Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 186 of 250
Found at i:58633918 original size:9 final size:9
Alignment explanation
Indices: 58633888--58633919 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
58633878 ATTTATATTT
58633888 TATTAAAAA
1 TATTAAAAA
*
58633897 TATAAAAAA
1 TATTAAAAA
58633906 TATTAAAAA
1 TATTAAAAA
58633915 TATTA
1 TATTA
58633920 TCATAGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATTAAAAA
Found at i:58635130 original size:7 final size:7
Alignment explanation
Indices: 58635115--58635147 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
58635105 TTATATAGGT
58635115 AATACTA
1 AATACTA
*
58635122 AATAATA
1 AATACTA
58635129 AATACTA
1 AATACTA
58635136 AATACTA
1 AATACTA
58635143 AATAC
1 AATAC
58635148 GAAACGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:58636317 original size:22 final size:21
Alignment explanation
Indices: 58636285--58636331 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
58636275 ACATAGCTTT
*
58636285 TTTG-CAAAAATTAGAGACAAC
1 TTTGACAAAAATT-GAGACAAA
58636306 TTTGACAAAAATTGAGACAAA
1 TTTGACAAAAATTGAGACAAA
58636327 TTTGA
1 TTTGA
58636332 GAGAATTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.28
Consensus pattern (21 bp):
TTTGACAAAAATTGAGACAAA
Found at i:58642082 original size:128 final size:127
Alignment explanation
Indices: 58641850--58642159 Score: 368
Period size: 128 Copynumber: 2.4 Consensus size: 127
58641840 CGAAACTCAG
* * * * ** * *
58641850 CACGGTAGGGCACGATTCCTCGAACTTCCTAACATTGAACATTGCCTTGTTTTAGAATTTAAAGA
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTCTTTTAGAATTTAAAAA
* * * *
58641915 ATACGAATGAAATTCTAAAGGAATATTTGATTATTTTGAATAAACGAGAAATCAAAACCCAA
66 ACACGAATGAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACGAGAAATCAAAACCCAA
* * * * *
58641977 CACGATAGGGCACGGTTCCCCGAATTTTCAAGCATCAAATATTGCATTCTTTTAGAATTTAGAAA
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTCTTTTAGAATTTA-AAA
* * * * * *
58642042 AACACGAGTGAAATTCTAAAGGAAGGTTCGATTATTTTGAACAAACGGGAAATCGAAACTCAG
65 AACACGAATGAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACGAGAAATCAAAACCCAA
***
58642105 CACGATAGGGCACGATTTTTCGAATTTCCAAACATCAAACATTGCCTTCGTTTTA
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTC-TTTTA
58642160 AGGTTTAAAC
Statistics
Matches: 150, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
127 49 0.33
128 96 0.64
129 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (127 bp):
CACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTCTTTTAGAATTTAAAAA
ACACGAATGAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACGAGAAATCAAAACCCAA
Found at i:58643274 original size:28 final size:29
Alignment explanation
Indices: 58643221--58643282 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
58643211 AGGAAACACT
* * *
58643221 TATATATATATATAATAGATTTAAAAACA
1 TATATATACATATAATAAATTTAAAAAAA
58643250 TATATATACATA-AATAAATTTAAAAAAA
1 TATATATACATATAATAAATTTAAAAAAA
58643278 TATAT
1 TATAT
58643283 GCGAGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
TATATATACATATAATAAATTTAAAAAAA
Found at i:58646452 original size:18 final size:19
Alignment explanation
Indices: 58646431--58646466 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58646421 TTAAATAGTA
58646431 TTAAAA-ATAATTTTATAT
1 TTAAAAGATAATTTTATAT
*
58646449 TTAAAAGATATTTTTATA
1 TTAAAAGATAATTTTATA
58646467 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAAAAGATAATTTTATAT
Found at i:58647990 original size:28 final size:29
Alignment explanation
Indices: 58647958--58648020 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 29
58647948 AAAAACAAAC
*
58647958 TTAAAAACCTGGG-TTTTGAAATCTATTT
1 TTAAAAACCTGGGTTTTTGAAACCTATTT
58647986 TT-AAAACCTGGGTTTTTGAAACCTATTT
1 TTAAAAACCTGGGTTTTTGAAACCTATTT
58648014 TTAAAAA
1 TTAAAAA
58648021 TCAACTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 10 0.31
28 18 0.56
29 4 0.12
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (29 bp):
TTAAAAACCTGGGTTTTTGAAACCTATTT
Found at i:58649885 original size:46 final size:50
Alignment explanation
Indices: 58649825--58649987 Score: 149
Period size: 52 Copynumber: 3.2 Consensus size: 50
58649815 TAGCCTCGCC
* *
58649825 ATGGTCTTACACGGATCACA-TATC-AT-ACA-GATGCCATATCCCAGAT
1 ATGGTCTTATACGGATCACATTATCAATCACACGATGCCATAGCCCAGAT
* *
58649871 ATGGTCTTATACGGAATCATATTATCATATCACACCGATGCCATAGCCCAGCT
1 ATGGTCTTATACGG-ATCACATTATCA-ATCACA-CGATGCCATAGCCCAGAT
* * * *
58649924 ATGGTCTTATACGGA-AACACGTATCACATTGCAC-CAATGCCATAGCCCAGCT
1 ATGGTCTTATACGGATCACA-TTATCA-A-T-CACACGATGCCATAGCCCAGAT
58649976 ATGGTCTTATAC
1 ATGGTCTTATAC
58649988 AGAAGCACAT
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
46 13 0.13
47 5 0.05
48 4 0.04
50 2 0.02
51 5 0.05
52 36 0.37
53 30 0.31
54 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (50 bp):
ATGGTCTTATACGGATCACATTATCAATCACACGATGCCATAGCCCAGAT
Found at i:58649921 original size:53 final size:52
Alignment explanation
Indices: 58649843--58649987 Score: 182
Period size: 53 Copynumber: 2.8 Consensus size: 52
58649833 ACACGGATCA
* * * * * *
58649843 CATATCATACAGATGCCATATCCCAGATATGGTCTTATACGGAATCATATTAT
1 CATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAACA-AGTAT
*
58649896 CATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAACACGTAT
1 CATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAACAAGTAT
* ** *
58649948 CACATTGCACCAATGCCATAGCCCAGCTATGGTCTTATAC
1 CATATCACACCGATGCCATAGCCCAGCTATGGTCTTATAC
58649988 AGAAGCACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 39 0.48
53 42 0.52
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (52 bp):
CATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAACAAGTAT
Found at i:58649971 original size:52 final size:53
Alignment explanation
Indices: 58649855--58649987 Score: 178
Period size: 52 Copynumber: 2.5 Consensus size: 53
58649845 TATCATACAG
* * * * * *
58649855 ATGCCATATCCCAGATATGGTCTTATACGGAATCATATTATCATATCACACCG
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAAACATAGTATCACATCACACCA
* **
58649908 ATGCCATAGCCCAGCTATGGTCTTATACGGAAACA-CGTATCACATTGCACCA
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAAACATAGTATCACATCACACCA
58649960 ATGCCATAGCCCAGCTATGGTCTTATAC
1 ATGCCATAGCCCAGCTATGGTCTTATAC
58649988 AGAAGCACAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 39 0.55
53 32 0.45
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
ATGCCATAGCCCAGCTATGGTCTTATACGGAAACATAGTATCACATCACACCA
Found at i:58653089 original size:12 final size:11
Alignment explanation
Indices: 58653053--58653091 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
58653043 AGATAAATAT
58653053 TATTTTATTAA
1 TATTTTATTAA
* *
58653064 TATTTTAATGA
1 TATTTTATTAA
58653075 TATATTTATTAA
1 TAT-TTTATTAA
58653087 TATTT
1 TATTT
58653092 ATTTAGCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:58653598 original size:46 final size:46
Alignment explanation
Indices: 58653531--58653664 Score: 250
Period size: 46 Copynumber: 2.9 Consensus size: 46
58653521 GCGTAATAAA
58653531 CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATAC
1 CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATAC
58653577 CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATAC
1 CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATAC
* *
58653623 CATGGCAACGTGACATGAAATGAACAAAACCATGGTTGAAAG
1 CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAG
58653665 GTGTAACACC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.19
Consensus pattern (46 bp):
CATGGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGATAC
Found at i:58654341 original size:6 final size:6
Alignment explanation
Indices: 58654330--58654407 Score: 97
Period size: 6 Copynumber: 12.8 Consensus size: 6
58654320 AACCAAAATG
58654330 AGAATC AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
* *
58654378 AGAATT ACGTGA-C AGAATC AGAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
58654408 GTGAATGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
5 3 0.05
6 55 0.87
7 4 0.06
8 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:58654562 original size:27 final size:26
Alignment explanation
Indices: 58654525--58654590 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
58654515 AGCATGGCTG
*
58654525 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
58654551 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
*
58654578 CCAAAATCAGATA
1 CCAGAA-CAGATA
58654591 ATGTGGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:58654796 original size:22 final size:22
Alignment explanation
Indices: 58654764--58654821 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
58654754 TAAATACGTT
*
58654764 TGGCACGAAGCCATAGTCAAGA
1 TGGCACAAAGCCATAGTCAAGA
* * *
58654786 TGGCACAAAGCCATATTCAGGT
1 TGGCACAAAGCCATAGTCAAGA
*
58654808 TGGCACAGAGCCAT
1 TGGCACAAAGCCAT
58654822 TAATAACGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (22 bp):
TGGCACAAAGCCATAGTCAAGA
Found at i:58654948 original size:27 final size:26
Alignment explanation
Indices: 58654909--58654991 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
58654899 TCGATCGGTC
* *
58654909 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAA
*
58654935 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAA
*
58654962 AACAGATATTTGTGGCATAGCCACCAA
1 AACAGATA-TTGTGGCAGAGCCACCAA
58654989 AAC
1 AAC
58654992 GCTTCCTCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.16
27 42 0.84
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAA
Found at i:58655221 original size:27 final size:27
Alignment explanation
Indices: 58655191--58655381 Score: 201
Period size: 27 Copynumber: 7.2 Consensus size: 27
58655181 GGTCAAATTT
* * *
58655191 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
*
58655218 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
*
58655245 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * * *
58655272 ATGATTCTACCCTATAAGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * *
58655299 GT-A---TATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
58655322 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * *
58655349 GAAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
58655376 GTAATT
1 GTAATT
58655382 TCACAATCAA
Statistics
Matches: 138, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
23 19 0.14
24 1 0.01
26 1 0.01
27 117 0.85
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCG
Found at i:58655425 original size:27 final size:27
Alignment explanation
Indices: 58655386--58656068 Score: 758
Period size: 27 Copynumber: 25.3 Consensus size: 27
58655376 GTAATTTCAC
* * *
58655386 AATCAAGGATAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655413 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655440 AA-CTGAGGGT-AAACTAGTAATTCTTTA
1 AATC-GAGGGTAAAAC-GGTAATTCTGTA
* * **
58655467 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655494 AATCGAGGGTAAAATGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655521 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655548 AA-CTGAGGGTAAAATGGTAATTCTCTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** * **
58655575 AATCGAGGGTAAAACTATAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655602 AATCAAGGGTAAAACGGTAATTCTCTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655629 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** *
58655656 AA-CTGAGGGTAAAATAGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
**
58655683 AATCGAGGGTAAAATAGTAATTCTGT-
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655709 AACCTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
58655737 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
58655764 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** *
58655791 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655818 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
58655845 AATCAAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655872 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** *
58655899 AATCGAGGGTAAAATAGTAATTCTAT-
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
58655925 AACCTGAGGGTAAAACGGTAATTCTATAA
1 AATC-GAGGGTAAAACGGTAATTCTGT-A
58655954 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
58655981 AA-CTGAGGGTAAAACGGTAATTCAGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
**
58656008 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
58656035 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
58656062 AATCGAG
1 AATCGAG
58656069 AGTACTTTGG
Statistics
Matches: 557, Mismatches: 76, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
26 17 0.03
27 501 0.90
28 36 0.06
29 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:58656083 original size:54 final size:54
Alignment explanation
Indices: 58655395--58656068 Score: 896
Period size: 54 Copynumber: 12.5 Consensus size: 54
58655385 CAATCAAGGA
* *
58655395 TAAAACGGTAATTCTATAAATCGAGGGTAAAA-CGATAATTTTGTAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAG-TAATTCTGTAAACTGAGGG
* * * ** *
58655449 T-AAACTAGTAATTCTTTAAATCAAGGGTAAAACGGTAATT-T-TACAAATCGAGGG
1 TAAAAC-GGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTA-AACT-GAGGG
* * * * **
58655503 TAAAATGATAATTCTGTAAATTGAGGGTAAAACGGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
* * * *
58655557 TAAAATGGTAATTCTCTAAATCGAGGGTAAAACTA-TAATT-T-TACAAATCAAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAA-TAGTAATTCTGTA-AACT-GAGGG
* *
58655611 TAAAACGGTAATTCTCTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
** *
58655665 TAAAATAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAACCTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
* * **
58655719 TAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
* *
58655773 TAAAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
*
58655827 TAAAACGGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
* *
58655881 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTATAACCTGAGGG
1 TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
**
58655935 TAAAACGGTAATTCTATAAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTAT-AAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
58655990 TAAAACGGTAATTC-AGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
1 TAAAACGGTAATTCTA-TAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
*
58656044 TAAAACGGTAATTCTGTAAATCGAG
1 TAAAACGGTAATTCTATAAATCGAG
58656069 AGTACTTTGG
Statistics
Matches: 552, Mismatches: 52, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
52 4 0.01
53 13 0.02
54 471 0.85
55 60 0.11
56 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (54 bp):
TAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGG
Found at i:58660087 original size:16 final size:17
Alignment explanation
Indices: 58660068--58660110 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
58660058 TTAATAGATT
58660068 TTTATTTAAATG-ATAA
1 TTTATTTAAATGTATAA
58660084 TTTATTATGAAATGTATAA
1 TTTATT-T-AAATGTATAA
58660103 TTT-TTTAA
1 TTTATTTAA
58660111 GTCATAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 7 0.29
19 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TTTATTTAAATGTATAA
Found at i:58664324 original size:18 final size:18
Alignment explanation
Indices: 58664303--58664346 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
58664293 ATTTAATACT
58664303 AAAAAAATATAGCAAATG
1 AAAAAAATATAGCAAATG
* ** *
58664321 AAAATAATATTTCAGATG
1 AAAAAAATATAGCAAATG
58664339 AAAAAAAT
1 AAAAAAAT
58664347 CATTTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.23
Consensus pattern (18 bp):
AAAAAAATATAGCAAATG
Found at i:58666948 original size:33 final size:33
Alignment explanation
Indices: 58666908--58666976 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
58666898 CAGTGAAACT
58666908 TTTGCTAGACTTTCAAAATCCTATGGGTTTTAC
1 TTTGCTAGACTTTCAAAATCCTATGGGTTTTAC
58666941 TTTGCTAGACTTTCAAAATCCTATGGGTTTTAC
1 TTTGCTAGACTTTCAAAATCCTATGGGTTTTAC
58666974 TTT
1 TTT
58666977 TTGCTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (33 bp):
TTTGCTAGACTTTCAAAATCCTATGGGTTTTAC
Found at i:58667427 original size:15 final size:15
Alignment explanation
Indices: 58667407--58667436 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58667397 AGCAATTTGT
58667407 TGAAGAGAACGTCTA
1 TGAAGAGAACGTCTA
*
58667422 TGAAGAGAATGTCTA
1 TGAAGAGAACGTCTA
58667437 CAACCACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (15 bp):
TGAAGAGAACGTCTA
Found at i:58668986 original size:589 final size:590
Alignment explanation
Indices: 58667915--58669094 Score: 2161
Period size: 589 Copynumber: 2.0 Consensus size: 590
58667905 CGTTCACTTT
58667915 CGTCCATATAGAATGTGTATAGCCACTATTTCAACACCAATCGGTTAGCCAAAAACTTTTTTGCG
1 CGTCCATATAGAATGTGTATAGCCACTATTTCAACACCAATCGGTTAGCCAAAAACTTTTTTGCG
58667980 TAAAGGGTTTCTAACATTTTCCATAAGGCGGATGTCATTTTCTCCATTAACACCTCTTACAATAC
66 TAAAGGGTTTCTAACATTTTCCATAAGGCGGATGTCATTTTCTCCATTAACACCTCTTACAATAC
*
58668045 ACTATTCGTAAGGCACAATTGAATTAGTGACAGGGCCTTCTCATCAAGCTCTCCCTTTCTGATTG
131 ACTATTCGTAAGGCACAATTGAATTAGTGACAGGGCCTTCTCATCAAGCTCTCCCTTTCTGACTG
58668110 ATGTAGATTATCGAGTTTTTTTTCCCGTAATGACCTTTTTCAGACCGTTCTAAACTAGAATTATT
196 ATGTAGATTATCGAGTTTTTTTTCCCGTAATGACCTTTTTCAGACCGTTCTAAACTAGAATTATT
58668175 GTCATCCAAACTTGACATTGATTGAAATTTGTGAAGTCATCAAACTTCTCAATGTTGAACCTTAT
261 GTCATCCAAACTTGACATTGATTGAAATTTGTGAAGTCATCAAACTTCTCAATGTTGAACCTTAT
58668240 TATTGGCCTCTCAAAACAGGTTGAATACGAAAATCGAATCAAGCTCTGATGTTAGTTAGTTGGGG
326 TATTGGCCTCTCAAAACAGGTTGAATACGAAAATCGAATCAAGCTCTGATGTTAGTTAGTTGGGG
* *
58668305 ATAAACTTGTATAAGCAACAAACAAGAAAAATAAAGAATAAATTGAAAAGATCGAACATACAAAT
391 ATAAACTTGTATAAGCAACAAAAAAGAAAAATAAAGAATAAATTGAAAAGATCGAACACACAAAT
* *
58668370 TTTACATAGAAAAACCCTTTCGAAAAGGATAAAAAACCACGGGCGAAAATAATTTCACTAAATTG
456 TTTACATAGAAAAAACCTTTCGAAAAGGATAAAAAACCACGGGCGAAAATAATTTCACTAAATCG
58668435 GCAAAAACGAAGACTACAAAAATGAAAATAAAAACTAAACCATGAAACCCAAAAATAAGAACCCT
521 GCAAAAACGAAGACTACAAAAATGAAAATAAAAACTAAACCATGAAACCCAAAAATAAGAACCCT
58668500 CAAAA
586 CAAAA
* * *
58668505 CGTCTATATAGAATGTGTATAGCCACTATTTCAACACCAATCGGTTAGCCATAAACTTTTTTGTG
1 CGTCCATATAGAATGTGTATAGCCACTATTTCAACACCAATCGGTTAGCCAAAAACTTTTTTGCG
*
58668570 TAAAGGGTTTCTAACATTTTTCATAAGGCGGATGTCATTTTCTCCATTAACACCTCTTACAATAC
66 TAAAGGGTTTCTAACATTTTCCATAAGGCGGATGTCATTTTCTCCATTAACACCTCTTACAATAC
*
58668635 ACTATTCGTAAGGCACAATTGAATTA-TAGACAGGGGCTTCTCATCAAGCTCTCCCCTTT-TGAC
131 ACTATTCGTAAGGCACAATTGAATTAGT-GACAGGGCCTTCTCATCAAGCTCT-CCCTTTCTGAC
58668698 TGATGTAGATTATCGAG-TTTTTTTCCCGTAATGACCTTTTTCAGACCGTTCTAAACTAGAATTA
194 TGATGTAGATTATCGAGTTTTTTTTCCCGTAATGACCTTTTTCAGACCGTTCTAAACTAGAATTA
* *
58668762 TTGTCATCCGAACTTGACATTGATTGAAATTTGTGATGTCATCAAACTTCTCAATGTTGAACCTT
259 TTGTCATCCAAACTTGACATTGATTGAAATTTGTGAAGTCATCAAACTTCTCAATGTTGAACCTT
* *
58668827 ATTGTTGGCCTCTCAAAATAGGTTGAATACGAAAATCGAATCAAGCTCTGATGTTAGTTAGTTGG
324 ATTATTGGCCTCTCAAAACAGGTTGAATACGAAAATCGAATCAAGCTCTGATGTTAGTTAGTTGG
*
58668892 GGATAAACTTGTATAAGCAACAAAAAAGAAAAATAAATAATAAATTGAAAAGATCGAACACACAA
389 GGATAAACTTGTATAAGCAACAAAAAAGAAAAATAAAGAATAAATTGAAAAGATCGAACACACAA
*
58668957 ATTTTACAT-GAAAAAACTTTTCCGAAAAGGATAAAAAACCACGGGCGAAAATAATTTCACTAAA
454 ATTTTACATAGAAAAAACCTTT-CGAAAAGGATAAAAAACCACGGGCGAAAATAATTTCACTAAA
58669021 TCGGCAAAAACGAAGACTACAAAAATGAAAATAAAAACTAAACCATGAAACCCAAAAATAAGAAC
518 TCGGCAAAAACGAAGACTACAAAAATGAAAATAAAAACTAAACCATGAAACCCAAAAATAAGAAC
58669086 CCTCAAAA
583 CCTCAAAA
58669094 C
1 C
58669095 TTAAACACAA
Statistics
Matches: 571, Mismatches: 16, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
588 10 0.02
589 360 0.63
590 195 0.34
591 6 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (590 bp):
CGTCCATATAGAATGTGTATAGCCACTATTTCAACACCAATCGGTTAGCCAAAAACTTTTTTGCG
TAAAGGGTTTCTAACATTTTCCATAAGGCGGATGTCATTTTCTCCATTAACACCTCTTACAATAC
ACTATTCGTAAGGCACAATTGAATTAGTGACAGGGCCTTCTCATCAAGCTCTCCCTTTCTGACTG
ATGTAGATTATCGAGTTTTTTTTCCCGTAATGACCTTTTTCAGACCGTTCTAAACTAGAATTATT
GTCATCCAAACTTGACATTGATTGAAATTTGTGAAGTCATCAAACTTCTCAATGTTGAACCTTAT
TATTGGCCTCTCAAAACAGGTTGAATACGAAAATCGAATCAAGCTCTGATGTTAGTTAGTTGGGG
ATAAACTTGTATAAGCAACAAAAAAGAAAAATAAAGAATAAATTGAAAAGATCGAACACACAAAT
TTTACATAGAAAAAACCTTTCGAAAAGGATAAAAAACCACGGGCGAAAATAATTTCACTAAATCG
GCAAAAACGAAGACTACAAAAATGAAAATAAAAACTAAACCATGAAACCCAAAAATAAGAACCCT
CAAAA
Found at i:58672723 original size:32 final size:32
Alignment explanation
Indices: 58672687--58672757 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
58672677 GTTTAGTTCA
*
58672687 CTGTAATGGAATAAGACTATAATTGAATAGAG
1 CTGTAATGGAATAAGACTATAATGGAATAGAG
* *
58672719 CTGTAATGGAATAAGGCTATAATGGAATAGCG
1 CTGTAATGGAATAAGACTATAATGGAATAGAG
58672751 CTGTAAT
1 CTGTAAT
58672758 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (32 bp):
CTGTAATGGAATAAGACTATAATGGAATAGAG
Found at i:58672757 original size:16 final size:16
Alignment explanation
Indices: 58672687--58672757 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
58672677 GTTTAGTTCA
*
58672687 CTGTAATGGAATAAGA
1 CTGTAATGGAATAAGG
* *
58672703 CTATAATTGAAT-AGAG
1 CTGTAATGGAATAAG-G
58672719 CTGTAATGGAATAAGG
1 CTGTAATGGAATAAGG
*
58672735 CTATAATGGAAT-AGCG
1 CTGTAATGGAATAAG-G
58672751 CTGTAAT
1 CTGTAAT
58672758 CAGTAATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 4 0.09
16 39 0.87
17 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAAGG
Found at i:58674543 original size:50 final size:50
Alignment explanation
Indices: 58674489--58674589 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
58674479 AATAATAACA
58674489 ACATGGCATGCAGTAAATAACAACAGTCAAACATGCATTTAGGTCAATTT
1 ACATGGCATGCAGTAAATAACAACAGTCAAACATGCATTTAGGTCAATTT
58674539 ACATGGCATGCAGTAAATAACAACAGTCAAACATGCATTTAGGTCAATTT
1 ACATGGCATGCAGTAAATAACAACAGTCAAACATGCATTTAGGTCAATTT
58674589 A
1 A
58674590 ACCCTAGGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (50 bp):
ACATGGCATGCAGTAAATAACAACAGTCAAACATGCATTTAGGTCAATTT
Found at i:58674612 original size:25 final size:27
Alignment explanation
Indices: 58674575--58674627 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
58674565 TCAAACATGC
58674575 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
58674601 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
58674627 A
1 A
58674628 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:58676145 original size:26 final size:26
Alignment explanation
Indices: 58676114--58676221 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
58676104 TGAAATGCCC
*
58676114 ATCATGGAACATTTACCTAAGCCATT
1 ATCATGGAACATTTACCTAACCCATT
58676140 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
58676166 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
58676192 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58676218 ATCA
1 ATCA
58676222 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:58683754 original size:23 final size:25
Alignment explanation
Indices: 58683727--58683773 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
58683717 CTCATTACCA
*
58683727 TTTAAA-AG-TTTTTTTTTTCATTG
1 TTTAAATAGATTTTTTATTTCATTG
58683750 TTTAAATAGATTTTTTATTTCATT
1 TTTAAATAGATTTTTTATTTCATT
58683774 AGTCTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 13 0.62
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTAAATAGATTTTTTATTTCATTG
Found at i:58684666 original size:22 final size:20
Alignment explanation
Indices: 58684633--58684678 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
58684623 TTTCCCCTTA
58684633 AATTCTGTTTTGATTTCAATTT
1 AATTCTGTTTTGA-TT-AATTT
58684655 AATTCCTG-TTTGATTAATTT
1 AATT-CTGTTTTGATTAATTT
58684675 AATT
1 AATT
58684679 ATTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.39
21 2 0.09
22 9 0.39
23 3 0.13
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (20 bp):
AATTCTGTTTTGATTAATTT
Found at i:58684863 original size:19 final size:18
Alignment explanation
Indices: 58684836--58684873 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
58684826 ATCTATTTCG
58684836 TTTTTTTATCT-TCTATTA
1 TTTTTTTAT-TATCTATTA
58684854 TTTTTATTATTATCTATTA
1 TTTTT-TTATTATCTATTA
58684873 T
1 T
58684874 GTATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTATTATCTATTA
Found at i:58689966 original size:27 final size:24
Alignment explanation
Indices: 58689914--58689972 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
58689904 GTAAAATGGG
*
58689914 TTTAAAATAAGGTATATAAAATAAT
1 TTTAAAATAAGGTATATAAAA-AAA
58689939 TTTAAAATAA-GTAATATATAAGAAAA
1 TTTAAAATAAGGT-ATATA-AA-AAAA
58689965 TTTAAAAT
1 TTTAAAAT
58689973 GTTATATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.07
25 15 0.50
26 12 0.40
27 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (24 bp):
TTTAAAATAAGGTATATAAAAAAA
Found at i:58691826 original size:20 final size:19
Alignment explanation
Indices: 58691766--58691831 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
58691756 ATAAAGTAAT
58691766 TAAAAATA-ATACTATATA
1 TAAAAATATATACTATATA
* * *
58691784 TATAAATATATACATGTACA
1 TAAAAATATATAC-TATATA
58691804 TAAAAATATATACTACTATA
1 TAAAAATATATACTA-TATA
*
58691824 TAATAATA
1 TAAAAATA
58691832 ATAATAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 7 0.18
19 5 0.13
20 26 0.68
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAAATATATACTATATA
Found at i:58691966 original size:25 final size:25
Alignment explanation
Indices: 58691922--58691988 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
58691912 ATATATATAT
*
58691922 ACATAATA-A-TATTAAGAATACGA
1 ACATAATATAGTATTAAAAATACGA
* *
58691945 ATATAATATAGTATTAAAAATACGT
1 ACATAATATAGTATTAAAAATACGA
*
58691970 GCATAATATAGTTATTAAA
1 ACATAATATAG-TATTAAA
58691989 GATATATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.19
24 1 0.03
25 21 0.58
26 7 0.19
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (25 bp):
ACATAATATAGTATTAAAAATACGA
Found at i:58692000 original size:26 final size:25
Alignment explanation
Indices: 58691920--58692006 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
58691910 GAATATATAT
*
58691920 ATACATAATA-A-TATTAAGAATAC
1 ATACATAATATAGTATTAAAAATAC
*
58691943 GA-ATATAATATAGTATTAAAAATAC
1 -ATACATAATATAGTATTAAAAATAC
* * * *
58691968 GTGCATAATATAGTTATTAAAGATAT
1 ATACATAATATAG-TATTAAAAATAC
58691994 ATACATATATATA
1 ATACATA-ATATA
58692007 ATAGAACATA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 7 0.14
24 2 0.04
25 20 0.41
26 15 0.31
27 5 0.10
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (25 bp):
ATACATAATATAGTATTAAAAATAC
Found at i:58693738 original size:12 final size:12
Alignment explanation
Indices: 58693721--58693746 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58693711 GCTGATACAA
58693721 TTGGGTTTTGGG
1 TTGGGTTTTGGG
58693733 TTGGGTTTTGGG
1 TTGGGTTTTGGG
58693745 TT
1 TT
58693747 TAATGTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (12 bp):
TTGGGTTTTGGG
Found at i:58693762 original size:22 final size:22
Alignment explanation
Indices: 58693734--58693806 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
58693724 GGTTTTGGGT
*
58693734 TGGGTTTTGGGTTTAATGTAAA
1 TGGGTTTTGGGTTTAGTGTAAA
**
58693756 TGGGTTTTGGGGTTCGGTGTAAA
1 TGGGTTTT-GGGTTTAGTGTAAA
* *
58693779 TGGGTCATGGGGTTTAGTGTAAA
1 TGGGT-TTTGGGTTTAGTGTAAA
58693802 TGGGT
1 TGGGT
58693807 CATGGAGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 8 0.19
23 33 0.79
24 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.40, T:0.40
Consensus pattern (22 bp):
TGGGTTTTGGGTTTAGTGTAAA
Found at i:58693776 original size:23 final size:23
Alignment explanation
Indices: 58693750--58693811 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
58693740 TTGGGTTTAA
** *
58693750 TGTAAATGGGTTTTGGGGTTCGG
1 TGTAAATGGGTCATGGGGTTCAG
*
58693773 TGTAAATGGGTCATGGGGTTTAG
1 TGTAAATGGGTCATGGGGTTCAG
58693796 TGTAAATGGGTCATGG
1 TGTAAATGGGTCATGG
58693812 AGCAAAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.05, G:0.40, T:0.35
Consensus pattern (23 bp):
TGTAAATGGGTCATGGGGTTCAG
Found at i:58694671 original size:89 final size:88
Alignment explanation
Indices: 58694391--58694799 Score: 570
Period size: 88 Copynumber: 4.6 Consensus size: 88
58694381 ACGTGAGCCA
*
58694391 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAATATAAATTGAAAAAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
*
58694456 TGAAAATACCTCAGTGTGTCCTG
66 TGAAAATACCTCAGCGTGTCCTG
* * *
58694479 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGAAAAAATAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
*
58694544 TGAAAATACCTCAGCGTGTCTTG
66 TGAAAATACCTCAGCGTGTCCTG
* *
58694567 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGAAAAAAATAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTG-AAAAAACAGAAA
*
58694632 TTAAAAATACC-CTAGCGTGTCCTG
65 TTGAAAATACCTC-AGCGTGTCCTG
* * ** * *
58694656 AGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTGAGAAGCAGAAATTG-AAAAGCAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAAATTGAAAAAACAGAA
* *
58694720 GTTGAAAATACCTCAGCGTGCCCTG
64 ATTGAAAATACCTCAGCGTGTCCTG
* * * * *
58694745 AGGCTCAACTCACCTCTCACAATATCAGTTGATTTTTGACAAACAGAAATTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAA
58694800 TTACCTCAGC
Statistics
Matches: 290, Mismatches: 25, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
87 18 0.06
88 136 0.47
89 120 0.41
90 1 0.00
91 15 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (88 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
TGAAAATACCTCAGCGTGTCCTG
Found at i:58694710 original size:14 final size:14
Alignment explanation
Indices: 58694693--58694727 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58694683 GTTGATTTTT
*
58694693 TTGAGAAGCAGAAA
1 TTGAAAAGCAGAAA
*
58694707 TTGAAAAGCAGAAG
1 TTGAAAAGCAGAAA
58694721 TTGAAAA
1 TTGAAAA
58694728 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.26, T:0.17
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:58694799 original size:178 final size:176
Alignment explanation
Indices: 58694301--58694859 Score: 574
Period size: 178 Copynumber: 3.3 Consensus size: 176
58694291 CGGCATGTGA
** * * *
58694301 TCCTGA-GCTCAACTCATTTCTCGCAATATGAATTGACTCTTT--AAAACAGACATT---AAAAC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAAAAC
* ** * *
58694360 AAAAATTGAAAATAGGTCAGCACGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
65 AGAAATTGAAAATACCTCAG--CGTG-CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
58694424 TTTTGAAGAATATAAATTG-AAAAAACAGAAATTGAAAATACCTCAGTGTG
127 TTTTGAA-AATATAAATTGAAAAAAACAGAAATTAAAAATACCTCAGCGTG
* * * * *
58694474 TCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGAAAAAATA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAAACA
* *
58694539 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
66 GAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
58694604 GAAAAATATAGATTGAAAAAAATAGAAATTAAAAATACC-CTAGCGTG
131 G-AAAATATAAATTGAAAAAAACAGAAATTAAAAATACCTC-AGCGTG
* * * *
58694651 TCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTGAGAAGCAGAAATTG-AAAAG
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAAAAA
* * *
58694715 CAGAAGTTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATCAGTTGA---
64 CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * *
58694777 -T-----T-T---TTG--ACAAACAGAAATTGAAATTACCTCAGCGTG
129 TTGAAAATATAAATTGAAAAAAACAGAAATTAAAAATACCTCAGCGTG
*
58694813 TCCTGAGGCTCAACTCACCTCTCGCCATATGAGTTGATTTTTGAAAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
58694860 TAGAAATAAA
Statistics
Matches: 335, Mismatches: 38, Indels: 39
0.81 0.09 0.09
Matches are distributed among these distances:
160 9 0.03
162 59 0.18
163 1 0.00
164 3 0.01
167 1 0.00
168 1 0.00
173 10 0.03
174 29 0.09
175 10 0.03
176 53 0.16
177 63 0.19
178 81 0.24
179 15 0.04
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (176 bp):
TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAAACA
GAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAATATAAATTGAAAAAAACAGAAATTAAAAATACCTCAGCGTG
Found at i:58694834 original size:73 final size:72
Alignment explanation
Indices: 58694707--58694866 Score: 239
Period size: 73 Copynumber: 2.2 Consensus size: 72
58694697 GAAGCAGAAA
*
58694707 TTGAAAAGCAGAAGTTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATCA
1 TTGAAAA-CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATCA
58694772 GTTGATTT
65 GTTGATTT
* * * * *
58694780 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCCATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATCA
58694845 GTTGATTT
65 GTTGATTT
*
58694853 TTGAAAATAGAAAT
1 TTGAAAACAGAAAT
58694867 AAAAACTTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 9 0.11
73 67 0.85
74 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (72 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATCAG
TTGATTT
Found at i:58706633 original size:25 final size:25
Alignment explanation
Indices: 58706589--58706655 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
58706579 ATATATATAT
*
58706589 ACATAATA-A-TATTAAGAATACGA
1 ACATAATATAGTATTAAAAATACGA
* *
58706612 ATATAATATAGTATTAAAAATACGT
1 ACATAATATAGTATTAAAAATACGA
*
58706637 GCATAATATAGTTATTAAA
1 ACATAATATAG-TATTAAA
58706656 GATATATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.19
24 1 0.03
25 21 0.58
26 7 0.19
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (25 bp):
ACATAATATAGTATTAAAAATACGA
Found at i:58706667 original size:26 final size:25
Alignment explanation
Indices: 58706587--58706673 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
58706577 GAATATATAT
*
58706587 ATACATAATA-A-TATTAAGAATAC
1 ATACATAATATAGTATTAAAAATAC
*
58706610 GA-ATATAATATAGTATTAAAAATAC
1 -ATACATAATATAGTATTAAAAATAC
* * * *
58706635 GTGCATAATATAGTTATTAAAGATAT
1 ATACATAATATAG-TATTAAAAATAC
58706661 ATACATATATATA
1 ATACATA-ATATA
58706674 ATAGAACATA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 7 0.14
24 2 0.04
25 20 0.41
26 15 0.31
27 5 0.10
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (25 bp):
ATACATAATATAGTATTAAAAATAC
Found at i:58706706 original size:3 final size:3
Alignment explanation
Indices: 58706692--58706722 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
58706682 TATACTAACG
*
58706692 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58706723 CAAAAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58707143 original size:24 final size:25
Alignment explanation
Indices: 58707109--58707173 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
58707099 AAAAGGATAC
*
58707109 GTATACGTAATATATA-TAAAAAAT
1 GTATACATAATATATACTAAAAAAT
*
58707133 GTATACATAATATAGTACTAAAATAT
1 GTATACATAATATA-TACTAAAAAAT
*
58707159 -T-TACATAGTATATAC
1 GTATACATAATATATAC
58707174 ATATTAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.08
24 23 0.64
25 3 0.08
26 7 0.19
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (25 bp):
GTATACATAATATATACTAAAAAAT
Found at i:58708346 original size:23 final size:22
Alignment explanation
Indices: 58708322--58708393 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
58708312 CTGATACAAT
*
58708322 TGGGTTTTGGGTTTAATGTAAA
1 TGGGTTTTGGGTTTAGTGTAAA
* *
58708344 TTGGTTTTGGGTTTGGTGTAAA
1 TGGGTTTTGGGTTTAGTGTAAA
* *
58708366 TGGGTCATGGGGTTTAGTGTAAA
1 TGGGT-TTTGGGTTTAGTGTAAA
58708389 TGGGT
1 TGGGT
58708394 CATGAGGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 23 0.55
23 19 0.45
ACGTcount: A:0.18, C:0.01, G:0.38, T:0.43
Consensus pattern (22 bp):
TGGGTTTTGGGTTTAGTGTAAA
Found at i:58708394 original size:23 final size:23
Alignment explanation
Indices: 58708330--58708397 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
58708320 ATTGGGTTTT
* * * *
58708330 GGGTTTAATGTAAATTGGT-TTT
1 GGGTTTAGTGTAAATGGGTCATG
*
58708352 GGGTTTGGTGTAAATGGGTCATG
1 GGGTTTAGTGTAAATGGGTCATG
58708375 GGGTTTAGTGTAAATGGGTCATG
1 GGGTTTAGTGTAAATGGGTCATG
58708398 AGGCAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.21, C:0.03, G:0.37, T:0.40
Consensus pattern (23 bp):
GGGTTTAGTGTAAATGGGTCATG
Found at i:58715221 original size:22 final size:22
Alignment explanation
Indices: 58715196--58715243 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
58715186 TTTTATTTTA
58715196 CATTATTATTGTCAACTTCCAG
1 CATTATTATTGTCAACTTCCAG
58715218 CATTATTATTGTCAACTTCCAG
1 CATTATTATTGTCAACTTCCAG
58715240 CATT
1 CATT
58715244 TATATACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (22 bp):
CATTATTATTGTCAACTTCCAG
Found at i:58715441 original size:46 final size:46
Alignment explanation
Indices: 58715369--58715501 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 46
58715359 GACAGGACAG
* * * *
58715369 GACAGAAATGAGCCATGTAAGTCCATATCAGATATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATGGCATTGGA
*
58715415 GACAGGAATGAGCCATGTAAACCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATTAG----ATATATGGCATTGGA
58715465 GACAGGAATGAGCCATGTAAGCCCATATTAGATATAT
1 GACAGGAATGAGCCATGTAAGCCCATATTAGATATAT
58715502 ATATGGCATT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
46 33 0.43
50 44 0.57
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (46 bp):
GACAGGAATGAGCCATGTAAGCCCATATTAGATATATGGCATTGGA
Found at i:58715475 original size:50 final size:50
Alignment explanation
Indices: 58715400--58715511 Score: 206
Period size: 50 Copynumber: 2.2 Consensus size: 50
58715390 TCCATATCAG
*
58715400 ATATATGGCTTTGGAGACAGGAATGAGCCATGTAAACCCATATTAGATAT
1 ATATATGGCATTGGAGACAGGAATGAGCCATGTAAACCCATATTAGATAT
*
58715450 ATATATGGCATTGGAGACAGGAATGAGCCATGTAAGCCCATATTAGATAT
1 ATATATGGCATTGGAGACAGGAATGAGCCATGTAAACCCATATTAGATAT
58715500 ATATATGGCATT
1 ATATATGGCATT
58715512 CATGTAAGTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (50 bp):
ATATATGGCATTGGAGACAGGAATGAGCCATGTAAACCCATATTAGATAT
Found at i:58720472 original size:241 final size:241
Alignment explanation
Indices: 58720049--58720531 Score: 930
Period size: 241 Copynumber: 2.0 Consensus size: 241
58720039 TATGGAAATA
*
58720049 ATTGACTAAATTATTAAGATTTTAATGACACTAACATACCATCCAAAGTGACACATGTAATTCAT
1 ATTGACTAAATTATTAAGATTTTAACGACACTAACATACCATCCAAAGTGACACATGTAATTCAT
*
58720114 AATTTTTTTTAAGAAGTTCATAAAAAATTTTAAAAAATATCCACATTAGCAATGGAGTATATGTG
66 AATTTTTTTTAAAAAGTTCATAAAAAATTTTAAAAAATATCCACATTAGCAATGGAGTATATGTG
58720179 AACAATCATACGGATTGTTGCATCAATATTGTTAAAATTTTAAGAGTTCAATTATTTTTTTATCC
131 AACAATCATACGGATTGTTGCATCAATATTGTTAAAATTTTAAGAGTTCAATTATTTTTTTATCC
*
58720244 AAAAAAGGAAAAAAGCAATTTAACTGCATTTTGAAAGTTGAAACTT
196 AAAAAAGGAAAAAAGCAATTTAAATGCATTTTGAAAGTTGAAACTT
58720290 ATTGACTAAATTATTAAGATTTTAACGACACTAACATACCATCCAAAGTGACACATGTAATTCAT
1 ATTGACTAAATTATTAAGATTTTAACGACACTAACATACCATCCAAAGTGACACATGTAATTCAT
*
58720355 AATTTTTTTTAAAAAGTTCATAAAAATTTTTAAAAAATATCCACATTAGCAATGGAGTATATGTG
66 AATTTTTTTTAAAAAGTTCATAAAAAATTTTAAAAAATATCCACATTAGCAATGGAGTATATGTG
58720420 AACAATCATACGGATTGTTGCATCAATATTGTTAAAATTTTAAGAGTTCAATTATTTTTTTATCC
131 AACAATCATACGGATTGTTGCATCAATATTGTTAAAATTTTAAGAGTTCAATTATTTTTTTATCC
58720485 AAAAAAGGAAAAAAGCAATTTAAATGCATTTTGAAAGTTGAAACTT
196 AAAAAAGGAAAAAAGCAATTTAAATGCATTTTGAAAGTTGAAACTT
58720531 A
1 A
58720532 ATAATTCAAA
Statistics
Matches: 238, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 238 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (241 bp):
ATTGACTAAATTATTAAGATTTTAACGACACTAACATACCATCCAAAGTGACACATGTAATTCAT
AATTTTTTTTAAAAAGTTCATAAAAAATTTTAAAAAATATCCACATTAGCAATGGAGTATATGTG
AACAATCATACGGATTGTTGCATCAATATTGTTAAAATTTTAAGAGTTCAATTATTTTTTTATCC
AAAAAAGGAAAAAAGCAATTTAAATGCATTTTGAAAGTTGAAACTT
Found at i:58728514 original size:37 final size:36
Alignment explanation
Indices: 58728445--58728522 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 36
58728435 ATAAGTGTAT
*
58728445 TTATTATAAAACTTAAAGTTAATATATAATATTATA
1 TTATAATAAAACTTAAAGTTAATATATAATATTATA
58728481 TTATAATAAAACTTAAACGTTAAGTATAT-ATATTATA
1 TTATAATAAAACTTAAA-GTTAA-TATATAATATTATA
58728518 TTATA
1 TTATA
58728523 TTATAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 16 0.41
37 18 0.46
38 5 0.13
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (36 bp):
TTATAATAAAACTTAAAGTTAATATATAATATTATA
Found at i:58728618 original size:25 final size:25
Alignment explanation
Indices: 58728548--58728621 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
58728538 AAAAGAAAAA
* *
58728548 AAAAG-AAAA-AGAATGAGAGAAAG
1 AAAAGAAAAAGAGAAAGAGAGAAGG
* * *
58728571 AAACGAAACAGAGAAGGAGAGAAGG
1 AAAAGAAAAAGAGAAAGAGAGAAGG
*
58728596 AAAAGAAAAAGAGAAAGAAAGAAGG
1 AAAAGAAAAAGAGAAAGAGAGAAGG
58728621 A
1 A
58728622 GAAAAGTCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 4 0.10
24 3 0.07
25 34 0.83
ACGTcount: A:0.66, C:0.03, G:0.30, T:0.01
Consensus pattern (25 bp):
AAAAGAAAAAGAGAAAGAGAGAAGG
Found at i:58738174 original size:59 final size:59
Alignment explanation
Indices: 58738109--58738228 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
58738099 AGTTTACAAG
58738109 TACCATCCATCAACCTTGAGAGGCAAGGCACAAATGACCATATTGTTACACTTTCCCAA
1 TACCATCCATCAACCTTGAGAGGCAAGGCACAAATGACCATATTGTTACACTTTCCCAA
58738168 TACCATCCATCAACCTTGAGAGGCAAGGCACAAATGACCATATTGTTACACTTTCCCAA
1 TACCATCCATCAACCTTGAGAGGCAAGGCACAAATGACCATATTGTTACACTTTCCCAA
58738227 TA
1 TA
58738229 GTCTTCTCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (59 bp):
TACCATCCATCAACCTTGAGAGGCAAGGCACAAATGACCATATTGTTACACTTTCCCAA
Found at i:58749258 original size:132 final size:132
Alignment explanation
Indices: 58749071--58749343 Score: 359
Period size: 132 Copynumber: 2.1 Consensus size: 132
58749061 TTCACAATTT
* * * *
58749071 TTTTAAAAACTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCAGAATCGTGCCCTAA
1 TTTTAAAAACTCTTTAAAACAAAGACAAGATTCGATATTTAGCAATTCGCAGAATCGTGCCCTAA
* * *
58749136 CGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAATC-GAGTATCCCTTCAAAATTTCGCTCAT
66 CGTGTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCAGA-TAACCCTTCAAAATTTCGCTCAT
58749200 GCC
130 GCC
* * * * *
58749203 TTTTAAGAACTCTTTAAAACAAAGATAAGGTTTGATATTTAGCAATTCGCGGAATCGTGCCCTAA
1 TTTTAAAAACTCTTTAAAACAAAGACAAGATTCGATATTTAGCAATTCGCAGAATCGTGCCCTAA
* * * * *
58749268 TGTGTTGGGTTGCAATTTCTCGTTTGCCCAAAAAAATCAGATAACCCTTCAAAATTTCACTCGTG
66 CGTGTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCAGATAACCCTTCAAAATTTCGCTCATG
*
58749333 TC
131 CC
*
58749335 TTCTAAAAA
1 TTTTAAAAA
58749344 TCCTCTAAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
132 118 0.98
133 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (132 bp):
TTTTAAAAACTCTTTAAAACAAAGACAAGATTCGATATTTAGCAATTCGCAGAATCGTGCCCTAA
CGTGTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCAGATAACCCTTCAAAATTTCGCTCATG
CC
Found at i:58749381 original size:132 final size:132
Alignment explanation
Indices: 58749074--58749382 Score: 354
Period size: 132 Copynumber: 2.3 Consensus size: 132
58749064 ACAATTTTTT
* * *
58749074 TAAAAACTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCAGAATCGTGCCCTAACGT
1 TAAAAACTCTCTAAAACGAAGGCAAGATTCGATATTTGACAATTCGCAGAATCGTGCCCTAACGT
* * * *
58749139 GTTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAGTATCCCTTCAAAATTTCGCTCATGCCT
66 GTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCGAGTAACCCTTCAAAATTTCACTCATGCCT
*
58749204 TT
131 TC
* * * ** * * * *
58749206 TAAGAACTCTTTAAAACAAAGATAAGGTTTGATATTT-AGCAATTCGCGGAATCGTGCCCTAATG
1 TAAAAACTCTCTAAAACGAAGGCAAGATTCGATATTTGA-CAATTCGCAGAATCGTGCCCTAACG
* * * *
58749270 TGTTGGGTTGCAATTTCTCGTTTGCCCAAAAAAATC-AGATAACCCTTCAAAATTTCACTCGTGT
65 TGTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCGAG-TAACCCTTCAAAATTTCACTCATGC
58749334 CTTC
129 CTTC
* * *
58749338 TAAAAA-TCCTCTAAAACGAAGGCAATACTCGATGTTTGACAATTC
1 TAAAAACT-CTCTAAAACGAAGGCAAGATTCGATATTTGACAATTC
58749383 ATGAATCATG
Statistics
Matches: 144, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
131 3 0.02
132 140 0.97
133 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (132 bp):
TAAAAACTCTCTAAAACGAAGGCAAGATTCGATATTTGACAATTCGCAGAATCGTGCCCTAACGT
GTTGGGTTGCAATTTCGCATTTGCCCAAAAAAATCGAGTAACCCTTCAAAATTTCACTCATGCCT
TC
Found at i:58751567 original size:20 final size:21
Alignment explanation
Indices: 58751544--58751582 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
58751534 GGTAAAAAGA
58751544 AAGTACAATAA-AATAAAAAT
1 AAGTACAATAATAATAAAAAT
*
58751564 AAGTATAATAATAATAAAA
1 AAGTACAATAATAATAAAA
58751583 CAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAGTACAATAATAATAAAAAT
Found at i:58751596 original size:14 final size:14
Alignment explanation
Indices: 58751570--58751610 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
58751560 AAATAAGTAT
58751570 AATAATAATAAAACA
1 AATAAT-ATAAAACA
*
58751585 AATAATATAAAATA
1 AATAATATAAAACA
*
58751599 AATAATAGAAAA
1 AATAATATAAAA
58751611 ATTCTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (14 bp):
AATAATATAAAACA
Found at i:58753373 original size:20 final size:21
Alignment explanation
Indices: 58753348--58753386 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
58753338 ATCCAATTAG
58753348 TTTAATTTATTT-ATTTAATT
1 TTTAATTTATTTGATTTAATT
58753368 TTTAATTTATTTGATTTAA
1 TTTAATTTATTTGATTTAA
58753387 CCAACTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTAATTTATTTGATTTAATT
Found at i:58761089 original size:24 final size:23
Alignment explanation
Indices: 58761045--58761090 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
58761035 TGATTTTTTA
*
58761045 TTTTATTTTATATGTTCAATTAC
1 TTTTATTTTATATATTCAATTAC
* *
58761068 TTTTAGTTTTATTTATTTAATTA
1 TTTTA-TTTTATATATTCAATTA
58761091 AATATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTATTTTATATATTCAATTAC
Found at i:58761327 original size:28 final size:27
Alignment explanation
Indices: 58761287--58761375 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
58761277 AACATTTAAT
58761287 AAATTTAGATACCAAATTGAACCTAAAA
1 AAATTTAGATACCAAATTGAA-CTAAAA
*
58761315 AAATTTAGATACCAAATTAGGACTCAAAA
1 AAATTTAGATACCAAATT-GAACT-AAAA
* * * *
58761344 AAGTTTAAATA-CAAATTTAAGTAAAA
1 AAATTTAGATACCAAATTGAACTAAAA
58761370 AAATTT
1 AAATTT
58761376 CAACGTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 9 0.17
27 2 0.04
28 26 0.50
29 15 0.29
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATTTAGATACCAAATTGAACTAAAA
Found at i:58765118 original size:17 final size:19
Alignment explanation
Indices: 58765082--58765119 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
58765072 GATAATTTTG
*
58765082 TATTTTATATGAATATATT
1 TATTTTATATGAATACATT
58765101 TATTTTAT-T-AATACATT
1 TATTTTATATGAATACATT
58765118 TA
1 TA
58765120 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TATTTTATATGAATACATT
Found at i:58766017 original size:21 final size:21
Alignment explanation
Indices: 58765993--58766033 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58765983 AAAATTATAG
58765993 AATACATTCAATAAATAAAAA
1 AATACATTCAATAAATAAAAA
** *
58766014 AATATTTTCAATAATTAAAA
1 AATACATTCAATAAATAAAA
58766034 TATGAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (21 bp):
AATACATTCAATAAATAAAAA
Found at i:58769381 original size:26 final size:24
Alignment explanation
Indices: 58769351--58769400 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
58769341 AAATAAAAAA
58769351 ATTTAAAAAT-ATAATAAATCAAATAT
1 ATTT-AAAATCATAA-AAA-CAAATAT
58769377 ATTTAAAATCATAAAAACAAATAT
1 ATTTAAAATCATAAAAACAAATAT
58769401 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 8 0.35
26 8 0.35
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTTAAAATCATAAAAACAAATAT
Found at i:58769414 original size:21 final size:21
Alignment explanation
Indices: 58769387--58769429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58769377 ATTTAAAATC
* *
58769387 ATAAAAACAAATATTAAAACAA
1 ATAAAAA-TAATACTAAAACAA
58769409 ATAAAAATAATACTAAAACAA
1 ATAAAAATAATACTAAAACAA
58769430 TTCTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAAAAATAATACTAAAACAA
Found at i:58769763 original size:14 final size:14
Alignment explanation
Indices: 58769744--58769778 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
58769734 GAACCTTTGG
58769744 TTCATATTTTCAAT
1 TTCATATTTTCAAT
58769758 TTCATATTTTCAAT
1 TTCATATTTTCAAT
58769772 TTCATAT
1 TTCATAT
58769779 CTAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCATATTTTCAAT
Found at i:58770034 original size:23 final size:23
Alignment explanation
Indices: 58769980--58770040 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
58769970 GATATATAAA
58769980 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
58770001 GTGCCTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
58770022 GTGCCTGAAATACGACACA
1 GTGCCTGAAATACGACACA
58770041 TAAAGTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
23 10 0.28
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:58770048 original size:23 final size:23
Alignment explanation
Indices: 58769977--58770052 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 23
58769967 TACGATATAT
58769977 AAAGTGCCT-AAA-ACGACACAC
1 AAAGTGCCTGAAATACGACACAC
* *
58769998 GAGGTGCCTG--ATACGACACAC
1 AAAGTGCCTGAAATACGACACAC
* * *
58770019 GAGGTGCCTGAAATACGACACAT
1 AAAGTGCCTGAAATACGACACAC
58770042 AAAGTGCCTGA
1 AAAGTGCCTGA
58770053 TCGATAAAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 26 0.57
23 19 0.41
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (23 bp):
AAAGTGCCTGAAATACGACACAC
Found at i:58781963 original size:19 final size:19
Alignment explanation
Indices: 58781935--58781971 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58781925 TAAGAAAATA
* *
58781935 ATATTTTATTATTATTATT
1 ATATTATATTACTATTATT
58781954 ATATTATATTACTATTAT
1 ATATTATATTACTATTAT
58781972 AATTAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATATTACTATTATT
Found at i:58784618 original size:17 final size:17
Alignment explanation
Indices: 58784582--58784618 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
58784572 CACATTCTCT
**
58784582 TTTTTCTTTTGTTTTTG
1 TTTTTCTTTTGTTTGAG
58784599 TTTTTCTTTTGTTTGAG
1 TTTTTCTTTTGTTTGAG
58784616 TTT
1 TTT
58784619 GAAAGTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.05, G:0.14, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTGTTTGAG
Found at i:58785970 original size:49 final size:49
Alignment explanation
Indices: 58785906--58786083 Score: 293
Period size: 49 Copynumber: 3.6 Consensus size: 49
58785896 ATGACTTCGA
58785906 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* *
58785955 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATTAG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* *
58786004 TCACGTGTGTAGTATTAAGTGCAGGCTACTACGTGTACCGAATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
* * *
58786053 TCTCATGTGTAGTACTAAGTGCATGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
58786084 TGCGTACCAG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 119 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
Found at i:58786091 original size:49 final size:49
Alignment explanation
Indices: 58785870--58786083 Score: 286
Period size: 49 Copynumber: 4.3 Consensus size: 49
58785860 ATATGATCAA
* * * *
58785870 TAAGTGCAGGCTACTATGCGTACTC-AATGACTTCGATCACGTGTGTAGTAC
1 TAAGTGCAGGCTACTACGTGTAC-CGAAT-AATT-GGTCACGTGTGTAGTAC
*
58785921 TAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTAC
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
* * * *
58785970 TAAGTGTAGGCTACTACGTGTACCGGATAATTAGTCACGTGTGTAGTAT
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
* *
58786019 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCTCATGTGTAGTAC
1 TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
*
58786068 TAAGTGCATGCTACTA
1 TAAGTGCAGGCTACTA
58786084 TGCGTACCAG
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
49 120 0.82
50 4 0.03
51 23 0.16
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (49 bp):
TAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACGTGTGTAGTAC
Found at i:58787554 original size:25 final size:26
Alignment explanation
Indices: 58787504--58787553 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
58787494 ATTAACTTAA
*
58787504 TTAGAGTGATTAAAATAAAATAAAAT
1 TTAGAGTGATCAAAATAAAATAAAAT
*
58787530 TTAGAGTGATCAAAATAAGATAAA
1 TTAGAGTGATCAAAATAAAATAAA
58787554 TCCGATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (26 bp):
TTAGAGTGATCAAAATAAAATAAAAT
Found at i:58792229 original size:23 final size:23
Alignment explanation
Indices: 58792203--58792251 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
58792193 CTTTAAAATA
* *
58792203 AATAGTTATTTTCTTTTTTATAT
1 AATACTTATTTTATTTTTTATAT
* *
58792226 AATACTTTTTTTATTTTTTATTT
1 AATACTTATTTTATTTTTTATAT
58792249 AAT
1 AAT
58792252 TTAATATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
AATACTTATTTTATTTTTTATAT
Found at i:58792609 original size:89 final size:88
Alignment explanation
Indices: 58792388--58792615 Score: 294
Period size: 89 Copynumber: 2.6 Consensus size: 88
58792378 ATGCAATTTG
* *
58792388 GGAACATGTCAATGGTGAACATTGAAATTGAGGGAAACCATGTTTGTGGGGAAGTAATTCAGTGG
1 GGAACATGTCAATGGTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGG
*
58792453 TGGAAACCATAAAAAGGCGATTCA
65 TGGAAACCATAAAAAGGCAATTCA
* * * * ** *
58792477 GGAATATGTCAATGGTGAACATTGAAATCAAAGAAAATTATGTTTATGGGGAAGTAACTCAATGG
1 GGAACATGTCAATGGTGAACATTGAAAT-GAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGG
* * *
58792542 TGGAAACCATAGAAGGGTAATTCA
65 TGGAAACCATAAAAAGGCAATTCA
* *
58792566 GGAACATGACAATGGTGAACATTGAAACTGAGGGGAACCATGTTTGTGGG
1 GGAACATGTCAATGGTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGG
58792616 TTAACTCAGA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
88 1 0.01
89 113 0.98
90 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (88 bp):
GGAACATGTCAATGGTGAACATTGAAATGAGGGAAACCATGTTTGTGGGGAAGTAACTCAATGGT
GGAAACCATAAAAAGGCAATTCA
Found at i:58795499 original size:45 final size:45
Alignment explanation
Indices: 58795449--58795540 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
58795439 ACTAAGATGA
58795449 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
1 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
*
58795494 TTGTACCATATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
1 TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
58795539 TT
1 TT
58795541 TAATCTGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (45 bp):
TTGTACCACATATGTCCAGATTGTTTTAATCCATATAAACTTTTC
Found at i:58796668 original size:216 final size:216
Alignment explanation
Indices: 58796290--58796941 Score: 1196
Period size: 216 Copynumber: 3.0 Consensus size: 216
58796280 GCTTCAGGTG
*
58796290 TGTATTACTTTATTTTGAACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
* *
58796355 TAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATAAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
*
58796420 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTA
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
58796485 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
* * *
58796506 TGTGTTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTTGTATTGGAGAATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
*
58796571 CAGCTGGTATGTGAGATTTTTTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
*
58796636 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGTGAGGATCTAATTG
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
58796701 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
*
58796722 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTTGAGCATTTT
1 TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
*
58796787 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTTAGTAAATGAATCTGGTAGTTGATTGGCA
66 CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
*
58796852 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGGTCTAATTG
131 ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
58796917 AGATAATGATGATCCATTCCA
196 AGATAATGATGATCCATTCCA
58796938 TGTA
1 TGTA
58796942 ATTTCTTTGA
Statistics
Matches: 419, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 419 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (216 bp):
TGTATTACTTTATTTTGCACTAACAATATACCCTATTGGGATATCAATTCGTATTGGAGCATTTT
CAGCTGGTATGTGAGATTTTGTAATTCTCTTTAGGTCAGTAAATGAATCTGGTAGTTGATTGGCA
ATGTTTTGCAAATGTGTGATCCTTTGAACTTCTTGTTCACATAGACTTGTGCGAGGATCTAATTG
AGATAATGATGATCCATTCCA
Found at i:58797979 original size:26 final size:25
Alignment explanation
Indices: 58797917--58798012 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 25
58797907 CAAAGTATAT
**
58797917 ATATAGTATT-AAAAATATGTACATA
1 ATAT-GTATTAAAAAATACATACATA
58797942 ATATG-ACGTTAAAAAATACATACATA
1 ATATGTA--TTAAAAAATACATACATA
* *
58797968 ATATAGTATTAAATATATACATAAGATA
1 ATAT-GTATTAAA-AAATACAT-ACATA
**
58797996 ATATGTAAAAAAAAATA
1 ATATGTATTAAAAAATA
58798013 GTATTCGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 6 0.11
26 26 0.46
27 14 0.25
28 9 0.16
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.31
Consensus pattern (25 bp):
ATATGTATTAAAAAATACATACATA
Found at i:58798307 original size:20 final size:20
Alignment explanation
Indices: 58798271--58798310 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
58798261 GTATATATAA
58798271 AAAAATATAACTAATAATATT
1 AAAAATATAAC-AATAATATT
58798292 AAAAATATATAC-ATAATAT
1 AAAAATATA-ACAATAATAT
58798311 ATATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 9 0.50
22 2 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATATAACAATAATATT
Found at i:58798308 original size:23 final size:24
Alignment explanation
Indices: 58798237--58798342 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 24
58798227 AATAAGGATA
*
58798237 ATATAAAAATATATACACGAAATAGTAT
1 ATATAAAAATATAT--AC-TAATA-TAT
*
58798265 ATATAAAAAAATATAACTAATA-AT
1 ATATAAAAATATAT-ACTAATATAT
58798289 AT-TAAAAATATATACATAATATAT
1 ATATAAAAATATATAC-TAATATAT
* * *
58798313 ATATATAAATATATACGATATATAC
1 ATATAAAAATATATACTA-ATATAT
58798338 ATATA
1 ATATA
58798343 TTAGAAATGA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.03
23 15 0.22
24 9 0.13
25 22 0.33
26 4 0.06
27 2 0.03
28 13 0.19
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (24 bp):
ATATAAAAATATATACTAATATAT
Found at i:58798341 original size:17 final size:16
Alignment explanation
Indices: 58798296--58798343 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
58798286 AATATTAAAA
*
58798296 ATATATACATAATATAT
1 ATATATACAT-ATATAG
*
58798313 ATATATAAATATATACG
1 ATATATACATATATA-G
58798330 ATATATACATATAT
1 ATATATACATATAT
58798344 TAGAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATATACATATATAG
Found at i:58799972 original size:42 final size:41
Alignment explanation
Indices: 58799818--58799973 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
58799808 TATGTTATCG
*
58799818 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
58799860 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
58799904 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
58799946 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
58799974 TGTCCGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:58802054 original size:26 final size:25
Alignment explanation
Indices: 58802015--58802130 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 25
58802005 AGTATGTATG
* *
58802015 TAATATAGTGTTAAAAATACATACA
1 TAATATAATATTAAAAATACATACA
*
58802040 TAATATAATTATTAAAAATATATACA
1 TAATATAA-TATTAAAAATACATACA
* * *
58802066 CAATATAATA--AAATATAC-GA-A
1 TAATATAATATTAAAAATACATACA
* *
58802087 TAATATGATATTAAAAATATATACA
1 TAATATAATATTAAAAATACATACA
*
58802112 TAATGTAA-AGTTAAAAATA
1 TAATATAATA-TTAAAAATA
58802131 ATATATATAA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
21 9 0.13
22 1 0.01
23 12 0.17
24 2 0.03
25 25 0.35
26 22 0.31
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (25 bp):
TAATATAATATTAAAAATACATACA
Found at i:58802147 original size:14 final size:15
Alignment explanation
Indices: 58802123--58802153 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
58802113 AATGTAAAGT
58802123 TAAAAATAATATATA
1 TAAAAATAATATATA
58802138 TAAAAA-AATATATA
1 TAAAAATAATATATA
58802152 TA
1 TA
58802154 CATAATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAATAATATATA
Found at i:58802177 original size:26 final size:27
Alignment explanation
Indices: 58802128--58802192 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
58802118 AAAGTTAAAA
*
58802128 ATAATATATATAAAAAAATATATATAC
1 ATAATATATATAAAAAAATATATACAC
* * *
58802155 ATAATATCTATTAAAAGA-ATATACAC
1 ATAATATATATAAAAAAATATATACAC
*
58802181 CTAATATATATA
1 ATAATATATATA
58802193 CATGTATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATATATATAAAAAAATATATACAC
Found at i:58802256 original size:67 final size:66
Alignment explanation
Indices: 58802185--58802316 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 66
58802175 ATACACCTAA
* * *
58802185 TATATATACATG-TATTAAAATAATGATAATATTAAAAAAAATAATTATTAATAATGTTACATAA
1 TATATATACATGCTATTAAAATAATAATAATATT-AAAAAAA-AACTATTAATAATATTACATAA
58802249 AAG
64 AAG
* * * *
58802252 TATATATATATGCCTGTTAAAATATTAATAATGTTAAAAAAAAACTATTAATAATATTACATAAA
1 TATATATACATG-CTATTAAAATAATAATAATATTAAAAAAAAACTATTAATAATATTACATAAA
58802317 GACATACATA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 32 0.57
68 7 0.12
69 17 0.30
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (66 bp):
TATATATACATGCTATTAAAATAATAATAATATTAAAAAAAAACTATTAATAATATTACATAAAA
G
Found at i:58802328 original size:67 final size:69
Alignment explanation
Indices: 58802199--58802329 Score: 169
Period size: 67 Copynumber: 1.9 Consensus size: 69
58802189 TATACATGTA
* * * * *
58802199 TTAAAATAATGATAATATTAAAAAAAATAATTATTAATAATGTTACATAAAAGTATATATATATG
1 TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAAAGCATACATATATG
58802264 CCTG
66 CCTG
* *
58802268 TTAAAATATTAATAATGTT-AAAAAAA-AACTATTAATAATATTACAT-AAAGACATACATATAT
1 TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAAAG-CATACATATAT
58802330 ATATTAAAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 4 0.07
67 27 0.50
68 7 0.13
69 16 0.30
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (69 bp):
TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAAAGCATACATATATG
CCTG
Found at i:58802328 original size:69 final size:69
Alignment explanation
Indices: 58802199--58802331 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 69
58802189 TATACATGTA
* * * * *
58802199 TTAAAATAATGATAATATTAAAAAAAATAATTATTAATAATGTTACATAAAAGTATATATATATG
1 TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAAAATACATATATATG
58802264 CCTG
66 CCTG
* *
58802268 TTAAAATATTAATAATGTT-AAAAAAA-AACTATTAATAATATTACATAAAGACATACATATATA
1 TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAA-A-ATACATATATA
58802331 T
64 T
58802332 ATTAAAGATG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 21 0.38
68 8 0.15
69 26 0.47
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (69 bp):
TTAAAATAATAATAATATTAAAAAAAATAACTATTAATAATATTACATAAAAATACATATATATG
CCTG
Found at i:58802488 original size:25 final size:26
Alignment explanation
Indices: 58802391--58802495 Score: 98
Period size: 25 Copynumber: 4.2 Consensus size: 26
58802381 AATAAGGATA
*
58802391 ATATAAAAATATATACACGAAATAGTAT
1 ATATAAAAATATATA-ACGATATA-TAT
*
58802419 ATATAAAAA-ATATAACTA-ATA-AT
1 ATATAAAAATATATAACGATATATAT
58802442 AT-TAAAAATATAT-AC-ATAATATAT
1 ATATAAAAATATATAACGAT-ATATAT
* *
58802466 ATATATAAATATAT-ACGATATATAC
1 ATATAAAAATATATAACGATATATAT
58802491 ATATA
1 ATATA
58802496 TTAGAAATGA
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
21 1 0.01
22 8 0.12
23 11 0.16
24 4 0.06
25 25 0.37
26 5 0.07
27 5 0.07
28 9 0.13
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (26 bp):
ATATAAAAATATATAACGATATATAT
Found at i:58802494 original size:17 final size:16
Alignment explanation
Indices: 58802449--58802496 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
58802439 AATATTAAAA
*
58802449 ATATATACATAATATAT
1 ATATATACAT-ATATAG
*
58802466 ATATATAAATATATACG
1 ATATATACATATATA-G
58802483 ATATATACATATAT
1 ATATATACATATAT
58802497 TAGAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATATACATATATAG
Found at i:58802679 original size:3 final size:3
Alignment explanation
Indices: 58802595--58802662 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
58802585 ATACTAGTAC
* * *
58802595 TAA TAA TAT TTA TAA TGAA T-A TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58802640 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
58802663 TATGCATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58802781 original size:26 final size:25
Alignment explanation
Indices: 58802715--58802857 Score: 98
Period size: 25 Copynumber: 5.8 Consensus size: 25
58802705 TAAGTATAAA
* ** *
58802715 ATAATAATAATATTAAAAGTATGTAT
1 ATAAT-ATAATATTAAAAATACATAC
* * *
58802741 GTAATATAGTGTTAAAAATACATAC
1 ATAATATAATATTAAAAATACATAC
*
58802766 ATAATATAATTATTAAAAATATATAC
1 ATAATATAA-TATTAAAAATACATAC
* * *
58802792 ACAATATAATA--AAATATAC-GA-
1 ATAATATAATATTAAAAATACATAC
* *
58802813 ATAATATGATATTAAAAATATATAC
1 ATAATATAATATTAAAAATACATAC
*
58802838 ATAATGTAA-AGTTAAAAATA
1 ATAATATAATA-TTAAAAATA
58802858 ATATATATAA
Statistics
Matches: 89, Mismatches: 22, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
21 9 0.10
22 1 0.01
23 12 0.13
24 2 0.02
25 39 0.44
26 26 0.29
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATAATATTAAAAATACATAC
Found at i:58802874 original size:14 final size:15
Alignment explanation
Indices: 58802850--58802880 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
58802840 AATGTAAAGT
58802850 TAAAAATAATATATA
1 TAAAAATAATATATA
58802865 TAAAAA-AATATATA
1 TAAAAATAATATATA
58802879 TA
1 TA
58802881 CATAATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAATAATATATA
Found at i:58802904 original size:26 final size:27
Alignment explanation
Indices: 58802855--58802919 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
58802845 AAAGTTAAAA
*
58802855 ATAATATATATAAAAAAATATATATAC
1 ATAATATATATAAAAAAATATATACAC
* * *
58802882 ATAATATCTATTAAAAGA-ATATACAC
1 ATAATATATATAAAAAAATATATACAC
*
58802908 CTAATATATATA
1 ATAATATATATA
58802920 CATGTATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATATATATAAAAAAATATATACAC
Found at i:58804304 original size:69 final size:70
Alignment explanation
Indices: 58804214--58804362 Score: 255
Period size: 70 Copynumber: 2.1 Consensus size: 70
58804204 TGGGCTATAT
58804214 GGGTGTGGATCAGGGTTTGTTTGGAATTGGGTTATTGGATTA-AAATTTGGGCTTTGGGTACTTA
1 GGGT-TGG-TCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTACTTA
58804278 GGGTATG
64 GGGTATG
* *
58804285 GGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAATTTTGGGCTTTGGGTACTTGGG
1 GGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTACTTAGG
58804350 GTATG
66 GTATG
58804355 GGGTTGGT
1 GGGTTGGT
58804363 AATTTGGTGG
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
69 33 0.44
70 38 0.51
71 4 0.05
ACGTcount: A:0.15, C:0.04, G:0.40, T:0.41
Consensus pattern (70 bp):
GGGTTGGTCAGGGTTTGTTTGGAATTGGGTTATTGGATTATAAATTTGGGCTTTGGGTACTTAGG
GTATG
Found at i:58807665 original size:5 final size:5
Alignment explanation
Indices: 58807655--58807699 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
58807645 AACATATGTG
58807655 AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAA
58807700 GAACACACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 33 0.87
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:58807681 original size:22 final size:22
Alignment explanation
Indices: 58807655--58807699 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
58807645 AACATATGTG
58807655 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
58807677 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
58807699 A
1 A
58807700 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAA
Found at i:58807682 original size:17 final size:17
Alignment explanation
Indices: 58807660--58807695 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
58807650 ATGTGAAAAT
58807660 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
58807677 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
58807694 AA
1 AA
58807696 TAAAGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:58809055 original size:12 final size:12
Alignment explanation
Indices: 58809040--58809064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58809030 TTCTTATAAC
58809040 ATAAATATTGTT
1 ATAAATATTGTT
58809052 ATAAATATTGTT
1 ATAAATATTGTT
58809064 A
1 A
58809065 ATAGCCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:58813813 original size:50 final size:52
Alignment explanation
Indices: 58813759--58813867 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 52
58813749 AATAAAGTAA
58813759 TGCATTATGTAACTTTCATGTTAG-TTAAGTATGCATCA-TAAA-TAATGACT
1 TGCATTATGTAACTTTCATGTTAGTTTAAGTATGCATCATTAAATTAA-GACT
* * *
58813809 TGCATTATGTAACTTTCATGTTAGTTTAAGTCTGCATTATTAAATTAAGTCT
1 TGCATTATGTAACTTTCATGTTAGTTTAAGTATGCATCATTAAATTAAGACT
58813861 TGCATTA
1 TGCATTA
58813868 AATAACTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 24 0.45
51 12 0.23
52 14 0.26
53 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (52 bp):
TGCATTATGTAACTTTCATGTTAGTTTAAGTATGCATCATTAAATTAAGACT
Found at i:58814028 original size:9 final size:9
Alignment explanation
Indices: 58814009--58814082 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
58813999 AGTTTATTTA
58814009 TTTAA-GTG
1 TTTAATGTG
58814017 TTTAATGTG
1 TTTAATGTG
58814026 TTT--TGTG
1 TTTAATGTG
58814033 TTTAATAAGTG
1 TTTAAT--GTG
*
58814044 TTCAAATGTG
1 TT-TAATGTG
*
58814054 TTTAATATG
1 TTTAATGTG
58814063 -TT--TGT-
1 TTTAATGTG
58814068 TTTAATGTG
1 TTTAATGTG
58814077 TTTAAT
1 TTTAAT
58814083 TGCAGGTGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 19
0.69 0.05 0.25
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 10 0.19
9 18 0.35
10 5 0.10
11 5 0.10
12 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.19, T:0.55
Consensus pattern (9 bp):
TTTAATGTG
Found at i:58826754 original size:293 final size:293
Alignment explanation
Indices: 58826227--58826817 Score: 1173
Period size: 293 Copynumber: 2.0 Consensus size: 293
58826217 AGGACAATTT
58826227 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
1 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
58826292 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
66 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
58826357 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
131 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
58826422 TAAAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCAT
196 TAAAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCAT
58826487 TATCAAATGGTGATGAAGCAGCTTTAATAATAA
261 TATCAAATGGTGATGAAGCAGCTTTAATAATAA
58826520 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
1 ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
58826585 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
66 GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
*
58826650 TAATGGTTAACATGGTCATAACTATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
131 TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
58826715 TAAAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCAT
196 TAAAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCAT
58826780 TATCAAATGGTGATGAAGCAGCTTTAATAATAA
261 TATCAAATGGTGATGAAGCAGCTTTAATAATAA
58826813 ATTGA
1 ATTGA
58826818 TGATAATAAT
Statistics
Matches: 297, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
293 297 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (293 bp):
ATTGAATCCCTAAAATAAAAAATATCGCCTTGATTTTAATTTCTTCTCATGAGTTATTTAAAAAT
GAATACATCACTTGATATGATATGCGATTGAGCATAATGCGGGAATGAATAAATATATCTAAGCA
TAATGGTTAACATGGTCATAACCATAATAAAATAAAATAACTACATAAAAAATTAAAAACATAGA
TAAAAAAAAATTGAACTGACTATCGTAAAATAATAATATAAGAACAAAATAATGGTAGATACCAT
TATCAAATGGTGATGAAGCAGCTTTAATAATAA
Found at i:58827163 original size:10 final size:10
Alignment explanation
Indices: 58827148--58827175 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
58827138 TACCCCTCAG
58827148 CACGCCACTA
1 CACGCCACTA
58827158 CACGCCACTA
1 CACGCCACTA
58827168 CACGCCAC
1 CACGCCAC
58827176 GTACCTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.54, G:0.11, T:0.07
Consensus pattern (10 bp):
CACGCCACTA
Found at i:58830996 original size:21 final size:20
Alignment explanation
Indices: 58830972--58831011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
58830962 AGAAATTGTT
58830972 ATTATATTATATTATTATTAC
1 ATTATATTATATTA-TATTAC
58830993 ATTATATTATATTATATTA
1 ATTATATTATATTATATTA
58831012 TATATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTATATTATATTATATTAC
Found at i:58831021 original size:5 final size:5
Alignment explanation
Indices: 58830971--58831014 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
58830961 AAGAAATTGT
*
58830971 TATTA TATTA TATTA TTATTA CATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TAT
58831015 ATTATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:58832777 original size:6 final size:6
Alignment explanation
Indices: 58832766--58832792 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58832756 ATGTGCCGAC
58832766 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
58832793 CGATTCGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:58832822 original size:45 final size:45
Alignment explanation
Indices: 58832772--58832880 Score: 182
Period size: 45 Copynumber: 2.4 Consensus size: 45
58832762 CGACTACTGT
*
58832772 TACTGTTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* * *
58832817 TACTGTTACTGTTACCGTTATCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
58832862 TACTGTTACTGTTACTGTT
1 TACTGTTACTGTTACTGTT
58832881 CCGGATTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:58832824 original size:51 final size:49
Alignment explanation
Indices: 58832749--58832881 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 49
58832739 TTACTGATCA
* * *
58832749 GGCAC-TTATGTGCCGACTACTGTTACTGTTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTT-C-GTTACCGATTC
*
58832799 GGCACTTTGTGTGTCGAATACTGTTACTGTTAC----CGTTATCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTCGTTACCGATTC
* *
58832844 AGCACTTTGTGTGTTGAATACTGTTACTGTTACTGTTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTC
58832882 CGGATTTGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
45 41 0.57
46 1 0.01
49 1 0.01
50 5 0.07
51 24 0.33
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (49 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTCGTTACCGATTC
Found at i:58833060 original size:18 final size:18
Alignment explanation
Indices: 58833038--58833302 Score: 147
Period size: 18 Copynumber: 14.3 Consensus size: 18
58833028 AAAGGTATAA
* *
58833038 AATAACTGATTATTTCTA
1 AATAACTGATTATTACTG
* *
58833056 AATAATTGACTATTACTG
1 AATAACTGATTATTACTG
* * *
58833074 GATAA-TAGACTGTTACTG
1 AATAACT-GATTATTACTG
*
58833092 AATAACTGAATATTACTG
1 AATAACTGATTATTACTG
*
58833110 AATAAATGATTATTACTG
1 AATAACTGATTATTACTG
* *
58833128 AATAACTGATTGTCACTG
1 AATAACTGATTATTACTG
* * *
58833146 AATAAATGACTGTTACTG
1 AATAACTGATTATTACTG
* * *
58833164 AATAACTTAATTGTTATTG
1 AATAAC-TGATTATTACTG
* *
58833183 AATATCTGATT-TTACTA
1 AATAACTGATTATTACTG
* * *
58833200 AATAATTGACTGTTACTG
1 AATAACTGATTATTACTG
* *
58833218 GATAACCGATCAATTGATTGATACTG
1 AATAA-C--T-GATT-A-T--TACTG
* *
58833244 AATAACTGGTTATTATTG
1 AATAACTGATTATTACTG
* * *
58833262 AATAATTGATTGTTACCG
1 AATAACTGATTATTACTG
* *
58833280 AATAACTGACTGTTACTG
1 AATAACTGATTATTACTG
58833298 AATAA
1 AATAA
58833303 ACAATTGTTC
Statistics
Matches: 189, Mismatches: 46, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
17 13 0.07
18 142 0.75
19 15 0.08
20 1 0.01
21 2 0.01
22 4 0.02
23 1 0.01
24 1 0.01
25 1 0.01
26 9 0.05
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (18 bp):
AATAACTGATTATTACTG
Found at i:58833204 original size:54 final size:55
Alignment explanation
Indices: 58833066--58833302 Score: 167
Period size: 54 Copynumber: 4.2 Consensus size: 55
58833056 AATAATTGAC
* * * * * *
58833066 TATTACTGGATAA-TAGACTGTTACTGAATAACTGAATATTACTGAATAA-ATGAT
1 TATTACTGAATAACT-GATTGTTACTGAATAAATGACTGTTACTGAATAACATAAT
* *
58833120 TATTACTGAATAACTGATTGTCACTGAATAAATGACTGTTACTGAATAACTTAAT
1 TATTACTGAATAACTGATTGTTACTGAATAAATGACTGTTACTGAATAACATAAT
* * * * * *
58833175 TGTTATTGAATATCTGATT-TTACTAAATAATTGACTGTTACTGGATAACCGATCAAT
1 TATTACTGAATAACTGATTGTTACTGAATAAATGACTGTTACTGAATAA-C-AT-AAT
* * * * * * * *
58833232 TGATTGATACTGAATAACTGGTTATTATTGAATAATTGATTGTTACCGAATAAC-TGAC
1 T-A-T--TACTGAATAACTGATTGTTACTGAATAAATGACTGTTACTGAATAACATAAT
*
58833290 TGTTACTGAATAA
1 TATTACTGAATAA
58833303 ACAATTGTTC
Statistics
Matches: 145, Mismatches: 28, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
54 76 0.52
55 21 0.14
56 2 0.01
57 4 0.03
58 2 0.01
59 2 0.01
61 14 0.10
62 24 0.17
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (55 bp):
TATTACTGAATAACTGATTGTTACTGAATAAATGACTGTTACTGAATAACATAAT
Found at i:58833697 original size:24 final size:24
Alignment explanation
Indices: 58833669--58833717 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
58833659 TGTAAAAGTA
58833669 TTGATGAAATAAGTAAATTATGGT
1 TTGATGAAATAAGTAAATTATGGT
58833693 TTGATGAAATAAGTAAATTATGGT
1 TTGATGAAATAAGTAAATTATGGT
58833717 T
1 T
58833718 GGCAACAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGATGAAATAAGTAAATTATGGT
Found at i:58834969 original size:33 final size:33
Alignment explanation
Indices: 58834900--58834997 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
58834890 CTATACCCAT
* * *
58834900 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
58834937 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
58834970 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
58834998 ATACATATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:58835259 original size:41 final size:41
Alignment explanation
Indices: 58835214--58835369 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
58835204 ACCGGCTCTT
*
58835214 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
58835255 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
58835296 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
58835337 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
58835370 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:58842595 original size:33 final size:33
Alignment explanation
Indices: 58842526--58842623 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
58842516 CTATACCCAT
* * *
58842526 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
58842563 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
58842596 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
58842624 ATACATATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:58842885 original size:41 final size:41
Alignment explanation
Indices: 58842840--58842995 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
58842830 ACCGGCTCTT
*
58842840 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
58842881 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
58842922 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
58842963 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
58842996 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:58847795 original size:46 final size:46
Alignment explanation
Indices: 58847723--58847815 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
58847713 ATTTATTTGA
* *
58847723 TTCTTCCCAATCTCTAACATTTGACTCACAAAATTGTATGCAAACT
1 TTCTCCCCAATCTCTAACATTTGACTCACAAAATTGTATACAAACT
58847769 TTCTCCCCAATCTCTAACATTTGACTCACAAAATTGTATACAAACT
1 TTCTCCCCAATCTCTAACATTTGACTCACAAAATTGTATACAAACT
58847815 T
1 T
58847816 ACAGTCTCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (46 bp):
TTCTCCCCAATCTCTAACATTTGACTCACAAAATTGTATACAAACT
Found at i:58849202 original size:20 final size:22
Alignment explanation
Indices: 58849173--58849214 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
58849163 AATAAAATTG
*
58849173 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
58849193 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
58849215 TATGACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:58851314 original size:17 final size:16
Alignment explanation
Indices: 58851272--58851314 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
58851262 AATATATTTT
58851272 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
58851288 TAGAAAATATTTTAAAA
1 TA-AAAATATTTTAAAA
58851305 TAAAATATAT
1 TAAAA-ATAT
58851315 GATTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAATATTTTAAAA
Done.