Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008183.1 Kokia drynarioides strain JFW-HI SEQ_122842, 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: 2343
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:395 original size:216 final size:216
Alignment explanation
Indices: 1--2343 Score: 2580
Period size: 216 Copynumber: 10.9 Consensus size: 216
* * * * * * *
1 TTCGAACTTCTCAAACTTTTACGAGTTATTTTTTAACTTC-AATTCCCTAAAGTATTCAACAAGA
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGA-TCCTTAAAGTATTCAAGACGA
* * * * *
65 TCCATT--TTCTAGAGCAATTTT-TCGAACATTCCATCCTTGGGAAATTGCATCATTTGATCTAA
65 TCCATTCCTTC--GAGCAATTTTCT-GAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAA
* * * *
127 ATAGATTGTCATTTTGTAAACAAGTTCTGGTCTTTGAATGAAAAAGTTATTTACGTGAGAATTGT
127 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
*
192 TTCTCTCTTTGTTCTTGGATGAACT
192 TTCTCTCTTTGTTCTTGGACGAACT
* * *
217 TTC-AAGCTTGTCAAACTTTTACTAGTTCTTTTATAACTTCTGATCCTTAAAGTATTCAAGACTA
1 TTCGAA-CTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGA
* * * *
281 TCCATTCCTTCGAGCAATTTTCTAAATATTCCATGCTCGGCAAATCGCATCATTTGGCCTAAATG
65 TCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAATA
* ** * *
346 GTTTGTCATTCTAAAAAAAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
130 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* *
411 TCTCTTTG-TCTCTGTACAAACT
195 TCTCTTTGTTCT-TGGACGAACT
* * * * * *
433 TTCTAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTC-GATTCCCTAAAGTATTCAACAAGA
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGA-TCCTTAAAGTATTCAAGACGA
** * * * * *
497 AACATTCGTTAGAGCAATTTTCTGAACATTCCGTGCTTGAG-AAATCGCATCATTTGGTTTAAAT
65 TCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCG-GCAAATCGCATCATTTGGTCTAAAT
* ** * **
561 ATTTTGTCATTTTGTTTACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGCAT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * *
626 CACTCTTGGTTCATGGACGAAC-
194 CTCTCTTTGTTCTTGGACGAACT
* * * ****
648 TCCTGAACTTGTCAAACTTTTAGGAGATCTTTTATAACTTAACTTCCTTAAAGTATTCAAGACGA
1 TTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGA
* * * *** * * *
713 CCCATTCCTTTGAG-TATTTTCTGAACATTCCATGCTCAAAAAATTGCATCATTCGGTCTAAAGA
65 TCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAATA
* * * *
777 GTTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAATAAAAAACTTATTTGCGTGAGAATTGTTTC
130 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* *
842 TCTCTTTCTTCTTGGATGAACT
195 TCTCTTTGTTCTTGGACGAACT
* * * * * * *
864 TTCAAACGTGTCAAACTTTTACGACTTATTTTATAACTTC-CATTCCTTAAAGTATTGAAGGCGA
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGA-TCCTTAAAGTATTCAAGACGA
* * ** * * * *
928 TCCAGTCCTTCGAGCAGTTTTCCAAACATTCCTTGCTCAAG-AAATCACAGCATTTGGTCTAAAT
65 TCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTC-GGCAAATCGCATCATTTGGTCTAAAT
* * *
992 AGATTGTCATTTAT-TAAACAGGTTTTGGTCGTTGAATTAAAAACTTATTTACGTGAGAATTGTT
129 AGTTTGTCATTT-TGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
1056 TCTCTCTTTGTTCTTGGACGAACT
193 TCTCTCTTTGTTCTTGGACGAACT
* * * * *
1080 TCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCATTAAAGTATTCAAGATGAT
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGAT
* ** * * * * *
1145 CTATTTTTTCGAGCAATTTTCTAAACATTCCATGCTCAAG-AAATCACATCAATTGGCCTAAATA
66 CCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTC-GGCAAATCGCATCATTTGGTCTAAATA
* * * * *
1209 ATTTGTCGTTTTGCAAACAAGTTTTGGCCTTTAAATTAAAAACTTA-TTACGTGAGAATTGTTTC
130 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* *
1273 TCTCTTAGTTCTTGGACGAACA
195 TCTCTTTGTTCTTGGACGAACT
* * ** * * * * *
1295 TTCGAACTTGTCAAACTTTTACGAGTTTTTTTTTAACTTTAGTTCCCTAAAGTATTCCACAAGAT
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGAT
* * * * **
1360 CCATT--TTCTAGAGCAATTTTCCGAACATTCCATCCTTGGGAAATTACATCATTTGGTCTAAAT
66 CCATTCCTTC--GAGCAATTTTCTGAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAAT
* * * *
1423 AGTTTGTTATTTTGTAAACAAGTTTTTGTCTTTGAATTCAGAACTTATTTACGTGAGAATTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
1488 CTCTCTTTGTTCTTGGACGAACT
194 CTCTCTTTGTTCTTGGACGAACT
* * *
1511 TCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAGGACGAT
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGAT
* ** * *
1576 CCATTCCTTTC-AGCAATATTCCAAATATTCTATGCTCGGCAAATCGCATC---TGGTCTAAATA
66 CCATTCC-TTCGAGCAATTTTCTGAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAATA
* * * * *
1637 GTTTGTCATTTTGCAAACAAGTTTTTGTCGTTGAATTGAAAACTTATTTACGTGAGAATTGCTTC
130 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
*
1702 TCTCTTTGTTCTTGGACGAGCT
195 TCTCTTTGTTCTTGGACGAACT
** * * * * * * * * *
1724 CCCAAACTTGTCAAACTTTTACAAGTTATTTTTTAAATTC-TATTCCCTAAAGTAATCAAGAAGA
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGA-TCCTTAAAGTATTCAAGACGA
* ** * *
1788 TCCATTCCTTTGAGCAATTTT-TCGAACATTTAATCCTCGGGAAATCGCATCATTTGGTCTAAAT
65 TCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAAT
* * * *
1852 AGTTTGTCATTTTGTATACAAGTTCTGGTCTTTGAATTGAAAAGTTATTTACGTGAGAATTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
*
1917 CTCTCTTTGTTCTTGGATGAACT
194 CTCTCTTTGTTCTTGGACGAACT
* * *
1940 TTCGAACTTGTCAAACTTTTACAAGTTCTTTGATAACTTCGGATCCTCAAAGTATTCAAGACGAT
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGAT
* * * *
2005 CCATTCTTTCGCGCAATTTT-TCGAACATTCCATGCTC-GCGAAATCGTATCATTTGGTCTATAT
66 CCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGGC-AAATCGCATCATTTGGTCTAAAT
* *
2068 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGGGAACTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * *
2133 CCCTCCTTGTTCTTTGATGAACT
194 CTCTCTTTGTTCTTGGACGAACT
* * *
2156 TTCGAACTTGTCAAACTTTTACTTA-TTCTTTTTTAACTTCGGATCCTTAAAGTATTTAAGACGA
1 TTCGAACTTGTCAAACTTTTAC-GAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGA
** * * *
2220 TCCATTCCTTTTAGCAATTTT-TCGAATATTCCATGCTCGACAAATCGTATCATTTGGTCTAAAT
65 TCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAAT
* * *
2284 AGTTTGTCGTTTTGCAAACAAGTTTTGGTCGTTGAATTAAAAACTTATTTACGTGAGAAT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
Statistics
Matches: 1784, Mismatches: 306, Indels: 74
0.82 0.14 0.03
Matches are distributed among these distances:
212 3 0.00
213 183 0.10
214 2 0.00
215 358 0.20
216 1220 0.68
217 12 0.01
218 3 0.00
219 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (216 bp):
TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGATCCTTAAAGTATTCAAGACGAT
CCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGGCAAATCGCATCATTTGGTCTAAATAG
TTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
CTCTTTGTTCTTGGACGAACT
Found at i:958 original size:431 final size:431
Alignment explanation
Indices: 5--2343 Score: 2749
Period size: 431 Copynumber: 5.4 Consensus size: 431
1 TTCG
* *
5 AACTTCTCAAACTTTTACGAGTTATTTTTTAACTTCAATTCCCTAAAGTATTCAACAAGATCCAT
1 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGATCCAT
* * * * * *
70 T--TTCTAGAGCAATTTTTCGAACATTCCATCCTTGGGAAATTGCATCATTTGATCTAAATAGAT
66 TCCTTC--GAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTT
* * *
133 TGTCATTTTGTAAACAAGTTCTGGTCTTTGAATGAAAAAGTTATTTACGTGAGAATTGTTTCTCT
129 TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
* * * **
198 CTTTGTTCTTGGATGAACT-TTCAAGCTTGTCAAACTTTTACTAGTTCTTTTATAACTTCTGATC
194 CTTTGTTCTTGGACGAACTCCTGAA-CTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATC
* * * *
262 CTTAAAGTATTCAAGACTATCCATTCCTTCGAGCAATTTTCTAAATATTCCATGCTCGGCAAATC
258 CTTAAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTCTAAACATTCCATGCTCGACAAATC
* * * ** * *
327 GCATCATTTGGCCTAAATGGTTTGTCATTCTAAAAAAAAATTTTGGTCTTTGAATTAAAAACTTA
323 GCATCA-TTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTA
* * *
392 TTTACGTGAGAATTGTTTCTCTCTTTG-TCTCTGTACAAACTTTCT
387 TTTACGTGAGAATTGTTTCTCTCTTTGTTCT-TGGACGAACTTTCA
**
437 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGAAACAT
1 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGATCCAT
* * * * * * * *
502 TCGTTAGAGCAATTTTCTGAACATTCCGTGCTTGAGAAATCGCATCATTTGGTTTAAATATTTTG
66 TCCTTCGAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
** * ** *
567 TCATTTTGTTTACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGCATCACTCT
131 TCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * ** * ***
632 TGGTTCATGGACGAACTCCTGAACTTGTCAAACTTTTAGGAGATCTTTTATAACTTAACTTCCTT
196 TTGTTCTTGGACGAACTCCTGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCCTT
* * * * * *
697 AAAGTATTCAAGACGACCCATTCCTTTGAG-TATTTTCTGAACATTCCATGCTCAAAAAATTGCA
261 AAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTCTAAACATTCCATGCTCGACAAATCGCA
* * * *
761 TCATTCGGTCTAAAGAGTTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAATAAAAAACTTATTT
326 TCATT-GGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
* * *
826 GCGTGAGAATTGTTTCTCTCTTTCTTCTTGGATGAACTTTCA
390 ACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCA
* * * * * * *** *
868 AACGTGTCAAACTTTTACGACTTATTTTATAACTTCCATTCCTTAAAGTATTGAAGGCGATCCAG
1 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGATCCAT
* * * * * * * *
933 TCCTTCGAGCAGTTTTCCAAACATTCCTTGCTCAAGAAATCACAGCATTTGGTCTAAATAGATTG
66 TCCTTCGAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* *
998 TCATTTAT-TAAACAGGTTTTGGTCGTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
131 TCATTT-TGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
*
1062 TTTGTTCTTGGACGAACTTCC-GAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCA
195 TTTGTTCTTGGACGAAC-TCCTGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCC
* * * * *
1126 TTAAAGTATTCAAGATGATCTATT-TTTTCGAGCAATTTTCTAAACATTCCATGCTCAAGAAATC
259 TTAAAGTATTCAAGACGATCCATTCCTTT-GAGCAATTTTCTAAACATTCCATGCTCGACAAATC
* * * * * * *
1190 ACATCAATTGGCCTAAATAATTTGTCGTTTTGCAAACAAGTTTTGGCCTTTAAATTAAAAACTTA
323 GCATC-ATTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTA
* * *
1255 -TTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACATTCG
387 TTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCA
* * *
1299 AACTTGTCAAACTTTTACGAGTTTTTTTTTAACTT-TAGTTCCCTAAAGTATTCCACAAGATCCA
1 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGA-TTCCCTAAAGTATTCAACAAGATCCA
* * **
1363 TT--TTCTAGAGCAATTTTCCGAACATTCCATCCTTGGGAAATTACATCATTTGGTCTAAATAGT
65 TTCCTTC--GAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGT
* * * *
1426 TTGTTATTTTGTAAACAAGTTTTTGTCTTTGAATTCAGAACTTATTTACGTGAGAATTGTTTCTC
128 TTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC
*
1491 TCTTTGTTCTTGGACGAACTTCC-GAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGAT
193 TCTTTGTTCTTGGACGAAC-TCCTGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGAT
* * * * * * *
1555 CCTTAAAGTATTCAGGACGATCCATTCCTTTCAGCAATATTCCAAATATTCTATGCTCGGCAAAT
257 CCTTAAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTCTAAACATTCCATGCTCGACAAAT
* * * *
1620 CGCATC--TGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTTGTCGTTGAATTGAAAACTTA
322 CGCATCATTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTA
* * **
1683 TTTACGTGAGAATTGCTTCTCTCTTTGTTCTTGGACGAGCTCCCA
387 TTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCA
* * * * *
1728 AACTTGTCAAACTTTTACAAGTTATTTTTTAAATTCTATTCCCTAAAGTAATCAAGAAGATCCAT
1 AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGATCCAT
* * ** *
1793 TCCTTTGAGCAATTTTTCGAACATTTAATCCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTG
66 TCCTTCGAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * *
1858 TCATTTTGTATACAAGTTCTGGTCTTTGAATTGAAAAGTTATTTACGTGAGAATTGTTTCTCTCT
131 TCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* * * * *
1923 TTGTTCTTGGATGAACT-TTCGAACTTGTCAAACTTTTACAAGTTCTTTGATAACTTCGGATCCT
196 TTGTTCTTGGACGAACTCCT-GAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCCT
* * *
1987 CAAAGTATTCAAGACGATCCATT-CTTTCGCGCAATTTT-TCGAACATTCCATGCTCG-CGAAAT
260 TAAAGTATTCAAGACGATCCATTCCTTT-GAGCAATTTTCT-AAACATTCCATGCTCGAC-AAAT
* *
2049 CGTATCATTTGGTCTATATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTT
322 CGCATCA-TTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTT
* * * * * * *
2114 ATTTACGTGGGAACTGTTTCCCTCCTTGTTCTTTGATGAACTTTCG
386 ATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCA
* * * * * *
2160 AACTTGTCAAACTTTTACTTA-TTCTTTTTTAACTTCGGA-TCCTTAAAGTATTTAAGACGATCC
1 AACTTGTCAAACTTTTAC-GAGTTATTTTTTAACTTC-GATTCCCTAAAGTATTCAACAAGATCC
** * * * * *
2223 ATTCCTTTTAGCAATTTTTCGAATATTCCATGCTCGACAAATCGTATCATTTGGTCTAAATAGTT
64 ATTCCTTCGAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTT
* * *
2288 TGTCGTTTTGCAAACAAGTTTTGGTCGTTGAATTAAAAACTTATTTACGTGAGAAT
129 TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
Statistics
Matches: 1617, Mismatches: 261, Indels: 58
0.84 0.13 0.03
Matches are distributed among these distances:
428 55 0.03
429 315 0.19
430 9 0.01
431 655 0.41
432 573 0.35
433 8 0.00
434 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (431 bp):
AACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGATCCAT
TCCTTCGAGCAATTTTCCGAACATTCCATCCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
TTGTTCTTGGACGAACTCCTGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTAGGATCCTT
AAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTCTAAACATTCCATGCTCGACAAATCGCA
TCATTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCA
Found at i:1388 original size:647 final size:644
Alignment explanation
Indices: 1--2343 Score: 2859
Period size: 647 Copynumber: 3.6 Consensus size: 644
* * * *
1 TTCGAACTTCTCAAACTTTTACGAGTTATTTTTTAACTTCAATTCCCTAAAGTATTCAACAAGAT
1 TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTCAACAAGAT
* * *
66 CCATT-TTCTAGAGCAATTTTTCGAACATTCCATCCTTGGGAAATTGCATCATTTGATCTAAATA
66 CCATTCTT-TAGAGCAATTTTCCGAACATTCCATCCTCGGGAAATTGCATCATTTGGTCTAAATA
* * * *
130 GATTGTCATTTTGTAAACAAGTTCTGGTCTTTGAATGAAAAAGTTATTTACGTGAGAATTGTTTC
130 GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* *
195 TCTCTTTGTTCTTGGATGAACTTTCAAGCTTGTCAAACTTTTACTAGTTCTTTTATAACTTCTGA
195 TCTCTTTGTTCTTGGATGAACTTTCAAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGA
* * *
260 TCCTTAAAGTATTCAAGACTATCCATTCCTTCGAGCAATTTTCTAAATATTCCATGCTCGGCAAA
260 TCCTTAAAGTATT-AAGACGATCCATTCCTTCGAGCAATTTTCCAAATATTCCATGCTCAGCAAA
* * * * ** * * *
325 TCGCATCATTTGGCCTAAATGGTTTGTCATTCTAAAAAAAAATTTTGGTCTTTGAATTAAAAACT
324 TCGCAGCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCGTTGAATTAAAAACT
* * * *
390 TATTTACGTGAGAATTGTTTCTCTCTTTG-TCTCTGTACAAACTTTCTAACTTGTCAAACTTTTA
389 TATTTACGTGAGAATTGTTTCTCTCTTTGTTCT-TGGACGAACTTCCAAACTTGTCAAACTTTTA
* * * *
454 CGAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAACAAGAAACATTCGTTAGAGCAATTTTC
453 CAAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAAGAAG-ATCATTC-TTTGAGCAATTTTC
* * * * *
519 TGAACATTCCGTGCTTGAGAAATCGCATCATTTGGTTTAAATATTTTGTCATTTTGTTTACAAGT
516 TGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTATACAAGT
* ** * * *
584 TTTGGTCTTTGAATTAAAAACTTATTTACGAGAGAATTGCATCACTCTTGGTTCATGGACGAAC
581 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAAC
* * * * * * * *
648 TCCTGAACTTGTCAAACTTTTAGGAGATCTTTTATAACTTAACTTCCTTAAAGTATTCAAGACGA
1 TTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTCAACAAGA
* * * * *** * *
713 CCCATTCCTTT-GAG-TATTTTCTGAACATTCCATGCTCAAAAAATTGCATCATTCGGTCTAAAG
65 TCCATT-CTTTAGAGCAATTTTCCGAACATTCCATCCTCGGGAAATTGCATCATTTGGTCTAAAT
* * * *
776 AGTTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAATAAAAAACTTATTTGCGTGAGAATTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * * * *
841 CTCTCTTTCTTCTTGGATGAACTTTCAAACGTGTCAAACTTTTACGACTTATTTTATAACTTC-C
194 CTCTCTTTGTTCTTGGATGAACTTTCAAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGG
* * * * *
905 ATTCCTTAAAGTATTGAAGGCGATCCAGTCCTTCGAGCAGTTTTCCAAACATTCCTTGCTCAAG-
259 A-TCCTTAAAGTATT-AAGACGATCCATTCCTTCGAGCAATTTTCCAAATATTCCATGCTC-AGC
* * * *
969 AAATCACAGCATTTGGTCTAAATAGATTGTCATTTAT-TAAACAGGTTTTGGTCGTTGAATTAAA
321 AAATCGCAGCATTTGGTCTAAATAGTTTGTCATTT-TGCAAACAAGTTTTGGTCGTTGAATTAAA
*
1033 AACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTT
385 AACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTGTCAAACTT
* * * * ** * *
1098 TTACTAGTTCTTTTATAACTTAGGA-TCATTAAAGTATTCAAGATGATCTATTTTTTCGAGCAAT
450 TTACAAGTTATTTTTTAACTT-CGATTCCCTAAAGTATTCAAGAAGATC-ATTCTTT-GAGCAAT
* * * * * * * *
1162 TTTCTAAACATTCCATGCTCAAGAAATCACATCAATTGGCCTAAATAATTTGTCGTTTTGCAAAC
512 TTTCTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTATAC
* *
1227 AAGTTTTGGCCTTTAAATTAAAAACTTA-TTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACG
577 AAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACG
1291 AAC
642 AAC
* * * *
1294 ATTCGAACTTGTCAAACTTTTACGAGTTTTTTTTTAACTTTAGTTCCCTAAAGTATTCCACAAGA
1 -TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTCAACAAGA
* *
1359 TCCATT-TTCTAGAGCAATTTTCCGAACATTCCATCCTTGGGAAATTACATCATTTGGTCTAAAT
65 TCCATTCTT-TAGAGCAATTTTCCGAACATTCCATCCTCGGGAAATTGCATCATTTGGTCTAAAT
* * * *
1423 AGTTTGTTATTTTGTAAACAAGTTTTTGTCTTTGAATTCAGAACTTATTTACGTGAGAATTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * *
1488 CTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGG
194 CTCTCTTTGTTCTTGGATGAACTTTCAAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGG
* * * *
1553 ATCCTTAAAGTATTCAGGACGATCCATTCCTTTC-AGCAATATTCCAAATATTCTATGCTCGGCA
259 ATCCTTAAAGTATT-AAGACGATCCATTCC-TTCGAGCAATTTTCCAAATATTCCATGCTCAGCA
* * *
1617 AAT--C-GCATCTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTTGTCGTTGAATTGAAAA
322 AATCGCAGCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCGTTGAATTAAAAA
* * *
1679 CTTATTTACGTGAGAATTGCTTCTCTCTTTGTTCTTGGACGAGCTCCCAAACTTGTCAAACTTTT
387 CTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTT
* * *
1744 ACAAGTTATTTTTTAAATTCTATTCCCTAAAGTAATCAAGAAGATCCATTCCTTTGAGCAATTTT
452 ACAAGTTATTTTTTAACTTCGATTCCCTAAAGTATTCAAGAAGAT-CATT-CTTTGAGCAATTTT
** * * *
1809 -TCGAACATTTAATCCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTATACAA
515 CT-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTATACAA
* * * * *
1873 GTTCTGGTCTTTGAATTGAAAAGTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGATGAA
579 GTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAA
1938 C
644 C
* * * * * *
1939 TTTCGAACTTGTCAAACTTTTACAAGTTCTTTGATAACTTCGGAT-CCTCAAAGTATTCAAGACG
1 -TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCT-AAAGTATTCAACAAG
* * * * * * * *
2003 ATCCATTCTTTCGCGCAATTTTTCGAACATTCCATGCTCGCGAAATCGTATCATTTGGTCTATAT
64 ATCCATTCTTTAGAGCAATTTTCCGAACATTCCATCCTCGGGAAATTGCATCATTTGGTCTAAAT
* *
2068 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGGGAACTGTTT
129 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * * *
2133 CCCTCCTTGTTCTTTGATGAACTTTCGAACTTGTCAAACTTTTACTTA-TTCTTTTTTAACTTCG
194 CTCTCTTTGTTCTTGGATGAACTTTCAAACTTGTCAAACTTTTAC-TAGTTCTTTTATAACTTCG
** * *
2197 GATCCTTAAAGTATTTAAGACGATCCATTCCTTTTAGCAATTTTTCGAATATTCCATGCTC-GAC
258 GATCCTTAAAGTA-TTAAGACGATCCATTCCTTCGAGCAATTTTCCAAATATTCCATGCTCAG-C
* * *
2261 AAATCGTATCATTTGGTCTAAATAGTTTGTCGTTTTGCAAACAAGTTTTGGTCGTTGAATTAAAA
321 AAATCGCAGCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCGTTGAATTAAAA
2326 ACTTATTTACGTGAGAAT
386 ACTTATTTACGTGAGAAT
Statistics
Matches: 1436, Mismatches: 228, Indels: 63
0.83 0.13 0.04
Matches are distributed among these distances:
643 3 0.00
644 235 0.16
645 312 0.22
646 104 0.07
647 639 0.44
648 140 0.10
649 1 0.00
650 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (644 bp):
TTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCCTAAAGTATTCAACAAGAT
CCATTCTTTAGAGCAATTTTCCGAACATTCCATCCTCGGGAAATTGCATCATTTGGTCTAAATAG
TTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
CTCTTTGTTCTTGGATGAACTTTCAAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGAT
CCTTAAAGTATTAAGACGATCCATTCCTTCGAGCAATTTTCCAAATATTCCATGCTCAGCAAATC
GCAGCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCGTTGAATTAAAAACTTA
TTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACAA
GTTATTTTTTAACTTCGATTCCCTAAAGTATTCAAGAAGATCATTCTTTGAGCAATTTTCTGAAC
ATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTATACAAGTTTTGG
TCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAAC
Done.