Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016407.1 Corchorus olitorius cultivar O-4 contig16440, 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: 66115
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:990 original size:333 final size:333
Alignment explanation
Indices: 141--1691 Score: 2148
Period size: 334 Copynumber: 4.7 Consensus size: 333
131 TTTTAGCGTT
* * * * * * *
141 GAGCATATGAAACTTGTTTTGATTTATTTAGAAATTAAGTTAGAAAAAATAAGAAATACGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATT
* * * ** *
206 TAAAGCGTGAAAAATCCTCCAATCTTTTTGAAGTTAAATTATACTATATTTTTTATGAGTATTTT
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATA-TATA--TTTTATAAGTATTTT
* * * * * * * *
271 AGCCAAAAAATTAAGGAAATATCTTTC-AGGTCA-ATTTTTACTAAATTTTAGCTAAAATCGTGT
128 ATCC-AAAAATTGAGGAAAAATTTTTCGA-GTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGT
* ** * * * * * *
334 AATAACCATCATAGTTTTTGGCTAAAAAAGCG-TTCAGGGGCCACGGCTCAGTTTTACATGATTT
191 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GAGACCCCGTCTCAGTTTTGCATGATTT
* * * * * * * ** *
398 TTGGCGCCAAGACTCATTGAGATATCCATATTCATCTAATCATATCCCAGCCACATTGGATTTAA
255 TTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAA
* *
463 AAATTTGTTTTTAC
320 GAATTTGCTTTTAC
* * * *
477 GAGTATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAGAAATATCAAAAAACGATAT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAT-GAAAAACGATAT
542 TAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTAT
65 TAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTAT
* *
607 CCAAAAATTGAGGAAAAGTTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACCA
130 CCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTA
*
672 ACCATCACGGTTTTTGACTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGC
195 ACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGC
* **
737 ACCGAGACTCCTTGAAATATCTATATTCATTTAATAAAATCTTAGAGACATTGCATTTAAGAATT
260 ACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATT
802 TGCTTTTAC
325 TGCTTTTAC
* *
811 GAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATT
* * * *
876 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCATTAAATTTTATACATTTTATAGGTATTTTATC
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
* * *
941 CAATAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCACACTTTTAGCCAAAATCGTGTACGT-
131 CAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTAC-TA
* * *
1005 ----TCACGGTTTTTGGCTAAAAACGTGTTTCGAGACACCGCCTCAGTTTTGCATGATTTTTGGC
195 ACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGC
1066 ACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATT
260 ACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATT
1131 TGCTTTTAC
325 TGCTTTTAC
* * *
1140 GAGCATCTGAATCTTATTTCGTTTTAATTAGAAATTAATTTAG-TAAAATATGAAAAACGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATT
* *
1204 AAAAGCGCGAAAAGTCCTCCAATTTTTTTGGCGTTTAATTATATATATATTTTATAAGTATTTTA
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCG-TTAAAT-TATATATATTTTATAAGTATTTTA
* * **
1269 TCCAAAAATTTAGGAAAAATTTTTTGAGTCATTTTTTTGCAAAATTTTAGTTAAAATCGTGTACT
129 TCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACT
1334 AACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGG
194 AACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGG
* *
1399 CCCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATATAAGAAT
259 CACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAAT
1464 TTGCTTTTAC
324 TTGCTTTTAC
* *
1474 GAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATT
* * *
1539 AAAAGCGTGAAAAGTCCTTCAATTTTTTTGGCGCTAAATTATATATATTTTGTAAGTATTTTATC
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
* ** * * *
1604 CAAAAATTGAGAAAAAAAATTTCGATTTATTTTTTTGCAAAATTTTAGTCAAAATCGTGTACTAA
131 CAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAA
* *
1669 CCATCACGTGTTTTGGGGTAAAA
196 CCATCACG-GTTTTTGGCTAAAA
1692 GTATTCGGGA
Statistics
Matches: 1086, Mismatches: 115, Indels: 30
0.88 0.09 0.02
Matches are distributed among these distances:
328 50 0.05
329 174 0.16
330 78 0.07
333 242 0.22
334 393 0.36
335 53 0.05
336 47 0.04
337 49 0.05
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (333 bp):
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATT
AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
CAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAA
CCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCA
CCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTT
GCTTTTAC
Found at i:1614 original size:663 final size:662
Alignment explanation
Indices: 141--1665 Score: 2144
Period size: 663 Copynumber: 2.3 Consensus size: 662
131 TTTTAGCGTT
* * * * * * * *
141 GAGCATATGAAACTTGTTTTGATTTATTTAGAAATTAAGTTAGAAAAAATAAGAAATACGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
* * * ** *
206 TAAAGCGTGAAAAATCCTCCAATCTTTTTGAAGTTAAATTATACTATATTTTTTATGAGTATTTT
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATA-TATA--TTTTATAAGTATTTT
* * * * * * *
271 AGCCAAAAAATTAAGGAAATATCTTTC-AGGTCA-ATTTTTACTAAATTTTAGCTAAAATCGTGT
128 ATCC-AAAAATTGAGGAAAAATATTTCGA-GTCATTTTTTTGC-AAATTTTAGCCAAAATCGTG-
* * * *
334 AATAACCATCATAGTTTTTGGCTAAAAAAGCGTTCAGGGGCCACGGCTCAGTTTTACATGATTTT
189 --T-ACCATCACAGTTTTTGGCTAAAAAAGCGTTCAGAGACCACGCCTCAGTTTTACATGATTTT
* * * * *
399 TGGCGCCAAGACTCATTGAGATATCCATATTCATCTAATCATATCCCAGCCACATTGGATTTAAA
251 TGGCACCAAGACTCATTGAAATATCCATATTCATCTAATAAAATCCCAGCCACATTGCATTTAAA
* * *
464 AATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTAGAAGAAATAT
316 AATTTGCTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATTAATTTAGAAGAAATAT
*
529 CAAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTT
381 CAAAAAACGATATTAAAAGCGCGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTT
*
594 ATAAGTATTTTATCCAAAAATTGAGGAAAAGTTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCA
446 ATAAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCA
659 AAATCGTGTACCAACCATCACGGTTTTTGACTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTG
511 AAATCGTGTACCAACCATCACGGTTTTTGACTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTG
* *
724 CATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATTTAATAAAATCTTAGAGACATT
576 CATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGACACATT
*
789 GCATTTAAGAATTTGCTTTTAC
641 GCATATAAGAATTTGCTTTTAC
*
811 GAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
* * * *
876 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCATTAAATTTTATACATTTTATAGGTATTTTATC
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
* * * **
941 CAATAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCACACTTTTAGCCAAAATCGTGTACGTT
131 CAAAAATTGAGGAAAAATATTTCGAGTCATTTTTTTGCA-AATTTTAGCCAAAATCGTGTACCAT
* * * *
1006 CACGGTTTTTGGCTAAAAACGTGTTTC-GAGA-CACCGCCTCAGTTTTGCATGATTTTTGGCACC
195 CACAGTTTTTGGCTAAAAAAGCG-TTCAGAGACCA-CGCCTCAGTTTTACATGATTTTTGGCACC
* * * ** *
1069 GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGC
258 AAGACTCATTGAAATATCCATATTCATCTAATAAAATCCCAGCCACATTGCATTTAAAAATTTGC
* * * *
1134 TTTTACGAGCATCTGAATCTTATTTCGTTTTAATTAGAAATTAATTTAGTA-AAATAT-GAAAAA
323 TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATTAATTTAGAAGAAATATCAAAAAA
*
1197 CGATATTAAAAGCGCGAAAAGTCCTCCAATTTTTTTGGCGTTTAATTATATATATATTTTATAAG
388 CGATATTAAAAGCGCGAAAAGTCCTCCAATTTTTTTGGCG-TTAAAT-TATATATATTTTATAAG
* * **
1262 TATTTTATCCAAAAATTTAGGAAAAATTTTTTGAGTCATTTTTTTGCAAAATTTTAGTTAAAATC
451 TATTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATC
* *
1327 GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGA
516 GTGTACCAACCATCACGGTTTTTGACTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGA
* *
1392 TTTTTGGCCCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATA
581 TTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGACACATTGCATA
1457 TAAGAATTTGCTTTTAC
646 TAAGAATTTGCTTTTAC
*
1474 GAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
1 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
* * *
1539 AAAAGCGTGAAAAGTCCTTCAATTTTTTTGGCGCTAAATTATATATATTTTGTAAGTATTTTATC
66 AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
* * * * *
1604 CAAAAATTGAGAAAAAAAATTTCGATTTATTTTTTTGCAAAATTTTAGTCAAAATCGTGTAC
131 CAAAAATTGAGGAAAAATATTTCGAGTCATTTTTTTGC-AAATTTTAGCCAAAATCGTGTAC
1666 TAACCATCAC
Statistics
Matches: 760, Mismatches: 87, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
661 44 0.06
662 13 0.02
663 540 0.71
664 5 0.01
666 23 0.03
667 40 0.05
669 3 0.00
670 92 0.12
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (662 bp):
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATT
AAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATC
CAAAAATTGAGGAAAAATATTTCGAGTCATTTTTTTGCAAATTTTAGCCAAAATCGTGTACCATC
ACAGTTTTTGGCTAAAAAAGCGTTCAGAGACCACGCCTCAGTTTTACATGATTTTTGGCACCAAG
ACTCATTGAAATATCCATATTCATCTAATAAAATCCCAGCCACATTGCATTTAAAAATTTGCTTT
TACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATTAATTTAGAAGAAATATCAAAAAACGA
TATTAAAAGCGCGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTT
TATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTA
CCAACCATCACGGTTTTTGACTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTT
GGCACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGACACATTGCATATAAGA
ATTTGCTTTTAC
Found at i:1919 original size:15 final size:14
Alignment explanation
Indices: 1896--1925 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1886 ATAAAAATTA
1896 AATATTTTTATTTT
1 AATATTTTTATTTT
1910 AATATATTTTATTTT
1 AATAT-TTTTATTTT
1925 A
1 A
1926 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:3404 original size:15 final size:15
Alignment explanation
Indices: 3372--3401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3362 TAAATTTCAA
3372 TAAAATAAAATATAT
1 TAAAATAAAATATAT
3387 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
3401 T
1 T
3402 TAATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:4224 original size:333 final size:333
Alignment explanation
Indices: 3612--5387 Score: 2582
Period size: 332 Copynumber: 5.3 Consensus size: 333
3602 GGTACTTTTA
*
3612 CACGGGTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
3677 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
66 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
* *
3742 TTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAACATGAAAAATGA
131 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGA
* * * * * * *
3806 TATTGAAATCGTGAAAAGTCCTCCAATTTTTTTTGGAGCTAAATTATATATATATTGTAAGTATC
196 TATTAAAAGCGTGAAAAGTCCTCCAA-TTTTTTTGGCGTTAAATTATATATATTTTATAAGTATT
3871 TTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGT
260 TTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGT
3936 ACCAACCAT
325 ACCAACCAT
* * *
3945 CACGATTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCACTGA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
*
4010 GACTCCTTGAAATATCTATATACATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
66 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
* *
4075 TTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTTGAAAAAATATGAAAAATGA
131 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGA
* ** * *
4140 TACTAAAAGATTGAAAAGTCCTCCAATTTTTTTGGCGGTAAATTATATATATTTTATAATTATTT
196 TATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTT
*
4205 TATCCAAAAATTGAGGAAAAATTTTTCGAGTCA-TTTTTTCCAAAATTTTAGCCAAAATCGTGTA
261 TATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTA
4269 CCAACCAT
326 CCAACCAT
** * *
4277 CACGGTTAATGGCTAAAAACGCGTTTCGAGAACCCGTCTCAGTTTTGCATGATTTTTGGCGCCAA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
** * * ** * * * *
4342 GACTCCTTGTGATATCCATATTCATCTAATCAAATCCCAGCCAAATTGGATTTAAAAATTTGTTT
66 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
* * * * * *
4407 TTACGAGAACCTAAATCTTGTTTCAATTTAATTAGATATTAATTCAAGAAAAATATGATGATATT
131 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TAGAAAAA-AT-ATG--A--
* *
4472 AAAAGTGTGAATATTAAAAGCGTGAAAAGTCCTCCATTTTTTTTGGCGTTAAATTTTATATATTT
189 AAAA---TG-ATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTT
* * *
4537 TATAAGTATTTTATCCATAAATTAAGGAAAACTTTTTCGAGTCATTTTTTTTGCAAAATTTTAGC
250 TATAAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCA-TTTTTTTGCAAAATTTTAGC
*
4602 CAAAATCGTGTACTC-ATCAT
314 CAAAATCGTGTAC-CAACCAT
*
4622 CACAGTTTTTGGCTAAAAACGCGTTTCGAGA-CCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
4686 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
66 GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
*
4751 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAACATGAAAAATGA
131 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGA
* * *
4816 TATTAAAAGCGTGAAAAGTCTTCCAATTTTTTTGGCGTTAAATTATCTATATATTATAAGTATTT
196 TATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTT
* * *
4881 TATCCAAAAATTTAGGAAAAATTTTTTGATTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTA
261 TATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTA
*
4946 CTAACCAT
326 CCAACCAT
* * * ** *
4954 CACGGTTTTTGGCTAATAACGCGTTTCGGGGACCCAG-CTCCA-TTTTATATGATTTTTGGCTCC
1 CACGGTTTTTGGCTAAAAACGCGTTTC-GAGACCCCGTCT-CAGTTTTGCATGATTTTTGGCGCC
* * * *
5017 GAAACTACTTCAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGC
64 GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGC
*
5082 TTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAATAT-AAAAAT
129 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAAT
*
5145 GATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTTGGCGTTGAATTATATATATTTTATAAGTA
194 GATATTAAAAGCGTGAAAAGTCCTCCAA-TTTTTTTGGCGTTAAATTATATATATTTTATAAGTA
5210 TTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGT
258 TTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGT
*
5275 GTACTAACCAT
323 GTACCAACCAT
* * * * ** *
5286 CACGGTTTTTGGCTAATAACGCGTTCCGGGGACCCAG-CTCCA-TTTTATATGATTTTTGGCTCC
1 CACGGTTTTTGGCTAAAAACGCGTTTC-GAGACCCCGTCT-CAGTTTTGCATGATTTTTGGCGCC
* * * *
5349 GAAACTACTTCAAATATCTATATTCATCTAATCAAATCT
64 GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCT
5388 GTGACACTAT
Statistics
Matches: 1310, Mismatches: 113, Indels: 41
0.89 0.08 0.03
Matches are distributed among these distances:
331 33 0.03
332 464 0.35
333 462 0.35
334 46 0.04
335 3 0.00
337 5 0.00
339 5 0.00
341 3 0.00
342 3 0.00
343 96 0.07
344 126 0.10
345 63 0.05
346 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (333 bp):
CACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGA
GACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTT
TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGA
TATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTT
TATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTA
CCAACCAT
Found at i:4487 original size:15 final size:15
Alignment explanation
Indices: 4467--4497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4457 AAATATGATG
*
4467 ATATTAAAAGTGTGA
1 ATATTAAAAGCGTGA
4482 ATATTAAAAGCGTGA
1 ATATTAAAAGCGTGA
4497 A
1 A
4498 AAGTCCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (15 bp):
ATATTAAAAGCGTGA
Found at i:4901 original size:676 final size:665
Alignment explanation
Indices: 3621--5387 Score: 2577
Period size: 676 Copynumber: 2.6 Consensus size: 665
3611 ACACGGGTTT
* *
3621 TGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTG
1 TGGCTAAAAACGCGTTTCGAGAACCCGTCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
*
3686 AAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAGCA
66 AAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAGCA
* *
3751 TCTCAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAACATG--AAAAATGATATTGAAA
131 TCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAA-ATGATAAAAATGATATTAAAA
* * * * * *
3814 TCGTGAAAAGTCCTCCAATTTTTTTTGGAGCTAAATTATATATATATTGTAAGTATCTTATCCAA
195 GCGTGAAAAGTCCTCCAATTTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAA
3879 AAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTAC-CAACC
260 AAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTC-ACC
*
3943 ATCACGATTTTTGGCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCACT
324 ATCACG-TTTTTGGCTAAAAACGCGTTTCGAGA-CCCGTCTCAGTTTTGCATGATTTTTGGCACC
*
4008 GAGACTCCTTGAAATATCTATATACATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGC
387 GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGC
* *
4073 TTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTTGAAAAAATATGAAAAAT
452 TTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAACATGAAAAAT
* * *
4138 GATACTAAAAGATTGAAAAGTCCTCCAATTTTTTTGGCGGTAAATTATATATATTTTATAATTAT
517 GATACTAAAAGAGTGAAAAGTCCTCCAATTTTTTTGGCGGTAAATTATATATATATTATAAGTAT
4203 TTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCA-TTTTTTCCAAAATTTTAGCCAAAATCGTG
582 TTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTCCAAAATTTTAGCCAAAATCGTG
4267 TACCAACCATCACGGTTAA
647 TACCAACCATCACGGTTAA
4286 TGGCTAAAAACGCGTTTCGAGAACCCGTCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
1 TGGCTAAAAACGCGTTTCGAGAACCCGTCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
** * ** * * * * *
4351 TGATATCCATATTCATCTAATCAAATCCCAGCCAAATTGGATTTAAAAATTTGTTTTTACGAGAA
66 AAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAGCA
* * * *
4416 CCTAAATCTTGTTTCAATTTAATTAGATATTAATTCAAGAAAAATATGATGATATTAAAAGTGTG
131 TCTAAATCTTGTTTCGATTTAATTAGAAATTAATT-TAG-AAAA-A--ATGATA--AAAA---TG
*
4481 AATATTAAAAGCGTGAAAAGTCCTCC-ATTTTTTTTGGCGTTAAATTTTATATATTTTATAAGTA
186 -ATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTTGGCGTTAAATTATATATATTTTATAAGTA
* * *
4545 TTTTATCCATAAATTAAGGAAAACTTTTTCGAGTCATTTTTTTTGCAAAATTTTAGCCAAAATCG
250 TTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCA-TTTTTTTGCAAAATTTTAGCCAAAATCG
*
4610 TGTACTCATCATCACAGTTTTTGGCTAAAAACGCGTTTCGAGACCCGTCTCAGTTTTGCATGATT
314 TGTACTCACCATCAC-GTTTTTGGCTAAAAACGCGTTTCGAGACCCGTCTCAGTTTTGCATGATT
*
4675 TTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTA
378 TTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTA
*
4740 AGAATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAC
443 AGAATTTGCTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAC
* * * * *
4805 ATGAAAAATGATATTAAAAGCGTGAAAAGTCTTCCAATTTTTTTGGCGTTAAATTATCTATATAT
508 ATGAAAAATGATACTAAAAGAGTGAAAAGTCCTCCAATTTTTTTGGCGGTAAATTATATATATAT
* * * *
4870 TATAAGTATTTTATCCAAAAATTTAGGAAAAATTTTTTGATTCATTTTTTTGCAAAATTTTAGCC
573 TATAAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTCCAAAATTTTAGCC
* **
4935 AAAATCGTGTACTAACCATCACGGTTTT
638 AAAATCGTGTACCAACCATCACGGTTAA
* * * ** * *
4963 TGGCTAATAACGCGTTTCGGGGACCCAG-CTCCA-TTTTATATGATTTTTGGCTCCGAA-ACTAC
1 TGGCTAAAAACGCGTTTCGAGAACCC-GTCT-CAGTTTTGCATGATTTTTGGCGCC-AAGACTCC
* *
5025 TTCAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTAACGA
63 TTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGA
*
5090 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAAT-ATAAAAATGATATTAA
128 GCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATGATAAAAATGATATTAA
*
5153 AAGCGTGAAAAGTCCTCCAATTTTTTTTGGCGTTGAATTATATATATTTTATAAGTATTTTATCC
193 AAGCGTGAAAAGTCCTCCAATTTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCC
*
5218 AAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAAC
258 AAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCAC
* * * **
5283 CATCACGGTTTTTGGCTAATAACGCGTTCCGGGGACCCAG-CTCCA-TTTTATATGATTTTTGGC
323 CATCAC-GTTTTTGGCTAAAAACGCGTTTC-GAGACCC-GTCT-CAGTTTTGCATGATTTTTGGC
* * * * *
5346 TCCGAAACTACTTCAAATATCTATATTCATCTAATCAAATCT
384 ACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCT
5388 GTGACACTAT
Statistics
Matches: 985, Mismatches: 94, Indels: 46
0.88 0.08 0.04
Matches are distributed among these distances:
664 87 0.09
665 280 0.28
666 5 0.01
667 4 0.00
668 5 0.01
669 3 0.00
670 3 0.00
671 3 0.00
673 5 0.01
674 3 0.00
676 313 0.32
677 267 0.27
678 7 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (665 bp):
TGGCTAAAAACGCGTTTCGAGAACCCGTCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
AAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAGCA
TCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATGATAAAAATGATATTAAAAG
CGTGAAAAGTCCTCCAATTTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAA
AATTGAGGAAAAATTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCACCAT
CACGTTTTTGGCTAAAAACGCGTTTCGAGACCCGTCTCAGTTTTGCATGATTTTTGGCACCGAGA
CTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTT
ACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAACATGAAAAATGATA
CTAAAAGAGTGAAAAGTCCTCCAATTTTTTTGGCGGTAAATTATATATATATTATAAGTATTTTA
TCCAAAAATTGAGGAAAAATTTTTCGAGTCATTTTTTTCCAAAATTTTAGCCAAAATCGTGTACC
AACCATCACGGTTAA
Found at i:9731 original size:239 final size:240
Alignment explanation
Indices: 9385--9829 Score: 653
Period size: 239 Copynumber: 1.9 Consensus size: 240
9375 TACGAGCATC
* * *
9385 TGAATCTTGTTTCGATTTGATTTGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAGACCG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAACCG
* * * * * *
9450 TTAAAAGTTCTCATATTTTTAGAGTTGAATTCTAAATATTTTATAGGTATTTTATCCAAAAATTG
66 TGAAAAGTCCTCATATTTTTAGAGCTAAATTATAAATATTTTATAAGTATTTTATCCAAAAATTG
*
9515 AAGAAAAATCTTTCGAGTCA-TTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACG
131 AAGAAAAATCTTTCGAATCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACG
*
9579 GTTTTTGGCTATAAACGTGTTTCGATACCCCGTCTCAGATTTGCA
196 GTTCTTGGCTATAAACGTGTTTCGATACCCCGTCTCAGATTTGCA
* * *
9624 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAATAT-AAAAATGATATTAAAAGCG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAACCG
* * * * *
9687 TGAAAAGTCCTCCAATTTTTTTGGCGCTAAATTATATATATTTTATAATTATTTTATCCAAAAAT
66 TGAAAAGTCCT-C-ATATTTTTAGAGCTAAATTATAAATATTTTATAAGTATTTTATCCAAAAAT
* * *
9752 TGAGGAAAAATTTTTCGAATCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTAGTAACCATCA
129 TGAAGAAAAATCTTTCGAATCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCA
9817 CGGTTCTTGGCTA
194 CGGTTCTTGGCTA
9830 ATAACGCGTT
Statistics
Matches: 181, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
237 25 0.14
238 9 0.05
239 94 0.52
240 53 0.29
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (240 bp):
TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAACCG
TGAAAAGTCCTCATATTTTTAGAGCTAAATTATAAATATTTTATAAGTATTTTATCCAAAAATTG
AAGAAAAATCTTTCGAATCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACG
GTTCTTGGCTATAAACGTGTTTCGATACCCCGTCTCAGATTTGCA
Found at i:10575 original size:332 final size:329
Alignment explanation
Indices: 9624--10693 Score: 1238
Period size: 332 Copynumber: 3.3 Consensus size: 329
9614 CAGATTTGCA
*
9624 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATAT-AAAAATGATATTAAAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCGT
* * *
9688 GAAAAGTCCTCCAAT-TTTTTTGGCGCTAAATTATATATATTTTATAATTATTTTATCCAAAAAT
66 GAAAAGCCCTCCAATATTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAAAT
*
9752 TGAGGAAAAATTTTTCGAATCATTTTTTTTGCAAAATTTTAGCCAAAATCGTGTAGTAACCATCA
131 TGAGGAAAAA-TTTTCG-ATCA-TTTTTTTGCAAAATTTTAGCCAAAATCGTGTAAT-ACCATCA
* * * * * * * *
9817 CGGTTCTTGGCTAATAACGCGTTCCGGGGACCCAGCTCAATTTTACATGATTTTTGACTCCG-GA
192 CGGTTTTTGGCTAAAAACGCGTTTC-GAGACCCTGCTCAGTTTTACATGATTTTTGGCGCCGAG-
* * * *
9881 ACT-ACTTGAAATATCTATATTCAAT-TAACCAAATCTCAGACACATTGGATTTATGGATATGTT
255 ACTCA-TTGAAATATCTATATTC-ATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
*
9944 TTTACGAGCATA
318 TTTACGAGCATC
* * * *
9956 TGAATCTTGTTTCGATTTTATTAGAAATTAATTT-GGAAAATAGGAAAAACGATATTAGAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCGT
* * * * *
10020 CAAAAGCCCTTC-ATCA-TTTTTGGAGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAA
66 GAAAAGCCCTCCAAT-ATTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCC--AAA
** *
10082 AATTGAGG--AAA---T--ATC--TTTTAGGTC--AATTTTA-CCAAAATTGTGTAATAACCATC
128 AATTGAGGAAAAATTTTCGATCATTTTTTTG-CAAAATTTTAGCCAAAATCGTGTAAT-ACCATC
* * * * * *
10135 ACAGTTTTTGGCTAAAAAAGCG-TTCAAGGGCCATAGCTCAGTTTTACATGATTTTTGGCGCCAA
191 ACGGTTTTTGGCTAAAAACGCGTTTCGA-GACCCT-GCTCAGTTTTACATGATTTTTGGCGCCGA
* * * **
10199 GACTCCTTGAGATATCCATATTCATCTAATCAAAT-TCCAGCCACATTGGATTTAAAAATTTGTT
254 GACTCATTGAAATATCTATATTCATCTAATCAAATCT-CAGCCACATTGGATTTAAGGATTTGTT
*
10263 TTTACGAGTATC
318 TTTACGAGCATC
*
10275 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTGAAAGCG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAATATGAAAAACGATATTAAAAGCG
* *
10340 TTAAAAGTCCTCCAAT-TTTTGTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAA
65 TGAAAAGCCCTCCAATATTTT-TTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAA
*
10404 ATTGAGGAAAAACTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACT-CCATCA
129 ATTGAGGAAAAA-TTTTCGA-TCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTAATACCATCA
* * *
10468 CGGTTTTTAGCTAAAAACTCGTTTCGAGACCCTGTCTCAGTTTTGCATGATTTTTGGCGCCGAGA
192 CGGTTTTTGGCTAAAAACGCGTTTCGAGACCCTG-CTCAGTTTTACATGATTTTTGGCGCCGAGA
* * * * *
10533 CTCATTAAAATATATATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTT
256 CTCATTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
*
10598 ATGAGCATC
321 ACGAGCATC
*
10607 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCATA-AAAAATATGAAAAACGATATTAAAAGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATT--TAGAAAAATATGAAAAACGATATTAAAAGC
*
10671 GTGAAAAGCCCTTCAATATTTTT
64 GTGAAAAGCCCTCCAATATTTTT
10694 AGCGTTGAGC
Statistics
Matches: 617, Mismatches: 83, Indels: 76
0.80 0.11 0.10
Matches are distributed among these distances:
318 8 0.01
319 153 0.25
320 9 0.01
321 53 0.09
322 21 0.03
323 20 0.03
324 3 0.00
327 2 0.00
329 1 0.00
330 2 0.00
331 30 0.05
332 273 0.44
333 27 0.04
334 15 0.02
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (329 bp):
TGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCGT
GAAAAGCCCTCCAATATTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAAAT
TGAGGAAAAATTTTCGATCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTAATACCATCACGGT
TTTTGGCTAAAAACGCGTTTCGAGACCCTGCTCAGTTTTACATGATTTTTGGCGCCGAGACTCAT
TGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
CATC
Found at i:10745 original size:98 final size:100
Alignment explanation
Indices: 10599--10800 Score: 250
Period size: 98 Copynumber: 2.0 Consensus size: 100
10589 TTTGTTTTTA
* * **
10599 TGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCATAAAAAATATGAAAAACGATAT
1 TGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAACAAAAACGATAT
* * * *
10664 TAAAAGTGTGAAAAGCCCTTCAATATTTTTAGCGT
66 TAAAAGCGTGAAAAACCCTCCAATATTTTTAGCAT
* *
10699 TGAGCATATGGAA-CTTGTTT-GA-TTCATTAGAAATTAAGTT-AGAAAAAATAACAAATACGAT
1 TGAGCATAT-GAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAGAAAAAATAACAAAAACGAT
* *
10760 ATTAAAAGCGTGAAAAACCCTCCAATCTTTTTGGCAT
64 ATTAAAAGCGTGAAAAACCCTCCAATATTTTTAGCAT
10797 TGAG
1 TGAG
10801 TTATATATTT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
98 66 0.75
99 4 0.05
100 15 0.17
101 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (100 bp):
TGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAACAAAAACGATAT
TAAAAGCGTGAAAAACCCTCCAATATTTTTAGCAT
Found at i:11097 original size:433 final size:431
Alignment explanation
Indices: 10280--11126 Score: 1021
Period size: 433 Copynumber: 2.0 Consensus size: 431
10270 GTATCTGAAT
* ** * *
10280 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTGAAAGCGTTAAA
1 CTTGTTTCGATTTAATTAGAAATTAAGTTAGAAAAAATAACAAAAACGATATTAAAAGCGTGAAA
** * * *
10345 AGTCCTCCAATTTTTGTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAAATTGAG
66 AACCCTCCAATCTTTGTTGGCATTAAATTATATATATTTTATAAGTATTTTAGCCAAAAATTGAG
* *
10410 GAAAAACTTTTCGAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCCATCACGGTTTT
131 GAAAAACTTTTCGAGTCATATTTTTACAAAATTTTAGCCAAAATCGTGTACTCCATCACGGTTTT
* * * * * *
10475 TAGCTAAAAACTCGTTTCGAGACCCTGTCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCATTA
196 TAGCTAAAAACGCGTTCCGAGACCCTATCACAATTTTACATGATTTTTGGCGCCGAGACTCATTA
* * * * * *
10540 AAATATATATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTATGAGCA
261 AAATATATATATTCATCAAATAAAATCTCAGACACATTGCATTTAAGGATATGTTTTGACGAGCA
*
10605 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCATAAAAAATATGAAAAACGATATTAAAAG
326 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-ATAAAAAATAGGAAAAACGATATTAAAAG
* * *
10670 TGTGAAAAGCCCTTCAATATTTTTAGCGTTGAGCATATGGAA
390 CGTCAAAAGCCCTTCAATAGTTTTAGCGTTGAGCATATGGAA
* *
10712 CTTGTTT-GA-TTCATTAGAAATTAAGTTAGAAAAAATAACAAATACGATATTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAAGTTAGAAAAAATAACAAAAACGATATTAAAAGCGTGAAA
* * *
10775 AACCCTCCAATCTTT-TTGGCATTGAGTTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAG
66 AACCCTCCAATCTTTGTTGGCATTAAATTATATATATTTTATAAGTATTTTAGCCAAAAATTGAG
* * ** * **
10838 GAGATA-TCTTTCTTGTCA-ATTTTTACAAAATTTTATCTGAAATCGTGTACTAACTAACCATCA
131 GAAAAACT-TTTCGAGTCATATTTTTACAAAATTTTAGCCAAAATCGTG---T-ACT--CCATCA
* * * *
10901 CGGTTTTTGGCTAATAACGCGTTCCGGGGACCC-ATCACAATTTTACATGATTTTTGGCTCCG-G
189 CGGTTTTTAGCTAAAAACGCGTTCC-GAGACCCTATCACAATTTTACATGATTTTTGGCGCCGAG
* * * * * *
10964 AACT-ACTTGAAATATCTATATTCATCAAATCAAATCTCGGACACATTGGATTTTTATGGATATG
253 -ACTCA-TTAAAATATATATATTCATCAAATAAAATCTCAGACACATTGCA--TTTAAGGATATG
* *
11028 TTTTGACGAGCATCTGAATCTTGTTTCGATTTTATTAGAAATTAATT-TGAAAAATAGGAAAAAC
314 TTTTGACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTATAAAAAATAGGAAAAAC
* *
11092 GATATTAGAAGCGTCAAAAGCCCTTTAATAGTTTT
379 GATATTAAAAGCGTCAAAAGCCCTTCAATAGTTTT
11127 GGAGTTAAAT
Statistics
Matches: 349, Mismatches: 54, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
427 25 0.07
428 39 0.11
429 16 0.05
430 60 0.17
431 5 0.01
432 9 0.03
433 135 0.39
434 6 0.02
435 54 0.15
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (431 bp):
CTTGTTTCGATTTAATTAGAAATTAAGTTAGAAAAAATAACAAAAACGATATTAAAAGCGTGAAA
AACCCTCCAATCTTTGTTGGCATTAAATTATATATATTTTATAAGTATTTTAGCCAAAAATTGAG
GAAAAACTTTTCGAGTCATATTTTTACAAAATTTTAGCCAAAATCGTGTACTCCATCACGGTTTT
TAGCTAAAAACGCGTTCCGAGACCCTATCACAATTTTACATGATTTTTGGCGCCGAGACTCATTA
AAATATATATATTCATCAAATAAAATCTCAGACACATTGCATTTAAGGATATGTTTTGACGAGCA
TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTATAAAAAATAGGAAAAACGATATTAAAAGC
GTCAAAAGCCCTTCAATAGTTTTAGCGTTGAGCATATGGAA
Found at i:11343 original size:332 final size:327
Alignment explanation
Indices: 10712--14465 Score: 3272
Period size: 332 Copynumber: 11.4 Consensus size: 327
10702 GCATATGGAA
* * ** *
10712 CTTGTTT-GA-TTCATTAGAAATTAAGTTAGAAAAAATAACAAATACGATATTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAA-TTTGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
** * * *
10775 AACCCTCCAATCTTTTTGGCA-TTGAGTTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGG
65 AGTCCTCCAATTTTTTTGG-AGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGG
* * ** * * **
10839 AGATATCTTTCTTGTCAATTTTTACAAAATTTTATCTGAAATCGTGTACTAACTAACCATCACGG
129 AAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTG---TAA-TAACCATCACGG
* ** * * * * *
10904 TTTTTGGCTAATAACGCGTTCCGGGGACCCATCACAATTTTACATGATTTTTGGCTCC-GGAACT
190 TTTTTGGCTAAAAACGCGTT-CGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG-ACT
* * * * * *
10968 ACTTGAAATATCTATATTCATCAAATCAAATCTCGGACACATTGGATTTTTATGGATATGTTTTG
252 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA--TTTAAGGATTTGTTTT-
11033 ACGAGCATCTGAAT
314 ACGAGCATCTGAAT
* * *
11047 CTTGTTTCGATTTTATTAGAAATTAATTTG-AAAAATAGGAAAAACGATATTAGAAGCGTCAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAA
* ** **
11111 GCCCTTTAATAGTTTTGGAGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAAATTGAGGA
66 GTCCTCCAATTTTTTTGGAGTTAAATTATATATTTTTATGAGTATTTTAGCC-AAAAATTGAGGA
* * * * *
11176 AATATCTTTCATGTCAATTTTTACAAAATTTTTGCCAAAATCGTGTAATAACCATCACAGTTTTT
130 AAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTT
* **
11241 GGCTAAAAAAGCGTTCAGGGGCCACGGCTCAGTTTTAAATGATTTTTGGCGCCAAGACTCCTTGA
195 GGCTAAAAACGCGTTC-GGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
* * ** *
11306 GATATAC-ATATTCATCTAATCAAATCCCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGTA
258 AATAT-CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTACGAGCA
* *
11370 CCTAAAT
321 TCTGAAT
* * *
11377 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACTATACTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTT-GAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
* * * * * *
11442 AGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTCATAAGTATTTTATCCAAAAATTTATG
65 AGTCCTCCAATTTTTTTGGAGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * * *
11507 AAAAATTTTTC-GATTCATTTATTTGCAAAGTTTTAGCCAAAATCGTGTACTAACCATCACGGTT
129 AAAAATCTTTCAG-GTCAATT-TTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTT
* * * *
11571 TTTGGCTAAAAACGCGTTTCGAGACCCGTCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTT
192 TTTGGCTAAAAACGCG-TTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* * * *
11636 GAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAGC
256 GAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTACGAGC
*
11701 ATTTGAAT
320 ATCTGAAT
* ** ** *
11709 CTTCTTTCGATTTAATTAGATTTTAATTTAGAAAAAATTCGAAAAATGATATTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTT-GAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
*** * * * *
11774 AGTCCTCCAATTTTTTTTTCGCTAAATTGTATATATTTTATAAGTATTTTATCCAAAAATTGAGG
65 AGTCCTCCAATTTTTTTGGAGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG
* * *
11839 AAAAATTTTTC-GAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTT
129 AAAAATCTTTCAG-GTCA-ATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTT
* * * * ** * *
11903 TTTGGCTAATAACGCGTTCCGGGGACCCAGCTCAATTTTACATGATTTTTGGCTTC-GGAACTAC
192 TTTGGCTAAAAACGCGTT-CGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG-ACTCC
* * * * *
11967 TTGAAATATCTATATTCATCTAGTCAAATCTCAGACACATTGTATTCTTATGGATATGTTTTTAC
254 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA-T-TTAAGGATTTG-TTTTAC
12032 GAGCATCTGAAT
316 GAGCATCTGAAT
* ** * *
12044 CTTGTTTCGATTTTATTAGAAATTAATTTGAAAAAGCAGGAAAAACGATATTAGAAGCGTCAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAA
* ** **
12109 GCCCTTTAATAGTTTTGGAGTTAAATTATATATTTTTTATGAGTATTTTAGCCAAAAAAAATTGA
66 GTCCTCCAATTTTTTTGGAGTTAAATTATATA-TTTTTATGAGTATTTTAGCC---AAAAATTGA
* * * * *
12174 GGAAATATCTTTCAGGTCAATTTTTACAAAATTTTTGCCAAAATCGTGTAATTACCATCACAGTT
127 GGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTT
* * * * *
12239 TTTGACTAAAAAAGCGTTCAGGGGCCATGACTCAGTTTTACATGATTTTTGGCGCCAAGACTCCT
192 TTTGGCTAAAAACGCGTTC-GGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
* * * * **
12304 TGAGATATCCATATTCATCTAATCAACTCCCAGCCACATTGGATTTAAAAATTTGTATTTACGAG
255 TGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT-TTTACGAG
* * *
12369 TACCTAAAT
319 CATCTGAAT
* *
12378 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTT-GAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
* * * * *
12443 AGTCCTCCAATTTTTTTGGGGTTAAATTATATATATTTCATAAGTATTTTATCCAAAAATTTAGG
65 AGTCCTCCAATTTTTTTGGAGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG
** *
12508 AAAAAT-TTTTTGAGTCATTTTTTTGCAAAATTTTAG-C-----C-------AA--A--ACGGTT
129 AAAAATCTTTCAG-GTCA-ATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTT
* ** *
12555 TTTGGCTACAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
192 TTTGGCTAAAAACGCG-TTCG-GGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
* * * *
12620 TGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGCTTTTACGAG
255 TGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTACGAG
12685 CATCTGAAT
319 CATCTGAAT
* * * *
12694 CTTGTTTCGATTTAATTAGAAATTAATTT-AGAAAAATATGAAAAATGATACTAAAAGCTTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTTGA-AAAAATAGGAAAAACGATATTAAAAGCGTGAAA
* * * *
12758 AGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATAAGTATTTTATCCAAAAATTTAGG
65 AGTCCTCCAATTTTTTTGGAGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * *
12823 AAAAATTTTTC-GAGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACGT---TATCACGGT
129 AAAAATCTTTCAG-GTCA-ATTTTTGCAAAATTTTAGCCAAAATCGTGTA-ATAACCATCACGGT
* ** * * **
12884 TTTTGCCTAAAAACGCGTTTCGAGACCCCGTCTCAGTTTTGCATGATTTTTAGCATCAAGACTCC
191 TTTTGGCTAAAAACGCG-TTCG-GGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * *
12949 TTGAAATATCTATATTCATCTAATAAAATCTTAGCGACATTGCATTTAAGGATTTGTTTTTACGA
254 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTACGA
13014 GCATCTGAAT
318 GCATCTGAAT
* * * *
13024 CTTGTTTCGATTTGATTAGAAATTAATTCAT-AAAAAATATGAAAAACGATATTAAAACCGTTAA
1 CTTGTTTCGATTTAATTAGAAATTAATT--TGAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* * * * * ** *
13088 AAGTTCTCCAATATTTTTGGAGTTGAATTATATA-TATTATGTGTATTTTAGAGAAATATTGAGA
64 AAGTCCTCCAATTTTTTTGGAGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAG-
* * * * *
13152 AAAAAAATATTTCTGGTCAATTTTTTCAAAATATTAG------TC--G----AA--AT--C--TT
128 -GAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTT
* ** * * * * * * * *
13199 GTAT---TAAAAACGTATTCTGGGCCTTGGTTCAGTGTTGCATGGTTTTTAGCTGCCGAGACTAC
192 -TTTGGCTAAAAACGCGTTCGGGGCC-CGGCTCAGTTTTGCATGATTTTTGGC-GCCAAGACTCC
* * *** **
13261 TTGAAATATCTATATTCATTTAATGAAATCTCATGCCACATTGGATTTAAGGATTTGTAAAATAA
254 TTGAAATATCTATATTCATCTAATCAAATCTCA-GCCACATTGGATTTAAGGATTTGTTTTACGA
*
13326 GCATATGAAT
318 GCATCTGAAT
* * * *
13336 CATGTTTCAATTTAATTAGAAATTAATTCTGAAAATAATAGGAAAAACGATATTAGAAGCATGAA
1 CTTGTTTCGATTTAATTAGAAATTAATT-TGAAAA-AATAGGAAAAACGATATTAAAAGCGTGAA
* * * * * *
13401 AAGTCCTTCAATCTTTTTGGCA-TTCAATTATATAAATTTTATGAGTATTGTGGCTC-AAAATTG
64 AAGTCCTCCAATTTTTTTGG-AGTTAAATTATAT-ATTTTTATGAGTATTTTAGC-CAAAAATTG
* * * * *
13464 AGG-AAATTACTTTCAGGAACGCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATC
126 AGGAAAAAT-CTTTCAGG---TCA-ATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATC
* * * *
13528 ACGGTTTTTTGGCTAAAAAAGGCGTTCTGGGGCCCTGGGTCAGTTTTGCATGATATTTGGCGCGA
186 ACGG-TTTTTGGCT-AAAAACGCGTTC-GGGGCCC-GGCTCAGTTTTGCATGATTTTTGGCGCCA
** * * * *
13593 AGACTCCATAAAATATATCCATATTCTTCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTG
247 AGACTCC-TTGAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG
* *
13658 TTCTTACGAGTATCTAAAT
310 TT-TTACGAGCATCTGAAT
* *
13677 CTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAAATAGCTAGGAAAAACGATATTAGAA--
1 CTTGTTTCGATTTAATTAGAAATTAATTT-G--A-AAAA-A--TAGGAAAAACGATATTAAAAGC
* * * * * * * * * *
13740 GTGAAAAAGGCTTTCAATTTTATTGGCGTTGAATTATATGTTTTTTTATGAGCATTTTTGCTC-G
59 GTG-AAAAGTCCTCCAATTTTTTTGGAGTTAAATTATA--TATTTTTATGAGTATTTTAGC-CAA
* * *
13804 AAATTGAGGAAAAATCTTTC-GGTCAATATTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
120 AAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCAT
* * * * *
13868 CACGGTTTTCGACTAAAAACGCGTTCCGGAGCTCGGCTCAGTTTTGCATGATTTTTGGTGCCAAG
185 CACGGTTTTTGGCTAAAAACGCGTT-CGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * * *
13933 ACTCCTTGAAAAATCTATATTCATCTAACCAAATCCCAGTCACATTGGATTTAAGGATTTGTTTT
249 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTT
13998 TACGAGCATCTGAAT
313 TACGAGCATCTGAAT
** * * *
14013 CTTGTTTCGATTTAATTAGAAATTAATCCGGAAAAAATTAGGAAAAACAATTTTAGAAGCGCT-A
1 CTTGTTTCGATTTAATTAGAAATTAAT-TTGAAAAAA-TAGGAAAAACGATATTAAAAGCG-TGA
* * * * * ** *
14077 AAAGCCCTTCGATCTTTTT-AACGTCGAATTATATATTTTTTATGAGTATTTTATCCAAAAATTG
63 AAAGTCCTCCAATTTTTTTGGA-GTTAAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTG
* * * * * *
14141 AGGAAATATCTTTCGGGTCAATTTTT-CAAAATTTTAGTCGAAATCGTGTACTAACCATAACGGT
126 AGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGT
* * ** * * * * * * * *
14205 TTTTTGCTATAAGTGTGTTCCGGTGCTACGACTCTGTATTGCATGATTTTTTGCGCCGAGACTCC
191 TTTTGGCTAAAAACGCGTT-CGGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * * * * ** *
14270 TAGAAATATCTTTATTAATATAATCAAA-CATTAGTCTTATTGGATTTAAGGATTTGCTTTTGCG
254 TTGAAATATCTATATTCATCTAATCAAATC-TCAGCCACATTGGATTTAAGGATTTG-TTTTACG
* *
14334 TGCATATGAAT
317 AGCATCTGAAT
* *
14345 CTTGTTTCGATTTAATTATAAATTAA-TT-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAA
* * * * *
14408 GTCCTCCAATCTTTTTGGCG-TAGAATTATATATATTTTATGATTTTTTTTGCCAAAAA
66 GTCCTCCAATTTTTTTGGAGTTA-AATTATATAT-TTTTATGAGTATTTTAGCCAAAAA
14466 AATTTTGGGT
Statistics
Matches: 2827, Mismatches: 457, Indels: 277
0.79 0.13 0.08
Matches are distributed among these distances:
310 3 0.00
311 25 0.01
312 90 0.03
313 78 0.03
314 5 0.00
315 148 0.05
316 151 0.05
317 22 0.01
318 3 0.00
320 1 0.00
321 1 0.00
322 1 0.00
323 2 0.00
324 2 0.00
325 1 0.00
327 3 0.00
328 67 0.02
329 29 0.01
330 228 0.08
331 196 0.07
332 637 0.23
333 171 0.06
334 125 0.04
335 208 0.07
336 267 0.09
337 44 0.02
338 34 0.01
339 32 0.01
340 60 0.02
341 98 0.03
342 2 0.00
343 2 0.00
344 6 0.00
345 29 0.01
346 51 0.02
347 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (327 bp):
CTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAA
GTCCTCCAATTTTTTTGGAGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
AAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACGGTTTTTG
GCTAAAAACGCGTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGA
AT
Found at i:17362 original size:27 final size:28
Alignment explanation
Indices: 17323--17382 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
17313 AAAGTATTTA
*
17323 ATTCCAATCTCATAGATTATCACTATGT
1 ATTCCAATCTCATAGATTATCAATATGT
*
17351 ATTCC-ATCTCATAGTTTATCAATATGT
1 ATTCCAATCTCATAGATTATCAATATGT
17378 ATTCC
1 ATTCC
17383 TTCTTGCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (28 bp):
ATTCCAATCTCATAGATTATCAATATGT
Found at i:22209 original size:14 final size:16
Alignment explanation
Indices: 22185--22216 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22175 TCCATATCCA
22185 AAAACAAAAACA-AAG
1 AAAACAAAAACAGAAG
22200 AAAA-AAAAACAGAAG
1 AAAACAAAAACAGAAG
22215 AA
1 AA
22217 CCCTTTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAACAAAAACAGAAG
Found at i:22805 original size:8 final size:8
Alignment explanation
Indices: 22793--22829 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
22783 GGGAGAGATT
22793 GAGAGAGAA
1 GAGAGA-AA
22802 -AGAGAAA
1 GAGAGAAA
22809 GAGAG-AA
1 GAGAGAAA
22816 GAGAGAAA
1 GAGAGAAA
22824 GAGAGA
1 GAGAGA
22830 GATTTTCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 9 0.35
8 17 0.65
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (8 bp):
GAGAGAAA
Found at i:38382 original size:6 final size:6
Alignment explanation
Indices: 38371--38398 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38361 GTTCCTTCCT
38371 GAAAGG GAAAGG GAAAGG GAAAGG GAAA
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAA
38399 ATATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:38921 original size:17 final size:17
Alignment explanation
Indices: 38895--38931 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
38885 GGTGATTGAG
38895 TGTTCCTTATGCTTCAA
1 TGTTCCTTATGCTTCAA
*
38912 TGTTCTTTATGCTTCAA
1 TGTTCCTTATGCTTCAA
38929 TGT
1 TGT
38932 CAAATAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.51
Consensus pattern (17 bp):
TGTTCCTTATGCTTCAA
Found at i:43098 original size:167 final size:168
Alignment explanation
Indices: 42807--43131 Score: 526
Period size: 167 Copynumber: 1.9 Consensus size: 168
42797 GTATCCTCCT
* *
42807 CTATCCTCCTCTTTCTTAGTATCCTCCCCCTTCCATAGAGGGAAATATGGCTTGTGTACAAAAAC
1 CTATCCTCCCCTTTCTTAGTATCCTCCCCCTTCCATAGAGGGAAATATGGCTTGGGTACAAAAAC
* * *
42872 CCCTTCCGTCCCTTCCATTTTAATATCCTCTTTCTTACGATAATCCCCTCCCTTTTCCCATATAT
66 CCCTTCCGTCCCTTCCATTTTAATATCCTCTTTCTTACGATAATCCACTACCGTTTCCCATATAT
42937 ATGGCTTGCGTACAAAATCCCCCTCCTCTTTCTTACAA
131 ATGGCTTGCGTACAAAATCCCCCTCCTCTTTCTTACAA
*** * *
42975 CTATCCTCCCCTTTCTTAGTATCCTCCTTTTTCCATGGAGGGAAATATGGCTTGGGTAC-AAAAT
1 CTATCCTCCCCTTTCTTAGTATCCTCCCCCTTCCATAGAGGGAAATATGGCTTGGGTACAAAAAC
* *
43039 CCCTTCCGTCCCTTCCGTTTTAATATCCTCTTTCTTACGATAATCTACTACCGTTTCCCATATAT
66 CCCTTCCGTCCCTTCCATTTTAATATCCTCTTTCTTACGATAATCCACTACCGTTTCCCATATAT
*
43104 ATGGCTTGCGTACAAAATCCCCTTCCTC
131 ATGGCTTGCGTACAAAATCCCCCTCCTC
43132 CTTACAATCC
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
167 91 0.63
168 53 0.37
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.36
Consensus pattern (168 bp):
CTATCCTCCCCTTTCTTAGTATCCTCCCCCTTCCATAGAGGGAAATATGGCTTGGGTACAAAAAC
CCCTTCCGTCCCTTCCATTTTAATATCCTCTTTCTTACGATAATCCACTACCGTTTCCCATATAT
ATGGCTTGCGTACAAAATCCCCCTCCTCTTTCTTACAA
Found at i:43117 original size:83 final size:79
Alignment explanation
Indices: 42851--43129 Score: 246
Period size: 84 Copynumber: 3.3 Consensus size: 79
42841 ATAGAGGGAA
* *
42851 ATATGGCTTGTGTACAAAAACCCCTTCCGTCCCTTCCATTTTAATATCCTCTTTCTTACGATAAT
1 ATATGGCTTGCGTAC-AAAATCCCTTCCGTCCCTTCC-TTTTAATATCCTCTTTCTTACGATAAT
42916 CCCCTCCCTTTTCCCATAT
64 --CCT-CCTTTTCCCATAT
* **
42935 ATATGGCTTGCGTACAAAATCCC--CC-TCCTCTTTCTTACAACTATCCTCCCCTTTCTTA-G-T
1 ATATGGCTTGCGTACAAAATCCCTTCCGTCC-CTTCCTTTTAA-TATCCT---CTTTCTTACGAT
* *
42995 -ATCCTCCTTTTTCCATGGAGGGAA
61 AATCCTCCTTTTCCCAT------AT
*
43019 ATATGGCTTGGGTACAAAATCCCTTCCGTCCCTTCCGTTTTAATATCCTCTTTCTTACGATAATC
1 ATATGGCTTGCGTACAAAATCCCTTCCGTCCCTTCC-TTTTAATATCCTCTTTCTTACGATAATC
*
43084 TACTACCGTTTCCCATAT
65 --CT-CCTTTTCCCATAT
43102 ATATGGCTTGCGTACAAAATCCCCTTCC
1 ATATGGCTTGCGTACAAAAT-CCCTTCC
43130 TCCTTACAAT
Statistics
Matches: 158, Mismatches: 15, Indels: 44
0.73 0.07 0.20
Matches are distributed among these distances:
78 10 0.06
79 3 0.02
80 7 0.04
81 14 0.09
82 1 0.01
83 36 0.23
84 53 0.34
85 1 0.01
86 15 0.09
87 7 0.04
88 2 0.01
89 9 0.06
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.37
Consensus pattern (79 bp):
ATATGGCTTGCGTACAAAATCCCTTCCGTCCCTTCCTTTTAATATCCTCTTTCTTACGATAATCC
TCCTTTTCCCATAT
Found at i:43161 original size:21 final size:21
Alignment explanation
Indices: 43132--43229 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
43122 CCCCTTCCTC
43132 CTTACAATCCGGCTTGTCTTT
1 CTTACAATCCGGCTTGTCTTT
* * *
43153 CTTAGAATCCGGCTTGT-GTA
1 CTTACAATCCGGCTTGTCTTT
* * *
43173 C--AAAATCC-CCTTCCTCTTT
1 CTTACAATCCGGCTT-GTCTTT
43192 CTTACAATCCGGCTTGTCTTT
1 CTTACAATCCGGCTTGTCTTT
* *
43213 CTTAGAATCCGACTTGT
1 CTTACAATCCGGCTTGT
43230 GTACAAAATC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
17 3 0.05
18 7 0.12
19 2 0.03
20 2 0.03
21 42 0.71
22 3 0.05
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (21 bp):
CTTACAATCCGGCTTGTCTTT
Found at i:43216 original size:60 final size:57
Alignment explanation
Indices: 43106--43247 Score: 239
Period size: 60 Copynumber: 2.4 Consensus size: 57
43096 CCATATATAT
*
43106 GGCTTGCGTACAAAATCCCCTTCCTCCTTACAATCCGGCTTGTCTTTCTTAGAATCC
1 GGCTTGTGTACAAAATCCCCTTCCTCCTTACAATCCGGCTTGTCTTTCTTAGAATCC
43163 GGCTTGTGTACAAAATCCCCTTCCTCTTTCTTACAATCCGGCTTGTCTTTCTTAGAATCC
1 GGCTTGTGTACAAAATCCCCTTCCTC---CTTACAATCCGGCTTGTCTTTCTTAGAATCC
*
43223 GACTTGTGTACAAAATCCCCTTCCT
1 GGCTTGTGTACAAAATCCCCTTCCT
43248 TTGGGGAAGG
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
57 25 0.31
60 55 0.69
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (57 bp):
GGCTTGTGTACAAAATCCCCTTCCTCCTTACAATCCGGCTTGTCTTTCTTAGAATCC
Found at i:43583 original size:78 final size:78
Alignment explanation
Indices: 43488--43655 Score: 318
Period size: 78 Copynumber: 2.2 Consensus size: 78
43478 ATATATGGCT
*
43488 TGCGTACAAAATCCCCTTCCTCTTTTTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATA
1 TGCGTACAAAATCCCCTTCCTCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATA
43553 TATGGCTTCGTCC
66 TATGGCTTCGTCC
*
43566 TGTGTACAAAATCCCCTTCCTCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATA
1 TGCGTACAAAATCCCCTTCCTCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATA
43631 TATGGCTTCGTCC
66 TATGGCTTCGTCC
43644 TGCGTACAAAAT
1 TGCGTACAAAAT
43656 AGCCAAAATC
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 87 1.00
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.38
Consensus pattern (78 bp):
TGCGTACAAAATCCCCTTCCTCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATA
TATGGCTTCGTCC
Found at i:43683 original size:138 final size:138
Alignment explanation
Indices: 43518--43791 Score: 539
Period size: 138 Copynumber: 2.0 Consensus size: 138
43508 TCTTTTTTCA
43518 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
1 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
*
43583 TCCTCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCG
66 TCCTCTTTCTTCAAGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCG
43648 TACAAAAT
131 TACAAAAT
43656 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
1 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
43721 TCCTCTTTCTTCAAGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCG
66 TCCTCTTTCTTCAAGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCG
43786 TACAAA
131 TACAAA
43792 TTCCCCTTCC
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.22, C:0.32, G:0.09, T:0.36
Consensus pattern (138 bp):
AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
TCCTCTTTCTTCAAGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCG
TACAAAAT
Found at i:43689 original size:60 final size:60
Alignment explanation
Indices: 43596--43715 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
43586 TCTTTCTTCA
43596 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAAT
1 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAAT
*
43656 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAAT
1 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAAT
43716 CCCCTTCCTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (60 bp):
AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAAT
Found at i:43789 original size:78 final size:78
Alignment explanation
Indices: 43656--43965 Score: 557
Period size: 78 Copynumber: 4.0 Consensus size: 78
43646 CGTACAAAAT
* *
43656 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGTGTACAAAATCCCCT
1 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCCCT
43721 TCCTCTTTCTTCA
66 TCCTCTTTCTTCA
*
43734 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAATTCCCCT
1 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCCCT
43799 TCCTCTTTCTTCA
66 TCCTCTTTCTTCA
* *
43812 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATGTATATGGCTTCGTCCTGCGTACAAATTCCCCT
1 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCCCT
43877 TCCTCTTTCTTCA
66 TCCTCTTTCTTCA
* *
43890 AGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCACT
1 AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCCCT
43955 TCCTCTTTCTT
66 TCCTCTTTCTT
43966 TTCCCATATA
Statistics
Matches: 224, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 224 1.00
ACGTcount: A:0.20, C:0.34, G:0.09, T:0.38
Consensus pattern (78 bp):
AGCCAAAAGCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAAATCCCCT
TCCTCTTTCTTCA
Found at i:43969 original size:51 final size:51
Alignment explanation
Indices: 43893--44016 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 51
43883 TTCTTCAAGC
43893 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
1 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
*
43944 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGTTTCGTCCTGCGTA
1 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
* *
43995 CAAATTCCCCTTCCTCTTTCTT
1 CAAAATCCACTTCCTCTTTCTT
44017 CAAGTCAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.19, C:0.32, G:0.08, T:0.41
Consensus pattern (51 bp):
CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
Found at i:43978 original size:129 final size:129
Alignment explanation
Indices: 43815--44080 Score: 496
Period size: 129 Copynumber: 2.1 Consensus size: 129
43805 TTCTTCAAGC
* *
43815 CAAAAGCCACTTCCTCTTTCTTTTCCCATGTATATGGCTTCGTCCTGCGTACAAATTCCCCTTCC
1 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAATTCCCCTTCC
43880 TCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
66 TCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
*
43944 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGTTTCGTCCTGCGTACAAATTCCCCTTCC
1 CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAATTCCCCTTCC
*
44009 TCTTTCTTCAAGTCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
66 TCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
44073 CAAAATCC
1 CAAAATCC
44081 CCTTTCGTTT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 133 1.00
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (129 bp):
CAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTACAAATTCCCCTTCC
TCTTTCTTCAAGCCAAAATCCACTTCCTCTTTCTTTTCCCATATATATGGCTTCGTCCTGCGTA
Found at i:44265 original size:15 final size:15
Alignment explanation
Indices: 44245--44275 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44235 CCTCTTTTGG
44245 AGGGAAATTTGGCTT
1 AGGGAAATTTGGCTT
44260 AGGGAAATTTGGCTT
1 AGGGAAATTTGGCTT
44275 A
1 A
44276 TCCTCTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (15 bp):
AGGGAAATTTGGCTT
Found at i:46727 original size:15 final size:16
Alignment explanation
Indices: 46709--46766 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
46699 AGTATCAATG
46709 GGAGGCAT-ATCCATA
1 GGAGGCATGATCCATA
46724 GGAGGCTTATGATCCATA
1 GGAGGC--ATGATCCATA
* *
46742 GAAGGCACAAGATCCATA
1 GGAGG--CATGATCCATA
46760 GGAGGCA
1 GGAGGCA
46767 GAACAGGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 6 0.17
16 2 0.06
17 2 0.06
18 24 0.69
20 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.17
Consensus pattern (16 bp):
GGAGGCATGATCCATA
Found at i:46740 original size:18 final size:18
Alignment explanation
Indices: 46717--46766 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
46707 TGGGAGGCAT
** *
46717 ATCCATAGGAGGCTTATG
1 ATCCATAGGAGGCACAAG
*
46735 ATCCATAGAAGGCACAAG
1 ATCCATAGGAGGCACAAG
46753 ATCCATAGGAGGCA
1 ATCCATAGGAGGCA
46767 GAACAGGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (18 bp):
ATCCATAGGAGGCACAAG
Found at i:46870 original size:57 final size:57
Alignment explanation
Indices: 46770--46996 Score: 397
Period size: 57 Copynumber: 4.0 Consensus size: 57
46760 GGAGGCAGAA
*
46770 CAGGAGATGGATCCTTTAGA---GGGGGATACCCTTTAATTCTAAAATCCTTACGAT
1 CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
46824 CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
1 CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
*
46881 CAGGAGATGGATCCTTTAGAGACGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
1 CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
**
46938 CAGGAGATGGATCCTTTAGAGGCGGGAAATACCCTTTAATTTTAAAATCCTTACGAT
1 CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
46995 CA
1 CA
46997 TCCATGGGTG
Statistics
Matches: 165, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
54 20 0.12
57 145 0.88
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (57 bp):
CAGGAGATGGATCCTTTAGAGGCGGGGGATACCCTTTAATTTTAAAATCCTTACGAT
Found at i:47296 original size:156 final size:154
Alignment explanation
Indices: 47018--47353 Score: 491
Period size: 156 Copynumber: 2.2 Consensus size: 154
47008 CTTCCGATCC
47018 ATGGGAGGCAGAAAGGTAATATCCTCTTTCTTATACCCTTCAGTTTTAAAATCCTTACGATCATC
1 ATGGGAGGCAGAAAGGTAATATCCTCTTTCTTATACCCTTCAGTTTTAAAATCCTTACGATCATC
* *
47083 CATGGGTGGCTTACGATCCATAGGCACAGGATCTATAGGAGGCAGAACAAGAGAT-G-GAT-A-C
66 CATGGGAGGCTTACGATCCATAGGCACAGGATCCATAGGAGGCAGAACAAGAGATGGAGATGACC
* *
47144 TTTAGAGGGGGCAGAACAGGATGT
131 TTTAGAAGGGGCAGAACAGGATAT
*
47168 ATGGGAGGCAGAAAGGTAATATTCTCTTTCTTATACCCTTCATGATCAGTTTTAAAATCCTTACG
1 ATGGGAGGCAGAAAGGTAATATCCTCTTTCTTATA-CC--C-T--TCAGTTTTAAAATCCTTACG
* *
47233 ATCATCCATGGGAGGCTTACGATCCATTGGCACAGGATCCATAGGAGGCAGAACAGGAGATGGAG
60 ATCATCCATGGGAGGCTTACGATCCATAGGCACAGGATCCATAGGAGGCAGAACAAGAGATGGAG
47298 ATGGATCCTTTAGAAGGGGCAGAACAGGATAT
125 AT-GA-CCTTTAGAAGGGGCAGAACAGGATAT
* *
47330 ATGCGAGGCAGAAAGCTAATATCC
1 ATGGGAGGCAGAAAGGTAATATCC
47354 CATGGCAGAA
Statistics
Matches: 164, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
150 34 0.21
151 2 0.01
153 1 0.01
154 1 0.01
156 77 0.47
157 1 0.01
158 3 0.02
160 1 0.01
162 44 0.27
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (154 bp):
ATGGGAGGCAGAAAGGTAATATCCTCTTTCTTATACCCTTCAGTTTTAAAATCCTTACGATCATC
CATGGGAGGCTTACGATCCATAGGCACAGGATCCATAGGAGGCAGAACAAGAGATGGAGATGACC
TTTAGAAGGGGCAGAACAGGATAT
Found at i:53521 original size:11 final size:11
Alignment explanation
Indices: 53502--53564 Score: 90
Period size: 11 Copynumber: 5.7 Consensus size: 11
53492 AGTGTCAATT
53502 GCACCGCTACC
1 GCACCGCTACC
* *
53513 GCACTGCTACT
1 GCACCGCTACC
53524 GCACCGCTACC
1 GCACCGCTACC
* *
53535 GCACTGCTACT
1 GCACCGCTACC
53546 GCACCGCTACC
1 GCACCGCTACC
53557 GCACCGCT
1 GCACCGCT
53565 CTACTAAACG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 44 1.00
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.16
Consensus pattern (11 bp):
GCACCGCTACC
Found at i:53526 original size:22 final size:22
Alignment explanation
Indices: 53501--53560 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
53491 CAGTGTCAAT
53501 TGCACCGCTACCGCACTGCTAC
1 TGCACCGCTACCGCACTGCTAC
53523 TGCACCGCTACCGCACTGCTAC
1 TGCACCGCTACCGCACTGCTAC
53545 TGCACCGCTACCGCAC
1 TGCACCGCTACCGCAC
53561 CGCTCTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.17
Consensus pattern (22 bp):
TGCACCGCTACCGCACTGCTAC
Found at i:54766 original size:224 final size:224
Alignment explanation
Indices: 54371--54824 Score: 836
Period size: 224 Copynumber: 2.0 Consensus size: 224
54361 TCAAGAATTA
* *
54371 AAAAGAATGTAGGGATCTGATAGGATTACCTTGCATGACCCTTCAGTACATGGACCACCAACCAA
1 AAAA-AATGTAGGGATCTAATAGGATTACCTTGCACGACCCTTCAGTACATGGACCACCAACCAA
54436 AGCAAAGCAATGATCCTAGCACAATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCTGCC
65 AGCAAAGCAATGATCCTAGCACAATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCTGCC
54501 ACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACAA
130 ACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACAA
* *
54566 TAATTGGTTGATAAATTTAAAAAGGAACTT
195 TAACTAGTTGATAAATTTAAAAAGGAACTT
*
54596 AAAAAATGTAGGGATCTAATAGGATTACCTTGCCCGACCCTTCAGTACATGGACCACCAACCAAA
1 AAAAAATGTAGGGATCTAATAGGATTACCTTGCACGACCCTTCAGTACATGGACCACCAACCAAA
* *
54661 GCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATTTGCTGCCA
66 GCAAAGCAATGATCCTAGCACAATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCTGCCA
54726 CCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACAAT
131 CCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACAAT
54791 AACTAGTTGATAAATTTAAAAAGGAACTT
196 AACTAGTTGATAAATTTAAAAAGGAACTT
54820 AAAAA
1 AAAAA
54825 TAAATCACGA
Statistics
Matches: 222, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
224 218 0.98
225 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (224 bp):
AAAAAATGTAGGGATCTAATAGGATTACCTTGCACGACCCTTCAGTACATGGACCACCAACCAAA
GCAAAGCAATGATCCTAGCACAATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCTGCCA
CCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACAAT
AACTAGTTGATAAATTTAAAAAGGAACTT
Found at i:55614 original size:542 final size:540
Alignment explanation
Indices: 54594--55649 Score: 1941
Period size: 542 Copynumber: 2.0 Consensus size: 540
54584 AAAAAGGAAC
54594 TTAAAAAATGTAGGGATCTAATAGGATTACCTTGCCCGACCCTTCAGTACATGGACCACCAACCA
1 TTAAAAAATGTAGGGATCTAATAGGATTACCTTGCCCGACCCTTCAGTACATGGACCACCAACCA
* *
54659 AAGCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATTTGCTGC
66 AAGCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCCGC
*
54724 CACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTGCCCCGTTTGCAACTCATCCAACAACA
131 CACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTACCCCGTTTGCAACTCATCCAACAACA
*
54789 ATAACTAGTTGATAAATTTAAAAAGGAACTTAAAAATAAATCACGAAAAATAAATCAAACGAACT
196 ATAACTAGTTGATAAATTTAAAAAGGAACTTAAAAATAAATCACGAAAAATAAATCAAACGAACC
*
54854 GAATTGAGCATAGATACACAATCTGAAACCGCCAATAAAAACTCGTTGTATCCAGCCACTACCCC
261 GAATTGAGCATAGATACACAATCTGAAACCGCCAATAAAAACACGTTGTATCCAGCCACTACCCC
54919 TATTGAGGAGGTAGAGCTCAATGGATACAAAGTTTTTATTGCCGGTTTCAGATTGTGTATCTACG
326 TATTGAGGAGGTAGAGCTCAATGGATACAAAGTTTTTATTGCCGGTTTCAGATTGTGTATCTACG
* ** *
54984 TAAGGGATAAATTTATTCGATGTTGGGCCCTTATTCTTTGGTCTCTTTTCTTAGGTACACAAAGG
391 TAAGGGATAAATGTATTCGATGCCGGGCCCTCATTCTTTGGTCTCTTTTCTTAGGTACACAAAGG
55049 TGATGGGATGTTTGGATCGGGATTGGCTTGAACCGTATATTCGACGGTGGAAGATGAAGTGTAAA
456 TGATGGGATGTTTGGATCGGGATTGGCTTGAACCGTATATTCGACGGTGGAAGATGAAGTGTAAA
55114 ACTCGGCAGGACACATAATT
521 ACTCGGCAGGACACATAATT
* *
55134 TTAAAAAATGTAGGGATCTGATAGGATTACCTTGCCCGATCCTTCAGTACATGGACCACCAACCA
1 TTAAAAAATGTAGGGATCTAATAGGATTACCTTGCCCGACCCTTCAGTACATGGACCACCAACCA
55199 AAGCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCCGC
66 AAGCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCCGC
* *
55264 CACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTACCCCGTTTGTAACTCATCCAATAACA
131 CACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTACCCCGTTTGCAACTCATCCAACAACA
55329 ATAACTAGTTGATAAATTTAAAAAGGAACTTAAAAAATAAATCACGAAAAAATAAATCAAACGAA
196 ATAACTAGTTGATAAATTTAAAAAGGAACTT-AAAAATAAATCACG-AAAAATAAATCAAACGAA
* *
55394 CCGAATTGAGCGTAGATACACAATCTGAAACCGGCAATAAAAACACGTTGTATCCAGCCACTACC
259 CCGAATTGAGCATAGATACACAATCTGAAACCGCCAATAAAAACACGTTGTATCCAGCCACTACC
55459 CCTATTGAGGAGGTAGAGCTCAATGGATACAAAGTTTTTATTGCCGGTTTCAGATTGTGTATCTA
324 CCTATTGAGGAGGTAGAGCTCAATGGATACAAAGTTTTTATTGCCGGTTTCAGATTGTGTATCTA
**
55524 CGTCGGGGATAAATGTATTCGATGCCGGGCCCTCATTCTTTGGTCTCTTTTCTTAGGTACACAAA
389 CGTAAGGGATAAATGTATTCGATGCCGGGCCCTCATTCTTTGGTCTCTTTTCTTAGGTACACAAA
55589 GGTGATGGGATGTTTGGATCGGGATTGGCTTGAACCGTATATTCGACGGTGGAAGATGAAG
454 GGTGATGGGATGTTTGGATCGGGATTGGCTTGAACCGTATATTCGACGGTGGAAGATGAAG
55650 CTGATTTGTG
Statistics
Matches: 497, Mismatches: 17, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
540 219 0.44
541 14 0.03
542 264 0.53
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (540 bp):
TTAAAAAATGTAGGGATCTAATAGGATTACCTTGCCCGACCCTTCAGTACATGGACCACCAACCA
AAGCAAAGCAATGATCCTAGCACCATTTCAGGACGCAAGCATGCTCTAACAAGCAAATCTGCCGC
CACCCTTAAGGCCACTCCAGTGCACCTAGACGCCCTTTACCCCGTTTGCAACTCATCCAACAACA
ATAACTAGTTGATAAATTTAAAAAGGAACTTAAAAATAAATCACGAAAAATAAATCAAACGAACC
GAATTGAGCATAGATACACAATCTGAAACCGCCAATAAAAACACGTTGTATCCAGCCACTACCCC
TATTGAGGAGGTAGAGCTCAATGGATACAAAGTTTTTATTGCCGGTTTCAGATTGTGTATCTACG
TAAGGGATAAATGTATTCGATGCCGGGCCCTCATTCTTTGGTCTCTTTTCTTAGGTACACAAAGG
TGATGGGATGTTTGGATCGGGATTGGCTTGAACCGTATATTCGACGGTGGAAGATGAAGTGTAAA
ACTCGGCAGGACACATAATT
Done.