Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009390.1 Kokia drynarioides strain JFW-HI SEQ_124097, 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: 26572
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:759 original size:216 final size:216
Alignment explanation
Indices: 375--2952 Score: 2849
Period size: 216 Copynumber: 12.1 Consensus size: 216
365 GCTCACATCA
* * *
375 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTCTGAACTTGTCAAATTTTTACG
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * * * *
440 AGTTCTGTTATAACTTCGGTTCCTTAATGTATTCAAGATGATCCATTCCTTTGAGCAATTTTCCG
66 AGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG
* ** * * *
505 AACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATATTTTGTCATTTTTGTAAACAA-TT
131 AACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA-TTTTGTTATCAACTT
**
569 TTTTTCTTTGAATTAAAAACTT
195 TTGGTCTTTGAATTAAAAACTT
* *
591 ATTTACGTGAGAATTGTTTCTCTATTGGTT-TTGAGACAAACTTCCGAACTTGTCAAACTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTG-GACGAACTTCCGAACTTGTCAAACTTTTAC
*
655 GAGTTCTTTTATAACTTTGGTTCCTTAAAGAATTTAAGACGATCCATTCCTTCGAGCAATTTTCC
65 GAGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCC
* *
720 AAACATTCCATGCTCGGGAAATCGCAT-AGTTTTGTCTAAATAGTTTGTCATTTTGTTATCAACT
130 GAACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTTATCAACT
*
784 TTTGATC-TTGAATTAAAAACTT
194 TTTGGTCTTTGAATTAAAAACTT
* * * *
806 ATTTACTTGAGAATTGTTTCTCTCTTGGTTCTTGGATGGACTTTCGAACTTGTCAAACTTTTACG
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * *
871 AGTTCTTTTATAACTTTGGCTCCTTAAAAAATT-AAGACGATCCATTCCTTCGAGTAATTTTCCG
66 AGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG
* * *
935 AACATTCCATGCTCGGAAAATCACAT-AGTTTAGTCTAAATAGTTTGTCATTTTGTTATCAACTT
131 AACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTTATCAACTT
999 TTGGTCTTTGAATTAAAAACTT
195 TTGGTCTTTGAATTAAAAACTT
* * *
1021 ATTTACGTAAGAATTGTTTCTCTCTTGGCTCATGGACGAACATT-CGAACTTGTCAAACTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTCCGAACTTGTCAAACTTTTAC
* *
1085 GAGTTCTTTTATAACTTTGGTT-CTATAAAGTATTCAAGATGATCCATTCCTTC-A--AA-----
65 GAGTTCTTTTATAACTTTGGTTCCT-TAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * * * * * * *
1141 C--A-ATT---TTCTCGAGAAATCGCATCATTTGGTTTAAATAGTTTGTCATATTCTAAACAAGT
129 CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACT
*
1200 TTTGGTCTTTGAATTAAAAACAT
194 TTTGGTCTTTGAATTAAAAACTT
*** *
1223 ATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTAAAGAACTTGTCAAACTTTTACA
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * * * * * * *
1286 AGATCCTTTATTACTTT-GTTTCTTAAAAAGTATTTAAGACGATCCATTCCTTTGAACAATTTTT
66 AGTTCTTTTATAACTTTGGTTCCTT--AAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
** ** * * *
1350 TAAACATTGTAAGCTCGGGAAATCGCAT-AGTTTTGTCTAAATAATTTGTCATTTTGTTATCAAC
129 CGAACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTTATCAAC
* * *
1414 TTTTGATC-ATGTATTAAAAACTT
193 TTTTGGTCTTTGAATTAAAAACTT
* **
1437 ATTTACGTGAGAATTGTTTCTCTATTGGTTCTAAGACGAACTTCCGAACTTGTC-AA-----ACG
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * *
1496 AGTTCTTTTATTACTTTGGTTCCTTAAA-ATATTGAAAATGATCCATTCCTTCGAGCAATTTTCC
66 AGTTCTTTTATAACTTTGGTTCCTTAAAGA-ATTCAAGACGATCCATTCCTTCGAGCAATTTTCC
* * * * * *
1560 GAACATTCCATTCTCGGGAAATCGTATCATTTGGCCTAAATACTTTTTCATTTTGTTATCAACCT
130 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACTT
* *
1625 TTGGTCTTT--A--AATAGCTT
195 TTGGTCTTTGAATTAAAAACTT
* * *
1643 ATTTTCGTGAGAATTGTTTCTCTCTTGGTT-TTGAGATGAACTTCCGAACTTGTCAATCTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTG-GACGAACTTCCGAACTTGTCAAACTTTTAC
*
1707 GAGTTCTTTTATAACTTTGGTTCCTTAAA-ATATTGAAGACGATCCATTCCTTCGAGCAATTTTC
65 GAGTTCTTTTATAACTTTGGTTCCTTAAAGA-ATTCAAGACGATCCATTCCTTCGAGCAATTTTC
** * * *
1771 TAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAGTAGTTTTTCATTTTGTTATCAACT
129 CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACT
* *
1836 TTTGGACTTTGAATTAAAAGCTT
194 TTTGGTCTTTGAATTAAAAACTT
* * * ** *
1859 ATTTGCGTCAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTTTGAACTTGTCAAACTTTTACA
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
** * *** *
1924 AGTTCCATTATAACTTCGGTTCCTTAATTTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCG
66 AGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG
*** * *
1989 AACATTCCATGCAT-AAAAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGCTATCAACTT
131 AACATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACTT
* *
2053 TTGGACTTTGAATTAAAAGCTT
195 TTGGTCTTTGAATTAAAAACTT
* * * * **
2075 ATTTGCATGAGAATTGTTTCTGTCTTGGTTCTTGTACGAACTTTTGAACTTGTCAAACTTTTACG
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
** *** * * *
2140 AGTTCGATTATAACTTTGGTTCCTTAATTTATTTAAGACGATTCATTCCTTCGAGCAATTTTTCG
66 AGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG
** * * *
2205 AACATTCCATGCAT-AAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTTGTAAACAATT
131 AACATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA-TTTTGTTATCAACT
*
2269 TTTTGTCTTTGAATTAAAAACTT
194 TTTGGTCTTTGAATTAAAAACTT
* *
2292 ATTTACGTGAGAAATTGTTTCTCTATTGGTTC-TGAGACAAACTTCCGAACTTGTCAAACTTTTA
1 ATTTACGTGAG-AATTGTTTCTCTCTTGGTTCTTG-GACGAACTTCCGAACTTGTCAAACTTTTA
*
2356 CGAGTTCTTTTATAACTTCGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
64 CGAGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * *
2421 CAAACATTCCATGCTCGGGAAATCACAT-AGTTTTGTCTAAATAGTTTGTCATTTTGTTATCAAC
129 CGAACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTTATCAAC
*
2485 TTTTGATC-TTGAATTAAAAACTT
193 TTTTGGTCTTTGAATTAAAAACTT
* * * *
2508 ATTTACGTAAGAATTGTTTCTCTCTTGGTTCATGGACAAACATCCCGAACTTGTCAAACTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTCCGAACTTGTCAAACTTTTAC
* * *
2573 GAGTTCTTTTATAACTTCGGTTCCATAAAGTATTCAAGACGATCCATTCCTT----CAA------
65 GAGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCC
* * * * * * * *
2628 GTA-ATT---T-CTCGGGAAACCGCATCATTTGGTTTAAATAGTTTGTCATATTCTAAACAAGTT
130 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACTT
*
2688 TTGGTCTTTGAATTAAAAA-TGC
195 TTGGTCTTTGAATTAAAAACT-T
*** *
2710 ATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTGAAGAACTTGTCAAACTTTTACA
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * * * ** * * *
2773 AGATCATTTATTACTTCGGTT-CTTAAAAAGTATTCAAGATAATCCATTCCTTTGAACAATTTTT
66 AGTTCTTTTATAACTTTGGTTCCTT--AAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * * * * *
2837 CGAACATTCCATGCTTGGGAAATCTCAT-AGTTTTGTCTAAATAATTTGTCATTTTGTTATAAAA
129 CGAACATTCCATGCTCGGGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTTATCAAC
* *
2901 TTTT-GACCTTGAATTAAAAACTT
193 TTTTGGTCTTTGAATTAAAAACTT
*
2924 ATTTACGTGAGAATTGTTTCTCTATTGGT
1 ATTTACGTGAGAATTGTTTCTCTCTTGGT
2953 GATACGGCCA
Statistics
Matches: 2028, Mismatches: 255, Indels: 158
0.83 0.10 0.06
Matches are distributed among these distances:
198 2 0.00
199 43 0.02
200 97 0.05
201 76 0.04
202 108 0.05
203 1 0.00
204 5 0.00
205 7 0.00
206 55 0.03
207 1 0.00
208 2 0.00
209 87 0.04
210 21 0.01
211 10 0.00
212 134 0.07
213 2 0.00
214 159 0.08
215 335 0.17
216 679 0.33
217 63 0.03
218 141 0.07
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (216 bp):
ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACG
AGTTCTTTTATAACTTTGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG
AACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTTATCAACTTT
TGGTCTTTGAATTAAAAACTT
Found at i:2428 original size:650 final size:646
Alignment explanation
Indices: 375--2952 Score: 2844
Period size: 650 Copynumber: 4.0 Consensus size: 646
365 GCTCACATCA
* * * *
375 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTCTGAACTTGTCAAATTTTTACG
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCATGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * * * *
440 AGTTCTGTTATAACTTCGGTTCCTTAATGTATTCAAGATGATCCATTCCTTTGAGCAATTTTCCG
66 AGTTCTTTTATAACTTCGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCA
* * *
505 AACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATATTTTGTCATTTTTGTAAACAA-TT
131 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCA-TTTTGTAAACAACTT
*** *
569 TTTTTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTT-TTGAGACAAACT
195 TTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTG-GACAAACT
* * * * *
633 TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGAATTTAAGACGAT
259 TCCGAACTTGTCAAACTTTTACAAGTTCCTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
* *
698 CCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAATCGCATAGTTTTGTCTAAATAG
324 CCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATAGTTTGGTCTAAATAG
* *
763 TTTGTCATTTTGTTATCAACTTTTGATCTTGAATTAAAAACTTATTTACTTGAGAATTGTTTCTC
389 TTTGTCATTTTGCTATCAACTTTTGATCTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC
* * * *
828 TCTTGGTTCTTGGATGGACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGCTC
454 TCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTATTATAACTTTGGTTC
* * *
893 CTTAAAA-AATTAAGACGATCCATTCCTTCGAGTAATTTTCCGAACATTCCATGCTCGGAAAATC
519 CTTAAAATATTTAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCT-GGGAAATC
* * * *
957 ACATAGTTTAGTCTAAATAGTTTGTCATTTTGTTATCAACTTTTGGTCTTTGAATTAAAAACTT
583 GCATAGTTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTT
* *
1021 ATTTACGTAAGAATTGTTTCTCTCTTGGCTCATGGACGAACATT-CGAACTTGTCAAACTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCATGGACGAAC-TTCCGAACTTGTCAAACTTTTAC
* * *
1085 GAGTTCTTTTATAACTTTGGTT-CTATAAAGTATTCAAGATGATCCATTCCTTC-A--AA-----
65 GAGTTCTTTTATAACTTCGGTTCCT-TAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * * * *
1141 C--A-ATT---TTCTCGAGAAATCGCATCATTTGGTTTAAATAGTTTGTCATATTCTAAACAAGT
129 CAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACT
* * *
1200 TTTGGTCTTTGAATTAAAAACATATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACT
194 TTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACT
*** * * * * *
1263 AAAGAACTTGTCAAACTTTTACAAGATCCTTTATTACTT-TGTTTCTTAAAAAGTATTTAAGACG
259 TCCGAACTTGTCAAACTTTTACAAGTTCCTTTATAACTTCGGTTCCTT--AAAGTATTCAAGACG
* * * ** * *
1327 ATCCATTCCTTTGAACAATTTTTTAAACATTGTAAGCTCGGGAAATCGCATAGTTTTGTCTAAAT
322 ATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATAGTTTGGTCTAAAT
* * * *
1392 AATTTGTCATTTTGTTATCAACTTTTGATCATGTATTAAAAACTTATTTACGTGAGAATTGTTTC
387 AGTTTGTCATTTTGCTATCAACTTTTGATCTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* ** * * *
1457 TCTATTGGTTCTAAGACGAACTTCCGAACTTGTC-AA-----ACGAGTTCTTTTATTACTTTGGT
452 TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTATTATAACTTTGGT
* * * *
1516 TCCTTAAAATATTGAAAATGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATTCTCGGGAAA
517 TCCTTAAAATATTTAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCT-GGGAAA
* * * * * * * * *
1581 TCGTATCA-TTTGGCCTAAATACTTTTTCATTTTGTTATCAACCTTTGGTCTTT--A--AATAGC
581 TCGCAT-AGTTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAC
1641 TT
645 TT
* * * *
1643 ATTTTCGTGAGAATTGTTTCTCTCTTGGTT-TTGAGATGAACTTCCGAACTTGTCAATCTTTTAC
1 ATTTACGTGAGAATTGTTTCTCTCTTGGTTCATG-GACGAACTTCCGAACTTGTCAAACTTTTAC
* *
1707 GAGTTCTTTTATAACTTTGGTTCCTTAAA-ATATTGAAGACGATCCATTCCTTCGAGCAATTTTC
65 GAGTTCTTTTATAACTTCGGTTCCTTAAAGA-ATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * * * * * *
1771 TAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAGTAGTTTTTCATTTTGTTATCAACT
129 CAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACT
* * * * *
1836 TTTGGACTTTGAATTAAAAGCTTATTTGCGTCAGAATTGTTTCTCTCTTGGTTCTTGCACGAACT
194 TTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACT
** * **
1901 TTTGAACTTGTCAAACTTTTACAAGTTCCATTATAACTTCGGTTCCTTAATTTATTCAAGACGAT
259 TCCGAACTTGTCAAACTTTTACAAGTTCCTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
* ***
1966 CCATTCCTTCGAGCAATTTTTCGAACATTCCATGCAT-AAAAAATCGCATCA-TTTGGTCTAAAT
324 CCATTCCTTCGAGCAATTTTTCAAACATTCCATGC-TCGGGAAATCGCAT-AGTTTGGTCTAAAT
* * * *
2029 AGTTTTTCATTTTGCTATCAACTTTTGGA-CTTTGAATTAAAAGCTTATTTGCATGAGAATTGTT
387 AGTTTGTCATTTTGCTATCAACTTTT-GATC-TTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * *
2093 TCTGTCTTGGTTCTTGTACGAACTTTTGAACTTGTCAAACTTTTACGAGTTCGATTATAACTTTG
450 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTATTATAACTTTG
** * * **
2158 GTTCCTTAATTTATTTAAGACGATTCATTCCTTCGAGCAATTTTTCGAACATTCCATGCATAAGA
515 GTTCCTTAAAATATTTAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGC-TGGGA
* *
2223 AATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTTGTAAACAATTTTTTGTCTTTGAATTAAA
579 AATCGCAT-AGTTTGGTCTAAATAGTTTGTCA-TTTTGTAAACAACTTTTGGTCTTTGAATTAAA
2287 AACTT
642 AACTT
* *
2292 ATTTACGTGAGAAATTGTTTCTCTATTGGTTC-TGAGACAAACTTCCGAACTTGTCAAACTTTTA
1 ATTTACGTGAG-AATTGTTTCTCTCTTGGTTCATG-GACGAACTTCCGAACTTGTCAAACTTTTA
2356 CGAGTTCTTTTATAACTTCGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
64 CGAGTTCTTTTATAACTTCGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTC
* * * * *
2421 CAAACATTCCATGCTCGGGAAATCACAT-AGTTTTGTCTAAATAGTTTGTCATTTTGTTATCAAC
129 CAAACATTCCATGCTCGAGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTAAACAAC
* *
2485 TTTT-GA-TCTTGAATTAAAAACTTATTTACGTAAGAATTGTTTCTCTCTTGGTTCATGGACAAA
193 TTTTGGACT-TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAA
* * * *
2548 CATCCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCATAAAGTATTCAAGAC
257 C-TTCCGAACTTGTCAAACTTTTACAAGTTCCTTTATAACTTCGGTTCCTTAAAGTATTCAAGAC
* * *
2613 GATCCATTCCTT----CAA---GT---A-ATT---T-CTCGGGAAACCGCATCA-TTTGGTTTAA
321 GATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCAT-AGTTTGGTCTAA
* * * * *
2662 ATAGTTTGTCATATT-CTAAACAAGTTTTGGTCTTTGAATTAAAAA-TGCATTTACGTGAGAATT
385 ATAGTTTGTCATTTTGCT-ATCAACTTTTGATC-TTGAATTAAAAACT-TATTTACGTGAGAATT
*** * * *
2725 G-TT-TCTCTTGGTTCTTGGACGAACTGAAGAACTTGTCAAACTTTTACAAGATC-ATTTATTAC
447 GTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTA-TTATAAC
* * ** * * *
2787 TTCGGTT-CTTAAAAAGTATTCAAGATAATCCATTCCTTTGAACAATTTTTCGAACATTCCATGC
511 TTTGGTTCCTT-AAAA-TATTTAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGC
* * * * *
2851 TTGGGAAATCTCATAGTTTTGTCTAAATAATTTGTCATTTTGTTATAA-AA-TTTT-GACCTTGA
574 -TGGGAAATCGCATAGTTTGGTCTAAATAGTTTGTCATTTTG-TA-AACAACTTTTGGTCTTTGA
2913 ATTAAAAACTT
636 ATTAAAAACTT
*
2924 ATTTACGTGAGAATTGTTTCTCTATTGGT
1 ATTTACGTGAGAATTGTTTCTCTCTTGGT
2953 GATACGGCCA
Statistics
Matches: 1648, Mismatches: 223, Indels: 137
0.82 0.11 0.07
Matches are distributed among these distances:
621 4 0.00
622 104 0.06
623 3 0.00
624 1 0.00
625 32 0.02
626 92 0.06
627 1 0.00
629 6 0.00
630 50 0.03
631 194 0.12
632 105 0.06
633 70 0.04
634 82 0.05
635 73 0.04
636 79 0.05
637 88 0.05
638 116 0.07
639 11 0.01
640 1 0.00
643 3 0.00
644 98 0.06
645 23 0.01
646 104 0.06
647 3 0.00
648 1 0.00
649 69 0.04
650 234 0.14
651 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (646 bp):
ATTTACGTGAGAATTGTTTCTCTCTTGGTTCATGGACGAACTTCCGAACTTGTCAAACTTTTACG
AGTTCTTTTATAACTTCGGTTCCTTAAAGAATTCAAGACGATCCATTCCTTCGAGCAATTTTCCA
AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
TGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTC
CGAACTTGTCAAACTTTTACAAGTTCCTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCC
ATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATAGTTTGGTCTAAATAGTT
TGTCATTTTGCTATCAACTTTTGATCTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
TTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTATTATAACTTTGGTTCCT
TAAAATATTTAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTGGGAAATCGCA
TAGTTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTT
Found at i:2823 original size:200 final size:201
Alignment explanation
Indices: 2458--2824 Score: 490
Period size: 200 Copynumber: 1.8 Consensus size: 201
2448 TAGTTTTGTC
* * * * *
2458 TAAATAGTTTGTCATTTTGTTATCAACTTTTGATCTTGAATTAAAAACTTATTTACGTAAGAATT
1 TAAATAGTTTGTCATATTCTAAACAACTTTTGATCTTGAATTAAAAACTCATTTACGTAAGAATT
** * * *
2523 GTTTCTCTCTTGGTTCATGGACAAACATCCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAAC
66 GTTTCTCTCTTGGTTCATGGACAAACATCAAGAACTTGTCAAACTTTTACAAGATCATTTATAAC
* *
2588 TTCGGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGTAATTTCTCGGGAAACCGCATCAT
131 TTCGGTTCCAAAAAGTATTCAAGACAATCCATTCCTTCAAGTAATTTCTCGGGAAACCGCATCAT
2653 TTGGTT
196 TTGGTT
* * *
2659 TAAATAGTTTGTCATATTCTAAACAAGTTTTGGTCTTTGAATTAAAAA-TGCATTTACGTGAGAA
1 TAAATAGTTTGTCATATTCTAAACAACTTTTGATC-TTGAATTAAAAACT-CATTTACGTAAGAA
* * * *
2723 TTG-TT-TCTCTTGGTTCTTGGACGAAC-TGAAGAACTTGTCAAACTTTTACAAGATCATTTATT
64 TTGTTTCTCTCTTGGTTCATGGACAAACATCAAGAACTTGTCAAACTTTTACAAGATCATTTATA
* *
2785 ACTTCGGTTCTTAAAAAGTATTCAAGATAATCCATTCCTT
129 ACTTCGGTTC-CAAAAAGTATTCAAGACAATCCATTCCTT
2825 TGAACAATTT
Statistics
Matches: 142, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
199 39 0.27
200 44 0.31
201 32 0.23
202 27 0.19
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (201 bp):
TAAATAGTTTGTCATATTCTAAACAACTTTTGATCTTGAATTAAAAACTCATTTACGTAAGAATT
GTTTCTCTCTTGGTTCATGGACAAACATCAAGAACTTGTCAAACTTTTACAAGATCATTTATAAC
TTCGGTTCCAAAAAGTATTCAAGACAATCCATTCCTTCAAGTAATTTCTCGGGAAACCGCATCAT
TTGGTT
Found at i:3768 original size:32 final size:32
Alignment explanation
Indices: 3732--3797 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
3722 TAGCTGAAAT
* ***
3732 TAATTAGTTGATTAATGTGTTTCAGGTACATG
1 TAATTAGCTGATTAATACATTTCAGGTACATG
3764 TAATTAGCTGATTAATACATTTCAGGTACATG
1 TAATTAGCTGATTAATACATTTCAGGTACATG
3796 TA
1 TA
3798 TGGATGGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (32 bp):
TAATTAGCTGATTAATACATTTCAGGTACATG
Found at i:5268 original size:214 final size:214
Alignment explanation
Indices: 4727--5998 Score: 1245
Period size: 214 Copynumber: 6.0 Consensus size: 214
4717 GATCGATCAA
* * * * *
4727 TTGGTTC-TGAGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAATTTTGGTTCC
1 TTGGTTCTTG-GACAAACTTTCAAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCC
* * * * *
4791 TTAAAATATTAAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCA
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCACAGGAAATCG
* * * * * *
4856 CAT-AGTTTGGTCTAAATAGTTTTTCATTTTGTTATCAACTTTTGGTATTTGAA-T---AACTTA
129 CATCA-TTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA
*
4916 TTTACGTAAGAATTGTTTCTCT
193 TTTACGTGAGAATTGTTTCTCT
* * * *
4938 TTATGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTATGAGTTTCATTATAACTTCGGTTCC
1 TT-GGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCC
* * * *
5003 TTAATGTATTCAAGACGATCTATTCGTTCGAGCAATTTTTCGAACATTCCATGCACAAGAAATCG
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCACAGGAAATCG
* * * * * * *
5068 CATCATATGGCCTAAATA-TTTGGCCATTTTCTACACAAGTTTTGGTCTTTGAATTAAAAACGTA
129 CATCATTTGGTCTAAATAGTTT-GTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA
*
5132 TTTAAGTGAGAATTGTTTCTC-
193 TTTACGTGAGAATTGTTTCTCT
* * * * * * *
5153 TTGGTTCTTGGACGAAC-TTCAGAACTAGTAAAACTTTTACAAGATCCTTTATTACTTCGGTTCT
1 TTGGTTCTTGGACAAACTTTCA-AACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCC
* * * * * * *
5217 TTAAAAGTATTCAAGATGA-CCATTCTTTCGAACAATTTCTCGAACATTCCATTCTCGGGAAATT
65 TT-AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT-TCGAACATTCCATGCACAGGAAATC
** * * * * * *
5281 AAATCATTTTGTCTAAATA-TTTTTCATTCTGTAAACATGTTTTCATCTTTGAATTAAAAACTCA
128 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA
5345 TTTACGTGAGAATTGTTTCTCT
193 TTTACGTGAGAATTGTTTCTCT
* ** *
5367 ATTGGTTCTAGGACAAACTTTTGAACTTGTCAAACTTTT---A----C----T---TT-GGTACC
1 -TTGGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCC
* * * * * * *
5417 TTAAAGTATTCAAGACTATCAATTCCTTCTAGCAATTTTCTGAACATTCTATTCTCATGAAATCG
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-GAACATTCCATGCACAGGAAATCG
* * **
5482 CATCATTTGGTCTAAATAGTATGTCATTTTATAAA-AAAATTT-ATCTTTGAATTAAAAACTTAT
129 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTAT
5545 TTACGTGAGAATTGTTTCTCT
194 TTACGTGAGAATTGTTTCTCT
* * *
5566 CTTGGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTATGAGTTTCGTTATAACTTCGGTTCC
1 -TTGGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCC
* * * * * *
5631 TTAAGGTATTCAAGACAATCCATTCCTTCCAGAAATTTTCTGAACATTCCATGCTA-GGGTAATC
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-GAACATTCCATGC-ACAGGAAATC
* * * * * *
5695 GAATCATTTGGTCTAAATAGTTTGTAATTTTGTAAACAAGTTTTGGTGTTTAAATTAAGAACTTA
128 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTA
*
5760 TTTATGTGAGAATTGTTTCTCT
193 TTTACGTGAGAATTGTTTCTCT
* * *** * *
5782 ATTGGTT-TTGCGACGAGCTTTCAAACTTCAAAAACTTTTACGAGTTCTTTTTATAACTTTGGTT
1 -TTGGTTCTTG-GACAAACTTTCAAACTTGTCAAACTTTTACGAGTTC-CTTTATAACTTCGGTT
* * * *
5846 CCTTAAAGCATTCAAGATGATCCATTCCTCCGAGCAATTTTCCGAACATTCCATGCACAAAAGAA
63 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-CGAACATTCCATGCAC--AGGAA
* * *
5911 ATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAGAAATTTTGATCTTTGAATTTAAAAC
125 ATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAAC
*
5976 TTATTTACGTGAGAATTGGTTCT
190 TTATTTACGTGAGAATTGTTTCT
5999 AATATGATTC
Statistics
Matches: 864, Mismatches: 156, Indels: 74
0.79 0.14 0.07
Matches are distributed among these distances:
199 92 0.11
200 60 0.07
201 14 0.02
202 1 0.00
204 1 0.00
206 1 0.00
208 1 0.00
210 1 0.00
211 5 0.01
212 144 0.17
213 65 0.08
214 187 0.22
215 53 0.06
216 99 0.11
217 60 0.07
218 1 0.00
219 79 0.09
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (214 bp):
TTGGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGTTCCT
TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCGAACATTCCATGCACAGGAAATCGCA
TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTATTT
ACGTGAGAATTGTTTCTCT
Found at i:5569 original size:414 final size:427
Alignment explanation
Indices: 4727--5998 Score: 1114
Period size: 414 Copynumber: 3.0 Consensus size: 427
4717 GATCGATCAA
* * * * * * ** * *
4727 TTGGTTC-TGAGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAATTTTGGTTCC
1 TTGGTTCTTG-GACAAACTTTCAAACTAGTAAAACTTTTACAAGATCCGTTATAACTTCGGTTCC
* * * * * *
4791 TTAAAATATTAAAGACGATCCATTCCTTCGAGCAATTTT-TCGAACATTCCATGCTCGGGAAATC
65 TTAAAGTATTCAAGACAATCCATTCCTTCCAGAAATTTTCT-GAACATTCCATGCTAGGGAAATC
* * * * * * * ** * * *
4855 ACAT-AGTTTGGTCTAAATAGTTTTTCATTTTGTTATCAACTTTTGGTATTTGAA-T---AACTT
129 AAATCA-TTTGGTCTAAATAGTTTGTAATTCTGTAAACAAGTTTTCATCTTTAAATTAAAAACTC
* * * * * * *** * *
4915 ATTTACGTAAGAATTGTTTCTCTTTATGTTCTTG-GACAAACTTTCAAACTTGTCAAACTTTTAT
193 ATTTACGTGAGAATTGTTTCTCTAT-TGGT-TTGCGAC-GA-GTACAAACTTCAAAAACTTGTAC
* * * * * *
4979 GAG--TTTCATTATAACTTCGGTTCCTTAATGTATTCAAGACGATCTATTCGTTCGAGCAATTTT
254 GAGAACTT--TTATAACTTTGGTTCCTTAAAGTATTCAAGACTATCAATTCCTTCGAGCAATTTT
* * * * *
5042 -TCGAACATTCCATGCACAAGAAATCGCATCATATGGCCTAAATA-TTTGGCCATTTTCTACACA
317 CT-GAACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTT-GTCATTTTATA-AAA
* * * *
5105 AGTTTTGGTCTTTGAATTAAAAACGTATTTAAGTGAGAATTGTT-TCTC
379 AATTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTC
* * * *
5153 TTGGTTCTTGGACGAAC-TTCAGAACTAGTAAAACTTTTACAAGATCCTTTATTACTTCGGTTCT
1 TTGGTTCTTGGACAAACTTTCA-AACTAGTAAAACTTTTACAAGATCCGTTATAACTTCGGTTCC
** * * * *
5217 TTAAAAGTATTCAAGATGA-CCATT-CTTTC-GAACAATTTCTCGAACATTCCATTCTCGGGAAA
65 TT-AAAGTATTCAAGACAATCCATTCCTTCCAGAA-ATTTTCT-GAACATTCCATGCTAGGGAAA
* * * * * *
5279 TTAAATCATTTTGTCTAAATA-TTTTTCATTCTGTAAACATGTTTTCATCTTTGAATTAAAAACT
127 TCAAATCATTTGGTCTAAATAGTTTGTAATTCTGTAAACAAGTTTTCATCTTTAAATTAAAAACT
* ***
5343 CATTTACGTGAGAATTGTTTCTCTATTGG-TT-CTA-G-G-ACAAACTT-TTGAACTTGT-C-A-
192 CATTTACGTGAGAATTGTTTCTCTATTGGTTTGCGACGAGTACAAACTTCAAAAACTTGTACGAG
* *
5399 AAC-TTT-T-ACTTTGGTACCTTAAAGTATTCAAGACTATCAATTCCTTCTAGCAATTTTCTGAA
257 AACTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACTATCAATTCCTTCGAGCAATTTTCTGAA
* * * * * *
5461 CATTCTATTCTCATGAAATCGCATCATTTGGTCTAAATAGTATGTCATTTTATAAAAAAATTT-A
322 CATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTATAAAAAATTTTGA
5525 TCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
387 TCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTCTCTC
* * ** * *
5567 TTGGTTCTTGGACAAACTTTCAAACTTGTCAAACTTTTATGAGTTTCGTTATAACTTCGGTTCCT
1 TTGGTTCTTGGACAAACTTTCAAACTAGTAAAACTTTTACAAGATCCGTTATAACTTCGGTTCCT
* * *
5632 TAAGGTATTCAAGACAATCCATTCCTTCCAGAAATTTTCTGAACATTCCATGCTAGGGTAATCGA
66 TAAAGTATTCAAGACAATCCATTCCTTCCAGAAATTTTCTGAACATTCCATGCTAGGGAAATCAA
* ** * * *
5697 ATCATTTGGTCTAAATAGTTTGTAATTTTGTAAACAAGTTTTGGTGTTTAAATTAAGAACTTATT
131 ATCATTTGGTCTAAATAGTTTGTAATTCTGTAAACAAGTTTTCATCTTTAAATTAAAAACTCATT
* * * *
5762 TATGTGAGAATTGTTTCTCTATTGGTTTTGCGACGAGCTTTCAAACTTCAAAAACTTTTACGAGT
196 TACGTGAGAATTGTTTCTCTATTGG-TTTGCGACGAG--TACAAACTTCAAAAACTTGTACGAGA
* * * * *
5827 TCTTTTTATAACTTTGGTTCCTTAAAGCATTCAAGA-TGATCCATTCCTCCGAGCAATTTTCCGA
258 AC-TTTTATAACTTTGGTTCCTTAAAGTATTCAAGACT-ATCAATTCCTTCGAGCAATTTTCTGA
*
5891 ACATTCCATGCACAAAAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAGAAATT
321 ACATTCCATGCAC--AAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTATAAA-AAATT
*
5956 TTGATCTTTGAATTTAAAACTTATTTACGTGAGAATTGGTTCT
383 TTGATCTTTGAATTAAAAACTTATTTACGTGAGAATT-GTTCT
5999 AATATGATTC
Statistics
Matches: 684, Mismatches: 118, Indels: 79
0.78 0.13 0.09
Matches are distributed among these distances:
412 32 0.05
413 21 0.03
414 184 0.27
415 79 0.12
416 5 0.01
417 2 0.00
418 4 0.01
419 1 0.00
420 8 0.01
421 7 0.01
423 7 0.01
424 8 0.01
425 37 0.05
426 97 0.14
427 17 0.02
428 2 0.00
429 30 0.04
430 2 0.00
431 56 0.08
433 41 0.06
434 6 0.01
435 37 0.05
436 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (427 bp):
TTGGTTCTTGGACAAACTTTCAAACTAGTAAAACTTTTACAAGATCCGTTATAACTTCGGTTCCT
TAAAGTATTCAAGACAATCCATTCCTTCCAGAAATTTTCTGAACATTCCATGCTAGGGAAATCAA
ATCATTTGGTCTAAATAGTTTGTAATTCTGTAAACAAGTTTTCATCTTTAAATTAAAAACTCATT
TACGTGAGAATTGTTTCTCTATTGGTTTGCGACGAGTACAAACTTCAAAAACTTGTACGAGAACT
TTTATAACTTTGGTTCCTTAAAGTATTCAAGACTATCAATTCCTTCGAGCAATTTTCTGAACATT
CCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTATAAAAAATTTTGATCTT
TGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTC
Found at i:6597 original size:74 final size:74
Alignment explanation
Indices: 6471--6620 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 74
6461 CTTTACAAAA
* *
6471 TGAAAGTGAACAGCCATCATTCATCATTTATAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAGCCATCATTCATCATTCAAAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
6536 ATGAAACAT
66 ATGAAACAT
* * * *
6545 TGAATGTGAATAGCTATCATTCATCATTCAAAAATGAATGTGTTTATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAGCCATCATTCATCATTCAAAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
6610 ATGAAACAT
66 ATGAAACAT
6619 TG
1 TG
6621 TATCCCTCCA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (74 bp):
TGAAAGTGAACAGCCATCATTCATCATTCAAAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
ATGAAACAT
Found at i:12150 original size:28 final size:28
Alignment explanation
Indices: 12118--12173 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12108 GAATCTAATA
12118 TTTTTCATTTAATTTCTTTTCATTTCTT
1 TTTTTCATTTAATTTCTTTTCATTTCTT
* *
12146 TTTTTCATTTATTTTCTTTTCTTTTCTT
1 TTTTTCATTTAATTTCTTTTCATTTCTT
12174 CCAAACAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTTCATTTAATTTCTTTTCATTTCTT
Found at i:14225 original size:216 final size:215
Alignment explanation
Indices: 13601--14337 Score: 923
Period size: 216 Copynumber: 3.4 Consensus size: 215
13591 GTTCAGAGAC
* *** *
13601 GAAC-TTCTGAACTTG-TCAACTTTTACGAGTTCTTTTATAACTTCATTTCCTTAAAGTATTGAA
1 GAACTTTC-GAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* *
13664 GACA-ATCCATTCCTTCGAGTAA-TTTCTCGAACATTCCATGCTCGGAAAATTGCATCATTTGGT
65 GA-AGATCCATTCCTTCGAGCAATTTTC-CGAACATTCCATGCTCGGAAAATCGCATCATTTGGT
* *
13727 CTAAATAGTTTTTCATTTTGTTATCAACCTTTGCTCTTTGAATTAAAAACTTATTTACGTGAGAA
128 CTAAATAGTTTTTCATTTTGTTATCAACTTTTGGTCTTTGAATTAAAAAC-TATTTACGTGAGAA
13792 TTGTTTCTCTCTTGGTTCTTGGAT
192 TTGTTTCTCTCTTGGTTCTTGGAT
* * * * *
13816 GAACTTTCAAACTTGTTAAACTTTT-CTGAGTTCTTTTATAAATTCGGTTCATCAAAGTATTCAA
1 GAACTTTCGAACTTGTTAAACTTTTAC-GAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* * * * **
13880 G-ATATCCATT-CTCTCGAGCTATTTTCTGAACATTCCATGCACAAAAAATCGCATCATTTGGTC
65 GAAGATCCATTCCT-TCGAGCAATTTTCCGAACATTCCATGCTCGGAAAATCGCATCATTTGGTC
* * * * * * *
13943 TAAATAGTTTGTCACTTTGTAAACAAATTTTGGTCTTTGAATTACAAAGCTATTTACGTAAGAAT
129 TAAATAGTTTTTCATTTTGTTATCAACTTTTGGTCTTTGAATTA-AAAACTATTTACGTGAGAAT
* ***
14008 TGTTTCTCTATTGGTTCGAAGAT
193 TGTTTCTCTCTTGGTTCTTGGAT
* * * *
14031 GAAC-TTCTGAACTTATTAAACTTTTACGAGTTCTTGTATAACTTTTGTTCCTTAAAGTATTGAA
1 GAACTTTC-GAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* * **
14095 GAAGATCTATTCCTTTGAGCAATTTTCCGAACATTCCATGCTCGGGTAATCGCATCATTTGGTCT
65 GAAGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCT
*
14160 AAATAGTTTTTCATTTTGTTATCAACTTTTGGTCTTTGAATTAAAAACTGATTTACATGAGAATT
130 AAATAGTTTTTCATTTTGTTATCAACTTTTGGTCTTTGAATTAAAAACT-ATTTACGTGAGAATT
14225 GTTTCTCTCTTGGTTCTTGGAT
194 GTTTCTCTCTTGGTTCTTGGAT
* * * *
14247 GAACTTTCGAACATGTCAAACTTTTACGAGTTTTTTTATAACTTTGGTTCCATAAAGTATTCAAG
1 GAACTTTCGAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* *
14312 ACGATCCATTCCTTTGAGCAATTTTC
66 AAGATCCATTCCTTCGAGCAATTTTC
14338 TTGGGAAATA
Statistics
Matches: 440, Mismatches: 69, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
214 6 0.01
215 181 0.41
216 248 0.56
217 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (215 bp):
GAACTTTCGAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
AAGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTA
AATAGTTTTTCATTTTGTTATCAACTTTTGGTCTTTGAATTAAAAACTATTTACGTGAGAATTGT
TTCTCTCTTGGTTCTTGGAT
Found at i:17830 original size:50 final size:51
Alignment explanation
Indices: 17776--17889 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 51
17766 TAGTTATGTT
17776 TGCATCATAAATAATGA-CATGCATAAAGTAACTTAC-ATGTTAGTTAAA-TA
1 TGCATCATAAATAAT-ACCATGCATAAAGTAAC-TACTATGTTAGTTAAAGTA
** * * * *
17826 TGCATCATAAATCCTACCATGCATTATGTAACTCCTATGTTAGTTAAAGTT
1 TGCATCATAAATAATACCATGCATAAAGTAACTACTATGTTAGTTAAAGTA
17877 TGCATCATTAAAT
1 TGCATCA-TAAAT
17890 CAAGTCATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
49 3 0.06
50 38 0.70
51 8 0.15
52 5 0.09
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (51 bp):
TGCATCATAAATAATACCATGCATAAAGTAACTACTATGTTAGTTAAAGTA
Found at i:17908 original size:52 final size:50
Alignment explanation
Indices: 17812--17908 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 50
17802 AGTAACTTAC
*
17812 ATGTTAGTTAAATATGCATCATAAATCCTACCATGCATTATGTAACTCCT
1 ATGTTAGTTAAATATGCATCATAAATCCAACCATGCATTATGTAACTCCT
* * *
17862 ATGTTAGTTAAAGTTTGCATCATTAAAT-CAAGTCATGCATTTTGTAA
1 ATGTTAGTTAAA-TATGCATCA-TAAATCCAA-CCATGCATTATGTAA
17909 TCCATAGTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 12 0.30
51 10 0.25
52 18 0.45
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (50 bp):
ATGTTAGTTAAATATGCATCATAAATCCAACCATGCATTATGTAACTCCT
Found at i:19138 original size:24 final size:23
Alignment explanation
Indices: 19106--19156 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
19096 TAGAAAAAGT
19106 AAAAAAAAA-TCGAAATATTGAAAA
1 AAAAAAAAATTCGAAAT-TT-AAAA
*
19130 AAAAAAAAATTCGAAGTTTAAAA
1 AAAAAAAAATTCGAAATTTAAAA
19153 AAAA
1 AAAA
19157 GAAGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 11 0.44
25 6 0.24
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAAAAAAATTCGAAATTTAAAA
Found at i:21891 original size:50 final size:50
Alignment explanation
Indices: 21825--21953 Score: 134
Period size: 50 Copynumber: 2.5 Consensus size: 50
21815 TTACATCCAT
*
21825 TAACTCTCATGATTAGTTAAGTTTGCATAATAAATAATGA-CATGCATAAAG
1 TAACTCACATG-TTAGTTAAGTTTGCATAATAAATAAT-ATCATGCATAAAG
* * * * ** * *
21876 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAGTTTGCATAATAAATAATATCATGCATAAAG
*
21926 TAACTCCCATGTTAGTTAAAGTTTGCAT
1 TAACTCACATGTTAGTT-AAGTTTGCAT
21954 CATTAAATCA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.02
50 45 0.71
51 17 0.27
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAGTTTGCATAATAAATAATATCATGCATAAAG
Found at i:25251 original size:15 final size:15
Alignment explanation
Indices: 25233--25271 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
25223 GACAAACACA
*
25233 TTGCGAGCACTGATG
1 TTGCGAGCACTCATG
* *
25248 TTGCCAACACTCATG
1 TTGCGAGCACTCATG
25263 TTGCGAGCA
1 TTGCGAGCA
25272 TGGATGAAGG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (15 bp):
TTGCGAGCACTCATG
Found at i:25842 original size:39 final size:39
Alignment explanation
Indices: 25796--25894 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
25786 TTAAATAGAG
25796 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
25835 TTTTAATGTGTCTTATTTTCATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
25874 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
25895 GACAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:25969 original size:32 final size:32
Alignment explanation
Indices: 25933--25998 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
25923 TAGCCGAAAT
* *
25933 TAATTAGCTGATTAATGTGTTTCAGGTACATG
1 TAATTAGCTGATTAATATATTTCAGGTACATG
25965 TAATTAGCTGATTAATATATTTCAGGTACATG
1 TAATTAGCTGATTAATATATTTCAGGTACATG
25997 TA
1 TA
25999 TGGATGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (32 bp):
TAATTAGCTGATTAATATATTTCAGGTACATG
Done.