Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 122 of 172
Found at i:40685140 original size:10 final size:10
Alignment explanation
Indices: 40685101--40685159 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
40685091 TTTATATATA
40685101 TTATAATTTT
1 TTATAATTTT
* *
40685111 TAAATAATTAT
1 T-TATAATTTT
*
40685122 TAATAATTTT
1 TTATAATTTT
40685132 TTATAA-TTT
1 TTATAATTTT
*
40685141 CTA-AATTTT
1 TTATAATTTT
*
40685150 TTATACTTTT
1 TTATAATTTT
40685160 AAACTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 2 0.05
9 10 0.26
10 19 0.49
11 8 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATAATTTT
Found at i:40685301 original size:24 final size:22
Alignment explanation
Indices: 40685266--40685312 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
40685256 AAATATTTTT
*
40685266 AATTTTTTAAATAAACATTTTAAA
1 AATTTTTAAAAT-AA-ATTTTAAA
40685290 AATTTTTAAAATAAATTTTAAA
1 AATTTTTAAAATAAATTTTAAA
40685312 A
1 A
40685313 CATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTTTAAAATAAATTTTAAA
Found at i:40685340 original size:19 final size:21
Alignment explanation
Indices: 40685303--40685342 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40685293 TTTTAAAATA
40685303 AATTTTAAAACATATTTATTT
1 AATTTTAAAACATATTTATTT
40685324 AATTTTAAAA-A-ATTTATTT
1 AATTTTAAAACATATTTATTT
40685343 TTTTGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTAAAACATATTTATTT
Found at i:40687146 original size:18 final size:18
Alignment explanation
Indices: 40687123--40687193 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
40687113 TCATCAATAT
*
40687123 TAATCAGTTATTCAGTAA
1 TAATCAATTATTCAGTAA
* *
40687141 TAATCATTTATTCAATAA
1 TAATCAATTATTCAGTAA
* * *
40687159 CAGTCAATTATTTAGTAA
1 TAATCAATTATTCAGTAA
*
40687177 TAACCAATTATTCAGTA
1 TAATCAATTATTCAGTA
40687194 CCTTTATTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (18 bp):
TAATCAATTATTCAGTAA
Found at i:40687559 original size:19 final size:21
Alignment explanation
Indices: 40687528--40687569 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
40687518 TTCAGTTTTC
40687528 AATCAGTATATATT-TCAATT
1 AATCAGTATATATTCTCAATT
40687548 AATCAG-ATATATTCTCAATT
1 AATCAGTATATATTCTCAATT
40687568 AA
1 AA
40687570 ATATATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (21 bp):
AATCAGTATATATTCTCAATT
Found at i:40689238 original size:6 final size:6
Alignment explanation
Indices: 40689208--40689276 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
40689198 AAGAAACATT
* * *
40689208 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
40689257 ATCAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
40689277 GAGGTCAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 2 0.04
6 45 0.87
7 4 0.08
8 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:40689266 original size:31 final size:30
Alignment explanation
Indices: 40689229--40689306 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
40689219 AATCAAAATG
*
40689229 AGAATCAGAATCAGAATCAGGTGACAG-AATC
1 AGAATCAGAATCAGAATCAGGTCA-AGTAA-C
*
40689260 AGAATCAGAATCAGAATGAGGTCAAGTAAC
1 AGAATCAGAATCAGAATCAGGTCAAGTAAC
* *
40689290 AAAATTAGAATCAGAAT
1 AGAATCAGAATCAGAAT
40689307 GTAAATGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.18
Consensus pattern (30 bp):
AGAATCAGAATCAGAATCAGGTCAAGTAAC
Found at i:40689473 original size:27 final size:26
Alignment explanation
Indices: 40689425--40689484 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
40689415 GCGAGGCTGC
*
40689425 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40689452 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
40689478 CAGATAT
1 CAGATAT
40689485 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40689529 original size:71 final size:67
Alignment explanation
Indices: 40689452--40689593 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
40689442 TCACCAGATA
* * *
40689452 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
40689517 GGCTGC
62 GGCTGC
* *
40689523 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
40689588 GC
66 GC
40689590 CAGA
1 CAGA
40689594 ATGCTTCTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:40689571 original size:27 final size:26
Alignment explanation
Indices: 40689523--40689574 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40689513 GCGAGGCTGC
*
40689523 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40689549 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
40689575 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40690133 original size:27 final size:27
Alignment explanation
Indices: 40690080--40690349 Score: 186
Period size: 27 Copynumber: 9.9 Consensus size: 27
40690070 AATAATCCTA
* * * *
40690080 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* **
40690107 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* ** * *
40690134 CAATGGTATTTCTATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTACAAA-C
* ** *
40690163 CAAGGGTATTTCTGTAATTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
* *
40690190 C-AGAGGTATTTTGGTAATTTTACAAAT
1 CAAG-GGTATTTCGGTAATTTTACAAAC
** *
40690217 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
40690244 C-AGTGGTATTTCGGTAATTTTACAAAC
1 CAAG-GGTATTTCGGTAATTTTACAAAC
* * *
40690271 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * * * *
40690298 TAGGGGTATTTTGGTAATTCTATCATA-
1 CAAGGGTATTTCGGTAATTTTA-CAAAC
* * *
40690325 CAGGGGTATTTCAGTAATTTCACAA
1 CAAGGGTATTTCGGTAATTTTACAA
40690350 TCGAGGGTAA
Statistics
Matches: 198, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
26 6 0.03
27 157 0.79
28 20 0.10
29 15 0.08
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTACAAAC
Found at i:40690333 original size:81 final size:81
Alignment explanation
Indices: 40690166--40690385 Score: 218
Period size: 81 Copynumber: 2.7 Consensus size: 81
40690156 AGAAAGTCAA
* ** *
40690166 GGGTATTTCTGTAATTTTGTAAATCAGAGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGG
1 GGGTATTTCAGTAATTTTACAAATCAGAGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGG
40690231 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * * *
40690247 TGGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTT
1 GGGTATTTCAGTAATTTTACAAATC-AGAGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTC
*
40690310 GGTAA-TTCTATCATA-CAG
64 GGTAATTTC-A-CAAACCAG
* *** **
40690328 GGGTATTTCAGTAATTTCAC-AATC-GAGGGTAAAATGGTAATTTTGTAAATAGAGGGTA
1 GGGTATTTCAGTAATTTTACAAATCAGA-GGTATTTTGGTAATTTTACAAATAGAGGGTA
40690386 AAATGGTAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
79 4 0.03
80 28 0.24
81 78 0.68
82 5 0.04
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.38
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCAGAGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGG
TAATTTCACAAACCAG
Found at i:40690513 original size:27 final size:27
Alignment explanation
Indices: 40690348--40690565 Score: 222
Period size: 27 Copynumber: 8.1 Consensus size: 27
40690338 GTAATTTCAC
40690348 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
40690375 AATAGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * *
40690402 AATCAAGGGTAAAATAGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * ** *
40690429 AATTGAGGATAAAATGGTAATCCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
40690456 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
40690483 AATCGAGGGTGAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *** *
40690510 AATCGGGGGTACTTTGGTAATTTT-TCT
1 AATCGAGGGTAAAATGGTAATTTTGT-A
*** *
40690537 AATCGAGGGTATTTTGGTAATTTGGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
40690564 AA
1 AA
40690566 CTAAAGTATT
Statistics
Matches: 158, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 156 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:40692066 original size:27 final size:27
Alignment explanation
Indices: 40692027--40692149 Score: 108
Period size: 27 Copynumber: 4.6 Consensus size: 27
40692017 GAAAGTAAAA
**
40692027 GGTATTTCT-GTAATTTTGTAAATCAGG
1 GGTATTT-TGGTAATTTTACAAATCAGG
*
40692054 GGTATTTTGGTAATTTTACAAAT-TGAG
1 GGTATTTTGGTAATTTTACAAATCAG-G
* * * * *
40692081 GGTATTTCGATAATTTTACAAACCTGT
1 GGTATTTTGGTAATTTTACAAATCAGG
* *
40692108 AGTATTTCGGTAATTTTACAAA-CTAGG
1 GGTATTTTGGTAATTTTACAAATC-AGG
40692135 GGTATTTTGGTAATT
1 GGTATTTTGGTAATT
40692150 CTATCATACA
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.04
27 74 0.94
28 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.43
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAATCAGG
Found at i:40692164 original size:81 final size:81
Alignment explanation
Indices: 40692028--40692177 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 81
40692018 AAAGTAAAAG
* ** * **
40692028 GTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC-GAT
1 GTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAATCAAGGGTATTTCAG-T
40692092 AATTTTACAAACCTGTA
65 AATTTTACAAACCTGTA
*
40692109 GTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTCTATCATA-CAAGGGTATTTCAG
1 GTATTTCGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTCTA-CAAATCAAGGGTATTTCAG
40692172 TAATTT
64 TAATTT
40692178 CATATTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 1 0.02
81 54 0.92
82 4 0.07
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (81 bp):
GTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAATCAAGGGTATTTCAGTA
ATTTTACAAACCTGTA
Found at i:40692349 original size:27 final size:27
Alignment explanation
Indices: 40692311--40692431 Score: 161
Period size: 27 Copynumber: 4.5 Consensus size: 27
40692301 CAAAAAATAA
40692311 TAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
* * *
40692338 TAAATTGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTG
* * *
40692365 CAAATCGAGGGTAAAATGGTAATTTTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
* *
40692392 TAAATCGAGGGTGAAACGGTAATTTTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
*
40692419 TAAATCGGGGGTA
1 TAAATCGAGGGTA
40692432 CTTTGGTAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGGTAATTCTG
Found at i:40692424 original size:54 final size:54
Alignment explanation
Indices: 40692310--40692458 Score: 174
Period size: 54 Copynumber: 2.8 Consensus size: 54
40692300 ACAAAAAATA
* * * *
40692310 ATAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATGGTAATTCT
1 ATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCT
* * *
40692364 ACAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTTT
1 ATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCT
* * ***
40692418 GTAAATCGGGGGTACTTTGGTAATTTTGCT-AATCGAGGGTA
1 ATAAATCGAGGGTAAAATGGTAATTTTG-TAAATCGAGGGTA
40692459 TTTTGGTAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 79 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (54 bp):
ATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCT
Found at i:40692439 original size:27 final size:26
Alignment explanation
Indices: 40692328--40692476 Score: 111
Period size: 27 Copynumber: 5.5 Consensus size: 26
40692318 AGGGTAAAAC
* * **
40692328 GGTAATTCTGTAAATTGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGT-ATTT
* ** **
40692355 GGTAATTCTACAAATCGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGT-ATTT
***
40692382 GGTAATTTTGTAAATCGAGGGTGAAAC
1 GGTAATTTTGTAAATCGAGGGT-ATTT
*
40692409 GGTAATTTTGTAAATCGGGGGTACTTT
1 GGTAATTTTGTAAATCGAGGGTA-TTT
40692436 GGTAATTTTGCT-AATCGAGGGTATTTT
1 GGTAATTTTG-TAAATCGAGGGTA-TTT
*
40692463 GGTAATTTGGTAAA
1 GGTAATTTTGTAAA
40692477 CTAAAGTATT
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.02
27 101 0.97
28 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
GGTAATTTTGTAAATCGAGGGTATTT
Found at i:40692452 original size:81 final size:81
Alignment explanation
Indices: 40692311--40692476 Score: 206
Period size: 81 Copynumber: 2.0 Consensus size: 81
40692301 CAAAAAATAA
*
40692311 TAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
*
40692376 TAAAATGGTAATTTTG
66 TAAAATGGTAATTTGG
* * * *** * * *
40692392 TAAATCGAGGGTGAAACGGTAATTTTGTAAATCGGGGGTACTTTGGTAATTTTGCTAATCGAGGG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
***
40692457 TATTTTGGTAATTTGG
66 TAAAATGGTAATTTGG
40692473 TAAA
1 TAAA
40692477 CTAAAGTATT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (81 bp):
TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
TAAAATGGTAATTTGG
Found at i:40693491 original size:16 final size:16
Alignment explanation
Indices: 40693467--40693534 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
40693457 TTAAATTTAT
*
40693467 TTATTATATAAATATC
1 TTATAATATAAATATC
*
40693483 TTATAATATAATTA-C
1 TTATAATATAAATATC
*
40693498 TTA-ATTAATAAATATC
1 TTATAAT-ATAAATATC
40693514 TTTTATAAATAGTAAATATC
1 --TTAT-AATA-TAAATATC
40693534 T
1 T
40693535 ATTAGTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.05
15 10 0.25
16 13 0.32
18 4 0.10
19 1 0.03
20 10 0.25
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (16 bp):
TTATAATATAAATATC
Found at i:40693625 original size:4 final size:4
Alignment explanation
Indices: 40693616--40693649 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40693606 AACGTTTGTC
40693616 TTTA TTTA TTTA TTTTA TTTA TTTA CTTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA
40693650 ATTAGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40693634 original size:9 final size:8
Alignment explanation
Indices: 40693616--40693649 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
40693606 AACGTTTGTC
40693616 TTTATTTA
1 TTTATTTA
40693624 TTTATTTTA
1 TTTA-TTTA
40693633 TTTATTTA
1 TTTATTTA
40693641 CTTTATTTA
1 -TTTATTTA
40693650 ATTAGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTTA
Found at i:40693634 original size:13 final size:13
Alignment explanation
Indices: 40693615--40693649 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
40693605 AAACGTTTGT
40693615 CTTTATTTATTTA
1 CTTTATTTATTTA
*
40693628 TTTTATTTATTTA
1 CTTTATTTATTTA
40693641 CTTTATTTA
1 CTTTATTTA
40693650 ATTAGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTATTTATTTA
Found at i:40695127 original size:24 final size:26
Alignment explanation
Indices: 40695081--40695132 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
40695071 TGACAAATCC
* * *
40695081 AAATAATTTTGAATTTTATAAGTTAT
1 AAATAATTTTGAATTTCAAAAGTAAT
40695107 AAAT-ATTTT-AATTTCAAAAGTAAT
1 AAATAATTTTGAATTTCAAAAGTAAT
40695131 AA
1 AA
40695133 TTCTGTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 5 0.22
26 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATAATTTTGAATTTCAAAAGTAAT
Found at i:40696509 original size:15 final size:16
Alignment explanation
Indices: 40696489--40696584 Score: 81
Period size: 15 Copynumber: 5.8 Consensus size: 16
40696479 ACCCCTCCTA
40696489 TTATATTATATAAT-G
1 TTATATTATATAATAG
40696504 TTATATTATATCATATAG
1 TTATATTATAT-A-ATAG
*
40696522 TATATAATATATTAATAG
1 T-TATATTATA-TAATAG
40696540 -TATA-TATATAATAG
1 TTATATTATATAATAG
* *
40696554 TTATACATTATATATTAC
1 TTAT--ATTATATAATAG
40696572 TTATTATTATATA
1 TTA-TATTATATA
40696585 TTGTTGTTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
14 6 0.09
15 18 0.26
16 5 0.07
17 11 0.16
18 17 0.25
19 10 0.15
20 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (16 bp):
TTATATTATATAATAG
Found at i:40696570 original size:7 final size:7
Alignment explanation
Indices: 40696490--40696586 Score: 56
Period size: 7 Copynumber: 12.9 Consensus size: 7
40696480 CCCCTCCTAT
40696490 TATATTA
1 TATATTA
40696497 TATAATGT-
1 TAT-AT-TA
40696505 TATATTA
1 TATATTA
40696512 TATCATATA
1 TAT-AT-TA
*
40696521 GTATATAA
1 -TATATTA
40696529 TATATTA
1 TATATTA
*
40696536 -ATAGTA
1 TATATTA
40696542 TATA-TA
1 TATATTA
40696548 TAATAGTTA
1 T-ATA-TTA
*
40696557 TACATTA
1 TATATTA
40696564 TATATTA
1 TATATTA
40696571 CTTATTATTA
1 --TA-TATTA
40696581 TATATT
1 TATATT
40696587 GTTGTTTATT
Statistics
Matches: 72, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
6 9 0.12
7 33 0.46
8 12 0.17
9 10 0.14
10 8 0.11
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (7 bp):
TATATTA
Found at i:40696575 original size:18 final size:17
Alignment explanation
Indices: 40696544--40696586 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
40696534 TAATAGTATA
* *
40696544 TATATAATAGTTATACAT
1 TATATATTACTTAT-CAT
*
40696562 TATATATTACTTATTAT
1 TATATATTACTTATCAT
40696579 TATATATT
1 TATATATT
40696587 GTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (17 bp):
TATATATTACTTATCAT
Found at i:40698794 original size:15 final size:17
Alignment explanation
Indices: 40698774--40698815 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
40698764 TTAGACCTCC
40698774 TACTATATTATAT-A-A
1 TACTATATTATATCATA
*
40698789 TACTATATCATATCATA
1 TACTATATTATATCATA
*
40698806 TAATATATTA
1 TACTATATTA
40698816 ATAGTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 1 0.05
17 9 0.41
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (17 bp):
TACTATATTATATCATA
Found at i:40710516 original size:18 final size:17
Alignment explanation
Indices: 40710484--40710517 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40710474 AATACAGGTG
*
40710484 ATGGTGATGATGATGGT
1 ATGGTGATGAGGATGGT
40710501 ATGGTGTATGAGGATGG
1 ATGGTG-ATGAGGATGG
40710518 AGATATGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (17 bp):
ATGGTGATGAGGATGGT
Found at i:40714047 original size:22 final size:22
Alignment explanation
Indices: 40714022--40714076 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
40714012 ACCTTTGAAA
40714022 CATATCACTTACATTAATAATT
1 CATATCACTTACATTAATAATT
* * *
40714044 CATATCACTTCCGTTTATAATT
1 CATATCACTTACATTAATAATT
40714066 CATATCACTTA
1 CATATCACTTA
40714077 TCACCTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.42
Consensus pattern (22 bp):
CATATCACTTACATTAATAATT
Found at i:40714590 original size:19 final size:19
Alignment explanation
Indices: 40714553--40714590 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40714543 GCCTAAACAT
*
40714553 ATTTTTACAAATTATAATA
1 ATTTTTACAAATTAAAATA
40714572 ATTTTT-CAAATTTAAAATA
1 ATTTTTACAAA-TTAAAATA
40714591 GGGGAACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTTACAAATTAAAATA
Found at i:40721706 original size:19 final size:19
Alignment explanation
Indices: 40721657--40721707 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
40721647 TTAGGTTCAT
40721657 TAAATTTAAAT-TATATTAC
1 TAAATTTAAATAT-TATTAC
* *
40721676 TAAATTT--CTATTATTAG
1 TAAATTTAAATATTATTAC
40721693 TAAATTTAAATATTA
1 TAAATTTAAATATTA
40721708 GAATCTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.50
18 1 0.04
19 12 0.46
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATTTAAATATTATTAC
Found at i:40722341 original size:16 final size:16
Alignment explanation
Indices: 40722332--40722387 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
40722322 TGGAATAGGA
*
40722332 TTATAATGGAATAGAAA
1 TTATAATGGAATA-AAG
*
40722349 CTATAATGGAATAAAG
1 TTATAATGGAATAAAG
* *
40722365 TTGTAATGGAATAGAG
1 TTATAATGGAATAAAG
40722381 TTATAAT
1 TTATAAT
40722388 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (16 bp):
TTATAATGGAATAAAG
Found at i:40722565 original size:26 final size:26
Alignment explanation
Indices: 40722536--40722612 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
40722526 AATAAATAAT
40722536 TTAATCATATTTTAATATAATTATTA
1 TTAATCATATTTTAATATAATTATTA
* *
40722562 TTAAAT-ATAATTTAATAATATATAATTTA
1 TT-AATCATATTTTAAT-ATA-ATTA-TTA
*
40722591 ATAA-CAT-TTTTAATATAATTAT
1 TTAATCATATTTTAATATAATTAT
40722613 GTTTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
24 1 0.02
25 3 0.07
26 14 0.34
27 12 0.29
28 7 0.17
29 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATCATATTTTAATATAATTATTA
Found at i:40722584 original size:15 final size:15
Alignment explanation
Indices: 40722566--40722594 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40722556 TTATTATTAA
40722566 ATATAATTTAATAAT
1 ATATAATTTAATAAT
40722581 ATATAATTTAATAA
1 ATATAATTTAATAA
40722595 CATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATTTAATAAT
Found at i:40728008 original size:46 final size:45
Alignment explanation
Indices: 40727955--40728212 Score: 209
Period size: 46 Copynumber: 5.6 Consensus size: 45
40727945 AGATTTGTGC
* *
40727955 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-GTATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTG-A-GATGAGA
* * * *
40728001 GCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTGAGATGAGA
* ** **
40728049 GCTAGTGTAAGACATGTCTGGGACATGCATAAGCCACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTGAG-ATGAGA
* * **
40728095 GCCAGTGTAAAACATGTTTGGGACATGCATCGGCCTCGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGATGAGA
* * * * *
40728141 ACCAGTGTCAGACATGTCTGGGACATGCGTCTG-CT-ACGA-GATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTGA-GATGA-GA
* *
40728185 GCTAGTGTAAGACATGCCTGGGACATGC
1 GCCAGTGTAAGACATGTCTGGGACATGC
40728213 GTCAGTACGG
Statistics
Matches: 167, Mismatches: 37, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
43 2 0.01
44 26 0.16
45 4 0.02
46 83 0.50
47 28 0.17
48 22 0.13
49 1 0.01
50 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGATGAGA
Found at i:40728076 original size:94 final size:92
Alignment explanation
Indices: 40727958--40728128 Score: 243
Period size: 94 Copynumber: 1.8 Consensus size: 92
40727948 TTTGTGCGCC
** ** * * *
40727958 AGTGTAAGACATGTCTGGGACATGCATCGGCCGTATTATGATAGCCAGTGTAAGACCATGTCTGA
1 AGTGTAAGACATGTCTGGGACATGCATAAGCCACAGTATGAGAGCCAGTGTAA-AACATGTCTGA
40728023 GACATGGCATCGGCATTGAGACGAGGGCT
65 GACAT-GCATCGGCATTGAGACGAGGGCT
* *
40728052 AGTGTAAGACATGTCTGGGACATGCATAAGCCACAGTATGAGAGCCAGTGTAAAACATGTTTGGG
1 AGTGTAAGACATGTCTGGGACATGCATAAGCCACAGTATGAGAGCCAGTGTAAAACATGTCTGAG
40728117 ACATGCATCGGC
66 ACATGCATCGGC
40728129 CTCGAGATGT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 8 0.12
93 13 0.19
94 47 0.69
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATAAGCCACAGTATGAGAGCCAGTGTAAAACATGTCTGAG
ACATGCATCGGCATTGAGACGAGGGCT
Found at i:40728252 original size:46 final size:43
Alignment explanation
Indices: 40728143--40728255 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 43
40728133 AGATGTTAAC
* * *
40728143 CAGTGTCAGACATGTCTGGGACATGCGTCTGCTACGAGATGTG
1 CAGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTG
*
40728186 CTAGTGTAAGACATGCCTGGGACATGCGTCAG-TACGGTTACATGTG
1 C-AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG
*
40728232 TCAGTGTAAGACCTGTCTGGGACA
1 -CAGTGTAAGACATGTCTGGGACA
40728256 AGGCATAGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.07
44 28 0.47
46 26 0.44
47 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
CAGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTG
Found at i:40734955 original size:22 final size:20
Alignment explanation
Indices: 40734930--40734970 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
40734920 ATTAATTTTA
40734930 ATTTTATGATATAAAAATAATT
1 ATTTTAT-AT-TAAAAATAATT
*
40734952 ATTTTATATTTAAAATAAT
1 ATTTTATATTAAAAATAAT
40734971 AAAATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTTATATTAAAAATAATT
Found at i:40735762 original size:111 final size:111
Alignment explanation
Indices: 40735568--40735789 Score: 345
Period size: 111 Copynumber: 2.0 Consensus size: 111
40735558 TAGAACATAT
* * * * * *
40735568 CAAATGCAAATGCAAAATCCTACCCCCATCTGCTACACACCATCTTTGATAATCTCTATATACCA
1 CAAATGCAAATGCAAAATCCTACCCCCATCCGCTACACACCATATATAATAATCTCTACACACCA
*
40735633 AATAGGGTATCAAATACCCATCCATCCCTACACACCGTACAGTGAC
66 AATAGGGTATCAAATACCCATCCATCCCTACACACCATACAGTGAC
* * *
40735679 CAAATGCAAATGCAACATCCTACCCCCATCCGTTACACACCATATATAATAATCTTTACACACCA
1 CAAATGCAAATGCAAAATCCTACCCCCATCCGCTACACACCATATATAATAATCTCTACACACCA
*
40735744 AATAGGGTATCAAATACCCATCCATCCCTACACACCATATAGTGAC
66 AATAGGGTATCAAATACCCATCCATCCCTACACACCATACAGTGAC
40735790 TGTATGTCAC
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.23
Consensus pattern (111 bp):
CAAATGCAAATGCAAAATCCTACCCCCATCCGCTACACACCATATATAATAATCTCTACACACCA
AATAGGGTATCAAATACCCATCCATCCCTACACACCATACAGTGAC
Found at i:40738702 original size:43 final size:42
Alignment explanation
Indices: 40738613--40738815 Score: 203
Period size: 43 Copynumber: 4.7 Consensus size: 42
40738603 AGTCCTGGTC
* * *
40738613 TTTAGCGACGCTTTTTAGAAAAACG-CGC-AGAAGACCAAGATT
1 TTTAGCGGCACTTTTTA-AAAAACGCCGCTA-AAGACCAAGACT
* * * ** *
40738655 TTTAGCAGCGCTTTTTGAATAAGTGCCGCTAAAGACAAAGACT
1 TTTAGCGGCACTTTTT-AAAAAACGCCGCTAAAGACCAAGACT
* *
40738698 TTTAGCGGCACTTTTTAAAAAAACGTCGCTAAAGACCAGGACT
1 TTTAGCGGCACTTTTT-AAAAAACGCCGCTAAAGACCAAGACT
* * *
40738741 TTTAGCGGTACTTTTTTAAAAACGCCGCTAAAGACCAGGACT
1 TTTAGCGGCACTTTTTAAAAAACGCCGCTAAAGACCAAGACT
*
40738783 TTTAGCGGCGCTTTTTTTAAAAAACGCCGCTAA
1 TTTAGCGGCAC--TTTTTAAAAAACGCCGCTAA
40738816 TTTGCCCAGT
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 51 0.38
43 63 0.47
44 20 0.15
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCACTTTTTAAAAAACGCCGCTAAAGACCAAGACT
Found at i:40738768 original size:85 final size:85
Alignment explanation
Indices: 40738613--40738815 Score: 230
Period size: 85 Copynumber: 2.4 Consensus size: 85
40738603 AGTCCTGGTC
* * * *
40738613 TTTAGCGACGCTTTTTAGAAAAACGCGC-AGAAGACCAAGATTTTTAGCAGCGCTTTTTGAATAA
1 TTTAGCGGCGCTTTTTAAAAAAACGCGCTA-AAGACCAAGACTTTTAGCAGCACTTTTTGAATAA
**
40738677 GTGCCGCTAAAGACAAAGACT
65 ACGCCGCTAAAGACAAAGACT
* * * * *
40738698 TTTAGCGGCACTTTTTAAAAAAACGTCGCTAAAGACCAGGACTTTTAGCGGTACTTTTTTAA-AA
1 TTTAGCGGCGCTTTTTAAAAAAACG-CGCTAAAGACCAAGACTTTTAGCAGCACTTTTTGAATAA
* *
40738762 ACGCCGCTAAAGACCAGGACT
65 ACGCCGCTAAAGACAAAGACT
*
40738783 TTTAGCGGCGCTTTTTTTAAAAAACGCCGCTAA
1 TTTAGCGGCGC-TTTTTAAAAAAACG-CGCTAA
40738816 TTTGCCCAGT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
85 51 0.52
86 47 0.47
87 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (85 bp):
TTTAGCGGCGCTTTTTAAAAAAACGCGCTAAAGACCAAGACTTTTAGCAGCACTTTTTGAATAAA
CGCCGCTAAAGACAAAGACT
Found at i:40739138 original size:21 final size:21
Alignment explanation
Indices: 40739109--40739156 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
40739099 TTCTGTTCTA
* *
40739109 CTCCTCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
40739130 CTCCGCCTCCCGCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
40739151 CTCCGC
1 CTCCGC
40739157 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.58, G:0.19, T:0.23
Consensus pattern (21 bp):
CTCCGCCTCCCGCGCTGCTGC
Found at i:40744074 original size:9 final size:9
Alignment explanation
Indices: 40744060--40744225 Score: 136
Period size: 9 Copynumber: 17.6 Consensus size: 9
40744050 ATGTATTAGT
40744060 TAAGTTATG
1 TAAGTTATG
40744069 TAAGTTATTATG
1 TAAG---TTATG
*
40744081 TACGTTATG
1 TAAGTTATG
*
40744090 TGAGTTATG
1 TAAGTTATG
*
40744099 TAAATTATG
1 TAAGTTATG
40744108 TAAGTTATG
1 TAAGTTATG
*
40744117 TGAGTTATG
1 TAAGTTATG
40744126 TAAGTTGTTATG
1 TAA---GTTATG
40744138 TAA-TTATG
1 TAAGTTATG
*
40744146 TAACTTATG
1 TAAGTTATG
*
40744155 TCAGTTATG
1 TAAGTTATG
40744164 TAAGTTGTCATG
1 TAAG-T-T-ATG
*
40744176 TAAATTATG
1 TAAGTTATG
*
40744185 TAAGTTATA
1 TAAGTTATG
*
40744194 TGAGTTATG
1 TAAGTTATG
40744203 TAAGTTATG
1 TAAGTTATG
* * *
40744212 CAATTTATT
1 TAAGTTATG
40744221 TAAGT
1 TAAGT
40744226 AATGATCAAT
Statistics
Matches: 125, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
8 8 0.06
9 90 0.72
10 2 0.02
11 2 0.02
12 23 0.18
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:40744829 original size:241 final size:241
Alignment explanation
Indices: 40744406--40744895 Score: 903
Period size: 241 Copynumber: 2.0 Consensus size: 241
40744396 TTAAGGTTAT
*
40744406 ATAAATATTCAATAGTAAATGAGATCGATAGAGCTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
40744471 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
40744536 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
*
40744601 GGTCAGCTATTGTTGTAATTTTAAT-GAACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATAG-ACAAACAAGCTACATGGTA
*
40744647 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
* *
40744712 TCATCATACGTGGTGTTGTTACACCTAGGGAGGATCCATTATATTTTACAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
*
40744777 ACCCGTCAGGTTTTCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
40744842 GGTCAGCTATTGTTGTAATTTTAATAGACAAACAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATAGACAAACAAGCTACATGGTA
40744888 AT-AATATT
1 ATAAATATT
40744896 AATTCATACT
Statistics
Matches: 242, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
240 6 0.02
241 235 0.97
242 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (241 bp):
ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
GGTCAGCTATTGTTGTAATTTTAATAGACAAACAAGCTACATGGTA
Found at i:40745417 original size:183 final size:183
Alignment explanation
Indices: 40745104--40745435 Score: 601
Period size: 183 Copynumber: 1.8 Consensus size: 183
40745094 CCTAGAACAT
* *
40745104 ATGTAAGATTATAAGATTAACACCAAAAATATTTCAGTTGAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAACACCAAAAATATTTCAATTGAAGCAAATATAAAAACTTTATCTAT
*
40745169 ATCAGTACCAAATATTAAGTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGTAGGAGG
66 ATCAGTACCAAATATTAAGTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
*
40745234 AGCAGGAAGCAGTAACTGAAATACATACAGCATTAATTCACTAATACAGACAC
131 AGCAAGAAGCAGTAACTGAAATACATACAGCATTAATTCACTAATACAGACAC
* *
40745287 ATGTAAGATTATAAGAGTGACACCAAATATATTTCAATTGAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAACACCAAAAATATTTCAATTGAAGCAAATATAAAAACTTTATCTAT
*
40745352 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAAGTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
40745417 AGCAAGAAGCAGTAACTGA
131 AGCAAGAAGCAGTAACTGA
40745436 TGCTGAATCT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 142 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAACACCAAAAATATTTCAATTGAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAAGTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAAGAAGCAGTAACTGAAATACATACAGCATTAATTCACTAATACAGACAC
Found at i:40748403 original size:22 final size:22
Alignment explanation
Indices: 40748375--40748417 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40748365 CCTAGATCAA
*
40748375 GCAATAATCACGAAGCTAACAC
1 GCAATAATCACAAAGCTAACAC
40748397 GCAATAATCACAAAGCTAACA
1 GCAATAATCACAAAGCTAACA
40748418 AAACATTAAT
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:0.49, C:0.26, G:0.12, T:0.14
Consensus pattern (22 bp):
GCAATAATCACAAAGCTAACAC
Found at i:40749037 original size:77 final size:77
Alignment explanation
Indices: 40748910--40749053 Score: 252
Period size: 77 Copynumber: 1.9 Consensus size: 77
40748900 CGTTCAAGGT
* *
40748910 AAAAAAACGCCCCTAATCCCCTAAAAATCCATTAAAAACGATGTCGTTTACTATTTTAATTTTTT
1 AAAAAAACGCCCCTAATCCCCTAAAAATCCATTAAAAACGATGCCATTTACTATTTTAATTTTTT
40748975 GCGGCGATTTTA
66 GCGGCGATTTTA
* *
40748987 AAAAAAACGCCGCTAATCCCCTAAATATCCATTAAAAACGATGCCATTTACTATTTTAATTTTTT
1 AAAAAAACGCCCCTAATCCCCTAAAAATCCATTAAAAACGATGCCATTTACTATTTTAATTTTTT
40749052 GC
66 GC
40749054 TCCCTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (77 bp):
AAAAAAACGCCCCTAATCCCCTAAAAATCCATTAAAAACGATGCCATTTACTATTTTAATTTTTT
GCGGCGATTTTA
Found at i:40750010 original size:80 final size:83
Alignment explanation
Indices: 40749890--40750089 Score: 282
Period size: 80 Copynumber: 2.4 Consensus size: 83
40749880 TTTTTTTTGC
* * * * *
40749890 TTTTTGTGGCGTTTTTGAAAAAAACGCCGGTACTCCCCTAAAAATCCAA-T-AAACGACGTCGTT
1 TTTTTGCGGCGTTTTTTAAAAAAACGCCGCTACTCTCCTAAAAATCCAATTAAAACGACGCCGTT
40749953 TTCGTTAAACTGCT-T-T
66 TTCGTTAAACTGCTATGT
*
40749969 TTTTTGCGGCGTTTTTTCAAAAAAACGCCGCTACTCTCCTAAATATCCAATTAAAACGACGCCGT
1 TTTTTGCGGCGTTTTTT-AAAAAAACGCCGCTACTCTCCTAAAAATCCAATTAAAACGACGCCGT
40750034 TTTCGTTAAACTGCTATGT
65 TTTCGTTAAACTGCTATGT
* * *
40750053 TTTTTGCGGCGTTTTTTAAATAAACGCCACTAATCTC
1 TTTTTGCGGCGTTTTTTAAAAAAACGCCGCTACTCTC
40750090 TTAGTTTTTA
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
79 15 0.14
80 29 0.27
81 1 0.01
82 26 0.24
83 18 0.17
84 18 0.17
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (83 bp):
TTTTTGCGGCGTTTTTTAAAAAAACGCCGCTACTCTCCTAAAAATCCAATTAAAACGACGCCGTT
TTCGTTAAACTGCTATGT
Found at i:40751281 original size:41 final size:41
Alignment explanation
Indices: 40751213--40751511 Score: 354
Period size: 41 Copynumber: 7.3 Consensus size: 41
40751203 TTATATGACT
* *
40751213 TTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* * *
40751254 TTTAGCGACGTTGTACCGAAAGTGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* * *
40751295 TTTAGCGGTGTTTTATCGAAAGCGCCGCTAATGCTATGGTC
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* *
40751336 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCCCTAGTC
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* * *
40751377 TTTAGCGGCGTTTTACTGAAAGCGCCTCTAATGCTCT-ATC
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* * * *
40751417 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGTTCT-ATT
1 TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
* * * * *
40751457 TTTAGCGGTGTTTTTTA-CTAAAACGCCGCTATTGCTCT-GTT
1 TTTAGCGGCG--TTTTACCGAAAGCGCCGCTAATGCTCTGGTC
40751498 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
40751512 TGGTAAAACG
Statistics
Matches: 224, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
39 4 0.02
40 46 0.21
41 169 0.75
42 5 0.02
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTC
Found at i:40758355 original size:29 final size:29
Alignment explanation
Indices: 40758311--40758368 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
40758301 TGGTACGAAT
40758311 ATGGCTAATTGCTTTGTGGAGTATAAATG
1 ATGGCTAATTGCTTTGTGGAGTATAAATG
* *
40758340 ATGGTTAATTGTTTTGTGGAGTATAAATG
1 ATGGCTAATTGCTTTGTGGAGTATAAATG
40758369 CTTGAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (29 bp):
ATGGCTAATTGCTTTGTGGAGTATAAATG
Found at i:40758384 original size:29 final size:29
Alignment explanation
Indices: 40758320--40758384 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
40758310 TATGGCTAAT
** *
40758320 TGCTTTGTGGAGTATAAATGATGGTTAAT
1 TGCTTTGTGGAGTATAAATGATGGAGAAA
* * *
40758349 TGTTTTGTGGAGTATAAATGCTTGAGAAA
1 TGCTTTGTGGAGTATAAATGATGGAGAAA
40758378 TGCTTTG
1 TGCTTTG
40758385 ATGAAATATG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.42
Consensus pattern (29 bp):
TGCTTTGTGGAGTATAAATGATGGAGAAA
Found at i:40763643 original size:6 final size:6
Alignment explanation
Indices: 40763593--40763665 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
40763583 AAAAGTCTAA
* ** * * * *
40763593 AAAAAT AACAAT AAACGT AAAAAT AGAAAT AAAACT AATACT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
40763641 AAAAAC AAAAA- CAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
40763666 TGGACTCAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
5 9 0.18
6 42 0.82
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:40767364 original size:21 final size:20
Alignment explanation
Indices: 40767340--40767387 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
40767330 GAAAAAATAG
*
40767340 AAAAAAAAATTAAACTAAAAC
1 AAAAAAAAATGAAA-TAAAAC
* *
40767361 AAAAATAAAGTGAAATAAAAT
1 AAAAA-AAAATGAAATAAAAC
40767382 AAAAAA
1 AAAAAA
40767388 TGGCTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAAAAAATGAAATAAAAC
Found at i:40770585 original size:10 final size:11
Alignment explanation
Indices: 40770570--40770598 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
40770560 TTCAAAGGTG
40770570 TGAATTGAAT-
1 TGAATTGAATA
40770580 TGAATTGAATA
1 TGAATTGAATA
40770591 TGAATTGA
1 TGAATTGA
40770599 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:40771201 original size:24 final size:24
Alignment explanation
Indices: 40771125--40771204 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
40771115 CTCTTTTATA
* *
40771125 AGCTTCTCGATTAACTGGCTTTTCGG
1 AGCTTC-CCATTAA-TGGCTTTCCGG
* * **
40771151 AGCTTCCCGA-TATTGGCTCTCATG
1 AGCTTCCC-ATTAATGGCTTTCCGG
40771175 AGCTTCCCATTAATGGCTTTCCGG
1 AGCTTCCCATTAATGGCTTTCCGG
40771199 AGCTTC
1 AGCTTC
40771205 TTGTTACATG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
23 1 0.02
24 31 0.74
25 3 0.07
26 7 0.17
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (24 bp):
AGCTTCCCATTAATGGCTTTCCGG
Found at i:40787905 original size:155 final size:155
Alignment explanation
Indices: 40787623--40787932 Score: 541
Period size: 155 Copynumber: 2.0 Consensus size: 155
40787613 TTATTAGTCT
* * *
40787623 TGAATAGGGATAATAACATATCTTAGGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCGA
1 TGAATAGGAATAATAACATAACTTAAGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCGA
*
40787688 TTCGGAGCCAGAATAATAAGTAAAGTCTAGGTGGATTTTTTCTTAGGTATTGTCTCAAGTCAATC
66 TTCGGAGCCAGAATAATAAGTAAAGTCTAGGTGGATTTTTTCTTAGGTATTATCTCAAGTCAATC
* *
40787753 GA-TTTTCCCAAAAGCAATTTCCCA
131 GATTTTTCCCAAAAGAAATTCCCCA
40787777 NTGAATAGGAATAATAACATAACTTAAGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCG
1 -TGAATAGGAATAATAACATAACTTAAGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCG
*
40787842 ATTCGGAGCCAGAATAATAAGTAAAGTCTAGGTGGATTTTTTCTTAGGTATTATCTTAAGTCAAT
65 ATTCGGAGCCAGAATAATAAGTAAAGTCTAGGTGGATTTTTTCTTAGGTATTATCTCAAGTCAAT
40787907 CGATTTTTCCCAAAAGAAATTCCCCA
130 CGATTTTTCCCAAAAGAAATTCCCCA
40787933 ATTCTTTTCT
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
155 127 0.86
156 20 0.14
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (155 bp):
TGAATAGGAATAATAACATAACTTAAGGATCTCTACGGAACAAGTTGAATGAATAAATCGTTCGA
TTCGGAGCCAGAATAATAAGTAAAGTCTAGGTGGATTTTTTCTTAGGTATTATCTCAAGTCAATC
GATTTTTCCCAAAAGAAATTCCCCA
Found at i:40809750 original size:26 final size:24
Alignment explanation
Indices: 40809720--40809769 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
40809710 AAATAAAAAA
*
40809720 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
40809746 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
40809770 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:40809789 original size:21 final size:21
Alignment explanation
Indices: 40809740--40809796 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
40809730 ATAATAAATC
*
40809740 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
40809760 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
40809782 AAATAATAATAAAAC
1 AAATAATATTAAAAC
40809797 GATTCTTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:40816897 original size:15 final size:15
Alignment explanation
Indices: 40816877--40816941 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
40816867 GTATCTTGGG
40816877 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
40816892 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
40816907 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
40816922 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
40816936 TTTCTT
1 TTTCTT
40816942 GTTATCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 11 0.26
15 31 0.72
16 1 0.02
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40816907 original size:30 final size:29
Alignment explanation
Indices: 40816872--40816941 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
40816862 GTATCGTATC
40816872 TTGGGTTTCTTTAT-TCTGGATTTCTTTAT
1 TTGGGTTTCTTTATCT-TGGATTTCTTTAT
*
40816901 TCTGGGTTTCTCTATCTTGGATTTCTTTAT
1 T-TGGGTTTCTTTATCTTGGATTTCTTTAT
*
40816931 TTGGTTTTCTT
1 TTGGGTTTCTT
40816942 GTTATCGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.25
30 26 0.72
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (29 bp):
TTGGGTTTCTTTATCTTGGATTTCTTTAT
Found at i:40838355 original size:8 final size:8
Alignment explanation
Indices: 40838342--40838376 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
40838332 CACAAGTTGC
40838342 TAGAGGAT
1 TAGAGGAT
40838350 TAGAGGAT
1 TAGAGGAT
40838358 TAGAGGAT
1 TAGAGGAT
40838366 TAGAGGAT
1 TAGAGGAT
40838374 TAG
1 TAG
40838377 GTGTGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (8 bp):
TAGAGGAT
Found at i:40858186 original size:19 final size:20
Alignment explanation
Indices: 40858132--40858179 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
40858122 GATCTCGTAC
40858132 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCATTTTCTCTGTT
40858152 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCATTTTCTCTGTT
40858172 TTTGGCCC
1 TTTGGCCC
40858180 GTTTCTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.27, G:0.17, T:0.52
Consensus pattern (20 bp):
TTTGGCCCATTTTCTCTGTT
Found at i:40858808 original size:85 final size:85
Alignment explanation
Indices: 40858665--40858834 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
40858655 TGCATGAAAA
40858665 TTAAATCTCCACCACTATAATTTAAGATGATACATCAATCAAAAGGTCTTTAGAGGGTTGTAGTG
1 TTAAATCTCCACCACTATAATTTAAGATGATACATCAATCAAAAGGTCTTTAGAGGGTTGTAGTG
*
40858730 AGGCTTGGTTAGGGGTTGTG
66 AGGCTTGGTTAGGGGGTGTG
40858750 TTAAATCTCCACCACTATAATTTAAGATGATACATCAATCAAAAGGTCTTTAGAGGGTTGTAGTG
1 TTAAATCTCCACCACTATAATTTAAGATGATACATCAATCAAAAGGTCTTTAGAGGGTTGTAGTG
40858815 AGGCTTGGTTAGGGGGTGTG
66 AGGCTTGGTTAGGGGGTGTG
40858835 GTCACAAGCT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (85 bp):
TTAAATCTCCACCACTATAATTTAAGATGATACATCAATCAAAAGGTCTTTAGAGGGTTGTAGTG
AGGCTTGGTTAGGGGGTGTG
Found at i:40867803 original size:35 final size:35
Alignment explanation
Indices: 40867756--40867825 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
40867746 GTTGCAAGAG
40867756 GCATTAGCTACAAAGTTAAAATTCAGCACTGCCTT
1 GCATTAGCTACAAAGTTAAAATTCAGCACTGCCTT
* *
40867791 GCATTAGGTACAAAGTTAAATTTCAGCACTGCCTT
1 GCATTAGCTACAAAGTTAAAATTCAGCACTGCCTT
40867826 TCATCCACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (35 bp):
GCATTAGCTACAAAGTTAAAATTCAGCACTGCCTT
Found at i:40869981 original size:46 final size:46
Alignment explanation
Indices: 40869931--40870103 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
40869921 TGGTTGAGCA
40869931 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
40869977 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40870022 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40870070 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40870104 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40870087 original size:93 final size:93
Alignment explanation
Indices: 40869928--40870098 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40869918 GGATGGTTGA
* *
40869928 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40869993 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
40870021 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40870086 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40870099 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:40886681 original size:46 final size:46
Alignment explanation
Indices: 40886521--40886693 Score: 145
Period size: 46 Copynumber: 3.7 Consensus size: 46
40886511 AACCTGCCCC
* * * *
40886521 TAAGTGAACTAGGACTCAACTCAACGAGCTCGGGCATTCGCATCTA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
* ** * * * * *
40886567 TAAATGAACTCTTATTCAACTCAACGAGTTCAGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC-ATTTGCATCCA
* * * *
40886615 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
40886660 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
40886694 TGCTCAATCA
Statistics
Matches: 97, Mismatches: 23, Indels: 14
0.72 0.17 0.10
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 2 0.02
46 53 0.55
47 24 0.25
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
Found at i:40894179 original size:46 final size:45
Alignment explanation
Indices: 40894112--40894279 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 45
40894102 CGCCCCTAAG
40894112 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTT-GCATCCATAAA
* * * *
40894158 TGAACTCGTACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCATCCATAAA
* * * * * *
40894205 CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGCTCGGGC-GTTGCATCCATAAA
40894251 TGAACTCGGACTCAACTCAACGAGCTCGG
1 TGAACTCGGACTCAACTCAACGAGCTCGG
40894280 ATGCTCAATC
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 53 0.54
47 27 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCATCCATAAA
Found at i:40894272 original size:93 final size:93
Alignment explanation
Indices: 40894113--40894283 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
40894103 GCCCCTAAGT
* * * *
40894113 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGTACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
40894178 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * *
40894206 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
40894271 CGAGCTCGGATGC
66 CGAGCTCGGATGC
40894284 TCAATCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:40912803 original size:40 final size:40
Alignment explanation
Indices: 40912748--40912827 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
40912738 GGGAATGTAC
40912748 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
40912788 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
40912828 TTAACTCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (40 bp):
AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
Found at i:40912837 original size:40 final size:40
Alignment explanation
Indices: 40912748--40912837 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
40912738 GGGAATGTAC
*
40912748 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
*
40912788 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
**
40912828 TTAACTCTTG
1 AGAACTCTTG
40912838 CTTCCATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (40 bp):
AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
Found at i:40915520 original size:34 final size:34
Alignment explanation
Indices: 40915477--40915545 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
40915467 CGAAGATAAT
* *
40915477 GCCAGTAGAACAGTTCATAGAGAGCTAATGGATG
1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
40915511 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
40915545 G
1 G
40915546 TTCATCACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (34 bp):
GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
Found at i:40921174 original size:14 final size:15
Alignment explanation
Indices: 40921144--40921180 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
40921134 GAAGATTATC
40921144 ACATTTTTATGTAAA
1 ACATTTTTATGTAAA
40921159 ACATTTTTATGTAAA
1 ACATTTTTATGTAAA
*
40921174 CCATTTT
1 ACATTTT
40921181 CCAGCATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (15 bp):
ACATTTTTATGTAAA
Found at i:40921550 original size:17 final size:18
Alignment explanation
Indices: 40921509--40921551 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40921499 TGTATTTACT
40921509 TATTATATAAGTAAATAG
1 TATTATATAAGTAAATAG
*
40921527 TAATATA-AAGTAAAATA-
1 TATTATATAAGT-AAATAG
40921544 TATTATAT
1 TATTATAT
40921552 TATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (18 bp):
TATTATATAAGTAAATAG
Found at i:40925472 original size:232 final size:232
Alignment explanation
Indices: 40925167--40925626 Score: 830
Period size: 232 Copynumber: 2.0 Consensus size: 232
40925157 TAACATCTAT
*
40925167 ATATCAAGACTTCATTTGCATAATTTCATTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
1 ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
*
40925232 ACTTCAATTCAACCAAAATATAACATCAAAATAAGTCAAATCACATGGCTTAACATATACACAAA
66 ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
*
40925297 AATAAGCTTAAGTCAAGATATCAAGTAGCAAAACTATCATCCCTTAAACTAGCCTATACATGCCA
131 AATAAGCTAAAGTCAAGATATCAAGTAGCAAAACTATCATCCCTTAAACTAGCCTATACATGCCA
*
40925362 TATTTACAAATTCACAAGTTTAAAAGTACCAATCGGA
196 TATTTACAAATTCACAAGTTCAAAAGTACCAATCGGA
*
40925399 ATATCAAGACTTCATTTGCATAATTTCGCTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
1 ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
* *
40925464 ATTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACATAAA
66 ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
* * *
40925529 AATATGCTAAAGTCAAGATATCAAGTAGCATAACTATCATCCTTTAAACTAGCCTATACATGCCA
131 AATAAGCTAAAGTCAAGATATCAAGTAGCAAAACTATCATCCCTTAAACTAGCCTATACATGCCA
40925594 TATTTACAAATTCACAAGTTCAAAAGTACCAAT
196 TATTTACAAATTCACAAGTTCAAAAGTACCAAT
40925627 TGAAATTTGA
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 218 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (232 bp):
ATATCAAGACTTCATTTGCATAATTTCACTCCATCTTTCCTTGCTAAAACATACCATAATTGAAC
ACTTCAATTCAACCAAAATATAACATCAAAATAAGCCAAATCACATGGCTTAACATATACACAAA
AATAAGCTAAAGTCAAGATATCAAGTAGCAAAACTATCATCCCTTAAACTAGCCTATACATGCCA
TATTTACAAATTCACAAGTTCAAAAGTACCAATCGGA
Found at i:40926148 original size:46 final size:46
Alignment explanation
Indices: 40926093--40926240 Score: 151
Period size: 46 Copynumber: 3.2 Consensus size: 46
40926083 AGCTGATAAA
40926093 CAGTAAGCTCTATTGAGCTGAAAATGGTAAGCCCTATTGAGCTGAA-
1 CAGTAAGCTCTATTGAGCTG-AAATGGTAAGCCCTATTGAGCTGAAT
* * *
40926139 CAGTAAGCTCTATCGAGCT-AAATCGGTAAGCTCC-AATGAGTTGAAT
1 CAGTAAGCTCTATTGAGCTGAAAT-GGTAAGC-CCTATTGAGCTGAAT
* * * * * *
40926185 CGGTAAGCTCCAATGAGCTGAAATAGTAAGCTCT-TACGAGCTGAAT
1 CAGTAAGCTCTATTGAGCTGAAATGGTAAGCCCTAT-TGAGCTGAAT
40926231 CAGTAAGCTC
1 CAGTAAGCTC
40926241 ATACGAGCTA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
44 4 0.05
45 17 0.20
46 58 0.70
47 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (46 bp):
CAGTAAGCTCTATTGAGCTGAAATGGTAAGCCCTATTGAGCTGAAT
Found at i:40926171 original size:23 final size:23
Alignment explanation
Indices: 40926089--40926250 Score: 97
Period size: 23 Copynumber: 7.1 Consensus size: 23
40926079 CCCGAGCTGA
*
40926089 TAAA-CAGTAAGCTCTATTGAGC
1 TAAATCAGTAAGCTCTATCGAGC
* * *
40926111 TGAAAAT-GGTAAGCCCTATTGAGC
1 T--AAATCAGTAAGCTCTATCGAGC
*
40926135 TGAA-CAGTAAGCTCTATCGAGC
1 TAAATCAGTAAGCTCTATCGAGC
* * *
40926157 TAAATCGGTAAGCTCCAAT-GAGT
1 TAAATCAGTAAGCT-CTATCGAGC
* * *
40926180 TGAATCGGTAAGCTCCAAT-GAGC
1 TAAATCAGTAAGCT-CTATCGAGC
40926203 TGAAAT-AGTAAGCTCT-TACGAGC
1 T-AAATCAGTAAGCTCTAT-CGAGC
*
40926226 TGAATCAGTAAGCTC-ATACGAGC
1 TAAATCAGTAAGCTCTAT-CGAGC
40926249 TA
1 TA
40926251 TGGTGAGTCC
Statistics
Matches: 112, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.01
22 24 0.21
23 62 0.55
24 25 0.22
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (23 bp):
TAAATCAGTAAGCTCTATCGAGC
Found at i:40927168 original size:31 final size:31
Alignment explanation
Indices: 40927133--40927194 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40927123 ATTATTAATA
40927133 ACTTAATTAACTAAATTACCAATATAACCTT
1 ACTTAATTAACTAAATTACCAATATAACCTT
40927164 ACTTAATTAACTAAATTACCAATATAACCTT
1 ACTTAATTAACTAAATTACCAATATAACCTT
40927195 GTTAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (31 bp):
ACTTAATTAACTAAATTACCAATATAACCTT
Found at i:40928688 original size:16 final size:16
Alignment explanation
Indices: 40928667--40928706 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
40928657 TTGAATATTT
*
40928667 AATTATTCATATAATA
1 AATTATTAATATAATA
40928683 AATTATTAATATAATA
1 AATTATTAATATAATA
40928699 AATTATTA
1 AATTATTA
40928707 TAATAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATTAATATAATA
Found at i:40928690 original size:19 final size:17
Alignment explanation
Indices: 40928675--40928712 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
40928665 TTAATTATTC
40928675 ATATAATAAATTATTA-
1 ATATAATAAATTATTAT
40928691 ATATAATAAATTATTAT
1 ATATAATAAATTATTAT
40928708 A-ATAA
1 ATATAA
40928713 ATCATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAATAAATTATTAT
Found at i:40928712 original size:16 final size:16
Alignment explanation
Indices: 40928667--40928712 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
40928657 TTGAATATTT
40928667 AATTATTCAT-ATAATA
1 AATTATT-ATAATAATA
40928683 AATTATTA-ATATAATA
1 AATTATTATA-ATAATA
40928699 AATTATTATAATAA
1 AATTATTATAATAA
40928713 ATCATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATTATAATAATA
Found at i:40928750 original size:13 final size:14
Alignment explanation
Indices: 40928734--40928775 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40928724 TTTCAATTTT
40928734 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
40928747 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
40928762 ATTTTAAATAATAT
1 ATTTT-AATAATAT
40928776 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:40928760 original size:16 final size:16
Alignment explanation
Indices: 40928738--40928774 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40928728 AATTTTATTT
40928738 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
40928755 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
40928770 TAATA
1 TAATA
40928775 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:40932938 original size:18 final size:18
Alignment explanation
Indices: 40932915--40932952 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40932905 TATTTCTCAA
*
40932915 TTCTCAATTCTCACACAT
1 TTCTCAATACTCACACAT
*
40932933 TTCTCAATAGTCACACAT
1 TTCTCAATACTCACACAT
40932951 TT
1 TT
40932953 TTTAGAAAAG
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:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (18 bp):
TTCTCAATACTCACACAT
Found at i:40933422 original size:21 final size:22
Alignment explanation
Indices: 40933396--40933451 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
40933386 TTTTGTCTTA
40933396 GGGCAGCTTGTTGA-TGAGTTG
1 GGGCAGCTTGTTGACTGAGTTG
* * *
40933417 GGGCAG-TAGGTAACTGAGTTG
1 GGGCAGCTTGTTGACTGAGTTG
*
40933438 GGGCAGCCTGTTGA
1 GGGCAGCTTGTTGA
40933452 ATTGGGGTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.18, C:0.12, G:0.43, T:0.27
Consensus pattern (22 bp):
GGGCAGCTTGTTGACTGAGTTG
Found at i:40933499 original size:21 final size:21
Alignment explanation
Indices: 40933453--40933492 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40933443 GCCTGTTGAA
*
40933453 TTGGGGTACCCTCTTGCTGGC
1 TTGGGGTACCCTATTGCTGGC
*
40933474 TTGGGGTAGCCTATTGCTG
1 TTGGGGTACCCTATTGCTG
40933493 AGTTGGGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGGGGTACCCTATTGCTGGC
Found at i:40934850 original size:40 final size:40
Alignment explanation
Indices: 40934733--40934852 Score: 206
Period size: 40 Copynumber: 3.0 Consensus size: 40
40934723 CGGATGATAA
* *
40934733 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
40934773 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
40934813 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
40934853 GAATATGTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 76 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40937422 original size:46 final size:46
Alignment explanation
Indices: 40937355--40937572 Score: 382
Period size: 46 Copynumber: 4.7 Consensus size: 46
40937345 AACCCGCCCC
* * *
40937355 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
***
40937401 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40937447 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40937493 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40937539 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40937573 TGCTCAACCA
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 165 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40942950 original size:8 final size:8
Alignment explanation
Indices: 40942939--40942966 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40942929 TTAAAACGAT
40942939 AAATGCCG
1 AAATGCCG
40942947 AAATGCCG
1 AAATGCCG
40942955 AAATGCCG
1 AAATGCCG
40942963 AAAT
1 AAAT
40942967 TCTGGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (8 bp):
AAATGCCG
Found at i:40943106 original size:21 final size:20
Alignment explanation
Indices: 40943080--40943119 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40943070 GCATTACGAT
40943080 AAGTTGGGCCTCAAGGGGCTG
1 AAGTTGGGCC-CAAGGGGCTG
*
40943101 AAGTTGGGCCCAATGGGCT
1 AAGTTGGGCCCAAGGGGCT
40943120 TTCGGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (20 bp):
AAGTTGGGCCCAAGGGGCTG
Found at i:40943348 original size:31 final size:31
Alignment explanation
Indices: 40943310--40943373 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40943300 CGTTTACAGT
40943310 AAAGGCTTCAGCCCAGTAATATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
* **
40943341 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
40943372 AA
1 AA
40943374 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:40947195 original size:265 final size:265
Alignment explanation
Indices: 40946712--40947244 Score: 976
Period size: 265 Copynumber: 2.0 Consensus size: 265
40946702 ATTACTTGTA
40946712 AAGAAATAACCAAATTTGATAATTAAAAATAAAATTCTAAAATCTAATAAAAATAAAAAGTAGTT
1 AAGAAATAACCAAATTTGATAATTAAAAATAAAATTCTAAAATCTAATAAAAATAAAAAGTAGTT
40946777 TTAATAAAAATAAAAAAAGAAACATAAAATAATAAATAAATGTTTTTAAACATCTTCATCGCTGG
66 TTAATAAAAATAAAAAAAGAAACATAAAATAATAAATAAATGTTTTTAAACATCTTCATCGCTGG
*
40946842 ATGGTTCGCAAGGTGGGACTGGCGATGAGATGTGAAGGTGCTGACAAATCTGCTGTAGAGTTGCA
131 ATGGTTCGCAAGGTGGGACTGGCGATGAGATGTGAAGGTGCTGACAAATCTGCTGTAGAGTAGCA
* * *
40946907 TCAATATTGTCAAATCGTTGAAAACACTGCTGCTCGAATTGAGTGAGGCACTCAGAGATGTCAGC
196 TCAATATTGTCAAATCATTGAAAACACTGCTGCTCGAATCGAGTAAGGCACTCAGAGATGTCAGC
*
40946972 ATTTG
261 ATATG
40946977 AAGAAATAACCAAATTTGATAATTAAAAATAAAATTCTAAAATCTAATAAAAATAAAAAGTAGTT
1 AAGAAATAACCAAATTTGATAATTAAAAATAAAATTCTAAAATCTAATAAAAATAAAAAGTAGTT
40947042 TTAATAAAAATAAAAAAAGAAACATAAAATAATAAATAAATGTTTTTAAACATCTTCATCGCTGG
66 TTAATAAAAATAAAAAAAGAAACATAAAATAATAAATAAATGTTTTTAAACATCTTCATCGCTGG
*
40947107 ATGGTTCGCAAGGTGGGACTGGCGATGAGATGTGGAGGTGCTGACAAATCTGCTGTAGAGTAGCA
131 ATGGTTCGCAAGGTGGGACTGGCGATGAGATGTGAAGGTGCTGACAAATCTGCTGTAGAGTAGCA
* * * *
40947172 TCAATGTTGTCAATTCATTGAAAACACTGCTGCTCGAATCGGGTAAGGCGCTCAGAGATGTCAGC
196 TCAATATTGTCAAATCATTGAAAACACTGCTGCTCGAATCGAGTAAGGCACTCAGAGATGTCAGC
40947237 ATATG
261 ATATG
40947242 AAG
1 AAG
40947245 CCGTCGCATG
Statistics
Matches: 258, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
265 258 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (265 bp):
AAGAAATAACCAAATTTGATAATTAAAAATAAAATTCTAAAATCTAATAAAAATAAAAAGTAGTT
TTAATAAAAATAAAAAAAGAAACATAAAATAATAAATAAATGTTTTTAAACATCTTCATCGCTGG
ATGGTTCGCAAGGTGGGACTGGCGATGAGATGTGAAGGTGCTGACAAATCTGCTGTAGAGTAGCA
TCAATATTGTCAAATCATTGAAAACACTGCTGCTCGAATCGAGTAAGGCACTCAGAGATGTCAGC
ATATG
Found at i:40949620 original size:28 final size:27
Alignment explanation
Indices: 40949557--40949708 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
40949547 ATATTAAGTC
* *
40949557 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
40949584 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
40949612 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
40949639 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
40949667 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
40949694 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40949709 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40949641 original size:55 final size:55
Alignment explanation
Indices: 40949557--40949733 Score: 264
Period size: 55 Copynumber: 3.2 Consensus size: 55
40949547 ATATTAAGTC
* * *
40949557 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
40949612 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
40949667 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
40949723 CGCACACTTAG
1 CGCACACTTAG
40949734 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 95 0.86
56 16 0.14
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40955340 original size:40 final size:40
Alignment explanation
Indices: 40955296--40955473 Score: 284
Period size: 40 Copynumber: 4.5 Consensus size: 40
40955286 AACCCAATTA
* * * *
40955296 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATG
1 CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
* * *
40955336 CCTTCGAGACTTAACCCGGTTATAATAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
*
40955376 CCTTCGGGACTTAACCCGAATATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
40955416 CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
40955456 CCTTCGGGACTTAACCCG
1 CCTTCGGGACTTAACCCG
40955474 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 126 1.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGATATAACAACCAGCACGAATG
Found at i:40978670 original size:43 final size:43
Alignment explanation
Indices: 40978622--40978757 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 43
40978612 CCCGGACGTA
* *
40978622 GTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAGG
1 GTCTTACATGTAATTCAATATCGATGCCTATGTCCCAGACACG
* * * *
40978665 GTCTTACATG-AAATCAGATAT-GATACCGATGTCCCAGACATG
1 GTCTTACATGTAATTCA-ATATCGATGCCTATGTCCCAGACACG
* * *
40978707 GTCTTATACGTAAATCTC-A-ATCGAGGCCTATGTCCCAGACACG
1 GTCTTACATGT-AAT-TCAATATCGATGCCTATGTCCCAGACACG
*
40978750 TTCTTACA
1 GTCTTACA
40978758 CGATGTCTCT
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
42 32 0.43
43 38 0.51
44 2 0.03
45 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
GTCTTACATGTAATTCAATATCGATGCCTATGTCCCAGACACG
Found at i:40981276 original size:30 final size:30
Alignment explanation
Indices: 40981240--40981309 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
40981230 GCAACAATCT
40981240 CAAAAACATAGAAATTATCAAAAATCAAAG
1 CAAAAACATAGAAATTATCAAAAATCAAAG
40981270 CAAAAACATAGAAATTATCAAAAATCAAAG
1 CAAAAACATAGAAATTATCAAAAATCAAAG
40981300 CAAAAACATA
1 CAAAAACATA
40981310 CCTCAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.16
Consensus pattern (30 bp):
CAAAAACATAGAAATTATCAAAAATCAAAG
Found at i:40991383 original size:9 final size:8
Alignment explanation
Indices: 40991368--40991393 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40991358 ACTTGTTCTT
40991368 TAAAAAAA
1 TAAAAAAA
40991376 TAAAAAAA
1 TAAAAAAA
40991384 TAAAAAAA
1 TAAAAAAA
40991392 TA
1 TA
40991394 CAATACTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:40998276 original size:34 final size:34
Alignment explanation
Indices: 40998224--40998300 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
40998214 AAATAGTCTA
* * *
40998224 GCCTAAGCCCTTATCAGTAGCAATATCAGTGTGG
1 GCCTTAGCCCTTATCAGTAGCAATAGCAATGTGG
*
40998258 GCCTTAGCCCATTA-CAGTAGCAGTAGCAATGTGG
1 GCCTTAGCCC-TTATCAGTAGCAATAGCAATGTGG
40998292 GCCTTAGCC
1 GCCTTAGCC
40998301 TAATTCAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.92
35 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (34 bp):
GCCTTAGCCCTTATCAGTAGCAATAGCAATGTGG
Found at i:40998310 original size:34 final size:33
Alignment explanation
Indices: 40998237--40998315 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
40998227 TAAGCCCTTA
* * * *
40998237 TCAGTAGCAATATCAGTGTGGGCCTTAGCCCAT
1 TCAGTAGCAGTAGCAATGTGGGCCTTAGCCAAT
40998270 TACAGTAGCAGTAGCAATGTGGGCCTTAGCCTAAT
1 T-CAGTAGCAGTAGCAATGTGGGCCTTAGCC-AAT
40998305 TCAGTA-CAGTA
1 TCAGTAGCAGTA
40998316 TTAGAGATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.15
34 31 0.77
35 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (33 bp):
TCAGTAGCAGTAGCAATGTGGGCCTTAGCCAAT
Found at i:41001930 original size:16 final size:16
Alignment explanation
Indices: 41001909--41001939 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41001899 AACCCAACCC
*
41001909 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
41001925 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
41001940 CCCATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:41002717 original size:27 final size:27
Alignment explanation
Indices: 41002687--41002751 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
41002677 GGGCATATTC
41002687 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
41002714 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
41002741 GTCTTTTTACC
1 GTCATTTTACC
41002752 TAATAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:41002753 original size:26 final size:26
Alignment explanation
Indices: 41002687--41002788 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 26
41002677 GGGCATATTC
41002687 GTCATTTTACCATACAAGGGTATTACG
1 GTCATTTTACC-TACAAGGGTATTACG
* *
41002714 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTA-CCTACAAGGG-TATTACG
* ***
41002741 GTCTTTTTACCTA-ATAGGGGTATTTTA
1 GTCATTTTACCTACA-A-GGGTATTACG
*
41002768 GTCATTTCATCCTACAAGGGT
1 GTCATTTTA-CCTACAAGGGT
41002789 GTTTTGGTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
25 1 0.02
26 5 0.09
27 43 0.74
28 8 0.14
29 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (26 bp):
GTCATTTTACCTACAAGGGTATTACG
Found at i:41002835 original size:27 final size:27
Alignment explanation
Indices: 41002805--41002909 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 27
41002795 GTAAATCTAC
41002805 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
41002832 AAACCAATGGTATTTCTA-TAATTTTGT
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* * **
41002859 AAATC-AGAGGTATTT-TGATAATTTTAC
1 AAACCAAG-GGTATTTCAG-TAATTTTGT
**
41002886 AAACTGAGGGTATTTCAGTAATTT
1 AAACCAAGGGTATTTCAGTAATTT
41002910 CACAAACTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.02
27 58 0.92
28 4 0.06
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:41002914 original size:27 final size:26
Alignment explanation
Indices: 41002877--41003004 Score: 98
Period size: 27 Copynumber: 4.8 Consensus size: 26
41002867 GGTATTTTGA
*
41002877 TAATTTTACAAACTGAGGGTATTTCAG
1 TAATTTCACAAACT-AGGGTATTTCAG
**
41002904 TAATTTCACAAACTAGTGGTATTTTGG
1 TAATTTCACAAACTAG-GGTATTTCAG
* **
41002931 TAATTTTACAAACTAGGGTTATTTTGG
1 TAATTTCACAAACTAGGG-TATTTCAG
**
41002958 TAA-TTCTACCCTA-TAGGGGTATTTCAG
1 TAATTTC-A-CAAACTA-GGGTATTTCAG
* *
41002985 TAATTTCACAATCGAGGGTA
1 TAATTTCACAAACTAGGGTA
41003005 AAACGGTAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
26 12 0.15
27 61 0.75
28 8 0.10
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
TAATTTCACAAACTAGGGTATTTCAG
Found at i:41003024 original size:27 final size:27
Alignment explanation
Indices: 41002994--41003089 Score: 138
Period size: 27 Copynumber: 3.5 Consensus size: 27
41002984 GTAATTTCAC
41002994 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
41003021 AATCGATGGTAAAAATGGTAATTTTGTA
1 AATCGAGGGT-AAAACGGTAATTTTGTA
* **
41003049 AATCGAGGGTAAAACAGTAAGGTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
41003076 AATCGAGGGTAAAA
1 AATCGAGGGTAAAA
41003090 TTTGGTAAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 36 0.59
28 25 0.41
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:41012542 original size:25 final size:24
Alignment explanation
Indices: 41012500--41012571 Score: 103
Period size: 23 Copynumber: 3.0 Consensus size: 24
41012490 GCTTTATCAT
*
41012500 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
41012525 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41012548 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41012572 CACTTCCTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
23 23 0.52
24 9 0.20
25 12 0.27
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:41012646 original size:20 final size:20
Alignment explanation
Indices: 41012621--41012659 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41012611 TATGATTACA
41012621 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
41012641 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
41012660 ACCCTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:41015251 original size:33 final size:30
Alignment explanation
Indices: 41015206--41015345 Score: 96
Period size: 31 Copynumber: 4.6 Consensus size: 30
41015196 TCAGTACAAT
* *
41015206 CTGGGCCAAAGCCCTATTCAGTCTCAACATATA
1 CTGGGCCGAAGCCCT-TT-AGT-TAAACATATA
* *
41015239 CTGGGCCGAAG-CCTTTTGTTAAACATTTA
1 CTGGGCCGAAGCCCTTTAGTTAAACATATA
*
41015268 CTGGGCCGAAGCCTTTTCA--TAAATCATATCA
1 CTGGGCCGAAGCCCTTT-AGTTAAA-CATAT-A
*
41015299 CTGGGCCGAAGCCTTTTCA--TAAATCATATCA
1 CTGGGCCGAAGCCCTTT-AGTTAAA-CATAT-A
41015330 CT-GGCCGAAG-CCTTTA
1 CTGGGCCGAAGCCCTTTA
41015346 CTGTAAGCGG
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.01
29 27 0.28
30 18 0.19
31 36 0.38
32 3 0.03
33 10 0.11
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
CTGGGCCGAAGCCCTTTAGTTAAACATATA
Found at i:41015305 original size:31 final size:31
Alignment explanation
Indices: 41015233--41015344 Score: 169
Period size: 31 Copynumber: 3.7 Consensus size: 31
41015223 TCAGTCTCAA
**
41015233 CATAT-ACTGGGCCGAAGCCTTTTGTTAAA-
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
41015262 CAT-TTACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41015292 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41015323 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
41015345 ACTGTAAGCG
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
28 1 0.01
29 25 0.32
30 16 0.21
31 35 0.45
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:41015593 original size:25 final size:25
Alignment explanation
Indices: 41015565--41015634 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
41015555 CTCTTTTAAT
* *
41015565 AACTGGCGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41015590 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41015615 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41015635 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41016508 original size:26 final size:25
Alignment explanation
Indices: 41016447--41016519 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
41016437 ATATTCGTCA
41016447 TTTTACCATATAGGGGTATTACGGTC
1 TTTTACC-TATAGGGGTATTACGGTC
**
41016473 ACTTACCCTATAGGGGCT-TTACGGTC
1 TTTTA-CCTATAGGGG-TATTACGGTC
41016499 TTTTTACCTATTAGGGGTATT
1 -TTTTACCTA-TAGGGGTATT
41016520 TTAGTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (25 bp):
TTTTACCTATAGGGGTATTACGGTC
Found at i:41016590 original size:27 final size:27
Alignment explanation
Indices: 41016560--41016685 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 27
41016550 GTAAATCTAC
41016560 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
41016587 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
41016613 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
** * ** *
41016643 AAATTAGGGGTATTTTGGTAATTTTAT
1 AAACCAAGGGTATTTCAGTAATTTTGT
**
41016670 AAACTGAGGGTATTTC
1 AAACCAAGGGTATTTC
41016686 GGAAATTTCA
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
26 1 0.01
27 53 0.66
28 7 0.09
29 18 0.22
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:41016692 original size:27 final size:26
Alignment explanation
Indices: 41016622--41016746 Score: 115
Period size: 27 Copynumber: 4.7 Consensus size: 26
41016612 TAGAAAGTCA
* ** *
41016622 AGGGTATTTCTGTAATTTTGTAAATT
1 AGGGTATTTCGGTAATTTTACAAACT
* *
41016648 AGGGGTATTTTGGTAATTTTATAAACT
1 A-GGGTATTTCGGTAATTTTACAAACT
* * *
41016675 GAGGGTATTTCGGAAATTTCACAAACC
1 -AGGGTATTTCGGTAATTTTACAAACT
*
41016702 AGTGGTATTTTGGTAATTTTACAAACT
1 AG-GGTATTTCGGTAATTTTACAAACT
*
41016729 AGGAGTATTTTGGTAATT
1 AGG-GTATTTCGGTAATT
41016747 CTACCCTATA
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.05
27 77 0.94
28 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAAACT
Found at i:41017744 original size:56 final size:57
Alignment explanation
Indices: 41017615--41017766 Score: 243
Period size: 56 Copynumber: 2.6 Consensus size: 57
41017605 TCTCATACAG
* *
41017615 GGTCTTACTCGTACACATATATCGGAATCACATATCGATGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATC-A-GATGCCAACGTATTAAACGT
*
41017674 GGTCTTACTCGCACACATATATCGGAATCACATATC-GATGCCAACGTTTTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGT
*
41017730 GGTCTTACTTGCACACATATATCGGAATCACATATCA
1 GGTCTTACTCGCACACATATATCGGAATCACATATCA
41017767 CAAGTCGAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
56 53 0.60
59 35 0.40
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (57 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGT
Found at i:41041369 original size:53 final size:54
Alignment explanation
Indices: 41041306--41041413 Score: 200
Period size: 53 Copynumber: 2.0 Consensus size: 54
41041296 ATTTATAATG
41041306 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGAC-GTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
*
41041359 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACATTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
41041413 T
1 T
41041414 ACATTGTGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (54 bp):
TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
Found at i:41045820 original size:46 final size:45
Alignment explanation
Indices: 41045745--41045873 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 45
41045735 CATTAGGTGG
* *
41045745 TATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGACCACTT-
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCG-CCA-TTA
*
41045791 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATT-A
* * * *
41045837 GACGAGAGCTAGTGTAAGACATGTCTTGGACATGCAT
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCAT
41045874 TAGCCTCGGG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 70 0.95
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATTA
Found at i:41046026 original size:49 final size:49
Alignment explanation
Indices: 41045942--41046058 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 49
41045932 GTTTGTCAGC
* *
41045942 GTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAGAGCTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
* * * * *
41045991 GTAAGACCTGTCTGGGACGTGGCATTGGC-CTCGATATATGAAAGTTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAAAGCTAGT
* * *
41046040 GTAACACCTATATGGGACA
1 GTAAGACCTGTCTGGGACA
41046059 CAACATCGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 1 0.02
49 55 0.98
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (49 bp):
GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
Found at i:41047313 original size:20 final size:21
Alignment explanation
Indices: 41047274--41047313 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41047264 GTCAACAGGG
*
41047274 CCACACGGACGTGTTGCCCTT
1 CCACACGGACGTGATGCCCTT
*
41047295 CCACACGGGCGT-ATGCCCT
1 CCACACGGACGTGATGCCCT
41047314 GTTTTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (21 bp):
CCACACGGACGTGATGCCCTT
Done.