Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005935.1 Kokia drynarioides strain JFW-HI SEQ_120316, 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: 8023
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Found at i:5045 original size:216 final size:216
Alignment explanation
Indices: 4711--6897 Score: 2660
Period size: 216 Copynumber: 10.1 Consensus size: 216
4701 TGGAACATTT
* * *
4711 AAATTGCATCATTTGGTCTAAATAGTTTGTCT-TTTAGTAAACAAGTTTTGGTCTTCGAATTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGT-TATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* *
4775 AACTTATACACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTT
65 AACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
* * * * *** *
4840 TTACAAGTTCTTTTATAACTTCGGTTTCTCATAGTATTTGTGATGATCCATTCCTTCAAGCAATT
130 TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATT
*
4905 TTTTGAACATTCCATGCTCGGG
195 TTCTGAACATTCCATGCTCGGG
* * * * *
4927 ATATCACATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTCTAGTATTTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* *
4992 ACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGTCGAACTTTCGAACTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* * ** * * *
5057 TACGAGCTCTTTTATAACTTTGGTTCCTTAAAACATTCAAGACGATCCATTCCTTCCAGTAAGTT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
* * *
5122 TCCGAACATTCCGTGCTCGAG
196 TCTGAACATTCCATGCTCGGG
* * * *
5143 ATATCGCATCATTTGGTCTACATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAATTTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* ** * ** *
5208 ACTTATATATGTGATCATTGTTTCTCTCTTGGTTCTTAGAAAAACTTTCGAAGTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* * * *
5273 TATGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAGATGATGCATTCCTTCCAA-CAATT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT-CAAGCAATT
* *
5337 TTCTGAACATTCCATTCTCGTG
195 TTCTGAACATTCCATGCTCGGG
* * * *
5359 AAATCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * * **
5424 ACTTATATATGTGAGAATTGTTTCTAT-TTAGTTCTTCCACGAACTTTCGAACTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* * * * *
5488 TACGAGTTCTTTTATAACTTCGGCTCCTT-AAGTATTAAAGACAATCCATTCCTTCGAGCAATAT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
* * * * *
5552 TCCGAATAATCCATGCTTGTG
196 TCTGAACATTCCATGCTCGGG
* *
5573 AAATCGCATCTTTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAAATTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTT-GAATTAAA
* * * * * * *
5638 ATCCTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTAGGACGAACTTTCTAACTAGTCAAAATT
65 AACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
* * ** * *
5703 CTATGAGTTCTTTTATAGTTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTTC-ATCAAT
130 TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCC-TTCAAGCAAT
**
5767 TTTCCT-AACATTCCATGCTCGAA
194 TTT-CTGAACATTCCATGCTCGGG
* * **
5790 AAATCGCATCAATTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTATTCTTTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * * *
5855 ACTTATATATGTGGGAATTGTTTCACTCTTGGTTCTTGGAC-AAGC-TTCTGAATTTGTCAAACT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA-CTTTC-GAACTTGTCAAACT
* * * **
5918 TTTACAAGTTCTTTTAAAACTTTGGTTCCTTAAAACATTCAAGACGATCCATTCCTTTC-AGCAA
129 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCC-TTCAAGCAA
*
5982 TTTTTTGAACATTCCATGCTCGGG
193 TTTTCTGAACATTCCATGCTCGGG
* * *
6006 AAATTGCATCATTTGGTCTAAAGAGTTT-TCCATTTTGTAAACAAGTTTTGGT-TTGTGAATTAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGT-TATTTTGTAAACAAGTTTTGGTCTT-TGAATTAA
* * * *
6069 AAACTTATTTATGTGAGAATT-TTTATCTCTTGATTCTTGGACGAACTTAT-GAACTTGTCAAAC
64 AAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-TCGAACTTGTCAAAC
* * * * * *
6132 TTTTATGCGTTCTTTTATAACTTCGTTTCCTTATAGTTTTCAAGACGATCAATTCCTTCCAA-CA
128 TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT-CAAGCA
* ** *
6196 ATGTTCCAAACATTCCATCCTCGGG
192 ATTTTCTGAACATTCCATGCTCGGG
* * * **
6221 AAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAATAAGTTTTTTTCTTTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * * *
6286 ACTTATATACTTGAGAATTGTTTCTCTCTGGGTTCTTGGACGAATTTTCGAATTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* * * * * ** *
6351 TACAAGTTATTTTATAACTTAGGTTCCTCATAGTATTCGTGACGATTCATTCCTTCAAGCAATTT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
* * *
6416 TTTAAACATTTCATGCTCGGG
196 TCTGAACATTCCATGCTCGGG
* *
6437 ATATTGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * * * *
6502 ACTTATATACGTGAAAATTGTTTCTCTCTTGGTTCTTGGTCAAACTTTCAAACTTGTCAAACATT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* ** *
6567 TACGAGTTCTTTTATAACTGT-GGTTCCATAAAAAATTCAAGACGATCCATTCCTTCTAGCAATT
131 TACGAGTTCTTTTATAACT-TCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATT
*
6631 TTCCGAACATTCCATGCTCGGG
195 TTCTGAACATTCCATGCTCGGG
* * * * *
6653 ATATCGCATCATTTGGTTTACATAGTTTGTTATTTCGTAAACAAGTTTTGGTCTTTAAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * *
6718 ACTTATATACGTGATAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
** *
6783 TACGAGTTCTTTTATAACTTCAATTCCTTAAAGTATTCAAGATGATCCATTCCTTCCAA-CAATT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT-CAAGCAATT
* * **
6847 TTTTGAACATTCCATTCTCGTT
195 TTCTGAACATTCCATGCTCGGG
* *
6869 AAATCGTATCATTTGGTTTAAATAGTTTG
1 AAATCGCATCATTTGGTCTAAATAGTTTG
6898 ACATCTTGGT
Statistics
Matches: 1671, Mismatches: 274, Indels: 52
0.84 0.14 0.03
Matches are distributed among these distances:
213 2 0.00
214 95 0.06
215 271 0.16
216 1203 0.72
217 96 0.06
218 4 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (216 bp):
AAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
TCTGAACATTCCATGCTCGGG
Found at i:6052 original size:647 final size:647
Alignment explanation
Indices: 4711--6897 Score: 2764
Period size: 647 Copynumber: 3.4 Consensus size: 647
4701 TGGAACATTT
* *
4711 AAATTGCATCATTTGGTCTAAATAGTTTGTC-TTTTAGTAAACAAGTTTTGGTCTTCGAATTAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT-GTAAACAAGTTTTGGTCTTTGAATTAAA
* * *
4775 AACTTATACACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTT
65 AACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
* * * *** *
4840 TTACAAGTTCTTTTATAACTTCGGTTTCTCATAGTATTTGTGATGATCCATTCCTT-CAAGCAAT
130 TTACGAGTTCTTTTATAACTTCGGTTCCTTATAGTATTCAAGACGATCCATTCCTTCCAA-CAAT
** * *
4904 TTTTTGAACATTCCATGCTCGGGATATCACATCATTTGGTCTAAATAGTTTGTTATTTTGTAAAC
194 TTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAAC
* * * *
4969 AAGTTCTAGTATTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGTCG
259 AAGTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACG
* **
5034 AACTTTCGAACTTGTCAAACTTTTACGAGCTCTTTTATAACTTTGGTTCCTTAAAACATTCAAGA
324 AACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAA-TTTGGTTCCTTAAAGTATTCAAGA
* * * *
5099 CGATCCATTCCTTCCAGT-AAGTTTCCGAACATTCCGTGCTCGAGATATCGCATCATTTGGTCTA
388 CGATCCATTCCTTTCA-TCAATTTTCCTAACATTCCATGCTCGAGATATCGCATCATTTGGTCTA
* * * **
5163 CATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAATTTAAAACTTATATATGTGATCATTG
452 AATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATATATGTGAAAATTG
* * * *
5228 TTTCTCTCTTGGTTCTTAGAAAAACTTTCGAAGTTGTCAAACTTTTATGAGTTCTTTTATAACTT
517 TTTCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
** ** * * * * * *
5293 CAGTTCCTTAAAGTATTCAAGATGATGCATTCCTTCCAACAATTTTCTGAACATTCCATTCTCGT
582 TGGTTCCTTAAAAAATTCAAGACGATCCATTCCTTTCAGCAATTTTCTGAACATTCCATGCTCGG
5358 G
647 G
* * *
5359 AAATCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* * **
5424 ACTTATATATGTGAGAATTGTTTCTAT-TTAGTTCTTCCACGAACTTTCGAACTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
* * * * * *
5488 TACGAGTTCTTTTATAACTTCGGCTCCTTA-AGTATTAAAGACAATCCATTCCTTCGAGCAATAT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTATAGTATTCAAGACGATCCATTCCTTCCAACAATTT
* * * * *
5552 TCCGAATAATCCATGCTTGTGAAATCGCATCTTTTGGTCTAAATAGTTTGTTATTTTGTAAACAA
196 TCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAA
* * * * * *
5617 GTTTTGGTCTTTAAAATTAAAATCCTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTAGGACGA
261 GTTTTAGTCTTT-GAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGA
* * * * * * *
5682 ACTTTCTAACTAGTCAAAATTCTATGAGTTCTTTTATAGTTTCGGTTCCTTAAAGTATTCAAGAT
325 ACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAATTT-GGTTCCTTAAAGTATTCAAGAC
* * *
5747 GATCCATTCCTTTCATCAATTTTCCTAACATTCCATGCTCGAAAAATCGCATCAATTGGTCTAAA
389 GATCCATTCCTTTCATCAATTTTCCTAACATTCCATGCTCGAGATATCGCATCATTTGGTCTAAA
* ** **
5812 TAGTTTGTCATTTTGTAAACAAGTTTTATTCTTTGAATTAAAAACTTATATATGTGGGAATTGTT
454 TAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATATATGTGAAAATTGTT
* * * * *
5877 TCACTCTTGGTTCTTGGACAAGC-TTCTGAATTTGTCAAACTTTTACAAGTTCTTTTAAAACTTT
519 TCTCTCTTGGTTCTTGGACAAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTT
* *
5941 GGTTCCTTAAAACATTCAAGACGATCCATTCCTTTCAGCAATTTTTTGAACATTCCATGCTCGGG
583 GGTTCCTTAAAAAATTCAAGACGATCCATTCCTTTCAGCAATTTTCTGAACATTCCATGCTCGGG
* *
6006 AAATTGCATCATTTGGTCTAAAGAGTTT-TCCATTTTGTAAACAAGTTTTGGT-TTGTGAATTAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGT-CATTTTGTAAACAAGTTTTGGTCTT-TGAATTAA
* * *
6069 AAACTTATTTATGTGAGAATT-TTTATCTCTT-GATTCTTGGACGAACTTAT-GAACTTGTCAAA
64 AAACTTATATACGTGAGAATTGTTTCTCTCTTAG-TTCTTGGACGAACTT-TCGAACTTGTCAAA
* * * * *
6131 CTTTTATGCGTTCTTTTATAACTTCGTTTCCTTATAGTTTTCAAGACGATCAATTCCTTCCAACA
127 CTTTTACGAGTTCTTTTATAACTTCGGTTCCTTATAGTATTCAAGACGATCCATTCCTTCCAACA
* * * * *
6196 ATGTTCCAAACATTCCATCCTCGGGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
192 ATTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAA
* ** * *
6261 ATAAGTTTTTTTCTTTGAATTAAAAACTTATATACTTGAGAATTGTTTCTCTCTGGGTTCTTGGA
257 ACAAGTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA
* * * * * * * **
6326 CGAATTTTCGAATTTGTCAAACTTTTACAAGTTATTTTATAACTTAGGTTCCTCATAGTATTCGT
322 CGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAA-TTTGGTTCCTTAAAGTATTCAA
* * * * * *
6391 GACGATTCATTCC-TTCAAGCAATTTT-TTAAACATTTCATGCTCGGGATATTGCATCATTTGGT
386 GACGATCCATTCCTTTC-ATCAATTTTCCT-AACATTCCATGCTCGAGATATCGCATCATTTGGT
*
6454 CTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATATACGTGAAAA
449 CTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATATATGTGAAAA
* * *
6519 TTGTTTCTCTCTTGGTTCTTGGTCAAACTTTCAAACTTGTCAAACATTTACGAGTTCTTTTATAA
514 TTGTTTCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAA
* * *
6584 CTGTGGTTCCATAAAAAATTCAAGACGATCCATTCC-TTCTAGCAATTTTCCGAACATTCCATGC
579 CTTTGGTTCCTTAAAAAATTCAAGACGATCCATTCCTTTC-AGCAATTTTCTGAACATTCCATGC
6648 TCGGG
643 TCGGG
* * * * * *
6653 ATATCGCATCATTTGGTTTACATAGTTTGTTATTTCGTAAACAAGTTTTGGTCTTTAAATTAAAA
1 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* *
6718 ACTTATATACGTGATAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAACTTT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
** * *
6783 TACGAGTTCTTTTATAACTTCAATTCCTTAAAGTATTCAAGATGATCCATTCCTTCCAACAATTT
131 TACGAGTTCTTTTATAACTTCGGTTCCTTATAGTATTCAAGACGATCCATTCCTTCCAACAATTT
** * ** * *
6848 TTTGAACATTCCATTCTCGTTAAATCGTATCATTTGGTTTAAATAGTTTG
196 TCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTG
6898 ACATCTTGGT
Statistics
Matches: 1316, Mismatches: 201, Indels: 44
0.84 0.13 0.03
Matches are distributed among these distances:
646 111 0.08
647 881 0.67
648 319 0.24
649 5 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (647 bp):
AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
ACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTCGAACTTGTCAAACTTT
TACGAGTTCTTTTATAACTTCGGTTCCTTATAGTATTCAAGACGATCCATTCCTTCCAACAATTT
TCCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAA
GTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA
CTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAATTTGGTTCCTTAAAGTATTCAAGACGA
TCCATTCCTTTCATCAATTTTCCTAACATTCCATGCTCGAGATATCGCATCATTTGGTCTAAATA
GTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATATATGTGAAAATTGTTTC
TCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGT
TCCTTAAAAAATTCAAGACGATCCATTCCTTTCAGCAATTTTCTGAACATTCCATGCTCGGG
Found at i:6500 original size:863 final size:861
Alignment explanation
Indices: 4711--6897 Score: 2879
Period size: 863 Copynumber: 2.5 Consensus size: 861
4701 TGGAACATTT
* *
4711 AAATTGCATCATTTGGTCTAAATAGTTTGTCT-TTTAGTAAACAAGTTTTGGTCTTCGAATTAAA
1 AAATTGCATCATTTGGTCTAAATAGTTTGT-TATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * *
4775 AACTTATACACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTT
65 AACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCAAACTTGTCAAA-AT
* * * * * ***
4840 TTACAAGTTCTTTTATAACTTCGGTTTCTCATAGTATTTGTGATGATCCATTCCTTCAAGCAATT
129 TTACGAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCAAGCAATT
* *
4905 TT-TTGAACATTCCATGCTCGGGATATCACATCATTTGGTCTAAATAGTTTGTTATTTTGTAAAC
194 TTCCT-AACATTCCATGCTCGGGATATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAAC
* * *
4969 AAGTTCTAGTATTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGTCG
258 AAGTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACG
*
5034 AACTT-TCGAACTTGTCAAACTTTTACGAGCTCTTTTATAACTTTGGTTCCTTAAAACATTCAAG
323 AACTTCT-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAACATTCAAG
* * ** * *
5098 ACGATCCATTCCTTCCAGTAAGTTTCCGAACATTCCGTGCTCGAGATATCGCATCATTTGGTCTA
387 ACGATCCATTCCTTCCAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTA
* * * **
5163 CATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAATTTAAAACTTATATATGTGATCATTG
452 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATATATGTGAGAATTG
* * *
5228 TTTCTCTCTTGGTTCTTAGAAAAACTTTCGAAGTTGTCAAACTTTTATGAGTTCTTTTATAACTT
517 TTTATCTCTTGATTCTTAGAAAAACTTTCGAACTTGTCAAACTTTTATGAGTTCTTTTATAACTT
* * ** * *
5293 CAGTTCCTTAAAGTATTCAAGATGATGCATTCCTTCCAACAATTTTCTGAACATTCCATTCTCGT
582 CAGTTCCTTAAAGTATTCAAGACGATGCATTCCTTCCAACAATGTTCCAAACATTCCATCCTCGG
5358 GAAATCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAATTAAA
647 GAAATCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAATTAAA
*
5423 AACTTATATATGTGAGAATTGTTTCTATTTAGTTCTTCCACGAACTTTCGAACTTGTCAAACTTT
712 AACTTATATATGTGAGAATTGTTTCTATTGAGTTCTTCCACGAACTTTCGAACTTGTCAAACTTT
* * * * *
5488 TACGAGTTCTTTTATAACTTCGGCTCCTTAAGTATTAAAGACAATCCATTCCTTCGAGCAATATT
777 TACAAGTTATTTTATAACTTAGGCTCCTCAAGTATTAAAGACAATCCATTCCTTCAAGCAATATT
* * * *
5553 CCGAATAATCCATGCTTGTG
842 CCAAACAATCCATGCTCGGG
* * *
5573 AAATCGCATCTTTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAAATTAAA
1 AAATTGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTT-GAATTAAA
* * * * * * *
5638 ATCCTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTAGGACGAACTTTCTAACTAGTCAAAATT
65 AACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCAAACTTGTCAAAATT
* * *
5703 CTATGAGTTCTTTTATAGTTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTTC-ATCAAT
130 -TACGAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCC-TTCAAGCAAT
** * * *
5767 TTTCCTAACATTCCATGCTCGAAAAATCGCATCAATTGGTCTAAATAGTTTGTCATTTTGTAAAC
193 TTTCCTAACATTCCATGCTCGGGATATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAAC
* * * * *
5832 AAGTTTTATTCTTTGAATTAAAAACTTATATATGTGGGAATTGTTTCACTCTTGGTTCTTGGAC-
258 AAGTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACG
* * *
5896 AAGCTTCTGAATTTGTCAAACTTTTACAAGTTCTTTTAAAACTTTGGTTCCTTAAAACATTCAAG
323 AA-CTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAACATTCAAG
* * *
5961 ACGATCCATTCCTTTCAGCAATTTTTTGAACATTCCATGCTCGGGAAATTGCATCATTTGGTCTA
387 ACGATCCATTCCTTCCAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTA
* * *
6026 AAGAGTTT-TCCATTTTGTAAACAAGTTTTGGT-TTGTGAATTAAAAACTTATTTATGTGAGAAT
452 AATAGTTTGT-CATTTTGTAAACAAGTTTTGGTCTT-TAAATTAAAAACTTATATATGTGAGAAT
* ** *
6089 T-TTTATCTCTTGATTCTTGGACGAACTTAT-GAACTTGTCAAACTTTTATGCGTTCTTTTATAA
515 TGTTTATCTCTTGATTCTTAGAAAAACTT-TCGAACTTGTCAAACTTTTATGAGTTCTTTTATAA
* *
6152 CTTC-GTTTCCTTATAGTTTTCAAGACGAT-CAATTCCTTCCAACAATGTTCCAAACATTCCATC
579 CTTCAG-TTCCTTAAAGTATTCAAGACGATGC-ATTCCTTCCAACAATGTTCCAAACATTCCATC
* * ** *
6215 CTCGGGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAATAAGTTTTTTTCTTTGAA
642 CTCGGGAAATCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAA
* * ** * *
6280 TTAAAAACTTATATACT-TGAGAATTGTTTCTCTCTGGGTTCTTGGACGAATTTTCGAATTTGTC
707 TTAAAAACTTATATA-TGTGAGAATTGTTTCTAT-TGAGTTCTTCCACGAACTTTCGAACTTGTC
* *** * *
6344 AAACTTTTACAAGTTATTTTATAACTTAGGTTCCTCATAGTATTCGTGACGATTCATTCCTTCAA
770 AAACTTTTACAAGTTATTTTATAACTTAGGCTCCTCA-AGTATTAAAGACAATCCATTCCTTCAA
* ** * *
6409 GCAATTTTTTAAACATTTCATGCTCGGG
834 GCAATATTCCAAACAATCCATGCTCGGG
*
6437 ATATTGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
1 AAATTGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
* *
6502 ACTTATATACGTGAAAATTGTTTCTCTCTTGGTTCTTGGTCAAACTTTCAAACTTGTCAAACATT
66 ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCAAACTTGTCAAA-ATT
* * ** * *
6567 TACGAGTTCTTTTATAACTGT-GGTTCCATAAAAAATTCAAGACGATCCATTCCTTCTAGCAATT
130 TACGAGTTCTTTTATAA-TTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCAAGCAATT
* * * *
6631 TTCCGAACATTCCATGCTCGGGATATCGCATCATTTGGTTTACATAGTTTGTTATTTCGTAAACA
194 TTCCTAACATTCCATGCTCGGGATATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACA
* * *
6696 AGTTTTGGTCTTTAAATTAAAAACTTATATACGTGATAATTGTTTCTCTCTTAGTTCTTGGACGA
259 AGTTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGA
* *** ** *
6761 ACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTTAAAGTATTCAAGAT
324 ACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAACATTCAAGAC
* * ** * *
6826 GATCCATTCCTTCCAACAATTTTTTGAACATTCCATTCTCGTTAAATCGTATCATTTGGTTTAAA
389 GATCCATTCCTTCCAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA
6891 TAGTTTG
454 TAGTTTG
6898 ACATCTTGGT
Statistics
Matches: 1140, Mismatches: 165, Indels: 38
0.85 0.12 0.03
Matches are distributed among these distances:
861 3 0.00
862 254 0.22
863 778 0.68
864 105 0.09
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (861 bp):
AAATTGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAA
ACTTATATACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTCAAACTTGTCAAAATTT
ACGAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCAAGCAATTTT
CCTAACATTCCATGCTCGGGATATCGCATCATTTGGTCTAAATAGTTTGTTATTTTGTAAACAAG
TTTTAGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAAC
TTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAACATTCAAGACGA
TCCATTCCTTCCAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATATATGTGAGAATTGTTTA
TCTCTTGATTCTTAGAAAAACTTTCGAACTTGTCAAACTTTTATGAGTTCTTTTATAACTTCAGT
TCCTTAAAGTATTCAAGACGATGCATTCCTTCCAACAATGTTCCAAACATTCCATCCTCGGGAAA
TCGTATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCATTGAATTAAAAACT
TATATATGTGAGAATTGTTTCTATTGAGTTCTTCCACGAACTTTCGAACTTGTCAAACTTTTACA
AGTTATTTTATAACTTAGGCTCCTCAAGTATTAAAGACAATCCATTCCTTCAAGCAATATTCCAA
ACAATCCATGCTCGGG
Found at i:7040 original size:156 final size:156
Alignment explanation
Indices: 6751--7053 Score: 417
Period size: 156 Copynumber: 1.9 Consensus size: 156
6741 CTCTCTTAGT
* * *
6751 TCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTTAAAG
1 TCTTGCACGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCAACTCCTTAAAG
* ** * * * ** ** *
6816 TATTCAAGATGATCCATTCCTTCCAACAATTTTTTGAACATTCCATTCTCGTTAAATCGTATCAT
66 TATTAAAGACAATCCATTCCTTCCAACAATATTCTGAACATTCAACGCTCGCGAAATCGCATCAT
*
6881 TTGGTTTAAATAGTTTGACATCTTGG
131 TTGGTCTAAATAGTTTGACATCTTGG
***
6907 TCTTGCACGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGCTCCTTAAAG
1 TCTTGCACGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCAACTCCTTAAAG
* * *
6972 TATTAAAGACAATCCATTCCTTCGAGCAATATTCTGAACATTCAACGCTCGCGAAATCGCATCTT
66 TATTAAAGACAATCCATTCCTTCCAACAATATTCTGAACATTCAACGCTCGCGAAATCGCATCAT
7037 TTGGTCTAAATAGTTTG
131 TTGGTCTAAATAGTTTG
7054 TTATTATGTA
Statistics
Matches: 126, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 126 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (156 bp):
TCTTGCACGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCAACTCCTTAAAG
TATTAAAGACAATCCATTCCTTCCAACAATATTCTGAACATTCAACGCTCGCGAAATCGCATCAT
TTGGTCTAAATAGTTTGACATCTTGG
Found at i:7265 original size:372 final size:372
Alignment explanation
Indices: 6552--7269 Score: 1008
Period size: 372 Copynumber: 1.9 Consensus size: 372
6542 CAAACTTTCA
* * * *
6552 AACTTGTCAAACATTTACGAGTTCTTTTATAACTGTGGTTCCATAAAAAATTCAAGACGATCCAT
1 AACTTGTCAAACATTTACAAGTTCTTTTATAACTGTGGCTCCATAAAAAATTAAAGACAATCCAT
* * * * * * * *
6617 TCCTTCTAGCAATTTTCCGAACATTCCATGCTCGGGATATCGCATCATTTGGTTTACATAGTTTG
66 TCCTTCGAGCAATATTCCGAACATTCAACGCTCGCGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * *
6682 TTATTTCGTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATATACGTGATAATTGTTTCTCTCT
131 TTATTTCGTAAACAAGTTTTAGTCTTTAAATTAAAAACCTATATACGTGAGAATTATTTCTCTCT
* * *
6747 TAGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTT
196 TAGTTCTAGGACAAACTTCCGAACTAGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTT
* * * ** *
6812 AAAGTATTCAAGATGATCCATTCCTTCCAACAATTTTTTGAACATTCCATTCTCGTTAAATCGTA
261 AAAGTATTCAAGACGATCCATTCCTTCCAACAATTTTCTGAACATTCCATGCTCGAGAAATCGCA
*
6877 TCATTTGGTTTAAATAGTTTGACATCTTGGTCTTGCACGAACTTCCG
326 TCATTTGGTCTAAATAGTTTGACATCTTGGTCTTGCACGAACTTCCG
* * * **
6924 AACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGCTCCTTAAAGTATTAAAGACAATCCAT
1 AACTTGTCAAACATTTACAAGTTCTTTTATAACTGTGGCTCCATAAAAAATTAAAGACAATCCAT
* *
6989 TCCTTCGAGCAATATTCTGAACATTCAACGCTCGCGAAATCGCATCTTTTGGTCTAAATAGTTTG
66 TCCTTCGAGCAATATTCCGAACATTCAACGCTCGCGAAATCGCATCATTTGGTCTAAATAGTTTG
* *
7054 TTATTAT-GTAAACAAGTTTTAGTCTTTAAATTAAAATCCTATTTACGTGAGAATTATTTCTCTC
131 TTATT-TCGTAAACAAGTTTTAGTCTTTAAATTAAAAACCTATATACGTGAGAATTATTTCTCTC
* * * **
7118 TTGGTTCTAGGACAAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAGCTTCGGTTCCT
195 TTAGTTCTAGGACAAACTTCCGAACTAGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCT
* * *
7183 TAAAGTATTCAAGACGATCCATTCCTTTCAGCAATTTTCCT-AACATTTCATGCTCGAGAAATCG
260 TAAAGTATTCAAGACGATCCATTCCTTCCAACAATTTT-CTGAACATTCCATGCTCGAGAAATCG
*
7247 CATCTTTTGGTCTAAATAGTTTG
324 CATCATTTGGTCTAAATAGTTTG
7270 TCATTTTGTA
Statistics
Matches: 300, Mismatches: 44, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
372 298 0.99
373 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (372 bp):
AACTTGTCAAACATTTACAAGTTCTTTTATAACTGTGGCTCCATAAAAAATTAAAGACAATCCAT
TCCTTCGAGCAATATTCCGAACATTCAACGCTCGCGAAATCGCATCATTTGGTCTAAATAGTTTG
TTATTTCGTAAACAAGTTTTAGTCTTTAAATTAAAAACCTATATACGTGAGAATTATTTCTCTCT
TAGTTCTAGGACAAACTTCCGAACTAGTCAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTT
AAAGTATTCAAGACGATCCATTCCTTCCAACAATTTTCTGAACATTCCATGCTCGAGAAATCGCA
TCATTTGGTCTAAATAGTTTGACATCTTGGTCTTGCACGAACTTCCG
Found at i:7592 original size:221 final size:220
Alignment explanation
Indices: 6901--7678 Score: 972
Period size: 216 Copynumber: 3.6 Consensus size: 220
6891 TAGTTTGACA
* * * * * *
6901 TCTTGG-TCTTGCACGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGCTC
1 TCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC
* * * * * * *
6965 CTTAAAGTATTAAAGACAATCCATTCCTTCGAGCAATATTCTGAACATTCAACGCTCGCGAAATC
66 CTTAAAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACATTCCATGCTCGGGAAATC
* *
7030 GCATCTTTTGGTCTAAATAGTTTG--T-T-ATTATGTAAACAAGTTTTAG-TCTTTAAATTAAAA
131 GCATCTTTTGGTCTAAATAGTTTGTTTGTCATTTTGTAAACAAGTTTT-GTTCTTTGAATTAAAA
* * * *
7090 TCCTATTTACGTGAGAATTATTTCTC
195 ACTTATATACGTGAGAATTGTTTCTC
* * *
7116 TCTTGGTTCTAGGACAAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAGCTTCGGTTC
1 TCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC
* * * *
7181 CTTAAAGTATTCAAGACGATCCATTCCTT-TCAGCAATTTTCCTAACATTTCATGCTCGAGAAAT
66 CTTAAAGTATTCAAGACAATCCATTCCTTCT-AGCAATTTTCCGAACATTCCATGCTCGGGAAAT
*
7245 CGCATCTTTTGGTCTAAATA----GTTTGTCATTTTGTAAACAAGTTTTGTTCTTTGAATTAAGA
130 CGCATCTTTTGGTCTAAATAGTTTGTTTGTCATTTTGTAAACAAGTTTTGTTCTTTGAATTAAAA
* *
7306 ACTTATATATGTGAGAATTGTGTCTC
195 ACTTATATACGTGAGAATTGTTTCTC
*
7332 TCTTGGTTCTTGGACAAACTTTCGAATTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC
1 TCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC
* *
7397 CTTAAA-CATTCAAGACAATCCATTCCTTCTAGCAATTTTCCAAACATTCCATGCTCGGGAAATC
66 CTTAAAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACATTCCATGCTCGGGAAATC
*
7461 GCATCTTTTGGTCTAAATAGTTTGTTTTTGTCATTTTCTAAACAAGTTTTGTTCTTTGAATTAAA
131 GCATCTTTTGGTCTAAATAGTTTG--TTTGTCATTTTGTAAACAAGTTTTGTTCTTTGAATTAAA
* *
7526 AACTTATGTACGTGATAATTGTTTCTC
194 AACTTATATACGTGAGAATTGTTTCTC
* * * * **
7553 TCTTGATTTTTGGACGAAC-TTCTGAATTTGTCAAACTTTTACGAGTTCTTTTATAACTTTAGTT
1 TCTTGGTTCTTGGACAAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
* ** ** * *
7617 CCTCT-GAGTATTCGTGATGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGGGA
65 CCT-TAAAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACATTCCATGCTCGGGA
7679 TATGATACGA
Statistics
Matches: 489, Mismatches: 57, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
212 1 0.00
214 1 0.00
215 78 0.16
216 239 0.49
219 1 0.00
220 3 0.01
221 119 0.24
222 47 0.10
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (220 bp):
TCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC
CTTAAAGTATTCAAGACAATCCATTCCTTCTAGCAATTTTCCGAACATTCCATGCTCGGGAAATC
GCATCTTTTGGTCTAAATAGTTTGTTTGTCATTTTGTAAACAAGTTTTGTTCTTTGAATTAAAAA
CTTATATACGTGAGAATTGTTTCTC
Done.