Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 24
Found at i:3808380 original size:22 final size:22
Alignment explanation
Indices: 3808352--3808404 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3808342 AATTTGGAAA
3808352 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
3808374 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3808396 ATCGCAACG
1 ATCGCAACG
3808405 CGATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:3808419 original size:21 final size:21
Alignment explanation
Indices: 3808393--3808531 Score: 102
Period size: 21 Copynumber: 6.7 Consensus size: 21
3808383 ACAACTGTAG
3808393 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
3808414 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
* ***
3808435 A-AATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
* *** *
3808455 ACTATCCCAACGC-AAAATGA
1 ACTATCGCAACGCGATTTTCA
** ***
3808475 AAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
3808496 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
3808517 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
3808532 AATGCAACGC
Statistics
Matches: 80, Mismatches: 36, Indels: 4
0.67 0.30 0.03
Matches are distributed among these distances:
20 22 0.28
21 58 0.73
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:3808450 original size:41 final size:41
Alignment explanation
Indices: 3808404--3808510 Score: 187
Period size: 41 Copynumber: 2.6 Consensus size: 41
3808394 CTATCGCAAC
*
3808404 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCGTT
1 GCGATTTTCAACTATCGCAACGCGAAATGAAAAATCGCGTT
* *
3808445 GCGATTTTCAACTATCCCAACGCAAAATGAAAAATCGCGTT
1 GCGATTTTCAACTATCGCAACGCGAAATGAAAAATCGCGTT
3808486 GCGATTTTCAACTATCGCAACGCGA
1 GCGATTTTCAACTATCGCAACGCGA
3808511 TTTTCAACTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (41 bp):
GCGATTTTCAACTATCGCAACGCGAAATGAAAAATCGCGTT
Found at i:3808539 original size:21 final size:21
Alignment explanation
Indices: 3808494--3808539 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3808484 TTGCGATTTT
** *
3808494 CAACTATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
3808515 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
3808536 CAAC
1 CAAC
3808540 GCGAATTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:3810554 original size:3 final size:3
Alignment explanation
Indices: 3810543--3810614 Score: 85
Period size: 3 Copynumber: 24.3 Consensus size: 3
3810533 TTAAATAATA
*
3810543 TAT TA- TAT TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * *
3810588 TA- TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3810615 TTTGCAGGCT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3810581 original size:22 final size:21
Alignment explanation
Indices: 3810543--3810606 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 21
3810533 TTAAATAATA
3810543 TATTAT-ATTATTATTATTAT
1 TATTATAATTATTATTATTAT
3810563 TATTATAATTACTTATTATTAT
1 TATTATAATTA-TTATTATTAT
* *
3810585 TATTAT-ATTATTAATACTAT
1 TATTATAATTATTATTATTAT
3810605 TA
1 TA
3810607 ATATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.40
21 8 0.20
22 16 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATAATTATTATTATTAT
Found at i:3815843 original size:106 final size:106
Alignment explanation
Indices: 3815658--3816502 Score: 1413
Period size: 106 Copynumber: 8.0 Consensus size: 106
3815648 TTGCTCGAGT
3815658 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
3815723 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
3815764 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
3815829 AGGGACCGCTGGTTGTCAACAAACAACTTTTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
3815870 GCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * * *
3815935 AGGGACCGTTGGTTGTCAACAAATAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
3815976 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
3816041 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
3816082 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
3816147 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
3816188 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
3816253 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
3816294 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
3816359 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * * * *
3816400 GTCAATTTCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
3816465 AGGGACCGCTGGTTGTCAATAAACAACTT-TCAACTTCA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
3816503 CGACGAAGGA
Statistics
Matches: 692, Mismatches: 47, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
105 7 0.01
106 685 0.99
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
Found at i:3816691 original size:84 final size:84
Alignment explanation
Indices: 3816537--3816809 Score: 368
Period size: 84 Copynumber: 3.2 Consensus size: 84
3816527 AGGCTATCTG
** * * * *
3816537 CCAAAGACCCCCGAGTTCGATTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTC
*
3816602 GAGAAGGGTTATCTTCCAA
66 GAGAAGGGCTATCTTCCAA
* * * *
3816621 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTC
*
3816686 AAGAAGGGCTAT-TTGCCAA
66 GAGAAGGGCTATCTT-CCAA
* * *
3816705 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGTACATCATTTGCAGCATAGCTTAAGTT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTC
*
3816770 GAGAAGGGCTATCTGCCAA
66 GAGAAGGGCTATCTTCCAA
*
3816789 CCAAAGACCTGACGAGTTCGA
1 CCAAAGACCT-TCGAGTTCGA
3816810 TTTCATTCAG
Statistics
Matches: 163, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.01
84 152 0.93
85 9 0.06
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTTCCAA
Found at i:3817049 original size:3 final size:3
Alignment explanation
Indices: 3817038--3817106 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
3817028 TTAAATAATA
*
3817038 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
3817082 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3817107 TTTGCAGGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3819511 original size:40 final size:40
Alignment explanation
Indices: 3819466--3819543 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
3819456 ATGACACGTG
**
3819466 TCTATTAACACAAATTTTTAATAACTTTAAAGTGGTAACA
1 TCTATTAACACAAATTTTTAATAACCCTAAAGTGGTAACA
*
3819506 TCTATTAACACAACTTTTTAATAACCCTAAAGTGGTAA
1 TCTATTAACACAAATTTTTAATAACCCTAAAGTGGTAA
3819544 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTATTAACACAAATTTTTAATAACCCTAAAGTGGTAACA
Found at i:3824775 original size:18 final size:19
Alignment explanation
Indices: 3824735--3824772 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3824725 TGGTTAACGA
*
3824735 AATGTAAGATTATCAGTGGG
1 AATGTAAGATTACCAG-GGG
3824755 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
3824773 AATAGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:3831295 original size:28 final size:28
Alignment explanation
Indices: 3831263--3831323 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
3831253 GTTTGGCTTA
* *
3831263 GGTTTTTTAAAGTTTGATATTCGGGTCG
1 GGTTTTTTAAAGTGTGATATTCGGATCG
* *
3831291 GGTTTTTTTAAGTGTGATATTTGGATCG
1 GGTTTTTTAAAGTGTGATATTCGGATCG
3831319 GGTTT
1 GGTTT
3831324 AGGGTTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (28 bp):
GGTTTTTTAAAGTGTGATATTCGGATCG
Found at i:3831841 original size:18 final size:18
Alignment explanation
Indices: 3831811--3831860 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
3831801 GTTTCAGATT
*
3831811 CAGATTCCAATTCCTTCA
1 CAGATTACAATTCCTTCA
* * *
3831829 CATATTACAATTCATTCG
1 CAGATTACAATTCCTTCA
*
3831847 CAGATTCCAATTCC
1 CAGATTACAATTCC
3831861 CTCATAAACA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
CAGATTACAATTCCTTCA
Found at i:3835206 original size:53 final size:53
Alignment explanation
Indices: 3835120--3835224 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
3835110 GCAGTTTATA
3835120 TATTTTGAATAATGGAATCAAATCTATTAAGAAAAATGATAAATAGAGTCAAT
1 TATTTTGAATAATGGAATCAAATCTATTAAGAAAAATGATAAATAGAGTCAAT
* * *
3835173 TATTTTGAGTAATGGAATCAAATCTGTTCAGAAAAATGATAAATAGAGTCAA
1 TATTTTGAATAATGGAATCAAATCTATTAAGAAAAATGATAAATAGAGTCAA
3835225 CTACAATGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (53 bp):
TATTTTGAATAATGGAATCAAATCTATTAAGAAAAATGATAAATAGAGTCAAT
Found at i:3847109 original size:21 final size:21
Alignment explanation
Indices: 3847083--3847127 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3847073 GATTTCTGGG
* *
3847083 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3847104 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3847125 CAA
1 CAA
3847128 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3848824 original size:13 final size:13
Alignment explanation
Indices: 3848806--3848868 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
3848796 TTATATGGCA
3848806 CTACGGTGCAATT
1 CTACGGTGCAATT
3848819 CTACGG-GC-A--
1 CTACGGTGCAATT
*
3848828 CTTCGGTGCAATT
1 CTACGGTGCAATT
3848841 CTACGG-GC-A--
1 CTACGGTGCAATT
*
3848850 CTTCGGTGCAATT
1 CTACGGTGCAATT
3848863 CTACGG
1 CTACGG
3848869 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:3848834 original size:22 final size:22
Alignment explanation
Indices: 3848802--3848882 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
3848792 ATCATTATAT
*
3848802 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3848824 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3848846 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
3848869 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3848883 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:3862200 original size:16 final size:16
Alignment explanation
Indices: 3862179--3862222 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
3862169 TAATAAATAA
3862179 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
**
3862195 ACGAACATAAATGAAC
1 ACGAACATAAACAAAC
3862211 ACGAACATAAAC
1 ACGAACATAAAC
3862223 GTTAGAGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.59, C:0.23, G:0.09, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:3862667 original size:24 final size:24
Alignment explanation
Indices: 3862630--3862692 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3862620 AGATTGGGTT
**
3862630 AAACATAAATGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
* *
3862654 GAATATAACCGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
3862678 AAACATAACCGAACG
1 AAACATAACCGAACG
3862693 TTCACGAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
AAACATAACCGAACGAACATAAAC
Found at i:3867045 original size:101 final size:101
Alignment explanation
Indices: 3866870--3867079 Score: 395
Period size: 101 Copynumber: 2.1 Consensus size: 101
3866860 AACCCACAAC
3866870 CAGCAACCGAGCAACGCTCGACACGAACGAGAGCAGGAACATTAATGATACGACACCCTCCCAAA
1 CAGCAACCGAGCAACGCTCGACACGAACGAGAGCAGGAACATTAATGATACGACACCCTCCCAAA
*
3866935 CACCATCACTCGAGCACTGCCTTGATAGACCTACAT
66 CACCATCACTCAAGCACTGCCTTGATAGACCTACAT
3866971 CAGCAACCGAGCAACGCTC-ACCACGAACGAGAGCAGGAACATTAATGATACGACACCCTCCCAA
1 CAGCAACCGAGCAACGCTCGA-CACGAACGAGAGCAGGAACATTAATGATACGACACCCTCCCAA
3867035 ACACCATCACTCAAGCACTGCCTTGATAGACCTACAT
65 ACACCATCACTCAAGCACTGCCTTGATAGACCTACAT
3867072 CAGCAACC
1 CAGCAACC
3867080 AGACAAACCA
Statistics
Matches: 107, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
100 1 0.01
101 106 0.99
ACGTcount: A:0.35, C:0.35, G:0.17, T:0.13
Consensus pattern (101 bp):
CAGCAACCGAGCAACGCTCGACACGAACGAGAGCAGGAACATTAATGATACGACACCCTCCCAAA
CACCATCACTCAAGCACTGCCTTGATAGACCTACAT
Found at i:3870960 original size:71 final size:71
Alignment explanation
Indices: 3870840--3870973 Score: 187
Period size: 71 Copynumber: 1.9 Consensus size: 71
3870830 TTTATGGTAA
* * * *
3870840 CAGTCCATTGATATATCATGAATATAGAACGCAAAATAAAAACTAAATAGTCAGATAAAACAATT
1 CAGTCCATTGAAATATCATGAATACAGAAAGCAAAATAAAAACTAAATAGTCAAATAAAACAATT
3870905 TAGAGT
66 TAGAGT
* * * * *
3870911 CAGTCCATTGAAATATCCTGAATACAGAAAGCAAGATTAAAATTGAATAGTCAAATAAAACAA
1 CAGTCCATTGAAATATCATGAATACAGAAAGCAAAATAAAAACTAAATAGTCAAATAAAACAA
3870974 CTTAAAATGG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (71 bp):
CAGTCCATTGAAATATCATGAATACAGAAAGCAAAATAAAAACTAAATAGTCAAATAAAACAATT
TAGAGT
Found at i:3879944 original size:3 final size:3
Alignment explanation
Indices: 3879936--3879969 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3879926 AAATTAGTTA
3879936 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
3879970 GAAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3879952 original size:13 final size:13
Alignment explanation
Indices: 3879934--3879962 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3879924 AAAAATTAGT
3879934 TAAATAATAATAA
1 TAAATAATAATAA
3879947 TAAATAATAATAA
1 TAAATAATAATAA
3879960 TAA
1 TAA
3879963 TAAAATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:3879957 original size:16 final size:16
Alignment explanation
Indices: 3879936--3879966 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3879926 AAATTAGTTA
3879936 AATAATAATAATAAAT
1 AATAATAATAATAAAT
3879952 AATAATAATAATAAA
1 AATAATAATAATAAA
3879967 ATAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:3881306 original size:10 final size:9
Alignment explanation
Indices: 3881282--3881330 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
3881272 ATGATAGAAT
3881282 TAATA-ATA
1 TAATATATA
*
3881290 TTATATATA
1 TAATATATA
3881299 TATATATATA
1 TA-ATATATA
3881309 TAAT-TATA
1 TAATATATA
3881317 TAATATA-A
1 TAATATATA
3881325 TAATAT
1 TAATAT
3881331 TACTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 19 0.53
9 8 0.22
10 9 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATATATA
Found at i:3882049 original size:106 final size:106
Alignment explanation
Indices: 3881865--3883481 Score: 2406
Period size: 106 Copynumber: 15.5 Consensus size: 106
3881855 GCATTGTTCC
* * * ** * * *
3881865 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
3881930 CCAGCCGTCCCTTCGTTGTGAAGTTGAACCTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3881971 GAGTCCAGTATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882036 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3882077 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----G--A-----AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882130 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3882171 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882236 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3882277 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882342 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3882383 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882448 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3882489 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882554 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3882595 GAGTCTAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882660 CCAGCGGTCCCTTCGACGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3882701 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
3882766 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3882807 GAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACA
* *
3882871 ACCAGCGGTCCCTTCGTTGTGAAGTTGAAATTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3882913 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3882978 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3883019 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
3883084 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3883125 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3883190 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3883231 GAGTCCATTATCCTTCGTTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACA
**
3883295 ACCAGTAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3883337 GAGTCCAATATCCTTCG-T-T---G-TG--A-T-G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
3883390 CCAGCGGTCCCCTCGTCGTGAAGTTGAAATTGTGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3883431 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAATTGGGAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAG
3883482 CCCCTTCGTC
Statistics
Matches: 1382, Mismatches: 100, Indels: 58
0.90 0.06 0.04
Matches are distributed among these distances:
94 160 0.12
95 5 0.00
96 1 0.00
97 1 0.00
98 2 0.00
99 1 0.00
100 6 0.00
101 1 0.00
102 2 0.00
103 1 0.00
104 2 0.00
105 7 0.01
106 1192 0.86
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3883554 original size:35 final size:35
Alignment explanation
Indices: 3883514--3883581 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3883504 CTCAAATGGC
**
3883514 ACGATATCCTCCGTTGTAGAGTTGAAATCGTGGGT
1 ACGATATCCTCCGTCATAGAGTTGAAATCGTGGGT
*
3883549 ACGATATCCTCCGTCATGGAGTTGAAATCGTGG
1 ACGATATCCTCCGTCATAGAGTTGAAATCGTGG
3883582 ATGACCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (35 bp):
ACGATATCCTCCGTCATAGAGTTGAAATCGTGGGT
Found at i:3887623 original size:3 final size:3
Alignment explanation
Indices: 3887615--3887648 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3887605 AAATTAGTTA
3887615 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
3887649 GAAAATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3887634 original size:16 final size:16
Alignment explanation
Indices: 3887613--3887644 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3887603 AAAAATTAGT
3887613 TAAATAATAATAATAA
1 TAAATAATAATAATAA
3887629 TAAATAATAATAATAA
1 TAAATAATAATAATAA
3887645 AATAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAATAATAATAA
Found at i:3887636 original size:13 final size:13
Alignment explanation
Indices: 3887618--3887645 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3887608 TTAGTTAAAT
3887618 AATAATAATAATA
1 AATAATAATAATA
3887631 AATAATAATAATA
1 AATAATAATAATA
3887644 AA
1 AA
3887646 ATAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:3888997 original size:23 final size:21
Alignment explanation
Indices: 3888966--3889010 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
3888956 ATGATAGAAT
*
3888966 TAATAATATTATATATATATATA
1 TAATAATATAATATA-ATA-ATA
*
3888989 TAATTATATAATATAATAATA
1 TAATAATATAATATAATAATA
3889010 T
1 T
3889011 TACTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAATATAATATAATAATA
Found at i:3889007 original size:8 final size:9
Alignment explanation
Indices: 3888968--3889010 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
3888958 GATAGAATTA
3888968 ATAATATTAT
1 ATAATA-TAT
3888978 ATATATATAT
1 ATA-ATATAT
3888988 ATAAT-TAT
1 ATAATATAT
3888996 ATAATATA-
1 ATAATATAT
3889004 ATAATAT
1 ATAATAT
3889011 TACTAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 15 0.48
9 4 0.13
10 9 0.29
11 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAATATAT
Found at i:3889729 original size:106 final size:106
Alignment explanation
Indices: 3889545--3891161 Score: 2415
Period size: 106 Copynumber: 15.5 Consensus size: 106
3889535 GCATTGTTCC
* * * * ** * *
3889545 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * *
3889610 CCAGCCGTCCCTTCATTGTGAAGTTGAACCTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3889651 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3889716 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3889757 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----G--A-----AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3889810 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3889851 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3889916 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3889957 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3890022 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3890063 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
3890128 CAAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3890169 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
3890234 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3890275 GAGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
3890340 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3890381 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
3890446 CCAGTGGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
3890487 GAGTCCACTATCATTCGCTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTCATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACA
*
3890551 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3890593 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3890658 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3890699 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
3890764 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3890805 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
3890870 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3890911 GAGTCCATTATCCTTCGTTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACA
**
3890975 ACCAGTAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3891017 GAATCCAATATCCTTCG-T-T---G-TG--A-T-G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
3891070 CCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGTGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3891111 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAATTGGGAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAG
3891162 CCCCTTCGTC
Statistics
Matches: 1384, Mismatches: 98, Indels: 58
0.90 0.06 0.04
Matches are distributed among these distances:
94 160 0.12
95 5 0.00
96 1 0.00
97 1 0.00
98 2 0.00
99 1 0.00
100 6 0.00
101 1 0.00
102 2 0.00
103 1 0.00
104 2 0.00
105 7 0.01
106 1194 0.86
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3891234 original size:35 final size:35
Alignment explanation
Indices: 3891194--3891261 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3891184 CTCAAATGGC
**
3891194 ACGATATCCTCCGTTGTAGAGTTGAAATCGTGGGT
1 ACGATATCCTCCGTCATAGAGTTGAAATCGTGGGT
*
3891229 ACGATATCCTCCGTCATGGAGTTGAAATCGTGG
1 ACGATATCCTCCGTCATAGAGTTGAAATCGTGG
3891262 ATGACCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (35 bp):
ACGATATCCTCCGTCATAGAGTTGAAATCGTGGGT
Found at i:3895305 original size:3 final size:3
Alignment explanation
Indices: 3895297--3895330 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3895287 AAATTAGTTA
3895297 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
3895331 GAAATTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3895316 original size:16 final size:16
Alignment explanation
Indices: 3895295--3895326 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3895285 AAAAATTAGT
3895295 TAAATAATAATAATAA
1 TAAATAATAATAATAA
3895311 TAAATAATAATAATAA
1 TAAATAATAATAATAA
3895327 AATAGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAATAATAATAA
Found at i:3895318 original size:13 final size:13
Alignment explanation
Indices: 3895300--3895327 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3895290 TTAGTTAAAT
3895300 AATAATAATAATA
1 AATAATAATAATA
3895313 AATAATAATAATA
1 AATAATAATAATA
3895326 AA
1 AA
3895328 ATAGAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:3896672 original size:16 final size:16
Alignment explanation
Indices: 3896646--3896684 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3896636 GATAGAATTA
3896646 ATAAT-ATTATAT-AT
1 ATAATAATTATATAAT
3896660 ATATATAATTATATAAT
1 ATA-ATAATTATATAAT
3896677 ATAATAAT
1 ATAATAAT
3896685 ATTCCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 2 0.09
16 12 0.55
17 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATAATTATATAAT
Found at i:3897519 original size:38 final size:36
Alignment explanation
Indices: 3897467--3897541 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
3897457 CATTAAATCT
* *
3897467 TTTTATATTTTAAATTTTGTAAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAA-TATACAAA
* *
3897504 TTTTATGAATTTAAATTTTTTAAAGAAAATATACAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATATACAAA
3897541 T
1 T
3897542 ATTTTCAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATATACAAA
Found at i:3898234 original size:24 final size:24
Alignment explanation
Indices: 3898207--3898255 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3898197 CGTTCATTTA
*
3898207 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
3898231 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
3898255 C
1 C
3898256 ATTTATGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.10, C:0.16, G:0.27, T:0.47
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:3898245 original size:14 final size:14
Alignment explanation
Indices: 3898217--3898255 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3898207 CGTTCGTGAA
3898217 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3898231 CG-T---TTATGTT
1 CGTTCGGTTATGTT
3898241 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3898255 C
1 C
3898256 ATTTATGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
13 1 0.05
14 10 0.48
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:3898260 original size:24 final size:24
Alignment explanation
Indices: 3898217--3898265 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3898207 CGTTCGTGAA
*
3898217 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
3898241 CGTTCGGTTATGTTCATTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
3898265 C
1 C
3898266 ATTCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.14, G:0.22, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCATTTATGTT
Found at i:3898275 original size:24 final size:24
Alignment explanation
Indices: 3898223--3898278 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3898213 TGAACGTTCG
* * *
3898223 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCATTTATGTTCATTCA
3898247 GTTATGTTCATTTATGTTCATTCA
1 GTTATGTTCATTTATGTTCATTCA
*
3898271 TTTATGTT
1 GTTATGTT
3898279 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (24 bp):
GTTATGTTCATTTATGTTCATTCA
Found at i:3899375 original size:16 final size:16
Alignment explanation
Indices: 3899354--3899420 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
3899344 GTCTCCAACG
3899354 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
3899370 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
3899386 TTTATGTTCGTGGTCG
1 TTTATGTTCGTGTTCA
3899402 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
3899416 TTTAT
1 TTTAT
3899421 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 1 0.02
16 41 0.87
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:3899393 original size:32 final size:32
Alignment explanation
Indices: 3899352--3899412 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3899342 GGGTCTCCAA
*
3899352 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGGTCATTTATGTTCGTGTT
*
3899384 CGTTTATGTTCGTGGTCGTTTATGTTCGT
1 CGTTTATGTTCGTGGTCATTTATGTTCGT
3899413 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.13, G:0.25, T:0.54
Consensus pattern (32 bp):
CGTTTATGTTCGTGGTCATTTATGTTCGTGTT
Found at i:3899508 original size:16 final size:16
Alignment explanation
Indices: 3899483--3899539 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
3899473 AAAAAAAATT
*
3899483 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
3899499 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
3899515 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
3899531 T-TT-ATTTAT
1 TGTTCATTTAT
3899540 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:3902830 original size:31 final size:31
Alignment explanation
Indices: 3902789--3902897 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
3902779 TAAAGATTTT
*
3902789 TGTTGATAATGCTCAATCCACTAGTATTGAA
1 TGTTAATAATGCTCAATCCACTAGTATTGAA
* *
3902820 TGTTAATAATGCTCATTCAACTAGTATTGAA
1 TGTTAATAATGCTCAATCCACTAGTATTGAA
*
3902851 TGTTAATAATGCTCAATCCACTAGTATGGAA
1 TGTTAATAATGCTCAATCCACTAGTATTGAA
* *
3902882 TGTTGATAATACTCAA
1 TGTTAATAATGCTCAA
3902898 ATTAGGTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTAATAATGCTCAATCCACTAGTATTGAA
Found at i:3906756 original size:2 final size:2
Alignment explanation
Indices: 3906683--3906739 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3906673 GTCACTTATC
3906683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3906725 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3906740 AACCCTTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3906932 original size:31 final size:31
Alignment explanation
Indices: 3906894--3906958 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
3906884 AACTAGATTC
3906894 TTTAAATAAAATAAAAATAAAAATTTTGATG
1 TTTAAATAAAATAAAAATAAAAATTTTGATG
3906925 TTTAAATAAAATAAAAATAAAAATTTTGATG
1 TTTAAATAAAATAAAAATAAAAATTTTGATG
3906956 TTT
1 TTT
3906959 GTAAATAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (31 bp):
TTTAAATAAAATAAAAATAAAAATTTTGATG
Found at i:3910787 original size:287 final size:286
Alignment explanation
Indices: 3910271--3910845 Score: 1053
Period size: 287 Copynumber: 2.0 Consensus size: 286
3910261 GTCACTGTTA
*
3910271 TTTTTTTTTGATAGGAAAAAAGGCCTCAATAAAACCCCCTTGGTGATTAACGGAACTTAACAATA
1 TTTTTTTTTGATACGAAAAAAGGCCTCAATAAAACCCCCTTGGTGATTAACGGAACTTAACAATA
3910336 GTTCCTTAATCCACACAAGGAGGAAAGGAGTGCCCTAGGATTCATTAAACTCAAATATAACAAAG
66 GTTCCTTAATCCACACAAGGAGGAAAGGAGTGCCCTAGGATTCATTAAACTCAAATATAACAAAG
*
3910401 TAATACAAACCAATCTCCCTCAAGAGATACATAACCAGAAAAAAACAGCCCTTAACAGAGCATAA
131 TAATACAAACCAATCTCCCTCAAGAGATACAAAACCAGAAAAAAACAGCCCTTAACAGAGCATAA
*
3910466 TTCAACCAATACCCGCCTTAGCTAGAACATCCGCCTCTATATTGGCTGTCCTACTAACCCAACTA
196 ATCAACCAATACCCGCCTTAGCTAGAACATCCGCCTCTATATTGGCTGTCCTACTAACCCAACTA
*
3910531 ATCAAACCTTCAAAAACACTAAGCTT
261 ATAAAACCTTCAAAAACACTAAGCTT
3910557 TTTTTTTTTGATACGAATAAAAGGCCTCAATAAAACCCCCTTGGTGATTAACGGAACTTAA-AAG
1 TTTTTTTTTGATACGAA-AAAAGGCCTCAATAAAACCCCCTTGGTGATTAACGGAACTTAACAA-
*
3910621 TAGTTCCTTAATCCACACAAGGAGGAAAGGAGTGCCCTAGGATTCATTAAACTCAAATATAGCAA
64 TAGTTCCTTAATCCACACAAGGAGGAAAGGAGTGCCCTAGGATTCATTAAACTCAAATATAACAA
* *
3910686 AGTAATACAAATCAATCTCCCTCAAGAGATACAAAACCAGAAAGAAACAGCCCTTAACAGAGCAT
129 AGTAATACAAACCAATCTCCCTCAAGAGATACAAAACCAGAAAAAAACAGCCCTTAACAGAGCAT
*
3910751 AAATCAACCAATACCCGCCTTAGCTAGGACATCCGCCTCTATATTGGCTGTCCTACTAACCCAAC
194 AAATCAACCAATACCCGCCTTAGCTAGAACATCCGCCTCTATATTGGCTGTCCTACTAACCCAAC
3910816 TAATAAAACCTTCAAAAACACTAAGCTT
259 TAATAAAACCTTCAAAAACACTAAGCTT
3910844 TT
1 TT
3910846 GAATAATGTC
Statistics
Matches: 279, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
286 18 0.06
287 261 0.94
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (286 bp):
TTTTTTTTTGATACGAAAAAAGGCCTCAATAAAACCCCCTTGGTGATTAACGGAACTTAACAATA
GTTCCTTAATCCACACAAGGAGGAAAGGAGTGCCCTAGGATTCATTAAACTCAAATATAACAAAG
TAATACAAACCAATCTCCCTCAAGAGATACAAAACCAGAAAAAAACAGCCCTTAACAGAGCATAA
ATCAACCAATACCCGCCTTAGCTAGAACATCCGCCTCTATATTGGCTGTCCTACTAACCCAACTA
ATAAAACCTTCAAAAACACTAAGCTT
Found at i:3914882 original size:173 final size:173
Alignment explanation
Indices: 3914586--3914933 Score: 642
Period size: 173 Copynumber: 2.0 Consensus size: 173
3914576 GGTAAGAATT
3914586 CATCTAAAAGTGTTCCAAATAAATTCTTTAATGGATTAAAAGTGACGGTTCTCCAAAGTGGCATT
1 CATCTAAAAGTGTTCCAAATAAATTCTTTAATGGATTAAAAGTGACGGTTCTCCAAAGTGGCATT
*
3914651 AGAGAATGCTCAAAGTTGTACTATTTGAACTGTAATGAGACGAAACGCCACATCCAGTATATCGG
66 AGAGAATGCTCAAAGTTGTACCATTTGAACTGTAATGAGACGAAACGCCACATCCAGTATATCGG
3914716 TCTGAACCACTCCTACCACCACGACTCCCAGGGTTATTGGCAC
131 TCTGAACCACTCCTACCACCACGACTCCCAGGGTTATTGGCAC
3914759 CATCTAAAAGTGTTCCAAATAAATTCTTTAATGGATTAAAAGTGACGGTTCTCCAAAGTGGCATT
1 CATCTAAAAGTGTTCCAAATAAATTCTTTAATGGATTAAAAGTGACGGTTCTCCAAAGTGGCATT
* * * *
3914824 AGAGAATGTTCAAAGTTGTACCATTTGAACTGTAATGAGACGAACCGCCACGTCCAGTATATTGG
66 AGAGAATGCTCAAAGTTGTACCATTTGAACTGTAATGAGACGAAACGCCACATCCAGTATATCGG
*
3914889 TCTGAACCACTCCTACCGCCACGACTCCCAGGGTTATTGGCAC
131 TCTGAACCACTCCTACCACCACGACTCCCAGGGTTATTGGCAC
3914932 CA
1 CA
3914934 CGAGACCTCG
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
173 169 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (173 bp):
CATCTAAAAGTGTTCCAAATAAATTCTTTAATGGATTAAAAGTGACGGTTCTCCAAAGTGGCATT
AGAGAATGCTCAAAGTTGTACCATTTGAACTGTAATGAGACGAAACGCCACATCCAGTATATCGG
TCTGAACCACTCCTACCACCACGACTCCCAGGGTTATTGGCAC
Found at i:3916841 original size:21 final size:21
Alignment explanation
Indices: 3916798--3916842 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3916788 TATCGCATTA
* **
3916798 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTCACAATG
*
3916819 CGATTTTCCTAATTCACAATG
1 CGATTTTCCAAATTCACAATG
3916840 CGA
1 CGA
3916843 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTCACAATG
Found at i:3917085 original size:22 final size:22
Alignment explanation
Indices: 3917060--3917125 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
3917050 GGCGACATCT
3917060 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
3917082 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
3917104 GTCTCCATCTCTGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3917126 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3917504 original size:20 final size:20
Alignment explanation
Indices: 3917462--3917531 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
3917452 TGATTCTGTC
*
3917462 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
3917481 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
3917501 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
3917521 GTTACGATTTT
1 GTTGCGATTTT
3917532 AAATTTCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 11 0.25
20 33 0.75
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:3917538 original size:20 final size:20
Alignment explanation
Indices: 3917495--3917538 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3917485 CGATAGTCAT
* * *
3917495 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAA
3917515 TTTCGTGTTACGATTTTAAA
1 TTTCGTGTTACGATTTTAAA
3917535 TTTC
1 TTTC
3917539 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAA
Found at i:3919299 original size:21 final size:22
Alignment explanation
Indices: 3919260--3919300 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3919250 AAATATTCTC
*
3919260 GTAATTTCACTTAGATTGCTTA
1 GTAAATTCACTTAGATTGCTTA
*
3919282 GTAAATTCA-TTAGGTTGCT
1 GTAAATTCACTTAGATTGCT
3919301 GCCAATACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (22 bp):
GTAAATTCACTTAGATTGCTTA
Found at i:3919445 original size:20 final size:20
Alignment explanation
Indices: 3919420--3919471 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3919410 AGAATAGTTT
*
3919420 ACTATCGCAATGCAAAAATG
1 ACTATCGCAACGCAAAAATG
*
3919440 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCAAAAATG
3919460 ACTATCGCAACG
1 ACTATCGCAACG
3919472 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCAAAAATG
Found at i:3919512 original size:32 final size:34
Alignment explanation
Indices: 3919443--3919532 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 34
3919433 AAAAATGACT
* * * *
3919443 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGACAATCGCAACAACAAA
*
3919477 ATCGCAATGCG-AAATGA-AATCGCAACAACAAA
1 ATCGCAACGCGAAAATGACAATCGCAACAACAAA
* *
3919509 ATCGCAACACGAAAATGACTATCG
1 ATCGCAACGCGAAAATGACAATCG
3919533 TAATGCGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 20 0.43
33 12 0.26
34 14 0.30
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACAATCGCAACAACAAA
Found at i:3919541 original size:20 final size:20
Alignment explanation
Indices: 3919518--3919577 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
3919508 AATCGCAACA
*
3919518 CGAAAATGACTATCGTAATG
1 CGAAAATGACTATCGCAATG
*
3919538 CGAAAATGAATATCGCAATG
1 CGAAAATGACTATCGCAATG
**
3919558 CGAATTTGACTATCGCAATG
1 CGAAAATGACTATCGCAATG
3919578 AAAGAATCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (20 bp):
CGAAAATGACTATCGCAATG
Found at i:3919650 original size:20 final size:20
Alignment explanation
Indices: 3919625--3919768 Score: 207
Period size: 20 Copynumber: 7.2 Consensus size: 20
3919615 TCTCTCGTTA
**
3919625 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
**
3919645 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
**
3919665 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
3919685 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
*
3919705 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
3919725 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
3919745 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
3919765 CGAT
1 CGAT
3919769 TTTAAGTTTC
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 119 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:3920293 original size:18 final size:19
Alignment explanation
Indices: 3920254--3920295 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
3920244 CTCACCTGTC
3920254 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
3920275 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
3920293 ATC
1 ATC
3920296 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:3920349 original size:42 final size:42
Alignment explanation
Indices: 3920277--3920359 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3920267 CCTCCCCTAT
* *
3920277 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGT-CCCTCCCAC
* * *
3920319 CGTTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCA
3920360 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:3921758 original size:14 final size:14
Alignment explanation
Indices: 3921739--3921774 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3921729 ATTGTTTAAT
3921739 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3921753 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3921767 TGATTTGT
1 TGATTTGT
3921775 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3921980 original size:33 final size:33
Alignment explanation
Indices: 3921918--3921981 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3921908 GAGAGAATTG
**
3921918 CATTGCGATTCTCTCGTTGCGATTTTCATTTCA
1 CATTGCGATTCTCTCGTTGCGATAGTCATTTCA
3921951 CATTGCGATTCTCTCGTTGCGATAGTCATTT
1 CATTGCGATTCTCTCGTTGCGATAGTCATTT
3921982 TCGCGTTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (33 bp):
CATTGCGATTCTCTCGTTGCGATAGTCATTTCA
Found at i:3921990 original size:20 final size:20
Alignment explanation
Indices: 3921965--3922058 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
3921955 GCGATTCTCT
*
3921965 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
3921985 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
3922005 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
3922025 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
3922045 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
3922059 AATGAATGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 66 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:3924475 original size:24 final size:24
Alignment explanation
Indices: 3924441--3924494 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3924431 CTGAAAAATC
3924441 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3924465 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3924489 ATCAAA
1 ATCAAA
3924495 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3925361 original size:20 final size:20
Alignment explanation
Indices: 3925336--3925402 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
3925326 AAATTCAGTA
3925336 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
3925356 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
3925376 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
3925396 TTGCGAT
1 TTGCGAT
3925403 TTACATATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:3925412 original size:20 final size:20
Alignment explanation
Indices: 3925389--3925505 Score: 207
Period size: 20 Copynumber: 5.8 Consensus size: 20
3925379 CGATAGTCAG
* *
3925389 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
3925409 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3925429 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3925449 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3925469 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3925489 ATTCGCATTGTGATTTA
1 ATTCGCATTGCGATTTA
3925506 GGAAAATCGC
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3925530 original size:21 final size:22
Alignment explanation
Indices: 3925501--3925543 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3925491 TCGCATTGTG
3925501 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGGAAAATCGCAACGCGA
*
3925523 ATTT-GGAAAATCGCAATGCGA
1 ATTTAGGAAAATCGCAACGCGA
3925544 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (22 bp):
ATTTAGGAAAATCGCAACGCGA
Found at i:3928907 original size:14 final size:14
Alignment explanation
Indices: 3928888--3928918 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3928878 TACATCTATG
3928888 TTCACAGGGATTAA
1 TTCACAGGGATTAA
3928902 TTCACAGGGATTAA
1 TTCACAGGGATTAA
3928916 TTC
1 TTC
3928919 CACAATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (14 bp):
TTCACAGGGATTAA
Found at i:3932030 original size:24 final size:24
Alignment explanation
Indices: 3932003--3932053 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3931993 ATAGGCTCTT
3932003 ATGCTTGGAAGCACCACATAGAGG
1 ATGCTTGGAAGCACCACATAGAGG
3932027 ATGCTTGGAAGCACCACATAGAGG
1 ATGCTTGGAAGCACCACATAGAGG
3932051 ATG
1 ATG
3932054 AACCAACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (24 bp):
ATGCTTGGAAGCACCACATAGAGG
Found at i:3937573 original size:31 final size:31
Alignment explanation
Indices: 3937535--3937628 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
3937525 CCCGAAGGAC
*
3937535 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
3937566 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3937597 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3937628 C
1 C
3937629 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:3941636 original size:31 final size:31
Alignment explanation
Indices: 3941598--3941691 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
3941588 CCCGAAGGAC
*
3941598 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
3941629 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3941660 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
3941691 C
1 C
3941692 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:3943746 original size:103 final size:103
Alignment explanation
Indices: 3943575--3943792 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
3943565 TAATGTCCAT
* *
3943575 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGAGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGAGTCTCACCA
3943640 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3943678 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGAGTCTCACCA
3943743 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3943781 AAGGACCACATA
1 AAGGACCACATA
3943793 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGAGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3944652 original size:64 final size:64
Alignment explanation
Indices: 3944544--3944764 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
3944534 TAATGAAGGT
* * * * *
3944544 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
3944607 G
64 G
* *
3944608 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
3944672 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
3944735 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3944765 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 126 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:3949355 original size:23 final size:23
Alignment explanation
Indices: 3949328--3949405 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
3949318 CACCACAGCT
*
3949328 CATATAATTGCACCAAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
3949351 CATATAATTGCACTGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
3949374 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
3949397 TATAATAAT
1 CAT-ATAAT
3949406 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:3949592 original size:103 final size:102
Alignment explanation
Indices: 3949412--3949628 Score: 371
Period size: 103 Copynumber: 2.1 Consensus size: 102
3949402 TAATGTCCAT
* * *
3949412 AAGGACCACATATCATTCCTTAAGAATCATATAATATGCTAGGGATCAAGTATATGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATAATATGCCAAGGATCAAGAATATGTCTCACCAG
3949477 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
3949514 AAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGAATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATA-ATATGCCAAGGATCAAGAATATGTCTCACCA
*
3949579 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3949617 AAGGACCACATA
1 AAGGACCACATA
3949629 AACCCTCGAC
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 32 0.30
103 76 0.70
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATAATATGCCAAGGATCAAGAATATGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3950488 original size:64 final size:64
Alignment explanation
Indices: 3950380--3950600 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
3950370 TAATGAAGGT
* * * * *
3950380 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
3950443 G
64 G
* *
3950444 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
3950508 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
3950571 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3950601 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 126 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:3969056 original size:29 final size:29
Alignment explanation
Indices: 3969022--3969088 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
3969012 CGAAACAAAC
3969022 GCGCTGAATACTGAACGGTTCAACATTCA
1 GCGCTGAATACTGAACGGTTCAACATTCA
3969051 GCGCTGAATACTGAACGGTTCAACATTCA
1 GCGCTGAATACTGAACGGTTCAACATTCA
3969080 GCGCTGAAT
1 GCGCTGAAT
3969089 GGTTCCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (29 bp):
GCGCTGAATACTGAACGGTTCAACATTCA
Found at i:3971464 original size:20 final size:20
Alignment explanation
Indices: 3971439--3971486 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
3971429 CTTTTTGCTC
3971439 CATATCTATTGTTGATTCTT
1 CATATCTATTGTTGATTCTT
*
3971459 CATATCTATTGTTGATTTTT
1 CATATCTATTGTTGATTCTT
3971479 CATATCTA
1 CATATCTA
3971487 CGAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (20 bp):
CATATCTATTGTTGATTCTT
Found at i:3985377 original size:60 final size:60
Alignment explanation
Indices: 3985284--3985403 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
3985274 CTCTACGATG
* * *
3985284 TCGACATTTAGGTCGAACAAGCTGGCAGTTGAATGTCT-TCCCCTTGAACTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCT-CCCTAGAACTTGAAGGCATC
*
3985344 TCGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGTCTCTCCCTAGAACTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCTCCCTAGAACTTGAAGGCATC
3985404 GTTTTACATG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (60 bp):
TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCTCCCTAGAACTTGAAGGCATC
Found at i:3992583 original size:22 final size:21
Alignment explanation
Indices: 3992535--3992586 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3992525 GTGGTATTTT
*
3992535 TATTATTTTCTTATATCGATA
1 TATTATTTTCTTATAACGATA
3992556 TATTATTTTCTATAATAAC-ATA
1 TATTATTTTCT-T-ATAACGATA
*
3992578 TTTTATTTT
1 TATTATTTT
3992587 ATTTCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 12 0.44
23 4 0.15
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATTTTCTTATAACGATA
Found at i:4015096 original size:28 final size:26
Alignment explanation
Indices: 4015050--4015136 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 26
4015040 GAGATAAAAA
4015050 TATATTAAACTTATTTTTATTTTAAATAT
1 TATATT-AA-TTA-TTTTATTTTAAATAT
*
4015079 TATATTGAATTTATTTTAGTTTAAA-A-
1 TATATT-AA-TTATTTTATTTTAAATAT
4015105 -ATATTACATT-TTTTATTTTAAATAT
1 TATATTA-ATTATTTTATTTTAAATAT
4015130 TATATTA
1 TATATTA
4015137 TTAAATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 11 0.22
24 4 0.08
25 6 0.12
26 6 0.12
27 1 0.02
28 11 0.22
29 11 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TATATTAATTATTTTATTTTAAATAT
Found at i:4024057 original size:20 final size:21
Alignment explanation
Indices: 4024032--4024124 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
4024022 TTTTCCCAAT
*
4024032 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4024052 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
4024073 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4024093 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4024114 TCGCAATGCGA
1 TCGCAATGCGA
4024125 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4024089 original size:41 final size:41
Alignment explanation
Indices: 4024032--4024124 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
4024022 TTTTCCCAAT
4024032 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4024073 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4024114 TCGCAATGCGA
1 TCGCAATGCGA
4024125 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:4024137 original size:41 final size:41
Alignment explanation
Indices: 4024051--4024185 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
4024041 GAATAAGTAA
** *
4024051 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
4024092 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
4024133 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
4024174 TTCGCAACGCGA
1 ATCGCAACGCGA
4024186 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:4024138 original size:20 final size:20
Alignment explanation
Indices: 4024113--4024206 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
4024103 AATTGGGAAA
*
4024113 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
4024133 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
4024154 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
4024174 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
4024194 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4024207 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:4024422 original size:22 final size:22
Alignment explanation
Indices: 4024394--4024437 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4024384 CACTCTCTCA
4024394 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
4024416 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
4024438 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4024726 original size:20 final size:20
Alignment explanation
Indices: 4024701--4024738 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4024691 CGATTCTCTC
4024701 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
4024721 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
4024739 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:4026079 original size:18 final size:18
Alignment explanation
Indices: 4026058--4026104 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4026048 TCCACTTCGG
*
4026058 GAGCCATCA-CCTCGCCCA
1 GAGCCATCATCC-CACCCA
*
4026076 GAGCTATCATCCCACCCA
1 GAGCCATCATCCCACCCA
4026094 GAGCCATCATC
1 GAGCCATCATC
4026105 TGATCGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.26, C:0.45, G:0.15, T:0.15
Consensus pattern (18 bp):
GAGCCATCATCCCACCCA
Found at i:4026648 original size:14 final size:14
Alignment explanation
Indices: 4026629--4026686 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4026619 ATGCGAAATG
4026629 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4026643 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4026659 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4026675 AAAATCGCAACG
1 AAAATCGCAACG
4026687 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4026671 original size:32 final size:33
Alignment explanation
Indices: 4026613--4026703 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
4026603 GGAAATGGCT
*
4026613 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4026646 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4026678 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
4026704 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:4026697 original size:19 final size:19
Alignment explanation
Indices: 4026575--4026708 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
4026565 TAGTTTACTT
* **
4026575 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
4026594 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
4026614 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4026633 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
4026647 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
4026665 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
4026679 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4026698 TCGCAATGCGA
1 TCGCAACGCGA
4026709 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 35 0.38
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4026739 original size:14 final size:14
Alignment explanation
Indices: 4026720--4026777 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4026710 TTGTGTTTCG
4026720 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4026734 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4026750 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
4026766 CGTTGCGATTTT
1 CGTTGCGATTTT
4026778 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4026754 original size:32 final size:33
Alignment explanation
Indices: 4026715--4026793 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
4026705 GCGATTTGTG
4026715 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
4026747 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
4026780 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
4026794 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:4026792 original size:19 final size:19
Alignment explanation
Indices: 4026734--4026851 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
4026724 GCGATTTTGT
4026734 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4026752 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
4026766 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
4026785 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
4026805 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4026824 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
4026844 TGTTGCGA
1 CGTTGCGA
4026852 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4028860 original size:14 final size:14
Alignment explanation
Indices: 4028841--4028931 Score: 83
Period size: 14 Copynumber: 5.8 Consensus size: 14
4028831 AACGCGAAAT
*
4028841 GAAAATCACAACGA
1 GAAAATCGCAACGA
4028855 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
4028873 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
4028888 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
4028906 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
4028921 GAAAATCGCAA
1 GAAAATCGCAA
4028932 TGCGATTTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
14 32 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 22 0.33
ACGTcount: A:0.51, C:0.19, G:0.20, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:4028877 original size:19 final size:16
Alignment explanation
Indices: 4028826--4028936 Score: 81
Period size: 14 Copynumber: 6.7 Consensus size: 16
4028816 AAAATAGACT
4028826 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCG-AA-GAAA
*
4028845 ATCACAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
4028859 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AA-GAAA
4028878 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
4028892 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AA-GAAA
4028911 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
4028925 ATCGCAATGCGA
1 ATCGCAA-GCGA
4028937 TTTTCATTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 28
0.72 0.02 0.26
Matches are distributed among these distances:
14 32 0.42
15 3 0.04
16 6 0.08
17 6 0.08
18 2 0.03
19 28 0.36
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.12
Consensus pattern (16 bp):
ATCGCAAGCGAAGAAA
Found at i:4028949 original size:33 final size:33
Alignment explanation
Indices: 4028826--4028936 Score: 204
Period size: 33 Copynumber: 3.4 Consensus size: 33
4028816 AAAATAGACT
* *
4028826 ATCGCAACGCGAAATGAAAATCACAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
4028859 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
4028892 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
4028925 ATCGCAATGCGA
1 ATCGCAATGCGA
4028937 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:4029012 original size:20 final size:20
Alignment explanation
Indices: 4028955--4029012 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
4028945 TCGCATTGCA
* *
4028955 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
4028975 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4028995 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4029013 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:4030123 original size:24 final size:24
Alignment explanation
Indices: 4030067--4030125 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
4030057 AGTCAGTATT
* *
4030067 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
4030091 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
4030115 CGAATTTTGAT
1 CGAAATTTGAT
4030126 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:4030317 original size:12 final size:12
Alignment explanation
Indices: 4030300--4030324 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4030290 ATATAATCCT
4030300 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4030312 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4030324 G
1 G
4030325 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4032639 original size:19 final size:19
Alignment explanation
Indices: 4032614--4032744 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
4032604 GGAAATTACT
4032614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
4032633 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4032647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
4032666 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
4032680 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
4032699 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
4032713 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4032732 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4032745 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4032656 original size:33 final size:33
Alignment explanation
Indices: 4032614--4032740 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
4032604 GGAAATTACT
*
4032614 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
4032647 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4032679 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4032713 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4032741 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4032721 original size:66 final size:66
Alignment explanation
Indices: 4032615--4032747 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
4032605 GAAATTACTA
* *
4032615 TCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4032680 T
66 T
*
4032681 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4032746 T
66 T
4032747 T
1 T
4032748 AATTTCGTGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:4032943 original size:14 final size:14
Alignment explanation
Indices: 4032924--4032960 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4032914 CATCAATTAA
4032924 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4032938 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4032952 ACAAATCAA
1 ACAAATCAA
4032961 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4034414 original size:21 final size:21
Alignment explanation
Indices: 4034348--4034414 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4034338 GTGAATCGGG
*
4034348 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
4034368 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
4034390 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
4034411 CTCT
1 CTCT
4034415 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:4034433 original size:42 final size:41
Alignment explanation
Indices: 4034348--4034470 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
4034338 GTGAATCGGG
* * * * *
4034348 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
4034390 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
4034432 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
4034471 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:4036508 original size:33 final size:33
Alignment explanation
Indices: 4036451--4036537 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
4036441 ACGAGATAAT
*
4036451 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
4036485 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
4036518 GACAATCGCAACCGCGAAAT
1 GAGAATCGCAA-CGCGAAAT
4036538 AAAAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 27 0.55
34 22 0.45
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:4036554 original size:19 final size:19
Alignment explanation
Indices: 4036426--4036591 Score: 127
Period size: 19 Copynumber: 9.1 Consensus size: 19
4036416 TCTTTTGGTT
*
4036426 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4036445 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4036465 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
4036483 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
4036499 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
4036517 ---A-GACAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
4036533 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4036552 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
4036571 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4036590 GA
1 GA
4036592 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 18 0.15
15 3 0.03
16 3 0.03
17 1 0.01
18 3 0.03
19 53 0.45
20 36 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4036620 original size:19 final size:19
Alignment explanation
Indices: 4036587--4036653 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4036577 AAAATCGCAA
**
4036587 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
4036606 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
4036625 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
4036645 TGCGATTTT
1 TGCGATTTT
4036654 CATTCTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4037200 original size:20 final size:20
Alignment explanation
Indices: 4037175--4037222 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4037165 ATGTAAATCA
*
4037175 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTAAGTATCG
*
4037195 CGTTGCGAAAGTAAGTATCT
1 CGTTGCGAAAGTAAGTATCG
4037215 CGTTGCGA
1 CGTTGCGA
4037223 TTTTGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
CGTTGCGAAAGTAAGTATCG
Found at i:4037260 original size:20 final size:20
Alignment explanation
Indices: 4037177--4037264 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
4037167 GTAAATCACG
* * *
4037177 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTAAGTATCGCA
* * *
4037197 TTGCGAAAGTAAGTATCTCG
1 TTGCGATAGTAAGTATCGCA
* * *
4037217 TTGCGATTTTGT-ATTATCGTA
1 TTGCGA--TAGTAAGTATCGCA
4037238 TTGCGATAGTAAGTATCGCA
1 TTGCGATAGTAAGTATCGCA
4037258 TTGCGAT
1 TTGCGAT
4037265 TTTCCCAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.06
20 38 0.70
21 11 0.20
22 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTAAGTATCGCA
Found at i:4037283 original size:41 final size:41
Alignment explanation
Indices: 4037190--4037285 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
4037180 CGAAAGTCAG
* * * ** *
4037190 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
**
4037231 TATCGTATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
4037273 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
4037286 TTACTTATTC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:4045043 original size:21 final size:21
Alignment explanation
Indices: 4045003--4045057 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
4044993 GATTCTTGAC
4045003 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
4045023 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
4045045 AATCGCAACGCGA
1 AATCGCAATGCGA
4045058 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:4045159 original size:20 final size:20
Alignment explanation
Indices: 4045045--4045293 Score: 236
Period size: 20 Copynumber: 12.4 Consensus size: 20
4045035 GATTTTACAG
* ** *
4045045 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
4045065 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
4045085 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
4045105 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4045125 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
4045145 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4045165 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4045185 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
4045205 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4045225 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4045245 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4045265 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4045285 AATCACAAC
1 AATCGCAAC
4045294 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 27, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 192 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:4046025 original size:24 final size:24
Alignment explanation
Indices: 4045986--4046032 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4045976 AAATTTGGTC
4045986 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
4046010 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
4046033 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:4046224 original size:12 final size:12
Alignment explanation
Indices: 4046207--4046231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4046197 ATATAATCCT
4046207 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4046219 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4046231 G
1 G
4046232 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4048567 original size:33 final size:33
Alignment explanation
Indices: 4048516--4048766 Score: 186
Period size: 33 Copynumber: 7.2 Consensus size: 33
4048506 CGGAAATTAC
* *
4048516 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
4048549 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
4048583 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
4048622 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
4048655 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
4048688 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
4048727 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
4048760 AATCGCA
1 AATCGCA
4048767 TTGCGATTCT
Statistics
Matches: 171, Mismatches: 27, Indels: 41
0.72 0.11 0.17
Matches are distributed among these distances:
32 9 0.05
33 63 0.37
34 43 0.25
35 3 0.02
36 1 0.01
37 1 0.01
38 17 0.10
39 24 0.14
40 10 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:4048593 original size:53 final size:53
Alignment explanation
Indices: 4048530--4048766 Score: 440
Period size: 53 Copynumber: 4.5 Consensus size: 53
4048520 GCAACGAGAG
* * *
4048530 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
4048583 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
4048636 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
4048688 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
4048741 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
4048767 TTGCGATTCT
Statistics
Matches: 180, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
52 52 0.29
53 128 0.71
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Done.