Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 10 of 12
Found at i:2442041 original size:2 final size:2
Alignment explanation
Indices: 2442034--2442064 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2442024 ATCCTAACCC
2442034 TA TA TA TA 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 T
2442065 TTAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2445909 original size:16 final size:16
Alignment explanation
Indices: 2445888--2445931 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
2445878 TGATTAAGCG
2445888 CTGAATGATTCAAATA
1 CTGAATGATTCAAATA
*
2445904 CTGAATGATTCAAATG
1 CTGAATGATTCAAATA
2445920 CTGAATGATTCA
1 CTGAATGATTCA
2445932 GAGGTTCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (16 bp):
CTGAATGATTCAAATA
Found at i:2452115 original size:10 final size:10
Alignment explanation
Indices: 2452096--2452126 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2452086 TATTTAATAA
2452096 ATAAATGAAC
1 ATAAATGAAC
*
2452106 ATAAACGAAC
1 ATAAATGAAC
2452116 ATAAATGAAC
1 ATAAATGAAC
2452126 A
1 A
2452127 CGAACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:2453249 original size:24 final size:24
Alignment explanation
Indices: 2453213--2453263 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2453203 GATTGAGTTA
* *
2453213 AACATAAATGAATGAATATAAACG
1 AACATAAACGAATGAACATAAACG
* *
2453237 AACATAACCGAATGAACATAACCG
1 AACATAAACGAATGAACATAAACG
2453261 AAC
1 AAC
2453264 GTTCATGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.16
Consensus pattern (24 bp):
AACATAAACGAATGAACATAAACG
Found at i:2453253 original size:14 final size:14
Alignment explanation
Indices: 2453236--2453262 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2453226 GAATATAAAC
2453236 GAACATAACCGAAT
1 GAACATAACCGAAT
2453250 GAACATAACCGAA
1 GAACATAACCGAA
2453263 CGTTCATGAA
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:0.52, C:0.22, G:0.15, T:0.11
Consensus pattern (14 bp):
GAACATAACCGAAT
Found at i:2454185 original size:2 final size:2
Alignment explanation
Indices: 2454180--2454212 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2454170 GAGAAAAATA
2454180 AT AT AT 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 AT AT AT A
2454213 ATGTAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2454248 original size:17 final size:17
Alignment explanation
Indices: 2454226--2454343 Score: 56
Period size: 17 Copynumber: 7.0 Consensus size: 17
2454216 TAAGGAAAAC
2454226 AAATAATAAAAAAGTAA
1 AAATAATAAAAAAGTAA
2454243 AAATAAGTAAAAATAAG-AA
1 AAATAA-T-AAAA-AAGTAA
*
2454262 AAAT-ATGATAATAA-TAA
1 AAATAAT-A-AAAAAGTAA
*
2454279 TAATAATAAACCAAA--AA
1 AAATAATAAA--AAAGTAA
* *
2454296 AGA-AAGAAAAATAGTAA
1 AAATAATAAAAA-AGTAA
2454313 AAAT-A-AAAAAA-TAA
1 AAATAATAAAAAAGTAA
*
2454327 AAAAAATAAAAAAGTAA
1 AAATAATAAAAAAGTAA
2454344 TATATATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 30
0.66 0.08 0.26
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 18 0.23
17 27 0.35
18 8 0.10
19 10 0.13
20 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (17 bp):
AAATAATAAAAAAGTAA
Found at i:2454254 original size:9 final size:10
Alignment explanation
Indices: 2454233--2454266 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2454223 AACAAATAAT
2454233 AAAA-AAGTA
1 AAAATAAGTA
2454242 AAAATAAGTA
1 AAAATAAGTA
2454252 AAAATAAG-A
1 AAAATAAGTA
2454261 AAAATA
1 AAAATA
2454267 TGATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 11 0.46
10 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAAATAAGTA
Found at i:2454277 original size:20 final size:19
Alignment explanation
Indices: 2454241--2454339 Score: 62
Period size: 17 Copynumber: 5.2 Consensus size: 19
2454231 ATAAAAAAGT
2454241 AAAAATAAGTAAAAATAAG
1 AAAAATAAGTAAAAATAAG
* * *
2454260 AAAAATATGATAATAATAAT
1 AAAAATAAG-TAAAAATAAG
* ** *
2454280 AATAATAAACCAAAAAAGAAAG
1 AAAAAT-AA-GTAAAAA-TAAG
2454302 AAAAAT-AGTAAAAATAA-
1 AAAAATAAGTAAAAATAAG
*
2454319 AAAAATAA-AAAAAATAA-
1 AAAAATAAGTAAAAATAAG
2454336 AAAA
1 AAAA
2454340 GTAATATATA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
17 18 0.30
18 3 0.05
19 13 0.22
20 14 0.23
21 5 0.08
22 7 0.12
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (19 bp):
AAAAATAAGTAAAAATAAG
Found at i:2454323 original size:9 final size:9
Alignment explanation
Indices: 2454291--2454339 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
2454281 ATAATAAACC
*
2454291 AAAAAAGAA
1 AAAAAATAA
*
2454300 AGAAAAATAG
1 A-AAAAATAA
*
2454310 TAAAAAT-A
1 AAAAAATAA
2454318 AAAAAATAA
1 AAAAAATAA
2454327 AAAAAATAA
1 AAAAAATAA
2454336 AAAA
1 AAAA
2454340 GTAATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 6 0.18
9 21 0.64
10 6 0.18
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2455478 original size:9 final size:9
Alignment explanation
Indices: 2455464--2455495 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2455454 ATAAAAATAC
2455464 ATATATAAT
1 ATATATAAT
2455473 ATATATAAT
1 ATATATAAT
2455482 ATATATAAT
1 ATATATAAT
*
2455491 GTATA
1 ATATA
2455496 CTCCTCATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:2457256 original size:182 final size:182
Alignment explanation
Indices: 2456946--2457580 Score: 1006
Period size: 182 Copynumber: 3.5 Consensus size: 182
2456936 TTTTTACTAT
* *
2456946 CGGTTTTGTCATTTCGAAACCGATTTTATCATATTTTTACCTGTTATATTATTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
2457011 ATTTTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
2457076 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTAC
* * * *
2457128 CGGTTTTGTCATTTCGAGACCGGTTTTGTTATATTTTTTCCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
2457193 ATTTTTATAAAGTATCGACAATTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
2457258 CGATACTTACAATAAAGTATCGACACTTTCAACATATCC-AGTAACGCTTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGA-TAGCGCTTTAC
* *
2457310 CGATTTTGTCATTTCGAGAACGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
2457375 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* * *
2457440 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAT
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTAC
* * * * *
2457492 CTGTTTTGTCATTTATG-GACCGGTTTTGTCAT-TTGTTTACATGTTATATTGTTATGGATCGAT
1 CGGTTTTGTCATTT-CGAGACCGATTTTATCATATT-TTTACCTGTTATATTGTTATGGATCGAT
2457555 ACATTTTTATAAAGTATCGACACTTT
64 ACATTTTTATAAAGTATCGACACTTT
2457581 CAATATATCC
Statistics
Matches: 414, Mismatches: 35, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
181 3 0.01
182 410 0.99
183 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTAC
Found at i:2457649 original size:112 final size:112
Alignment explanation
Indices: 2457451--2457914 Score: 757
Period size: 112 Copynumber: 4.1 Consensus size: 112
2457441 GATACTTATA
* * * *
2457451 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTATCTGTTTTGTCATTTATGGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2457516 TTTGTCATTTGTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
* *
2457563 ATAAAGTATCGACACTTTCAATATATCCGGCAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2457628 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
2457675 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2457740 TTTGTCATTTTTTTACATGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
* * *
2457787 ATAAAGTATCGACACTTTCAATATATCTGATAGCGCTTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2457852 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCA-TTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
*
2457900 ATAAAGTATCAACAC
1 ATAAAGTATCGACAC
2457915 AAACCAACAA
Statistics
Matches: 331, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 279 0.84
113 52 0.16
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTT
Found at i:2459244 original size:32 final size:31
Alignment explanation
Indices: 2459208--2459283 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
2459198 TTTTGTTGGA
* *
2459208 TTTAAGGGTTAAAATGATATTTTTAAT-TAAAG
1 TTTAAGGGTTAAAATGACA-TTTT-ATCTAAAC
** *
2459240 TTTAAATGTTAAATTGACATTTTATCTAAAC
1 TTTAAGGGTTAAAATGACATTTTATCTAAAC
*
2459271 TTTAAGGATTAAA
1 TTTAAGGGTTAAA
2459284 TTAAAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 2 0.06
31 18 0.51
32 15 0.43
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTAAGGGTTAAAATGACATTTTATCTAAAC
Found at i:2465790 original size:23 final size:23
Alignment explanation
Indices: 2465764--2465816 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2465754 CTTTAGTAAT
2465764 TAAATATAATTAACATAACCAAA
1 TAAATATAATTAACATAACCAAA
*
2465787 TAAATATAATTAACATAACCAAT
1 TAAATATAATTAACATAACCAAA
2465810 TAAATAT
1 TAAATAT
2465817 TTTGAAGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATATAATTAACATAACCAAA
Found at i:2466288 original size:14 final size:14
Alignment explanation
Indices: 2466269--2466299 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2466259 GATACTTGTA
*
2466269 TATTGGATAAATTG
1 TATTGGATAAAATG
2466283 TATTGGATAAAATG
1 TATTGGATAAAATG
2466297 TAT
1 TAT
2466300 GTAACTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (14 bp):
TATTGGATAAAATG
Found at i:2467377 original size:30 final size:30
Alignment explanation
Indices: 2467341--2467401 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2467331 AACGGGTGAT
2467341 ACATCCCCGAGCAAGAACAATATGAAGTTG
1 ACATCCCCGAGCAAGAACAATATGAAGTTG
2467371 ACATCCCCGAGCAAGAACAATATGAAGTTG
1 ACATCCCCGAGCAAGAACAATATGAAGTTG
2467401 A
1 A
2467402 TTTGTGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (30 bp):
ACATCCCCGAGCAAGAACAATATGAAGTTG
Found at i:2469115 original size:64 final size:64
Alignment explanation
Indices: 2469000--2469121 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
2468990 TTGTTTGAAG
* * **
2469000 GTGTATCGATGCACAGGTAGTGCATCGATGCACTCTTTTAAAATAGAAACATCGAATGCAATTA
1 GTGTATCGATGCAAAGGCAGTGCATCGATGCACTCTAATAAAATAGAAACATCGAATGCAATTA
*
2469064 GTGTATCGATGCATAAGGCA-TGCATCGATGCA-TCCTAATAATAATA-CAACATCGAATG
1 GTGTATCGATGCA-AAGGCAGTGCATCGATGCACT-CTAATAA-AATAGAAACATCGAATG
2469122 TATTTTATGC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 1 0.02
64 41 0.82
65 8 0.16
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCAAAGGCAGTGCATCGATGCACTCTAATAAAATAGAAACATCGAATGCAATTA
Found at i:2470438 original size:63 final size:63
Alignment explanation
Indices: 2470360--2470524 Score: 260
Period size: 63 Copynumber: 2.6 Consensus size: 63
2470350 GAGTTGAGGG
* *
2470360 TATACCTATGTTCTACGGAATATATGGACATAATTACCTATGTCTTTCGAGACATATGGACAC
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
* * *
2470423 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGATATATGGACAG
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
* *
2470486 TATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
2470525 GGTTCTTCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 7 0.07
63 88 0.93
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (63 bp):
TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
Found at i:2470530 original size:31 final size:31
Alignment explanation
Indices: 2470362--2470549 Score: 159
Period size: 31 Copynumber: 6.0 Consensus size: 31
2470352 GTTGAGGGTA
*
2470362 TACCTATGTTCTACGGAATATATGGACA-TAAT
1 TACCTATGTTCTACGGAACATATGGACAGT--T
* * *
2470394 TACCTATG-TCTTTC-GAGACATATGGACACTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
2470425 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
*** * *
2470457 TACCTATG-TCTTTTGAGATATATGGACAGTA
1 TACCTATGTTCTACGGA-ACATATGGACAGTT
*
2470488 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * * *
2470519 TACCTAGGTTCTTCGGAACCTATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
2470550 GCCGATGATC
Statistics
Matches: 125, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
31 76 0.61
32 48 0.38
33 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:2470577 original size:30 final size:30
Alignment explanation
Indices: 2470536--2470607 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2470526 GTTCTTCGGA
* * *
2470536 ACCTATGGATAGTTGCCGATGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
2470566 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
2470596 ACCTCTGGATAG
1 ACCTCTGGATAG
2470608 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:2474224 original size:7 final size:7
Alignment explanation
Indices: 2474212--2474236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2474202 TGTAAACTAT
2474212 GTGATAA
1 GTGATAA
2474219 GTGATAA
1 GTGATAA
2474226 GTGATAA
1 GTGATAA
2474233 GTGA
1 GTGA
2474237 CTATATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (7 bp):
GTGATAA
Found at i:2475135 original size:32 final size:32
Alignment explanation
Indices: 2475099--2475200 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
2475089 TCTACGGAAT
2475099 ATATGGACATAATTACCTATGTCTTTCGAGAC
1 ATATGGACATAATTACCTATGTCTTTCGAGAC
*
2475131 ATATGGACACT-A-TACCTATGT-TCTACG-GAAC
1 ATATGGACA-TAATTACCTATGTCT-TTCGAG-AC
* *
2475162 ATATGGACAGAATTACCTATGTCTTTTGAGAC
1 ATATGGACATAATTACCTATGTCTTTCGAGAC
2475194 ATATGGA
1 ATATGGA
2475201 TAGTATACCT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
30 2 0.03
31 24 0.41
32 30 0.51
33 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
ATATGGACATAATTACCTATGTCTTTCGAGAC
Found at i:2475156 original size:63 final size:63
Alignment explanation
Indices: 2475078--2475242 Score: 260
Period size: 63 Copynumber: 2.6 Consensus size: 63
2475068 GAGTTGAGGG
* *
2475078 TATACCTATGTTCTACGGAATATATGGACATAATTACCTATGTCTTTCGAGACATATGGACAC
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
* * *
2475141 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGATAG
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
* *
2475204 TATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
2475243 GGTTCTTCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 7 0.07
63 88 0.93
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (63 bp):
TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAC
Found at i:2475248 original size:31 final size:31
Alignment explanation
Indices: 2475080--2475267 Score: 159
Period size: 31 Copynumber: 6.0 Consensus size: 31
2475070 GTTGAGGGTA
*
2475080 TACCTATGTTCTACGGAATATATGGACA-TAAT
1 TACCTATGTTCTACGGAACATATGGACAGT--T
* * *
2475112 TACCTATG-TCTTTC-GAGACATATGGACACTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
2475143 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
*** * *
2475175 TACCTATG-TCTTTTGAGACATATGGATAGTA
1 TACCTATGTTCTACGGA-ACATATGGACAGTT
*
2475206 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * * *
2475237 TACCTAGGTTCTTCGGAACCTATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
2475268 GCCGAGGATC
Statistics
Matches: 125, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
31 76 0.61
32 48 0.38
33 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:2475306 original size:30 final size:30
Alignment explanation
Indices: 2475262--2475325 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2475252 GAACCTATGG
* *
2475262 ATAGTTGCCGAGGATCTTTATGACCTCTGA
1 ATAGTTACCAAGGATCTTTATGACCTCTGA
*
2475292 ATAGTTACCAAGGATCTTTATGACCTCTGG
1 ATAGTTACCAAGGATCTTTATGACCTCTGA
2475322 ATAG
1 ATAG
2475326 GTCCTTCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
ATAGTTACCAAGGATCTTTATGACCTCTGA
Found at i:2479859 original size:31 final size:31
Alignment explanation
Indices: 2479806--2479923 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
2479796 GTTCTACGGA
**
2479806 ACATATGGACAAAATTACCTATGTCTTTCGAG
1 ACATATGGACAGTA-TACCTATGTCTTTCGAG
* *
2479838 ATATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGTATACCTATGTCT-TTCGAG
* *
2479868 AACATATGGATAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGTA-TACCTATGTCTTTCGAG
*
2479901 ACATATGGACAATATACCTATGT
1 ACATATGGACAGTATACCTATGT
2479924 TCTAAGTAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.03
31 32 0.46
32 34 0.49
33 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTCTTTCGAG
Found at i:2479864 original size:63 final size:63
Alignment explanation
Indices: 2479786--2479942 Score: 260
Period size: 63 Copynumber: 2.5 Consensus size: 63
2479776 AGAGTCGAGG
*
2479786 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGATATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
* *
2479849 GTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
* * *
2479912 ATATACCTATGTTCTAAGTAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
2479943 GTTTACCTAG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:2479936 original size:31 final size:30
Alignment explanation
Indices: 2479787--2479971 Score: 142
Period size: 31 Copynumber: 5.9 Consensus size: 30
2479777 GAGTCGAGGG
2479787 TATACCTATGTTCTACGGAACATATGGACAA
1 TATACCTATGTTCTAC-GAACATATGGACAA
* * * *
2479818 AATTACCTATG-TCTTTCGAGATATATGGACAG
1 TA-TACCTATGTTC-TACGA-ACATATGGACAA
*
2479850 TATACCTATGTTCTACGGAACATATGGATAGA
1 TATACCTATGTTCTAC-GAACATATGGACA-A
*
2479882 -ATTACCTATG-TCTTTCGAGACATATGGACAA
1 TA-TACCTATGTTC-TACGA-ACATATGGACAA
* *
2479913 TATACCTATGTTCTAAGTAACATATGGACAG
1 TATACCTATGTTCTACG-AACATATGGACAA
* * * *
2479944 TTTACCTAGGTTCTTCGGAACCTATGGA
1 TATACCTATGTTCTAC-GAACATATGGA
2479972 TAGTTGCCGA
Statistics
Matches: 122, Mismatches: 19, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
31 72 0.59
32 50 0.41
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
TATACCTATGTTCTACGAACATATGGACAA
Found at i:2480004 original size:30 final size:30
Alignment explanation
Indices: 2479963--2480034 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2479953 GTTCTTCGGA
* * *
2479963 ACCTATGGATAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCGTTATG
*
2479993 ACGTCTGGATAGTTACCGAGGATCGTTATG
1 ACCTCTGGATAGTTACCGAGGATCGTTATG
2480023 ACCTCTGGATAG
1 ACCTCTGGATAG
2480035 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCGTTATG
Found at i:2480847 original size:100 final size:98
Alignment explanation
Indices: 2480673--2480913 Score: 304
Period size: 100 Copynumber: 2.4 Consensus size: 98
2480663 GGTGTTACAC
* * *
2480673 TACCGGTTTGTTTAAAGTTATAATATTAATGTAAAGGGTAAACTATTTACATCTTAACCAATTAA
1 TACCGGTTTGTTTAAAG-TATAATATTAATGTAAACGGTAAA-TATTTACAACTTAACCAATAAA
* * *
2480738 AATAGAATAGGCGTTACATATTACGTTAAACTAAA
64 AATAAAATAGACGCTACATATTACGTTAAACTAAA
**
2480773 TACCGGTTTGTTTAAATGTATAATATTAATGTAAACGGTCAAATATTTACAACTTAACCGGTAAA
1 TACCGGTTTGTTTAAA-GTATAATATTAATGTAAACGGT-AAATATTTACAACTTAACCAATAAA
* **
2480838 AATAAAATAGACGCTACCTATTACGTTAAACTATC
64 AATAAAATAGACGCTACATATTACGTTAAACTAAA
* * *
2480873 TACCGGTTTGTTTGAAGGT-TAATAATAATGTAAACAGTAAA
1 TACCGGTTTGTTT-AAAGTATAATATTAATGTAAACGGTAAA
2480914 ATAAAATAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
98 3 0.02
99 17 0.14
100 98 0.79
101 6 0.05
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (98 bp):
TACCGGTTTGTTTAAAGTATAATATTAATGTAAACGGTAAATATTTACAACTTAACCAATAAAAA
TAAAATAGACGCTACATATTACGTTAAACTAAA
Found at i:2480920 original size:75 final size:76
Alignment explanation
Indices: 2480836--2480992 Score: 217
Period size: 75 Copynumber: 2.1 Consensus size: 76
2480826 TTAACCGGTA
* * * * * *
2480836 AAAATAAAATAGACGCTACCTATTACGTTAAACTATCTACCGGTTTGTTTGAAGGT-TAATAATA
1 AAAATAAAATAAACGCTACATATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATAATA
*
2480900 ATGTAAACAGT
66 ATGTAAACAAT
* *
2480911 AAAATAAAATAAATGCTACATATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATATTA
1 AAAATAAAATAAACGCTACATATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATAATA
*
2480976 TTGTAAACAAT
66 ATGTAAACAAT
2480987 AAAATA
1 AAAATA
2480993 TTTACAACTT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 49 0.69
76 22 0.31
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (76 bp):
AAAATAAAATAAACGCTACATATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATAATA
ATGTAAACAAT
Found at i:2481133 original size:75 final size:75
Alignment explanation
Indices: 2481010--2481239 Score: 302
Period size: 75 Copynumber: 3.1 Consensus size: 75
2481000 CTTAACCGGT
* * * *
2481010 TAAAATAAAATAGGAGATATCTATTACGTTAAATTACCTACTGGTTTGTTTAAAAGTTAATAATA
1 TAAAATAAAATAGGAGCTATCTATTACGTTAAACTAGCTACTGATTTGTTTAAAAGTTAATAATA
2481075 ATGTAAACGG
66 ATGTAAACGG
* * * *
2481085 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAGCTA-TCAATTTGTTTAAAGGTTAATAAT
1 TAAAATAAAATAGGAGCTATCTATTACGTTAAACTAGCTACT-GATTTGTTTAAAAGTTAATAAT
*
2481149 AATGTAAACAG
65 AATGTAAACGG
* * * *
2481160 TAAAATAAAACA-AACACTATCTATTACGTTAAACTAGCTACTGATTTGTTAAAAAGTATAATAA
1 TAAAATAAAATAGGA-GCTATCTATTACGTTAAACTAGCTACTGATTTGTTTAAAAGT-TAATAA
2481224 TAATGTAAACGG
64 TAATGTAAACGG
2481236 TAAA
1 TAAA
2481240 CTATTTACAA
Statistics
Matches: 133, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
74 1 0.01
75 110 0.83
76 22 0.17
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGGAGCTATCTATTACGTTAAACTAGCTACTGATTTGTTTAAAAGTTAATAATA
ATGTAAACGG
Found at i:2481286 original size:250 final size:251
Alignment explanation
Indices: 2480831--2481343 Score: 683
Period size: 250 Copynumber: 2.0 Consensus size: 251
2480821 ACAACTTAAC
* ** *
2480831 CGGTAAAAATAAAATAGACGCTACCTATTACGTTAAACTATCTACCGGTTTGTTTGAAGGTTAAT
1 CGGT-AAAATAAAATAGACGCTACCTATTACGTTAAACTAGCTACCAATTTGTTTAAAGGTTAAT
* ** *
2480896 AATAATGTAAACAGTAAAATAAAATAAATGCTACATATTACGTTAAACTACCTACCGGTTTGTGT
65 AATAATGTAAACAGTAAAATAAAACAAACACTACATATTACGTTAAACTACCTACCGATTTGTGT
* * **
2480961 AAAAGTATAATATTATTGTAAACAATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGAG
130 AAAAGTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCAATTAAAATAAAATAGGAG
* * * *
2481026 ATATCTATTACGTTAAATTACCTA-CTGGTTTGTTTAAAAGT-TAATAATAATGTAAA
195 ATACCTATTACGTTAAACTACCTAGC-AGTTTATTTAAAAGTATAATAATAATGTAAA
** *
2481082 CGGTAAAATAAAATAGGTGCTACCTATTACGTTAAACTAGCTATCAATTTGTTTAAAGGTTAATA
1 CGGTAAAATAAAATAGACGCTACCTATTACGTTAAACTAGCTACCAATTTGTTTAAAGGTTAATA
* *
2481147 ATAATGTAAACAGTAAAATAAAACAAACACTATC-TATTACGTTAAACTAGCTACTGATTTGT-T
66 ATAATGTAAACAGTAAAATAAAACAAACACTA-CATATTACGTTAAACTACCTACCGATTTGTGT
** * * * *
2481210 AAAAAGTATAATAATAATGTAAACGGTAAACTATTTACAACTTAACCAATTAAAATAGAATATGT
130 -AAAAGTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCAATTAAAATAAAATAGGA
* * *
2481275 GTTACCTATTACGTTAAACTACCTAGCAGTTTATTTAAATGTATAATATTAATGTAAA
194 GATACCTATTACGTTAAACTACCTAGCAGTTTATTTAAAAGTATAATAATAATGTAAA
*
2481333 CGGTGAAATAA
1 CGGTAAAATAA
2481344 TTATAACTTA
Statistics
Matches: 227, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
249 1 0.00
250 196 0.86
251 30 0.13
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (251 bp):
CGGTAAAATAAAATAGACGCTACCTATTACGTTAAACTAGCTACCAATTTGTTTAAAGGTTAATA
ATAATGTAAACAGTAAAATAAAACAAACACTACATATTACGTTAAACTACCTACCGATTTGTGTA
AAAGTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCAATTAAAATAAAATAGGAGA
TACCTATTACGTTAAACTACCTAGCAGTTTATTTAAAAGTATAATAATAATGTAAA
Found at i:2481391 original size:350 final size:349
Alignment explanation
Indices: 2480931--2481588 Score: 894
Period size: 350 Copynumber: 1.9 Consensus size: 349
2480921 AAATGCTACA
* * * *
2480931 TATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATATTATTGTAAACAATAAAATATTT
1 TATTACGTTAAACTACCTACCAGTTTATGTAAAAGTATAATATTAATGTAAACAATAAAATAATT
** * * * **
2480996 ACAACTTAACCGGTTAAAATAAAATAGGAGATATCTATTACGTTAAATTACCTA-CTGGTTTGTT
66 ACAACTTAACCGAATAAAATAAAATAGGAGATACCTATCACGTTAAACTACCTATC-AATTTGTT
* * * * *
2481060 TAAA-AGTTAATAATAATGTAAACGGTAAAATAAAATAGGTGCTACCTATTACGTTAAACTAGCT
130 TAAAGA-TTAATAATAATGAAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTACCT
* *
2481124 A-TCAATTTGTTTAAAGGTTAATAATAATGTAAAC-AGTAAAATAAAACAAACACTATCTATTAC
194 ACT-AATTCGTTTAAAGGTTAATAATAATGTAAACGA-TAAAATAAAACAAACACTACCTATTAC
*
2481187 GTTAAACTAGCTACT-GATTTGTTAAAAAGTATAATAATAATGTAAACGGTAAACTATTTACAAC
257 GTTAAACAAGCTACTAG-TTTGTTAAAAAGT-TAATAATAATGTAAACGGTAAACTATTTACAAC
2481251 TTAACCAATTAAAATAGAATATGTGTTACC
320 TTAACCAATTAAAATAGAATATGTGTTACC
* * * ** *
2481281 TATTACGTTAAACTACCTAGCAGTTTATTTAAATGTATAATATTAATGTAAACGGTGAAATAATT
1 TATTACGTTAAACTACCTACCAGTTTATGTAAAAGTATAATATTAATGTAAACAATAAAATAATT
* * * * **
2481346 ATAACTTAACCGAATAGAATAAAATAGGCGCTACCTATCACGTTAAACTATTTATCAATTTGTTT
66 ACAACTTAACCGAATAAAATAAAATAGGAGATACCTATCACGTTAAACTACCTATCAATTTGTTT
*
2481411 AAAGATTAATAATAATGAAAACAGTAAAATAAAATAGGCGCTACATATTACTTTAAACTACCTAC
131 AAAGATTAATAATAATGAAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTAC
** * *
2481476 TGGTTCGTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAATAGACACTACCTATTACGTTA
196 TAATTCGTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAACAAACACTACCTATTACGTTA
*
2481541 AACAAGCTACTAGTTTGTTTAAAAGTTAATAATAATGTAAACGGTAAA
261 AACAAGCTACTAGTTTGTTAAAAAGTTAATAATAATGTAAACGGTAAA
2481589 ATAAAATATG
Statistics
Matches: 266, Mismatches: 37, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
349 22 0.08
350 239 0.90
351 5 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (349 bp):
TATTACGTTAAACTACCTACCAGTTTATGTAAAAGTATAATATTAATGTAAACAATAAAATAATT
ACAACTTAACCGAATAAAATAAAATAGGAGATACCTATCACGTTAAACTACCTATCAATTTGTTT
AAAGATTAATAATAATGAAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTAC
TAATTCGTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAACAAACACTACCTATTACGTTA
AACAAGCTACTAGTTTGTTAAAAAGTTAATAATAATGTAAACGGTAAACTATTTACAACTTAACC
AATTAAAATAGAATATGTGTTACC
Found at i:2481412 original size:100 final size:100
Alignment explanation
Indices: 2481180--2481438 Score: 258
Period size: 100 Copynumber: 2.6 Consensus size: 100
2481170 CAAACACTAT
* * * * *
2481180 CTATTACGTTAAACTAGCTA-CTGATTTGTTAAAAAGTATAATAATAATGTAAACGGTAAACTAT
1 CTATCACGTTAAACTACCTAGC-AATTTGTTTAAAAGTATAATAATAATGTAAACGGTAAACTAA
* * * *
2481244 TTACAACTTAACCAATTAAAATAGAATATGTGTTAC
65 TTACAACTTAACCAATTAAAATAAAATAGGCGCTAC
* * * * *
2481280 CTATTACGTTAAACTACCTAGCAGTTTATTTAAATGTATAATATTAATGTAAACGGTGAAA-TAA
1 CTATCACGTTAAACTACCTAGCAATTTGTTTAAAAGTATAATAATAATGTAAACGGT-AAACTAA
* *
2481344 TTATAACTTAACCGAA-TAGAATAAAATAGGCGCTAC
65 TTACAACTTAACC-AATTAAAATAAAATAGGCGCTAC
** * * *
2481380 CTATCACGTTAAACTATTTATCAATTTGTTT-AAAG-ATTAATAATAATGAAAACAGTAAA
1 CTATCACGTTAAACTACCTAGCAATTTGTTTAAAAGTA-TAATAATAATGTAAACGGTAAA
2481439 ATAAAATAGG
Statistics
Matches: 131, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
98 4 0.03
99 19 0.15
100 102 0.78
101 6 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (100 bp):
CTATCACGTTAAACTACCTAGCAATTTGTTTAAAAGTATAATAATAATGTAAACGGTAAACTAAT
TACAACTTAACCAATTAAAATAAAATAGGCGCTAC
Found at i:2481452 original size:75 final size:74
Alignment explanation
Indices: 2481363--2481639 Score: 306
Period size: 75 Copynumber: 3.7 Consensus size: 74
2481353 AACCGAATAG
* ** *
2481363 AATAAAATAGGCGCTACCTATCACGTTAAACTATTTA-TCAATTTGTTTAAAGATTAATAATAAT
1 AATAAAATAGGCGCTACCTATTACGTTAAACTACCTACT-AGTTTGTTTAAAGATTAATAATAAT
*
2481427 GAAAACAGTAA
65 GTAAAC-GTAA
* * * * *
2481438 AATAAAATAGGCGCTACATATTACTTTAAACTACCTACTGGTTCGTTTAAAGGTTAATAATAATG
1 AATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTAGTTTGTTTAAAGATTAATAATAATG
2481503 TAAACGATAA
66 TAAACG-TAA
* * * *
2481513 AATAAAATAGACACTACCTATTACGTTAAACAAGCTACTAGTTTGTTTAAA-AGTTAATAATAAT
1 AATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTAGTTTGTTTAAAGA-TTAATAATAAT
2481577 GTAAACGGTAA
65 GTAAAC-GTAA
* * * * * * *
2481588 AATAAAATATGTGGTACTTATTACGTTAAACTAACTACCAGTTTGTTAAAAG
1 AATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTAGTTTGTTTAAAG
2481640 GTATAAAATA
Statistics
Matches: 168, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
74 1 0.01
75 165 0.98
76 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (74 bp):
AATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTAGTTTGTTTAAAGATTAATAATAATG
TAAACGTAA
Found at i:2481469 original size:175 final size:175
Alignment explanation
Indices: 2480735--2481517 Score: 596
Period size: 175 Copynumber: 4.5 Consensus size: 175
2480725 CTTAACCAAT
* * * ** *
2480735 TAAAATAGAATAGGCGTTACATATTACGTTAAACTAAATACCGGTTTGTTTAAATGTATAATATT
1 TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
* * *
2480800 AATGTAAACGGTCAAATATTTACAACTTAACCGGTAA-A-AATAAAATAGACGCTACCTATTACG
66 AATGTAAACGGTAAAATAATTACAACTTAACC-G-AATAGAATAAAATAGGCGCTACCTATTACG
* ** * *
2480863 TTAAACTATCTACCGGTTTGTTTGAAGGTTAATAATAATGTAAACAG
129 TTAAACTATCTATCAATTTGTTTAAAGATTAATAATAATGTAAACAG
** * *
2480910 TAAAATAAAATAAATGCTACATATTACGTTAAACTACCTACCGGTTTGTGTAAAAGTATAATATT
1 TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
* ** * ** * * * *
2480975 ATTGTAAACAATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGAGATATCTATTACGTT
66 AATGTAAACGGTAAAATAATTACAACTTAACCGAATAGAATAAAATAGGCGCTACCTATTACGTT
* * ** *
2481040 AAATTACCTA-CTGGTTTGTTTAAA-AGTTAATAATAATGTAAACGG
131 AAACTATCTATC-AATTTGTTTAAAGA-TTAATAATAATGTAAACAG
* * * ** *
2481085 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAGCTATCAATTTGTTTAAAGGT-TAATAAT
1 TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
* * * * * * * *
2481149 AATGTAAACAGTAAAATAA-AACAAACACT-ATCTATTACG-TTAAACTA---GCTA-CTGATT-
66 AATGTAAACGGTAAAATAATTAC-AAC-TTAACCGAATA-GAATAAAATAGGCGCTACCT-ATTA
* * * * * * * * *
2481206 TGTTAAAAAGTAT-AAT-AATAATG--TAAACGGTAAACTATTTACAACT-TAACCAAT
127 CGTT--AAACTATCTATCAAT-TTGTTTAAA-GATTAA-TA---ATAA-TGTAAAC-AG
* * * * * * * *
2481260 TAAAATAGAATATGTGTTACCTATTACGTTAAACTACCTAGCAGTTTATTTAAATGTATAATATT
1 TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
* * *
2481325 AATGTAAACGGTGAAATAATTATAACTTAACCGAATAGAATAAAATAGGCGCTACCTATCACGTT
66 AATGTAAACGGTAAAATAATTACAACTTAACCGAATAGAATAAAATAGGCGCTACCTATTACGTT
* *
2481390 AAACTATTTATCAATTTGTTTAAAGATTAATAATAATGAAAACAG
131 AAACTATCTATCAATTTGTTTAAAGATTAATAATAATGTAAACAG
* * * * *
2481435 TAAAATAAAATAGGCGCTACATATTACTTTAAACTACCTACTGGTTCGTTTAAAGGT-TAATAAT
1 TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
*
2481499 AATGTAAACGATAAAATAA
66 AATGTAAACGGTAAAATAA
2481518 AATAGACACT
Statistics
Matches: 470, Mismatches: 104, Indels: 69
0.73 0.16 0.11
Matches are distributed among these distances:
169 4 0.01
170 9 0.02
171 11 0.02
172 5 0.01
173 2 0.00
174 69 0.15
175 292 0.62
176 43 0.09
177 1 0.00
178 6 0.01
179 12 0.03
180 12 0.03
181 4 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (175 bp):
TAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATATT
AATGTAAACGGTAAAATAATTACAACTTAACCGAATAGAATAAAATAGGCGCTACCTATTACGTT
AAACTATCTATCAATTTGTTTAAAGATTAATAATAATGTAAACAG
Found at i:2481640 original size:150 final size:150
Alignment explanation
Indices: 2481363--2481649 Score: 355
Period size: 150 Copynumber: 1.9 Consensus size: 150
2481353 AACCGAATAG
* * * **
2481363 AATAAAATAGGCGCTACCTATCACGTTAAACTATTTATCAATTTGTTTAAAGATTAATAATAATG
1 AATAAAATAGACACTACCTATCACGTTAAACAAGCTATCAATTTGTTTAAAGATTAATAATAATG
* * ** *
2481428 AAAACAGTAAAATAAAATAGGCGCTACATATTACTTTAAACTACCTACTGGTTCGTTTAAAGGT-
66 AAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTAACTACCAGTTCGTTAAAAGGTA
2481492 TAATAATAATGTAAACGATAA
131 TAA-AATAATGTAAACGATAA
* *
2481513 AATAAAATAGACACTACCTATTACGTTAAACAAGCTA-CTAGTTTGTTTAAA-AGTTAATAATAA
1 AATAAAATAGACACTACCTATCACGTTAAACAAGCTATC-AATTTGTTTAAAGA-TTAATAATAA
* * * * * * *
2481576 TGTAAACGGTAAAATAAAATATGTGGTACTTATTACGTTAAACTAACTACCAGTTTGTTAAAAGG
64 TGAAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTAACTACCAGTTCGTTAAAAGG
2481641 TATAAAATA
129 TATAAAATA
2481650 TTTACAACTT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
149 2 0.02
150 110 0.96
151 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (150 bp):
AATAAAATAGACACTACCTATCACGTTAAACAAGCTATCAATTTGTTTAAAGATTAATAATAATG
AAAACAGTAAAATAAAATAGGCGCTACATATTACGTTAAACTAACTACCAGTTCGTTAAAAGGTA
TAAAATAATGTAAACGATAA
Found at i:2487610 original size:2 final size:2
Alignment explanation
Indices: 2487603--2487638 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2487593 TGCCATTCGG
2487603 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
2487639 GTGTTAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2489316 original size:13 final size:15
Alignment explanation
Indices: 2489289--2489325 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2489279 CGATCTCCAA
2489289 TTTTCATTTGAC-TTT
1 TTTTC-TTTGACTTTT
2489304 TTTTCTTTG-CTTTT
1 TTTTCTTTGACTTTT
2489318 TTTTCTTT
1 TTTTCTTT
2489326 TTGCTGCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.71
15 5 0.24
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTCTTTGACTTTT
Found at i:2504233 original size:18 final size:19
Alignment explanation
Indices: 2504210--2504247 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2504200 CCCAGTAATC
2504210 TTATTCCC-TGGTAATCTT
1 TTATTCCCATGGTAATCTT
2504228 TTATTCCCATTGGTAATCTT
1 TTATTCCCA-TGGTAATCTT
2504248 ACATTCTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (19 bp):
TTATTCCCATGGTAATCTT
Found at i:2505670 original size:2 final size:2
Alignment explanation
Indices: 2505663--2505693 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2505653 GCATGAAGGC
2505663 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2505694 AAACCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:2507480 original size:16 final size:14
Alignment explanation
Indices: 2507448--2507475 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2507438 CACATTATGC
2507448 ATACATTTAACAGA
1 ATACATTTAACAGA
2507462 ATACATTTAACAGA
1 ATACATTTAACAGA
2507476 GAATAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
ATACATTTAACAGA
Found at i:2519802 original size:11 final size:10
Alignment explanation
Indices: 2519782--2519819 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
2519772 TTCATGGATT
2519782 TTAAAA-AAA
1 TTAAAATAAA
2519791 TTTAAAATAAA
1 -TTAAAATAAA
2519802 TTAAACATAAA
1 TTAAA-ATAAA
2519813 TTAAAAT
1 TTAAAAT
2519820 TTTGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:2520824 original size:2 final size:2
Alignment explanation
Indices: 2520817--2520843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2520807 TCAAGAGAAA
2520817 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2520844 TGGGGAGAGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2523175 original size:2 final size:2
Alignment explanation
Indices: 2523168--2523204 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2523158 AGAACATAGC
2523168 TA TA TA TA TA TA TA 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 TA T
2523205 TGTGATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2524246 original size:17 final size:17
Alignment explanation
Indices: 2524224--2524260 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2524214 GGTCTGACCC
2524224 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
2524241 GACCCGACTCGACCGTT
1 GACCCGACCCGACCGTT
2524258 GAC
1 GAC
2524261 AGTTGACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:2524267 original size:7 final size:7
Alignment explanation
Indices: 2524251--2524282 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2524241 GACCCGACTC
2524251 GACCGTT
1 GACCGTT
*
2524258 GACAGTT
1 GACCGTT
2524265 GACCGTT
1 GACCGTT
2524272 GACCGTT
1 GACCGTT
2524279 GACC
1 GACC
2524283 ACCTTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:2531412 original size:19 final size:20
Alignment explanation
Indices: 2531388--2531444 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
2531378 GCTGGAATTG
*
2531388 ACCGGTTTGACCGGTTC-GA
1 ACCGGTTTGATCGGTTCTGA
*
2531407 ACCGGTCTGATCGG-TCTGA
1 ACCGGTTTGATCGGTTCTGA
*
2531426 ACCCGTTTGATCGG-TCTGA
1 ACCGGTTTGATCGGTTCTGA
2531445 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 2 0.06
19 31 0.94
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (20 bp):
ACCGGTTTGATCGGTTCTGA
Found at i:2531478 original size:17 final size:17
Alignment explanation
Indices: 2531442--2531480 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2531432 TTGATCGGTC
*
2531442 TGACCCGACCCGACCAT
1 TGACCCGACCCGAACAT
*
2531459 TGACCCGACCCGAACGT
1 TGACCCGACCCGAACAT
2531476 TGACC
1 TGACC
2531481 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGAACAT
Found at i:2533693 original size:8 final size:9
Alignment explanation
Indices: 2533674--2533704 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2533664 ACCAATATTT
*
2533674 AAAATATAA
1 AAAAAATAA
2533683 AAAAAATAA
1 AAAAAATAA
2533692 AAAAAATAA
1 AAAAAATAA
2533701 AAAA
1 AAAA
2533705 TCATATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2535292 original size:21 final size:21
Alignment explanation
Indices: 2535263--2535307 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2535253 ATTCTGACTA
2535263 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2535284 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
2535305 TCG
1 TCG
2535308 AAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2535337 original size:20 final size:20
Alignment explanation
Indices: 2535309--2535398 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
2535299 CCTAATTCGA
2535309 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** * *
2535329 AACGCGAATTTGGAAAATTGC
1 AATGCGAA-TACGTAAATCGC
*
2535350 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
2535370 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
2535390 AATGCGAAT
1 AATGCGAAT
2535399 TTGACTATCG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:2535625 original size:22 final size:22
Alignment explanation
Indices: 2535599--2535660 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
2535589 ACATCCGTTC
2535599 CCATCTCCGACGAAATCAGTC-
1 CCATCTCCGACGAAATCAGTCT
* *
2535620 CTCATCGCCGACGATATCAGTCT
1 C-CATCTCCGACGAAATCAGTCT
*
2535643 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
2535661 TTCACGGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:2536056 original size:20 final size:20
Alignment explanation
Indices: 2536012--2536085 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
2536002 GTGATTTTCA
*
2536012 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
2536032 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * **
2536052 TTTCGTGTTGTGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
*
2536072 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
2536086 TTAAAGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2536086 original size:20 final size:20
Alignment explanation
Indices: 2535998--2536087 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
2535988 GCGATTCTGC
*
2535998 CGTTGTGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
2536017 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
2536037 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
2536057 TGTTGTGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2536077 TGTTGCGATTT
1 CGTTGCGATTT
2536088 AAAGTTTCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 11 0.19
20 48 0.81
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2536095 original size:20 final size:20
Alignment explanation
Indices: 2536052--2536095 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2536042 CGATAGTCAT
* ** *
2536052 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
2536072 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
2536092 TTTC
1 TTTC
2536096 ATAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:2537984 original size:20 final size:20
Alignment explanation
Indices: 2537959--2538094 Score: 86
Period size: 20 Copynumber: 7.5 Consensus size: 20
2537949 AGAATAGTTT
2537959 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2537979 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
2537999 ACTATCGTAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2538015 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
*
2538032 A-AATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
2538047 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** **
2538065 ACTATCGCTGTGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2538085 ACTATCGCAA
1 ACTATCGCAA
2538095 CGAAAGAATC
Statistics
Matches: 92, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
14 13 0.14
15 1 0.01
16 11 0.12
17 8 0.09
18 10 0.11
20 49 0.53
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2538107 original size:86 final size:87
Alignment explanation
Indices: 2537962--2538126 Score: 260
Period size: 86 Copynumber: 1.9 Consensus size: 87
2537952 ATAGTTTACT
* *
2537962 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGTAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
2538027 AAATG-AAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
*** **
2538048 ATCGCAATGCGAAAATGACTATCGCTGTGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
2538113 AAATGAAAATCGCA
66 AAATGAAAATCGCA
2538127 TTGCGATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 63 0.89
87 8 0.11
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (87 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:2538160 original size:34 final size:36
Alignment explanation
Indices: 2538122--2538208 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 36
2538112 GAAATGAAAA
2538122 TCGCATTGCGATTC-TCTCG-TTGCGATAGTCATTT
1 TCGCATTGCGATTCATCTCGATTGCGATAGTCATTT
*
2538156 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGAT--TCA-TCTCG-ATTGCGATAGTCATTT
*
2538196 TCGCGTTGCGATT
1 TCGCATTGCGATT
2538209 TTGTTGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
34 12 0.27
36 2 0.04
38 5 0.11
40 26 0.58
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (36 bp):
TCGCATTGCGATTCATCTCGATTGCGATAGTCATTT
Found at i:2538166 original size:20 final size:20
Alignment explanation
Indices: 2538141--2538207 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
2538131 GATTCTCTCG
2538141 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2538161 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2538181 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2538201 TTGCGAT
1 TTGCGAT
2538208 TTTGTTGTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2538219 original size:34 final size:33
Alignment explanation
Indices: 2538122--2538221 Score: 92
Period size: 40 Copynumber: 2.8 Consensus size: 33
2538112 GAAATGAAAA
* *
2538122 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATT-TTTTGTTGCGATAGTCATTT
2538156 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGAT--T--TTTT-G--TTGCGATAGTCATTT
*
2538196 TCGCGTTGCGATTTTGTTGTTGCGAT
1 TCGCATTGCGATTTT-TTGTTGCGAT
2538222 TTTTATTTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
34 19 0.35
36 4 0.07
37 4 0.07
38 2 0.04
40 26 0.47
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTTTGTTGCGATAGTCATTT
Found at i:2538832 original size:21 final size:21
Alignment explanation
Indices: 2538767--2538842 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
2538757 GGCATCCCCT
*
2538767 ATCATTCAAGAGGCCTCTATC
1 ATCATTCAAGAGGCCACTATC
** * * **
2538788 ATCCCTCAAGAGTCCCCTCCC
1 ATCATTCAAGAGGCCACTATC
*
2538809 ATCATTCAAGAGGCCACTGTC
1 ATCATTCAAGAGGCCACTATC
* *
2538830 ATCTTTGAAGAGG
1 ATCATTCAAGAGG
2538843 TCCCTCCCAA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCATTCAAGAGGCCACTATC
Found at i:2538841 original size:42 final size:42
Alignment explanation
Indices: 2538767--2538862 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
2538757 GGCATCCCCT
*
2538767 ATCATTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCCCTCCC
1 ATCATTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCC
* ** *
2538809 ATCATTCAAGAGGCCACTGTCATCTTTGAAGAGGTCCCTCCC
1 ATCATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCC
* *
2538851 AACATTCTAGAG
1 ATCATTCAAGAG
2538863 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (42 bp):
ATCATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCC
Found at i:2540249 original size:14 final size:14
Alignment explanation
Indices: 2540230--2540264 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2540220 ATTGTTTAAT
2540230 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2540244 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2540258 TGATTTG
1 TGATTTG
2540265 CTTAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2540459 original size:34 final size:33
Alignment explanation
Indices: 2540371--2540466 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
2540361 AAAACAGACT
* **
2540371 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
2540405 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2540438 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2540467 CGAAACTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2540462 original size:20 final size:19
Alignment explanation
Indices: 2540404--2540471 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
2540394 GCAACGAGAG
2540404 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2540423 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2540437 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2540457 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2540472 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2540501 original size:20 final size:20
Alignment explanation
Indices: 2540476--2540569 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
2540466 GCGAAACTAA
2540476 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
*
2540496 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
* *
2540516 TTCCGCATTGCGATAGTCA-
1 TTTCGCGTTGCGATAGTCAT
*
2540535 TTTCTGTGTTGCGATAGTCAT
1 TTTC-GCGTTGCGATAGTCAT
*
2540556 ATTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2540570 TTCCGCGTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.05
20 58 0.91
21 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2543033 original size:24 final size:24
Alignment explanation
Indices: 2542999--2543052 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2542989 CTGAAAAATC
2542999 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2543023 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2543047 ATCAAA
1 ATCAAA
2543053 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2543901 original size:20 final size:20
Alignment explanation
Indices: 2543876--2543919 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2543866 AAATTCAGTA
*
2543876 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2543896 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
2543916 TTGC
1 TTGC
2543920 AATTTACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2543932 original size:20 final size:20
Alignment explanation
Indices: 2543909--2544005 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
2543899 CGATAGTCAG
*
2543909 ATTCGCGTTGCAATTTACAT
1 ATTCGCATTGCAATTTACAT
* *
2543929 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCAATTTACAT
* * * *
2543949 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGC-AATTTACAT
* *
2543970 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCAATTTACAT
2543990 ATTCGCATTGCGAATT
1 ATTCGCATTGC-AATT
2544006 AGGAAAATCG
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
20 42 0.71
21 17 0.29
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCAATTTACAT
Found at i:2544017 original size:41 final size:41
Alignment explanation
Indices: 2543931--2544017 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
2543921 ATTTACATAT
* * *
2543931 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
* **
2543972 TCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
2544013 TCGCA
1 TCGCA
2544018 ACGCGAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
Found at i:2548384 original size:11 final size:11
Alignment explanation
Indices: 2548368--2548424 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
2548358 AAAATTACAT
2548368 TATTAAAAATA
1 TATTAAAAATA
2548379 TATTAAAAATA
1 TATTAAAAATA
* **
2548390 AATTATTAATA
1 TATTAAAAATA
*
2548401 -ATTATAAAT-
1 TATTAAAAATA
*
2548410 TTTTAAAAATA
1 TATTAAAAATA
2548421 TATT
1 TATT
2548425 TTTAAATGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 15 0.41
11 22 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2548427 original size:14 final size:14
Alignment explanation
Indices: 2548381--2548430 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
2548371 TAAAAATATA
*
2548381 TTAAAAATAAATTA
1 TTAAAAATAAATTT
2548395 TTAATAATTATAAATTT
1 TTAA-AA--ATAAATTT
*
2548412 TTAAAAATATATTT
1 TTAAAAATAAATTT
2548426 TTAAA
1 TTAAA
2548431 TGTAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAAATAAATTT
Found at i:2555169 original size:2 final size:2
Alignment explanation
Indices: 2555162--2555202 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2555152 GTTGGGCTTT
2555162 TA TA TA TA TA TA TA TA TA 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 TA TA TA T
2555203 TTGTTGGACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2556993 original size:29 final size:30
Alignment explanation
Indices: 2556944--2557017 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
2556934 GTCGGGTCAG
* **
2556944 ACCGGTCAAACCGGTTTGAACCAGTTG-AA
1 ACCGGTTAAACCGGTCAGAACCAGTTGAAA
* * *
2556973 ATCGGTTAAATCGGTCAGAACCGGTTGAAA
1 ACCGGTTAAACCGGTCAGAACCAGTTGAAA
2557003 ACCGGTTAAACCGGT
1 ACCGGTTAAACCGGT
2557018 TTCCAGCAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (30 bp):
ACCGGTTAAACCGGTCAGAACCAGTTGAAA
Found at i:2557015 original size:9 final size:9
Alignment explanation
Indices: 2556944--2557018 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
2556934 GTCGGGTCAG
*
2556944 ACCGGTCAA
1 ACCGGTTAA
*
2556953 ACCGGTTTGA
1 ACCGG-TTAA
*
2556963 ACCAGTTGAA
1 ACCGGTT-AA
*
2556973 ATCGGTTAA
1 ACCGGTTAA
* *
2556982 ATCGGTCAGA
1 ACCGGTTA-A
2556992 ACCGGTTGAAA
1 ACCGGTT--AA
2557003 ACCGGTTAA
1 ACCGGTTAA
2557012 ACCGGTT
1 ACCGGTT
2557019 TCCAGCAGCC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 25 0.48
10 18 0.35
11 8 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:2564201 original size:7 final size:7
Alignment explanation
Indices: 2564189--2564219 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2564179 GTCAAAGAAA
2564189 GTCAACG
1 GTCAACG
2564196 GTCAACG
1 GTCAACG
*
2564203 GTCAATG
1 GTCAACG
2564210 GTCAACG
1 GTCAACG
2564217 GTC
1 GTC
2564220 CGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:2564237 original size:22 final size:22
Alignment explanation
Indices: 2564209--2564251 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2564199 AACGGTCAAT
*
2564209 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGATCCGGTCGGGTCG
*
2564231 GGTCAACGATCGGGTCGGGTC
1 GGTCAACGATCCGGTCGGGTC
2564252 AAACCGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.19
Consensus pattern (22 bp):
GGTCAACGATCCGGTCGGGTCG
Found at i:2564262 original size:9 final size:9
Alignment explanation
Indices: 2564248--2564327 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
2564238 GATCGGGTCG
2564248 GGTCAAACC
1 GGTCAAACC
2564257 GGTCAAACC
1 GGTCAAACC
* *
2564266 TGTTCAGACC
1 -GGTCAAACC
2564276 GGTCAAACC
1 GGTCAAACC
*
2564285 GGTTGAAACC
1 GG-TCAAACC
2564295 GGTCAGAACC
1 GGTCA-AACC
*
2564305 GGTTGAAAACC
1 GG-T-CAAACC
*
2564316 GGTTAAACC
1 GGTCAAACC
2564325 GGT
1 GGT
2564328 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
9 28 0.48
10 22 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2564278 original size:19 final size:19
Alignment explanation
Indices: 2564250--2564328 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 19
2564240 TCGGGTCGGG
*
2564250 TCAAACCGGTCAAACCTGT
1 TCAAACCGGTCAAACCGGT
*
2564269 TCAGACCGGTCAAACCGGT
1 TCAAACCGGTCAAACCGGT
*
2564288 TGAAACCGGTCAGAACCGGT
1 TCAAACCGGTCA-AACCGGT
* *
2564308 TGAAAACCGGTTAAACCGGT
1 T-CAAACCGGTCAAACCGGT
2564328 T
1 T
2564329 TCCAGCAGCC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
19 27 0.52
20 16 0.31
21 9 0.17
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (19 bp):
TCAAACCGGTCAAACCGGT
Found at i:2564317 original size:11 final size:10
Alignment explanation
Indices: 2564280--2564328 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
2564270 CAGACCGGTC
2564280 AAACCGGTTG
1 AAACCGGTTG
*
2564290 AAACCGG-TC
1 AAACCGGTTG
2564299 AGAACCGGTTG
1 A-AACCGGTTG
2564310 AAAACCGGTT-
1 -AAACCGGTTG
2564320 AAACCGGTT
1 AAACCGGTT
2564329 TCCAGCAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 11 0.32
10 13 0.38
11 9 0.26
12 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:2564447 original size:29 final size:30
Alignment explanation
Indices: 2564376--2564435 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2564366 CAATTTAAGG
2564376 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2564407 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2564436 TTTAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2564551 original size:22 final size:22
Alignment explanation
Indices: 2564525--2564567 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2564515 TTCAAGATTG
*
2564525 CCCAGGGGGTACAGATTCCCCC
1 CCCAGGGGGTACAGATACCCCC
2564547 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
2564568 GGGTATAGAT
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:0.21, C:0.40, G:0.28, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:2564577 original size:15 final size:15
Alignment explanation
Indices: 2564553--2564582 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2564543 CCCCCCCAGG
2564553 GGGTACAGATACCCC
1 GGGTACAGATACCCC
*
2564568 GGGTATAGATACCCC
1 GGGTACAGATACCCC
2564583 CTGCAGGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:2564658 original size:22 final size:21
Alignment explanation
Indices: 2564616--2564657 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2564606 AACAGAATGT
2564616 TCAGGGGGTACCGATTCCCCC
1 TCAGGGGGTACCGATTCCCCC
2564637 TCAGGGGGTACCGATTCCCCC
1 TCAGGGGGTACCGATTCCCCC
2564658 CCTGTTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.19
Consensus pattern (21 bp):
TCAGGGGGTACCGATTCCCCC
Found at i:2564803 original size:20 final size:22
Alignment explanation
Indices: 2564765--2564804 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2564755 TTTGAGTATA
2564765 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2564787 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2564805 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2565057 original size:34 final size:32
Alignment explanation
Indices: 2565018--2565087 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2565008 TTTTGTAAAG
* *
2565018 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2565052 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2565084 GGGA
1 GGGA
2565088 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2566600 original size:19 final size:20
Alignment explanation
Indices: 2566576--2566613 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2566566 TAAAGATAAT
2566576 TTGATTTTGAAAA-CAAAAG
1 TTGATTTTGAAAATCAAAAG
2566595 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAATCAAAA
2566614 TCAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAATCAAAAG
Found at i:2567973 original size:29 final size:30
Alignment explanation
Indices: 2567902--2567961 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2567892 CAATTTAAGG
2567902 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2567933 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2567962 TTTAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2568076 original size:21 final size:21
Alignment explanation
Indices: 2568051--2568114 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
2568041 TTCAAGATTG
* *
2568051 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
2568072 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
2568093 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
2568114 C
1 C
2568115 TGCAGGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:2568174 original size:21 final size:21
Alignment explanation
Indices: 2568148--2568190 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2568138 ACAGAATGTT
2568148 CAGGGGGTACCGATTCCCCCC
1 CAGGGGGTACCGATTCCCCCC
2568169 CAGGGGGTACCGATTCCCCCC
1 CAGGGGGTACCGATTCCCCCC
2568190 C
1 C
2568191 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CAGGGGGTACCGATTCCCCCC
Found at i:2568334 original size:20 final size:22
Alignment explanation
Indices: 2568296--2568335 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2568286 TTTGAGTATA
2568296 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2568318 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2568336 ATATACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2568588 original size:34 final size:32
Alignment explanation
Indices: 2568549--2568618 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2568539 TTTTGTAAAG
* *
2568549 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2568583 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2568615 GGGA
1 GGGA
2568619 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2571926 original size:44 final size:43
Alignment explanation
Indices: 2571846--2571961 Score: 142
Period size: 44 Copynumber: 2.7 Consensus size: 43
2571836 GACAAGTTAG
* * *
2571846 CCACTTGCACAACTTGTCAACTTGCCAACCAAGGATGAATTATC
1 CCACGTGCACAAGTTGGCAACTTGCCAACCAAGGATGAA-TATC
* * * *
2571890 CCATGTGCTCAAGTTGGCAACTTGCTAACCAAGGATGAATATT
1 CCACGTGCACAAGTTGGCAACTTGCCAACCAAGGATGAATATC
* *
2571933 CCACGTGCACAAGTTGGCTACTTGTCAAC
1 CCACGTGCACAAGTTGGCAACTTGCCAAC
2571962 TTGCCAATTT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
43 27 0.45
44 33 0.55
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
CCACGTGCACAAGTTGGCAACTTGCCAACCAAGGATGAATATC
Found at i:2576574 original size:17 final size:17
Alignment explanation
Indices: 2576552--2576592 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2576542 TTATCCCATG
*
2576552 TGCACAAGTTGGTC-ACT
1 TGCACAACTT-GTCAACT
2576569 TGCACAACTTGTCAACT
1 TGCACAACTTGTCAACT
2576586 TGC-CAAC
1 TGCACAAC
2576593 CTAGGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (17 bp):
TGCACAACTTGTCAACT
Found at i:2576664 original size:43 final size:44
Alignment explanation
Indices: 2576569--2576667 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 44
2576559 GTTGGTCACT
* * * *
2576569 TGCACAACTTGTCAACTTGCCAACCTAGGATGAATTATCCCATG
1 TGCACAAGTTGGCAACTTACCAACCAAGGATGAATTATCCCATG
* * *
2576613 TTCTCAAGTTGGCAACTTACTAACCAAGGATGAA-TATCCCATG
1 TGCACAAGTTGGCAACTTACCAACCAAGGATGAATTATCCCATG
2576656 TGCACAAGTTGG
1 TGCACAAGTTGG
2576668 ATTGCAAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 19 0.41
44 27 0.59
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
TGCACAAGTTGGCAACTTACCAACCAAGGATGAATTATCCCATG
Found at i:2581170 original size:2 final size:2
Alignment explanation
Indices: 2581159--2581190 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2581149 ACCATGATAC
2581159 AT AT -T 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 AT AT AT A
2581191 CAGCCTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2588807 original size:11 final size:11
Alignment explanation
Indices: 2588787--2588817 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2588777 CACTACATAC
*
2588787 AATACGATTCA
1 AATACAATTCA
2588798 AATACAATTCA
1 AATACAATTCA
2588809 AATACAATT
1 AATACAATT
2588818 TTGAAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (11 bp):
AATACAATTCA
Found at i:2592656 original size:24 final size:24
Alignment explanation
Indices: 2592604--2592650 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2592594 ATGTAGTCTT
*
2592604 ATTAAATTTTAAAATTTTATTTAA
1 ATTAAATTTTAAAATTATATTTAA
2592628 ATTAAAGTTTTAAAATTATATTT
1 ATTAAA-TTTTAAAATTATATTT
2592651 TTTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTAAATTTTAAAATTATATTTAA
Found at i:2604792 original size:21 final size:21
Alignment explanation
Indices: 2604766--2604834 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
2604756 TCATCTCCGT
* *
2604766 AGGGTTACATTCTGATCCCGC
1 AGGGTTACATTCCGAGCCCGC
2604787 AGGGTTACATTCCGAGCCCGC
1 AGGGTTACATTCCGAGCCCGC
*
2604808 AGGGTTGCATTCCGAGCCCGC
1 AGGGTTACATTCCGAGCCCGC
2604829 AGGGTT
1 AGGGTT
2604835 TTATACCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.23
Consensus pattern (21 bp):
AGGGTTACATTCCGAGCCCGC
Found at i:2605403 original size:33 final size:32
Alignment explanation
Indices: 2605354--2605444 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
2605344 AAATGTTTTT
2605354 AAAATACAAATTATATTATTCGAAATTAAAATA
1 AAAATA-AAATTATATTATTCGAAATTAAAATA
* * *
2605387 AAAATAAAAATAATATTA-TCGAAATTTAAAGTT
1 AAAAT-AAAATTATATTATTCGAAA-TTAAAATA
*
2605420 AAAAT-AAATTATAGTATTCGAAATT
1 AAAATAAAATTATATTATTCGAAATT
2605445 TAACATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 11 0.22
32 12 0.24
33 26 0.52
34 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.34
Consensus pattern (32 bp):
AAAATAAAATTATATTATTCGAAATTAAAATA
Found at i:2605446 original size:32 final size:32
Alignment explanation
Indices: 2605352--2605454 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
2605342 ATAAATGTTT
*
2605352 TTAAAATACAAATTATATTATTCGAAA-TTAAAA
1 TTAAAAT--AAATTATAATATTCGAAATTTAAAA
* * *
2605385 TAAAAATAAA-AATAATATTATCGAAATTTAAAG
1 TTAAAATAAATTATAATA-T-TCGAAATTTAAAA
* *
2605418 TTAAAATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAATTATAATATTCGAAATTTAAAA
2605450 TTAAA
1 TTAAA
2605455 TTTCAACTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 22 0.39
33 21 0.37
34 5 0.09
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (32 bp):
TTAAAATAAATTATAATATTCGAAATTTAAAA
Found at i:2606348 original size:128 final size:128
Alignment explanation
Indices: 2606120--2606610 Score: 864
Period size: 128 Copynumber: 3.9 Consensus size: 128
2606110 ATGACTTCAC
2606120 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
* * *
2606185 AAATAATGGAAGGCGCGCCCCAGAGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTACTG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
*
2606248 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
*
2606313 AAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
2606376 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
* *
2606441 AAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTACTG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
*
2606504 ATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TGACA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
*
2606568 AAATAATGGAAGGTGCG-CCCCGGGAACGCG-CTTCTAT-TGAATA
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC-ATGTGAATA
2606611 ATACTCCGAT
Statistics
Matches: 350, Mismatches: 12, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
125 10 0.03
126 15 0.04
127 20 0.06
128 305 0.87
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACA
AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
Found at i:2606721 original size:8 final size:8
Alignment explanation
Indices: 2606685--2606722 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2606675 ACAAGCTTTC
2606685 AATTCTCA
1 AATTCTCA
*
2606693 AATTCCCA
1 AATTCTCA
*
2606701 AACTCT-A
1 AATTCTCA
2606708 AATTCTCA
1 AATTCTCA
2606716 AATTCTC
1 AATTCTC
2606723 TGAAAATGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
AATTCTCA
Found at i:2609751 original size:23 final size:23
Alignment explanation
Indices: 2609725--2609771 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2609715 TATTTAAATG
*
2609725 AATGTTTTTG-TTTATAATAATTT
1 AATGTTATTGATTTAT-ATAATTT
2609748 AATGTTATTGCATTTATATAATTT
1 AATGTTATTG-ATTTATATAATTT
2609772 GTCAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 7 0.33
25 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (23 bp):
AATGTTATTGATTTATATAATTT
Found at i:2611209 original size:22 final size:22
Alignment explanation
Indices: 2611184--2611225 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2611174 GAGTCAAGAT
2611184 TAAAAATT-TAAAATATAAAGGC
1 TAAAAATTATAAAAT-TAAAGGC
*
2611206 TAAAACTTATAAAATTAAAG
1 TAAAAATTATAAAATTAAAG
2611226 TATAAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (22 bp):
TAAAAATTATAAAATTAAAGGC
Found at i:2611231 original size:22 final size:22
Alignment explanation
Indices: 2611184--2611231 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2611174 GAGTCAAGAT
*
2611184 TAAAAATTTAAAATATAAAGGC
1 TAAAAATTTAAAATATAAAGGA
* *
2611206 TAAAACTTATAAAAT-TAAAGTA
1 TAAAAATT-TAAAATATAAAGGA
2611228 TAAA
1 TAAA
2611232 GGTTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (22 bp):
TAAAAATTTAAAATATAAAGGA
Found at i:2616189 original size:35 final size:34
Alignment explanation
Indices: 2616127--2616201 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
2616117 AGTCAATTTC
*
2616127 AAATAAAAATATAATTTTAAGAATTAAATTAAA-T
1 AAATAAAAATATAAATTTAAGAATTAAA-TAAATT
*
2616161 AAATATAAAATGATAAATTTAA-ATTTAAATAAATT
1 AAATA-AAAAT-ATAAATTTAAGAATTAAATAAATT
2616196 AAATAA
1 AAATAA
2616202 CATGTAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 10 0.28
35 17 0.47
36 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (34 bp):
AAATAAAAATATAAATTTAAGAATTAAATAAATT
Found at i:2616238 original size:24 final size:24
Alignment explanation
Indices: 2616211--2616258 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2616201 ACATGTAAGG
2616211 ATTAAACCAAAA-TAATTATAAAAA
1 ATTAAACCAAAATTAA-TATAAAAA
**
2616235 ATTAAATTAAAATTAATATAAAAA
1 ATTAAACCAAAATTAATATAAAAA
2616259 TAAATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTAAACCAAAATTAATATAAAAA
Found at i:2616262 original size:22 final size:21
Alignment explanation
Indices: 2616224--2616267 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
2616214 AAACCAAAAT
2616224 AATTATAAAAAATTAAATTAA
1 AATTATAAAAAATTAAATTAA
2616245 AATTAATATAAAAA-TAAATTAA
1 AATT-ATA-AAAAATTAAATTAA
2616267 A
1 A
2616268 TTGAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTATAAAAAATTAAATTAA
Found at i:2622088 original size:17 final size:17
Alignment explanation
Indices: 2622066--2622102 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2622056 ACCGGCCCCT
2622066 AAATTTAAAATAAATAA
1 AAATTTAAAATAAATAA
2622083 AAATTTAAAATAAATAA
1 AAATTTAAAATAAATAA
2622100 AAA
1 AAA
2622103 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTTAAAATAAATAA
Found at i:2622107 original size:16 final size:17
Alignment explanation
Indices: 2622066--2622108 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2622056 ACCGGCCCCT
*
2622066 AAATTTAAAATAAATAA
1 AAATGTAAAATAAATAA
*
2622083 AAATTTAAAATAAATAA
1 AAATGTAAAATAAATAA
2622100 AAA-GTAAAA
1 AAATGTAAAA
2622109 AAAAACTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATGTAAAATAAATAA
Found at i:2626315 original size:29 final size:31
Alignment explanation
Indices: 2626282--2626341 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
2626272 ACGGTAATTG
*
2626282 CTTTC-ACA-CATCTGTATGTAGTAACCTTT
1 CTTTCGACATCATCTGTATGTAATAACCTTT
*
2626311 CTTTCGTACATTATCTGTATGTAATAACCTT
1 CTTTCG-ACATCATCTGTATGTAATAACCTT
2626342 GTGCGAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
31 3 0.12
32 18 0.69
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (31 bp):
CTTTCGACATCATCTGTATGTAATAACCTTT
Found at i:2627345 original size:2 final size:2
Alignment explanation
Indices: 2627338--2627368 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2627328 ACTTTCTGTA
2627338 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2627369 AACATCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2632103 original size:20 final size:21
Alignment explanation
Indices: 2632062--2632104 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2632052 TGACATGATA
2632062 TTTTAAAAAAATATTTTAATT
1 TTTTAAAAAAATATTTTAATT
* *
2632083 TTTTTAAAAAATGTTTT-ATT
1 TTTTAAAAAAATATTTTAATT
2632103 TT
1 TT
2632105 AAAACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAAAAAAATATTTTAATT
Found at i:2645795 original size:26 final size:26
Alignment explanation
Indices: 2645766--2645824 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
2645756 TTCAAAAAAC
*
2645766 AGTTCGCGGACAAACCCTAACCCTTA
1 AGTTCCCGGACAAACCCTAACCCTTA
*
2645792 AGTTCCCGGACAAACCCTATCCCTTA
1 AGTTCCCGGACAAACCCTAACCCTTA
2645818 AGTTCCC
1 AGTTCCC
2645825 ATATCCTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.27, C:0.37, G:0.14, T:0.22
Consensus pattern (26 bp):
AGTTCCCGGACAAACCCTAACCCTTA
Found at i:2650176 original size:2 final size:2
Alignment explanation
Indices: 2650169--2650213 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2650159 ATAGAATTAT
2650169 TA TA TA TA 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 TA
2650211 TA T
1 TA T
2650214 TGCCATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2650289 original size:30 final size:30
Alignment explanation
Indices: 2650248--2650319 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
2650238 AATGGAAGTA
*
2650248 AATTATTAATGTTATACTTAAAACGGTTTT
1 AATTGTTAATGTTATACTTAAAACGGTTTT
2650278 AATTGTTAATGTTATACTTAAAACGGTTTT
1 AATTGTTAATGTTATACTTAAAACGGTTTT
2650308 AATTGTGTAATG
1 AATTGT-TAATG
2650320 GTTAGATATG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 35 0.88
31 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.46
Consensus pattern (30 bp):
AATTGTTAATGTTATACTTAAAACGGTTTT
Done.