Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 88 of 109
Found at i:28134169 original size:18 final size:18
Alignment explanation
Indices: 28134143--28134185 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28134133 GACTCGAAAA
* *
28134143 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
28134161 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
28134179 AGGAAAC
1 AGGAAAC
28134186 GTACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:28154431 original size:22 final size:22
Alignment explanation
Indices: 28154403--28154552 Score: 93
Period size: 22 Copynumber: 7.0 Consensus size: 22
28154393 NNNNNNNNNN
28154403 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
*
28154425 GTTTTTAAGTTAAGAG-TTA--
1 GTTTTTAAGTTAAGGGTTTAGG
*
28154444 GTGTTTAAGGTT-AGGG----GG
1 GTTTTTAA-GTTAAGGGTTTAGG
* * **
28154462 TTTTAAATTAAGTCAAGGGTTTAAA
1 GTTT---TTAAGTTAAGGGTTTAGG
* *
28154487 GTTTTTAAGTCATGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
28154509 GTTTGTAAGTTAAGTGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
28154531 GTTTTAAAGTCAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
28154552 G
1 G
28154553 ATTAGGGTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 23
0.69 0.14 0.16
Matches are distributed among these distances:
18 2 0.02
19 10 0.10
20 5 0.05
21 17 0.18
22 60 0.62
25 3 0.03
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.41
Consensus pattern (22 bp):
GTTTTTAAGTTAAGGGTTTAGG
Found at i:28154528 original size:44 final size:43
Alignment explanation
Indices: 28154470--28154552 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 43
28154460 GGTTTTAAAT
* *
28154470 TAAGTCAAGGGTTTAAAGTTTTTAAGTCATGGGTTTAGGGTTTG
1 TAAGTCAAGGGTTTAAAGTTTTAAAGTCAAGGG-TTAGGGTTTG
* * **
28154514 TAAGTTAAGTGTTTAGGGTTTTAAAGTCAAGGGTTAGGG
1 TAAGTCAAGGGTTTAAAGTTTTAAAGTCAAGGGTTAGGG
28154553 ATTAGGGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 6 0.18
44 27 0.82
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.39
Consensus pattern (43 bp):
TAAGTCAAGGGTTTAAAGTTTTAAAGTCAAGGGTTAGGGTTTG
Found at i:28154591 original size:27 final size:26
Alignment explanation
Indices: 28154561--28154611 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
28154551 GGATTAGGGT
*
28154561 TTAAGGTTTAAGGTTAAGAGATTTAAA
1 TTAAGGGTTAAGGTTAAG-GATTTAAA
* *
28154588 TTAAGGGTTAGGGTTTAGGATTTA
1 TTAAGGGTTAAGGTTAAGGATTTA
28154612 GGTTTTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (26 bp):
TTAAGGGTTAAGGTTAAGGATTTAAA
Found at i:28154611 original size:7 final size:7
Alignment explanation
Indices: 28154591--28154631 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
28154581 ATTTAAATTA
28154591 AGGG-TT
1 AGGGTTT
28154597 AGGGTTT
1 AGGGTTT
*
28154604 AGGATTT
1 AGGGTTT
*
28154611 AGGTTTT
1 AGGGTTT
28154618 AGGGTTT
1 AGGGTTT
28154625 AGGGTTT
1 AGGGTTT
28154632 GTCAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:28157065 original size:51 final size:51
Alignment explanation
Indices: 28157021--28157120 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
28157011 AATTATTTAA
28157021 AAATAGGGATTTAAGAGAAATTTAAG-AGGAATTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAG-AATTTAAGAAGGAATTTGAGAGCAAATTGAGATT
* * **
28157072 AAATATGGATTTCAGAGAATTTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAATTTAAGAAGGAATTTGAGAGCAAATTGAGA
28157121 GGAAATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 6 0.14
51 38 0.86
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAATTTAAGAAGGAATTTGAGAGCAAATTGAGATT
Found at i:28157118 original size:11 final size:11
Alignment explanation
Indices: 28157098--28157155 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
28157088 GAATTTTGGA
*
28157098 AGGAATTTGAG
1 AGGAAATTGAG
*
28157109 AGCAAATTGAG
1 AGGAAATTGAG
*
28157120 AGGAAATTTAG
1 AGGAAATTGAG
28157131 AGGAAATTGAG
1 AGGAAATTGAG
28157142 AGGAAATTTGAG
1 AGGAAA-TTGAG
28157154 AG
1 AG
28157156 AGGATTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 34 0.83
12 7 0.17
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:28157123 original size:22 final size:23
Alignment explanation
Indices: 28157101--28157155 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
28157091 TTTTGGAAGG
28157101 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
*
28157124 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
28157146 AATTTGAGAG
1 AATTTGAGAG
28157156 AGGATTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGGA
Found at i:28157863 original size:19 final size:17
Alignment explanation
Indices: 28157820--28157872 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
28157810 AAAAAAAGAT
28157820 AAAAAAATTCTAAAAAA
1 AAAAAAATTCTAAAAAA
*
28157837 AGTTAAAAATTCTAAATAATA
1 A--AAAAAATTCTAAA-AA-A
*
28157858 AAAAAATTTCTAAAA
1 AAAAAAATTCTAAAA
28157873 TAACTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 23 0.79
20 2 0.07
21 2 0.07
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAAAATTCTAAAAAA
Found at i:28161428 original size:21 final size:24
Alignment explanation
Indices: 28161380--28161428 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
28161370 CAGAGGTTGA
*
28161380 TATCTATTTTCTTTCTTCGTTTCAT
1 TATCTATTTTCTTTATTC-TTTCAT
28161405 TATCTATTTT-TTTATT-TTTC-T
1 TATCTATTTTCTTTATTCTTTCAT
28161426 TAT
1 TAT
28161429 ATACGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
24 5 0.22
25 10 0.43
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (24 bp):
TATCTATTTTCTTTATTCTTTCAT
Found at i:28174638 original size:12 final size:12
Alignment explanation
Indices: 28174621--28174646 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28174611 TAAAATAGGG
28174621 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28174633 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28174645 TT
1 TT
28174647 AGACAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:28174706 original size:40 final size:40
Alignment explanation
Indices: 28174652--28174749 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
28174642 CGTTTAGACA
* *
28174652 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGC-TTTACG
1 AAAAACGCCGCTAAAAATCGAGCATTAACGGCGCATTT-CG
* * * *
28174692 TAAAACGCCGCTAAAGATCGAGTATTAACGGCGCATTTTG
1 AAAAACGCCGCTAAAAATCGAGCATTAACGGCGCATTTCG
28174732 AAAAACGCCGCTAAAAAT
1 AAAAACGCCGCTAAAAAT
28174750 AAGTATTAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAACGGCGCATTTCG
Found at i:28174891 original size:41 final size:41
Alignment explanation
Indices: 28174828--28175064 Score: 330
Period size: 41 Copynumber: 5.8 Consensus size: 41
28174818 TTTTGAGGCA
***
28174828 TTTAGCGGCGTTTTTTATAAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* *
28174869 TTTAGTGGTGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* *
28174910 TTTAGCGGCATTTTTGGGAAAGCGCCGCTAATTCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* *
28174951 TTTAGCGGCGTTTTTGGGAAAGCGCTGCTAATGCTCGGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* * * *
28174992 TTTAGCGGCGTTTTTGAGAATGCGCCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
** *
28175033 TTTAGCGGCGTTTTTGAAAAAGCGCCTCTAAT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAT
28175065 AATAAAATCT
Statistics
Matches: 174, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 174 1.00
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
Found at i:28176819 original size:58 final size:58
Alignment explanation
Indices: 28176745--28177014 Score: 522
Period size: 58 Copynumber: 4.7 Consensus size: 58
28176735 CTACATTGAT
**
28176745 AATTTTAACCGCAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
1 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
28176803 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
1 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
28176861 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
1 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
28176919 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
1 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
28176977 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAAT
1 AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAAT
28177015 TTTAACCAAA
Statistics
Matches: 210, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 210 1.00
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (58 bp):
AATTTTAACCAAAAAATTAGATGTTTAAATTAAAAAATAAAAAAAATTAGTATCTCAA
Found at i:28181907 original size:42 final size:42
Alignment explanation
Indices: 28181848--28182106 Score: 254
Period size: 42 Copynumber: 6.1 Consensus size: 42
28181838 ATAATTTTTT
* * * *
28181848 TAAAGGTTATG-TTTTTAGCGGCGTTTTTGCAAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGAA-AAGCGCCGC
* * ** *
28181890 TAAAGGT-TTGTTCTTTAGCGGCGTTTGTAATAAAAGCGCCTC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGT-GGAAAAGCGCCGC
* * *
28181932 TAAAGGTCATGATCTTTAGCGGCGATTGTGGGAGAAGCGCCAC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGT-GGAAAAGCGCCGC
* * * * * *
28181975 TAAAGATCGTGGTCTATAGCGGCGTTTGTGGGAAAGCACCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAGCGCCGC
* *
28182017 TAAAGGTCGTGGTCTTTAGCGGCGTTTGTGCG-AAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTG-GAAAAGCGCCGC
* *
28182059 TAAAGGTCATGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGG
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGG-AAAAGCGCCGC
28182102 TAAAG
1 TAAAG
28182107 TTAGCGACGC
Statistics
Matches: 181, Mismatches: 30, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
41 3 0.02
42 110 0.61
43 68 0.38
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (42 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAGCGCCGC
Found at i:28182096 original size:85 final size:86
Alignment explanation
Indices: 28181848--28182106 Score: 294
Period size: 85 Copynumber: 3.1 Consensus size: 86
28181838 ATAATTTTTT
* * * * * * *
28181848 TAAAGGTTATG-TTTTTAGCGGCGTTTTTGCAAGAAGCGCCGCTAAAGGT-TTGTTCTTTAGCGG
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGCGAGAAGCGCCGCTAAAGGTCATGATCTATAGCGG
* *
28181911 CGTTTGT-AATAAAAGCGCCTC
66 CGTTTGTGGA-AAAAGCGCCGC
* * * * * *
28181932 TAAAGGTCATGATCTTTAGCGGCGATTGTGGGAGAAGCGCCACTAAAGATCGTGGTCTATAGCGG
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGCGAGAAGCGCCGCTAAAGGTCATGATCTATAGCGG
* *
28181997 CGTTTGTGG-GAAAGCACCGC
66 CGTTTGTGGAAAAAGCGCCGC
* *
28182017 TAAAGGTCGTGGTCTTTAGCGGCGTTTGTGCGA-AAGCGCCGCTAAAGGTCATGATCTATAGCGG
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGCGAGAAGCGCCGCTAAAGGTCATGATCTATAGCGG
*
28182081 CGTTTGTGGAAAAAGCGCCGG
66 CGTTTGTGGAAAAAGCGCCGC
28182102 TAAAG
1 TAAAG
28182107 TTAGCGACGC
Statistics
Matches: 145, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
84 46 0.32
85 81 0.56
86 18 0.12
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (86 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGCGAGAAGCGCCGCTAAAGGTCATGATCTATAGCGG
CGTTTGTGGAAAAAGCGCCGC
Found at i:28182106 original size:127 final size:128
Alignment explanation
Indices: 28181863--28182099 Score: 325
Period size: 127 Copynumber: 1.9 Consensus size: 128
28181853 GTTATGTTTT
* * * * *
28181863 TAGCGGCGTTTTTGCAAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTGTAATAAAAGCG
1 TAGCGGCGTTTGTGCAAGAAGCACCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTAACAAAAGCG
* * * *
28181928 CCTCTAAAGGTCATGATCTTTAGCGGCGATTGTGGGAGAAGCGCCACTAAAGATCGTGGTCTA
66 CCGCTAAAGGTCATGATCTATAGCGGCGATTGTGGAAAAAGCGCCACTAAAGATCGTGGTCTA
** * *
28181991 TAGCGGCGTTTGTGGGA-AAGCACCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGT-GCGAAAGC
1 TAGCGGCGTTTGTGCAAGAAGCACCGCTAAAGGT-GTGGTCTTTAGCGGCGTTTGTAACAAAAGC
*
28182054 GCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGAAAAAGCGCC
65 GCCGCTAAAGGTCATGATCTATAGCGGCGATTGTGGAAAAAGCGCC
28182100 GGTAAAGTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
127 61 0.65
128 33 0.35
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (128 bp):
TAGCGGCGTTTGTGCAAGAAGCACCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTAACAAAAGCG
CCGCTAAAGGTCATGATCTATAGCGGCGATTGTGGAAAAAGCGCCACTAAAGATCGTGGTCTA
Found at i:28182182 original size:22 final size:22
Alignment explanation
Indices: 28182154--28182196 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28182144 TAGTGGCGCT
*
28182154 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
28182176 AAAAAGCGCTGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
28182197 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:28182359 original size:28 final size:28
Alignment explanation
Indices: 28182316--28182371 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28182306 ATTTTTTTTA
* *
28182316 TTTATAATGTACATATACATACATACAT
1 TTTATAATATACATATACACACATACAT
* *
28182344 TTTATAATATATATATACACATATACAT
1 TTTATAATATACATATACACACATACAT
28182372 GTACATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (28 bp):
TTTATAATATACATATACACACATACAT
Found at i:28182458 original size:16 final size:19
Alignment explanation
Indices: 28182437--28182481 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
28182427 CTTGTATTTC
28182437 TTTATATACG-T-TATA-A
1 TTTATATACGCTATATATA
*
28182453 TTTATACACGCCTATATATA
1 TTTATATACG-CTATATATA
28182473 TTTATATAC
1 TTTATATAC
28182482 ATAGTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 1 0.04
19 4 0.17
20 9 0.39
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTATATACGCTATATATA
Found at i:28182626 original size:29 final size:29
Alignment explanation
Indices: 28182578--28182721 Score: 182
Period size: 30 Copynumber: 4.9 Consensus size: 29
28182568 AAAAAAATAA
* *
28182578 AAATTATATTTT-AGCCCCTAAACTTTTTG
1 AAATTACATTTTGA-CCCCTAAATTTTTTG
* *
28182607 AAATTACATTTTGACACCTAAATTTTTCTA
1 AAATTACATTTTGACCCCTAAATTTTT-TG
* *
28182637 AAATTATATTTTGACCCCTAAAATTTTTG
1 AAATTACATTTTGACCCCTAAATTTTTTG
*
28182666 AAATTACATTTTGACCCATAAAATTTTTTG
1 AAATTACATTTTGACCCCT-AAATTTTTTG
*
28182696 AAATTACATTATGACCCCTAAATTTT
1 AAATTACATTTTGACCCCTAAATTTT
28182722 CTCAAAATTA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
29 47 0.47
30 52 0.53
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAATTTTTTG
Found at i:28182645 original size:59 final size:59
Alignment explanation
Indices: 28182577--28182721 Score: 199
Period size: 59 Copynumber: 2.5 Consensus size: 59
28182567 AAAAAAAATA
*
28182577 AAAATTATATTTT-AGCCCCTAAACTTTTTGAAATTACATTTTGACACC-T-AAATTTTTCT
1 AAAATTATATTTTGA-CCCCTAAAATTTTTGAAATTACATTTTGAC-CCATAAAATTTTT-T
28182636 AAAATTATATTTTGACCCCTAAAATTTTTGAAATTACATTTTGACCCATAAAATTTTTT
1 AAAATTATATTTTGACCCCTAAAATTTTTGAAATTACATTTTGACCCATAAAATTTTTT
* * *
28182695 GAAATTACATTATGACCCCT-AAATTTT
1 AAAATTATATTTTGACCCCTAAAATTTT
28182722 CTCAAAATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
58 9 0.11
59 61 0.77
60 9 0.11
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (59 bp):
AAAATTATATTTTGACCCCTAAAATTTTTGAAATTACATTTTGACCCATAAAATTTTTT
Found at i:28182953 original size:14 final size:15
Alignment explanation
Indices: 28182934--28182965 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
28182924 AGGCCCCGAA
28182934 TCAAAAAAAA-AGTT
1 TCAAAAAAAAGAGTT
28182948 TCAAAAAAAAGAGTT
1 TCAAAAAAAAGAGTT
28182963 TCA
1 TCA
28182966 GCAGCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.22
Consensus pattern (15 bp):
TCAAAAAAAAGAGTT
Found at i:28182954 original size:15 final size:15
Alignment explanation
Indices: 28182936--28182965 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28182926 GCCCCGAATC
28182936 AAAAAAAAAGTTTCA
1 AAAAAAAAAGTTTCA
*
28182951 AAAAAAAGAGTTTCA
1 AAAAAAAAAGTTTCA
28182966 GCAGCAAAAG
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:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (15 bp):
AAAAAAAAAGTTTCA
Found at i:28183111 original size:20 final size:22
Alignment explanation
Indices: 28183082--28183125 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
28183072 GAAGAAGAAG
28183082 AAGAAGAAGAAAGAAA-GAAAA
1 AAGAAGAAGAAAGAAAGGAAAA
28183103 AAGAA-AAGAAAGAAAGGAAAA
1 AAGAAGAAGAAAGAAAGGAAAA
28183124 AA
1 AA
28183126 ATTATTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAAGAAAGGAAAA
Found at i:28183191 original size:16 final size:16
Alignment explanation
Indices: 28183150--28183197 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
28183140 TCGGGTCAGA
28183150 CCGACCCGACCCACGAAT
1 CCGACCCGA-CC-CGAAT
*
28183168 CGCGACCCGACCCGGAT
1 C-CGACCCGACCCGAAT
28183185 CCGACCCGACCCG
1 CCGACCCGACCCG
28183198 CAACAGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 5 0.18
18 3 0.11
19 8 0.29
ACGTcount: A:0.21, C:0.52, G:0.23, T:0.04
Consensus pattern (16 bp):
CCGACCCGACCCGAAT
Found at i:28183361 original size:24 final size:24
Alignment explanation
Indices: 28183333--28183378 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28183323 ACAGCAAGTG
28183333 CAGGCCCAGTGCAGCAGCAGGCTC
1 CAGGCCCAGTGCAGCAGCAGGCTC
*
28183357 CAGGCCTAGTGCAGCAGCAGGC
1 CAGGCCCAGTGCAGCAGCAGGC
28183379 CAACCCAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.35, T:0.09
Consensus pattern (24 bp):
CAGGCCCAGTGCAGCAGCAGGCTC
Found at i:28183453 original size:34 final size:33
Alignment explanation
Indices: 28183384--28183454 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
28183374 CAGGCCAACC
*
28183384 CAGCAGGCCCACAACGCCAGGCCCAAATCGCCAG
1 CAGCAGGCCAACAACGCCAGGCCCAAA-CGCCAG
* *
28183418 CAGCAGGCCTAACAGCGCCCAGGCCCAAA-GGCAG
1 CAGCAGGCC-AACAACG-CCAGGCCCAAACGCCAG
28183452 CAG
1 CAG
28183455 GCCAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 16 0.50
35 5 0.16
36 11 0.34
ACGTcount: A:0.30, C:0.41, G:0.27, T:0.03
Consensus pattern (33 bp):
CAGCAGGCCAACAACGCCAGGCCCAAACGCCAG
Found at i:28183481 original size:17 final size:16
Alignment explanation
Indices: 28183459--28183498 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
28183449 CAGCAGGCCA
28183459 AAAAAAGAGAAAAAAAG
1 AAAAAAGA-AAAAAAAG
28183476 AAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
*
28183492 GAAAAAG
1 AAAAAAG
28183499 CCCGAGTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:28183484 original size:15 final size:16
Alignment explanation
Indices: 28183460--28183489 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28183450 AGCAGGCCAA
28183460 AAAAAGAGAAAAAAAG
1 AAAAAGAGAAAAAAAG
28183476 AAAAA-AGAAAAAAA
1 AAAAAGAGAAAAAAA
28183490 AGGAAAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAAAAG
Found at i:28183496 original size:8 final size:9
Alignment explanation
Indices: 28183459--28183497 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
28183449 CAGCAGGCCA
28183459 AAAAAAGAG
1 AAAAAAGAG
28183468 AAAAAA-AG
1 AAAAAAGAG
*
28183476 AAAAAAGAA
1 AAAAAAGAG
28183485 AAAAAAG-G
1 AAAAAAGAG
28183493 AAAAA
1 AAAAA
28183498 GCCCGAGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:28183670 original size:32 final size:34
Alignment explanation
Indices: 28183620--28183682 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
28183610 ATATTCTTGT
*
28183620 TTTTTTTAAAGCATTTTTTTAT-TTCGTATTAGG
1 TTTTTTTAAAGCATTTTTTTATAGTCGTATTAGG
28183653 TTTTTTTAAAGCA-TTTTTTATAGTCGTATT
1 TTTTTTTAAAGCATTTTTTTATAGTCGTATT
28183683 TAATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.60
Consensus pattern (34 bp):
TTTTTTTAAAGCATTTTTTTATAGTCGTATTAGG
Found at i:28183695 original size:34 final size:33
Alignment explanation
Indices: 28183620--28183695 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
28183610 ATATTCTTGT
* *
28183620 TTTTTTTAAAGCATTTTTTTATTTCGTATTAGG
1 TTTTTTTAAAGCATTTTTTTATGTCGTATTAGA
28183653 TTTTTTTAAAGCA-TTTTTTATAGTCGTATTTA-A
1 TTTTTTTAAAGCATTTTTTTAT-GTCGTA-TTAGA
28183686 TTTTATTTAA
1 TTTT-TTTAA
28183696 TTTCATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 8 0.21
33 22 0.58
34 8 0.21
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (33 bp):
TTTTTTTAAAGCATTTTTTTATGTCGTATTAGA
Found at i:28183853 original size:18 final size:18
Alignment explanation
Indices: 28183832--28183940 Score: 69
Period size: 17 Copynumber: 5.7 Consensus size: 18
28183822 TGAAACACTT
28183832 AAAAATTCTCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
*
28183849 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
28183867 AAAAAATAATTTTCGTGTTTTC
1 ---AAA-AATTCTCGTGTTTTC
*
28183889 AAAAAAAAATTTCTCGTCTTTT-
1 ----AAAAA-TTCTCGTGTTTTC
* *
28183911 AAAGATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
28183929 AAAAATTTTCGT
1 AAAAATTCTCGT
28183941 ATTTCTAAGA
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
17 22 0.29
18 19 0.25
21 3 0.04
22 17 0.22
23 16 0.21
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:28183905 original size:23 final size:22
Alignment explanation
Indices: 28183849--28183933 Score: 99
Period size: 22 Copynumber: 4.0 Consensus size: 22
28183839 CTCGTGTTTC
28183849 AAAAATTTTCGTGTTTTCAAAA
1 AAAAATTTTCGTGTTTTCAAAA
*
28183871 AATAATTTTCGTGTTTTCAAAA
1 AAAAATTTTCGTGTTTTCAAAA
*
28183893 AAAAATTTCTCGTCTTTT-----
1 AAAAATTT-TCGTGTTTTCAAAA
*
28183911 AAAGATTTTCGTGTTTTCAAAA
1 AAAAATTTTCGTGTTTTCAAAA
28183933 A
1 A
28183934 TTTTCGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
17 8 0.15
18 7 0.13
22 29 0.56
23 8 0.15
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (22 bp):
AAAAATTTTCGTGTTTTCAAAA
Found at i:28183945 original size:17 final size:17
Alignment explanation
Indices: 28183893--28183968 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
28183883 GTTTTCAAAA
* *
28183893 AAAAATTTCTCGTCTTTT
1 AAAAATTT-TCGTATTTC
* *
28183911 AAAGATTTTCGTGTTTTC
1 AAAAATTTTCGT-ATTTC
28183929 AAAAATTTTCGTATTTC
1 AAAAATTTTCGTATTTC
* *
28183946 TAAGATTCTT-GTATTTCC
1 AAAAATT-TTCGTATTT-C
28183964 AAAAA
1 AAAAA
28183969 AAAATGTCCG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 19 0.41
18 27 0.59
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (17 bp):
AAAAATTTTCGTATTTC
Found at i:28183967 original size:35 final size:36
Alignment explanation
Indices: 28183893--28183968 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 36
28183883 GTTTTCAAAA
* * *
28183893 AAAAATTTCTCGTCTTTTAAAGATTTTCGTGTTTTC
1 AAAAATTTCTCGTATTTTAAAGATTTTCGTATTTCC
28183929 AAAAATTT-TCGTATTTCT-AAGATTCTT-GTATTTCC
1 AAAAATTTCTCGTATTT-TAAAGATT-TTCGTATTTCC
28183964 AAAAA
1 AAAAA
28183969 AAAATGTCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 24 0.69
36 11 0.31
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (36 bp):
AAAAATTTCTCGTATTTTAAAGATTTTCGTATTTCC
Found at i:28187549 original size:129 final size:129
Alignment explanation
Indices: 28187383--28187631 Score: 383
Period size: 129 Copynumber: 1.9 Consensus size: 129
28187373 ACTCCACTGT
* * **
28187383 AACTTCAGGGAGATAATACTGGATGTGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTA
1 AACTTCAGGGAGATAAAACTGAATACGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGT-
*
28187448 G-TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTGTTCCATTGC
65 GTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGTTCCATTGC
* * *
28187512 AACTTCTGGGAGATAAAACTGAATACGATCTGTTCTACTGTAACTTTAGAGAGATAAGATCTGTG
1 AACTTCAGGGAGATAAAACTGAATACGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTG
* * *
28187577 TTTTTAATTCGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTG
66 TTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTG
28187632 ATTAACTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 107 0.99
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (129 bp):
AACTTCAGGGAGATAAAACTGAATACGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTG
TTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGTTCCATTGC
Found at i:28187703 original size:50 final size:50
Alignment explanation
Indices: 28187648--28187929 Score: 240
Period size: 50 Copynumber: 5.6 Consensus size: 50
28187638 TACAATGTCG
* *
28187648 AGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * * * ** **
28187698 AGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGTAATGTTA
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * ** *
28187748 GGGAAGCAAGATTCGTTGTTGTAGCTTCAATCTGTTCCACTGCACCACCA
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* *** * ** * ** * *
28187798 AGGAAGTAAGATTCACCGTTACGGCTTCAATCTTTTTAATTGCAATGTCG
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
28187848 GGGAAGCAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCA
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * **
28187898 AGGAAGTAAGATTCACCATTACAGCTTCAATC
1 AGGAAGTAAGATTCGCCGTTGTAGCTTCAATC
28187930 ATTTCACTGT
Statistics
Matches: 172, Mismatches: 60, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
50 172 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (50 bp):
AGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
Found at i:28187817 original size:100 final size:100
Alignment explanation
Indices: 28187640--28187935 Score: 423
Period size: 100 Copynumber: 3.0 Consensus size: 100
28187630 TGATTAACTA
* *
28187640 CAATGTC-GAGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAG
1 CAATGTCAG-GGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAG
* **
28187704 TAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTG
65 TAAGATTCACCGTTACGGCTTCAATCTTTTCAATTG
* * * *
28187740 TAATGTTAGGGAAGCAAGATTCGTTGTTGTAGCTTCAATCTGTTCCACTGCACCACCAAGGAAGT
1 CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
*
28187805 AAGATTCACCGTTACGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTACGGCTTCAATCTTTTCAATTG
* * **
28187840 CAATGTCGGGGAAGCAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
1 CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
* * *
28187905 AAGATTCACCATTACAGCTTCAATCATTTCA
66 AAGATTCACCGTTACGGCTTCAATCTTTTCA
28187936 CTGTAATGCC
Statistics
Matches: 173, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
100 172 0.99
101 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
CAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
AAGATTCACCGTTACGGCTTCAATCTTTTCAATTG
Found at i:28188192 original size:45 final size:45
Alignment explanation
Indices: 28188134--28188569 Score: 340
Period size: 45 Copynumber: 9.8 Consensus size: 45
28188124 TTCTGATCTA
* *
28188134 CTTCACTGCCAGTACAGAAAGGCAATG-TCTGCTATCTTCAGTCTG
1 CTTCGCTGTCAGTACAGAAAGGCAA-GATCTGCTATCTTCAGTCTG
* * * * * * *
28188179 CTCCACTGTCAGTATAGGAAGGCAAGGT-TGGTGTCTTC-GATCTG
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAG-TCTG
* *
28188223 CTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTTTG
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAGTCTG
* * * * * * *
28188268 CTCCGCTGTCAGTACAGGAATGCAAG-GCTGGTGTCTTC-GATCTA
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAG-TCTG
* * * *
28188312 CTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCCG
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAGTCTG
* * * * * *
28188357 TTTCGCTGTCAATACAGAAAGGTAAG-GCT-CGTGTCTTC-GATCTA
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGC-TATCTTCAG-TCTG
* * *
28188401 CTTCGCTGTCAGTACAGAAAGACAAGATATGCTATCTTTAGTCTG
1 CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAGTCTG
* *
28188446 CTTCGCTGTCAGTACA-AGAAGGTAAGATCTGCTATCTTCAGCCTG
1 CTTCGCTGTCAGTACAGA-AAGGCAAGATCTGCTATCTTCAGTCTG
* * * * *
28188491 CTTCGCTGTCAGTACA-AGAAGACAAG-GCTGGTGTCTTC-GATCTA
1 CTTCGCTGTCAGTACAGA-AAGGCAAGATCTGCTATCTTCAG-TCTG
**
28188535 CTTTACTGTCAGTACATG-AAGGCAAGATCTGCTAT
1 CTTCGCTGTCAGTACA-GAAAGGCAAGATCTGCTAT
28188570 TTTTAGTTTA
Statistics
Matches: 309, Mismatches: 65, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
43 4 0.01
44 136 0.44
45 165 0.53
46 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (45 bp):
CTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAGTCTG
Found at i:28188245 original size:89 final size:89
Alignment explanation
Indices: 28188123--28188516 Score: 450
Period size: 89 Copynumber: 4.4 Consensus size: 89
28188113 AAGGCTACTG
* * * *
28188123 CTTCTGATCTACTTCACTGCCAGTACAGAAAGGCAATG-TCTGCTATCTTCAGTCTGCTCCACTG
1 CTTC-GATCTACTTCGCTGTCAGTACAGGAAGGCAA-GATCTGCTATCTTCAGTCTGCTCCGCTG
* *
28188187 TCAGTATAGGAAGGCAAGGTTGGTGT
64 TCAGTACAGGAAGGCAAGGCTGGTGT
* *
28188213 CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTTTGCTCCGCTGTC
1 CTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
*
28188278 AGTACAGGAATGCAAGGCTGGTGT
66 AGTACAGGAAGGCAAGGCTGGTGT
* * * * *
28188302 CTTCGATCTACTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCCGTTTCGCTGTC
1 CTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
* * * *
28188367 AATACAGAAAGGTAAGGCTCGTGT
66 AGTACAGGAAGGCAAGGCTGGTGT
* * * * *
28188391 CTTCGATCTACTTCGCTGTCAGTACAGAAAGACAAGATATGCTATCTTTAGTCTGCTTCGCTGTC
1 CTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
* * * * *
28188456 AGTACAAGAAGGTAAGATCTGCTAT
66 AGTACAGGAAGGCAAG-GCTGGTGT
* * * *
28188481 CTTC-AGCCTGCTTCGCTGTCAGTACAAGAAGACAAG
1 CTTCGA-TCTACTTCGCTGTCAGTACAGGAAGGCAAG
28188517 GCTGGTGTCT
Statistics
Matches: 261, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
88 1 0.00
89 222 0.85
90 38 0.15
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (89 bp):
CTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
AGTACAGGAAGGCAAGGCTGGTGT
Found at i:28188460 original size:134 final size:134
Alignment explanation
Indices: 28188312--28188576 Score: 356
Period size: 134 Copynumber: 2.0 Consensus size: 134
28188302 CTTCGATCTA
* * *
28188312 CTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCC-GTTTCGCTGTCAATAC-AGA
1 CTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAG-CCTGCTTCGCTGTCAATACAAG-
** *
28188375 AAGGTAAGGCTCGTGTCTTCGATCTACTTCGCTGTCAGTACA-GAAAGACAAGATATGCTATCTT
64 AAGACAAGGCTCGTGTCTTCGATCTACTTCACTGTCAGTACATG-AAGACAAGATATGCTATCTT
28188439 TAGTCTG
128 TAGTCTG
* * *
28188446 CTTCGCTGTCAGTACAAGAAGGTAAGATCTGCTATCTTCAGCCTGCTTCGCTGTCAGTACAAGAA
1 CTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAGCCTGCTTCGCTGTCAATACAAGAA
* * * * *
28188511 GACAAGGCTGGTGTCTTCGATCTACTTTACTGTCAGTACATGAAGGCAAGATCTGCTATTTTTAG
66 GACAAGGCTCGTGTCTTCGATCTACTTCACTGTCAGTACATGAAGACAAGATATGCTATCTTTAG
28188576 T
131 T
28188577 TTACTCCGCT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
133 2 0.02
134 109 0.96
135 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (134 bp):
CTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAGCCTGCTTCGCTGTCAATACAAGAA
GACAAGGCTCGTGTCTTCGATCTACTTCACTGTCAGTACATGAAGACAAGATATGCTATCTTTAG
TCTG
Found at i:28197844 original size:16 final size:16
Alignment explanation
Indices: 28197819--28197855 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28197809 AAATAAAAAT
28197819 AAAATTACATT-ATAA
1 AAAATTACATTAATAA
28197834 AAAAGTTACATTAATAA
1 AAAA-TTACATTAATAA
28197851 AAAAT
1 AAAAT
28197856 CACAAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:28197990 original size:105 final size:104
Alignment explanation
Indices: 28197817--28198166 Score: 349
Period size: 105 Copynumber: 3.5 Consensus size: 104
28197807 TCAAATAAAA
** * * *
28197817 ATAAAATTACATTATAAAAAAGTTACATTAATAAAAAATCACAAAA-CACTAAACTAAACACTAA
1 ATAAAATTATTTTAAAAAAAATTTACATTACTAAAAAATCACAAAACCACTAAACTAAACACTAA
*
28197881 CAATTTATATAACCTAATCATTAATTACTAACAAAAAAACT
66 CAATTTATA-AA-CTAATCATAAATTACTAACAAAAAAACT
28197922 ATAAAATTATTTTAAAAAAAATTTACATTACTAAAAAATCACAAAACCA-TAAACTAAACACTAA
1 ATAAAATTATTTTAAAAAAAATTTACATTACTAAAAAATCACAAAACCACTAAACTAAACACTAA
*
28197986 CAATTTATAAACTAATCATAAATTACTAACAAAATAACT
66 CAATTTATAAACTAATCATAAATTACTAACAAAAAAACT
* ** * *
28198025 ATAACA-T-TTAAAAAAAAGAATTTACATTACT-----AT---TAAATCAC---A--AAACACTA
1 ATAAAATTATTTTAAAAAA-AATTTACATTACTAAAAAATCACAAAACCACTAAACTAAACACTA
* * * *
28198075 ACAATTTGTAAACTAATTATAAATTACTAACGAAATAACT
65 ACAATTTATAAACTAATCATAAATTACTAACAAAAAAACT
* *** * *
28198115 ATAAAAATATTTTTTTAATATTTTACATTACTAAAAAATCACAAAA-CACTAA
1 ATAAAATTATTTTAAAAAAAATTTACATTACTAAAAAATCACAAAACCACTAA
28198167 CATAAATTAC
Statistics
Matches: 205, Mismatches: 24, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
90 50 0.24
91 13 0.06
92 5 0.02
94 5 0.02
96 2 0.01
97 2 0.01
98 3 0.01
99 3 0.01
101 8 0.04
102 14 0.07
103 31 0.15
104 2 0.01
105 65 0.32
106 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.29
Consensus pattern (104 bp):
ATAAAATTATTTTAAAAAAAATTTACATTACTAAAAAATCACAAAACCACTAAACTAAACACTAA
CAATTTATAAACTAATCATAAATTACTAACAAAAAAACT
Found at i:28198604 original size:45 final size:44
Alignment explanation
Indices: 28198523--28198613 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
28198513 ACCTCTATTC
*
28198523 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
28198567 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
28198612 CA
1 CA
28198614 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:28198613 original size:16 final size:16
Alignment explanation
Indices: 28198592--28198629 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28198582 TTGATTTGCT
*
28198592 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
28198608 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28198624 AATACA
1 ATTACA
28198630 GCGAACCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28211960 original size:20 final size:18
Alignment explanation
Indices: 28211929--28211979 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28211919 AGAAGTTTTG
28211929 ATTTTTTT-AATTTAATA
1 ATTTTTTTGAATTTAATA
* *
28211946 GTTCTTTTATGAATTTTATA
1 ATT-TTTT-TGAATTTAATA
28211966 ATTTTTTTGAATTT
1 ATTTTTTTGAATTT
28211980 TTATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 5 0.18
20 10 0.36
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (18 bp):
ATTTTTTTGAATTTAATA
Found at i:28211988 original size:7 final size:7
Alignment explanation
Indices: 28211978--28212007 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28211968 TTTTTTGAAT
28211978 TTTTATA
1 TTTTATA
28211985 TTTTATA
1 TTTTATA
28211992 TTTTATA
1 TTTTATA
28211999 TTTT-TA
1 TTTTATA
28212005 TTT
1 TTT
28212008 GACATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATA
Found at i:28212735 original size:22 final size:19
Alignment explanation
Indices: 28212717--28212755 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
28212707 TTTTCTTTAT
28212717 ATTTTGTTTCTTCTTTCTTTG
1 ATTTTGTTTC--CTTTCTTTG
28212738 ATTTTGTTTCCTTTCTTT
1 ATTTTGTTTCCTTTCTTT
28212756 CAGCCTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (19 bp):
ATTTTGTTTCCTTTCTTTG
Found at i:28212854 original size:24 final size:25
Alignment explanation
Indices: 28212810--28212856 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
28212800 CATTTTGCAT
**
28212810 TTTTTTGTGTTGTTATTGGTGTGAA
1 TTTTTTGTGTTGTTAAGGGTGTGAA
28212835 TTTTTTG-GTTGTTAAGGGTGTG
1 TTTTTTGTGTTGTTAAGGGTGTG
28212857 GTGAGGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (25 bp):
TTTTTTGTGTTGTTAAGGGTGTGAA
Found at i:28216291 original size:19 final size:19
Alignment explanation
Indices: 28216256--28216298 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28216246 AATATGAAAT
**
28216256 ATATATATATATTTACAAA
1 ATATATATATAAGTACAAA
*
28216275 ATATATATATAAGTACAAT
1 ATATATATATAAGTACAAA
28216294 ATATA
1 ATATA
28216299 AGAAAATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATATATATAAGTACAAA
Found at i:28216977 original size:26 final size:26
Alignment explanation
Indices: 28216948--28217025 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 26
28216938 ATAATGCATA
28216948 TATATATATTATAAAAACAATGCGTG
1 TATATATATTATAAAAACAATGCGTG
* * *
28216974 TATA-CTA-TAT-AAAA-AATGCATATA
1 TATATATATTATAAAAACAATGC--GTG
28216998 TATATATATTATAAAAAACAATGCGTG
1 TATATATATTAT-AAAAACAATGCGTG
28217025 T
1 T
28217026 GTACGAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
22 5 0.13
23 4 0.10
24 8 0.21
25 4 0.10
26 7 0.18
27 2 0.05
28 4 0.10
29 5 0.13
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.35
Consensus pattern (26 bp):
TATATATATTATAAAAACAATGCGTG
Found at i:28216999 original size:22 final size:22
Alignment explanation
Indices: 28216947--28217005 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
28216937 TATAATGCAT
28216947 ATATATATATTATAAAAACAATGC
1 ATATATATA-TAT-AAAACAATGC
* *
28216971 GTGTATACTATATAAAA-AATGC
1 ATATATA-TATATAAAACAATGC
28216993 ATATATATATATA
1 ATATATATATATA
28217006 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.20
22 10 0.33
23 4 0.13
24 8 0.27
25 2 0.07
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
ATATATATATATAAAACAATGC
Found at i:28217047 original size:3 final size:3
Alignment explanation
Indices: 28217039--28217120 Score: 57
Period size: 3 Copynumber: 28.3 Consensus size: 3
28217029 CGAATATAGA
* **
28217039 AAT AAT AAT AAT AAT GAT AAT AAAT AAT -AT AAT AAT AAAT AAT GGT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT
* * *
28217085 -AT AAT GAT AAT AA- CAT AA- AAA AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28217121 GCTAAAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
2 8 0.13
3 48 0.77
4 6 0.10
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28219084 original size:33 final size:33
Alignment explanation
Indices: 28219047--28219112 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
28219037 GGTGACAGGG
28219047 TTTGCACGTACATGTAAAATAAACAATTTTATA
1 TTTGCACGTACATGTAAAATAAACAATTTTATA
* *
28219080 TTTGCATGTACGTGTAAAATAAACAATTTTATA
1 TTTGCACGTACATGTAAAATAAACAATTTTATA
28219113 AAACAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (33 bp):
TTTGCACGTACATGTAAAATAAACAATTTTATA
Found at i:28223096 original size:11 final size:11
Alignment explanation
Indices: 28223080--28223152 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
28223070 TTAGATAGAA
28223080 ATTAAATTAAT
1 ATTAAATTAAT
28223091 ATTAAATTAAT
1 ATTAAATTAAT
*
28223102 A-T--ATTATT
1 ATTAAATTAAT
* *
28223110 ATCTAGATAAAT
1 AT-TAAATTAAT
28223122 ATTAAATTAA-
1 ATTAAATTAAT
28223132 ATTTAATATTAA-
1 A-TTAA-ATTAAT
28223144 ATT-AATTAA
1 ATTAAATTAA
28223153 AAAATATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.12
9 5 0.10
10 4 0.08
11 24 0.47
12 12 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
ATTAAATTAAT
Found at i:28223180 original size:14 final size:14
Alignment explanation
Indices: 28223142--28223184 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
28223132 ATTTAATATT
*
28223142 AAATTAA-TTAAAA
1 AAATTAATTTGAAA
28223155 AATATTATATTTGAAA
1 AA-ATTA-ATTTGAAA
28223171 AAATTAATTTGAAA
1 AAATTAATTTGAAA
28223185 TTAAATTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 12 0.46
15 5 0.19
16 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
AAATTAATTTGAAA
Found at i:28229469 original size:19 final size:18
Alignment explanation
Indices: 28229400--28229472 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
28229390 CAACCAAAAA
* *
28229400 TTTGCTTCTATTGATGTT
1 TTTGTTTCTATTGAAGTT
*
28229418 TTGTGTTTCTATTTAAGTCT
1 TT-TGTTTCTATTGAAGT-T
*
28229438 TTTGTTT-GAGTTGAAGTT
1 TTTGTTTCTA-TTGAAGTT
*
28229456 TTTGCTTTCTGTTGAAG
1 TTTG-TTTCTATTGAAG
28229473 AGAAGAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 8 0.19
19 32 0.74
20 3 0.07
ACGTcount: A:0.14, C:0.08, G:0.21, T:0.58
Consensus pattern (18 bp):
TTTGTTTCTATTGAAGTT
Found at i:28232602 original size:2 final size:2
Alignment explanation
Indices: 28232595--28232619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28232585 CATCATATGT
28232595 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28232620 TTACTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28236050 original size:17 final size:17
Alignment explanation
Indices: 28236030--28236064 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28236020 CTTTTTTTCC
**
28236030 TTTTATTTGTTTTATTA
1 TTTTATTTACTTTATTA
28236047 TTTTATTTACTTTATTA
1 TTTTATTTACTTTATTA
28236064 T
1 T
28236065 AATTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTTACTTTATTA
Found at i:28246696 original size:26 final size:26
Alignment explanation
Indices: 28246667--28246736 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
28246657 CCATACGAGT
* *
28246667 ATGTAATCAGGAAGCTCTTTTGAACC
1 ATGTAATCGGGAAGCTCTTGTGAACC
* *
28246693 ATGTAA-CGGGAAGCTCATGTGAGCC
1 ATGTAATCGGGAAGCTCTTGTGAACC
*
28246718 ATATAAT-GGGAAGCTCTTG
1 ATGTAATCGGGAAGCTCTTG
28246737 CAAGCCAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 31 0.84
26 6 0.16
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (26 bp):
ATGTAATCGGGAAGCTCTTGTGAACC
Found at i:28246742 original size:25 final size:25
Alignment explanation
Indices: 28246691--28246847 Score: 94
Period size: 25 Copynumber: 6.3 Consensus size: 25
28246681 CTCTTTTGAA
* * **
28246691 CCATGTAACGGGAAGCTCATGTGAG
1 CCATATAATGGGAAGCTCATGCAAG
*
28246716 CCATATAATGGGAAGCTCTTGCAAG
1 CCATATAATGGGAAGCTCATGCAAG
* * *
28246741 CCA-ATTATTGGGAAGCTCATACGAG
1 CCATA-TAATGGGAAGCTCATGCAAG
* * * *
28246766 CCATA-AACGGGAATCTCAAGAAAG
1 CCATATAATGGGAAGCTCATGCAAG
*
28246790 CCAT-TAATTGGGAAGGTCATG-AGAG
1 CCATATAA-TGGGAAGCTCATGCA-AG
28246815 CC-TA-ATATCGGGAAGCTCATG-AGAG
1 CCATATA-AT-GGGAAGCTCATGCA-AG
28246840 CCATATAA
1 CCATATAA
28246848 CAGGATGCTC
Statistics
Matches: 101, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
24 23 0.23
25 73 0.72
26 4 0.04
27 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (25 bp):
CCATATAATGGGAAGCTCATGCAAG
Found at i:28246857 original size:25 final size:25
Alignment explanation
Indices: 28246800--28246882 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
28246790 CCATTAATTG
* * *
28246800 GGAAGGTCATGAGAGCCTAATATCG
1 GGAAGCTCATGAGAGCCTAATAACA
28246825 GGAAGCTCATGAGAGCC-ATATAACA
1 GGAAGCTCATGAGAGCCTA-ATAACA
* * *
28246850 GGATGCTCATAAGAG-CTAAATAACG
1 GGAAGCTCATGAGAGCCT-AATAACA
*
28246875 GGACGCTC
1 GGAAGCTC
28246883 TTGCAAGTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 2 0.04
25 45 0.94
26 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCTAATAACA
Found at i:28248324 original size:28 final size:24
Alignment explanation
Indices: 28248262--28248329 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 24
28248252 TGCAGGGTTT
28248262 TTTACTAAAATAGGGTAAAAAAAA
1 TTTACTAAAATAGGGTAAAAAAAA
28248286 TTGTACTAAAATAGGATGTCAAAAAAATA
1 TT-TACTAAAATAGG--GT-AAAAAAA-A
*
28248315 TTTACCAAAAT-GGGT
1 TTTACTAAAATAGGGT
28248330 TACTTTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 2 0.05
25 14 0.37
27 4 0.11
28 15 0.39
29 3 0.08
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (24 bp):
TTTACTAAAATAGGGTAAAAAAAA
Found at i:28248524 original size:27 final size:27
Alignment explanation
Indices: 28248494--28248558 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
28248484 CCTATCAGGT
28248494 AGGCGCCAATGAATGTGCCTCAT-AGAG
1 AGGCGCCAATGAATGTGCCTCATAAG-G
28248521 AGGCGCCAATGAATGTGCCTCATAAGG
1 AGGCGCCAATGAATGTGCCTCATAAGG
28248548 AGGCGCCAATG
1 AGGCGCCAATG
28248559 GTGGCCTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTCATAAGG
Found at i:28248709 original size:14 final size:13
Alignment explanation
Indices: 28248680--28248719 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
28248670 AGAAAAAAAA
*
28248680 AAGAGAGAAAGGAG
1 AAGA-AGAAAGAAG
28248694 AAGAAGAGAAGAAG
1 AAGAAGA-AAGAAG
28248708 AAGAAGAAAGAA
1 AAGAAGAAAGAA
28248720 AAAAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAG
Found at i:28248919 original size:23 final size:23
Alignment explanation
Indices: 28248892--28248939 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
28248882 CGGATTAGTA
28248892 TTTTGTATGAATATTCTAATTTT
1 TTTTGTATGAATATTCTAATTTT
*
28248915 TTTTGTATGAATATTGTAATTTT
1 TTTTGTATGAATATTCTAATTTT
28248938 TT
1 TT
28248940 ATGAATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.62
Consensus pattern (23 bp):
TTTTGTATGAATATTCTAATTTT
Found at i:28248942 original size:19 final size:19
Alignment explanation
Indices: 28248891--28248980 Score: 108
Period size: 19 Copynumber: 4.5 Consensus size: 19
28248881 TCGGATTAGT
* *
28248891 ATTTTGTATGAATATTCTA
1 ATTTTTTATGAATATTGTA
28248910 ATTTTTTTTGTATGAATATTGTA
1 A---TTTTT-TATGAATATTGTA
28248933 ATTTTTTATGAATATTGTA
1 ATTTTTTATGAATATTGTA
*
28248952 ATTTTGTATGAATATTGTA
1 ATTTTTTATGAATATTGTA
28248971 ATTATTTTAT
1 ATT-TTTTAT
28248981 AATTAAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
19 35 0.56
20 10 0.16
22 4 0.06
23 13 0.21
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (19 bp):
ATTTTTTATGAATATTGTA
Found at i:28249120 original size:19 final size:20
Alignment explanation
Indices: 28249073--28249121 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
28249063 TTTGGATTAG
28249073 TATTTTGTATGAATATTGTA
1 TATTTTGTATGAATATTGTA
*
28249093 TTTTTTTGTATGAATATTGTA
1 -TATTTTGTATGAATATTGTA
28249114 -ATTTTGTA
1 TATTTTGTA
28249122 ATTTTGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
21 19 0.73
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (20 bp):
TATTTTGTATGAATATTGTA
Found at i:28249121 original size:29 final size:28
Alignment explanation
Indices: 28249088--28249172 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 28
28249078 TGTATGAATA
28249088 TTGTATTTTTTTGTATGAATATTGTAATT
1 TTGTA-TTTTTTGTATGAATATTGTAATT
* * *
28249117 TTGTA-ATTTTGTATGAATATTTTAATA
1 TTGTATTTTTTGTATGAATATTGTAATT
28249144 TTGTAATTTTTTGTATGAATATTGTAATT
1 TTGT-ATTTTTTGTATGAATATTGTAATT
28249173 ATTTTATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.48
28 1 0.02
29 24 0.50
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (28 bp):
TTGTATTTTTTGTATGAATATTGTAATT
Found at i:28249131 original size:27 final size:28
Alignment explanation
Indices: 28249095--28249172 Score: 122
Period size: 27 Copynumber: 2.8 Consensus size: 28
28249085 ATATTGTATT
28249095 TTTTTGTATGAATATTGTAATTTTGTAA
1 TTTTTGTATGAATATTGTAATTTTGTAA
* *
28249123 -TTTTGTATGAATATTTTAATATTGTAA
1 TTTTTGTATGAATATTGTAATTTTGTAA
28249150 TTTTTTGTATGAATATTGTAATT
1 -TTTTTGTATGAATATTGTAATT
28249173 ATTTTATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.57
29 19 0.43
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (28 bp):
TTTTTGTATGAATATTGTAATTTTGTAA
Found at i:28249139 original size:61 final size:61
Alignment explanation
Indices: 28248873--28249113 Score: 273
Period size: 61 Copynumber: 4.0 Consensus size: 61
28248863 ATATTTAGTG
* * * *
28248873 TTTATAG-TTCGGATTAGTATTTTGTATGAATATTCTAATT-TTTTTTGTATGAATATTGTAA
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTTTAT-AATGAATATTGT-A
* * * *
28248934 TTT-T--TTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAA-ATTTGTA
1 TTTATAGTTTTGGAT-TAGT-ATTTTGTATGAATATTGTAATTATTTTATAATGAATA-TTGTA
* *
28248994 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTA
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTA
* *
28249055 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGT-ATTTTTTTGT-ATGAATATTGTA
1 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTA
28249114 ATTTTGTAAT
Statistics
Matches: 155, Mismatches: 16, Indels: 20
0.81 0.08 0.10
Matches are distributed among these distances:
59 14 0.09
60 17 0.11
61 110 0.71
62 8 0.05
63 6 0.04
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (61 bp):
TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATGAATATTGTA
Found at i:28249283 original size:60 final size:60
Alignment explanation
Indices: 28249165--28249286 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
28249155 TGTATGAATA
* * * * **
28249165 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATGGTTGTGT
*
28249225 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTGGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATGGTTGTGT
28249285 TT
1 TT
28249287 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATGGTTGTGT
Found at i:28251061 original size:6 final size:6
Alignment explanation
Indices: 28251050--28251079 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28251040 GCATCATGCA
*
28251050 CCAGAG CCAGAG CCAGAG CCAGTG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
28251080 ACGGAACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.33, T:0.03
Consensus pattern (6 bp):
CCAGAG
Found at i:28252498 original size:27 final size:27
Alignment explanation
Indices: 28252463--28252540 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
28252453 GAAAAATTAG
*
28252463 ACCATTGGCGCCTCTCAACAT-GGCACC
1 ACCAATGGCGCCTCTC-ACATAGGCACC
* *
28252490 ACTAATGGCGCCTCTCAGATAGGCACC
1 ACCAATGGCGCCTCTCACATAGGCACC
* * *
28252517 ACCATTGGCGCCTCTGAGATAGGC
1 ACCAATGGCGCCTCTCACATAGGC
28252541 GCCAATACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (27 bp):
ACCAATGGCGCCTCTCACATAGGCACC
Found at i:28255066 original size:13 final size:15
Alignment explanation
Indices: 28255036--28255067 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28255026 ATATTTCATG
28255036 CATTTCATCAATAAT
1 CATTTCATCAATAAT
28255051 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
28255064 CATT
1 CATT
28255068 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:28255669 original size:6 final size:6
Alignment explanation
Indices: 28255632--28255674 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
28255622 CCAAACACAC
* *
28255632 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
28255675 TTCAACACNN
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (6 bp):
CAGTAA
Found at i:28261160 original size:181 final size:182
Alignment explanation
Indices: 28260855--28261217 Score: 710
Period size: 181 Copynumber: 2.0 Consensus size: 182
28260845 GATTAAAAAT
28260855 TAAAAATGAGTAAACAAATAAATATTAATTGAAATATTTAATGAAACTATTTTTTTAAAACAAAT
1 TAAAAATGAGTAAACAAATAAATATTAATTGAAATATTTAATGAAACTATTTTTTTAAAACAAAT
28260920 AATATATAAAAAAAATTAATTAAACAGGCTGAGGACCGAATTGAAATCGGGCTAAAAAATCAAAG
66 AATATATAAAAAAAATTAATTAAACAGGCTGAGGACCGAATTGAAATCGGGCTAAAAAATCAAAG
28260985 TTTAAATTGCAAATAAATAAAACAGGGTTGCCAGGGGAATGAAATGAAACGC
131 TTTAAATTGCAAATAAATAAAACAGGGTTGCCAGGGGAATGAAATGAAACGC
*
28261037 TAAAAATGATTAAACAAAT-AATATTAATTGAAATATTTAATGAAACTATTTTTTTAAAACAAAT
1 TAAAAATGAGTAAACAAATAAATATTAATTGAAATATTTAATGAAACTATTTTTTTAAAACAAAT
28261101 AATATATAAAAAAAATTAATTAAACAGGCTGAGGACCGAATTGAAATCGGGCTAAAAAATCAAAG
66 AATATATAAAAAAAATTAATTAAACAGGCTGAGGACCGAATTGAAATCGGGCTAAAAAATCAAAG
28261166 TTTAAATTGCAAATAAATAAAACAGGGTTGCCAGGGGAATGAAATGAAACGC
131 TTTAAATTGCAAATAAATAAAACAGGGTTGCCAGGGGAATGAAATGAAACGC
28261218 GCGCAAAGCG
Statistics
Matches: 180, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
181 162 0.90
182 18 0.10
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (182 bp):
TAAAAATGAGTAAACAAATAAATATTAATTGAAATATTTAATGAAACTATTTTTTTAAAACAAAT
AATATATAAAAAAAATTAATTAAACAGGCTGAGGACCGAATTGAAATCGGGCTAAAAAATCAAAG
TTTAAATTGCAAATAAATAAAACAGGGTTGCCAGGGGAATGAAATGAAACGC
Found at i:28267908 original size:31 final size:31
Alignment explanation
Indices: 28267873--28267941 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
28267863 TAACCCAGTA
*
28267873 ACTTAAATAAAAAATTTTGAATAGTTTAGTG
1 ACTTAAATAAAAAATTTTGAATAGTTTAATG
* *
28267904 ACTTAAATGAAAACTTTTGAATAGTTTAATG
1 ACTTAAATAAAAAATTTTGAATAGTTTAATG
28267935 AC-TAAAT
1 ACTTAAAT
28267942 TATAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 5 0.14
31 30 0.86
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTTGAATAGTTTAATG
Found at i:28269340 original size:16 final size:16
Alignment explanation
Indices: 28269303--28269342 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28269293 TTGATAAAAT
* *
28269303 TAAAACTAATTATTAT
1 TAAAATTAATTATTAG
*
28269319 TAAAATTAATTTTTAG
1 TAAAATTAATTATTAG
28269335 TAAAATTA
1 TAAAATTA
28269343 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:28269472 original size:75 final size:74
Alignment explanation
Indices: 28269337--28269476 Score: 253
Period size: 75 Copynumber: 1.9 Consensus size: 74
28269327 ATTTTTAGTA
*
28269337 AAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
1 AAATTATCAAATTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
28269402 AAAATTATC
66 AAAATTATC
*
28269411 AAATTATTAAATGTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAG
1 AAATTATCAAAT-TATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAG
28269476 T
65 T
28269477 TTACATTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
74 11 0.17
75 52 0.83
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (74 bp):
AAATTATCAAATTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
AAAATTATC
Found at i:28269714 original size:19 final size:19
Alignment explanation
Indices: 28269687--28269743 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 19
28269677 TCTGTCGGGG
*
28269687 AAATGAAATTGAAAACTAA
1 AAATAAAATTGAAAACTAA
28269706 AAATAAAATTGAAAACATAA
1 AAATAAAATTGAAAAC-TAA
28269726 AAATAAAATTGAAAACTA
1 AAATAAAATTGAAAACTA
28269744 TAAGTCCAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (19 bp):
AAATAAAATTGAAAACTAA
Found at i:28271060 original size:92 final size:92
Alignment explanation
Indices: 28270903--28273104 Score: 4377
Period size: 92 Copynumber: 23.9 Consensus size: 92
28270893 TCCACTCCTC
28270903 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28270968 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28270995 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271060 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271087 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271152 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271179 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271244 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271271 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271336 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271363 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271428 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271455 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271520 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271547 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271612 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271639 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271704 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271731 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271796 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271823 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271888 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28271915 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28271980 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272007 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272072 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272099 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272164 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272191 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272256 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272283 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272348 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272375 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272440 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272467 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272532 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272559 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272624 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272651 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272716 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272743 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272808 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272835 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272900 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
28272927 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28272992 AAATATACAAATAGGTTAAAACAAAAT
66 AAATATACAAATAGGTTAAAACAAAAT
* * *
28273019 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATGCAAATAGATTCATATTTTATT
1 GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
28273084 AAATATACAAATAGGTTAAAA
66 AAATATACAAATAGGTTAAAA
28273105 ATTGTAGCTT
Statistics
Matches: 2107, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 2107 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (92 bp):
GCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAATAGGTTTATATTTTATT
AAATATACAAATAGGTTAAAACAAAAT
Found at i:28274014 original size:17 final size:18
Alignment explanation
Indices: 28273992--28274032 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28273982 GACTGAGATA
*
28273992 AGAATT-CTGTTCATAAC
1 AGAATTCCTGTTCACAAC
*
28274009 AGAATTCCTGTTTACAAC
1 AGAATTCCTGTTCACAAC
28274027 AGAATT
1 AGAATT
28274033 GTAGATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
AGAATTCCTGTTCACAAC
Found at i:28275917 original size:407 final size:407
Alignment explanation
Indices: 28275162--28275974 Score: 1563
Period size: 407 Copynumber: 2.0 Consensus size: 407
28275152 TTGGTAAAGC
* *
28275162 TTTCTCACGACGTAGTGGAGGTGTAGACCGCTCTAAATTATGGTGCTCTCACTATGGAAAACATC
1 TTTCTCACAACGTAGTGGAGGTGTAGACCGCTCTAAATTATGGTACTCTCACTATGGAAAACATC
28275227 GACACTCGAAGGAAGAATGCTACCATATAATCGGGTTCCCCGATGGTTGGAAAGCACGTCAGAAG
66 GACACTCGAAGGAAGAATGCTACCATATAATCGGGTTCCCCGATGGTTGGAAAGCACGTCAGAAG
* *
28275292 GAAAGACAGCCAACAGGGTCAGCAGCTGCAGCAACTGGCCAAGACAACAACGTTGGGATAGGAGA
131 GAAAGACAGCCAACAGGGTCAGCAGCTGCAGCAACTGGCCAAGACAACAACGTTGGGACAAGAGA
28275357 ACAAATGGGAGAAAACATAGGAGGTGCAAATCAGGCAGCCGGGATTGAAAAAGGCAGAAATATGT
196 ACAAATGGGAGAAAACATAGGAGGTGCAAATCAGGCAGCCGGGATTGAAAAAGGCAGAAATATGT
28275422 TCTCTAACATAGGTAAAGGGGCTGGAAATTATTTTTCCAACCCCCCACTTATTGATTCCGAAAGT
261 TCTCTAACATAGGTAAAGGGGCTGGAAATTATTTTTCCAACCCCCCACTTATTGATTCCGAAAGT
28275487 TTGTTACCCTCTCCATGTTTTAAATCCCATATTGGTGCTGCAAATATATGTGTATCCGGATCACA
326 TTGTTACCCTCTCCATGTTTTAAATCCCATATTGGTGCTGCAAATATATGTGTATCCGGATCACA
28275552 AAAAAATTCCCAATGGG
391 AAAAAATTCCCAATGGG
* *
28275569 TTTCTCACAACGTAGTGGATGTGTAGACCGCTCTAAATTATGGTACTCTCACTGTGGAAAACATC
1 TTTCTCACAACGTAGTGGAGGTGTAGACCGCTCTAAATTATGGTACTCTCACTATGGAAAACATC
28275634 GACACTCGAAGGAAGAATGCTACCATATAATCGGGTTCCCCGATGGTTGGAAAGCACGTCAGAAG
66 GACACTCGAAGGAAGAATGCTACCATATAATCGGGTTCCCCGATGGTTGGAAAGCACGTCAGAAG
28275699 GAAAGACAGCCAACAGGGTCAGCAGCTGCAGCAACTGGCCAAGACAACAACGTTGGGACAAGAGA
131 GAAAGACAGCCAACAGGGTCAGCAGCTGCAGCAACTGGCCAAGACAACAACGTTGGGACAAGAGA
28275764 ACAAATGGGAGAAAACATAGGAGGTGCAAATCAGGCAGCCGGGATTGAAAAAGGCAGAAATATGT
196 ACAAATGGGAGAAAACATAGGAGGTGCAAATCAGGCAGCCGGGATTGAAAAAGGCAGAAATATGT
28275829 TCTCTAACATAGGTAAAGGGGCTGGAAATTATTTTTCCAACCCCCCACTTATTGATTCCGAAAGT
261 TCTCTAACATAGGTAAAGGGGCTGGAAATTATTTTTCCAACCCCCCACTTATTGATTCCGAAAGT
*
28275894 TTGTTACCCTCTCCATGTTTTAAATCCCATGTTGGTGCTGCAAATATATGTGTATCCGGATCACA
326 TTGTTACCCTCTCCATGTTTTAAATCCCATATTGGTGCTGCAAATATATGTGTATCCGGATCACA
28275959 AAAAAATTCCCAATGG
391 AAAAAATTCCCAATGG
28275975 TTGTTTGATT
Statistics
Matches: 399, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
407 399 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (407 bp):
TTTCTCACAACGTAGTGGAGGTGTAGACCGCTCTAAATTATGGTACTCTCACTATGGAAAACATC
GACACTCGAAGGAAGAATGCTACCATATAATCGGGTTCCCCGATGGTTGGAAAGCACGTCAGAAG
GAAAGACAGCCAACAGGGTCAGCAGCTGCAGCAACTGGCCAAGACAACAACGTTGGGACAAGAGA
ACAAATGGGAGAAAACATAGGAGGTGCAAATCAGGCAGCCGGGATTGAAAAAGGCAGAAATATGT
TCTCTAACATAGGTAAAGGGGCTGGAAATTATTTTTCCAACCCCCCACTTATTGATTCCGAAAGT
TTGTTACCCTCTCCATGTTTTAAATCCCATATTGGTGCTGCAAATATATGTGTATCCGGATCACA
AAAAAATTCCCAATGGG
Found at i:28278041 original size:93 final size:93
Alignment explanation
Indices: 28277890--28278075 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
28277880 GATACTCCCA
28277890 CTGATGAAGTTATTCATGTAGAATCTCAGGATAATGCGCCTGAGTCTAATTCGGAAGAGAATAGA
1 CTGATGAAGTTATTCATGTAGAATCTCAGGATAATGCGCCTGAGTCTAATTCGGAAGAGAATAGA
*
28277955 TATGTGTTGCCTCCTAGGAGTACTCGAG
66 TATGTGTTGCCTCCCAGGAGTACTCGAG
*
28277983 CTGATGAAGTTATTCATGTAGAATCTCAGGATAATGCGCCTGAGTCTAATTTGGAAGAGAATAGA
1 CTGATGAAGTTATTCATGTAGAATCTCAGGATAATGCGCCTGAGTCTAATTCGGAAGAGAATAGA
28278048 TATGTGTTGCCTCCCAGGAGTACTCGAG
66 TATGTGTTGCCTCCCAGGAGTACTCGAG
28278076 GTATTCCCCC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (93 bp):
CTGATGAAGTTATTCATGTAGAATCTCAGGATAATGCGCCTGAGTCTAATTCGGAAGAGAATAGA
TATGTGTTGCCTCCCAGGAGTACTCGAG
Found at i:28281858 original size:16 final size:17
Alignment explanation
Indices: 28281837--28281870 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28281827 TATATTTTTT
28281837 AAACAT-AAAAAACTTA
1 AAACATAAAAAAACTTA
28281853 AAACATAAAAAAACTTA
1 AAACATAAAAAAACTTA
28281870 A
1 A
28281871 TATATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (17 bp):
AAACATAAAAAAACTTA
Found at i:28289997 original size:13 final size:12
Alignment explanation
Indices: 28289978--28290034 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 12
28289968 TTGTTTTAAT
28289978 AATTTTTT-AAA
1 AATTTTTTAAAA
28289989 AATATTTTTAAAA
1 AAT-TTTTTAAAA
*
28290002 CCATTTTTTAAATTA
1 -AATTTTTTAAA--A
28290017 AATTCTTTTAAAA
1 AATT-TTTTAAAA
28290030 AATTT
1 AATTT
28290035 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 3 0.08
12 6 0.16
13 16 0.42
14 5 0.13
15 8 0.21
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTTTTAAAA
Found at i:28290132 original size:91 final size:92
Alignment explanation
Indices: 28290016--28290199 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 92
28290006 TTTTTAAATT
28290016 AAATTCTTTTAAAAAATTTAAAATTAAAAAACTCAAAATAAAATTGATACAAAACTGTTTATTTA
1 AAATTCTTTTAAAAAATTTAAAATTAAAAAACTCAAAATAAAATTGATACAAAACTGTTTATTTA
28290081 ATTTAACTATTTTCTAAAACTGTTTCC
66 ATTTAACTATTTTCTAAAACTGTTTCC
28290108 AAATTCTTTT-AAAAATTTAAAATTAAAAAACTCAAAATAAAATTGATACAAAACTGTTTATTTA
1 AAATTCTTTTAAAAAATTTAAAATTAAAAAACTCAAAATAAAATTGATACAAAACTGTTTATTTA
28290172 ATTTAACTATTTTCTAAAACTGTTTCC
66 ATTTAACTATTTTCTAAAACTGTTTCC
28290199 A
1 A
28290200 TTTTTTCATA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 82 0.89
92 10 0.11
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (92 bp):
AAATTCTTTTAAAAAATTTAAAATTAAAAAACTCAAAATAAAATTGATACAAAACTGTTTATTTA
ATTTAACTATTTTCTAAAACTGTTTCC
Found at i:28292942 original size:22 final size:23
Alignment explanation
Indices: 28292914--28292960 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28292904 GCAGTAGAAG
*
28292914 AAGAAG-AGAAAAACAAAGGAAA
1 AAGAAGAAGAAAAACAAAGAAAA
* *
28292936 AAGAAGAAGAAGAAGAAAGAAAA
1 AAGAAGAAGAAAAACAAAGAAAA
28292959 AA
1 AA
28292961 TGGAGATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAGAAGAAAAACAAAGAAAA
Found at i:28294728 original size:15 final size:15
Alignment explanation
Indices: 28294697--28294727 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28294687 GAAACCTTGC
28294697 TTCTTCTTCTTTTTT
1 TTCTTCTTCTTTTTT
28294712 TTCTT-TTCTTTTTT
1 TTCTTCTTCTTTTTT
28294726 TT
1 TT
28294728 TACACTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTCTTCTTTTTT
Found at i:28314163 original size:12 final size:12
Alignment explanation
Indices: 28314146--28314198 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
28314136 TCGAATAAGC
28314146 ATGTATATATAT
1 ATGTATATATAT
28314158 ATGTATATATAT
1 ATGTATATATAT
*
28314170 AATGCTAGAATATAT
1 -ATG-TA-TATATAT
**
28314185 ATACATATATAT
1 ATGTATATATAT
28314197 AT
1 AT
28314199 AAAAGTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:28325604 original size:46 final size:42
Alignment explanation
Indices: 28325541--28325626 Score: 120
Period size: 41 Copynumber: 2.0 Consensus size: 42
28325531 TTATGAAGGA
28325541 AATAAATACCTAATATAATAGAGAAAATAAATAAAACTAAAACTCTT
1 AATAAATACCTAATATAAT-----AAATAAATAAAACTAAAACTCTT
28325588 AATAAA-ACCTAATATAATAAATAAATAAAACTAAAACTC
1 AATAAATACCTAATATAATAAATAAATAAAACTAAAACTC
28325627 CTGTTGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
41 21 0.54
46 12 0.31
47 6 0.15
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (42 bp):
AATAAATACCTAATATAATAAATAAATAAAACTAAAACTCTT
Found at i:28333457 original size:15 final size:15
Alignment explanation
Indices: 28333399--28333468 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
28333389 TTTTTTTAAT
* *
28333399 TCTTTTATTTCTCTC
1 TCTTTTTTTTCTTTC
*
28333414 TCTTTATTTT-TTT-
1 TCTTTTTTTTCTTTC
* * *
28333427 TCTATTTTGTCGTTC
1 TCTTTTTTTTCTTTC
28333442 TCTTTTTTTTCTTTC
1 TCTTTTTTTTCTTTC
28333457 TTCTTCTTTTTT
1 -TCTT-TTTTTT
28333469 TAATGTCTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
13 7 0.17
14 4 0.10
15 20 0.49
16 4 0.10
17 6 0.15
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (15 bp):
TCTTTTTTTTCTTTC
Found at i:28333855 original size:2 final size:2
Alignment explanation
Indices: 28333848--28333872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28333838 TAAGAAAGAA
28333848 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28333873 ATTTGTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28336738 original size:21 final size:22
Alignment explanation
Indices: 28336712--28336754 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
28336702 GGGCCAGGGT
28336712 ATTGGGCTTAG-GTTTAGGCTA
1 ATTGGGCTTAGTGTTTAGGCTA
*
28336733 ATTGGGCTTAGTGTTTGGGCTA
1 ATTGGGCTTAGTGTTTAGGCTA
28336755 GGTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (22 bp):
ATTGGGCTTAGTGTTTAGGCTA
Found at i:28340619 original size:27 final size:26
Alignment explanation
Indices: 28340589--28340648 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
28340579 GAGGTGACTC
28340589 TATATATAAAATT-TTAATAAATAAAAA
1 TATATATAAAATTATT-A-AAATAAAAA
*
28340616 TATAT-T-AAATTATTAAATTAAAAA
1 TATATATAAAATTATTAAAATAAAAA
28340640 TA-ATATAAA
1 TATATATAAA
28340649 TATATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 2 0.07
24 11 0.38
25 8 0.28
26 3 0.10
27 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TATATATAAAATTATTAAAATAAAAA
Found at i:28340994 original size:22 final size:23
Alignment explanation
Indices: 28340969--28341017 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
28340959 ATTGTAAGTA
*
28340969 ACACAA-ATTTAAACACA-TAACT
1 ACACAATA-TTAAAAACATTAACT
*
28340991 ACACCATATTAAAAACATTAACT
1 ACACAATATTAAAAACATTAACT
28341014 ACAC
1 ACAC
28341018 TATAACTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (23 bp):
ACACAATATTAAAAACATTAACT
Found at i:28342353 original size:93 final size:93
Alignment explanation
Indices: 28342194--28342369 Score: 253
Period size: 93 Copynumber: 1.9 Consensus size: 93
28342184 ATAATGGAGA
* * * **
28342194 TATTCAAGGGGTTAAATCCGCATCCGCATCAAATAATATTTTTACTATTCGAAAAATTGTCATCT
1 TATTCAAGGGGTTAAATACGCATCCGCAACAAATAATATTTTTACTATCCGAAAAATTACCATCT
28342259 CTACCTAAACTTTGTTTTTACTATCCAT
66 CTACCTAAACTTTGTTTTTACTATCCAT
* ** * *
28342287 TATTCATGGGGTTAAATACGCATCCGCAACGGATAGTATTTTTATTATCCGAAAAATTACCATCT
1 TATTCAAGGGGTTAAATACGCATCCGCAACAAATAATATTTTTACTATCCGAAAAATTACCATCT
*
28342352 CTACCTAGACTTTGTTTT
66 CTACCTAAACTTTGTTTT
28342370 GAGTTTGAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (93 bp):
TATTCAAGGGGTTAAATACGCATCCGCAACAAATAATATTTTTACTATCCGAAAAATTACCATCT
CTACCTAAACTTTGTTTTTACTATCCAT
Found at i:28342549 original size:18 final size:18
Alignment explanation
Indices: 28342528--28342562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28342518 TTATATTTTA
28342528 GGCTTATACAATATATTG
1 GGCTTATACAATATATTG
**
28342546 GGCTTATTTAATATATT
1 GGCTTATACAATATATT
28342563 TGGCCTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (18 bp):
GGCTTATACAATATATTG
Found at i:28342657 original size:62 final size:62
Alignment explanation
Indices: 28342584--28342708 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
28342574 ATTTTATTAT
*
28342584 TAATAATTTTAAATAATCGGTTAATTATTTGATTTTGAACCGAATTAATCGTTAACTAAAAA
1 TAATAATTTTAAATAATCGGTTAATTATTTGATCTTGAACCGAATTAATCGTTAACTAAAAA
*
28342646 TAATAATTTTAAGTAATCGGTTAATTATTTGATCTTGAACCGAATTAATCGTTAACTAAAAA
1 TAATAATTTTAAATAATCGGTTAATTATTTGATCTTGAACCGAATTAATCGTTAACTAAAAA
28342708 T
1 T
28342709 TCAAAAAACT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (62 bp):
TAATAATTTTAAATAATCGGTTAATTATTTGATCTTGAACCGAATTAATCGTTAACTAAAAA
Found at i:28342786 original size:26 final size:26
Alignment explanation
Indices: 28342757--28342806 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28342747 ATGGCTGACG
*
28342757 GAAATAATTCAATTAGATCGATTACT
1 GAAATAATTCAATTAAATCGATTACT
28342783 GAAATAATTCAATTAAATCGATTA
1 GAAATAATTCAATTAAATCGATTA
28342807 ATTTGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (26 bp):
GAAATAATTCAATTAAATCGATTACT
Found at i:28351743 original size:28 final size:27
Alignment explanation
Indices: 28351673--28351743 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 27
28351663 ATTTATAAAC
* **
28351673 TAAAATATAAATTTTTATTTTTTTAGGT
1 TAAAATAT-AATTTTAATTTTTAAAGGT
* *
28351701 CAAAACTA-AAATTTAATTTTTAAAGAGT
1 TAAAA-TATAATTTTAATTTTTAAAG-GT
28351729 TAAAATATAATTTTA
1 TAAAATATAATTTTA
28351744 GCATTAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
27 15 0.45
28 16 0.48
29 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (27 bp):
TAAAATATAATTTTAATTTTTAAAGGT
Found at i:28354450 original size:27 final size:28
Alignment explanation
Indices: 28354392--28354459 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
28354382 ATGGGTTTTT
* * *
28354392 TTATAAAAATGATATTAAAAATAAATTGA
1 TTATAAAAAT-AAAGTAAAAATAAATTAA
28354421 TTATAAAAATAAAGTAAAAA-AAATTAA
1 TTATAAAAATAAAGTAAAAATAAATTAA
**
28354448 TTACGAAAATAA
1 TTATAAAAATAA
28354460 GATATTTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 16 0.47
28 8 0.24
29 10 0.29
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.29
Consensus pattern (28 bp):
TTATAAAAATAAAGTAAAAATAAATTAA
Found at i:28355415 original size:21 final size:22
Alignment explanation
Indices: 28355384--28355426 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28355374 CATATTGGAT
28355384 TTTTGAGAAAA-GTATAATAAAA
1 TTTTGAGAAAATGTA-AATAAAA
28355406 TTTTG-GAAAATGTAAATAAAA
1 TTTTGAGAAAATGTAAATAAAA
28355427 GTATTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (22 bp):
TTTTGAGAAAATGTAAATAAAA
Found at i:28356662 original size:29 final size:28
Alignment explanation
Indices: 28356601--28356662 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
28356591 CATTTGTACT
*
28356601 TTTTTAAATTTGAAATTTGGTCTATGTA
1 TTTTTAAATTTGAAATTTAGTCTATGTA
* *
28356629 CTTTTAAATTT-AAGATTTTAGTCTATTTA
1 TTTTTAAATTTGAA-A-TTTAGTCTATGTA
28356658 TTTTT
1 TTTTT
28356663 TGGACAGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.07
28 11 0.39
29 15 0.54
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (28 bp):
TTTTTAAATTTGAAATTTAGTCTATGTA
Found at i:28368364 original size:13 final size:12
Alignment explanation
Indices: 28368334--28368376 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
28368324 AATTTCATTT
28368334 AATTTTTATATA
1 AATTTTTATATA
28368346 AATTTTTA-ATA
1 AATTTTTATATA
28368357 AATGTTTT-TATA
1 AAT-TTTTATATA
28368369 TAATTTTT
1 -AATTTTT
28368377 TTGAATGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.21
12 19 0.68
13 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
AATTTTTATATA
Found at i:28368377 original size:13 final size:13
Alignment explanation
Indices: 28368336--28368378 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
28368326 TTTCATTTAA
*
28368336 TTTTTATATAAAT
1 TTTTTATATAATT
* *
28368349 TTTTAATA-AATG
1 TTTTTATATAATT
28368361 TTTTTATATAATT
1 TTTTTATATAATT
28368374 TTTTT
1 TTTTT
28368379 GAATGAACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:28369205 original size:124 final size:122
Alignment explanation
Indices: 28369073--28369302 Score: 318
Period size: 124 Copynumber: 1.9 Consensus size: 122
28369063 GAAAATAAAG
* *
28369073 AAAAGAAAACCCCTTTCATCATTTTCCTTCAATTTCAAGCTTAAGGTATGGTTTTTCT-TCAATT
1 AAAAGAAAACCCCTTTCATCATTTTCCTTCAATTTCAAGCTTAAGGCATGATTTTTCTAT-AA--
* *
28369137 TTTTTTTTATAAATTTTGAATCTTTGAAATTTGCTTTACATATAAGTTTGGGAAAAGGAA
63 TTTTTTTTATAAATTTTAAATCTTTGAAACTTGCTTTACATATAAGTTTGGGAAAAGGAA
* * * * *
28369197 AAAAGAAAATCCCTTTCATCATTTTCCTTCAATTTTAAGTTTAATGCATTATTTTTCTATAATTT
1 AAAAGAAAACCCCTTTCATCATTTTCCTTCAATTTCAAGCTTAAGGCATGATTTTTCTATAATTT
* * *
28369262 TTTTTATAGATTTTAAATGTTTGAAGCTTGCTTTACATATA
66 TTTTTATAAATTTTAAATCTTTGAAACTTGCTTTACATATA
28369303 CATACCAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
122 39 0.42
124 53 0.57
125 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (122 bp):
AAAAGAAAACCCCTTTCATCATTTTCCTTCAATTTCAAGCTTAAGGCATGATTTTTCTATAATTT
TTTTTATAAATTTTAAATCTTTGAAACTTGCTTTACATATAAGTTTGGGAAAAGGAA
Found at i:28375760 original size:21 final size:22
Alignment explanation
Indices: 28375734--28375775 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28375724 AACAGTTCAA
* *
28375734 ATTTTT-TTCATTTATTAAAAG
1 ATTTTTCTGCATTTATCAAAAG
28375755 ATTTTTCTGCATTTATCAAAA
1 ATTTTTCTGCATTTATCAAAA
28375776 CTATGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTTTTCTGCATTTATCAAAAG
Found at i:28383178 original size:14 final size:15
Alignment explanation
Indices: 28383144--28383179 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
28383134 ACAAATAGAA
28383144 CAAAAAGGATTAAAC
1 CAAAAAGGATTAAAC
28383159 CAAAAAGGATTAAAC
1 CAAAAAGGATTAAAC
28383174 CAAAAA
1 CAAAAA
28383180 TATAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.14, G:0.11, T:0.11
Consensus pattern (15 bp):
CAAAAAGGATTAAAC
Found at i:28384783 original size:4 final size:4
Alignment explanation
Indices: 28384774--28384896 Score: 72
Period size: 4 Copynumber: 30.8 Consensus size: 4
28384764 TTTTAATTCT
* * * * **
28384774 TTTA TTTA TTTA TTTA CTTA TTTA CTTG TTTA TTTA TTCA -TTA TTCC
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
28384821 TTTGA TTTTA TTAA TTTA TTTG TTCA TTTA CTTA TTTA TTCA TATA -TTA
1 TTT-A -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
28384870 TTGA TTTA TTTTT TTTA TTT- TTTA TTT
1 TTTA TTTA -TTTA TTTA TTTA TTTA TTT
28384897 TAATCCTTGT
Statistics
Matches: 85, Mismatches: 28, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
3 7 0.08
4 71 0.84
5 4 0.05
6 3 0.04
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:28384831 original size:53 final size:53
Alignment explanation
Indices: 28384773--28384893 Score: 133
Period size: 53 Copynumber: 2.3 Consensus size: 53
28384763 ATTTTAATTC
* * *
28384773 TTTTATTTATTTATTTACTT-ATTTACTTGTTTATTTAT-TCATTATTCCTTTGA
1 TTTTATTTATTTATTTACTTCATTTACTTATTTATTCATAT-ATTATTCATTT-A
* * *
28384826 TTTTATTAATTTATTT-GTTCATTTACTTATTTATTCATATATTATTGATTTA
1 TTTTATTTATTTATTTACTTCATTTACTTATTTATTCATATATTATTCATTTA
*
28384878 TTTTTTTTATTT-TTTA
1 TTTTATTTATTTATTTA
28384894 TTTTAATCCT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
51 3 0.05
52 13 0.23
53 40 0.70
54 1 0.02
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (53 bp):
TTTTATTTATTTATTTACTTCATTTACTTATTTATTCATATATTATTCATTTA
Found at i:28384945 original size:26 final size:26
Alignment explanation
Indices: 28384916--28385001 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
28384906 TATTCATTTA
28384916 TTTATTATCCCTTCATTTATTATTAT
1 TTTATTATCCCTTCATTTATTATTAT
* * **
28384942 TTTATT-TTCTTTCATCGATTATTTAT
1 TTTATTATCCCTTCATTTATTA-TTAT
*
28384968 TTTATTTATGCCTTCA-TTATTATTAT
1 TTTA-TTATCCCTTCATTTATTATTAT
28384994 TATTATTA
1 T-TTATTA
28385002 CTATTTTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
25 11 0.23
26 22 0.46
27 9 0.19
28 6 0.12
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATTATCCCTTCATTTATTATTAT
Found at i:28384991 original size:3 final size:3
Alignment explanation
Indices: 28384983--28385021 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
28384973 TTATGCCTTC
*
28384983 ATT ATT ATT ATT ATT ATT ACT ATT -TT ATT ATT ATCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
28385022 TATCTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28385106 original size:3 final size:3
Alignment explanation
Indices: 28385098--28385126 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28385088 AAATTTATTG
28385098 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28385127 ACTTACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28388432 original size:21 final size:22
Alignment explanation
Indices: 28388407--28388447 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28388397 AAGTCTAAAC
* *
28388407 AAGATTGAAGTGCT-AAAGCGA
1 AAGATAGAAGAGCTCAAAGCGA
28388428 AAGATAGAAGAGCTCAAAGC
1 AAGATAGAAGAGCTCAAAGC
28388448 CGCACTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.15
Consensus pattern (22 bp):
AAGATAGAAGAGCTCAAAGCGA
Found at i:28388840 original size:19 final size:20
Alignment explanation
Indices: 28388805--28388854 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
28388795 GCCTCTTATT
28388805 GCATT-CATTTCATTCATCA
1 GCATTACATTTCATTCATCA
*
28388824 GCATTACATTTCA-TCATCT
1 GCATTACATTTCATTCATCA
*
28388843 GCATTAAATTTC
1 GCATTACATTTC
28388855 CCAAAAAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (20 bp):
GCATTACATTTCATTCATCA
Found at i:28392034 original size:18 final size:15
Alignment explanation
Indices: 28391999--28392037 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
28391989 TACGATTCAA
28391999 AAGAAGAAAGAGCTG
1 AAGAAGAAAGAGCTG
28392014 AAGAAGAAAGAGCTG
1 AAGAAGAAAGAGCTG
*
28392029 GAGAAGAAA
1 AAGAAGAAA
28392038 CAAGAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.33, T:0.05
Consensus pattern (15 bp):
AAGAAGAAAGAGCTG
Done.