Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_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: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:2004573 original size:17 final size:16
Alignment explanation
Indices: 2004551--2004607 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
2004541 AATTGGAGTA
2004551 CAAAAAGAAAGAAAAGT
1 CAAAAAG-AAGAAAAGT
*
2004568 CAAAAAGAAGAAAAATT
1 CAAAAAGAAG-AAAAGT
2004585 CAAAAAGAAGAAAAG-
1 CAAAAAGAAGAAAAGT
2004600 -AAAAAGAA
1 CAAAAAGAA
2004608 AATGATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.22
16 7 0.19
17 22 0.59
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (16 bp):
CAAAAAGAAGAAAAGT
Found at i:2004618 original size:31 final size:32
Alignment explanation
Indices: 2004551--2004632 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
2004541 AATTGGAGTA
2004551 CAAAAAGAAAGAAAAGTCAAAAAGAAGAAAAATT
1 CAAAAAG-AAGAAAAG-CAAAAAGAAGAAAAATT
* *
2004585 CAAAAAGAAGAAAAG-AAAAAGAA-AATGATTT
1 CAAAAAGAAGAAAAGCAAAAAGAAGAA-AAATT
2004616 CAAAAAG-AG-AAAGCAAA
1 CAAAAAGAAGAAAAGCAAA
2004633 GCCAAGGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 4 0.09
30 7 0.16
31 18 0.41
33 8 0.18
34 7 0.16
ACGTcount: A:0.70, C:0.06, G:0.16, T:0.09
Consensus pattern (32 bp):
CAAAAAGAAGAAAAGCAAAAAGAAGAAAAATT
Found at i:2006773 original size:23 final size:23
Alignment explanation
Indices: 2006743--2006791 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2006733 ACACAATTCA
2006743 TGAATGTGGGGAATTAAAGGACG
1 TGAATGTGGGGAATTAAAGGACG
2006766 TGAATGTGGGGAATTAAAGGACG
1 TGAATGTGGGGAATTAAAGGACG
2006789 TGA
1 TGA
2006792 CCTTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.39, T:0.22
Consensus pattern (23 bp):
TGAATGTGGGGAATTAAAGGACG
Found at i:2026670 original size:19 final size:18
Alignment explanation
Indices: 2026641--2026676 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2026631 GTTCTTTAGG
*
2026641 TTATTTTCTTTTTCATTT
1 TTATTTTCTTTTGCATTT
2026659 TTATTGTTCTTTTGCATT
1 TTATT-TTCTTTTGCATT
2026677 ATCTAACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (18 bp):
TTATTTTCTTTTGCATTT
Found at i:2031239 original size:20 final size:20
Alignment explanation
Indices: 2031214--2031253 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2031204 GAATCTGGTA
*
2031214 CAAAACATCTTGGTACACGT
1 CAAAACATCATGGTACACGT
2031234 CAAAACATCATGGTACACGT
1 CAAAACATCATGGTACACGT
2031254 TGTTGGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (20 bp):
CAAAACATCATGGTACACGT
Found at i:2035013 original size:19 final size:20
Alignment explanation
Indices: 2034972--2035013 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2034962 CATCTTAAAC
2034972 TTAGCTCATAATGTCATTAT
1 TTAGCTCATAATGTCATTAT
2034992 TTAGCTCAT-ATG-CATGTAT
1 TTAGCTCATAATGTCAT-TAT
2035011 TTA
1 TTA
2035014 CACGTGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (20 bp):
TTAGCTCATAATGTCATTAT
Found at i:2035435 original size:17 final size:17
Alignment explanation
Indices: 2035415--2035449 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2035405 TTTAGGGAAG
2035415 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
2035432 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
2035449 T
1 T
2035450 GACTCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:2041934 original size:50 final size:50
Alignment explanation
Indices: 2041829--2041935 Score: 121
Period size: 50 Copynumber: 2.1 Consensus size: 50
2041819 TCACACTCCA
* * *
2041829 ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
* *
2041879 GTTTTCCTTTTCATTGCGACTAGGAGGGATT-GATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGG-TTGGATAGAGACA-TAT-CATCGT
2041929 ATTTTCC
1 ATTTTCC
2041936 ATATATCCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
49 3 0.06
50 39 0.81
51 6 0.12
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
Found at i:2043346 original size:15 final size:16
Alignment explanation
Indices: 2043313--2043370 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
2043303 GGAAGATTAC
*
2043313 TTGTCTCCACTTGGCT
1 TTGTCTCCACTTAGCT
2043329 TTGTCTCCACTT-GCT
1 TTGTCTCCACTTAGCT
*
2043344 TTGTCTTCACTTAGCT
1 TTGTCTCCACTTAGCT
2043360 TTGTCTCCACT
1 TTGTCTCCACT
2043371 AGACATCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.09, C:0.31, G:0.14, T:0.47
Consensus pattern (16 bp):
TTGTCTCCACTTAGCT
Found at i:2043408 original size:44 final size:44
Alignment explanation
Indices: 2043354--2043441 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
2043344 TTGTCTTCAC
2043354 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
1 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
*
2043398 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGGCCAA
1 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
2043442 GGAACTTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (44 bp):
TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
Found at i:2051664 original size:22 final size:22
Alignment explanation
Indices: 2051630--2051676 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2051620 ATTATTATGG
* *
2051630 AACCTTCGGCCATGCAT-ATCTT
1 AACCTACGACCATGCATGAT-TT
2051652 AACCTACGACCATGCATGATTT
1 AACCTACGACCATGCATGATTT
2051674 AAC
1 AAC
2051677 TCCTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (22 bp):
AACCTACGACCATGCATGATTT
Found at i:2059069 original size:21 final size:21
Alignment explanation
Indices: 2059025--2059065 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2059015 TCTTTATTTC
* *
2059025 ATTTCATTTATTATCTTTCTT
1 ATTTCATTGATTATCTTCCTT
2059046 ATTTCATTGATT-TCTTCCTT
1 ATTTCATTGATTATCTTCCTT
2059066 TATTAACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTCATTGATTATCTTCCTT
Found at i:2064356 original size:91 final size:90
Alignment explanation
Indices: 2064248--2064567 Score: 419
Period size: 91 Copynumber: 3.5 Consensus size: 90
2064238 TATTCTTTAT
** * **
2064248 TTTCATTTATCTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA-TTTTCTTTATGGCATCCTT
* * *
2064313 TCATGCCGATAATGCACCATTGTGTG
65 TCATGCCGATAATGCACCGTTATGTA
* ** *
2064339 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA-TTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTC-TTTATGGCATCCTT
* *
2064403 TCATGCCTATAATGCACCGTTATGCATT
65 TCATGCCGATAATGCACCGTTATG--TA
*
2064431 TTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
* *
2064495 CATGTCGATAATGCACCGTTATGCA
66 CATGCCGATAATGCACCGTTATGTA
* *
2064520 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTT
2064568 CATTTATTCA
Statistics
Matches: 202, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
89 8 0.04
90 76 0.38
91 111 0.55
92 7 0.03
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
CATGCCGATAATGCACCGTTATGTA
Found at i:2064369 original size:45 final size:45
Alignment explanation
Indices: 2064248--2064574 Score: 433
Period size: 45 Copynumber: 7.2 Consensus size: 45
2064238 TATTCTTTAT
** * **
2064248 TTTCATTTATCTCATCCTTTCATGCCTATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* **
2064293 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTGTGTG
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* ** *
2064339 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
2064384 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
2064429 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * *
2064475 TTTTATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
2064520 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
2064565 TTTCATTTAT
1 TTTCATTTAT
2064575 TCATTCATTT
Statistics
Matches: 247, Mismatches: 29, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
44 6 0.02
45 163 0.66
46 70 0.28
47 8 0.03
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
Found at i:2064492 original size:136 final size:136
Alignment explanation
Indices: 2064248--2064567 Score: 541
Period size: 136 Copynumber: 2.4 Consensus size: 136
2064238 TATTCTTTAT
** *
2064248 TTTCATTTATCTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* **
2064313 TCATGCCGATAATGCACCATTGTGTGTCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
2064378 TATGCA
131 TATGCA
*
2064384 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* * *
2064449 TCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGTCGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
2064514 TATGCA
131 TATGCA
*
2064520 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTT
2064568 CATTTATTCA
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 173 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (136 bp):
TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
TATGCA
Found at i:2065104 original size:45 final size:45
Alignment explanation
Indices: 2065046--2065253 Score: 242
Period size: 45 Copynumber: 4.6 Consensus size: 45
2065036 TCAGTATCGG
* * * *
2065046 TAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* *
2065091 TAATGAACCGTTATGCATTTTTC-TTAATGGCATCCTTT-ACTGCCTA
1 TAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCA-TGCCTA
* *
2065137 TAATGCACCATTATGCATTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* *
2065182 TAATGCACCGTTATGCA-TTCTAATTATGGAATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTC-ATTTATGGCATCCTTTCATGCCTA
* * *
2065227 TAATGCACCATTATACATTTAATTTAT
1 TAATGCACCGTTATGCATTTCATTTAT
2065254 TCATTCATTT
Statistics
Matches: 138, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
44 7 0.05
45 91 0.66
46 36 0.26
47 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (45 bp):
TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
Found at i:2065670 original size:672 final size:676
Alignment explanation
Indices: 2064365--2066796 Score: 3674
Period size: 672 Copynumber: 3.6 Consensus size: 676
2064355 CTTTCATGTA
* *
2064365 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * * *
2064430 TTTTCTTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCCTTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* *
2064495 CATGTCGATAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
2064560 ATGCATTTCATTTATTCATTCATTTTAGAGAAGTTCATACTCCAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * * * * *
2064625 TTCATATACAAAATGCAAATATATTAACTAATGTAAAACATACATAAAATCACAATATTCTAATA
261 TT-ATATACATAATG-AAAAATA-TAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
2064690 TGACTCATTGTC-AATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTC
323 TGACTCATTG-CGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTC
* *
2064754 ACTAATAAGATATAATGATGTCC-AGCTATTCAGCAACTTTATCTTTGCCCTTTTTCTTGCTAGA
387 ACTAATAAGATGTAATGATGTCCGA-CTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGA
*
2064818 CTCAGGAGCTTGGTTATGATCTACACAAACATCCATTAAAGACACATATCATACCAAATGTTAGT
451 CTCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGT
* * *
2064883 ATATTCCATAACATTTATACCTTAATAAAACTCAAAAGTACTATTATTTCAATTTCTATAACAAT
516 ATATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAAT
* ** * * * * *
2064948 CTCAACTTATCTTATAGTTACATGTTGAATAGTGTTGGTACGCTACCATGGTATCGATACTTCTA
581 TTCAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTA
*
2065013 TACAATGGTACCGATACTCATTTTCAGTATC
646 TACTATGGTACCGATACTCATTTTCAGTATC
* * * *
2065044 GGTAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTATAATGAACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
*
2065109 TTTTCTTAATGGCATCCTTT-ACTGCCTATAATGCACCATTATGCATTTCATTTATGGCATCCTT
66 TTTTCTTAATGGCATCCTTTCA-TGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATT
* *
2065173 TCATGCCGATAATGCACCGTTATGCA-TTCTAATTATGGA-ATCCTTTCATGCCTATAATGCACC
130 TCATGCCGAAAATGCACCGTTATGCATTTC-ATTTAT-GACATCCTTTCATGCCTATAATGCACC
* * *
2065236 ATTATACATTTAATTTATTCATTCATTTTACAGAAGTTCGTACTCTAAAACTCATTCATAATAT-
193 ATTATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATC
* *
2065300 CATTT-TATACATAATG-AAAATATAACTATTGTAAAACATACATTAAATCACAACATTCTAGTT
258 CTTTTATATACATAATGAAAAATATAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
* *
2065363 TGACTCATTGTGAATCTTCCTCATCTCATATAAATACAATGAATGTACTCAC-TGATAATCCTCA
323 TGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTCA
* * * *
2065427 CTAACAATATGTAATGATGTCCGACTATTCAACAACTTTATCTTTTCCCTTTTTCTTACTAGACT
388 CTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGACT
*
2065492 CAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAATTGTTAGTAT
453 CAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTAT
* *
2065557 ATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAAATTCTGTAACAATTT
518 ATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATTT
* * *
2065622 CATCTAATTTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTATA
583 CAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTATA
* *
2065687 TTATGGTACCGATACTCCTTTTCAGTATC
648 CTATGGTACCGATACTCATTTTCAGTATC
* * * *
2065716 GATAATGCACCGTTATGCATTTTATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * *
2065781 TTTTCTTAATGGCATCCATTCATGCCTATAATGCACCATTATGCATTTCATTTGTAGCATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* * *
2065846 CATGCC-AAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* *
2065910 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGGACTCTAAAACTCATTCATAATATCTTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * *
2065975 TTCATAAACATAATGAAAAATATATTATCTACTGTAAAACATACAGTAAATCACAACATTCTAAT
261 TT-ATATACATAATGAAAAATATA--A-CTATTGTAAAACATACATTAAATCACAACATTCTAAT
* * * * *
2066040 TTGACTCATTGCAAATATTCCTCATCTCATATAAATACAATGAATGTGCTCACTTGATAATCCTC
322 TTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTC
*
2066105 ACTAATAAGATGTAATGATGTCTGACTATTCAACAACTTTATCTTTGCCC-TTTTCTTGCTAGAC
387 ACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
* * * *
2066169 TTAGGTGCTTGGTTATGATCTATACAAGCATCCATTAAAGATACATATCATACCAAATGTTAGTA
452 TCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
*
2066234 TATTCCCTAATA-TTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
517 TATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
* * *
2066298 TCAACTTATCTTATAGTTACATTCTCAATAGTATCGGTTCCCTACCATGGTATAGATACTTATAT
582 TCAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTAT
2066363 ACTATGGTACCGATACTCATTTTCAGTATC
647 ACTATGGTACCGATACTCATTTTCAGTATC
* * *
2066393 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG-CTATAATGCACCGTTATGCAG
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * * *
2066457 TTTTCTTAATGGCATCCTTTCATGCCTATAATTCACCATTATGCATTTCACTTGTGGTATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
*
2066522 CATGCCGAAAATG-ATCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
2066586 ATGTATTTCATTTATTCATTCATTGTATAGAAGTTCGTACTATAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* *
2066651 TTCATATAAATAATG-AAAATGTTAACTATTGTAAAACATACATT-AATCACAACATTCTAATTT
261 TT-ATATACATAATGAAAAAT-ATAACTATTGTAAAACATACATTAAATCACAACATTCTAATTT
* * * * *
2066714 CACTCATTACGAATCTTCCTCATCTCATTTAAACACAATAAATGTACTCACCTGAT-ATCCTCAC
324 GACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTCAC
2066778 TAATAAGATGTAATGATGT
389 TAATAAGATGTAATGATGT
2066797 TATTTGGTTT
Statistics
Matches: 1595, Mismatches: 140, Indels: 44
0.90 0.08 0.02
Matches are distributed among these distances:
670 1 0.00
671 131 0.08
672 466 0.29
673 104 0.07
674 16 0.01
675 13 0.01
676 216 0.14
677 183 0.11
678 175 0.11
679 288 0.18
680 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (676 bp):
GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
TTATATACATAATGAAAAATATAACTATTGTAAAACATACATTAAATCACAACATTCTAATTTGA
CTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTCACTA
ATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGACTCAG
GAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTATATT
CCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATTTCAA
CTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTATACTA
TGGTACCGATACTCATTTTCAGTATC
Found at i:2065873 original size:44 final size:45
Alignment explanation
Indices: 2065717--2065924 Score: 217
Period size: 45 Copynumber: 4.6 Consensus size: 45
2065707 TTCAGTATCG
* * * * *
2065717 ATAATGCACCGTTATGCATTTTATTCATGGCATCATTTCATACCT
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCT
* * *
2065762 ATAATG-AACAGTTATGCATTTTTC-TTAATGGCATCCA-TTCATGCCT
1 ATAATGCACCA-TTATGCA--TTTCATTTATAGCAT-CATTTCATGCCT
*
2065808 ATAATGCACCATTATGCATTTCATTTGTAGCATCATTTCATGCC-
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCT
* ** * * *
2065852 AAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCT
2065897 ATAATGCACCATTATGCATTTCATTTAT
1 ATAATGCACCATTATGCATTTCATTTAT
2065925 TCATTCATTT
Statistics
Matches: 135, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
44 45 0.33
45 52 0.39
46 30 0.22
47 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (45 bp):
ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCT
Found at i:2065934 original size:89 final size:90
Alignment explanation
Indices: 2065717--2065924 Score: 276
Period size: 89 Copynumber: 2.3 Consensus size: 90
2065707 TTCAGTATCG
* * * * * *
2065717 ATAATGCACCGTTATGCATTTTATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCATT
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCTAAAATGAACAGTTATACA-T
2065782 TTTCTTAATGGCATCCATTCATGCCT
65 TTTCTTAATGGCATCCATTCATGCCT
* * * *
2065808 ATAATGCACCATTATGCATTTCATTTGTAGCATCATTTCATGCC-AAAATGCACGGTTATACA-T
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCTAAAATGAACAGTTATACATT
* *
2065871 TTCATTTATGGCATCCTTTCATGCCT
66 TTC-TTAATGGCATCCATTCATGCCT
2065897 ATAATGCACCATTATGCATTTCATTTAT
1 ATAATGCACCATTATGCATTTCATTTAT
2065925 TCATTCATTT
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 4 0.04
89 47 0.46
90 14 0.14
91 38 0.37
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (90 bp):
ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCTAAAATGAACAGTTATACATT
TTCTTAATGGCATCCATTCATGCCT
Found at i:2066448 original size:44 final size:45
Alignment explanation
Indices: 2066394--2066600 Score: 258
Period size: 44 Copynumber: 4.6 Consensus size: 45
2066384 TTCAGTATCG
2066394 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG-CT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
*
2066438 ATAATGCACCGTTATGCAGTTTTC-TTAATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCATGCCT
* * * * * * *
2066484 ATAATTCACCATTATGCATTTCACTTGTGGTATCATTTCATGCCG
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* * *
2066529 AAAATG-ATCGTTATGCATTTCATTTATGACATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* *
2066573 ATAATGCACCATTATGTATTTCATTTAT
1 ATAATGCACCGTTATGCATTTCATTTAT
2066601 TCATTCATTG
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
44 57 0.42
45 56 0.41
46 22 0.16
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (45 bp):
ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
Found at i:2066523 original size:45 final size:45
Alignment explanation
Indices: 2066394--2066600 Score: 240
Period size: 45 Copynumber: 4.6 Consensus size: 45
2066384 TTCAGTATCG
*
2066394 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG-CT
1 ATAATGCACCGTTATGCATTTCACTTATGGCATCCTTTCATGCCT
*
2066438 ATAATGCACCGTTATGCAGTTT-TCTTAATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCA-TTTCACTT-ATGGCATCCTTTCATGCCT
* * * * * *
2066484 ATAATTCACCATTATGCATTTCACTTGTGGTATCATTTCATGCCG
1 ATAATGCACCGTTATGCATTTCACTTATGGCATCCTTTCATGCCT
* * * *
2066529 AAAATG-ATCGTTATGCATTTCATTTATGACATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCACTTATGGCATCCTTTCATGCCT
* * *
2066573 ATAATGCACCATTATGTATTTCATTTAT
1 ATAATGCACCGTTATGCATTTCACTTAT
2066601 TCATTCATTG
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
44 55 0.41
45 59 0.44
46 21 0.16
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (45 bp):
ATAATGCACCGTTATGCATTTCACTTATGGCATCCTTTCATGCCT
Found at i:2066609 original size:89 final size:88
Alignment explanation
Indices: 2066394--2066609 Score: 240
Period size: 89 Copynumber: 2.4 Consensus size: 88
2066384 TTCAGTATCG
* * * * *
2066394 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTATAATGCACCGTTATGCAGTT
1 ATAATGCACCATTATGCATTTCATTTAT-TCATCATTTCATGCGAAAATGCACCGTTATGCAG-T
*
2066459 TTCTTAATGGCATCCTTTCATGCCT
64 TTCTTAATGACATCCTTTCATGCCT
* ** *
2066484 ATAATTCACCATTATGCATTTCACTTGTGGT-ATCATTTCATGCCGAAAATG-ATCGTTATGCA-
1 ATAATGCACCATTATGCATTTCA-TT-TATTCATCATTTCATG-CGAAAATGCACCGTTATGCAG
*
2066546 TTTCATTTATGACATCCTTTCATGCCT
63 TTTC-TTAATGACATCCTTTCATGCCT
*
2066573 ATAATGCACCATTATGTATTTCATTTATTCATTCATT
1 ATAATGCACCATTATGCATTTCATTTATTCA-TCATT
2066610 GTATAGAAGT
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
87 2 0.02
88 7 0.07
89 46 0.44
90 41 0.39
91 8 0.08
92 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (88 bp):
ATAATGCACCATTATGCATTTCATTTATTCATCATTTCATGCGAAAATGCACCGTTATGCAGTTT
CTTAATGACATCCTTTCATGCCT
Found at i:2068983 original size:45 final size:45
Alignment explanation
Indices: 2068861--2069172 Score: 412
Period size: 45 Copynumber: 6.9 Consensus size: 45
2068851 TATTCTTTAT
*
2068861 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
2068906 TTTTTC-TTTATGGCAACCTTTCATGCCAATAATTCACCGTTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * **
2068952 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATTATATA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* **
2068997 TTTCATTTATGGCATCCTTTTATGCATATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
2069042 TTTTTC-TTTATGGCATCCTTTCATGTCGATAATGCACCGTTATACA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
2069088 TTTCATTTATGACATCCTTTCATGCCGATAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
2069133 TTTCATTTATGGTATCGTTTCATGCCTATAATGCACCGTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTT
2069173 TTTAGAGTTC
Statistics
Matches: 230, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
44 8 0.03
45 142 0.62
46 72 0.31
47 8 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:2069052 original size:91 final size:89
Alignment explanation
Indices: 2068861--2069172 Score: 412
Period size: 91 Copynumber: 3.4 Consensus size: 89
2068851 TATTCTTTAT
* * *
2068861 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTC-TTTATGGCAACCT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAT--ATATTTCATTTATGGCATCCT
*
2068925 TTCATGCCAATAATTCACCGTTATGCA
64 TTCATG-CAATAATGCACCGTTATGCA
* *
2068952 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATTATATATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATATATTTCATTTATGGCATCCTTT
*
2069017 TATGCATATAATGCACCGTTATGCA
66 CATGCA-ATAATGCACCGTTATGCA
* * *
2069042 TTTTTC-TTTATGGCATCCTTTCATGTCGATAATGCACCGTTATACATTTCATTTATGACATCCT
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATATATTTCATTTATGGCATCCT
* *
2069106 TTCATGCCGATAATGTACCGTTATGCA
64 TTCATG-CAATAATGCACCGTTATGCA
* * *
2069133 TTTCATTTATGGTATCGTTTCATGCCTATAATGCACCGTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTT
2069173 TTTAGAGTTC
Statistics
Matches: 198, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
89 12 0.06
90 65 0.33
91 116 0.59
92 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (89 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATATATTTCATTTATGGCATCCTTT
CATGCAATAATGCACCGTTATGCA
Found at i:2069105 original size:136 final size:136
Alignment explanation
Indices: 2068861--2069172 Score: 489
Period size: 136 Copynumber: 2.3 Consensus size: 136
2068851 TATTCTTTAT
2068861 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCAACCTT
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCAACCTT
* * * *
2068926 TCATGCCAATAATTCACCGTTATGCATTTCATTTATGGCATCCTTTCATGTCGATAATGCACCAT
66 TCATGCCAATAATGCACCGTTATACATTTCATTTATGACATCCTTTCATGCCGATAATGCACCAT
*
2068991 TATATA
131 TATACA
* * *
2068997 TTTCATTTATGGCATCCTTTTATGCATATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCAACCTT
* * * *
2069062 TCATGTCGATAATGCACCGTTATACATTTCATTTATGACATCCTTTCATGCCGATAATGTACCGT
66 TCATGCCAATAATGCACCGTTATACATTTCATTTATGACATCCTTTCATGCCGATAATGCACCAT
*
2069127 TATGCA
131 TATACA
* *
2069133 TTTCATTTATGGTATCGTTTCATGCCTATAATGCACCGTT
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTT
2069173 TTTAGAGTTC
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
136 159 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (136 bp):
TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCAACCTT
TCATGCCAATAATGCACCGTTATACATTTCATTTATGACATCCTTTCATGCCGATAATGCACCAT
TATACA
Found at i:2069723 original size:21 final size:19
Alignment explanation
Indices: 2069697--2069735 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
2069687 CTCAAAGCAA
2069697 TATCGATACTAATTGCATCAG
1 TATCGATACT-ATT-CATCAG
2069718 TATCGATACTATTCATCA
1 TATCGATACTATTCATCA
2069736 TAATTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TATCGATACTATTCATCAG
Found at i:2071762 original size:17 final size:17
Alignment explanation
Indices: 2071742--2071793 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
2071732 TTTAGGGAAG
2071742 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
2071759 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
2071776 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
2071793 T
1 T
2071794 GACTATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:2073705 original size:17 final size:18
Alignment explanation
Indices: 2073668--2073705 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2073658 GCTAAATTGA
* *
2073668 TGAGATCTTTTCATCTTT
1 TGAGATCTTTTCATATGT
2073686 TGAG-TCTTTTCATATGT
1 TGAGATCTTTTCATATGT
2073703 TGA
1 TGA
2073706 TTATAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (18 bp):
TGAGATCTTTTCATATGT
Found at i:2077800 original size:21 final size:21
Alignment explanation
Indices: 2077776--2077824 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2077766 ATCGAGGAAA
*
2077776 AGACATCCCTGAACGATCAAG
1 AGACATCCCTGAACGATAAAG
2077797 AGACATCCCTGAACGATAAAG
1 AGACATCCCTGAACGATAAAG
2077818 AGACATC
1 AGACATC
2077825 ATAACAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (21 bp):
AGACATCCCTGAACGATAAAG
Found at i:2092137 original size:28 final size:27
Alignment explanation
Indices: 2092095--2092163 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
2092085 ATTGGAGTGA
2092095 AAAAAGAAAA-T--AAAAGACA-AAAAG
1 AAAAAGAAAATTCGAAAAGA-ATAAAAG
2092119 AAGAAA-AAAATTCAGAAAAGAATAAAAG
1 AA-AAAGAAAATTC-GAAAAGAATAAAAG
2092147 AAAAAGAAAATTCGAAA
1 AAAAAGAAAATTCGAAA
2092164 CAAAAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
24 6 0.16
25 4 0.11
27 8 0.21
28 20 0.53
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (27 bp):
AAAAAGAAAATTCGAAAAGAATAAAAG
Found at i:2094737 original size:19 final size:20
Alignment explanation
Indices: 2094710--2094753 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2094700 AGCATTTATC
*
2094710 TTCAAT-AAAATTATGTATT
1 TTCAATAAAAATCATGTATT
* *
2094729 TTCATTAAAAATCATGTGTT
1 TTCAATAAAAATCATGTATT
2094749 TTCAA
1 TTCAA
2094754 AGGGGTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (20 bp):
TTCAATAAAAATCATGTATT
Found at i:2095125 original size:13 final size:14
Alignment explanation
Indices: 2095088--2095127 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2095078 TAAGATACTA
*
2095088 TTTCCATCAACATC
1 TTTCCATCACCATC
*
2095102 TTTCTATCACCATC
1 TTTCCATCACCATC
2095116 -TTCCATCACCAT
1 TTTCCATCACCAT
2095128 TCACGCCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:2100373 original size:15 final size:16
Alignment explanation
Indices: 2100353--2100395 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2100343 AGTTATCATC
2100353 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
2100368 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
2100384 AAAATAACTATA
1 ATAATAACTATA
2100396 TTAAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:2100774 original size:13 final size:13
Alignment explanation
Indices: 2100756--2100789 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2100746 AAGATACTAT
2100756 TTCCATCACCATC
1 TTCCATCACCATC
2100769 TTCCATCACCATC
1 TTCCATCACCATC
*
2100782 TTTCATCA
1 TTCCATCA
2100790 ACATTCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (13 bp):
TTCCATCACCATC
Found at i:2102685 original size:16 final size:16
Alignment explanation
Indices: 2102664--2102707 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2102654 TGGAAGATTG
*
2102664 CTTGTCTCCACTTGAC
1 CTTGTCTCCACTTAAC
2102680 CTTGTCTCCACTTAAC
1 CTTGTCTCCACTTAAC
* *
2102696 TTTGTTTCCACT
1 CTTGTCTCCACT
2102708 GGCCATCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.09, T:0.43
Consensus pattern (16 bp):
CTTGTCTCCACTTAAC
Found at i:2102875 original size:22 final size:22
Alignment explanation
Indices: 2102824--2102875 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
2102814 CACCATGAGA
* *
2102824 CCATGCAAATTGTAACATTCGG
1 CCATGCATATTGTAACATACGG
* *
2102846 CCATGCATTTTGTAACCTACGG
1 CCATGCATATTGTAACATACGG
2102868 CCATGCAT
1 CCATGCAT
2102876 GTTCAAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (22 bp):
CCATGCATATTGTAACATACGG
Found at i:2106795 original size:16 final size:15
Alignment explanation
Indices: 2106759--2106801 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2106749 TGGATGATTG
*
2106759 TTTGTCTCCACTTGA
1 TTTGTCTCCACTTAA
2106774 TCTTGTCTCCACTTAA
1 T-TTGTCTCCACTTAA
*
2106790 CTTTGTTTCCAC
1 -TTTGTCTCCAC
2106802 CAGCCATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.14, C:0.30, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTGTCTCCACTTAA
Found at i:2111548 original size:631 final size:631
Alignment explanation
Indices: 2110294--2111552 Score: 2413
Period size: 631 Copynumber: 2.0 Consensus size: 631
2110284 TACAAAAAGA
2110294 AAGCATAATATAAGCTAAGTATTTGAAGTAAATAACTTATAATATGAAGATGTGACCTATAGGTT
1 AAGCATAATATAAGCTAAGTATTTGAAGTAAATAACTTATAATATGAAGATGTGACCTATAGGTT
2110359 ATAATAATAACTCATGCATCATATGATAATGAATGAATATTATTACAACTATAGATTATATGCTT
66 ATAATAATAACTCATGCATCATATGATAATGAATGAATATTATTACAACTATAGATTATATGCTT
2110424 GAATATCAATCAATGATACAAACCATATAATGAATGCACAAAGTATGGTAATTCAAGTATAGTCT
131 GAATATCAATCAATGATACAAACCATATAATGAATGCACAAAGTATGGTAATTCAAGTATAGTCT
2110489 AATCTTCATATGTATGCTCATAATAGTATATAATGCATAAATAAGTAAATATAAGATAAAGAAAG
196 AATCTTCATATGTATGCTCATAATAGTATATAATGCATAAATAAGTAAATATAAGATAAAGAAAG
2110554 GAAGAACTCCCTTAGAACTAGTTTTGAATAACCTCCATGGTGTGATCAAGTCATGGAGAAAAATT
261 GAAGAACTCCCTTAGAACTAGTTTTGAATAACCTCCATGGTGTGATCAAGTCATGGAGAAAAATT
2110619 GGAGCAAGACAGGATCACATCATCCTCCCCTTCTTTTAGGCGATTTGTCCTCAAATAGAAGTAGT
326 GGAGCAAGACAGGATCACATCATCCTCCCCTTCTTTTAGGCGATTTGTCCTCAAATAGAAGTAGT
2110684 TTGTCATTGAAGACCTTCTTGATGTAGGAAGGATTGAATCATTATGTTCTCCTTGAGAATCTCCC
391 TTGTCATTGAAGACCTTCTTGATGTAGGAAGGATTGAATCATTATGTTCTCCTTGAGAATCTCCC
2110749 ATGAAATGTTCAACTCATTGTTCTATCTTGTTTGTGTTGGTTTGATTCAACATTTCTCTATGTGA
456 ATGAAATGTTCAACTCATTGTTCTATCTTGTTTGTGTTGGTTTGATTCAACATTTCTCTATGTGA
2110814 AGACTTGTGTCTCTTGTAGTCCTCCTTGATGTACTTTGGAAACATAATATTTTTCATCGATGAAG
521 AGACTTGTGTCTCTTGTAGTCCTCCTTGATGTACTTTGGAAACATAATATTTTTCATCGATGAAG
*
2110879 ATTATTTTTTGATCAATCTTTTTACTTGGAATAACACATCCATAAG
586 AATATTTTTTGATCAATCTTTTTACTTGGAATAACACATCCATAAG
2110925 AAGCAT-A-ATAAGCTAAGTATTTGAAGTAAATAACTTATAATATGAAGATGTGACCTATAGGTT
1 AAGCATAATATAAGCTAAGTATTTGAAGTAAATAACTTATAATATGAAGATGTGACCTATAGGTT
2110988 ATAATAATAACTCATGC-TCATATGATAAATGAATGAATA-TATTACAACTATAGATTATATGCT
66 ATAATAATAACTCATGCATCATATGAT-AATGAATGAATATTATTACAACTATAGATTATATGCT
2111051 TGAATATCAATCAATGATACAAACCAT-TAATGAATGCACAAAGTATGGTAATTCAAGTATAGTC
130 TGAATATCAATCAATGATACAAACCATATAATGAATGCACAAAGTATGGTAATTCAAGTATAGTC
2111115 TAATCTTCATATGTATGCTCATAATAGTATATAATGCATAAATAAGTAAATATAAGATAAAGAAA
195 TAATCTTCATATGTATGCTCATAATAGTATATAATGCATAAATAAGTAAATATAAGATAAAGAAA
2111180 GGAAGAACTCCCTTAGAACTAGTTTTGAATAACCTCCATGGTGTGATCAAGTCATGGAG-AAAAT
260 GGAAGAACTCCCTTAGAACTAGTTTTGAATAACCTCCATGGTGTGATCAAGTCATGGAGAAAAAT
2111244 TGGAGCAAGACAGGATCACATCATCCTCCCCTTCTTTTAGGCGATTTGTCCTCAAATAGAAGTAG
325 TGGAGCAAGACAGGATCACATCATCCTCCCCTTCTTTTAGGCGATTTGTCCTCAAATAGAAGTAG
2111309 TTTGTCATTGAAGACCTTCTTGATGTAGGAAGGATTGAATCATTATGTTCTCCTTGAGAAGATTC
390 TTTGTCATTGAAGACCTTCTTGATGTAGGAAGGATTGAATCATTATGTTCTCCTTGAG-A-A-TC
2111374 TCCCCATGAAATGTTCAACCTCATTGTTCTATCTTGTTTGTGTTGGTTTGATTCAACATTTCTCT
452 T-CCCATGAAATGTTCAA-CTCATTGTTCTATCTTGTTTGTGTTGGTTTGATTCAACATTTCTCT
2111439 ATGTGAAGACTTGTGTCTCTTGTAGTCCTCCTTGATGTACTTTGGAAACATAATATTTTTCATCG
515 ATGTGAAGACTTGTGTCTCTTGTAGTCCTCCTTGATGTACTTTGGAAACATAATATTTTTCATCG
2111504 ATGAAGAATATTTTTTGATCAATCTTTTTACTTGGAATAACACATCCAT
580 ATGAAGAATATTTTTTGATCAATCTTTTTACTTGGAATAACACATCCAT
2111553 TGGAGAAGGT
Statistics
Matches: 621, Mismatches: 1, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
626 128 0.21
627 162 0.26
628 61 0.10
629 88 0.14
630 17 0.03
631 165 0.27
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (631 bp):
AAGCATAATATAAGCTAAGTATTTGAAGTAAATAACTTATAATATGAAGATGTGACCTATAGGTT
ATAATAATAACTCATGCATCATATGATAATGAATGAATATTATTACAACTATAGATTATATGCTT
GAATATCAATCAATGATACAAACCATATAATGAATGCACAAAGTATGGTAATTCAAGTATAGTCT
AATCTTCATATGTATGCTCATAATAGTATATAATGCATAAATAAGTAAATATAAGATAAAGAAAG
GAAGAACTCCCTTAGAACTAGTTTTGAATAACCTCCATGGTGTGATCAAGTCATGGAGAAAAATT
GGAGCAAGACAGGATCACATCATCCTCCCCTTCTTTTAGGCGATTTGTCCTCAAATAGAAGTAGT
TTGTCATTGAAGACCTTCTTGATGTAGGAAGGATTGAATCATTATGTTCTCCTTGAGAATCTCCC
ATGAAATGTTCAACTCATTGTTCTATCTTGTTTGTGTTGGTTTGATTCAACATTTCTCTATGTGA
AGACTTGTGTCTCTTGTAGTCCTCCTTGATGTACTTTGGAAACATAATATTTTTCATCGATGAAG
AATATTTTTTGATCAATCTTTTTACTTGGAATAACACATCCATAAG
Found at i:2119338 original size:14 final size:14
Alignment explanation
Indices: 2119319--2119347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2119309 GTGATGGATG
2119319 ATGGTGATGGAAAT
1 ATGGTGATGGAAAT
2119333 ATGGTGATGGAAAT
1 ATGGTGATGGAAAT
2119347 A
1 A
2119348 GTATCTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (14 bp):
ATGGTGATGGAAAT
Found at i:2125981 original size:5 final size:5
Alignment explanation
Indices: 2125956--2125989 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
2125946 ACCAGCACTC
*
2125956 AAAAG AAGAAG AAAAG CAAAG AAAAG AAAAG AAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAA
2125990 TAAGTTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2137669 original size:7 final size:7
Alignment explanation
Indices: 2137657--2137682 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2137647 ACAAAACCCT
2137657 AATAAAG
1 AATAAAG
2137664 AATAAAG
1 AATAAAG
2137671 AATAAAG
1 AATAAAG
2137678 AATAA
1 AATAA
2137683 CGAAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:2146706 original size:35 final size:35
Alignment explanation
Indices: 2146662--2146760 Score: 153
Period size: 35 Copynumber: 2.8 Consensus size: 35
2146652 ATAAGGGGAT
*
2146662 GGTGATGATATAGGCATGAAATGGTGATAGAAGAA
1 GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
* * *
2146697 GGTGATGATATAGGCGTGCAATGGTGATGGAAGAT
1 GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
2146732 GGTGATGATATAGGCGTGAAAATGGTGAT
1 GGTGATGATATAGGCGTG-AAATGGTGAT
2146761 GAAAGATGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 49 0.84
36 9 0.16
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.25
Consensus pattern (35 bp):
GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
Found at i:2147993 original size:22 final size:22
Alignment explanation
Indices: 2147967--2148035 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2147957 ATAGTATATT
2147967 TTAATAACTTATATCTCACATA
1 TTAATAACTTATATCTCACATA
* * * *
2147989 TTAATGGA-TAAGT-TATCA-ACA
1 TTAAT-AACTTA-TATCTCACATA
2148010 -TAATAACTTATATCTCACATA
1 TTAATAACTTATATCTCACATA
2148031 TTAAT
1 TTAAT
2148036 GGATAAGTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 2 0.06
20 10 0.30
21 4 0.12
22 15 0.45
23 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAATAACTTATATCTCACATA
Found at i:2148015 original size:42 final size:42
Alignment explanation
Indices: 2147968--2148059 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
2147958 TAGTATATTT
2147968 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
1 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
2148010 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
1 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
2148052 TAATAACT
1 TAATAACT
2148060 ATAGGTATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (42 bp):
TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
Found at i:2155843 original size:32 final size:30
Alignment explanation
Indices: 2155772--2155844 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
2155762 CTTGGCTTGC
* *
2155772 TTTCTTTTTTTTGACTTTTCTTCTTTTTCTT
1 TTTC-TTTTTCTGAATTTTCTTCTTTTTCTT
* *
2155803 TTCCCTTTTTCTGAATTTTCATTCTTTTTGTAT
1 TT-TCTTTTTCTGAATTTTC-TTCTTTTTCT-T
2155836 TTTCTTTTT
1 TTTCTTTTT
2155845 TAACTCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 15 0.44
32 16 0.47
33 3 0.09
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (30 bp):
TTTCTTTTTCTGAATTTTCTTCTTTTTCTT
Found at i:2163511 original size:13 final size:13
Alignment explanation
Indices: 2163493--2163523 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2163483 CTCTAGCTAG
2163493 CTCAAATGTCCAA
1 CTCAAATGTCCAA
*
2163506 CTCAAATGTCCAG
1 CTCAAATGTCCAA
2163519 CTCAA
1 CTCAA
2163524 GTCAACTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (13 bp):
CTCAAATGTCCAA
Found at i:2164574 original size:18 final size:18
Alignment explanation
Indices: 2164551--2164599 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
2164541 ATTTCTATGG
2164551 TGGATGTTTAATGGGAGT
1 TGGATGTTTAATGGGAGT
2164569 TGGATGTTTAATGGGAGT
1 TGGATGTTTAATGGGAGT
* *
2164587 TGGTTGCTTAATG
1 TGGATGTTTAATG
2164600 ATGGATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (18 bp):
TGGATGTTTAATGGGAGT
Found at i:2164986 original size:36 final size:36
Alignment explanation
Indices: 2164945--2165016 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2164935 CATCTTCAAA
*
2164945 AAGCTTTTCTTCATTTGAATTGTCCTCTAAATGTTC
1 AAGCTTTTCTTCATTTGAATTGTCCTCTAAACGTTC
*
2164981 AAGCTTTTCTTCATTTGAATTTTCCTCTAAACGTTC
1 AAGCTTTTCTTCATTTGAATTGTCCTCTAAACGTTC
2165017 TCCTTCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (36 bp):
AAGCTTTTCTTCATTTGAATTGTCCTCTAAACGTTC
Found at i:2166346 original size:21 final size:21
Alignment explanation
Indices: 2166320--2166364 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2166310 TAAAACACCT
2166320 GATGTCTCTTGATCATTCAGG
1 GATGTCTCTTGATCATTCAGG
2166341 GATGTCTCTTGATCATTCAGG
1 GATGTCTCTTGATCATTCAGG
2166362 GAT
1 GAT
2166365 ATCTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (21 bp):
GATGTCTCTTGATCATTCAGG
Found at i:2176913 original size:20 final size:21
Alignment explanation
Indices: 2176876--2176914 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2176866 TATGGTCTTG
*
2176876 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGATGATGATGAA
*
2176897 ATGAA-GATGATGGTGATG
1 ATGAAGGATGATGATGATG
2176915 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGATGATGATGAA
Found at i:2178147 original size:2 final size:2
Alignment explanation
Indices: 2178130--2178163 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2178120 TCATAATAAC
*
2178130 TA TA TG TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2178164 GATAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2178200 original size:43 final size:43
Alignment explanation
Indices: 2178122--2178204 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
2178112 AGTTATCATC
* *
2178122 ATAATAACTATATGTATAATATATATATATATATATATATATG
1 ATAATAACTATATGTATAAAATATAAATATATATATATATATG
*
2178165 ATAATAACTATCT-TATAAAATATGAAATA-AGTATATATAT
1 ATAATAACTATATGTATAAAATAT-AAATATA-TATATATAT
2178205 GTGTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 10 0.29
43 25 0.71
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.41
Consensus pattern (43 bp):
ATAATAACTATATGTATAAAATATAAATATATATATATATATG
Found at i:2189093 original size:29 final size:28
Alignment explanation
Indices: 2189055--2189146 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 28
2189045 ACGAAATTAG
*
2189055 CACCATTTTTAAAAATAATTACAAATATAA
1 CACCA-TTTTCAAAATAATTACAAA-ATAA
*
2189085 CACCATTTTCAAAATAATTACCAAAATAT
1 CACCATTTTCAAAATAATTA-CAAAATAA
* *
2189114 CACCATTTTCAAAATATTTACGAAAATAT
1 CACCATTTTCAAAATAATTAC-AAAATAA
2189143 CACC
1 CACC
2189147 CCCATCAACG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
28 1 0.02
29 47 0.82
30 9 0.16
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.32
Consensus pattern (28 bp):
CACCATTTTCAAAATAATTACAAAATAA
Found at i:2192681 original size:23 final size:26
Alignment explanation
Indices: 2192634--2192685 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
2192624 TATTCCATCT
*
2192634 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2192660 TTATTTCA-TT-ATTTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2192683 TTA
1 TTA
2192686 ACCATATTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 7 0.28
25 2 0.08
26 8 0.32
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTACCTTTA
Found at i:2192949 original size:21 final size:21
Alignment explanation
Indices: 2192910--2192949 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2192900 GGAGTGTAAA
* *
2192910 AAGAAAAGAAAAGACAAAAAT
1 AAGAAAAAAAAAAACAAAAAT
*
2192931 AAGAAAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAACAAAA
2192950 GTAAAAGATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (21 bp):
AAGAAAAAAAAAAACAAAAAT
Found at i:2201655 original size:21 final size:22
Alignment explanation
Indices: 2201631--2201672 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2201621 GATACCACCA
*
2201631 TGAA-GGAACTGATTCCCCCTT
1 TGAAGGGAACCGATTCCCCCTT
2201652 TGAAGGGGAACCGATTCCCCC
1 TGAA-GGGAACCGATTCCCCC
2201673 CCCATAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (22 bp):
TGAAGGGAACCGATTCCCCCTT
Found at i:2204362 original size:21 final size:21
Alignment explanation
Indices: 2204336--2204375 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2204326 CATATTGCTT
2204336 AGAGGGAA-CTGATTCCCCCCA
1 AGAGGGAATC-GATTCCCCCCA
*
2204357 AGAGGGTATCGATTCCCCC
1 AGAGGGAATCGATTCCCCC
2204376 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (21 bp):
AGAGGGAATCGATTCCCCCCA
Found at i:2210389 original size:32 final size:31
Alignment explanation
Indices: 2210347--2210423 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 31
2210337 AGGCACAAAA
*
2210347 ACAAATATAAAAAAATATATATA-AATAA-AAT
1 ACAAAAATAAAAAAATA-ATA-ACAATAACAAT
*
2210378 ACATAAAATAAAGAAGATAATAACAATAACAAT
1 ACA-AAAATAAA-AAAATAATAACAATAACAAT
2210411 ACAAAAATAAAAA
1 ACAAAAATAAAAA
2210424 TAGAAGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 6 0.15
32 23 0.57
33 11 0.28
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (31 bp):
ACAAAAATAAAAAAATAATAACAATAACAAT
Found at i:2210439 original size:15 final size:15
Alignment explanation
Indices: 2210419--2210450 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2210409 ATACAAAAAT
*
2210419 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
2210434 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
2210449 AA
1 AA
2210451 TGAAGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:2210477 original size:16 final size:17
Alignment explanation
Indices: 2210456--2210518 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
2210446 TAAAATGAAG
2210456 TATATA-AAATAATAAA
1 TATATAGAAATAATAAA
*
2210472 TATATATAACAT-AT-AA
1 TATATAGAA-ATAATAAA
*
2210488 T-TATAGTAATAA-AAA
1 TATATAGAAATAATAAA
*
2210503 TATATAAAAATAATAA
1 TATATAGAAATAATAA
2210519 TGATATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 18 0.49
17 6 0.16
18 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TATATAGAAATAATAAA
Found at i:2212317 original size:110 final size:108
Alignment explanation
Indices: 2212078--2212328 Score: 287
Period size: 110 Copynumber: 2.3 Consensus size: 108
2212068 AGTATTGTTC
* * *
2212078 CGAGTCCAATAT-CCTCTGTCGTGAAGTTGAAA-T-ATGCTCTGGAACTGGGAAATTGTTTGTTG
1 CGAGTCCAATATCCCTC-GTTGTGAAGTTGAAATTGATGCTATGGAACTGGAAAATTGTTTGTTG
*
2212140 ACAGCCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
65 ACAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
* * **
2212184 CGAGTTCAATATCCTTCACTGTGAAGTTGAAATTGATGCTGAATGAGAA-T-GAAAAGTTGTTTG
1 CGAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGATGCT--ATG-GAACTGGAAAA-TTGTTTG
* * ** *
2212247 TTGATAATCAGTCGCCCCTTCGTTATGAAGTTGAGCTTGTTTTGTCT
62 TTGACAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
* *
2212294 CGAGTCCAATATCCCTCGTTGTGAAATTAAAATTG
1 CGAGTCCAATATCCCTCGTTGTGAAGTTGAAATTG
2212329 GCTCTGAAAC
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
106 23 0.19
107 4 0.03
108 5 0.04
109 4 0.03
110 80 0.67
111 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (108 bp):
CGAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGATGCTATGGAACTGGAAAATTGTTTGTTGA
CAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCT
Found at i:2212336 original size:110 final size:110
Alignment explanation
Indices: 2212130--2212328 Score: 290
Period size: 110 Copynumber: 1.8 Consensus size: 110
2212120 AACTGGGAAA
* *
2212130 TTGTTTGTTGACAGCCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* * *
2212195 TCCTTCACTGTGAAGTTGAAATTGATGCTGAATGAGAATGAAAAG
66 TCCCTCACTGTGAAATTAAAATTGATGCTGAATGAGAATGAAAAG
* * ** *
2212240 TTGTTTGTTGATAATCAGTCGCCCCTTCGTTATGAAGTTGAGCTTGTTTTGTCTCGAGTCCAATA
1 TTGTTTGTTGACAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
**
2212305 TCCCTCGTTGTGAAATTAAAATTG
66 TCCCTCACTGTGAAATTAAAATTG
2212329 GCTCTGAAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 77 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAGTCGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
TCCCTCACTGTGAAATTAAAATTGATGCTGAATGAGAATGAAAAG
Found at i:2212441 original size:43 final size:43
Alignment explanation
Indices: 2212375--2212456 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
2212365 AGCCTCAAAT
* * *
2212375 GGTATGATATCCTCCGTATTGGAGTTGAAATCGTGGATGTGCG
1 GGTACGATATCCTCCGTAGTGGAGTTGAAATCGCGGATGTGCG
*
2212418 GGTACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATG
1 GGTACGATATCCTCCGTAGTGGAGTTGAAATCGCGGATG
2212457 GCTCCTTCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
GGTACGATATCCTCCGTAGTGGAGTTGAAATCGCGGATGTGCG
Found at i:2213452 original size:11 final size:10
Alignment explanation
Indices: 2213427--2213451 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2213417 AAGATTTTCA
2213427 TTTTTGTTTT
1 TTTTTGTTTT
2213437 TTTTTGTTTT
1 TTTTTGTTTT
2213447 TTTTT
1 TTTTT
2213452 TACTTAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:2223864 original size:13 final size:13
Alignment explanation
Indices: 2223835--2223876 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2223825 GAGTCACAAA
*
2223835 AAAAAATATAAA-
1 AAAATATATAAAT
2223847 AAAATATATAAAT
1 AAAATATATAAAT
*
2223860 AAAATACATAAAAT
1 AAAATATAT-AAAT
2223874 AAA
1 AAA
2223877 GAAGATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:2223963 original size:16 final size:17
Alignment explanation
Indices: 2223942--2224004 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
2223932 TAAAATGAAG
2223942 TATATA-AAATAATAAA
1 TATATATAAATAATAAA
2223958 TATATATAACAT-AT-AA
1 TATATATAA-ATAATAAA
2223974 T-TATAGT-AATAA-AAA
1 TATATA-TAAATAATAAA
2223989 TATATATAAATAATAA
1 TATATATAAATAATAA
2224005 TGATATATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 19 0.49
17 6 0.15
18 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
TATATATAAATAATAAA
Found at i:2224002 original size:19 final size:19
Alignment explanation
Indices: 2223980--2224036 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
2223970 ATAATTATAG
2223980 TAATAAAAATATATATAAA
1 TAATAAAAATATATATAAA
** *
2223999 TAATAATGATATATGAAAAA
1 TAATAAAAATATAT-ATAAA
* *
2224019 GAATTAAAAGTATATATA
1 TAA-TAAAAATATATATA
2224037 TATATACAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
TAATAAAAATATATATAAA
Found at i:2228940 original size:18 final size:18
Alignment explanation
Indices: 2228896--2228933 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2228886 AGGCATTTGA
* *
2228896 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
2228914 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
2228932 TC
1 TC
2228934 TCGTGCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.24, T:0.47
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:2230576 original size:22 final size:22
Alignment explanation
Indices: 2230494--2230575 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
2230484 AGAACCCCAG
*
2230494 GGGGGTATCGATTCCCC-TACA
1 GGGGGTATCGATTCCCCTTAAA
* *
2230515 GGGGG-ATTGATTCCCCTTTTAA
1 GGGGGTATCGATTCCCC-TTAAA
* *
2230537 GGGGGAATCGGTTCCCCTTAAA
1 GGGGGTATCGATTCCCCTTAAA
2230559 GGGGGGTATCGATTCCC
1 -GGGGGTATCGATTCCC
2230576 TCTACACTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 10 0.20
21 5 0.10
22 11 0.22
23 23 0.47
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTAAA
Found at i:2235226 original size:17 final size:18
Alignment explanation
Indices: 2235187--2235228 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2235177 AAGTAGTGTT
*
2235187 CTTGAAAGAAAAATGAAT
1 CTTGAAAGAAAAATGAAG
* *
2235205 ATTGAATGAAAAAT-AAG
1 CTTGAAAGAAAAATGAAG
2235222 CTTGAAA
1 CTTGAAA
2235229 TGCTCAAACT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
CTTGAAAGAAAAATGAAG
Found at i:2251430 original size:26 final size:26
Alignment explanation
Indices: 2251371--2251421 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2251361 AGCCATTTTA
2251371 TTTCATCT-TTATTTCATTTCATTTCT
1 TTTCAT-TATTATTTCATTTCATTTCT
2251397 TTTCATTATTATTTCA-TT-ATTTCT
1 TTTCATTATTATTTCATTTCATTTCT
2251421 T
1 T
2251422 CCTTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTCATTATTATTTCATTTCATTTCT
Found at i:2260286 original size:23 final size:20
Alignment explanation
Indices: 2260255--2260299 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
2260245 AGCCCTCTCT
2260255 TTTCTATCTTTATTTCATTTCA
1 TTTCTATCTTTA-TT-ATTTCA
2260277 TTTCTTATCTTTATTATTTCA
1 TTTC-TATCTTTATTATTTCA
2260298 TT
1 TT
2260300 ATTTCTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTATCTTTATTATTTCA
Found at i:2260311 original size:23 final size:26
Alignment explanation
Indices: 2260264--2260315 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
2260254 TTTTCTATCT
*
2260264 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2260290 TTATTTCA-TT-ATTTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2260313 TTA
1 TTA
2260316 ATCATATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 7 0.28
25 2 0.08
26 8 0.32
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTACCTTTA
Found at i:2269355 original size:13 final size:13
Alignment explanation
Indices: 2269339--2269396 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
2269329 AATAAAAAGG
2269339 GCAAAAAAAAGAA
1 GCAAAAAAAAGAA
2269352 GCAAAAAACAA-AA
1 GCAAAAAA-AAGAA
2269365 G-AACAAAAAAGAA
1 GCAA-AAAAAAGAA
*
2269378 -CAAAAAGAAAAAA
1 GCAAAAA-AAAGAA
2269391 G-AAAAA
1 GCAAAAA
2269397 GGGACAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
12 7 0.18
13 29 0.76
14 2 0.05
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
GCAAAAAAAAGAA
Found at i:2269371 original size:15 final size:15
Alignment explanation
Indices: 2269341--2269397 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
2269331 TAAAAAGGGC
2269341 AAAAAAAAGAAGCAA
1 AAAAAAAAGAAGCAA
2269356 AAAACAAAAGAA-CAA
1 AAAA-AAAAGAAGCAA
* *
2269371 AAAAGAACAAAAAGAAA
1 AAAA-AA-AAGAAGCAA
2269388 AAAGAAAAAG
1 AAA-AAAAAG
2269398 GGACAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 13 0.38
16 13 0.38
17 7 0.21
18 1 0.03
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAGCAA
Found at i:2269383 original size:26 final size:26
Alignment explanation
Indices: 2269343--2269393 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2269333 AAAAGGGCAA
2269343 AAAAAAGAAGCAAAA-AACAAAAGAAC
1 AAAAAAGAAGCAAAAGAA-AAAAGAAC
2269369 AAAAAAGAA-CAAAAAGAAAAAAGAA
1 AAAAAAGAAGC-AAAAGAAAAAAGAA
2269394 AAAGGGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.04
26 20 0.87
27 2 0.09
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAGCAAAAGAAAAAAGAAC
Found at i:2269395 original size:23 final size:24
Alignment explanation
Indices: 2269343--2269407 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
2269333 AAAAGGGCAA
*
2269343 AAAAAAGAAGCAAAAAACAAAAGAAC
1 AAAAAAGAA-C-AAAAAGAAAAGAAC
*
2269369 AAAAAAGAACAAAAAGAAAA-AAG
1 AAAAAAGAACAAAAAGAAAAGAAC
* *
2269392 AAAAAGGGACAAAAAG
1 AAAAAAGAACAAAAAG
2269408 CACATGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.46
24 9 0.26
25 1 0.03
26 9 0.26
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAGAACAAAAAGAAAAGAAC
Found at i:2269984 original size:22 final size:22
Alignment explanation
Indices: 2269956--2269998 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2269946 GCTACCCCAG
*
2269956 CAAACCTTTGAGCATCCAATGC
1 CAAACCTTTGAGCATCAAATGC
2269978 CAAACCTTTGAGCATCAAATG
1 CAAACCTTTGAGCATCAAATG
2269999 AACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2270859 original size:36 final size:37
Alignment explanation
Indices: 2270812--2270946 Score: 100
Period size: 36 Copynumber: 3.8 Consensus size: 37
2270802 CAGATGATTA
* *
2270812 TCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
** ** * * *
2270848 TCTCGCTTGAGACCG-TTTTC--ACTAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
*
2270882 TCTCGCTTGAGATAGTTTTTCTTGAAACAA-ACTTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
* * * * *
2270918 TCTCCCATGAGACAGTTTCTCTTGAAACA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACA
2270947 TCTTTGAAAT
Statistics
Matches: 76, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
33 6 0.08
34 16 0.21
35 10 0.13
36 41 0.54
37 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (37 bp):
TCTCGCTTGAGATAGTTTTTCTTAAAACAAGACTTTG
Found at i:2270995 original size:63 final size:62
Alignment explanation
Indices: 2270888--2271009 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 62
2270878 TTTATCTCGC
* * *
2270888 TTGAGATAGTTTTTCTTGAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACATCT
1 TTGAAATAGTTTTCCTTAAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACATCT
* * *
2270950 TTGAAATATGTTTTCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGAAACA
1 TTGAAATA-GTTTTCCTTAAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
2271010 AATTTTGTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 7 0.13
63 46 0.87
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (62 bp):
TTGAAATAGTTTTCCTTAAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACATCT
Found at i:2271044 original size:36 final size:36
Alignment explanation
Indices: 2270969--2271046 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
2270959 GTTTTCCTTA
* ** *
2270969 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
* *
2271005 AAACAAATTTTGTCTCCCATGGGGCAGTTTCGCTCG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
2271041 AAACAA
1 AAACAA
2271047 CACATTGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
Found at i:2271469 original size:65 final size:65
Alignment explanation
Indices: 2271388--2271610 Score: 328
Period size: 64 Copynumber: 3.5 Consensus size: 65
2271378 TTGGAATTCA
* *
2271388 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
*
2271453 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAA-AAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * *
2271517 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
2271582 C
65 C
* * *
2271583 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
2271611 ATATTGGACT
Statistics
Matches: 146, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
63 21 0.14
64 63 0.43
65 49 0.34
66 13 0.09
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
Found at i:2271653 original size:170 final size:171
Alignment explanation
Indices: 2271453--2271788 Score: 629
Period size: 171 Copynumber: 2.0 Consensus size: 171
2271443 TCCCAGTATC
*
2271453 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAA-AAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
2271517 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
66 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
2271582 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
2271623 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
* *
2271688 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
66 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
*
2271753 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
2271789 CCTCGAAACA
Statistics
Matches: 161, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
170 47 0.29
171 114 0.71
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (171 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:2271674 original size:235 final size:231
Alignment explanation
Indices: 2271296--2271752 Score: 731
Period size: 235 Copynumber: 2.0 Consensus size: 231
2271286 CGAGAAAGCT
*
2271296 CAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTCCCAATCCAATTTCAA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATCCAATTTCAA
* *
2271361 CTTCATAGCGAAGGATATTGGAATTCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
66 CTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
* * *
2271426 GGTTGTTAACAAAAATTTCCCAGTATCAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
131 GGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
* *
2271491 GGTTGTCAA-AAA-AATTTCCCAGTTTAAGACAACA
196 GGCTGTCAACAAACAACTTCCCAGTTTAAGACAACA
*
2271525 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAA--T-----CCA
2271590 ATTTCAACTTCACAGCGAAGGATATTGG-ACTCAAGACAACACAAGTTCAACTTCACAACGAAGG
59 ATTTCAACTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAAGG
* *
2271654 GGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTAAGACAGCACAAGTTCAACTTCACAACGAAGG
124 GGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGG
2271719 GGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
189 GGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
2271753 CAGAGTCAAT
Statistics
Matches: 208, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
229 52 0.25
231 1 0.00
235 110 0.53
236 33 0.16
237 12 0.06
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (231 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATCCAATTTCAA
CTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
GGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCT
GGCTGTCAACAAACAACTTCCCAGTTTAAGACAACA
Found at i:2271702 original size:65 final size:66
Alignment explanation
Indices: 2271622--2271781 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 66
2271612 TATTGGACTC
* *
2271622 AAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAGT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAGT
2271685 TT
65 TT
2271687 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
2271752 T
66 T
* * * *
2271753 CAG--AG-TCAATTTCAACTTCACAGCGAAGG
1 AAGACAGCACAAGTTCAACTTCACAACGAAGG
2271782 ATATTGGCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 21 0.24
64 2 0.02
65 50 0.57
66 12 0.14
67 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (66 bp):
AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
T
Found at i:2271736 original size:106 final size:104
Alignment explanation
Indices: 2271517--2271718 Score: 273
Period size: 106 Copynumber: 1.9 Consensus size: 104
2271507 TCCCAGTTTA
2271517 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
* * * * *
2271582 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
* *
2271621 CAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAG
1 --AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAA
2271684 TTTAAGACAGCACAAGTTCAACTTCACAACGAAGG
63 TTTAAG--AGC-CAAGTTCAACTTCACAACGAAGG
2271719 GGCCGCTGGC
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
104 2 0.02
105 11 0.13
106 50 0.57
107 3 0.03
108 21 0.24
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (104 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
Found at i:2281433 original size:13 final size:14
Alignment explanation
Indices: 2281415--2281443 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2281405 TGTTTCTATG
2281415 TGAATACAAGT-TA
1 TGAATACAAGTATA
2281428 TGAATACAAGTATA
1 TGAATACAAGTATA
2281442 TG
1 TG
2281444 TTTAGGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (14 bp):
TGAATACAAGTATA
Found at i:2281688 original size:23 final size:24
Alignment explanation
Indices: 2281662--2281706 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2281652 CGATCATTTG
*
2281662 GGACATTTCTATGTGGT-CTTTTA
1 GGACATTTCTACGTGGTACTTTTA
2281685 GGACATTTCTACGTGGTACTTT
1 GGACATTTCTACGTGGTACTTT
2281707 GGTGCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (24 bp):
GGACATTTCTACGTGGTACTTTTA
Found at i:2283683 original size:35 final size:35
Alignment explanation
Indices: 2283636--2283711 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
2283626 TACTATCTAT
* *
2283636 ACCATCTCCCATCTCCATATCACACCTATGTCATC
1 ACCATCTCCCATCTCCATATCACACCTATATAATC
* * *
2283671 ACCATCTTCCATCTCCATTTCACGCCTATATAATC
1 ACCATCTCCCATCTCCATATCACACCTATATAATC
2283706 ACCATC
1 ACCATC
2283712 CCATTATCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.41, G:0.03, T:0.30
Consensus pattern (35 bp):
ACCATCTCCCATCTCCATATCACACCTATATAATC
Found at i:2284124 original size:12 final size:12
Alignment explanation
Indices: 2284086--2284129 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2284076 CAAGTGCTGC
*
2284086 AACAAAATGAAA
1 AACAAAAAGAAA
*
2284098 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
*
2284111 AACAAAAAGCAA
1 AACAAAAAGAAA
2284123 AACAAAA
1 AACAAAA
2284130 GACTCCTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.02
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:2287617 original size:35 final size:35
Alignment explanation
Indices: 2287565--2287640 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
2287555 TCCTACCTAT
* *
2287565 ACCATCTCCCATCTCCATATCACGCCTATATCATC
1 ACCATCTCCCATATCCATATCACGCCTATATAATC
* * *
2287600 ACCATCTTCCATATCCATTTCACGCCTCTATAATC
1 ACCATCTCCCATATCCATATCACGCCTATATAATC
2287635 ACCATC
1 ACCATC
2287641 CCATTATCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.41, G:0.03, T:0.30
Consensus pattern (35 bp):
ACCATCTCCCATATCCATATCACGCCTATATAATC
Found at i:2287795 original size:15 final size:15
Alignment explanation
Indices: 2287775--2287820 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
2287765 TTTGATATCA
2287775 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
2287790 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
2287805 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
2287821 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:2288933 original size:17 final size:18
Alignment explanation
Indices: 2288913--2288950 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2288903 CCATTAATGA
*
2288913 AAGGTTACCTTAC-TAAC
1 AAGGTGACCTTACATAAC
2288930 AAGGTGACCTTACATAAC
1 AAGGTGACCTTACATAAC
2288948 AAG
1 AAG
2288951 TTGTTTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (18 bp):
AAGGTGACCTTACATAAC
Found at i:2290592 original size:19 final size:20
Alignment explanation
Indices: 2290568--2290610 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2290558 AGCATTTATC
*
2290568 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
2290587 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
2290607 TTCA
1 TTCA
2290611 AAGGGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:2291003 original size:35 final size:35
Alignment explanation
Indices: 2290954--2291032 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
2290944 ACTATCTGTT
* *
2290954 CATCACCATCTTCCATGACCATTGCACGCCTATAA
1 CATCACCATATTCCATCACCATTGCACGCCTATAA
* *
2290989 CATCACCATATTCCATCACCATTTCACGCCTATAT
1 CATCACCATATTCCATCACCATTGCACGCCTATAA
2291024 CATCACCAT
1 CATCACCAT
2291033 TCCTTAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.28
Consensus pattern (35 bp):
CATCACCATATTCCATCACCATTGCACGCCTATAA
Found at i:2293965 original size:21 final size:22
Alignment explanation
Indices: 2293925--2293965 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2293915 CCAGCAAAAA
2293925 AAATCAAAGCACTCAAAAGAAG
1 AAATCAAAGCACTCAAAAGAAG
*
2293947 AAATGAAAGCACT-AAAAGA
1 AAATCAAAGCACTCAAAAGA
2293966 GGACGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.10
Consensus pattern (22 bp):
AAATCAAAGCACTCAAAAGAAG
Found at i:2299393 original size:5 final size:5
Alignment explanation
Indices: 2299371--2299418 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
2299361 TCCAGCACTC
*
2299371 AAAAG AAGAA- AAAA- AAAAG AAAAG AAAAG AAAAG -AAAT AAAAG AAAAG
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2299419 TTGAAGCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 9 0.24
5 27 0.71
6 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:2299395 original size:19 final size:19
Alignment explanation
Indices: 2299371--2299418 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2299361 TCCAGCACTC
2299371 AAAAGAAGAA-AAAAAAAAG
1 AAAAGAA-AAGAAAAAAAAG
* *
2299390 AAAAGAAAAGAAAAGAAAT
1 AAAAGAAAAGAAAAAAAAG
2299409 AAAAGAAAAG
1 AAAAGAAAAG
2299419 TTGAAGCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAAAAG
Found at i:2299412 original size:14 final size:13
Alignment explanation
Indices: 2299371--2299418 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
2299361 TCCAGCACTC
*
2299371 AAAAGAAGAAAAAA
1 AAAAGAA-AAAAAG
2299385 AAAAGAAAAGAAAAG
1 AAAAG-AAA-AAAAG
2299400 AAAAGAAATAAAAG
1 AAAAGAAA-AAAAG
2299414 AAAAG
1 AAAAG
2299419 TTGAAGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:2303440 original size:21 final size:21
Alignment explanation
Indices: 2303401--2303440 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2303391 ATGCATTCAT
* * *
2303401 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
2303422 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
2303441 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:2305633 original size:24 final size:23
Alignment explanation
Indices: 2305576--2305634 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
2305566 ATTCTTTTCT
*
2305576 TTTCTTCTTCTTTTGAGTGCTGGA
1 TTTCTT-TTCTTTTGAGTGCTGCA
* *
2305600 TTTTTCTTTCTTTTGAGTGCTTCA
1 TTTCT-TTTCTTTTGAGTGCTGCA
2305624 CTTTCTTTTCT
1 -TTTCTTTTCT
2305635 ATTTTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.07, C:0.19, G:0.14, T:0.61
Consensus pattern (23 bp):
TTTCTTTTCTTTTGAGTGCTGCA
Found at i:2310019 original size:15 final size:16
Alignment explanation
Indices: 2309980--2310021 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2309970 ATGTTATAAG
*
2309980 ATAGTTATTTTCATCT
1 ATAGTTATTATCATCT
2309996 ATA-TATATTAT-ATCT
1 ATAGT-TATTATCATCT
2310011 ATAGTTATTAT
1 ATAGTTATTAT
2310022 GATGATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (16 bp):
ATAGTTATTATCATCT
Found at i:2313163 original size:18 final size:18
Alignment explanation
Indices: 2313123--2313164 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2313113 TAGGCATGAG
2313123 TTCA-TTTAAGCATGCAT
1 TTCATTTTAAGCATGCAT
*
2313140 TGCATTTTAAGCAT-CTAT
1 TTCATTTTAAGCATGC-AT
2313158 TTCATTT
1 TTCATTT
2313165 AATAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (18 bp):
TTCATTTTAAGCATGCAT
Found at i:2313188 original size:18 final size:17
Alignment explanation
Indices: 2313158--2313223 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
2313148 AAGCATCTAT
2313158 TTCATTTAA-TAAAGTTAG
1 TTCA-TTAATTAAA-TTAG
*
2313176 TTCATTAATTAAACTAG
1 TTCATTAATTAAATTAG
* * *
2313193 TTCATAAATCAAACTAAG
1 TTCATTAATTAAA-TTAG
*
2313211 TTCATTTATTAAA
1 TTCATTAATTAAA
2313224 CTAACTCTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (17 bp):
TTCATTAATTAAATTAG
Found at i:2313224 original size:18 final size:18
Alignment explanation
Indices: 2313174--2313227 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
2313164 TAATAAAGTT
2313174 AGTTCATTAATTAAACT-
1 AGTTCATTAATTAAACTA
* *
2313191 AGTTCATAAATCAAACTA
1 AGTTCATTAATTAAACTA
*
2313209 AGTTCATTTATTAAACTA
1 AGTTCATTAATTAAACTA
2313227 A
1 A
2313228 CTCTTAATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (18 bp):
AGTTCATTAATTAAACTA
Found at i:2328643 original size:20 final size:19
Alignment explanation
Indices: 2328602--2328644 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2328592 AGTATTTATC
* *
2328602 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTACT
*
2328621 TTCATTAAAAATCATGTGCT
1 TTCATT-AAAATCATGTACT
2328641 TTCA
1 TTCA
2328645 AAGGAGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCATTAAAATCATGTACT
Found at i:2328994 original size:14 final size:14
Alignment explanation
Indices: 2328975--2329001 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2328965 TTATAAGATA
2328975 ATATTTCCATCACC
1 ATATTTCCATCACC
2328989 ATATTTCCATCAC
1 ATATTTCCATCAC
2329002 TTTCACGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATTTCCATCACC
Found at i:2341123 original size:10 final size:10
Alignment explanation
Indices: 2341093--2341143 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 10
2341083 TTCTAAAAAA
2341093 TACTGTAGCAAT
1 TACTGTAGC--T
2341105 TACTGTAGCT
1 TACTGTAGCT
*
2341115 TATTGTAGCAGT
1 TACTGTAGC--T
2341127 TACTGTAGCT
1 TACTGTAGCT
2341137 TACTGTA
1 TACTGTA
2341144 ATAATGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 17 0.49
12 18 0.51
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (10 bp):
TACTGTAGCT
Found at i:2341124 original size:22 final size:22
Alignment explanation
Indices: 2341093--2341143 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2341083 TTCTAAAAAA
2341093 TACTGTAGCAATTACTGTAGCT
1 TACTGTAGCAATTACTGTAGCT
* *
2341115 TATTGTAGCAGTTACTGTAGCT
1 TACTGTAGCAATTACTGTAGCT
2341137 TACTGTA
1 TACTGTA
2341144 ATAATGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (22 bp):
TACTGTAGCAATTACTGTAGCT
Found at i:2343565 original size:19 final size:20
Alignment explanation
Indices: 2343519--2343567 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2343509 AAACCCCTTC
**
2343519 GAAAATACATGATTTTTTAT
1 GAAAATACATGATTTTAAAT
2343539 GAAAATACATGA-TTTAAAT
1 GAAAATACATGATTTTAAAT
*
2343558 GAATATACAT
1 GAAAATACAT
2343568 ACTCTTGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (20 bp):
GAAAATACATGATTTTAAAT
Found at i:2351690 original size:8 final size:8
Alignment explanation
Indices: 2351677--2351705 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2351667 AAACATTTTA
2351677 AAAAAATT
1 AAAAAATT
2351685 AAAAAATT
1 AAAAAATT
2351693 -AAAAATT
1 AAAAAATT
2351700 AAAAAA
1 AAAAAA
2351706 AAAGGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:2351714 original size:5 final size:5
Alignment explanation
Indices: 2351700--2351747 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
2351690 ATTAAAAATT
* * *
2351700 AAAAA AAAAG GAAAG AAAAG CAAAAAA AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG AAAAG AAAAG A
2351748 TTCTAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 32 0.89
7 4 0.11
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2351718 original size:21 final size:22
Alignment explanation
Indices: 2351700--2351745 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2351690 ATTAAAAATT
*
2351700 AAAAAAAAAGGAAAGAAAAGCA
1 AAAAAAAAAGAAAAGAAAAGCA
2351722 AAAAAAAAAGAAAAGAAAAG-A
1 AAAAAAAAAGAAAAGAAAAGCA
2351743 AAA
1 AAA
2351746 GATTCTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGAAAAGAAAAGCA
Found at i:2351724 original size:17 final size:16
Alignment explanation
Indices: 2351711--2351745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2351701 AAAAAAAAGG
2351711 AAAGAAAAGCAAAAAAA
1 AAAGAAAAG-AAAAAAA
2351728 AAAGAAAAGAAAAGAAA
1 AAAGAAAAGAAAA-AAA
2351745 A
1 A
2351746 GATTCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAAA
Found at i:2355899 original size:26 final size:25
Alignment explanation
Indices: 2355851--2355899 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2355841 TATTTCAATG
*
2355851 ATATGTATAACATGATCAACTAAGC
1 ATATGTATAACATAATCAACTAAGC
2355876 ATATGATAGTAACATAAT-AACTAA
1 ATATG-TA-TAACATAATCAACTAA
2355900 CATGTGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 8 0.38
27 8 0.38
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (25 bp):
ATATGTATAACATAATCAACTAAGC
Found at i:2361688 original size:23 final size:23
Alignment explanation
Indices: 2361637--2361685 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2361627 AGGGACAAGT
* * *
2361637 GCCTTACATCATGTGGTATCAGA
1 GCCTTACATCAAGCGGTATCAAA
2361660 GCCTTACATCAAGCGGTAATCAAA
1 GCCTTACATCAAGCGGT-ATCAAA
2361684 GC
1 GC
2361686 TTAGGTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
GCCTTACATCAAGCGGTATCAAA
Found at i:2372251 original size:30 final size:28
Alignment explanation
Indices: 2372202--2372260 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
2372192 AAGAAATGAC
* *
2372202 AAAAAAAGAAGAAAAAAATTCAGAAAAG
1 AAAAAAAGAAAAAAAAAATTCAAAAAAG
2372230 AAAAAAAGAAAAAAAAGAAATTCAAAAAAG
1 AAAAAAAG-AAAAAAA-AAATTCAAAAAAG
2372260 A
1 A
2372261 GAAAGCAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 8 0.30
29 6 0.22
30 13 0.48
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (28 bp):
AAAAAAAGAAAAAAAAAATTCAAAAAAG
Found at i:2389660 original size:18 final size:18
Alignment explanation
Indices: 2389633--2389677 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2389623 TGTAGGAGTC
2389633 TTTTTC-TTTTATT-TTT
1 TTTTTCTTTTTATTCTTT
2389649 ATTTTTCTTTTTATTCTTT
1 -TTTTTCTTTTTATTCTTT
*
2389668 CTTTTCTTTT
1 TTTTTCTTTT
2389678 CTTTTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTATTCTTT
Found at i:2389672 original size:12 final size:12
Alignment explanation
Indices: 2389639--2389672 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2389629 AGTCTTTTTC
*
2389639 TTTTATTTTTAT
1 TTTTCTTTTTAT
2389651 TTTTCTTTTTAT
1 TTTTCTTTTTAT
2389663 TCTTTCTTTT
1 T-TTTCTTTT
2389673 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTAT
Found at i:2394189 original size:13 final size:13
Alignment explanation
Indices: 2394171--2394196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2394161 GAAACCTGTC
2394171 ACATACCTTTTCA
1 ACATACCTTTTCA
2394184 ACATACCTTTTCA
1 ACATACCTTTTCA
2394197 TATTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Done.