Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007703.1 Hibiscus syriacus cultivar Beakdansim tig00109916_pilon, 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: 1017536
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:430926 original size:2 final size:2
Alignment explanation
Indices: 430915--430966 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
430905 TTTAAAAACT
430915 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
430954 TA -A TA TA -A TA TA T
1 TA TA TA TA TA TA TA T
430967 GATTTTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:431032 original size:35 final size:36
Alignment explanation
Indices: 430956--431052 Score: 128
Period size: 36 Copynumber: 2.7 Consensus size: 36
430946 TATAATATTA
**
430956 ATATAATATATGATTTT-TAAAACATTTTGAAAACTT
1 ATATAATATAT-ATTTTGTAAAACATTTTGAAAAAAT
430992 ATATAATATATATTTTGTAAAACATTTTGAAAAAAT
1 ATATAATATATATTTTGTAAAACATTTTGAAAAAAT
*
431028 -TATAATATATAGTTTTG-AAATCATT
1 ATATAATATATA-TTTTGTAAAACATT
431053 ATAATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
35 23 0.41
36 33 0.59
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATAATATATATTTTGTAAAACATTTTGAAAAAAT
Found at i:431053 original size:24 final size:24
Alignment explanation
Indices: 431016--431075 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
431006 TTGTAAAACA
431016 TTTTGAAAAAATTATAATATATAG
1 TTTTGAAAAAATTATAATATATAG
**
431040 TTTTGAAATCATTATAATATATAG
1 TTTTGAAAAAATTATAATATATAG
*
431064 TTTTTAAAAAAT
1 TTTTGAAAAAAT
431076 GCATTTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (24 bp):
TTTTGAAAAAATTATAATATATAG
Found at i:431231 original size:28 final size:30
Alignment explanation
Indices: 431184--431242 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
431174 TAGTTTTAAA
*
431184 TTTCTTTTTTATTATTTTTATCAT-TATTT
1 TTTCTTTTTTATTATGTTTATCATATATTT
*
431213 TTTCTTTTTTATT-TGTTTATTATATATTT
1 TTTCTTTTTTATTATGTTTATCATATATTT
431242 T
1 T
431243 ATTAATTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (30 bp):
TTTCTTTTTTATTATGTTTATCATATATTT
Found at i:432356 original size:26 final size:26
Alignment explanation
Indices: 432299--432359 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
432289 GTTACTTTTG
* * * *
432299 TATATATGTTTTTTATCATTTTTATG
1 TATATATATTGTTTATCATTATTATA
* *
432325 TGTATATATTGTTTATTATTATTATA
1 TATATATATTGTTTATCATTATTATA
432351 TATATATAT
1 TATATATAT
432360 ATACACTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (26 bp):
TATATATATTGTTTATCATTATTATA
Found at i:432544 original size:5 final size:5
Alignment explanation
Indices: 432532--432580 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
432522 TATAAATTTC
*
432532 TTTA- TTTAT TTTAT TTTAT TTTA- TTTAT TTTA- TTCAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
432579 TT
1 TT
432581 ATCTAACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
4 11 0.28
5 29 0.73
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:432551 original size:14 final size:14
Alignment explanation
Indices: 432532--432582 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
432522 TATAAATTTC
432532 TTTATTTATTTTAT
1 TTTATTTATTTTAT
432546 TTTATTT-TATTTAT
1 TTTATTTAT-TTTAT
*
432560 TTTATTCATTTTAT
1 TTTATTTATTTTAT
432574 TTTATTTAT
1 TTTATTTAT
432583 CTAACATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 1 0.03
14 31 0.94
15 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:432582 original size:9 final size:9
Alignment explanation
Indices: 432532--432580 Score: 71
Period size: 9 Copynumber: 5.2 Consensus size: 9
432522 TATAAATTTC
432532 TTTATTTAT
1 TTTATTTAT
432541 TTTATTTTAT
1 TTTA-TTTAT
432551 TTTATTTAT
1 TTTATTTAT
*
432560 TTTATTCAT
1 TTTATTTAT
432569 TTTATTTTAT
1 TTTA-TTTAT
432579 TT
1 TT
432581 ATCTAACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTAT
Found at i:433283 original size:27 final size:27
Alignment explanation
Indices: 433237--433290 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
433227 AGAAACCCTA
*
433237 AAAAAATCATTTATTAGAAAAAAACCC
1 AAAAAATCATTAATTAGAAAAAAACCC
* * *
433264 AAAATATCATTAATTGGAAAAATACCC
1 AAAAAATCATTAATTAGAAAAAAACCC
433291 CAAGCTACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAAAATCATTAATTAGAAAAAAACCC
Found at i:436091 original size:3 final size:3
Alignment explanation
Indices: 436085--436128 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
436075 GAAGAAGATG
436085 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
436129 TGATATTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:436332 original size:17 final size:17
Alignment explanation
Indices: 436310--436355 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
436300 GTTAAACTTT
436310 GTTTAAATTATAATTAA
1 GTTTAAATTATAATTAA
*
436327 GTTTAAATTTATTAATTTA
1 GTTTAAA-TTA-TAATTAA
436346 -TTTAAATTAT
1 GTTTAAATTAT
436356 CTGTAACACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 9 0.35
19 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
GTTTAAATTATAATTAA
Found at i:436349 original size:18 final size:18
Alignment explanation
Indices: 436310--436353 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
436300 GTTAAACTTT
436310 GTTTAAA-TTATAATTAA
1 GTTTAAATTTATAATTAA
*
436327 GTTTAAATTTATTAATTTA
1 GTTTAAATTTA-TAATTAA
436346 -TTTAAATT
1 GTTTAAATT
436354 ATCTGTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
GTTTAAATTTATAATTAA
Found at i:436906 original size:54 final size:54
Alignment explanation
Indices: 436818--436948 Score: 174
Period size: 54 Copynumber: 2.4 Consensus size: 54
436808 GATATTACCC
* *
436818 TTCAAGGGTATCGATACCTCCTCATGGTATCGATACCGAA-ATAACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACC-AATATAACATTCGATGT
**
436872 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
* **
436926 TTTAAAAGTATCGATACCATCCT
1 TTCAAGGGTATCGATACC-TCCT
436949 TCAGGTATTG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
53 2 0.03
54 62 0.91
55 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
Found at i:443005 original size:54 final size:55
Alignment explanation
Indices: 442947--443053 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 55
442937 CAAGGGTATC
442947 GATACCAAAATAACATTCGATGTTTTAAGGGTATAGATACC-TCCTCAAGGTACT
1 GATACCAAAATAACATTCGATGTTTTAAGGGTATAGATACCATCCTCAAGGTACT
** * * *
443001 GATACCAATCTGACATTCGATGTTTTAAGGGTATCGATACCATCCTTAAGGTA
1 GATACCAAAATAACATTCGATGTTTTAAGGGTATAGATACCATCCTCAAGGTA
443054 TCGATACTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 37 0.79
55 10 0.21
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (55 bp):
GATACCAAAATAACATTCGATGTTTTAAGGGTATAGATACCATCCTCAAGGTACT
Found at i:446474 original size:55 final size:55
Alignment explanation
Indices: 446296--446456 Score: 270
Period size: 55 Copynumber: 2.9 Consensus size: 55
446286 TAGAAAATTA
446296 CACTATGTGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGG
* *
446350 CACTATGTGTGCAAAACTAAGAAATTCATAATAATTTTATGAATTTCTGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGG
* * *
446405 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGTATTTCCGTAT
1 CACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTAT
446457 TGGCGATACG
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 12 0.12
55 88 0.88
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (55 bp):
CACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGG
Found at i:448347 original size:81 final size:81
Alignment explanation
Indices: 446602--448321 Score: 2533
Period size: 81 Copynumber: 21.3 Consensus size: 81
446592 AATTATGCCA
* * * *
446602 GTTAAATACCTTTGAATAAAAGATTAATGACC-ATGTTGTGCATTTGACAGAAATGTGTTAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTA-GCTGTGCATTTGACAGAAATGTGTCAATTA
446666 TGCCAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* * *
446683 GTTAAATACCTTTGAGTAAAATA-TAATGGCCTATG-TATGCATTTGACAGAAAGGTGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTA-GCTGTGCATTTGACAGAAATGTGTCAATTA
446746 TGCCAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* *
446763 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
446828 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
*
446844 GTTAAATACCTTTGAGTAAAAGATT-A-GGCCTAGCTGTGCATTTGACATAAATGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
446907 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
*
446923 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
446988 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* ** * *
447004 GTTAAATACCTTTGAGT-AAATATTAATGGCCTAGCTGTGCATTTTCCAAAAATGTGTCAACTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
*
447068 GCCAGTTAGATGAAAT
66 GCCAGTTAGATGAAAG
447084 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
* *
447149 GCCAATTAGATGAAAT
66 GCCAGTTAGATGAAAG
* *
447165 GTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAAGGTGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAG-AAATGTGTCAATTA
* *
447230 TGCCAGTTAAAAGAAAG
65 TGCCAGTTAGATGAAAG
* * **
447247 GTTAAATACCTTTGAGTAAAATATTAATGGCCTAGCCGTGCATTTTCCAGAAATGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
447312 G-CAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* * * *
447327 GTTAAATACTTTTGAGTAAAATATTAATGGCCTAGCTGTGCATTTGATAGAAATGTTTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
* *
447392 GTCAGTTAAATGAAAG
66 GCCAGTTAGATGAAAG
* *
447408 GTTAAATACCTTTGAGTAAACA-ATTAATGGCCTAGCTGTGCATCTGACAGAAAGGTGTCAATTA
1 GTTAAATACCTTTGAGTAAA-AGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTA
**
447472 TGCCAGTTAGATGAATT
65 TGCCAGTTAGATGAAAG
* * * *
447489 GTTAAATACTTTTGAGTAAAATATTAATAGCCTAGTTGTGCATTTGACAGAAA-GATGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATG-TGTCAATTA
447553 TGCCAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* * *
447570 GTTAAATACCTTGGAGTAAAAGATTAATGGCCTATCTGTGCATTTGAAAGAAATGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
* *
447635 GCCAGTTAGACGGAAG
66 GCCAGTTAGATGAAAG
* * * * *
447651 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGTATTTGACAGAAAGGTGTTAGTTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
* *
447716 GCCAATTAGATGGAAG
66 GCCAGTTAGATGAAAG
* *
447732 GTTAAATACCTTTGAGTAAAAAATTAATGGCCTAGCTGTGCATTTGACAGAAAAGATGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATG-TGTCAATTA
*
447797 TGCTAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* * *
447814 GTTAACTACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
*
447879 GCCAATTAGATGAAAG
66 GCCAGTTAGATGAAAG
*
447895 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
447960 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
** *
447976 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGAAGTGCATTTGACAGAAATGTGTCTATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
448041 GCCAGTTAGAT-AAAG
66 GCCAGTTAGATGAAAG
* ** * * * *
448056 GTTAGATATATTTGAGTAAAAGATTAGTGGCCTAGTTGTGCATTTGACATAAAAGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
448121 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* * * *
448137 GTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTACATTTGACAAAAATATGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
*
448202 GTCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* * * * * * * *
448218 GTTAAATACTTTTGAGTAAAAGACTAATAGCCTAACTGTGCCTTTGGCAAAAATGTGTCAATCAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
* *
448283 GTCAGTTATATGAAAG
66 GCCAGTTAGATGAAAG
*
448299 GTTAAATACCTTTGGGTAAAAGA
1 GTTAAATACCTTTGAGTAAAAGA
448322 CTAAATGTCT
Statistics
Matches: 1491, Mismatches: 134, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
79 75 0.05
80 292 0.20
81 979 0.66
82 145 0.10
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTAT
GCCAGTTAGATGAAAG
Found at i:451005 original size:23 final size:23
Alignment explanation
Indices: 450979--451026 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
450969 ATAAAGTACA
*
450979 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
451002 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
451025 AT
1 AT
451027 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:451478 original size:23 final size:23
Alignment explanation
Indices: 451452--451514 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
451442 ATATAACCAC
451452 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
451475 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
451498 TACCTATTACATCATAT
1 TACCTATTACATTATAT
451515 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:451899 original size:430 final size:430
Alignment explanation
Indices: 451100--453438 Score: 4398
Period size: 430 Copynumber: 5.4 Consensus size: 430
451090 TTATAATATG
451100 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
* * *
451165 TC-AA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATGAATTTAATAATTTTATTTGCA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
451228 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAACAATA
451293 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
195 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
451358 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
260 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
*
451423 AAAAGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
325 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
451488 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
451529 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
451594 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
451659 CAAAAAATTATTTTATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
451724 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
196 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
* *
451789 TCACTCAAAAGATAACCTTCAATTAATGTTTTCCACAGTGAAAAAAATATAGACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
451854 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
*
451919 TCTAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
451959 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
* *
452024 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTACA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
452089 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
452154 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
196 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
452219 TCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATAGACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
452284 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
452349 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
452389 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
452454 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
452519 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
*
452584 TATATATCGTAACGTAAAAAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAAC
196 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
452649 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAGTATAGACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
* **
452714 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACAATATATATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
452779 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
452819 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
452884 TC-AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
452948 C-AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
*
453012 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATTTCTTAAAAC
196 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
453077 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAGTATAGACACTTTTATAAA
261 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
* *
453142 AAGAATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATGCCTATTACATTA
326 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
*
453207 TATAAGCGCTACCTATTACATCATATTTTTACATATTATA
391 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
453247 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
453312 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
453377 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAA
453439 CATTAACCAA
Statistics
Matches: 1870, Mismatches: 36, Indels: 7
0.98 0.02 0.00
Matches are distributed among these distances:
428 357 0.19
429 191 0.10
430 1219 0.65
431 103 0.06
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (430 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:451908 original size:23 final size:23
Alignment explanation
Indices: 451882--451944 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
451872 ATATAACCAC
451882 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
451905 TACCTATTACATTATCTAAGCGC
1 TACCTATTACATTATATAAACGA
*
451928 TACCTATTACATCATAT
1 TACCTATTACATTATAT
451945 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:452338 original size:23 final size:23
Alignment explanation
Indices: 452312--452374 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
452302 ATATAACCAC
452312 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
452335 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
452358 TACCTATTACATCATAT
1 TACCTATTACATTATAT
452375 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:452795 original size:23 final size:23
Alignment explanation
Indices: 452732--452804 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
452722 ATACTTTACA
*
452732 ATATAACCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
* **
452755 ATATAAACAATATATATTACATT
1 ATATAAACACTACCTATTACATT
* * *
452778 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
452801 ATAT
1 ATAT
452805 TTTTACCTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:453198 original size:23 final size:23
Alignment explanation
Indices: 453170--453232 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
453160 ATATAACCAC
453170 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
453193 TGCCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
453216 TACCTATTACATCATAT
1 TACCTATTACATTATAT
453233 TTTTACATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:456600 original size:183 final size:183
Alignment explanation
Indices: 456075--456564 Score: 892
Period size: 183 Copynumber: 2.7 Consensus size: 183
456065 TTAAAATTAC
456075 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
456140 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* *
456205 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAACGT
*
456258 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATTAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
456323 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* *
456388 ATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAACCGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAACGT
* *
456441 CGACACGTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
456505 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATA
65 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATA
456565 TCGATAGCAT
Statistics
Matches: 297, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 294 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAACGT
Found at i:458533 original size:3 final size:3
Alignment explanation
Indices: 458525--458590 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
458515 ACTTGTTTAG
* * * * * * *
458525 ATC ATC ATC ATC ATT ATC ATC ATC GTC GTC ATC ATC TTC ATC GTT AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
458573 TTC ATC GTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC
458591 GTCAGCTTCA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:458575 original size:12 final size:12
Alignment explanation
Indices: 458560--458602 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
458550 TCGTCATCAT
*
458560 CTTCATCGTTAG
1 CTTCATCGTCAG
*
458572 CTTCATCGTCAT
1 CTTCATCGTCAG
*
458584 CATCATCGTCAG
1 CTTCATCGTCAG
458596 CTTCATC
1 CTTCATC
458603 TTCATTGACC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.37
Consensus pattern (12 bp):
CTTCATCGTCAG
Found at i:458583 original size:24 final size:24
Alignment explanation
Indices: 458556--458607 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
458546 ATCGTCGTCA
* *
458556 TCATCTTCATCGTTAGCTTCATCG
1 TCATCATCATCGTCAGCTTCATCG
*
458580 TCATCATCATCGTCAGCTTCATCT
1 TCATCATCATCGTCAGCTTCATCG
458604 TCAT
1 TCAT
458608 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (24 bp):
TCATCATCATCGTCAGCTTCATCG
Found at i:460412 original size:200 final size:200
Alignment explanation
Indices: 460069--461245 Score: 2219
Period size: 200 Copynumber: 5.9 Consensus size: 200
460059 TTTAAATTAA
460069 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
460134 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
460199 TCGACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
460264 AAAAC
196 AAAAC
460269 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
460334 CTTGTACCGATTAGATTGAAAAATTACATATTGCATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
460399 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
460464 AAAAC
196 AAAAC
*
460469 TATCGACGCAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
460534 CTTGTACCGATTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
460599 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
460664 AAAAC
196 AAAAC
*
460669 TATCGACACAAACTAAAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
460734 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
460799 CCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
460864 AAAAC
196 AAAAC
460869 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
460934 CTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
460999 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
461064 AAAAA
196 AAAAC
*
461069 TATCAACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
461134 CTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTTGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
* *
461199 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
461246 GGCCATATTG
Statistics
Matches: 958, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 958 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
AAAAC
Found at i:461410 original size:19 final size:19
Alignment explanation
Indices: 461364--461412 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
461354 TTATATTCAC
*
461364 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
461383 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
461402 ATACAAAATTA
1 ATACAAAATTA
461413 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:463250 original size:33 final size:33
Alignment explanation
Indices: 463204--463269 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
463194 CATCTTAATA
* *
463204 TCACTCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
463237 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
463270 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:463328 original size:21 final size:21
Alignment explanation
Indices: 463303--463367 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
463293 CCCCTTATGC
* *
463303 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
463324 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
463345 CTATCAAGTTTCTCTTGGACT
1 CTCTCAAGTTTCTCTTCGACT
463366 CT
1 CT
463368 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:465605 original size:17 final size:18
Alignment explanation
Indices: 465583--465625 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
465573 ATATATCCGG
465583 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
465600 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
465620 TATCAT
1 TATCAT
465626 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:465634 original size:20 final size:19
Alignment explanation
Indices: 465588--465648 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
465578 TCCGGTATCA
465588 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
465607 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* * *
465628 TTTTACCTGTTATATCGTT
1 TTTTACCGGTTTTATCATT
465647 TT
1 TT
465649 GGATCGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:465796 original size:20 final size:20
Alignment explanation
Indices: 465769--465815 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
465759 TCCGGTAACG
465769 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
465788 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
465809 TTTTACC
1 TTTTACC
465816 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:465859 original size:181 final size:182
Alignment explanation
Indices: 465555--466027 Score: 727
Period size: 181 Copynumber: 2.6 Consensus size: 182
465545 CGTACTTACG
* *
465555 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
465620 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
465685 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
465736 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
465801 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
465866 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * *
465918 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGATT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
465982 TTGTCATAGTTTTACTTGTTATATCGTTTTGGATCG-TCACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGAT-ACATTTTT
466028 AATTTGGATC
Statistics
Matches: 267, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
181 170 0.64
182 96 0.36
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:466839 original size:27 final size:28
Alignment explanation
Indices: 466808--466865 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
466798 AAGTTGTGTA
* *
466808 TGGGTTATTATTT-TAATTAATG-TTTTT
1 TGGGTTATT-TTTCTAATAAATGAATTTT
466835 TGGGTTATTTTTCTAATAAATGAATTTT
1 TGGGTTATTTTTCTAATAAATGAATTTT
466863 TGG
1 TGG
466866 ATTTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 17 0.63
28 7 0.26
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (28 bp):
TGGGTTATTTTTCTAATAAATGAATTTT
Found at i:466981 original size:14 final size:14
Alignment explanation
Indices: 466964--467004 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
466954 AATTTATATA
466964 ATTAATATTTAATG
1 ATTAATATTTAATG
*
466978 ATTAATATATTTAATT
1 ATT-A-ATATTTAATG
466994 ATTAATATTTA
1 ATTAATATTTA
467005 TTTTGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTAATATTTAATG
Found at i:466989 original size:16 final size:16
Alignment explanation
Indices: 466968--467001 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
466958 TATATAATTA
466968 ATATTTAATGATTAAT
1 ATATTTAATGATTAAT
*
466984 ATATTTAATTATTAAT
1 ATATTTAATGATTAAT
467000 AT
1 AT
467002 TTATTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATTTAATGATTAAT
Found at i:473247 original size:37 final size:36
Alignment explanation
Indices: 473172--473247 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
473162 TTTTTATATT
*
473172 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
473208 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
473245 TTT
1 TTT
473248 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:478115 original size:47 final size:46
Alignment explanation
Indices: 478019--478116 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 46
478009 TCGAATAAAT
**
478019 GCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTAATC-AACAA
* *
478066 GCATGCGAATTAGATATCATGCGGTTAGGATTT-TTGTTAAT-AACAAA
1 GCATGCGAACTAGAAATCATGCGGTTAGG-TTTATT-TTAATCAAC-AA
478113 GCAT
1 GCAT
478117 AGGGTAGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
46 3 0.07
47 35 0.80
48 6 0.14
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (46 bp):
GCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTAATCAACAA
Found at i:485300 original size:42 final size:42
Alignment explanation
Indices: 485240--485673 Score: 339
Period size: 42 Copynumber: 10.5 Consensus size: 42
485230 ATCAGTAAGT
* * *
485240 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* * * * *
485282 GCCATCAGTAAGTTTTTCGAGTATGATGATTAAATCCTTCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
** ** * * * * *
485324 GTAATTTGTAAG-CCTTC-ACCAAAGA-GTAGTG-AAGCAAAT---
1 GCCATCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATC-ATTCGG
* *
485363 -CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* * * * *
485404 GTCATCAGTAAGTCTTTCGAACATGATGATGAAGTCTTTTGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* * * *
485446 GCCATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTTGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
** * *
485488 ATCATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* * *
485530 GCCATCAGTAAGTATTTCGAGCATGATAATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
*
485572 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* *** * * * *
485614 GTCATTTTTTAGTCTTTCGAGCAAGATAAT-AAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* *
485655 GTCATCCA-TAAGTCCTTCG
1 GCCAT-CAGTAAGTCTTTCG
485674 GGTCATCCAT
Statistics
Matches: 316, Mismatches: 63, Indels: 27
0.78 0.16 0.07
Matches are distributed among these distances:
38 10 0.03
39 11 0.03
40 5 0.02
41 34 0.11
42 256 0.81
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
Found at i:485369 original size:135 final size:137
Alignment explanation
Indices: 485110--485374 Score: 417
Period size: 135 Copynumber: 1.9 Consensus size: 137
485100 GGGCCATCAA
* *
485110 TAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATG
1 TAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAG-ATGATGATG
* ** *
485175 ATTAAGTTTTTCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGTAAGT
65 ATTAAATCCTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATCAGTAAGT
485240 GCCATTAG
130 GCCATTAG
* * *
485248 TAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTTTTTCGAG-T-ATGATGA
1 TAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGATGATGATGA
*
485311 TTAAATCCTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGT
66 TTAAATCCTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATCAGTAAGT
485375 CTTTCGAGCA
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
135 66 0.56
136 1 0.01
138 50 0.43
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (137 bp):
TAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGATGATGATGA
TTAAATCCTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATCAGTAAGTG
CCATTAG
Found at i:485520 original size:126 final size:126
Alignment explanation
Indices: 485364--485673 Score: 390
Period size: 126 Copynumber: 2.5 Consensus size: 126
485354 GAAGCAAATC
* *
485364 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCAGTAAGTCTTTCGAACATG
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTCATCAGTAAGTCTTTCGAACATG
* * * * * * *
485429 ATGATGAAGTCTTTTGGGCCATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGAT
66 ATAATGAAATCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCATTCGGAT
* * *
485490 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGCCATCAGTAAGTATTTCGAGCATG
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTCATCAGTAAGTCTTTCGAACATG
* * * *
485555 ATAATTAAATCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGT
66 ATAATGAAATCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCATTCGGAT
*** * * * *
485616 CATTTTTTAGTCTTTCGAGCAAGATAA-TAAATCCTTCGGGTCATCCA-TAAGTCCTTCG
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTCAT-CAGTAAGTCTTTCG
485674 GGTCATCCAT
Statistics
Matches: 158, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
125 24 0.15
126 134 0.85
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (126 bp):
CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTCATCAGTAAGTCTTTCGAACATG
ATAATGAAATCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCATTCGGAT
Found at i:485670 original size:20 final size:20
Alignment explanation
Indices: 485642--485696 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
485632 GAGCAAGATA
485642 ATAAATCCTTCGGGTCATCC
1 ATAAATCCTTCGGGTCATCC
*
485662 ATAAGTCCTTCGGGTCATCC
1 ATAAATCCTTCGGGTCATCC
*
485682 ATAATTCCTTCGGGT
1 ATAAATCCTTCGGGT
485697 AGGATGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (20 bp):
ATAAATCCTTCGGGTCATCC
Found at i:486180 original size:53 final size:53
Alignment explanation
Indices: 486117--486313 Score: 290
Period size: 53 Copynumber: 3.7 Consensus size: 53
486107 ATCAAACCAT
*
486117 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
486170 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
486223 AAGACTGTTCGAGTTCTACTTCCTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
* *
486276 AAGATTGTTCGAGTTCTACACCCTGAAGCAATAGGGAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAG
486314 AAAACCTTTT
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
53 129 0.98
54 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:487074 original size:45 final size:45
Alignment explanation
Indices: 487010--487100 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
487000 CAAAAAGGGG
487010 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
*
487055 TACTTATTTCTATGTTTCCATTTTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
487100 T
1 T
487101 GTACATGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (45 bp):
TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
Found at i:487786 original size:2 final size:2
Alignment explanation
Indices: 487775--487813 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
487765 TACTTTAATG
487775 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
487814 CATTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:490246 original size:53 final size:53
Alignment explanation
Indices: 489923--490247 Score: 239
Period size: 53 Copynumber: 6.2 Consensus size: 53
489913 TATGCATGTG
** * * *
489923 AGAAATTATAAAAATGTGAGTCTGTCATTTATTGATGA-AGATGTATG-TGAGCA
1 AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATA-ATGTATGCTGA-CA
* * * * *
489976 AGAAAATAAGAAAATGTGAGTATTTCATTTATGTATGATGATGTATGC-GAACA
1 AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATAATGTATGCTG-ACA
* * * * * * *
490029 AGAAATTAGG-AAACGACGAGTTTTTCATTTATGGATAATGATGTGTGATGGCA
1 AGAAATTAGGAAAATG-TGAGTTTTTCATTTATGGATGATAATGTATGCTGACA
* * * * * * * * * *
490082 ATAAATTAGGAAAATATAAGTCTTTCATTTATGGATTACAATTTTTGCAGGCA
1 AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATAATGTATGCTGACA
* * * * * *
490135 AGACATT-GGAAAATGTGACTATTTCATTTATGGATAATGATGTATGC-AAGCA
1 AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATAATGTATGCTGA-CA
* * *
490187 AAAAATTAGGAAAATGTTAGTTTTTCATTTATGGATGATAATGTATGCTGATA
1 AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATAATGTATGCTGACA
490240 AGAAATTA
1 AGAAATTA
490248 ATAAAAAGTT
Statistics
Matches: 209, Mismatches: 54, Indels: 18
0.74 0.19 0.06
Matches are distributed among these distances:
52 42 0.20
53 161 0.77
54 6 0.03
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (53 bp):
AGAAATTAGGAAAATGTGAGTTTTTCATTTATGGATGATAATGTATGCTGACA
Found at i:493907 original size:20 final size:21
Alignment explanation
Indices: 493856--493911 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
493846 ACAAGGTATA
493856 AAGTACCAAAGTTATAAACATTC
1 AAGTACCAAA--TATAAACATTC
493879 AAGTAACCAAATA-AAACATTC
1 AAGT-ACCAAATATAAACATTC
493900 AAGTACCAAATA
1 AAGTACCAAATA
493912 CCAAATAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 2 0.06
23 4 0.12
24 6 0.19
ACGTcount: A:0.54, C:0.18, G:0.07, T:0.21
Consensus pattern (21 bp):
AAGTACCAAATATAAACATTC
Found at i:494945 original size:64 final size:63
Alignment explanation
Indices: 494855--495015 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
494845 ATTGTTTAAG
* * *
494855 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
494918 T
63 T
* * * * *
494919 ATGCATCGATGCATAAGGAGTACATCGATGCATCCCCATTAAATAAAAACATTGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
494983 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
495016 ACATTCATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.88
65 7 0.09
66 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:495730 original size:30 final size:30
Alignment explanation
Indices: 495694--495757 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
495684 AAGGAACATA
* *
495694 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
495724 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
495754 TGGA
1 TGGA
495758 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:496702 original size:15 final size:15
Alignment explanation
Indices: 496684--496728 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
496674 TCATCATGAG
*
496684 CATCATCCATGTGCT
1 CATCATCCATATGCT
496699 CATC-TCCATCATGCT
1 CATCATCCAT-ATGCT
496714 CATCATCCATATGCT
1 CATCATCCATATGCT
496729 TACCGTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.22, C:0.36, G:0.09, T:0.33
Consensus pattern (15 bp):
CATCATCCATATGCT
Found at i:497642 original size:23 final size:23
Alignment explanation
Indices: 497599--497644 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
497589 ATATGTTTAA
*
497599 AAGAAGTTAAAAATGATTTTAGG
1 AAGAAGTTAAAAATGAATTTAGG
*
497622 AAGAA-TTAAAACTGAAATTTAGG
1 AAGAAGTTAAAAATG-AATTTAGG
497645 GTGAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (23 bp):
AAGAAGTTAAAAATGAATTTAGG
Found at i:499358 original size:3 final size:3
Alignment explanation
Indices: 499350--499377 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
499340 GTTGGCTACT
499350 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
499378 TGGTAGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:501231 original size:30 final size:30
Alignment explanation
Indices: 501190--501248 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
501180 TTTTGATAAA
* * *
501190 TTTTGATAAATTCGATTAAGTCTAAAATCT
1 TTTTAATAAATTCAATTAAGTCCAAAATCT
501220 TTTTAATAAATTCAATTAAGTCCAAAATC
1 TTTTAATAAATTCAATTAAGTCCAAAATC
501249 AATTTACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (30 bp):
TTTTAATAAATTCAATTAAGTCCAAAATCT
Found at i:502509 original size:53 final size:53
Alignment explanation
Indices: 502446--502921 Score: 414
Period size: 53 Copynumber: 9.1 Consensus size: 53
502436 AAGATGTTTT
** ** *
502446 AAAATGCGAGTCTTAAAACTATGGATGATGATGTATACATGAAATAAATTAGG
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
* *
502499 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACGTGCAAGAAATTAGG
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
** * **
502552 AAAATATGAGTCTTTCATTTATGGATGATGATGTATGCGAACAAA-AAATTA-G
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATAC-ATGAAAGAAATTAGG
* * * * *
502604 TAAAT--GTGTCTTTAATTTATGGATGATGATGTATAC-GGATAAGAAATTAGT
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGA-AAGAAATTAGG
* ** * *
502655 AAAAGGTAAGTCTTTCATTTATGGATGATGATGTATGC-GGACAAGAAATT-GG
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGA-AAGAAATTAGG
* * * * * * * *
502707 GAAGTGTGTGTATTTCATTTATGGATGAT-ATGTATGCAGGCAAGAAATTAGG
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
* * *
502759 AAAA-GATGAGTCTTTCATTGATGGATGATGATGTATGCGA-GAAAGAAATTAGG
1 AAAATG-CGAGTCTTTCATTTATGGATGATGATGTATAC-ATGAAAGAAATTAGG
** **** *
502812 AAAATGTTAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGA
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
** * * ** *
502865 AAAATGTTAGTCTTTCATTCATGGATGATGATGTATGCGGGTAAGAAATTAGG
1 AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
502918 AAAA
1 AAAA
502922 AGTGAGTATC
Statistics
Matches: 359, Mismatches: 51, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 34 0.09
51 20 0.06
52 55 0.15
53 243 0.68
54 4 0.01
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (53 bp):
AAAATGCGAGTCTTTCATTTATGGATGATGATGTATACATGAAAGAAATTAGG
Found at i:502650 original size:103 final size:102
Alignment explanation
Indices: 502465--502921 Score: 485
Period size: 106 Copynumber: 4.4 Consensus size: 102
502455 GTCTTAAAAC
* * *
502465 TATGGATGATGATGTATAC-ATGA-AATAAATTAGGAAAATGCGAGTCTTTCATTTATGGATGAT
1 TATGGATGATGATGTATGCGA--ACAAGAAATTA-GAAAAT--GTGTCTTTCATTTATGGATGAT
*
502528 GATGTATACGTGCAAGAAATTAGGAAAATATGAGTCTTTCATT
61 GATGTATACG-GCAAGAAATTAGGAAAAGATGAGTCTTTCATT
* * *
502571 TATGGATGATGATGTATGCGAACAAAAAATTAGTAAATGTGTCTTTAATTTATGGATGATGATGT
1 TATGGATGATGATGTATGCGAACAAGAAATTAGAAAATGTGTCTTTCATTTATGGATGATGATGT
* * * *
502636 ATACGGATAAGAAATTAGTAAAAGGTAAGTCTTTCATT
66 ATACGG-CAAGAAATTAGGAAAAGATGAGTCTTTCATT
* * ** *
502674 TATGGATGATGATGTATGCGGACAAGAAATTGGGAAGTGTGTGTATTTCATTTATGGATGAT-AT
1 TATGGATGATGATGTATGCGAACAAGAAATT-AGAA-AATGTGTCTTTCATTTATGGATGATGAT
*
502738 GTATGCAGGCAAGAAATTAGGAAAAGATGAGTCTTTCATT
64 GTATAC-GGCAAGAAATTAGGAAAAGATGAGTCTTTCATT
*
502778 GATGGATGATGATGTATGCGAGA-AAGAAATTAGGAAAATGTTAGTCTTTCATTTATGGATGATG
1 TATGGATGATGATGTATGCGA-ACAAGAAATTA-GAAAATG-T-GTCTTTCATTTATGGATGATG
** *
502842 ATGTATGTGGGAAAGAAATTA-GAAAA-ATGTTAGTCTTTCATT
62 ATGTAT-ACGGCAAGAAATTAGGAAAAGATG--AGTCTTTCATT
* ***
502884 CATGGATGATGATGTATGCGGGTAAGAAATTAGGAAAA
1 TATGGATGATGATGTATGCGAACAAGAAATTA-GAAAA
502922 AGTGAGTATC
Statistics
Matches: 301, Mismatches: 35, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
102 1 0.00
103 87 0.29
104 70 0.23
105 54 0.18
106 88 0.29
107 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (102 bp):
TATGGATGATGATGTATGCGAACAAGAAATTAGAAAATGTGTCTTTCATTTATGGATGATGATGT
ATACGGCAAGAAATTAGGAAAAGATGAGTCTTTCATT
Found at i:502913 original size:210 final size:208
Alignment explanation
Indices: 502466--502919 Score: 603
Period size: 210 Copynumber: 2.2 Consensus size: 208
502456 TCTTAAAACT
* * * * * * *
502466 ATGGATGATGATGTATACATGA-AATAAATTAGGAAAATGCGAGTCTTTCATTTATGGATGATGA
1 ATGGATGATGATGTATGC-GGACAAGAAATTAGG-AAGTGTGTGTATTTCATTTATGGATGATGA
* *
502530 TGTATACGTGCAAGAAATTAGGAAAATATGAGTCTTTCATTTATGGATGATGATGTATGCGAACA
64 TGTATACGTGCAAGAAATTAGGAAAAGATGAGTCTTTCATTGATGGATGATGATGTATGCGAACA
* *
502595 AAAAATTAGTAAATGTGTCTTTAATTTATGGATGATGATGTATACGGATAAGAAATTAGTAAAAG
129 AAAAATTAGAAAATGTGTCTTTAATTTATGGATGATGATGTATACGGATAAGAAATTAGAAAAAG
*
502660 GTAAGTCTTTCATTT
194 GTAAGTCTTTCATTC
*
502675 ATGGATGATGATGTATGCGGACAAGAAATTGGGAAGTGTGTGTATTTCATTTATGGATGAT-ATG
1 ATGGATGATGATGTATGCGGACAAGAAATTAGGAAGTGTGTGTATTTCATTTATGGATGATGATG
*
502739 TATGCAG-GCAAGAAATTAGGAAAAGATGAGTCTTTCATTGATGGATGATGATGTATGCGAGA-A
66 TATAC-GTGCAAGAAATTAGGAAAAGATGAGTCTTTCATTGATGGATGATGATGTATGCGA-ACA
* * **
502802 AGAAATTAGGAAAATGTTAGTCTTTCATTTATGGATGATGATGTATGTGGGA-AAGAAATTAGAA
129 AAAAATTA-GAAAATG-T-GTCTTTAATTTATGGATGATGATGTAT-ACGGATAAGAAATTAGAA
* *
502866 AAATGTTAGTCTTTCATTC
190 AAAGGTAAGTCTTTCATTC
**
502885 ATGGATGATGATGTATGCGGGTAAGAAATTAGGAA
1 ATGGATGATGATGTATGCGGACAAGAAATTAGGAA
502920 AAAGTGAGTA
Statistics
Matches: 215, Mismatches: 23, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
207 66 0.31
208 34 0.16
209 27 0.13
210 85 0.40
211 3 0.01
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (208 bp):
ATGGATGATGATGTATGCGGACAAGAAATTAGGAAGTGTGTGTATTTCATTTATGGATGATGATG
TATACGTGCAAGAAATTAGGAAAAGATGAGTCTTTCATTGATGGATGATGATGTATGCGAACAAA
AAATTAGAAAATGTGTCTTTAATTTATGGATGATGATGTATACGGATAAGAAATTAGAAAAAGGT
AAGTCTTTCATTC
Found at i:509779 original size:2 final size:2
Alignment explanation
Indices: 509772--509798 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
509762 TTGATATAAG
509772 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
509799 ATGTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:510643 original size:29 final size:29
Alignment explanation
Indices: 510565--510634 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
510555 TAATTCTACA
*
510565 GTGACCAAGGAGGTCGTCATGCACTCCGG
1 GTGACCAAGGAGGTCGACATGCACTCCGG
*
510594 GCGACCAAGGAGGTCGACATGCACT-CGCG
1 GTGACCAAGGAGGTCGACATGCACTCCG-G
510623 GTGACCAAGGAG
1 GTGACCAAGGAG
510635 CGATGCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.13
Consensus pattern (29 bp):
GTGACCAAGGAGGTCGACATGCACTCCGG
Found at i:511254 original size:21 final size:21
Alignment explanation
Indices: 511229--511272 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
511219 AATCTAGTTA
*
511229 ATTAGTTTGTTAGTATAAATT
1 ATTAGTGTGTTAGTATAAATT
* *
511250 ATTAGTGTGTTAGTTTAAGTT
1 ATTAGTGTGTTAGTATAAATT
511271 AT
1 AT
511273 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTGTGTTAGTATAAATT
Found at i:511282 original size:28 final size:30
Alignment explanation
Indices: 511249--511311 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
511239 TAGTATAAAT
511249 TATTAGTGTGTTAGTTT-AAGT-TATATTA
1 TATTAGTGTGTTAGTTTAAAGTATATATTA
* *
511277 TATTAGTTTGTTAGTTTAAATTATATATTA
1 TATTAGTGTGTTAGTTTAAAGTATATATTA
511307 TATTA
1 TATTA
511312 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 16 0.52
29 3 0.10
30 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
TATTAGTGTGTTAGTTTAAAGTATATATTA
Found at i:511331 original size:49 final size:49
Alignment explanation
Indices: 511223--511334 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 49
511213 AACTAAAATC
* * * ***
511223 TAGTTAATTAGTTTGTTAGTATAAATTATTAGTGTGTTAGTTTAAGTTA
1 TAGTTAATTAGTTTGTTAGTATAAATTATTAGTATATTAGTATAAAAAA
* *
511272 TA-TTATATTAGTTTGTTAGTTTAAATTATATATTATATTA-TATAAAAAA
1 TAGTTA-ATTAGTTTGTTAGTATAAATTAT-TAGTATATTAGTATAAAAAA
511321 TAGTTAATTAGTTT
1 TAGTTAATTAGTTT
511335 ATTAAATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
48 3 0.06
49 39 0.75
50 10 0.19
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (49 bp):
TAGTTAATTAGTTTGTTAGTATAAATTATTAGTATATTAGTATAAAAAA
Found at i:511800 original size:17 final size:17
Alignment explanation
Indices: 511778--511838 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
511768 GATAATTTCC
511778 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
* *
511795 GTTTAAAAATATTTAATGTT
1 GTTTAAAAA-A-ATATTG-T
*
511815 GTTTTAAAAAAATATTTT
1 G-TTTAAAAAAATATTGT
511833 GTTTAA
1 GTTTAA
511839 TTTATATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.40
18 3 0.09
19 7 0.20
20 3 0.09
21 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:514560 original size:11 final size:11
Alignment explanation
Indices: 514544--514613 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
514534 CTGAAGGACT
514544 GCAATAATGCA
1 GCAATAATGCA
514555 GCAATAATGCA
1 GCAATAATGCA
* * *
514566 ACAATAAGGGCT
1 GCAATAA-TGCA
514578 GCAATAATGCA
1 GCAATAATGCA
*
514589 GCAATAAGTGCT
1 GCAATAA-TGCA
514601 GCAATAATGCA
1 GCAATAATGCA
514612 GC
1 GC
514614 TGAATTCACG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 31 0.63
12 18 0.37
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:514612 original size:23 final size:23
Alignment explanation
Indices: 514544--514613 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
514534 CTGAAGGACT
*
514544 GCAATAA-TGCAGCAATAATGCA
1 GCAATAAGTGCTGCAATAATGCA
* *
514566 ACAATAAGGGCTGCAATAATGCA
1 GCAATAAGTGCTGCAATAATGCA
514589 GCAATAAGTGCTGCAATAATGCA
1 GCAATAAGTGCTGCAATAATGCA
514612 GC
1 GC
514614 TGAATTCACG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 6 0.14
23 36 0.86
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (23 bp):
GCAATAAGTGCTGCAATAATGCA
Found at i:514807 original size:29 final size:29
Alignment explanation
Indices: 514765--514876 Score: 170
Period size: 29 Copynumber: 3.9 Consensus size: 29
514755 GAGGAACGTT
514765 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
*
514794 GGACGCCGGGCGTGCATAGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
*
514823 GGACGTCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
* ***
514852 GGTCATTGGGCGTGCATGGCGACCT
1 GGACGCCGGGCGTGCATGGCGACCT
514877 CCTTGGTGGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.20, C:0.26, G:0.38, T:0.17
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:520082 original size:14 final size:14
Alignment explanation
Indices: 520035--520086 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
520025 TAAAGATGAT
* *
520035 ATAAAAGTAAGAAA
1 ATAAAAATAATAAA
* *
520049 ATATAAA-AATATA
1 ATAAAAATAATAAA
*
520062 ATTAAAATAATAAA
1 ATAAAAATAATAAA
520076 ATAAAAATAAT
1 ATAAAAATAAT
520087 TTAGTAATTG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:528675 original size:14 final size:14
Alignment explanation
Indices: 528648--528706 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
528638 TATTTATATA
528648 AATAATAA--AAAT
1 AATAATAATGAAAT
*
528660 AATAACAATGAAAT
1 AATAATAATGAAAT
* *
528674 AATAATTAAAGCAAT
1 AATAA-TAATGAAAT
*
528689 AATAATAATAAAAT
1 AATAATAATGAAAT
528703 AATA
1 AATA
528707 TTGCAAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.19
14 19 0.51
15 11 0.30
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (14 bp):
AATAATAATGAAAT
Found at i:528783 original size:29 final size:29
Alignment explanation
Indices: 528734--528795 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
528724 AATAAAAGGA
* *
528734 ATTAAAAATATAGTAT-TAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAAATG-AAAAT
528763 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAAATGAAAAT
528792 -TTAA
1 ATTAA
528796 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATATCAAAAATGAAAAT
Found at i:530000 original size:14 final size:15
Alignment explanation
Indices: 529980--530014 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
529970 TTTGTTATTA
529980 GGTTTGGGCCAGTCT
1 GGTTTGGGCCAGTCT
*
529995 -GTTTGGGCGAGTCT
1 GGTTTGGGCCAGTCT
530009 GGTTTG
1 GGTTTG
530015 TAATCGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.06, C:0.14, G:0.43, T:0.37
Consensus pattern (15 bp):
GGTTTGGGCCAGTCT
Found at i:530088 original size:22 final size:22
Alignment explanation
Indices: 530061--530106 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
530051 ATTAATTATT
530061 TAATAA-ATATAAT-ATAACATAA
1 TAATAATA-ATAATAATAA-ATAA
530083 TAATAATAATAATAATAAATAA
1 TAATAATAATAATAATAAATAA
530105 TA
1 TA
530107 TAAGCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATAAATAA
Found at i:530091 original size:19 final size:19
Alignment explanation
Indices: 530069--530106 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
530059 TTTAATAAAT
530069 ATAAT-ATAACATAATAATA
1 ATAATAATAACA-AATAATA
*
530088 ATAATAATAATAAATAATA
1 ATAATAATAACAAATAATA
530107 TAAGCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAACAAATAATA
Found at i:530658 original size:113 final size:113
Alignment explanation
Indices: 530430--530658 Score: 275
Period size: 113 Copynumber: 2.0 Consensus size: 113
530420 TAGAGTCATG
*
530430 CAAAAGGTCGAACAAGCTTTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTCGAACAAGATTTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCA
** * * * ** *
530495 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAA
66 TTATGAACTGACTCTGGAAAAGCTGATCAATCAAGTCAAAAAGTTAAA
* * *
530543 CAAAAGGTTGAACAA-ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTCGAACAAGATT-TTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTC
* * *
530607 ATTATGAACTCGAC-CTGGAAATGCTGATGAATTCAAG-CAAAAAGTTGAA
65 ATTATGAACT-GACTCTGGAAAAGCTGATCAA-TCAAGTCAAAAAGTTAAA
530656 CAA
1 CAA
530659 GTTCTTCTCA
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
112 2 0.02
113 90 0.92
114 6 0.06
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (113 bp):
CAAAAGGTCGAACAAGATTTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCA
TTATGAACTGACTCTGGAAAAGCTGATCAATCAAGTCAAAAAGTTAAA
Found at i:530739 original size:61 final size:61
Alignment explanation
Indices: 530597--530744 Score: 253
Period size: 61 Copynumber: 2.4 Consensus size: 61
530587 TCTTCAGATG
**
530597 AGTTCTTCTCATTATGAAC-TCGACCTGGAAATGCTGATGAATTCAAGCAAAAAGTTGAACA
1 AGTTCTTCTCATTATGAACTTC-TTCTGGAAATGCTGATGAATTCAAGCAAAAAGTTGAACA
530658 AGTTCTTCTCATTATGAACTTCTTCTGGAAATGCTGATGAATTCAAGCAAAAAGTTGAACA
1 AGTTCTTCTCATTATGAACTTCTTCTGGAAATGCTGATGAATTCAAGCAAAAAGTTGAACA
*
530719 AGTTCTTCTCATTATAAACTTCTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
530745 TCTTTCTTCA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
61 81 0.98
62 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (61 bp):
AGTTCTTCTCATTATGAACTTCTTCTGGAAATGCTGATGAATTCAAGCAAAAAGTTGAACA
Found at i:531154 original size:111 final size:113
Alignment explanation
Indices: 530692--531236 Score: 706
Period size: 111 Copynumber: 4.9 Consensus size: 113
530682 CTGGAAATGC
* * *
530692 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCTTTCTTCAGA
1 TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * *
530757 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAG
66 TGAGTTCTTCTCATTATGAACTCTATCTGGAAAAGTTGATCCATCGAG
* * * *
530805 TGATGAATTTAAACAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGA
1 TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * * ** * * * *
530870 TGAGTTCTTCTCATTATAAACTCTAACTGGCACTGCTGATTCACCGAA
66 TGAGTTCTTCTCATTATGAACTCTATCTGGAAAAGTTGATCCATCGAG
* * *
530918 TGATGAATTCAAACGAAAGGTTAAACAAGTTCTTCT--TCTATGAACTTCTTCTTCCTTCTTCAG
1 TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT-TATGAACTTCTTCTTCCTTCTTCAG
530981 ATGAGTTCTTCTCATTATGAACTCT-TCTGGAAAAGTTGATCCATCGAG
65 ATGAGTTCTTCTCATTATGAACTCTATCTGGAAAAGTTGATCCATCGAG
* * ** * *
531029 TAATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATA
1 TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * * *
531094 TAAGTTCTTCTCATTATGAGCT-T-TCTGGTAATGTTGATCCATCGAG
66 TGAGTTCTTCTCATTATGAACTCTATCTGGAAAAGTTGATCCATCGAG
* * * *
531140 TGATGAATTCGAGCAAAAGGTTGAACAAGTTCATCTCATTATGAACTTCTTCTTTCTTATTCAGA
1 TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
531205 TGAGTTCTTCTCATTATGAATTCT-TCTGGAAA
66 TGAGTTCTTCTCATTATGAACTCTATCTGGAAA
531237 TGCTGATGAC
Statistics
Matches: 371, Mismatches: 57, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
111 142 0.38
112 101 0.27
113 128 0.35
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCTATCTGGAAAAGTTGATCCATCGAG
Found at i:531400 original size:77 final size:76
Alignment explanation
Indices: 531241--531473 Score: 412
Period size: 76 Copynumber: 3.1 Consensus size: 76
531231 TGGAAATGCT
* * * *
531241 GATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGTACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
531306 TAGGACTTACA
66 TAGGACTTACA
531317 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACT
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACT
531382 GTAGGACTTACA
65 GTAGGACTTACA
*
531394 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
531459 TAGGACTTACA
66 TAGGACTTACA
531470 GATG
1 GATG
531474 TGGGAAATAG
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
76 76 0.50
77 75 0.50
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:532179 original size:22 final size:22
Alignment explanation
Indices: 532151--532271 Score: 224
Period size: 22 Copynumber: 5.5 Consensus size: 22
532141 AATAAAGCTT
*
532151 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
532173 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
532195 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
532217 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
532239 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
532261 TCATCTTTGAA
1 TCATCTTTGAA
532272 GAGTGTAGAT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 98 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:532695 original size:50 final size:50
Alignment explanation
Indices: 532640--532781 Score: 266
Period size: 50 Copynumber: 2.8 Consensus size: 50
532630 TAACTGGTTC
*
532640 GTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTACTCAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACTCAGAT
532690 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACTCAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACTCAGAT
*
532740 GTAAAACATTTGGCAACACATTCATCCTTTCCTGTGGTTTCT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCT
532782 GCTCGAATTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (50 bp):
GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACTCAGAT
Found at i:535063 original size:114 final size:114
Alignment explanation
Indices: 534863--535079 Score: 371
Period size: 114 Copynumber: 1.9 Consensus size: 114
534853 CATGCAGTTC
* * *
534863 ATCTTTCAATTCCAATAATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
534928 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
* * * *
534977 ATCTTTCAAATCCAATGATTGGTTTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
535042 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
535080 CGAGAACGTG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
ATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
Found at i:537693 original size:2 final size:2
Alignment explanation
Indices: 537686--537737 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
537676 ACAACAAAGG
537686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537728 AT AT AT AT AT
1 AT AT AT AT AT
537738 TAAAGGATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:540731 original size:14 final size:14
Alignment explanation
Indices: 540697--540750 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
540687 CATAAAAATA
* *
540697 CAAATGCAAAGATG
1 CAAATGTAAATATG
540711 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
540726 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
540740 TAAATGTAAAT
1 CAAATGTAAAT
540751 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:542358 original size:28 final size:26
Alignment explanation
Indices: 542303--542360 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
542293 AAACATTAAT
*
542303 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
542329 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
542357 AAAA
1 AAAA
542361 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:543238 original size:26 final size:28
Alignment explanation
Indices: 543179--543240 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
543169 TAAATAATAT
*
543179 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
543209 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
543234 AAATAAT
1 AAATAAT
543241 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:544521 original size:14 final size:15
Alignment explanation
Indices: 544501--544535 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
544491 TTTATTATTA
*
544501 GGTTTGGGCCAGTCT
1 GGTTTGGGACAGTCT
544516 -GTTTGGGACAGTCT
1 GGTTTGGGACAGTCT
544530 GGTTTG
1 GGTTTG
544536 TAATCGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.09, C:0.14, G:0.40, T:0.37
Consensus pattern (15 bp):
GGTTTGGGACAGTCT
Found at i:544609 original size:22 final size:22
Alignment explanation
Indices: 544582--544627 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
544572 ATTAATGATT
544582 TAATAA-ATATAAT-ATAACATAA
1 TAATAATA-ATAATAATAA-ATAA
544604 TAATAATAATAATAATAAATAA
1 TAATAATAATAATAATAAATAA
544626 TA
1 TA
544628 TAAGCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATAAATAA
Found at i:544612 original size:19 final size:19
Alignment explanation
Indices: 544590--544627 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
544580 TTTAATAAAT
544590 ATAAT-ATAACATAATAATA
1 ATAATAATAACA-AATAATA
*
544609 ATAATAATAATAAATAATA
1 ATAATAATAACAAATAATA
544628 TAAGCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAACAAATAATA
Found at i:546533 original size:21 final size:20
Alignment explanation
Indices: 546499--546591 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
546489 GATTCTGACT
* * *
546499 ATCGCATTGAGATTTCCCAA
1 ATCGCAATGCGATTACCCAA
**
546519 ATTCGCAATGCGATTACGTAA
1 A-TCGCAATGCGATTACCCAA
**
546540 ATCGCAATGCGATTACGTAA
1 ATCGCAATGCGATTACCCAA
* * **
546560 ATCGCAATGCTAATACGTAA
1 ATCGCAATGCGATTACCCAA
546580 ATCGCAATGCGA
1 ATCGCAATGCGA
546592 ATATGTGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 49 0.77
21 15 0.23
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATTACCCAA
Found at i:546544 original size:41 final size:40
Alignment explanation
Indices: 546499--546588 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
546489 GATTCTGACT
* * *
546499 ATCGCATTGAGATTTCCCAAATTCGCAATGCGATTACGTAA
1 ATCGCAATGAGATTACCCAAA-TCGCAATGCGAATACGTAA
* ** *
546540 ATCGCAATGCGATTACGTAAATCGCAATGCTAATACGTAA
1 ATCGCAATGAGATTACCCAAATCGCAATGCGAATACGTAA
546580 ATCGCAATG
1 ATCGCAATG
546589 CGAATATGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 26 0.62
41 16 0.38
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (40 bp):
ATCGCAATGAGATTACCCAAATCGCAATGCGAATACGTAA
Found at i:546546 original size:20 final size:20
Alignment explanation
Indices: 546521--546591 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
546511 TTTCCCAAAT
546521 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
546541 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
546561 TCGCAATGCTAATACGTAAA
1 TCGCAATGCGATTACGTAAA
546581 TCGCAATGCGA
1 TCGCAATGCGA
546592 ATATGTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:547636 original size:20 final size:20
Alignment explanation
Indices: 547611--547664 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
547601 GACATTCATT
547611 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
* *
547631 TGACTATTGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
547651 TGACTATCGCAACG
1 TGACTATCGCAACG
547665 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:547693 original size:33 final size:34
Alignment explanation
Indices: 547656--547731 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
547646 GGAAATGACT
547656 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
* *
547689 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
547723 ATCGCAACG
1 ATCGCAACG
547732 CGAAATTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 24 0.60
34 16 0.40
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
Found at i:549390 original size:41 final size:42
Alignment explanation
Indices: 549284--549392 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 42
549274 TCTAGAATGT
* *
549284 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGTGGCCTCTTGAACGA
* * ** *
549326 TGGGAGGGGACTCTTGAGGGATGATAG-GGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGTGGCCTCTTGAACGA
*
549367 TAGGG-GAGTCCTCTTGAACGATGACA
1 T-GGGAGAGGCCTCTTGAACGATGACA
549393 TGTGAGTCGG
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 29 0.55
42 22 0.42
43 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGTGGCCTCTTGAACGA
Found at i:549907 original size:20 final size:20
Alignment explanation
Indices: 549882--550010 Score: 94
Period size: 20 Copynumber: 6.8 Consensus size: 20
549872 AATCGCAACG
*
549882 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
*
549902 AATGACTATCGCAATGCG-A
1 AATGACTATCGCAACGCGAA
**
549921 AATGAAAATCGCAA--C-AA
1 AATGACTATCGCAACGCGAA
*
549938 CAA--A--ATCGCAACGTGAA
1 -AATGACTATCGCAACGCGAA
* *
549955 AATGACTATTGCAATGCGAA
1 AATGACTATCGCAACGCGAA
* *
549975 AATGACTATTGCAATGCGAA
1 AATGACTATCGCAACGCGAA
**
549995 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
550011 AGAGAATTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.08
16 3 0.03
17 4 0.05
18 3 0.03
19 13 0.15
20 58 0.66
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:550062 original size:20 final size:20
Alignment explanation
Indices: 550023--550134 Score: 170
Period size: 20 Copynumber: 5.6 Consensus size: 20
550013 AGAATTCTTT
* **
550023 CGTTTCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
550043 CATTGCGATAATCATTTTCG
1 CGTTGCGATAGTCATTTTCG
550063 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
550083 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
550103 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
550123 CATTGCGATAGT
1 CGTTGCGATAGT
550135 AAACTATTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:552073 original size:20 final size:20
Alignment explanation
Indices: 552015--552081 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
552005 GAAACTTTAA
* **
552015 ATCGCAACACGACAATGAAA
1 ATCGCAACACGAAAATGACT
552035 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
552055 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
552075 ATCGCAA
1 ATCGCAA
552082 TGCAAGAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:552515 original size:22 final size:22
Alignment explanation
Indices: 552453--552518 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
552443 TGACCGTGAA
* *
552453 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
552475 TGATATCGTCGGCGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
552497 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
552519 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:552725 original size:20 final size:20
Alignment explanation
Indices: 552700--552808 Score: 80
Period size: 20 Copynumber: 5.4 Consensus size: 20
552690 ATGTAAATCA
552700 CATTGCGATAGT-CAGATTCG
1 CATTGCGAT-GTACAGATTCG
* *
552720 CATTGCGATTTACATATTCG
1 CATTGCGATGTACAGATTCG
*
552740 CATTGCGATTTAC-GTATTCG
1 CATTGCGATGTACAG-ATTCG
* * *
552760 CATTGCGATTTTCCAAATTCG
1 CATTGCGA-TGTACAGATTCG
* * *
552781 CGTTGCGATTTAC-GTATTTG
1 CATTGCGATGTACAG-ATTCG
552801 CATTGCGA
1 CATTGCGA
552809 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.01
20 57 0.77
21 16 0.22
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
CATTGCGATGTACAGATTCG
Found at i:552792 original size:41 final size:40
Alignment explanation
Indices: 552715--552808 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
552705 CGATAGTCAG
*
552715 ATTCGCATTGCGATTTACATATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
* *
552755 ATTCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACGT
*
552796 ATTTGCATTGCGA
1 ATTCGCATTGCGA
552809 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
Found at i:552831 original size:21 final size:21
Alignment explanation
Indices: 552805--552850 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
552795 TATTTGCATT
552805 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
552826 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
552847 GCGA
1 GCGA
552851 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:553169 original size:30 final size:30
Alignment explanation
Indices: 553091--553178 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
553081 GTCTTAATCT
* **
553091 AAAATATATTTTAATCTTATCACAAC--TTA
1 AAAATATATTTT-ATTTTATCTTAACTTTTA
*
553120 AAATTATATTTTATTTTTTATCTTAACTTTTA
1 AAAATATATTTTA--TTTTATCTTAACTTTTA
*
553152 AAAATATATTTTATTTTATTTTAACTT
1 AAAATATATTTTATTTTATCTTAACTT
553179 ATTACATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.02
29 11 0.22
30 22 0.45
32 15 0.31
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (30 bp):
AAAATATATTTTATTTTATCTTAACTTTTA
Found at i:553198 original size:32 final size:32
Alignment explanation
Indices: 553124--553223 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 32
553114 AACTTAAAAT
* *
553124 TATATTTTATT-TTTTATCTTAACTT-TTAAA
1 TATATTATATTATTTTATATTAACTTATTAAA
* * * *
553154 AATA-TATTTTATTTTATTTTAACTTATTACA
1 TATATTATATTATTTTATATTAACTTATTAAA
* *
553185 TATATTATATTA--TTAAATTAAATTATTAAA
1 TATATTATATTATTTTATATTAACTTATTAAA
553215 TATATTATA
1 TATATTATA
553224 GTCTTTCCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.07
30 39 0.70
31 7 0.12
32 6 0.11
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATTATATTATTTTATATTAACTTATTAAA
Found at i:553323 original size:18 final size:18
Alignment explanation
Indices: 553290--553339 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
553280 AAAAATAAGA
*
553290 ATAAAATATATCTTTTAAC
1 ATAAAA-ATATATTTTAAC
*
553309 TTAAAAATATATTTTAAC
1 ATAAAAATATATTTTAAC
553327 AT-AAAATATATTT
1 ATAAAAATATATTT
553340 AAAAATAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 11 0.39
18 12 0.43
19 5 0.18
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAAATATATTTTAAC
Found at i:553325 original size:60 final size:60
Alignment explanation
Indices: 553258--553385 Score: 206
Period size: 60 Copynumber: 2.1 Consensus size: 60
553248 AATTTATCCT
553258 TATTTTAACA-AAAATATATATTAAAAATAAGAATAAAATATAT-CTTTTAACTTAAAAATA
1 TATTTTAACATAAAATATAT-TTAAAAATAAGAATAAAATATATAC-TTTAACTTAAAAATA
*
553318 TATTTTAACATAAAATATATTTAAAAATAAGAATACAATATATACTTTAACTTAAAAATA
1 TATTTTAACATAAAATATATTTAAAAATAAGAATAAAATATATACTTTAACTTAAAAATA
*
553378 TATGTTAA
1 TATTTTAA
553386 AATATAATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
60 54 0.84
61 10 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (60 bp):
TATTTTAACATAAAATATATTTAAAAATAAGAATAAAATATATACTTTAACTTAAAAATA
Found at i:553334 original size:17 final size:17
Alignment explanation
Indices: 553290--553339 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
553280 AAAAATAAGA
553290 ATAAAATATATCTTTTAAC
1 ATAAAATATA--TTTTAAC
*
553309 TTAAAAATATATTTTAAC
1 AT-AAAATATATTTTAAC
553327 ATAAAATATATTT
1 ATAAAATATATTT
553340 AAAAATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 8 0.29
19 1 0.04
20 8 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATATATTTTAAC
Found at i:553347 original size:17 final size:17
Alignment explanation
Indices: 553312--553352 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
553302 TTTTAACTTA
* *
553312 AAAATATATTTTAACAT
1 AAAATATATTTAAAAAT
553329 AAAATATATTTAAAAAT
1 AAAATATATTTAAAAAT
553346 AAGAATA
1 AA-AATA
553353 CAATATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATATATTTAAAAAT
Found at i:554731 original size:159 final size:158
Alignment explanation
Indices: 554228--555222 Score: 1037
Period size: 159 Copynumber: 6.3 Consensus size: 158
554218 TGTGATATAT
* * * *
554228 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACCTAAAATAAAAGATGAAGTGAAGAAATAAGAA
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAAGGATGAAGTGAAGAAAAAAGGA
*** *
554293 AATTATGAAAAATTGAGGGACTAAATTGAAAAATAGAAAAAAAATTTATCAAAAAGCGAAATTGA
66 AATTATGAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTA-TTATCAAAAAGAGAAATTGA
* * * *
554358 AAGTACATATATATTCTATGGTGGTTTAA
130 AAGTACATATGTATTCTACGATGGTTTAG
* * * *
554387 TAGTATGTGGTTCAAATTTGAT-AAAAACAGACTTAAAATAAAGGATGAATTAAAGGGGAAAAAA
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAAGGATGAAGTGAA---GAAAAAA
* * *
554451 GGAAATTATGAAAAATTGAGGGATTAAACTTAAAAAAATAGGAACAA--TGTTATCAAAAAGAGA
63 GGAAATTATGAAAAATTGAGGGACTAAA-TT-GAAAAATA-GAA-AATTTATTATCAAAAAGAGA
* * * ** *
554514 AATTGAAAGTAAATAGGTATTCTAATG-TGGAATAT
124 AATTGAAAGTACATATGTATTCT-ACGATGGTTTAG
* * * *
554549 GAGTA--TGGTTCAAATTTGGTAAAAAAAAAGACCTAAAATAAAGGATGAAGCGAAGAAATAAGG
1 GAGTATGTGGTTCAAATTTGGT-AAAAAACAGACTTAAAATAAAGGATGAAGTGAAGAAAAAAGG
*
554612 AAATTATGAAAAACTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGAAATTGA
65 AAATTATGAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGAAATTGA
* *
554677 AAGTACATATGTATTATACGGTGGTTTAG
130 AAGTACATATGTATTCTACGATGGTTTAG
* * * *
554706 GAGTATGTGGTTCAAATTTGAT-AAAAAC-GAACTTAAAATAAATGATGAATTGAA-AAAAAAAG
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAG-ACTTAAAATAAAGGATGAAGTGAAGAAAAAAGG
* * * * *
554768 AAATTATGAAAAATTGAGGGATTAAACTGAAAAAATAGAAAA--AAGTATCAAAAAGAGAAACTG
65 AAATTATGAAAAATTGAGGGACTAAATTG-AAAAATAGAAAATTTATTATCAAAAAGAGAAATTG
* * *
554831 AAAGTACATATGTATTCAACTATAGTTTAG
129 AAAGTACATATGTATTCTACGATGGTTTAG
** * * *
554861 GAACATGTGGTTCAAATTTGAT-AAAAATAGACTTAAAATAAAGGATGAATTGAAGAAAAAAAAA
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAAGGATGAAGTGAAG---AAAAAA
* * * *** * **
554925 GGAAATTATGAAAAATTGAGGGAATAAATTGAAAAATAAAAAATTTGTTATTGGAAAGATACTTT
63 GGAAATTATGAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGAAATT
**
554990 GAAAGTACATA-GTATTCTACGATAATTTAG
128 GAAAGTACATATGTATTCTACGATGGTTTAG
* * * * * *
555020 GAGCATATGGTTCAAATTTGGT-AAAAACATACTTAAAATAAAGGAAGAAGAGAAGAAAAAAAGA
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAAGGATGAAGTGAAG-AAAAAAGG
* * *
555084 AAATTATGAAAAAATTGAGAGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAATAGAAATT
65 AAATTATG-AAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTATTATC-AAAAAGAGAAATT
* * *
555149 AAAAGAACATATATATTCTACGATGGTTTAG
128 GAAAGTACATATGTATTCTACGATGGTTTAG
* * * * *
555180 GAGCATGTCGTTTAAATTTGGTAAAAAAAAGATTTAAAATAAA
1 GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAA
555223 TAATGAAATC
Statistics
Matches: 700, Mismatches: 108, Indels: 54
0.81 0.13 0.06
Matches are distributed among these distances:
155 93 0.13
156 39 0.06
157 105 0.15
158 79 0.11
159 179 0.26
160 70 0.10
161 49 0.07
162 71 0.10
163 10 0.01
164 3 0.00
165 2 0.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (158 bp):
GAGTATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAAGGATGAAGTGAAGAAAAAAGGA
AATTATGAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGAAATTGAA
AGTACATATGTATTCTACGATGGTTTAG
Found at i:556022 original size:25 final size:26
Alignment explanation
Indices: 555971--556024 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
555961 TTTTACGTTA
555971 GGAGACAAACTTATAAAAATTTAAGG
1 GGAGACAAACTTATAAAAATTTAAGG
*
555997 GGAGACAAACTTAT-AAAATTTTAGG
1 GGAGACAAACTTATAAAAATTTAAGG
556022 GGA
1 GGA
556025 CTATAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (26 bp):
GGAGACAAACTTATAAAAATTTAAGG
Found at i:562547 original size:34 final size:34
Alignment explanation
Indices: 562488--562554 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
562478 TTCTTGAGAG
*
562488 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
562522 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
562555 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:564463 original size:650 final size:639
Alignment explanation
Indices: 563224--564510 Score: 1887
Period size: 650 Copynumber: 2.0 Consensus size: 639
563214 TGTTTTAAGA
* * * * * * * *
563224 GTGTGTTTGGTTCACAGAATGTAAGATTATCAGCGGGAATGAAAGATTATTAGGGAATAGGGTTA
1 GTGTGTTTAGTTCACAGAATGTAAGATTACCAGCGAGAATAAAAGATTATCAGAGAATAAGATTA
*
563289 CTGAGAATATTGTATTTTGTGTTTGGTTGGTTTAGCAGAAATGTAAGATTACCGTGTTTGGTTAA
66 ATGAGAATATTGTATTTTGTGTTTGGTTGGTTTAGCAGAAATGTAAGATTACCGTGTTTGGTTAA
*
563354 ATGAATAAAAGATTATTGGAATGTATAGACCAAATTGTCCTTTTTATAAATTTGTTTTTTAACAA
131 AGGAATAAAAGATTATTGGAATGTATAGACCAAATTGTCCTTTTTATAAATTTGTTTTTTAACAA
* *
563419 GTTGGAAAATATTTATATATTTTCTTTAAAAGATTTAAATTTATATAATTTATATAATTTTTTTA
196 GTTGGAAAATATTTATATATTTTCTTTAAAAGATTTAAATTCATACAATTTATATAATTTTTTTA
* *
563484 CAAGATTGAAAATATAAAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAAAACCTGAACTTCAT
261 CAAAATTGAAAATATAAAAAGGTTTAATGAAAGGATAAAATTTTATTTTAAAACCTGAACTTCAT
* *
563549 ATAAAATTTTAATTATAGATTTTTTTGTAAATTTAAAAGAGTTTAAGGATAAATTTGTAATTTAA
326 ATAAAATTTTAATTATAGATTTTTTTGTAAATCTAAAAGAGTTTAAGAATAAATTTGTAATTTAA
* * * * * **
563614 CCTTCGTAGAATTTTTACTATTCAATGACAGGATAATGATAAATTTGAAAGAACATTTTTTAAGG
391 CATTCGTAGAAGTTTTACTATTCAATGACAGAATAAAGATAAATTTGAAAGAAAAAATTTTAAGG
*
563679 ACATTTTAGTCCAAAACACCGGTAATCCAACAATACCTAAGGCAAGGGAGGTAATGACATTCCCG
456 ACATTTTAGTCCAAAACACCGGTAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCG
* * *
563744 GTAATATACCCAAAAAAATTCACTATTGGTAATGTAAGATTACCAGGAATGACATTCCCGACCAA
521 ATAATATACCCAAAAAAATCCACTATTGGTAATGTAAGATTACCAGGAATGACATTCCCGACAAA
** * * *
563809 CCAAACGGGGGAATGCGGATTCCATTCCCATGTGAATCTCACATTTCCCAACGG
586 CCAAACGGAAGAATGCGAATTCCATTCCCATGGGAATCTCACATTCCCCAACGG
** *
563863 GTGTGTTTAGTTCATGGAATGTAAGATTACCAGTGAGAATAAAAGATTATCAGAGAATAAGATTA
1 GTGTGTTTAGTTCACAGAATGTAAGATTACCAGCGAGAATAAAAGATTATCAGAGAATAAGATTA
* * * *
563928 ATGGGAATGTTGTATTTTGTGTTTGGTTGGTTTAGTAGGAATGTAAGATTACCGTGTTTGGTTAA
66 ATGAGAATATTGTATTTTGTGTTTGGTTGGTTTAGCAGAAATGTAAGATTACCGTGTTTGGTTAA
*
563993 AGGAATAAAAGATTATTGGAATGTATATTTGACCAAATTGT-CTTTATTATATATTTGTTTTTTT
131 AGGAATAAAAGATTATTGGAATGTATA---GACCAAATTGTCCTTT-TTATAAATTTG-TTTTTT
* *
564057 AACAAGTTGGAAAATATTTATATATATTTTCTTTTAAA-ATTTAAATTCGTACAATTTATATACT
191 AACAAGTTGGAAAATA-TT-TATATATTTTCTTTAAAAGATTTAAATTCATACAATTTATATA--
* **
564121 TTTTTTTTACAAAATTGAAAATATAAAAAGGTTTAAT-AGAAGGATAAAATTTTATTTTAACCCC
252 ATTTTTTTACAAAATTGAAAATATAAAAAGGTTTAATGA-AAGGATAAAATTTTATTTTAAAACC
* *
564185 TTAACTTCATATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGAATAAAT
316 TGAACTTCATATAAAATTTTAATTATAGA-TTTTTTTGTAAATCTAAAAGAGTTTAAGAATAAAT
* **
564250 TTGTAATTTAACATTCGTAGAAGTTTTATTATTCAATGACAGAATAAAGATATTTTTGAAAAGGA
380 TTGTAATTTAACATTCGTAGAAGTTTTACTATTCAATGACAGAATAAAGATAAATTTG-AAA-G-
* ** *
564315 AAAAAATTTTAAGGGCATTTTAGTCCAAAACGTCGGTAATCCAATAATACCTAAGGAAAGGGAGG
442 AAAAAATTTTAAGGACATTTTAGTCCAAAACACCGGTAATCCAACAATACCTAAGGAAAGGGAGG
* * *
564380 TAATGACATTCCCGATAATATGCCCAAACAAATCCACTATTGGTAATGTAAGATTACCGGGAATG
507 TAATGACATTCCCGATAATATACCCAAAAAAATCCACTATTGGTAATGTAAGATTACCAGGAATG
* * *
564445 ACATTCCCGGCAAACCAAACGGAAGAATGTGAATTCCATTCCCATGGGAATCTCATATTCCCCAA
572 ACATTCCCGACAAACCAAACGGAAGAATGCGAATTCCATTCCCATGGGAATCTCACATTCCCCAA
564510 C
637 C
564511 CAAACACACC
Statistics
Matches: 574, Mismatches: 60, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
639 140 0.24
641 4 0.01
642 21 0.04
643 22 0.04
644 23 0.04
645 18 0.03
646 85 0.15
647 83 0.14
648 3 0.01
649 1 0.00
650 174 0.30
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (639 bp):
GTGTGTTTAGTTCACAGAATGTAAGATTACCAGCGAGAATAAAAGATTATCAGAGAATAAGATTA
ATGAGAATATTGTATTTTGTGTTTGGTTGGTTTAGCAGAAATGTAAGATTACCGTGTTTGGTTAA
AGGAATAAAAGATTATTGGAATGTATAGACCAAATTGTCCTTTTTATAAATTTGTTTTTTAACAA
GTTGGAAAATATTTATATATTTTCTTTAAAAGATTTAAATTCATACAATTTATATAATTTTTTTA
CAAAATTGAAAATATAAAAAGGTTTAATGAAAGGATAAAATTTTATTTTAAAACCTGAACTTCAT
ATAAAATTTTAATTATAGATTTTTTTGTAAATCTAAAAGAGTTTAAGAATAAATTTGTAATTTAA
CATTCGTAGAAGTTTTACTATTCAATGACAGAATAAAGATAAATTTGAAAGAAAAAATTTTAAGG
ACATTTTAGTCCAAAACACCGGTAATCCAACAATACCTAAGGAAAGGGAGGTAATGACATTCCCG
ATAATATACCCAAAAAAATCCACTATTGGTAATGTAAGATTACCAGGAATGACATTCCCGACAAA
CCAAACGGAAGAATGCGAATTCCATTCCCATGGGAATCTCACATTCCCCAACGG
Found at i:569848 original size:38 final size:38
Alignment explanation
Indices: 569771--569848 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
569761 TTATATTTTC
* * *
569771 AATTTTGTAAAAGAAATTATATAAATTTTATGAATTTA
1 AATTTTGTAAAAGAAAATATATAAATTTTATCAACTTA
*
569809 AATTTT-TTAAAGAAAATATATAAATATTT-TCCAACTTA
1 AATTTTGTAAAAGAAAATATATAAAT-TTTAT-CAACTTA
569847 AA
1 AA
569849 AAATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 18 0.53
38 16 0.47
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (38 bp):
AATTTTGTAAAAGAAAATATATAAATTTTATCAACTTA
Found at i:570774 original size:34 final size:35
Alignment explanation
Indices: 570715--570784 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
570705 AGCAAAACAT
570715 GTAAATAGCGACAGACTTTCAGATTTGCCGATCAC
1 GTAAATAGCGACAGACTTTCAGATTTGCCGATCAC
* *
570750 GTAAATAGCGGC-GACTTTCGGATTTGCCGATCAC
1 GTAAATAGCGACAGACTTTCAGATTTGCCGATCAC
570784 G
1 G
570785 GTCGTTTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (35 bp):
GTAAATAGCGACAGACTTTCAGATTTGCCGATCAC
Found at i:577042 original size:31 final size:31
Alignment explanation
Indices: 576970--577035 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
576960 AGTTATGTCG
576970 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
* *
577001 GGGACCATATTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGA
577032 GGGA
1 GGGA
577036 TTATATTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:579616 original size:31 final size:30
Alignment explanation
Indices: 579578--579655 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
579568 CTTTTAAAAC
* * *
579578 TTGCAATATAATCCCCCAGTATTTAGTCTGT
1 TTGCAATATGATCCCCAAG-ATTTAGTCCGT
*
579609 TTGCAATATGTTCCCTCAAGATTTAGTCCGT
1 TTGCAATATGATCCC-CAAGATTTAGTCCGT
579640 TTGCAATATGATCCCC
1 TTGCAATATGATCCCC
579656 GACATAACTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 37 0.90
32 3 0.07
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (30 bp):
TTGCAATATGATCCCCAAGATTTAGTCCGT
Found at i:583797 original size:21 final size:21
Alignment explanation
Indices: 583773--583817 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
583763 AAGTAAAATT
*
583773 GTGCATCGATGCACTTCTACA
1 GTGCATCGATGCACTGCTACA
583794 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
583815 GTG
1 GTG
583818 ATTTTCGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:584524 original size:18 final size:18
Alignment explanation
Indices: 584501--584535 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
584491 CCACGTAGAA
584501 ATGTCCCGAAGAACCACT
1 ATGTCCCGAAGAACCACT
*
584519 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGAACCAC
584536 AATCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGAACCACT
Found at i:584675 original size:23 final size:23
Alignment explanation
Indices: 584645--584688 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
584635 ATTACATATA
584645 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
584668 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
584689 CCCTCGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:586251 original size:21 final size:21
Alignment explanation
Indices: 586225--586266 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
586215 CCAGAATGGG
*
586225 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
586246 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
586267 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:586478 original size:29 final size:31
Alignment explanation
Indices: 586446--586505 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
586436 AAATTTTGAA
*
586446 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
586475 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
586506 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:589350 original size:34 final size:32
Alignment explanation
Indices: 589297--589366 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
589287 ACCTTACAAC
* *
589297 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACCAGAACCTT
*
589329 TCCCTAGCTTTTACACGGGCTAAGCCAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACCAGAACCTT
589363 TCCC
1 TCCC
589367 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACCAGAACCTT
Done.