Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 130 of 255
Found at i:41713119 original size:30 final size:31
Alignment explanation
Indices: 41713043--41713125 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
41713033 TCAGTCTCGA
41713043 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41713073 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41713104 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
41713126 ACTGTAAGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 18 0.35
31 34 0.65
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:41713373 original size:25 final size:25
Alignment explanation
Indices: 41713345--41713414 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41713335 CTCTTTTAAT
*
41713345 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41713370 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41713395 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41713415 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41714372 original size:27 final size:27
Alignment explanation
Indices: 41714342--41714393 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
41714332 GTAAATATGC
*
41714342 AAACTAAGGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
41714369 AAACCAATGGTATTTCTATAATTTT
1 AAACCAAGGGTATTTCTATAATTTT
41714394 TCTGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:41714553 original size:27 final size:27
Alignment explanation
Indices: 41714397--41714733 Score: 158
Period size: 27 Copynumber: 12.5 Consensus size: 27
41714387 TAATTTTTCT
*
41714397 GTAATTTTGTAAAT-TAGGGGTATTTTG
1 GTAATTTTGTAAATCGA-GGGTATTTTG
** * ***
41714424 GTAATTTTACAAATTGAGGGTATTCCA
1 GTAATTTTGTAAATCGAGGGTATTTTG
* *** *
41714451 ATAATTTCACAAA-CCAGTGGTATTTTG
1 GTAATTTTGTAAATCGAG-GGTATTTTG
** *
41714478 GTAATTTTACAAA-CTAGGGGTATTTTG
1 GTAATTTTGTAAATCGA-GGGTATTTTG
* * * *
41714505 GTAATTTTGTAAACCAATGGTATTTTA
1 GTAATTTTGTAAATCGAGGGTATTTTG
***
41714532 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTTTGTAAATCGAGGGTATTTTG
* * * ***
41714559 ATAATTCTGTAAATAGAGGGTAAAATG
1 GTAATTTTGTAAATCGAGGGTATTTTG
* ** ***
41714586 GTAATTCTGTAAATTAAGGGTAAAATG
1 GTAATTTTGTAAATCGAGGGTATTTTG
* * ****
41714613 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTTTGTAAATCGAGGGTATTTTG
* ***
41714640 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTTTGTAAATCGAGGGTATTTTG
* *
41714667 GTAATTCTGTAAATCGAGGGTACTTTG
1 GTAATTTTGTAAATCGAGGGTATTTTG
** * * *
41714694 GTAATTTTACAAATTGAGGATATTTTA
1 GTAATTTTGTAAATCGAGGGTATTTTG
*
41714721 GTAATTTGGTAAA
1 GTAATTTTGTAAA
41714734 CTAAAGTATT
Statistics
Matches: 253, Mismatches: 53, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
26 2 0.01
27 247 0.98
28 4 0.02
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (27 bp):
GTAATTTTGTAAATCGAGGGTATTTTG
Found at i:41714696 original size:81 final size:81
Alignment explanation
Indices: 41714503--41714699 Score: 259
Period size: 81 Copynumber: 2.4 Consensus size: 81
41714493 AGGGGTATTT
* * * * * * * *
41714503 TGGTAATTTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATGATAATTCTG
1 TGGTAATTCTGTAAATCAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTG
41714568 TAAATAGAGGGTAAAA
66 TAAATAGAGGGTAAAA
* ** *
41714584 TGGTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTG
1 TGGTAATTCTGTAAATCAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTG
*
41714649 TAAATCGAGGGTAAAA
66 TAAATAGAGGGTAAAA
* *
41714665 TGGTAATTCTGTAAATCGAGGGTACTTTGGTAATT
1 TGGTAATTCTGTAAATCAAGGGTAATTTGGTAATT
41714700 TTACAAATTG
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 98 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (81 bp):
TGGTAATTCTGTAAATCAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTG
TAAATAGAGGGTAAAA
Found at i:41714699 original size:54 final size:54
Alignment explanation
Indices: 41714532--41714688 Score: 251
Period size: 54 Copynumber: 2.9 Consensus size: 54
41714522 TGGTATTTTA
* * *
41714532 GTAATTTTGTAAATCGAGGGTAAAATGATAATTCTGTAAATAGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
** * *
41714586 GTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
41714640 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTA
41714689 CTTTGGTAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATG
Found at i:41716969 original size:30 final size:31
Alignment explanation
Indices: 41716893--41716975 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
41716883 TCAGTCACGA
41716893 CATAT-ACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
* * *
41716923 CATATCATTGGGCCGAAGCCTTTTCATAAGT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
41716954 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTAGGCCGAAGCCTTT
41716976 ACTGTAAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.38
31 30 0.62
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTTCATAAAT
Found at i:41717223 original size:25 final size:25
Alignment explanation
Indices: 41717195--41717264 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
41717185 TTCTTTTAAT
*
41717195 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41717220 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
41717245 AACTGAGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41717265 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:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41718103 original size:27 final size:26
Alignment explanation
Indices: 41718073--41718150 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
41718063 CAGCATGTTC
*
41718073 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
* *
41718100 GTCACTTTACCCTATAGGGGCT-TTATG
1 GTCATTTTA-CCTATAGGGG-TATTACG
*
41718127 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-TAGGGGTATT
41718151 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 34 0.81
28 3 0.07
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:41718363 original size:27 final size:27
Alignment explanation
Indices: 41718232--41718384 Score: 150
Period size: 27 Copynumber: 5.7 Consensus size: 27
41718222 AGAAAGCCAA
**
41718232 GGGTATTTCT-GTAATTTTGTAAA-TCAG
1 GGGTATTT-TGGTAATTTTACAAACT-AG
*
41718259 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
41718285 AGTGTATTTTGGTAATTTCACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
41718313 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
** * *
41718340 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
41718367 TGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
41718385 GTAAATCGAG
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.02
27 103 0.96
28 2 0.02
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:41718385 original size:27 final size:27
Alignment explanation
Indices: 41718191--41718398 Score: 136
Period size: 27 Copynumber: 7.6 Consensus size: 27
41718181 GTAAATCTAC
* *
41718191 TTTGTAAACCAATGGTATTTCT-ATAAT
1 TTTGTAAACCAAGGGTATTT-TGGTAAT
41718218 TTT-TAGAAAGCCAAGGGTATTTCT-GTAAT
1 TTTGT--AAA-CCAAGGGTATTT-TGGTAAT
* *
41718247 TTTGTAAATCAGGGGTATTTTGGTAAT
1 TTTGTAAACCAAGGGTATTTTGGTAAT
** *** *
41718274 TTTACAAATTGAGTGTATTTTGGTAAT
1 TTTGTAAACCAAGGGTATTTTGGTAAT
*** *
41718301 TTCACAAA-CTAGTGGTATTTTGGTAAT
1 TTTGTAAACCAAG-GGTATTTTGGTAAT
** * *
41718328 TTTACAAACTAGGGGTATTTTGGTAAT
1 TTTGTAAACCAAGGGTATTTTGGTAAT
* *
41718355 TTTGTAAACCAATGGTATTTTAGTAAT
1 TTTGTAAACCAAGGGTATTTTGGTAAT
* *
41718382 TTTGTAAATCGAGGGTA
1 TTTGTAAACCAAGGGTA
41718399 AAACTGTAAT
Statistics
Matches: 147, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
26 4 0.03
27 115 0.78
28 7 0.05
29 20 0.14
30 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TTTGTAAACCAAGGGTATTTTGGTAAT
Found at i:41718398 original size:54 final size:54
Alignment explanation
Indices: 41718191--41718398 Score: 188
Period size: 54 Copynumber: 3.8 Consensus size: 54
41718181 GTAAATCTAC
* * *
41718191 TTTGTAAACCAATGGTATTTCTA-TAATTTTTAGAAAGCCAAGGGTATTTCT-GTAAT
1 TTTGTAAACCAATGGTATTT-TAGTAA-TTTTACAAA-TCGAGGGTATTT-TGGTAAT
* ** * * *
41718247 TTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGTGTATTTTGGTAAT
1 TTTGTAAACCAATGGTATTTTAGTAATTTTACAAATCGAGGGTATTTTGGTAAT
*** * * * *
41718301 TTCACAAACTAGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAAT
1 TTTGTAAACCAATGGTATTTTAGTAATTTTACAAATCGA-GGGTATTTTGGTAAT
**
41718355 TTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 TTTGTAAACCAATGGTATTTTAGTAATTTTACAAATCGAGGGTA
41718399 AAACTGTAAT
Statistics
Matches: 121, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
53 2 0.02
54 88 0.73
55 11 0.09
56 20 0.17
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (54 bp):
TTTGTAAACCAATGGTATTTTAGTAATTTTACAAATCGAGGGTATTTTGGTAAT
Found at i:41718407 original size:27 final size:27
Alignment explanation
Indices: 41718377--41718506 Score: 183
Period size: 27 Copynumber: 4.8 Consensus size: 27
41718367 TGGTATTTTA
*
41718377 GTAATTTTGTAAATCGAGGGTAAAACT
1 GTAATTCTGTAAATCGAGGGTAAAACT
41718404 GTAATTCTGTAAATCGAGGGTAAAAC-
1 GTAATTCTGTAAATCGAGGGTAAAACT
*
41718430 GTTAATTCTGTAAATTGAGGGTAAAA-T
1 G-TAATTCTGTAAATCGAGGGTAAAACT
* * *
41718457 GGTAATTCTATAAATCGAAGGTAAAACG
1 -GTAATTCTGTAAATCGAGGGTAAAACT
41718485 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
41718507 CTTTGGTAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.01
27 89 0.98
28 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACT
Found at i:41718425 original size:81 final size:81
Alignment explanation
Indices: 41718340--41718519 Score: 189
Period size: 81 Copynumber: 2.2 Consensus size: 81
41718330 TACAAACTAG
* * *** * * * *
41718340 GGGTATTTTGGTAATTTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACTG
1 GGGTAATTTGGTAATTTTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAAGGTAAAACGG
41718405 TAATTCTGTAAATCGA
66 TAATTCTGTAAATCGA
*** * * *** *
41718421 GGGTAAAACGTTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATAAATCGAAGGTAAAACGG
1 GGGTAATTTGGTAATTTTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAAGGTAAAACGG
41718486 TAATTCTGTAAATCGA
66 TAATTCTGTAAATCGA
*
41718502 GGGTACTTTGGTAATTTT
1 GGGTAATTTGGTAATTTT
41718520 ACAAATTGAG
Statistics
Matches: 75, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (81 bp):
GGGTAATTTGGTAATTTTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAAGGTAAAACGG
TAATTCTGTAAATCGA
Found at i:41718526 original size:81 final size:81
Alignment explanation
Indices: 41718377--41718530 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
41718367 TGGTATTTTA
* * * * * **
41718377 GTAATTTTGTAAATCGAGGGTAAAACTGTAATTCTGTAAATCGAGGGTAAAACGTTAATTCTGTA
1 GTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTACA
41718442 AATTGAGGGTAAAATG
66 AATTGAGGGTAAAATG
**** *
41718458 GTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTACA
1 GTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTACA
41718523 AATTGAGG
66 AATTGAGG
41718531 ACATTTTCGT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (81 bp):
GTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTACA
AATTGAGGGTAAAATG
Found at i:41718543 original size:81 final size:81
Alignment explanation
Indices: 41718371--41718544 Score: 177
Period size: 81 Copynumber: 2.1 Consensus size: 81
41718361 AACCAATGGT
* * * * *
41718371 ATTTTAGTAATTTTGTAAATCGAGGGTAAAACTGTAATTCTGTAAATCGAGGGTAAAACGTTAAT
1 ATTTTAGTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAAT
** **
41718436 TCTGTAAATTGAGGGT
66 TCTACAAATTGAGGAC
*** * ****
41718452 AAAATGGTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTACTTTGGTAAT
1 ATTTTAGTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAAT
*
41718517 TTTACAAATTGAGGAC
66 TCTACAAATTGAGGAC
*
41718533 ATTTTCGTAATT
1 ATTTTAGTAATT
41718545 TGGTAAACCA
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (81 bp):
ATTTTAGTAATTCTATAAATCGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAAT
TCTACAAATTGAGGAC
Found at i:41731039 original size:33 final size:33
Alignment explanation
Indices: 41730992--41731070 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
41730982 TTGTTTGTAT
*
41730992 ACTGTACTGAAATGGGCTAAGGCCTAGACTGCC
1 ACTGTACTGAAATGGGCTAAGGCCCAGACTGCC
* *
41731025 ACTGTTACTG-AATGGGCTTAGGCCCAGACTGCT
1 ACTG-TACTGAAATGGGCTAAGGCCCAGACTGCC
*
41731058 ACTGCTACCGAAA
1 ACTG-TACTGAAA
41731071 GAGGGGCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (33 bp):
ACTGTACTGAAATGGGCTAAGGCCCAGACTGCC
Found at i:41732345 original size:43 final size:43
Alignment explanation
Indices: 41732289--41732433 Score: 168
Period size: 43 Copynumber: 3.4 Consensus size: 43
41732279 TTAACAAGAC
** * **
41732289 ATGATTATGTGTAAGACCATGTCTGAGACATTTTCATC-ATAT
1 ATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATAT
*
41732331 -TGCGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTAT
1 AT--GATTACATGTAAGACCATGTCTGGGACATTGGCATCGATAT
* * *
41732375 ATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAC
1 ATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATAT
*
41732418 ATGATAACATGTAAGA
1 ATGATTACATGTAAGA
41732434 GCATATCTAG
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
43 81 0.94
44 3 0.03
45 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (43 bp):
ATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATAT
Found at i:41748423 original size:22 final size:21
Alignment explanation
Indices: 41748361--41748420 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
41748351 AGGGATTCGT
* *
41748361 ATGAGTGCTCGCAAGGGCTCAC
1 ATGAG-GCTCGCAGGGGTTCAC
* * *
41748383 ATGGGGTTCTCAAGGGGTTCAC
1 ATGAGGCTCGC-AGGGGTTCAC
41748405 ATGAGGCTCGCAGGGG
1 ATGAGGCTCGCAGGGG
41748421 GTTTACAGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.20, C:0.22, G:0.38, T:0.20
Consensus pattern (21 bp):
ATGAGGCTCGCAGGGGTTCAC
Found at i:41749611 original size:13 final size:13
Alignment explanation
Indices: 41749595--41749619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41749585 AAATGATTTC
41749595 TTGAAAATTTTGT
1 TTGAAAATTTTGT
41749608 TTGAAAATTTTG
1 TTGAAAATTTTG
41749620 ACGTTTGAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTGAAAATTTTGT
Found at i:41751233 original size:50 final size:50
Alignment explanation
Indices: 41751166--41751413 Score: 199
Period size: 50 Copynumber: 4.9 Consensus size: 50
41751156 TAAGACAGTT
* * *
41751166 TTAGGTCACGTATGTAGTACTAAGTGCAGGCTCCTACGTGTACCAGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
** * * * ** **
41751216 TTAGGTCGTATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCTACAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* ** * * * * * * * *
41751266 CTTCGAACACGTGTGTAGTACTAAGTGCAAGATACTACATATATCACATGG
1 -TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* * * * * *
41751317 TTAGGTCACGTGTGTAATACTAAGTGTAGGCTACTACATGTATCGGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* * *
41751367 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
41751414 AAGCTTCGAT
Statistics
Matches: 147, Mismatches: 50, Indels: 2
0.74 0.25 0.01
Matches are distributed among these distances:
50 115 0.78
51 32 0.22
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
Found at i:41756919 original size:52 final size:52
Alignment explanation
Indices: 41756802--41756979 Score: 233
Period size: 51 Copynumber: 3.5 Consensus size: 52
41756792 CGGATACCCG
* * * *
41756802 GTGGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTA-CCTTCTTCAAAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCTTTCTTCAAAAA
41756853 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCAAAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCAAAAA
*
41756905 GTGGCCTTCACATAGTAGCACACTTGTGACC-AAGCTATCTCTT-TTC--AAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCT-TTCTTCAAAAA
* *
41756954 GTGGCCATCACATTGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
41756980 AGTCACTAGT
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
49 26 0.22
51 45 0.39
52 45 0.39
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCAAAAA
Found at i:41761081 original size:54 final size:54
Alignment explanation
Indices: 41760949--41761081 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 54
41760939 GTGGCAAGGT
* * * *
41760949 CATGTAACTCACTATGACCGTATGGCTTAGGGTCACACGTAATTGTCGCCAGGC
1 CATGTAACTCTCTATGACCGTGTGGCTCAGGGTCACACGGAATTGTCGCCAGGC
* * * * ** *
41761003 CATATAACTCTTTAAG-CTCGTGTGGCTCAGGGTCACGCGGCCTTGTCGTCAGGC
1 CATGTAACTCTCTATGAC-CGTGTGGCTCAGGGTCACACGGAATTGTCGCCAGGC
*
41761057 CATGTAACTCTCTATGACCATGTGG
1 CATGTAACTCTCTATGACCGTGTGG
41761082 ACCAACTTGC
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
53 1 0.02
54 60 0.97
55 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (54 bp):
CATGTAACTCTCTATGACCGTGTGGCTCAGGGTCACACGGAATTGTCGCCAGGC
Found at i:41767605 original size:40 final size:40
Alignment explanation
Indices: 41767554--41767752 Score: 228
Period size: 40 Copynumber: 5.1 Consensus size: 40
41767544 ATAACGGGGT
* * * * *
41767554 TAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTCTGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCCGGGC
* *
41767594 TAAGTCCCGAAGGCTTTTGTGCGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGC
*
41767634 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGC
* *
41767674 TAAGTCCCGAAGGCATTTGTGCTAGTGACCATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGC
* * **
41767714 TAAGGCCCGATGGC--TT-TGCGAGTGGTTATATCC-GGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGC
41767750 TAA
1 TAA
41767753 ATCGCAAAGA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
36 6 0.04
37 13 0.09
38 2 0.01
40 119 0.84
41 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGC
Found at i:41775817 original size:40 final size:40
Alignment explanation
Indices: 41775762--41775874 Score: 156
Period size: 40 Copynumber: 2.8 Consensus size: 40
41775752 ATTGATAACG
* * *
41775762 GGGTTAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTTC
1 GGGTTAAGTCCCGAAGGCATTTGTGCTAGTGACTACA-TCC
* *
41775802 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCC
1 GGGTTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCC
*
41775842 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAC
1 GGGTTAAGTCCCGAAGGCATTTGTGCTAGTGAC
41775875 CATATCCAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 63 0.98
41 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (40 bp):
GGGTTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCC
Found at i:41775887 original size:40 final size:39
Alignment explanation
Indices: 41775766--41775903 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
41775756 ATAACGGGGT
* * * *
41775766 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTTCGGGT
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAA-TCCGGGC
* *
41775806 TAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATCCGGGC
* *
41775846 TAAGTCCCGAAGGCATTTGTGCTAGTGACCATATCCAGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATCCGGGC
* *
41775886 TAAGGCCCGATGGC-TTTG
1 TAAGTCCCGAAGGCATTTG
41775904 CAAGTGGTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 4 0.05
40 79 0.94
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (39 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATCCGGGC
Found at i:41798185 original size:6 final size:6
Alignment explanation
Indices: 41798166--41798221 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
41798156 GTTGAGTCCA
* * * *
41798166 TTTA-T TTTATTT TTTATT TTTCTT ATTATT TCTATT TTTATG TTTATT
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
41798214 GTTATT TT
1 TTTATT TT
41798222 CTTAGACTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
5 4 0.10
6 30 0.77
7 5 0.13
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:41798196 original size:24 final size:23
Alignment explanation
Indices: 41798167--41798221 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
41798157 TTGAGTCCAT
* *
41798167 TTATTTTATTTTTTATTTTTCTTA
1 TTATTTTA-TTTTTATGTTTATTA
*
41798191 TTATTTCTATTTTTATGTTTATTG
1 TTATTT-TATTTTTATGTTTATTA
41798215 TTATTTT
1 TTATTTT
41798222 CTTAGACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.89
25 2 0.07
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (23 bp):
TTATTTTATTTTTATGTTTATTA
Found at i:41802808 original size:17 final size:17
Alignment explanation
Indices: 41802766--41802808 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
41802756 TTTTAATCCG
41802766 TTTAGTGTTGTGTTGAAT
1 TTTA-TGTTGTGTTGAAT
*
41802784 TTTTTGTTGATGTTGAA-
1 TTTATGTTG-TGTTGAAT
41802801 TTTATGTT
1 TTTATGTT
41802809 TTGGCAGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.16, C:0.00, G:0.23, T:0.60
Consensus pattern (17 bp):
TTTATGTTGTGTTGAAT
Found at i:41805475 original size:76 final size:72
Alignment explanation
Indices: 41805345--41805506 Score: 236
Period size: 76 Copynumber: 2.2 Consensus size: 72
41805335 TAAAGATAAA
*
41805345 AAGTGTGGTAATGAGAAAATACATGTGTTGTATTGTTCCATTCACTTTTATAGGTAGGTTATTCG
1 AAGTGTGGTAATGAGAAAATACATGTGTTGTATTGTTCCATTCAATTTTATAGGT---TT-TTCG
41805410 ATTACTATGAG
62 ATTACTATGAG
* *
41805421 AAGTGTGGTAATGAGAAAATACATGTGTTGTATTGTT-CATTTCAATTTTGTAGGTTTTTTGATT
1 AAGTGTGGTAATGAGAAAATACATGTGTTGTATTGTTCCA-TTCAATTTTATAGGTTTTTCGATT
41805485 ACTATGAG
65 ACTATGAG
*
41805493 AAGTTTGGTAATGA
1 AAGTGTGGTAATGA
41805507 AAAGGTGATT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
72 27 0.33
73 2 0.02
75 2 0.02
76 50 0.62
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (72 bp):
AAGTGTGGTAATGAGAAAATACATGTGTTGTATTGTTCCATTCAATTTTATAGGTTTTTCGATTA
CTATGAG
Found at i:41816236 original size:28 final size:29
Alignment explanation
Indices: 41816204--41816317 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
41816194 TACCTGTATC
* *
41816204 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
41816232 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
41816261 TGGCCCATGAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
41816290 TAGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
41816318 ATCATGCTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 26 0.36
29 46 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:41816570 original size:16 final size:16
Alignment explanation
Indices: 41816529--41816571 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41816519 GTAGCCAAAC
41816529 TTTCGGCTTTTCAACA
1 TTTCGGCTTTTCAACA
** *
41816545 TTTCAACTTTTCAGCA
1 TTTCGGCTTTTCAACA
41816561 TTTCGGCTTTT
1 TTTCGGCTTTT
41816572 GCCGATACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCAACA
Found at i:41817668 original size:16 final size:17
Alignment explanation
Indices: 41817636--41817671 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41817626 ACAAAGAAAG
*
41817636 TTTGGGATTTCAGAATT
1 TTTGGGATTTCAAAATT
41817653 TTTGGG-TTTCAAAATT
1 TTTGGGATTTCAAAATT
41817669 TTT
1 TTT
41817672 AGGGCATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (17 bp):
TTTGGGATTTCAAAATT
Found at i:41821099 original size:6 final size:6
Alignment explanation
Indices: 41821088--41821116 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41821078 AGCCATATAA
41821088 TAAAAT TAAAA- TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
41821117 CACAAAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:41821102 original size:11 final size:11
Alignment explanation
Indices: 41821086--41821116 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
41821076 CGAGCCATAT
41821086 AATAAAATTAA
1 AATAAAATTAA
41821097 AATAAAATTAA
1 AATAAAATTAA
41821108 AATTAAAAT
1 AA-TAAAAT
41821117 CACAAAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATTAA
Found at i:41824918 original size:30 final size:30
Alignment explanation
Indices: 41824874--41824962 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
41824864 CAAAGATAAC
*
41824874 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
41824903 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
41824933 AAGATATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
41824963 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:41824922 original size:15 final size:14
Alignment explanation
Indices: 41824874--41824956 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
41824864 CAAAGATAAC
*
41824874 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
41824888 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
41824903 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
41824918 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
41824933 AAGATATCCAGGATA
1 AAGA-AACCCGAATA
41824948 AAGAAACCC
1 AAGAAACCC
41824957 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.11
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:41824962 original size:15 final size:15
Alignment explanation
Indices: 41824885--41824962 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
41824875 AGAAAACCGA
41824885 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
41824900 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
41824914 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
41824929 AATAAAGATATCCAGG
1 -ATAAAGAAATCCAAG
*
41824945 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
41824960 ATA
1 ATA
41824963 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:41827948 original size:46 final size:45
Alignment explanation
Indices: 41827881--41828055 Score: 154
Period size: 46 Copynumber: 3.8 Consensus size: 45
41827871 TGTAACCCGC
* *
41827881 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * * *
41827927 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** ** ***
41827973 ACATCTCTCGAACTCGGACTCAACTCAACGAATTCAAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
41828020 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
41828056 ATGCCCAAAT
Statistics
Matches: 98, Mismatches: 26, Indels: 10
0.73 0.19 0.07
Matches are distributed among these distances:
45 1 0.01
46 65 0.66
47 30 0.31
48 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:41827996 original size:93 final size:93
Alignment explanation
Indices: 41827888--41828060 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
41827878 CGCCCATAAG
* *** *
41827888 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAACTCAAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41827953 ACAAGCTCGGATGCCTAGTTACATCTCT
66 ACAAGCTCGGATGCCTAGTTACATCTCT
* *
41827981 CGAACTCGGACTCAACTCAACGAATTCAAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAACTCAAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
41828046 ACGAGTTCGGATGCC
66 ACAAGCTCGGATGCC
41828061 CAAATATCCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAACTCAAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGCTCGGATGCCTAGTTACATCTCT
Found at i:41835484 original size:64 final size:64
Alignment explanation
Indices: 41835404--41835587 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
41835394 AGACATTATG
* * *
41835404 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * * *
41835468 ATGTAGCTAGGTCGCATGCATGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41835533 AA
63 AA
* * * *
41835535 ACTG--GCTTGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
41835588 CGAACTATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 24 0.25
66 19 0.20
67 31 0.32
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41841802 original size:18 final size:20
Alignment explanation
Indices: 41841767--41841808 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
41841757 CTAAGAAGGA
41841767 AAAGTAACTAAATAAGTTC-
1 AAAGTAACTAAATAAGTTCT
* *
41841786 AAAG-AACTTAATGAGTTCT
1 AAAGTAACTAAATAAGTTCT
41841805 AAAG
1 AAAG
41841809 GAAACATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (20 bp):
AAAGTAACTAAATAAGTTCT
Found at i:41847380 original size:46 final size:45
Alignment explanation
Indices: 41847313--41847487 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 45
41847303 TGTAACCCGC
41847313 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTT-ACAT
41847359 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTACAT
* * * * * * *
41847409 CTC-T---CGAACTCGGACTTAACTCAACGAGTTCTGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-GTTACAT
*
41847452 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
41847488 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 10, Indels: 20
0.78 0.07 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 62 0.57
47 25 0.23
48 1 0.01
49 1 0.01
50 6 0.06
51 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTACAT
Found at i:41847480 original size:93 final size:93
Alignment explanation
Indices: 41847321--41847491 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
41847311 GCCCATAAGT
* *
41847321 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
41847386 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * * **
41847414 GAACTCGGACTTAACTCAACGAGTTCTGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
41847479 CGAGTTCGGATGC
66 CGAGCTCGGATGC
41847492 TCAACCATCC
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:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:41847507 original size:46 final size:45
Alignment explanation
Indices: 41847318--41847507 Score: 140
Period size: 46 Copynumber: 4.1 Consensus size: 45
41847308 CCCGCCCATA
** *
41847318 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-ACATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACATCC-T
41847363 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTC-A---ACATC-CT
* * * * ***
41847413 --CGAACTCGGACTTAACTCAACGAGTTCTGA--CATTTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-TCAACATCC-T
*
41847456 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAA-CATCCT
41847503 AGTGA
1 AGTGA
41847508 CATGTCACTT
Statistics
Matches: 113, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
45 2 0.02
46 64 0.57
47 28 0.25
48 6 0.05
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACATCCT
Found at i:41854381 original size:16 final size:17
Alignment explanation
Indices: 41854350--41854382 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41854340 TTCATAAGTA
*
41854350 TATATTAATCATTTCAT
1 TATATCAATCATTTCAT
41854367 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
41854383 GCACCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:41854842 original size:46 final size:46
Alignment explanation
Indices: 41854663--41854846 Score: 224
Period size: 46 Copynumber: 4.0 Consensus size: 46
41854653 TTATCTTTGA
* * * * * *
41854663 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGT
* * **
41854709 CATGTTGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGT
* * * *
41854755 CATGCTGCCATGGTATCTTTCAAGCATGGTCTTATTCATTTCCCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGT
* *
41854801 CATGTTGCCATGGTATCTTTCAACCATGGGCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGT
41854847 TCTTTCAACC
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGT
Found at i:41854842 original size:92 final size:92
Alignment explanation
Indices: 41854663--41854834 Score: 247
Period size: 92 Copynumber: 1.9 Consensus size: 92
41854653 TTATCTTTGA
* * ** *
41854663 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATTTT
1 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCCCATCATGTTGCCATGGTATCTT
*
41854728 TCAACCATGGTCTTACACATTTCATGT
66 TCAACCATGGGCTTACACATTTCATGT
* * *
41854755 CATGCTGCCATGGTATCTTTCAAGC-ATGGTCTTATTCATTTCCCATCATGTTGCCATGGTATCT
1 CATGATGCCATAGTATCTTTCAA-CTATGGTCTTACTCATTTCCCATCATGTTGCCATGGTATCT
41854819 TTCAACCATGGGCTTA
65 TTCAACCATGGGCTTA
41854835 TTCATTTCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 69 0.99
93 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.40
Consensus pattern (92 bp):
CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCCCATCATGTTGCCATGGTATCTT
TCAACCATGGGCTTACACATTTCATGT
Found at i:41854900 original size:46 final size:46
Alignment explanation
Indices: 41854848--41854972 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
41854838 ATTTCCCGTT
** * * *
41854848 CTTTCAACCATGGTCTTATTCATTTCATATCTGGTTGTCATGGTAC
1 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATAC
*
41854894 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATAT
1 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATAC
41854940 CTTTCAACCATGGTCTTACACATTTCATATCAG
1 CTTTCAACCATGGTCTTACACATTTCATATCAG
41854973 AGAGCACACT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (46 bp):
CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATAC
Found at i:41854918 original size:77 final size:77
Alignment explanation
Indices: 41854770--41854919 Score: 212
Period size: 77 Copynumber: 1.9 Consensus size: 77
41854760 TGCCATGGTA
* * *
41854770 TCTTTCAAGCATGGTCTTATTCATTTCCCATCATGTTGCCATGGTATCTTTCAACCATGGGCTTA
1 TCTTTCAACCATGGTCTTATTCATTTCACATCATGTTGCCATGGTACCTTTCAACCATGGGCTTA
**
41854835 TTCATTTCCCGT
66 CACATTTCCCGT
* * *
41854847 TCTTTCAACCATGGTCTTATTCATTTCATATC-TGGTTGTCATGGTACCTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTATTCATTTCACATCAT-GTTGCCATGGTACCTTTCAACCATGGGCTT
41854911 ACACATTTC
65 ACACATTTC
41854920 ATATCAGGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.02
77 63 0.98
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (77 bp):
TCTTTCAACCATGGTCTTATTCATTTCACATCATGTTGCCATGGTACCTTTCAACCATGGGCTTA
CACATTTCCCGT
Found at i:41854945 original size:123 final size:123
Alignment explanation
Indices: 41854726--41854957 Score: 322
Period size: 123 Copynumber: 1.9 Consensus size: 123
41854716 CCATGGTATT
* * * **
41854726 TTTCAACCATGGTCTTACACATTTCATGTCATGCTGCCATGGTATCTTTCAAGCATGGTCTTATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTACCTTTCAACCATGGTCTTACA
* * *
41854791 CATTTCCCATCATGTTGCCATGGTATCTTTCAACCATGGGCTTATTCATTTCCCGTTC
66 CATTTCACATCAGGTTGCCATGATATCTTTCAACCATGGGCTTATTCATTTCCCGTTC
** * *
41854849 TTTCAACCATGGTCTTATTCATTTCATATC-TGGTTGTCATGGTACCTTTCAACCATGGTCTTAC
1 TTTCAACCATGGTCTTACACATTTCATATCAT-GCTGCCATGGTACCTTTCAACCATGGTCTTAC
* *
41854913 ACATTTCATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
65 ACATTTCACATCAGGTTGCCATGATATCTTTCAACCATGGGCTTA
41854958 CACATTTCAT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
122 1 0.01
123 93 0.99
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (123 bp):
TTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTACCTTTCAACCATGGTCTTACA
CATTTCACATCAGGTTGCCATGATATCTTTCAACCATGGGCTTATTCATTTCCCGTTC
Found at i:41857998 original size:28 final size:28
Alignment explanation
Indices: 41857958--41858012 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
41857948 AAACCATTGG
*
41857958 TCCCAACGGCTAATTAAATAGTCGTTGA
1 TCCCAACAGCTAATTAAATAGTCGTTGA
41857986 TCCCAACAGCTAATTAAATAGTCGTTG
1 TCCCAACAGCTAATTAAATAGTCGTTG
41858013 TGGAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (28 bp):
TCCCAACAGCTAATTAAATAGTCGTTGA
Found at i:41859629 original size:30 final size:29
Alignment explanation
Indices: 41859562--41859629 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
41859552 ATTAACAAAA
*
41859562 TTAAGAATTTAGTCTTTGTATTTTTATTTC
1 TTAA-AATTTAGTCTTTCTATTTTTATTTC
*
41859592 ATAAAATTTAGTCTTTCTATTTTTCATATT-
1 TTAAAATTTAGTCTTTCTATTTTT-AT-TTC
41859622 TTAAAATT
1 TTAAAATT
41859630 CAAGTCCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 19 0.58
30 12 0.36
31 2 0.06
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.57
Consensus pattern (29 bp):
TTAAAATTTAGTCTTTCTATTTTTATTTC
Found at i:41861417 original size:11 final size:11
Alignment explanation
Indices: 41861401--41861425 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41861391 TTGAGAGAAA
41861401 AAATCATTTTT
1 AAATCATTTTT
41861412 AAATCATTTTT
1 AAATCATTTTT
41861423 AAA
1 AAA
41861426 AGTAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCATTTTT
Found at i:41870180 original size:24 final size:23
Alignment explanation
Indices: 41870128--41870181 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
41870118 GGATTTTTGC
* *
41870128 GTACAATCAAAGGTGCAATCGGAT
1 GTAC-ATCAAAGGTGCAACCGGAG
*
41870152 TTACATCAAGAGGTGCAACCGGAG
1 GTACATCAA-AGGTGCAACCGGAG
41870176 GTACAT
1 GTACAT
41870182 ATGAAAGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (23 bp):
GTACATCAAAGGTGCAACCGGAG
Found at i:41872775 original size:18 final size:19
Alignment explanation
Indices: 41872752--41872790 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
41872742 ATATATTCAC
41872752 ACATTTTCA-CAATTCAAT
1 ACATTTTCATCAATTCAAT
41872770 ACATTTTCATTCAATTCAAT
1 ACATTTTCA-TCAATTCAAT
41872790 A
1 A
41872791 TCAATACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTTCATCAATTCAAT
Found at i:41873447 original size:33 final size:33
Alignment explanation
Indices: 41873410--41873476 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41873400 CAATTAAACT
41873410 TCAAACTTTAAAATCCCTAATTTCCCCTTTTTC
1 TCAAACTTTAAAATCCCTAATTTCCCCTTTTTC
41873443 TCAAACTTTAAAATCCCTAATTTCCCCTTTTTC
1 TCAAACTTTAAAATCCCTAATTTCCCCTTTTTC
41873476 T
1 T
41873477 TTCTTTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (33 bp):
TCAAACTTTAAAATCCCTAATTTCCCCTTTTTC
Found at i:41873729 original size:8 final size:8
Alignment explanation
Indices: 41873718--41873758 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
41873708 TTTTTATTTA
41873718 ATAATAAT
1 ATAATAAT
41873726 ATAAT-AT
1 ATAATAAT
41873733 A-ATATAAT
1 ATA-ATAAT
41873741 ATAATAAT
1 ATAATAAT
*
41873749 CTAATAAT
1 ATAATAAT
41873757 AT
1 AT
41873759 GTTTTAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 1 0.04
7 5 0.18
8 21 0.75
9 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATAAT
Found at i:41873731 original size:5 final size:5
Alignment explanation
Indices: 41873716--41873746 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
41873706 TTTTTTTATT
41873716 TAATAA TAATA TAATA TAATA TAATA TAATA
1 TAAT-A TAATA TAATA TAATA TAATA TAATA
41873747 ATCTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:41874474 original size:58 final size:58
Alignment explanation
Indices: 41874381--41874494 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 58
41874371 TAGCATATCT
*
41874381 TCAACTTAATTTTCCACATTCATTGAAGTCCACTAGATGCAGTAGCCACCTTACATCC
1 TCAACTTAATTTTACACATTCATTGAAGTCCACTAGATGCAGTAGCCACCTTACATCC
* * * *
41874439 TCAACTTAATTTTACGCATTCATTGAAGTCTACTAGATGTAGTAGCTACCTTACAT
1 TCAACTTAATTTTACACATTCATTGAAGTCCACTAGATGCAGTAGCCACCTTACAT
41874495 GCACCAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (58 bp):
TCAACTTAATTTTACACATTCATTGAAGTCCACTAGATGCAGTAGCCACCTTACATCC
Found at i:41877681 original size:46 final size:46
Alignment explanation
Indices: 41877629--41877741 Score: 226
Period size: 46 Copynumber: 2.5 Consensus size: 46
41877619 AGTGTGCTCT
41877629 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41877675 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41877721 CTGATATGAAATGTGTAAGAC
1 CTGATATGAAATGTGTAAGAC
41877742 ACCATGGCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:41877751 original size:32 final size:32
Alignment explanation
Indices: 41877705--41877773 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
41877695 CCATGGTTGA
*
41877705 AAGATACCATGGCAACCTGATATGAAATGTGT
1 AAGACACCATGGCAACCTGATATGAAATGTGT
41877737 AAGACACCATGGCAACCTGATATGAAATGTGT
1 AAGACACCATGGCAACCTGATATGAAATGTGT
41877769 AAGAC
1 AAGAC
41877774 CATGGTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (32 bp):
AAGACACCATGGCAACCTGATATGAAATGTGT
Found at i:41877793 original size:78 final size:78
Alignment explanation
Indices: 41877659--41877819 Score: 304
Period size: 78 Copynumber: 2.1 Consensus size: 78
41877649 CCATGGTTGA
*
41877659 AAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AAGACACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
41877724 ATATGAAATGTGT
66 ATATGAAATGTGT
*
41877737 AAGACACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 AAGACACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
41877802 ATATGAAATGTGT
66 ATATGAAATGTGT
41877815 AAGAC
1 AAGAC
41877820 CATGTTTGAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (78 bp):
AAGACACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
ATATGAAATGTGT
Found at i:41877794 original size:46 final size:46
Alignment explanation
Indices: 41877737--41877980 Score: 330
Period size: 46 Copynumber: 5.3 Consensus size: 46
41877727 TGAAATGTGT
* * *
41877737 AAGACACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGA
1 AAGATACCATGGCAACGTGATATGAAATGAGTAAGACCATGGTTGA
* *
41877783 AAGATACCATGGCAACGTGATATGAAATGTGTAAGACCATGTTTGA
1 AAGATACCATGGCAACGTGATATGAAATGAGTAAGACCATGGTTGA
**
41877829 AAGATACCATAACAACGTGATATGAAATG-GATAAGACCATGGTTGA
1 AAGATACCATGGCAACGTGATATGAAATGAG-TAAGACCATGGTTGA
*
41877875 AAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGA
1 AAGATACCATGGCAACGTGATATGAAATGAGTAAGACCATGGTTGA
* * * *
41877921 AAGATACCATGGAAACATGACA-GAAAATGAGTAAGACCATAGTTGA
1 AAGATACCATGGCAACGTGATATG-AAATGAGTAAGACCATGGTTGA
* *
41877967 AAGACACTATGGCA
1 AAGATACCATGGCA
41877981 TCATGTCAAA
Statistics
Matches: 178, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
45 2 0.01
46 176 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
AAGATACCATGGCAACGTGATATGAAATGAGTAAGACCATGGTTGA
Found at i:41877850 original size:124 final size:124
Alignment explanation
Indices: 41877629--41877865 Score: 413
Period size: 124 Copynumber: 1.9 Consensus size: 124
41877619 AGTGTGCTCT
41877629 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
**
41877694 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTG-TAAGACACCATGGCAAC
66 ACCATGGTTGAAAGATACCATAACAACCTGATATGAAATG-GATAAGACACCATGGCAAC
*
41877753 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
* *
41877818 ACCATGTTTGAAAGATACCATAACAACGTGATATGAAATGGATAAGAC
66 ACCATGGTTGAAAGATACCATAACAACCTGATATGAAATGGATAAGAC
41877866 CATGGTTGAA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
123 1 0.01
124 106 0.99
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (124 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
ACCATGGTTGAAAGATACCATAACAACCTGATATGAAATGGATAAGACACCATGGCAAC
Found at i:41881634 original size:47 final size:47
Alignment explanation
Indices: 41881571--41881882 Score: 476
Period size: 47 Copynumber: 6.7 Consensus size: 47
41881561 ATGATAGTAT
41881571 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41881618 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG---A
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41881662 ---C-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
41881705 TGCCTATTGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
41881752 GGCCTAATGGCCGATGTGATGCATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
* *
41881801 GGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
41881850 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
41881883 CCCGAAGGGC
Statistics
Matches: 247, Mismatches: 8, Indels: 17
0.91 0.03 0.06
Matches are distributed among these distances:
40 38 0.15
41 1 0.00
43 1 0.00
44 1 0.00
46 1 0.00
47 114 0.46
49 87 0.35
50 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:41881695 original size:87 final size:90
Alignment explanation
Indices: 41881574--41881882 Score: 435
Period size: 87 Copynumber: 3.3 Consensus size: 90
41881564 ATAGTATGGC
41881574 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41881639 AATGTGAAAGTGTATATATGTG-A-
66 AATGTGAAAGTGTATATATGTGAAG
* *
41881662 C-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAATGCCTATTGGCCGATGTGATG
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41881726 AATGTGAAAGTGTATATATGTGATAAGG
66 AATGTGAAAGTGTATATATGTG--AA-G
* * *
41881754 CCTAATGGCCGATGTGATGCATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCAATGTG
1 -CTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
41881819 ATGAATGTGAAAGTGTATATATATGTGATAGGG
63 ATGAATGTGAAAGTG--TATATATGTGA-A--G
41881852 CCTAATGGCCGATGTGATGAATGTGATAAGT
1 -CTAATGGCCGATGTGATGAATGTGA-AAGT
41881883 CCCGAAGGGC
Statistics
Matches: 199, Mismatches: 8, Indels: 17
0.89 0.04 0.08
Matches are distributed among these distances:
87 83 0.42
88 1 0.01
90 1 0.01
93 1 0.01
94 27 0.14
96 44 0.22
97 1 0.01
98 37 0.19
99 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (90 bp):
CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGTATATATGTGAAG
Found at i:41881701 original size:25 final size:25
Alignment explanation
Indices: 41881671--41881749 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
41881661 ACAATGGCCG
41881671 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
*** * ****
41881696 ATGTGAT-AATG-CCTATTG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
41881718 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
41881743 ATGTGAT
1 ATGTGAT
41881750 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41881810 original size:49 final size:47
Alignment explanation
Indices: 41881663--41881882 Score: 341
Period size: 49 Copynumber: 4.6 Consensus size: 47
41881653 TATATGTGAC
*
41881663 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAATGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
*
41881710 ATTGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* *
41881757 AATGGCCGATGTGATGCATGTGAAAGTGTATATATATGTGATAGGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
* *
41881806 AATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
41881855 AATGGCCGATGTGATGAATGTGATAAGT
1 AATGGCCGATGTGATGAATGTGA-AAGT
41881883 CCCGAAGGGC
Statistics
Matches: 162, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
47 71 0.44
49 87 0.54
50 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.31
Consensus pattern (47 bp):
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
Found at i:41881817 original size:134 final size:134
Alignment explanation
Indices: 41881572--41881882 Score: 415
Period size: 134 Copynumber: 2.2 Consensus size: 134
41881562 TGATAGTATG
41881572 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
* * **
41881637 TGAATGTGAAAGTGTATATATGTGACAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
66 TGAATGTGAAAGTGTATATATGTGACAAGGGCCAATGTGACCAATGTGAAAGTGTATATATGTGA
41881702 TAAT
131 TAAT
*
41881706 GCCTATTGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
* * **
41881771 TGCATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
66 TGAATGTGAAAGTG--TATATATGTG--A----C-AAGGGCCAATGTGACCAATGTGAAAGTG--
**
41881836 TATATATGTGATAGG
120 TATATATGTGATAAT
41881851 GCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GCCTAATGGCCGATGTGATGAATGTGA-AAGT
41881883 CCCGAAGGGC
Statistics
Matches: 159, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
134 77 0.48
136 10 0.06
138 1 0.01
142 1 0.01
143 27 0.17
145 39 0.25
146 4 0.03
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.31
Consensus pattern (134 bp):
GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
TGAATGTGAAAGTGTATATATGTGACAAGGGCCAATGTGACCAATGTGAAAGTGTATATATGTGA
TAAT
Found at i:41882056 original size:37 final size:37
Alignment explanation
Indices: 41882000--41882078 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41881990 CCAAGCTCTA
* * *
41882000 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41882037 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41882074 AAGAC
1 AAGAC
41882079 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41883979 original size:43 final size:43
Alignment explanation
Indices: 41883931--41884033 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
41883921 TTGGTTTTCA
41883931 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
*
41883974 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
41884017 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
41884034 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
Found at i:41884050 original size:29 final size:29
Alignment explanation
Indices: 41884015--41884086 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
41884005 GTTGTGAGAT
* *
41884015 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
41884044 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
*
41884073 TGGCACTATGTGTG
1 TGGCACTAAGTGTG
41884087 TGAACCCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.13
29 33 0.87
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:41884496 original size:40 final size:40
Alignment explanation
Indices: 41884373--41884687 Score: 298
Period size: 40 Copynumber: 7.9 Consensus size: 40
41884363 TCGAATGATG
* ** *
41884373 TCCGGGATAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
41884413 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
41884453 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
41884493 TCCGGGCTAAGTTCC-AAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
41884532 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
41884572 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
** ** * * * *
41884612 TCCATGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
41884652 TCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
41884688 CGTGTATTCG
Statistics
Matches: 229, Mismatches: 41, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
39 38 0.17
40 172 0.75
41 19 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:41884516 original size:80 final size:80
Alignment explanation
Indices: 41884373--41884672 Score: 338
Period size: 80 Copynumber: 3.8 Consensus size: 80
41884363 TCGAATGATG
* * ** * *
41884373 TCCGGGATAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
* * * *
41884435 TTGGTGCGAGTTACTAAA
64 TTCGTGCTAGTGA-TATA
*
41884453 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCC-AAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
*
41884517 CATGCTAGTGATATA
66 CGTGCTAGTGATATA
*
41884532 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
41884597 CGTGCTAGTGATATA
66 CGTGCTAGTGATATA
** ** * * * * * *
41884612 TCCATGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAG
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAG
41884673 TAATCATGCT
Statistics
Matches: 190, Mismatches: 26, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
79 59 0.31
80 118 0.62
81 7 0.04
82 6 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
CGTGCTAGTGATATA
Found at i:41888339 original size:49 final size:47
Alignment explanation
Indices: 41888093--41888411 Score: 548
Period size: 47 Copynumber: 6.7 Consensus size: 47
41888083 ATGATAGTAT
41888093 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41888140 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
41888187 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41888234 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
41888281 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
*
41888330 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
*
41888379 GGCCTAATGGCTGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
41888412 CCCGAAGGGC
Statistics
Matches: 263, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
47 171 0.65
49 88 0.33
50 4 0.02
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.31
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:41890177 original size:40 final size:40
Alignment explanation
Indices: 41890147--41890356 Score: 260
Period size: 40 Copynumber: 5.3 Consensus size: 40
41890137 GGACTAAGAT
* *
41890147 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
41890187 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
41890227 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * **
41890267 CCGAAGGCATTCGTGTGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
41890307 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
41890346 CCGAAGGCATT
1 CCGAAGGCATT
41890357 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:41890231 original size:80 final size:80
Alignment explanation
Indices: 41890147--41890356 Score: 314
Period size: 80 Copynumber: 2.6 Consensus size: 80
41890137 GGACTAAGAT
*
41890147 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
41890212 AATCCGGGTTAAGTC
66 AATCCGGGTTAAGTC
* * ** *
41890227 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTGTTA
1 CCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
41890292 AATCCGGGTTAAGTC
66 AATCCGGGTTAAGTC
* * * * *
41890307 CCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 CCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
41890357 TGAACGAGGA
Statistics
Matches: 115, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 34 0.30
80 81 0.70
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
AATCCGGGTTAAGTC
Found at i:41898177 original size:39 final size:40
Alignment explanation
Indices: 41898083--41898290 Score: 287
Period size: 40 Copynumber: 5.3 Consensus size: 40
41898073 GGACTAAGAT
* * * **
41898083 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
41898123 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGT-
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
41898162 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
*
41898202 CCGAAGGCATTCGTGTGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
41898242 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGT-
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
41898280 CCGAAGGCATT
1 CCGAAGGCATT
41898291 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
38 11 0.07
39 61 0.39
40 84 0.54
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:41898194 original size:79 final size:78
Alignment explanation
Indices: 41898077--41898290 Score: 304
Period size: 79 Copynumber: 2.7 Consensus size: 78
41898067 ATATCCGGAC
* *
41898077 TAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG
1 TAAG-TCCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG
41898142 TTGTTAAATCCGGGT
64 TTGTTAAATCCGGGT
** *
41898157 TAAGTCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGT
1 TAAGTCCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT
41898222 TGTTAAATCCGGGT
65 TGTTAAATCCGGGT
* * * *
41898236 TAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGT-CCGAAGGCATT
1 TAAGT-CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
41898291 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 14 0.12
79 92 0.76
80 15 0.12
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (78 bp):
TAAGTCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT
GTTAAATCCGGGT
Found at i:41904950 original size:40 final size:40
Alignment explanation
Indices: 41904906--41905086 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
41904896 GCTACTAGCT
41904906 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
41904946 CAAATGCCTTCGGGACTTAGCCCGGTGATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
41904986 CAAATGCCTTCGGGACTTAGCCCGGATAAAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41905026 CAAATGCCTTCGAGA-TTAGCCCGGATT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
*
41905065 CAAATGCCTTCGAGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
41905087 TGGGTATCAA
Statistics
Matches: 130, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 33 0.25
40 97 0.75
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41905005 original size:80 final size:79
Alignment explanation
Indices: 41904873--41905086 Score: 290
Period size: 80 Copynumber: 2.7 Consensus size: 79
41904863 AAACCAAGTA
* * * *
41904873 CCTTCGGAGTTTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
1 CCTTC-GAGATTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAAA
41904936 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* *
41904952 CCTTCGGGACTTAGCCCGG-TGATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAAA
1 CCTTCGAGA-TTAGCCCGGAT-ATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAAA
41905016 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* * *
41905032 CCTTCGAGATTAGCCCGGATTTAGTCACTAGCACAAATGCCTTCGAGACTTAGCC
1 CCTTCGAGATTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
41905087 TGGGTATCAA
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 2 0.02
79 51 0.43
80 66 0.55
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGAGATTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAAAGT
AACTCGCACAAATG
Found at i:41913074 original size:40 final size:40
Alignment explanation
Indices: 41913030--41913174 Score: 238
Period size: 40 Copynumber: 3.6 Consensus size: 40
41913020 GCTACTAGCT
41913030 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
41913070 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41913110 CAAATGCCTTCGGGACTTAGCCCGAATT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCG-GTTATAGTAACTCGCA
41913150 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
41913175 GTATCAATCC
Statistics
Matches: 98, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
40 97 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41913129 original size:80 final size:80
Alignment explanation
Indices: 41913007--41913174 Score: 252
Period size: 80 Copynumber: 2.1 Consensus size: 80
41912997 CCTTCGGAGT
* * *
41913007 TTAG-CCGGATATAGCTACTAGCTCAAATGCCTTCGGGACTTAGCCCG-GTTATAGTAACTCGCA
1 TTAGCCCGGATATAGCTACTAGCACAAATGCCTTCGGGACTTAGCCCGAATT-TAGTAACTAGCA
41913070 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* *
41913086 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTCACTAGCA
1 TTAGCCCGGATATAGCT-ACTAGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTAACTAGCA
41913150 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
41913166 TTAGCCCGG
1 TTAGCCCGG
41913175 GTATCAATCC
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
79 5 0.06
80 74 0.91
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATATAGCTACTAGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTAACTAGCAC
AAATGCCTTCGGGAC
Found at i:41921023 original size:14 final size:14
Alignment explanation
Indices: 41921004--41921037 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
41920994 TTCCATGGCC
*
41921004 GTGTTGATAAGTCA
1 GTGTTGAGAAGTCA
41921018 GTGTTGAGAAGTCA
1 GTGTTGAGAAGTCA
41921032 GTGTTG
1 GTGTTG
41921038 CCCACGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.35, T:0.35
Consensus pattern (14 bp):
GTGTTGAGAAGTCA
Found at i:41922500 original size:22 final size:22
Alignment explanation
Indices: 41922475--41922517 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41922465 TCTCCCTATT
*
41922475 TTGCTGCCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
* *
41922497 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
41922518 TATTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:41922712 original size:18 final size:19
Alignment explanation
Indices: 41922684--41922729 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
41922674 TTATTGGGAA
41922684 ATATGTA-TTTTAATGTTT
1 ATATGTATTTTTAATGTTT
* *
41922702 TTA-GTATTTTTGATGTTT
1 ATATGTATTTTTAATGTTT
41922720 ATATGTATTT
1 ATATGTATTT
41922730 AAAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
ATATGTATTTTTAATGTTT
Found at i:41922745 original size:11 final size:11
Alignment explanation
Indices: 41922729--41922759 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41922719 TATATGTATT
41922729 TAAAAATTATA
1 TAAAAATTATA
*
41922740 TAAAAATAATA
1 TAAAAATTATA
41922751 TAAAAATTA
1 TAAAAATTA
41922760 ACACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:41925548 original size:37 final size:37
Alignment explanation
Indices: 41925493--41925567 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
41925483 CTTTCCGGAG
*
41925493 TTAGTATACAATCCGGATTACATGTTATGGTTTAGGA
1 TTAGTATACAATCCGGATTACATGTCATGGTTTAGGA
* *
41925530 TTAGTATGCAATCTGGATTACATGTCATGGTTTAGGA
1 TTAGTATACAATCCGGATTACATGTCATGGTTTAGGA
41925567 T
1 T
41925568 CCATGGCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (37 bp):
TTAGTATACAATCCGGATTACATGTCATGGTTTAGGA
Found at i:41928473 original size:37 final size:37
Alignment explanation
Indices: 41928423--41928501 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
41928413 TTATTACGAA
* *
41928423 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
41928460 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
41928497 GTCTT
1 GTCTT
41928502 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:41928698 original size:47 final size:47
Alignment explanation
Indices: 41928620--41929046 Score: 692
Period size: 47 Copynumber: 9.1 Consensus size: 47
41928610 CCCTTCGGGA
* * * * * * *
41928620 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41928667 CCTGTCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41928714 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41928761 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928808 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41928855 CTTATCACACATATACACTTTCACATTCATCACTTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928902 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928949 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41928996 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41929043 CTTA
1 CTTA
41929047 CTATCATTTC
Statistics
Matches: 357, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 357 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41938414 original size:329 final size:329
Alignment explanation
Indices: 41937816--41938481 Score: 1332
Period size: 329 Copynumber: 2.0 Consensus size: 329
41937806 CACTTAGGAA
41937816 AGAGGAGGCAGAGTAGGAAGCAAGGTTTTACTTAAGGAAAGCCGATTGATCCATCTCAAGAGCCG
1 AGAGGAGGCAGAGTAGGAAGCAAGGTTTTACTTAAGGAAAGCCGATTGATCCATCTCAAGAGCCG
41937881 AATTCATCATCAAGACTGGAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGGTCTTCTTATGTT
66 AATTCATCATCAAGACTGGAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGGTCTTCTTATGTT
41937946 TTGTTATCTTTATGCTTTTGAGATGTTTTCTTTCATAAGTATGAACTAAACCCCTAAATACCTAA
131 TTGTTATCTTTATGCTTTTGAGATGTTTTCTTTCATAAGTATGAACTAAACCCCTAAATACCTAA
41938011 GGGGAATAAAACCTAAGACAGATCTTGTTATTATTATCTGAATTGTATGATAAATATTTGACTTG
196 GGGGAATAAAACCTAAGACAGATCTTGTTATTATTATCTGAATTGTATGATAAATATTTGACTTG
41938076 TTCTTAATTATGTGCTCTTAATTCTTGTTTTGATATTCCAGGATATTAATTCAAGTTAAGCTCTT
261 TTCTTAATTATGTGCTCTTAATTCTTGTTTTGATATTCCAGGATATTAATTCAAGTTAAGCTCTT
41938141 ATTC
326 ATTC
41938145 AGAGGAGGCAGAGTAGGAAGCAAGGTTTTACTTAAGGAAAGCCGATTGATCCATCTCAAGAGCCG
1 AGAGGAGGCAGAGTAGGAAGCAAGGTTTTACTTAAGGAAAGCCGATTGATCCATCTCAAGAGCCG
41938210 AATTCATCATCAAGACTGGAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGGTCTTCTTATGTT
66 AATTCATCATCAAGACTGGAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGGTCTTCTTATGTT
41938275 TTGTTATCTTTATGCTTTTGAGATGTTTTCTTTCATAAGTATGAACTAAACCCCTAAATACCTAA
131 TTGTTATCTTTATGCTTTTGAGATGTTTTCTTTCATAAGTATGAACTAAACCCCTAAATACCTAA
41938340 GGGGAATAAAACCTAAGACAGATCTTGTTATTATTATCTGAATTGTATGATAAATATTTGACTTG
196 GGGGAATAAAACCTAAGACAGATCTTGTTATTATTATCTGAATTGTATGATAAATATTTGACTTG
41938405 TTCTTAATTATGTGCTCTTAATTCTTGTTTTGATATTCCAGGATATTAATTCAAGTTAAGCTCTT
261 TTCTTAATTATGTGCTCTTAATTCTTGTTTTGATATTCCAGGATATTAATTCAAGTTAAGCTCTT
41938470 ATTC
326 ATTC
41938474 AGAGGAGG
1 AGAGGAGG
41938482 AATAGACCCT
Statistics
Matches: 337, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
329 337 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (329 bp):
AGAGGAGGCAGAGTAGGAAGCAAGGTTTTACTTAAGGAAAGCCGATTGATCCATCTCAAGAGCCG
AATTCATCATCAAGACTGGAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGGTCTTCTTATGTT
TTGTTATCTTTATGCTTTTGAGATGTTTTCTTTCATAAGTATGAACTAAACCCCTAAATACCTAA
GGGGAATAAAACCTAAGACAGATCTTGTTATTATTATCTGAATTGTATGATAAATATTTGACTTG
TTCTTAATTATGTGCTCTTAATTCTTGTTTTGATATTCCAGGATATTAATTCAAGTTAAGCTCTT
ATTC
Found at i:41951951 original size:58 final size:58
Alignment explanation
Indices: 41951859--41951978 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
41951849 AGTCATTCCT
41951859 TTTCATTGGTTTTGCATTTTGGTAAGTCTAACTTTCAGTATGGGTGTGATTCTTTTTC
1 TTTCATTGGTTTTGCATTTTGGTAAGTCTAACTTTCAGTATGGGTGTGATTCTTTTTC
*
41951917 TTTCATTGGTTTTGCATTTTGGTAAGTCTGACTTTCAGTATGGGTGTGATTCTTTTTC
1 TTTCATTGGTTTTGCATTTTGGTAAGTCTAACTTTCAGTATGGGTGTGATTCTTTTTC
41951975 TTTC
1 TTTC
41951979 TCCCTCTTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.14, C:0.12, G:0.21, T:0.53
Consensus pattern (58 bp):
TTTCATTGGTTTTGCATTTTGGTAAGTCTAACTTTCAGTATGGGTGTGATTCTTTTTC
Found at i:41954635 original size:6 final size:6
Alignment explanation
Indices: 41954624--41954665 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
41954614 TTTTTTCAGC
* * *
41954624 CCCAAA CCCAAA TCCAAA TCCAAA CCCAAA TCCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
41954666 TCTAATTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (6 bp):
CCCAAA
Found at i:41954646 original size:12 final size:12
Alignment explanation
Indices: 41954624--41954667 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
41954614 TTTTTTCAGC
*
41954624 CCCAAACCCAAA
1 CCCAAATCCAAA
*
41954636 TCCAAATCCAAA
1 CCCAAATCCAAA
41954648 CCCAAATCCAAA
1 CCCAAATCCAAA
41954660 CCCAAATC
1 CCCAAATC
41954668 TAATTCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.48, C:0.43, G:0.00, T:0.09
Consensus pattern (12 bp):
CCCAAATCCAAA
Found at i:41954648 original size:18 final size:18
Alignment explanation
Indices: 41954624--41954665 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
41954614 TTTTTTCAGC
41954624 CCCAAACCCAAATCCAAA
1 CCCAAACCCAAATCCAAA
*
41954642 TCCAAACCCAAATCCAAA
1 CCCAAACCCAAATCCAAA
41954660 CCCAAA
1 CCCAAA
41954666 TCTAATTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (18 bp):
CCCAAACCCAAATCCAAA
Found at i:41956716 original size:65 final size:65
Alignment explanation
Indices: 41956637--41956768 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
41956627 GTTTTCATTT
*
41956637 AAGTTATTTGATAGTTAAAATCTTCATGGTATGACTTTTTCCTCTCTCACCTCCGACATCAATTG
1 AAGTTATTTGATAGTTAAAATCTTCATGGTATGACCTTTTCCTCTCTCACCTCCGACATCAATTG
*
41956702 AAGTTATTTGATAGTTAAAATCTTCGTGGTATGACCTTTTCCTCTCTCACCTCCGACATCAATTG
1 AAGTTATTTGATAGTTAAAATCTTCATGGTATGACCTTTTCCTCTCTCACCTCCGACATCAATTG
41956767 AA
1 AA
41956769 AGGGTAAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (65 bp):
AAGTTATTTGATAGTTAAAATCTTCATGGTATGACCTTTTCCTCTCTCACCTCCGACATCAATTG
Found at i:41959964 original size:19 final size:19
Alignment explanation
Indices: 41959933--41959978 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
41959923 GTTTATGGTA
*
41959933 ATTA-AATAATATTTATTT
1 ATTATAATAATATTTATCT
*
41959951 ATTATAATAGTATTTATCT
1 ATTATAATAATATTTATCT
41959970 -TTATAATAA
1 ATTATAATAA
41959979 ATAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATAATAATATTTATCT
Found at i:41960055 original size:7 final size:7
Alignment explanation
Indices: 41960043--41960073 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
41960033 TGATATTATG
41960043 TTTTAAT
1 TTTTAAT
41960050 TTTTAAT
1 TTTTAAT
41960057 TTTTAAT
1 TTTTAAT
*
41960064 CTTTAAT
1 TTTTAAT
41960071 TTT
1 TTT
41960074 GAAATTTAAA
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:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:41960528 original size:13 final size:13
Alignment explanation
Indices: 41960497--41960529 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41960487 TTGATAGATA
*
41960497 TTAAATTTAAAAT
1 TTAAATATAAAAT
41960510 TT-AATATAAAAT
1 TTAAATATAAAAT
41960522 TTAAATAT
1 TTAAATAT
41960530 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAAAAT
Found at i:41960628 original size:7 final size:7
Alignment explanation
Indices: 41960610--41960645 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
41960600 ATTATATTAT
41960610 TTTTGAA
1 TTTTGAA
41960617 TTTTTGAA
1 -TTTTGAA
*
41960625 TTTTAAA
1 TTTTGAA
41960632 TTTTGAA
1 TTTTGAA
41960639 TTTTGAA
1 TTTTGAA
41960646 CTTTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (7 bp):
TTTTGAA
Found at i:41962402 original size:7 final size:7
Alignment explanation
Indices: 41962390--41962418 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41962380 TGCCCCCGTC
41962390 ACCCTCT
1 ACCCTCT
41962397 ACCCTCT
1 ACCCTCT
41962404 ACCCTCT
1 ACCCTCT
41962411 ACCCTCT
1 ACCCTCT
41962418 A
1 A
41962419 AACCTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.55, G:0.00, T:0.28
Consensus pattern (7 bp):
ACCCTCT
Found at i:41964330 original size:27 final size:26
Alignment explanation
Indices: 41964260--41964323 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
41964250 TACATCAATA
*
41964260 AGGGGTATATCAGTC-TTTTACCTCAT
1 AGGGGTATAAC-GTCATTTTACCTCAT
* * *
41964286 AGGGTTATAATGTCATTTTACCTCTT
1 AGGGGTATAACGTCATTTTACCTCAT
41964312 AGGGGTATAACG
1 AGGGGTATAACG
41964324 ATTATTTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 3 0.10
26 28 0.90
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (26 bp):
AGGGGTATAACGTCATTTTACCTCAT
Found at i:41969157 original size:46 final size:46
Alignment explanation
Indices: 41969084--41969340 Score: 215
Period size: 46 Copynumber: 5.5 Consensus size: 46
41969074 GTGTCAATGC
* *
41969084 CATGTCCCTGACATGATCTTACTCTGACTATCATCTCGTAGCTGACG
1 CATGTCCCAGACATG-TCTTACACTGACTATCATCTCGTAGCTGACG
* * *
41969131 CATGTTCCAGACATGTCTTACACTGACTATCATCTCATAGCCGACG
1 CATGTCCCAGACATGTCTTACACTGACTATCATCTCGTAGCTGACG
* * *
41969177 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTCG-AGGTCGATG
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTCGTAGCT-GACG
* * * *
41969223 CATGTCCCAGACATGTCTTACA-TTAGC-ACTCGTCTC-AATGCCGATAC-
1 CATGTCCCAGACATGTCTTACACTGA-CTA-TCATCTCGTA-GCTG--ACG
* * * *
41969270 CATGTCCCAGACATGGTCTTACACTGACTTTCATGAT-GT-GTCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCAT-CTCGTAG-CTGACG
41969317 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
41969341 AGCTCACATA
Statistics
Matches: 171, Mismatches: 23, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
45 4 0.02
46 104 0.61
47 44 0.26
48 16 0.09
49 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTCGTAGCTGACG
Found at i:41969361 original size:94 final size:91
Alignment explanation
Indices: 41969083--41969342 Score: 241
Period size: 92 Copynumber: 2.8 Consensus size: 91
41969073 GGTGTCAATG
* * * * *
41969083 CCATGTCCCTGACATGATCTTACTCTGAC-TATCATCTCGTAGCT-GACGCATGTTCCAGACATG
1 CCATGTCCCAGACATG-TCTTACACTGACTTA-CA-CTCG-AGGTCGATGCATGTCCCAGACATG
41969146 TCTTACACT-GACTATC-ATCTC-ATAGCCG--A
62 TCTTACACTAGAC--TCGA-CTCAAT-GCCGATA
*
41969175 CGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGTCGATGCATGTCCCAGACATGTC
1 C-CATGTCCCAGACATGTCTTACACTGACTTACA-CTCGAGGTCGATGCATGTCCCAGACATGTC
* *
41969240 TTACATTAGCACTCGTCTCAATGCCGATA
64 TTACACTAG-ACTCGACTCAATGCCGATA
*
41969269 CCATGTCCCAGACATGGTCTTACACTGACTTTCA-T-GATGTGTCCGATGCATGTCCCAGACATG
1 CCATGTCCCAGACAT-GTCTTACACTGACTTACACTCGA-G-GT-CGATGCATGTCCCAGACATG
41969332 TCTTACACTAG
62 TCTTACACTAG
41969343 CTCACATAAG
Statistics
Matches: 144, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
91 5 0.03
92 54 0.38
93 35 0.24
94 50 0.35
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (91 bp):
CCATGTCCCAGACATGTCTTACACTGACTTACACTCGAGGTCGATGCATGTCCCAGACATGTCTT
ACACTAGACTCGACTCAATGCCGATA
Found at i:41974048 original size:55 final size:55
Alignment explanation
Indices: 41973936--41974048 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 55
41973926 CGTGGGCAAC
* * * *
41973936 ACTGACTTTTGAACACGGCTATGACACATGCCCATGCTGCCTGTCCATGTTCAAT
1 ACTGACTTTGGAACACGGCTATGACACACGCCCATGCTGCCTATCCATGTCCAAT
* * * *
41973991 ACTGACTTTGGGACACGGCTATGAGACACG-CC-TGTTTGACCTATCCATGTCCTAT
1 ACTGACTTTGGAACACGGCTATGACACACGCCCATG-CTG-CCTATCCATGTCCAAT
41974046 ACT
1 ACT
41974049 AACTCAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
53 2 0.04
54 4 0.08
55 42 0.88
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (55 bp):
ACTGACTTTGGAACACGGCTATGACACACGCCCATGCTGCCTATCCATGTCCAAT
Found at i:41974734 original size:26 final size:26
Alignment explanation
Indices: 41974698--41974747 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
41974688 GCTTAGTAAG
41974698 TCCATATGAAAATAATAAGCATTAAT
1 TCCATATGAAAATAATAAGCATTAAT
41974724 TCCATATGAAAATAATAAGCATTA
1 TCCATATGAAAATAATAAGCATTA
41974748 TAATAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (26 bp):
TCCATATGAAAATAATAAGCATTAAT
Found at i:41977471 original size:46 final size:45
Alignment explanation
Indices: 41977277--41977546 Score: 131
Period size: 46 Copynumber: 5.8 Consensus size: 45
41977267 CATAGCATAT
* * * *
41977277 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTATC
1 AATGTCGATG-CATGTCCTAGACAT-GTCTTACACTAGCTC-TCTCTC
* * * ** * *
41977325 AA-GTCGATGCCATGTCCCAGGCATGGTCTTACACT-GACACAGTTTG
1 AATGTCGATG-CATGTCCTAGACAT-GTCTTACACTAG-CTCTCTCTC
* * * *
41977371 TA-GCCGATGCATGT-TTCAGAGATGTCTTACACTAGCT-TACATCTC
1 AATGTCGATGCATGTCCT-AGACATGTCTTACACTAGCTCT-C-TCTC
* * * *
41977416 GAGGCCGATGCATATCCTAGACATGTCTTACACTAGCTCTCGTCTC
1 AATGTCGATGCATGTCCTAGACATGTCTTACACTAGCTCTC-TCTC
* * * *
41977462 AATGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-TAT-
1 AATGTCGATG-CATGTCCTAGACAT-GTCTTACACTAGCTCTCTCTC
* *
41977507 AATGTGGCCGATGTATGTCCTAGACATGTCTTACATTAGC
1 AATGT---CGATGCATGTCCTAGACATGTCTTACACTAGC
41977547 ACACAAATGA
Statistics
Matches: 173, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
44 11 0.06
45 18 0.10
46 65 0.38
47 57 0.33
48 22 0.13
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGTCGATGCATGTCCTAGACATGTCTTACACTAGCTCTCTCTC
Found at i:41984496 original size:46 final size:46
Alignment explanation
Indices: 41984296--41984609 Score: 221
Period size: 46 Copynumber: 6.7 Consensus size: 46
41984286 GTATAATGCT
* * * *
41984296 GATGCTATGTCCCAGACATGGTCTTACACTGGTTCATC-TATC-AAGTC
1 GATGC-ATGTCCCAGACAT-GTCTTACACTAGCTC-TCATATCGAGGCC
* * * * *
41984343 GATGCCATGTCCCAAACATGATCTCACGCTAACTCTCACATATCTG-TGCC
1 GATG-CATGTCCCAGACATG-TCTTACACTAGCTCT--CATATC-GAGGCC
* * * * * *
41984393 GATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATGTTGTA-TCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATATCG-AGGCC
*
41984439 AATGCATGTCCCAGACATGTCTTACACTAGCT-TCCATATCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATATCGAGGCC
* * * *
41984485 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATCGAGGCC
* * *
41984531 GATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-ATCGAGGCC
*
41984579 AATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
41984610 GCACAAATGA
Statistics
Matches: 211, Mismatches: 38, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
44 10 0.05
45 16 0.08
46 72 0.34
47 54 0.26
48 25 0.12
49 5 0.02
50 28 0.13
51 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATCGAGGCC
Found at i:41985461 original size:29 final size:28
Alignment explanation
Indices: 41985373--41985498 Score: 94
Period size: 29 Copynumber: 4.4 Consensus size: 28
41985363 GGTTACCGTC
* *
41985373 CCTTTTCATATTCAATAGTCAAAACC-AT
1 CCTTTTCATAATCAATAG-CCAAACCTAT
* * * *
41985401 CGCTTTTCATTAATCGATGGTCATCACC-AT
1 C-CTTTTCA-TAATCAATAGCCA-AACCTAT
*
41985431 CCATTTTCATAATCAATAGCTAAACCTAT
1 CC-TTTTCATAATCAATAGCCAAACCTAT
* * *
41985460 CCTTTTCATATTCAATAGCCGAAGCTAT
1 CCTTTTCATAATCAATAGCCAAACCTAT
41985488 CCCTTTTCATA
1 -CCTTTTCATA
41985499 TTCGATGGTT
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
28 26 0.34
29 32 0.42
30 19 0.25
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (28 bp):
CCTTTTCATAATCAATAGCCAAACCTAT
Found at i:41987579 original size:46 final size:46
Alignment explanation
Indices: 41987432--41987653 Score: 198
Period size: 46 Copynumber: 4.7 Consensus size: 46
41987422 TCACTTGTGT
* ***
41987432 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGGGATGA
* * ** * * *
41987478 AAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGGGATGA
* *
41987526 GTGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGGGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGGGATG-A
* * *
41987573 -AGCTAGTGTAAGATATGTCTGAGACATGCGTCGG-CT-GTGAGATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCG-G-GATGA
* *
41987618 TAGTTAGTGTAAGATCATGTCTGGGACATGGCATCG
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
41987654 ACACCTTACC
Statistics
Matches: 140, Mismatches: 28, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
44 1 0.01
45 4 0.03
46 69 0.49
47 40 0.29
48 26 0.19
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGGGATGA
Found at i:41987652 original size:94 final size:94
Alignment explanation
Indices: 41987434--41987653 Score: 259
Period size: 94 Copynumber: 2.3 Consensus size: 94
41987424 ACTTGTGTGA
**
41987434 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGGATGAAAGCCAGTGTAAGACCATGTC
* *
41987499 TGGGACATGGCATCGGTATTGAGACGAGT
66 TGAGACATGGCATCGGTAGTGAGACGAGT
* * * * * *
41987528 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGGGATGTAAGCTAGTGTAAGA-TATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGGATGAAAGCCAGTGTAAGACCATGTC
* *
41987592 TGAGACAT-GCGTCGGCT-GTGAGATGA-T
66 TGAGACATGGCATCGG-TAGTGAGACGAGT
*
41987619 AGTTAGTGTAAGATCATGTCTGGGACATGGCATCG
1 -GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
41987654 ACACCTTACC
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
91 1 0.01
92 24 0.22
93 26 0.24
94 57 0.53
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.25
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGGATGAAAGCCAGTGTAAGACCATGTC
TGAGACATGGCATCGGTAGTGAGACGAGT
Found at i:41996626 original size:26 final size:26
Alignment explanation
Indices: 41996596--41996655 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
41996586 AAAGCGCCTG
41996596 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAAGAAGCTCACAA
* ** * *
41996622 AGAGCCTTTAATCGGGAAGCTTACGA
1 AGAGCCATTAATCAAGAAGCTCACAA
41996648 AGAGCCAT
1 AGAGCCAT
41996656 ATATCGAGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAAGAAGCTCACAA
Found at i:41997728 original size:16 final size:13
Alignment explanation
Indices: 41997694--41997721 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41997684 TTTTATTTTA
41997694 TTATTTATCATCT
1 TTATTTATCATCT
41997707 TTATTTATCATCT
1 TTATTTATCATCT
41997720 TT
1 TT
41997722 TCAATTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:41999750 original size:40 final size:41
Alignment explanation
Indices: 41999706--41999782 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
41999696 TCGCAACTGC
*
41999706 TTGACCTTTTACGGCATTTTT-TAATAAATGCCACTAATGA
1 TTGACCTTTTACGGCATTTTTATAATAAACGCCACTAATGA
* ** *
41999746 TTGACCTTTTGCGGTGTTTTTATCATAAACGCCACTA
1 TTGACCTTTTACGGCATTTTTATAATAAACGCCACTA
41999783 TAGCTCTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 18 0.58
41 13 0.42
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (41 bp):
TTGACCTTTTACGGCATTTTTATAATAAACGCCACTAATGA
Found at i:42011732 original size:70 final size:70
Alignment explanation
Indices: 42011591--42012179 Score: 513
Period size: 70 Copynumber: 8.4 Consensus size: 70
42011581 TTAGCACGAA
* * * * * ** *
42011591 CTCAAGCTCCTAGCTTTGATTTTAAGGTTCATAGGTTCAACA-TGCAGCCTCCAAAATAGTTAGC
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
*
42011655 ATGAG
66 GTGAG
* * * * *
42011660 CTCAAGCTTCCAACTGTGATCTTAAGGCTCGCAGGTTGAACACCACAACCTCCAAAATAGTTAGT
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
*
42011725 GTTAG
66 GTGAG
* ** * * * * * *
42011730 CTCAAGCTCCTAGTTGTGATTTTATGGCGCACAGGTTCAACATCGTAGCCTCCAAAATAGTTAGC
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
*
42011795 GCGAG
66 GTGAG
* ** ** *
42011800 CTCAAGCACCCAGA-TGTGATCTTAAGGCTCATAGGTTCAACATTGTAGCCTCTC-AAATAGTTA
1 CTCAAGCTCCCA-ACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTC-CAAAATAGTTA
*
42011863 GCATGAG
64 GCGTGAG
* * *** *
42011870 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGTATGTTCAACTTTGCAG-CTAACAAAATAGTTAG
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCT-CCAAAATAGTTAG
*
42011934 CATGAG
65 CGTGAG
* * * * * * * * * *
42011940 TTCAAACTCCCAACTGTGATCTTAAGGCTTGCAGGTTTAACAGCACAGCCTTCTAAACAGTTAGT
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
*
42012005 GTAAG
66 GTGAG
** ** * * *
42012010 CTCAAGCTCCCAGTTGTGATCTTAAGGCTTACAAGTTCAACACTGCAGCCTCCAAAATAGTTAAC
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
*
42012075 GCGAG
66 GTGAG
* * * * ** *
42012080 GTCAAACTCCCAGCTGTGATCTTAAGGCTCGCAAGTTCAACACCATAGCCTCCTAAATAGTTAGC
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
42012145 -TAGAG
66 GT-GAG
*
42012150 CTCAAACTCCCAACTGTGATCTTAAGGCTC
1 CTCAAGCTCCCAACTGTGATCTTAAGGCTC
42012180 ACAAGCTCAA
Statistics
Matches: 419, Mismatches: 93, Indels: 15
0.80 0.18 0.03
Matches are distributed among these distances:
69 37 0.09
70 379 0.90
71 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (70 bp):
CTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGCAGCCTCCAAAATAGTTAGC
GTGAG
Found at i:42011836 original size:140 final size:140
Alignment explanation
Indices: 42011591--42012182 Score: 586
Period size: 140 Copynumber: 4.2 Consensus size: 140
42011581 TTAGCACGAA
* * * *
42011591 CTCAAGCTCCTAGCTT-TGATTTTAAGGTTCATAGGTTCAACAT-GCAGCCTCCAAAATAGTTAG
1 CTCAAGCTCCCAG-TTGTGATCTTAAGGCTCACAGGTTCAACATCGCAGCCTCCAAAATAGTTAG
* * * * * *
42011654 CATGAGCTCAAGCTTCCAACTGTGATCTTAAGGCTCGCAGGTTGAACACCACAACCTCCAAAATA
65 CACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCACAGCCTCCTAAATA
*
42011719 GTTAGTGTTAG
130 GTTAGTGTAAG
* * * * *
42011730 CTCAAGCTCCTAGTTGTGATTTTATGGCGCACAGGTTCAACATCGTAGCCTCCAAAATAGTTAGC
1 CTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTCAACATCGCAGCCTCCAAAATAGTTAGC
* * * ** ****
42011795 GCGAGCTCAAGCACCCAGA-TGTGATCTTAAGGCTCATAGGTTCAACATTGTAGCCT-CTCAAAT
66 ACGAGCTCAAACTCCCA-ACTGTGATCTTAAGGCTCGCAGGTTCAACACCACAGCCTCCT-AAAT
** *
42011858 AGTTAGCATGAG
129 AGTTAGTGTAAG
** ** * * * *
42011870 CTCAAGCTCCCAACTGTGATCTTAAGGCTCGTATGTTCAACTTTGCAG-CTAACAAAATAGTTAG
1 CTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTCAACATCGCAGCCT-CCAAAATAGTTAG
* * * * * * *
42011934 CATGAGTTCAAACTCCCAACTGTGATCTTAAGGCTTGCAGGTTTAACAGCACAGCCTTCTAAACA
65 CACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCACAGCCTCCTAAATA
42011999 GTTAGTGTAAG
130 GTTAGTGTAAG
* * *
42012010 CTCAAGCTCCCAGTTGTGATCTTAAGGCTTACAAGTTCAACA-CTGCAGCCTCCAAAATAGTTAA
1 CTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTCAACATC-GCAGCCTCCAAAATAGTTAG
* * * * *
42012074 CGCGAGGTCAAACTCCCAGCTGTGATCTTAAGGCTCGCAAGTTCAACACCATAGCCTCCTAAATA
65 CACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCACAGCCTCCTAAATA
*
42012139 GTTAG-CTAGAG
130 GTTAGTGTA-AG
* **
42012150 CTCAAACTCCCAACTGTGATCTTAAGGCTCACA
1 CTCAAGCTCCCAGTTGTGATCTTAAGGCTCACA
42012183 AGCTCAAAAA
Statistics
Matches: 366, Mismatches: 77, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
138 2 0.01
139 42 0.11
140 317 0.87
141 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (140 bp):
CTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTCAACATCGCAGCCTCCAAAATAGTTAGC
ACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCACAGCCTCCTAAATAG
TTAGTGTAAG
Found at i:42011930 original size:210 final size:209
Alignment explanation
Indices: 42011569--42012182 Score: 631
Period size: 210 Copynumber: 2.9 Consensus size: 209
42011559 TTTATATGAT
* * * * * * * *
42011569 CCTCCAAAGCAGTTAGCACGAACTCAAGCTCCTAGCTTTGATTTTAAGGTTCATAGGTTCAACAT
1 CCTCCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGATGTGATCTTAAGGCTCATAGGTTCAACAT
* * *
42011634 GCAGCCTCCAAAATAGTTAGCATGAGCTCAAGCTTCCAACTGTGATCTTAAGGCTCGCAGGTTGA
66 GCAGCCTCCAAAATAGTTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAAGTTCA
* ** * * * ** * *
42011699 ACACCACAACCTCCAAAATAGTTAGTGTTAGCTCAAGCTCCTAGTTGTGATTTTATGGCGCACAG
131 ACACCACAACCTACAAAATAGTTAGCATGAGCTCAAACTCCCAACTGTGATCTTAAGGCGCACAG
* **
42011764 GTTCAACATCGTAG
196 GTTCAACAGCACAG
* *
42011778 CCTCCAAAATAGTTAGCGCGAGCTCAAGCACCCAGATGTGATCTTAAGGCTCATAGGTTCAACAT
1 CCTCCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGATGTGATCTTAAGGCTCATAGGTTCAACA-
* * *
42011843 TGTAGCCTCTC-AAATAGTTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGTATGTT
65 TGCAGCCTC-CAAAATAGTTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAAGTT
**** * * ***
42011907 CAACTTTGC-AGCTAACAAAATAGTTAGCATGAGTTCAAACTCCCAACTGTGATCTTAAGGCTTG
129 CAACACCACAACCT-ACAAAATAGTTAGCATGAGCTCAAACTCCCAACTGTGATCTTAAGGCGCA
*
42011971 CAGGTTTAACAGCACAG
193 CAGGTTCAACAGCACAG
* * * ** * * * *
42011988 CCTTCTAAACAGTTAGTGTAAGCTCAAGCTCCCAGTTGTGATCTTAAGGCTTACAAGTTCAACAC
1 CCTCCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGATGTGATCTTAAGGCTCATAGGTTCAACA-
* ** * * *
42012053 TGCAGCCTCCAAAATAGTTAACGCGAGGTCAAACTCCCAGCTGTGATCTTAAGGCTCGCAAGTTC
65 TGCAGCCTCCAAAATAGTTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAAGTTC
* * * * *
42012118 AACACCATAGCCTCCTAAATAGTTAGC-TAGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCAC
130 AACACCACAACCTACAAAATAGTTAGCAT-GAGCTCAAACTCCCAACTGTGATCTTAAGGCGCAC
42012182 A
194 A
42012183 AGCTCAAAAA
Statistics
Matches: 328, Mismatches: 71, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
209 59 0.18
210 266 0.81
211 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (209 bp):
CCTCCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGATGTGATCTTAAGGCTCATAGGTTCAACAT
GCAGCCTCCAAAATAGTTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAAGTTCA
ACACCACAACCTACAAAATAGTTAGCATGAGCTCAAACTCCCAACTGTGATCTTAAGGCGCACAG
GTTCAACAGCACAG
Found at i:42015762 original size:39 final size:39
Alignment explanation
Indices: 42015719--42016092 Score: 448
Period size: 39 Copynumber: 9.6 Consensus size: 39
42015709 CATATTCACT
* * *
42015719 TTTAAGCATATATCACATTACACATGTAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
42015758 TTTAAACA-ATGTCACAATACTCATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
42015796 TTTAAGCATA-ATTTACAGTCCTCATATAATCACATAACA
1 TTTAAGCATATA-TCACAATACTCATATAATCACATAACA
* * * *
42015835 TTTAAGCATATATCATAGTGCTCATATAATCATATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * **
42015874 TTTAATCATATA-CTATAATACTCATATAATCACATAATG
1 TTTAAGCATATATC-ACAATACTCATATAATCACATAACA
* * **
42015913 TTTAAGCATATGTCACAATACTCATATAGTCACATAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
42015952 TTTAAGAATATATCACAAAACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * **
42015991 TTTAAGCATATATCACAATACTCATATAATAACAAAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
42016030 TTTAAGCTTATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
42016069 TTAAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
42016093 AAGACATATT
Statistics
Matches: 285, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
38 33 0.12
39 250 0.88
40 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:42015869 original size:8 final size:8
Alignment explanation
Indices: 42015817--42015911 Score: 63
Period size: 8 Copynumber: 12.1 Consensus size: 8
42015807 TTTACAGTCC
42015817 TCATATAA
1 TCATATAA
*
42015825 TCACATAA
1 TCATATAA
*
42015833 -CATTTAA
1 TCATATAA
*
42015840 GCATAT-A
1 TCATATAA
**
42015847 TCATAGTGC
1 TCATA-TAA
42015856 TCATATAA
1 TCATATAA
42015864 TCATATAA
1 TCATATAA
*
42015872 -CATTTAA
1 TCATATAA
*
42015879 TCATATAC
1 TCATATAA
*
42015887 T-ATAATAC
1 TCAT-ATAA
42015895 TCATATAA
1 TCATATAA
*
42015903 TCACATAA
1 TCATATAA
42015911 T
1 T
42015912 GTTTAAGCAT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
7 18 0.26
8 43 0.63
9 7 0.10
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (8 bp):
TCATATAA
Done.