGTTT-CGCATGTTCTTTTA-AACCTTCAGTTCCATAAAGTATTAATAA
66 CTTCCGAACTTGACAAACTTTACG-A-GTTCTTCTATAA-CTTTAGTTCCTTAAAGTATTCATGA
* * *** * * *
3561 CGATCAATTCCTTCTAGCAATTTTCCAAACATTGCATGCACGGGAAATCGCATCATTTTGTCTAA
128 CGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
3626 ATAGTTTGTCA-TTTCTAAACAA
193 ATAGTTTGTCATTTTCTAAACAA
* * * *
3648 CTTTTAGTCTTTGAATTAAAAACCTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTAGATGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* * * * * * * * *
3713 CTTCCAAACTTGACGAACTTCTATGAGTTCTTCAATAACTTTGGTTTCTTATAGTATTCAGGACA
66 CTTCCGAACTTGACAAACTT-TACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGACG
* ** * *
3778 ATCCATTCATTATAGCAGTTTTTTGAACATTCCATGCTCGGGAAGGT-GCATCATTTGGTCTAAA
130 ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAA-ATCGCATCATTTGGTCTAAA
* * *
3842 TACTTTATCATTTTCTAAACTA
194 TAGTTTGTCATTTTCTAAACAA
* * * * *
3864 CTTTTGGTCTGTGAATGAAATACTTTTTTA--TTAGAGTTGTTTTTATCTTGGTTCTTGGATGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
* * * *
3927 CTTTCGAACTTGGCAAACATTTACGAGTTCTTTTATAACTTTAGTTCCATAAAGTATTCATGACG
66 CTTCCGAACTTGACAAAC-TTTACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGACG
* ** * **
3992 ATCCATTCCTTCGAGCAATTTTTTGAACATTTCATGCTTTGGAAATCGCATAATTTTTTCTAAAC
130 ATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA-
**
4057 TA-TTTGTCATTTGGTAAACAA
194 TAGTTTGTCATTTTCTAAACAA
* * * ***
4078 CTTTTGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGAAATTGGATGAA
1 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
** * *
4143 CTTCTAAACTTGACAAACTTTAACGAGTTCTTCTATAAC-TTCGATTCTTTAAAGTATTCAT-AC
66 CTTCCGAACTTGACAAACTTT-ACGAGTTCTTCTATAACTTTAG-TTCCTTAAAGTATTCATGAC
* * * * * * *
4206 GATCCATTCCTTCGAGTAATTTTTTGAACTTTCCATGCTTGGGAAATCACACCATTTTGTCTACA
129 GATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
** *
4271 TAGTTTGTCATTTGGTATACAA
194 TAGTTTGTCATTTTCTAAACAA
*
4293 CTTTTGGTCATTT-AATTAAAAACTTATTTACGTGAGA
1 CTTTTGGTC-TTTGAATGAAAAACTTATTTACGTGAGA
4330 ATTTATTATC
Statistics
Matches: 1153, Mismatches: 305, Indels: 113
0.73 0.19 0.07
Matches are distributed among these distances:
204 2 0.00
205 154 0.13
206 296 0.26
207 14 0.01
209 9 0.01
212 9 0.01
213 1 0.00
214 185 0.16
215 236 0.20
216 246 0.21
217 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.39
Consensus pattern (215 bp):
CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTGTTTTTCTCTTGGTTCTTGGATGAA
CTTCCGAACTTGACAAACTTTACGAGTTCTTCTATAACTTTAGTTCCTTAAAGTATTCATGACGA
TCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATA
GTTTGTCATTTTCTAAACAA
Found at i:3929 original size:627 final size:622
Alignment explanation
Indices: 2600--4128 Score: 1885
Period size: 627 Copynumber: 2.4 Consensus size: 622
2590 GAAATCGCAT
* * *
2600 CTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGTTATTTCTCTCCTGGTTCTTGGACGAA
1 CTTTTGGTATGTGAATGAAAAACTTATTTAC-TGAGAGTTATTTCTATCCTGGTTCTTGGA-GAA
2665 CTTCTGAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACA
64 ---CTGAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACA
*
2730 ATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGTATCATTTGGTCTAAAT
126 ATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
*
2795 AGTTTGCCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTT
191 AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTT
2860 CTCTCTTTGAACTTCCGAACTTGATTAAGTTTCGCAAGTTCTTTTAAACCTTCAGTTCCATAAAG
256 CTCTCTTTGAACTTCCGAACTTGATTAAGTTTCGCAAGTTCTTTTAAACCTTCAGTTCCATAAAG
*
2925 TATTCATAACGATCAATTCCTTCTAGCAATTTTCCAAACATTCCATGCACGGGAAATCGAATCAT
321 TATTAATAACGATCAATTCCTTCTAGCAATTTTCCAAACATTCCATGCACGGGAAATCGAATCAT
* *
2990 TTTGTCTAAATAGTTTGTCATTTCTATACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTG
386 TTTGTCTAAATAGTTTGTCATTTCTAAACAACTTTTAGTCTTTGAATTAAAAACCTATTTACGTG
*******************
3055 AGAGTTGTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTTGACANNNNNNNNNNNNNNNNNNN
451 AGAGTTGTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTTGACAAGTTCTTCAATAACTTTGG
*******************************
3120 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGAGCAATTTTTTGAACATTCCATGCTCGAGAA
516 TTTCTTATAGTATTCAGGACAATCCATTCATTAGAGCAATTTTTTGAACATTCCATGCTCGAGAA
*
3185 ATCGCATCATTTGGTCTAAATACTTTGTCATTTTCTAAACGA
581 ATCGCATCATTTGGTCTAAATACTTTATCATTTTCTAAACGA
* * *
3227 CTTTTGGTATTTGAATGAAAAACTTATTTACGTGGGAGTTATTTCTCTCCTGGTTCTTGGACGAA
1 CTTTTGGTATGTGAATGAAAAACTTATTTAC-TGAGAGTTATTTCTATCCTGGTTCTTGGA-GAA
3292 CTTCTGAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACA
64 ---CTGAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACA
3357 ATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
126 ATCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAT
3422 AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTT
191 AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTT
* *
3487 CTCTCTTTGAACTTTCGAACTTGATTAAGTTTCGCATGTTCTTTTAAACCTTCAGTTCCATAAAG
256 CTCTCTTTGAACTTCCGAACTTGATTAAGTTTCGCAAGTTCTTTTAAACCTTCAGTTCCATAAAG
* *
3552 TATTAATAACGATCAATTCCTTCTAGCAATTTTCCAAACATTGCATGCACGGGAAATCGCATCAT
321 TATTAATAACGATCAATTCCTTCTAGCAATTTTCCAAACATTCCATGCACGGGAAATCGAATCAT
3617 TTTGTCTAAATAGTTTGTCATTTCTAAACAACTTTTAGTCTTTGAATTAAAAACCTATTTACGTG
386 TTTGTCTAAATAGTTTGTCATTTCTAAACAACTTTTAGTCTTTGAATTAAAAACCTATTTACGTG
3682 AGAGTTGTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTTGACGAACTTCTATGAGTTCTTCA
451 AGAGTTGTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTT---G-A---C-A--AGTTCTTCA
* *
3747 ATAACTTTGGTTTCTTATAGTATTCAGGACAATCCATTCATTATAGCAGTTTTTTGAACATTCCA
506 ATAACTTTGGTTTCTTATAGTATTCAGGACAATCCATTCATTAGAGCAATTTTTTGAACATTCCA
* * *
3812 TGCTCGGGAAGGT-GCATCATTTGGTCTAAATACTTTATCATTTTCTAAACTA
571 TGCTCGAGAA-ATCGCATCATTTGGTCTAAATACTTTATCATTTTCTAAACGA
* * * * * * *
3864 CTTTTGGTCTGTGAATGAAATACTTTTTTA-TTAGAGTTGTTTTTATCTTGGTTCTTGGATGAAC
1 CTTTTGGTATGTGAATGAAAAACTTATTTACTGAGAGTTATTTCTATCCTGGTTCTTGGA-GAAC
** * * * * * * *
3928 TTTCGAACTTGGCAAACATTTACGAGTTCTTTTATAACTTTAGTTCCATAAAGTATTCATGACGA
65 --T-GAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACAA
* * * * ** * **
3993 TCCATTCCTTCGAGCAATTTTTTGAACATTTCATGCTTTGGAAATCGCATAATTTTTTCTAAACT
127 TCCATTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA-T
* * * * * *
4058 A-TTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGTTT
191 AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTT
4122 CTCTCTT
256 CTCTCTT
4129 GGAAATTGGA
Statistics
Matches: 785, Mismatches: 102, Indels: 22
0.86 0.11 0.02
Matches are distributed among these distances:
627 486 0.62
630 1 0.00
631 1 0.00
632 1 0.00
634 2 0.00
635 197 0.25
636 2 0.00
637 94 0.12
638 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.39
Consensus pattern (622 bp):
CTTTTGGTATGTGAATGAAAAACTTATTTACTGAGAGTTATTTCTATCCTGGTTCTTGGAGAACT
GAACTTGTAAAACTTTTACCAGTTCATCTATAACTTTCGTTCCTTAAAGTATTCATGACAATCCA
TTCCTTCAAGCAATTTTCTGAACGTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTT
GTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACTTAAGAATTGTTTCTCTC
TTTGAACTTCCGAACTTGATTAAGTTTCGCAAGTTCTTTTAAACCTTCAGTTCCATAAAGTATTA
ATAACGATCAATTCCTTCTAGCAATTTTCCAAACATTCCATGCACGGGAAATCGAATCATTTTGT
CTAAATAGTTTGTCATTTCTAAACAACTTTTAGTCTTTGAATTAAAAACCTATTTACGTGAGAGT
TGTTTTTCTCTTGGTTCTTAGATGAACTTCCAAACTTGACAAGTTCTTCAATAACTTTGGTTTCT
TATAGTATTCAGGACAATCCATTCATTAGAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGC
ATCATTTGGTCTAAATACTTTATCATTTTCTAAACGA
Done.