Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 74 of 106
Found at i:28202696 original size:29 final size:28
Alignment explanation
Indices: 28202649--28202822 Score: 177
Period size: 29 Copynumber: 6.0 Consensus size: 28
28202639 TAGCAGCTTT
*
28202649 AACATGTTTGTCTTAATTTAGAAAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
28202677 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
28202706 AATATTTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
28202736 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
28202765 AACATATTTGTCTCAATTTAGACAAGATAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* * *
28202795 AATATTTTTGTCTTAATTAAAGACAAGA
1 AACATGTTTGTCTTAATT-TAGACAAGA
28202823 GTTGTCTTAA
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 37 0.30
29 38 0.30
30 30 0.24
31 20 0.16
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:28202761 original size:59 final size:58
Alignment explanation
Indices: 28202649--28202811 Score: 204
Period size: 59 Copynumber: 2.8 Consensus size: 58
28202639 TAGCAGCTTT
* * * * * *
28202649 AACATGTTTGTCTTAATTTAGAAAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATATTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
* * *
28202706 AATATTTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
1 AACATATTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
*
28202765 AACATATTTGTCTCAATTTAGACAAGATAAAATA-TTTTTGTCTTAAT
1 AACATATTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAAT
28202812 TAAAGACAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 17 0.19
58 26 0.29
59 48 0.53
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (58 bp):
AACATATTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
Found at i:28202799 original size:28 final size:28
Alignment explanation
Indices: 28202649--28202822 Score: 172
Period size: 28 Copynumber: 6.0 Consensus size: 28
28202639 TAGCAGCTTT
* *
28202649 AACATGTTTGTCTTAATTTAGAAAAGAA
1 AACATATTTGTCTTAATTTAGACAAGAA
*
28202677 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
* *
28202706 AATATTTTTGTCTTAATTTAAGACAAGAA
1 AACATATTTGTCTTAATTT-AGACAAGAA
* *
28202735 AA-ATATTTTTTATCTTAATCTAGACAAGAA
1 AACATA---TTTGTCTTAATTTAGACAAGAA
*
28202765 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATATTTGTCTTAATTTAGACAAGA-A
*
28202794 AA-ATATTTTTGTCTTAATTAAAGACAAGA
1 AACATA--TTTGTCTTAATT-TAGACAAGA
28202823 GTTGTCTTAA
Statistics
Matches: 125, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
28 42 0.34
29 39 0.31
30 22 0.18
31 22 0.18
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.37
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:28205078 original size:20 final size:20
Alignment explanation
Indices: 28205033--28205076 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
28205023 AAATATCTCT
28205033 TTCTTCTAGCAACTTCTTCA
1 TTCTTCTAGCAACTTCTTCA
28205053 TTCTTC-AGCAACTT-TTC-
1 TTCTTCTAGCAACTTCTTCA
28205070 TTCTTCT
1 TTCTTCT
28205077 TCTTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
19 8 0.35
20 6 0.26
ACGTcount: A:0.16, C:0.30, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCTTCTAGCAACTTCTTCA
Found at i:28205914 original size:37 final size:37
Alignment explanation
Indices: 28205873--28205991 Score: 177
Period size: 37 Copynumber: 3.2 Consensus size: 37
28205863 TGTTAGGTGG
* *
28205873 TGATGTTGAAGTGTACGAGTAGGGAGTGCACACATGA
1 TGATGATGAAGTGTGCGAGTAGGGAGTGCACACATGA
*
28205910 TGATGATGGAGTGTGCGAGTAGGGAGTGCACACATGA
1 TGATGATGAAGTGTGCGAGTAGGGAGTGCACACATGA
* *
28205947 TGATAAT-AGAGTGTGTGAGTAGGGAGTGCACACATGA
1 TGATGATGA-AGTGTGCGAGTAGGGAGTGCACACATGA
28205984 TGATGATG
1 TGATGATG
28205992 TATGTATATA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.29, C:0.09, G:0.37, T:0.24
Consensus pattern (37 bp):
TGATGATGAAGTGTGCGAGTAGGGAGTGCACACATGA
Found at i:28213578 original size:37 final size:37
Alignment explanation
Indices: 28213537--28213640 Score: 190
Period size: 37 Copynumber: 2.8 Consensus size: 37
28213527 TTGAAGTCTA
28213537 CGAGTAGGGAGTGCACACATGATGATGATGGAGTGTG
1 CGAGTAGGGAGTGCACACATGATGATGATGGAGTGTG
* *
28213574 CGAGTAGGGAGTGCACACATGATGATAATAGAGTGTG
1 CGAGTAGGGAGTGCACACATGATGATGATGGAGTGTG
28213611 CGAGTAGGGAGTGCACACATGATGATGATG
1 CGAGTAGGGAGTGCACACATGATGATGATG
28213641 TATGTATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.30, C:0.12, G:0.38, T:0.21
Consensus pattern (37 bp):
CGAGTAGGGAGTGCACACATGATGATGATGGAGTGTG
Found at i:28216751 original size:59 final size:61
Alignment explanation
Indices: 28216684--28216807 Score: 189
Period size: 59 Copynumber: 2.1 Consensus size: 61
28216674 TCTCTGCAAT
* * *
28216684 GAGATTCAATCTCGCTGCAGTGAAATTTCTACCCAG-AAACAG-ATGTTTCTCGCTACAGC
1 GAGATTCAATCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTACAGC
**
28216743 GAGATTCAATCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTGTAGC
1 GAGATTCAATCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTACAGC
28216804 GAGA
1 GAGA
28216808 ACGCATTTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 34 0.59
60 6 0.10
61 18 0.31
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (61 bp):
GAGATTCAATCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTTTCTCGCTACAGC
Found at i:28217230 original size:43 final size:43
Alignment explanation
Indices: 28217178--28217296 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
28217168 TCACCAGCTC
* * * * *
28217178 ATGCCCACTTTCTACTCGCACATGACTGGGTCATCAC-CGGGTT
1 ATGCGCACTTCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
*
28217221 ATGCGCACTTCCTACTCGCACATAACCGGGTCATCCTTGGCTT
1 ATGCGCACTTCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* * *
28217264 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTTCCTACTCGCACATAACCGGGTCA
28217297 ATATAATTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCGCACTTCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:28231954 original size:42 final size:42
Alignment explanation
Indices: 28231866--28231999 Score: 205
Period size: 42 Copynumber: 3.2 Consensus size: 42
28231856 AGCTAGGTCA
* * * * *
28231866 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCAGG
1 TCATCATCAGCTCATGTGCACTCCC-ACACGCACATAGCTAGG
28231909 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
1 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
*
28231951 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
28231993 TCATCAT
1 TCATCAT
28232000 GATCATATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 62 0.73
43 23 0.27
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATCATCAGCTCATGTGCACTCCCACACGCACATAGCTAGG
Found at i:28233820 original size:2 final size:2
Alignment explanation
Indices: 28233813--28233843 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28233803 AAATCATTAG
28233813 AT AT AT 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 AT AT AT A
28233844 AAGGAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28237030 original size:50 final size:49
Alignment explanation
Indices: 28236967--28237072 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 49
28236957 GGATTTTTTA
** *
28236967 TTTTTAATGGGAAGTGATAACCCTCACACAACCCATAAGGAGATTCTTGC
1 TTTTTAACAGGAAGCGATAACCCTCACACAACCCATAAGGA-ATTCTTGC
* * *
28237017 TTTTTAACAGGAAGCGATAACCCTTACACAATCCATAATGAATTCTTGC
1 TTTTTAACAGGAAGCGATAACCCTCACACAACCCATAAGGAATTCTTGC
28237066 TTTTTAA
1 TTTTTAA
28237073 GGGGATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 15 0.30
50 35 0.70
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (49 bp):
TTTTTAACAGGAAGCGATAACCCTCACACAACCCATAAGGAATTCTTGC
Found at i:28242445 original size:23 final size:23
Alignment explanation
Indices: 28242419--28242462 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28242409 TATTTTTTGG
* *
28242419 AACATAAATATTCTATTTTTCTA
1 AACATAAATACTCTATATTTCTA
*
28242442 AACATGAATACTCTATATTTC
1 AACATAAATACTCTATATTTC
28242463 CATTCTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (23 bp):
AACATAAATACTCTATATTTCTA
Found at i:28247690 original size:18 final size:19
Alignment explanation
Indices: 28247667--28247706 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28247657 TAAGTGGAGA
28247667 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
28247685 ATTTTATGAATAAAATAAT
1 ATTTTATGAATAAAATAAT
28247704 ATT
1 ATT
28247707 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:28248808 original size:5 final size:4
Alignment explanation
Indices: 28248788--28248855 Score: 50
Period size: 4 Copynumber: 16.2 Consensus size: 4
28248778 CAGTGGCTGG
* *
28248788 AGAA AGAA AGAAA AGAGA AG-A A-AA AGAAA AAAA AGAGA GGAA AGAAA
1 AGAA AGAA AG-AA AGA-A AGAA AGAA AG-AA AGAA AGA-A AGAA AG-AA
*
28248835 AGAA AGAA AGAA AGGA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
28248856 AAAAATATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
3 4 0.08
4 30 0.59
5 17 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28248815 original size:20 final size:20
Alignment explanation
Indices: 28248790--28248847 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
28248780 GTGGCTGGAG
28248790 AAAGAAAGAAAAGAGAAGAA
1 AAAGAAAGAAAAGAGAAGAA
* *
28248810 AAAGAAAAAAAAGAGAGGAA
1 AAAGAAAGAAAAGAGAAGAA
*
28248830 AGA-AAAG-AAAGA-AAGAA
1 AAAGAAAGAAAAGAGAAGAA
28248847 A
1 A
28248848 GGAAGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 3 0.09
20 20 0.61
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAAGAGAAGAA
Found at i:28258783 original size:69 final size:70
Alignment explanation
Indices: 28258705--28258884 Score: 220
Period size: 75 Copynumber: 2.5 Consensus size: 70
28258695 ATCACATAAC
* **
28258705 TTTAGGAATTTCTTTTGAAGTAGGAAACTATTTCCTATGAATTTCCC-AAATTAAAATACTATCC
1 TTTAGGAATTTCTTTTGAAGTAGGAAACAATTTCCTATGAATCACCCAAAATTAAAATACTATCC
28258769 TTAAT
66 TTAAT
* **
28258774 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATATTATGAATCACCCAAAATTAAAATTT
1 TTTAGGAATTTCTTTTGAAGTAGGAAACAATTTCC-----TATGAATCACCCAAAATTAAAATAC
28258839 TATCCTTAAT
61 TATCCTTAAT
* *
28258849 TTTAGGAATTGC-TTTGAAAATAGGAAACAATTTCCT
1 TTTAGGAATTTCTTTTG-AAGTAGGAAACAATTTCCT
28258885 TTTTTTTCTT
Statistics
Matches: 95, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
69 33 0.35
70 1 0.01
74 13 0.14
75 48 0.51
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (70 bp):
TTTAGGAATTTCTTTTGAAGTAGGAAACAATTTCCTATGAATCACCCAAAATTAAAATACTATCC
TTAAT
Found at i:28261327 original size:27 final size:27
Alignment explanation
Indices: 28261292--28261354 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
28261282 CACAACGTAG
28261292 GGGCAAAATGGTCATTTTGCCATCCGA
1 GGGCAAAATGGTCATTTTGCCATCCGA
28261319 GGGCAAAATGGTCATTTTGCCATCCGA
1 GGGCAAAATGGTCATTTTGCCATCCGA
28261346 GGGCAAAAT
1 GGGCAAAAT
28261355 TGGAATGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (27 bp):
GGGCAAAATGGTCATTTTGCCATCCGA
Found at i:28263712 original size:13 final size:13
Alignment explanation
Indices: 28263694--28263720 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28263684 AAGAAAATGG
28263694 AATATTTTTATTT
1 AATATTTTTATTT
28263707 AATATTTTTATTT
1 AATATTTTTATTT
28263720 A
1 A
28263721 GTTTGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATATTTTTATTT
Found at i:28270884 original size:9 final size:9
Alignment explanation
Indices: 28270861--28270915 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
28270851 AAACAACTAA
28270861 TTAA-TTTT
1 TTAATTTTT
28270869 TT-A-TTTT
1 TTAATTTTT
28270876 TTAATTTTT
1 TTAATTTTT
28270885 TTAATTTTT
1 TTAATTTTT
**
28270894 TTAATTTAA
1 TTAATTTTT
28270903 TTAATTTTAT
1 TTAATTTT-T
28270913 TTA
1 TTA
28270916 GCGATAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 7 0.17
8 3 0.08
9 27 0.68
10 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTAATTTTT
Found at i:28270910 original size:24 final size:24
Alignment explanation
Indices: 28270861--28270911 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28270851 AAACAACTAA
** *
28270861 TTAATTTTTTATTTTTTAATTTTT
1 TTAATTTTTTATAATTTAATTATT
28270885 TTAATTTTTT-TAATTTAATTAATT
1 TTAATTTTTTATAATTTAATT-ATT
28270909 TTA
1 TTA
28270912 TTTAGCGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTAATTTTTTATAATTTAATTATT
Found at i:28270914 original size:14 final size:14
Alignment explanation
Indices: 28270867--28270915 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
28270857 CTAATTAATT
*
28270867 TTTTATTT-TTTAA
1 TTTTATTTAATTAA
*
28270880 TTTT-TTTAATT-T
1 TTTTATTTAATTAA
28270892 TTTTAATTTAATTAA
1 TTTT-ATTTAATTAA
28270907 TTTTATTTA
1 TTTTATTTA
28270916 GCGATAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 7 0.24
13 6 0.21
14 12 0.41
15 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTAATTAA
Found at i:28275872 original size:35 final size:34
Alignment explanation
Indices: 28275826--28275894 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 34
28275816 AAAATCAAAG
*
28275826 AAATTTTACCTTTGCTTGATCAAATCCTTGAATNT
1 AAATTTTACCTTTACTTGATCAAATCCTTGAAT-T
28275861 AAATTTTACCTTTACTTGATCAAATCCTTGAATT
1 AAATTTTACCTTTACTTGATCAAATCCTTGAATT
28275895 CTAACACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.43
Consensus pattern (34 bp):
AAATTTTACCTTTACTTGATCAAATCCTTGAATT
Found at i:28280482 original size:313 final size:313
Alignment explanation
Indices: 28279906--28280539 Score: 1044
Period size: 313 Copynumber: 2.0 Consensus size: 313
28279896 AAAGGGCATT
*
28279906 ATTGTCAAGTAATGTCAAAAATTGGATAAAAACAATTAAAATTATAATGAAGAACATTTTTGAAT
1 ATTGTCAAGTAATGCCAAAAATTGGATAAAAACAATTAAAATTATAATGAAGAACATTTTTGAAT
**
28279971 TAGACTTATGCAGAAGGTTATTTCTCATAATTTTCTCTTTAAATTGAGAATAATTTATTATTATC
66 TAGACTTATAAAGAAGGTTATTTCTCATAATTTTCTCTTTAAATTGAGAATAATTTATTATTATC
*
28280036 TAATTGTACTTGGCTCCTTAAAATTAAATTTTGGATTCATTGCTACTCAGAATTATTTTATTACG
131 TAATTGTACTTGGCTCCTTAAAATTAAATTTTGGATTCATTGCTACTCAAAATTATTTTATTACG
* *
28280101 ATTATACTTTCTATGCATATATTCAAATTCATAAGAAAAGTGCAAAGTTATGTCCGTAAATGTCC
196 ATTATACTTTCTATACATATATTCAAATTCATAAGAAAAGTGCAAAGTTATGTCCGTAAATATCC
* *
28280166 CTCTTAGAAATTCTTTCTTGATTGGGTGAACAATGAACTCGATCTCTTCTACA
261 CTCTTAGAAATTCTTTCTTGATTGGGTGAAAAATGAACTAGATCTCTTCTACA
* * *
28280219 GTTGTCAAGTAATGCCAAAAATTGGATAAAAATAATTAGAATTATAATG-AGAAACATTTTTGAA
1 ATTGTCAAGTAATGCCAAAAATTGGATAAAAACAATTAAAATTATAATGAAG-AACATTTTTGAA
28280283 TTAGACTTATAAAGAAGGTTATTTCTCATAATTTT-T-TTTAAAAATTGAGAATAATTTATTATT
65 TTAGACTTATAAAGAAGGTTATTTCTCATAATTTTCTCTTT--AAATTGAGAATAATTTATTATT
28280346 ATCTAATTGTACTTGGCTCCTTAAAATTAAATTTTGGA-TC-TGTCGCTACTCAAAATTATTTTA
128 ATCTAATTGTACTTGGCTCCTTAAAATTAAATTTTGGATTCAT-T-GCTACTCAAAATTATTTTA
* * * *
28280409 TTATGATTATACTTTCTATACGTATATTCAAATTCATAAGAAAAGTGTAAAGTTATGTCCTTAAA
191 TTACGATTATACTTTCTATACATATATTCAAATTCATAAGAAAAGTGCAAAGTTATGTCCGTAAA
*
28280474 TATCCCTCTTAGAAATTCTTTCTTGATTGGGTGAAAAATGAACTAGATCTCTTTTACA
256 TATCCCTCTTAGAAATTCTTTCTTGATTGGGTGAAAAATGAACTAGATCTCTTCTACA
28280532 ATTGTCAA
1 ATTGTCAA
28280540 TGGGTAAAAT
Statistics
Matches: 299, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
311 4 0.01
312 6 0.02
313 289 0.97
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (313 bp):
ATTGTCAAGTAATGCCAAAAATTGGATAAAAACAATTAAAATTATAATGAAGAACATTTTTGAAT
TAGACTTATAAAGAAGGTTATTTCTCATAATTTTCTCTTTAAATTGAGAATAATTTATTATTATC
TAATTGTACTTGGCTCCTTAAAATTAAATTTTGGATTCATTGCTACTCAAAATTATTTTATTACG
ATTATACTTTCTATACATATATTCAAATTCATAAGAAAAGTGCAAAGTTATGTCCGTAAATATCC
CTCTTAGAAATTCTTTCTTGATTGGGTGAAAAATGAACTAGATCTCTTCTACA
Found at i:28287474 original size:91 final size:91
Alignment explanation
Indices: 28287375--28287550 Score: 282
Period size: 91 Copynumber: 1.9 Consensus size: 91
28287365 TATTTAATAT
* *
28287375 GGGGACAATAATCATATTACCCGTGGGTATTGTAATTTTTTTATTC-ATTAAAATTATAAATTAT
1 GGGGACAATAATCATATTACCCGAGGGTATTGTAATTTTTTTATTCAATT-AAATAATAAATTAT
* *
28287439 TTGATCGAATGTATAATTTTTTTAAAA
65 TGGATCAAATGTATAATTTTTTTAAAA
*
28287466 GGGGACAATAATCATATTACCTGAGGGTATTGTAATTTTTTTATTCAATTAAATAATAAATTATT
1 GGGGACAATAATCATATTACCCGAGGGTATTGTAATTTTTTTATTCAATTAAATAATAAATTATT
*
28287531 GGATTAAATGTATAATTTTT
66 GGATCAAATGTATAATTTTT
28287551 ATTTATTGTA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 75 0.96
92 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (91 bp):
GGGGACAATAATCATATTACCCGAGGGTATTGTAATTTTTTTATTCAATTAAATAATAAATTATT
GGATCAAATGTATAATTTTTTTAAAA
Found at i:28289561 original size:21 final size:21
Alignment explanation
Indices: 28289518--28289562 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28289508 ATAGGCAGAG
* *
28289518 AATAAAGTGAATATTGTACCA
1 AATAAAGTGAACATTGCACCA
* *
28289539 AATAAGGTGAACATTGCATCA
1 AATAAAGTGAACATTGCACCA
28289560 AAT
1 AAT
28289563 TAGGGAGTTG
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:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (21 bp):
AATAAAGTGAACATTGCACCA
Found at i:28297966 original size:20 final size:20
Alignment explanation
Indices: 28297931--28297983 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28297921 AAAACTAATC
*
28297931 AATAACAAACAAATTAAAAGA
1 AATAACATA-AAATTAAAAGA
*
28297952 AATAACATAAAATTAAAATA
1 AATAACATAAAATTAAAAGA
* *
28297972 ACTAACTTAAAA
1 AATAACATAAAA
28297984 GTAACCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (20 bp):
AATAACATAAAATTAAAAGA
Found at i:28299328 original size:20 final size:20
Alignment explanation
Indices: 28299303--28299372 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
28299293 TTAACACAAC
28299303 AAAACATGCAAATCACAAAT
1 AAAACATGCAAATCACAAAT
* *
28299323 AAAACATGTAAAT-A-AACT
1 AAAACATGCAAATCACAAAT
*
28299341 AACA-ATGCAAATCACAAAT
1 AAAACATGCAAATCACAAAT
*
28299360 AAAACATGTAAAT
1 AAAACATGCAAAT
28299373 AAACTAACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 7 0.17
20 19 0.47
ACGTcount: A:0.60, C:0.16, G:0.06, T:0.19
Consensus pattern (20 bp):
AAAACATGCAAATCACAAAT
Found at i:28299354 original size:37 final size:37
Alignment explanation
Indices: 28299308--28299382 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
28299298 ACAACAAAAC
28299308 ATGCAAATCACAAATAAAACATGTAAATAAACTAACA
1 ATGCAAATCACAAATAAAACATGTAAATAAACTAACA
28299345 ATGCAAATCACAAATAAAACATGTAAATAAACTAACA
1 ATGCAAATCACAAATAAAACATGTAAATAAACTAACA
28299382 A
1 A
28299383 AATTCTAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (37 bp):
ATGCAAATCACAAATAAAACATGTAAATAAACTAACA
Found at i:28299525 original size:6 final size:6
Alignment explanation
Indices: 28299511--28299642 Score: 123
Period size: 6 Copynumber: 22.8 Consensus size: 6
28299501 AAAGGAAAAG
*
28299511 AATAGAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAC
1 AATA-AT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
* * * * * *
28299560 AATAAC AATAA- AGTAA- AATAAT AAAAAT AAAAAT AAAAAT AATAAA
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
* * *
28299606 AATAAA AATAAA AATAA- AATGA- AATAA- AATAA- AATAA
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAA
28299643 ACCAAAACTG
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
5 26 0.22
6 86 0.74
7 4 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (6 bp):
AATAAT
Found at i:28299536 original size:15 final size:15
Alignment explanation
Indices: 28299511--28299642 Score: 123
Period size: 15 Copynumber: 9.1 Consensus size: 15
28299501 AAAGGAAAAG
28299511 AATAGATAATAATAAT
1 AATA-ATAATAATAAT
28299527 AATAATAATAATAAT
1 AATAATAATAATAAT
28299542 AATAATAATAATAAT
1 AATAATAATAATAAT
* *
28299557 AACAATAACAATAA-
1 AATAATAATAATAAT
* *
28299571 AGTAA-AATAATAAA
1 AATAATAATAATAAT
* *
28299585 AATAAAAATAAAAAT
1 AATAATAATAATAAT
* *
28299600 AATAAAAATAAAAAT
1 AATAATAATAATAAT
* *
28299615 AAAAATAA-AATGA-
1 AATAATAATAATAAT
28299628 AATAA-AATAA-AAT
1 AATAATAATAATAAT
28299641 AA
1 AA
28299643 ACCAAAACTG
Statistics
Matches: 98, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
12 3 0.03
13 15 0.15
14 10 0.10
15 66 0.67
16 4 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:28299542 original size:21 final size:21
Alignment explanation
Indices: 28299511--28299642 Score: 123
Period size: 21 Copynumber: 6.5 Consensus size: 21
28299501 AAAGGAAAAG
28299511 AATAGATAATAATAATAATAAT
1 AATA-ATAATAATAATAATAAT
28299533 AATAATAATAATAATAATAAT
1 AATAATAATAATAATAATAAT
* * *
28299554 AATAACAATAACAATAA-AGT
1 AATAATAATAATAATAATAAT
* *
28299574 AA-AATAATAAAAATAAAAAT
1 AATAATAATAATAATAATAAT
* * *
28299594 AAAAATAATAAAAATAAAAAT
1 AATAATAATAATAATAATAAT
* *
28299615 AAAAATAA-AATGA-AATAA-
1 AATAATAATAATAATAATAAT
28299633 AATAA-AATAA
1 AATAATAATAA
28299643 ACCAAAACTG
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
17 2 0.02
18 6 0.06
19 16 0.16
20 11 0.11
21 58 0.60
22 4 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAATAATAATAATAATAAT
Found at i:28306540 original size:121 final size:119
Alignment explanation
Indices: 28306326--28306566 Score: 401
Period size: 121 Copynumber: 2.0 Consensus size: 119
28306316 TAAGAATCGC
*** *
28306326 ATCATTTGGAGTTCTGTATCTCGAGATATGACCAAAATACTGAAACATATGCAAGCAGATTCTAG
1 ATCATTTGGAGTTCTGTAGAGCGAGATATAACCAAAATACTGAAACATATGCAAGCAGATTCTAG
28306391 GTCTTTCAACATCTTACTTTCCAAAATTAAGCCTAAATCACCTTTAATCCTACAA
66 GTCTTTCAACATCTTACTTTCCAAAATTAAGCCT-AATCACCTTTAATCCTACAA
* **
28306446 NATCATTTGGAGTTCTGTAGAGCGAGTTATAATTAAAATACTGAAACATATGCAAGCAGATTCTA
1 -ATCATTTGGAGTTCTGTAGAGCGAGATATAACCAAAATACTGAAACATATGCAAGCAGATTCTA
28306511 GGTCTTTCAACATCTTACTTTCCAAAATTAAGCCTAATCACCTTTAATCCTACAA
65 GGTCTTTCAACATCTTACTTTCCAAAATTAAGCCTAATCACCTTTAATCCTACAA
28306566 A
1 A
28306567 AAATATAAGA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
119 1 0.01
120 20 0.18
121 92 0.81
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (119 bp):
ATCATTTGGAGTTCTGTAGAGCGAGATATAACCAAAATACTGAAACATATGCAAGCAGATTCTAG
GTCTTTCAACATCTTACTTTCCAAAATTAAGCCTAATCACCTTTAATCCTACAA
Found at i:28306618 original size:19 final size:20
Alignment explanation
Indices: 28306594--28306635 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28306584 AATAATAAAC
28306594 AAATTAAAA-AAATAACATA
1 AAATTAAAATAAATAACATA
* *
28306613 AAATTAAAATAACTAACTTA
1 AAATTAAAATAAATAACATA
28306633 AAA
1 AAA
28306636 GTAACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATTAAAATAAATAACATA
Found at i:28306644 original size:20 final size:20
Alignment explanation
Indices: 28306606--28306644 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28306596 ATTAAAAAAA
*
28306606 TAACATAAAATTAAAATAAC
1 TAACATAAAAGTAAAATAAC
* *
28306626 TAACTTAAAAGTAACATAA
1 TAACATAAAAGTAAAATAA
28306645 TTATAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (20 bp):
TAACATAAAAGTAAAATAAC
Found at i:28310340 original size:20 final size:21
Alignment explanation
Indices: 28310310--28310348 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28310300 AAAAACGTGA
28310310 TTTTCCCTTTGAATTTTCTAG
1 TTTTCCCTTTGAATTTTCTAG
*
28310331 TTTT-CCTTTGATTTTTCT
1 TTTTCCCTTTGAATTTTCT
28310349 CTTTTCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64
Consensus pattern (21 bp):
TTTTCCCTTTGAATTTTCTAG
Found at i:28322368 original size:34 final size:35
Alignment explanation
Indices: 28322302--28322369 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
28322292 AATCACTTTG
* *
28322302 GGTTTTAGTTTAGCCCGTGAAAAACTAGTGTAAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAA
* * *
28322337 GGTTTTAGTTGAG-CCTTGAAAAGCCATTGTAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
28322370 GCTTAGTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (35 bp):
GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAA
Found at i:28330563 original size:7 final size:7
Alignment explanation
Indices: 28330551--28330586 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
28330541 ATATAGATAT
28330551 AGTTTGA
1 AGTTTGA
28330558 AGTTTGA
1 AGTTTGA
28330565 AGTTTGA
1 AGTTTGA
28330572 AGTTTGA
1 AGTTTGA
28330579 AGTTTGA
1 AGTTTGA
28330586 A
1 A
28330587 CCTTGAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (7 bp):
AGTTTGA
Found at i:28330592 original size:21 final size:21
Alignment explanation
Indices: 28330551--28330592 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28330541 ATATAGATAT
**
28330551 AGTTTGAAGTTTGAAGTTTGA
1 AGTTTGAAGTTTGAACCTTGA
28330572 AGTTTGAAGTTTGAACCTTGA
1 AGTTTGAAGTTTGAACCTTGA
28330593 GGAGACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (21 bp):
AGTTTGAAGTTTGAACCTTGA
Found at i:28334025 original size:2 final size:2
Alignment explanation
Indices: 28334020--28334066 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
28334010 ACACACACAC
28334020 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
28334062 AT AT A
1 AT AT A
28334067 CATACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28334769 original size:22 final size:22
Alignment explanation
Indices: 28334709--28334770 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
28334699 ATTTCAGGTA
* **
28334709 AATGTATC-AATACATTGAGGC
1 AATGTATCGGATACATTTCGGC
28334730 AATGTATCGGATACATTTCGGC
1 AATGTATCGGATACATTTCGGC
28334752 AATGTATCGGATACATTTC
1 AATGTATCGGATACATTTC
28334771 AAACAGAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 8 0.22
22 29 0.78
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (22 bp):
AATGTATCGGATACATTTCGGC
Found at i:28345334 original size:25 final size:25
Alignment explanation
Indices: 28345304--28345356 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
28345294 AGATCCTCTC
28345304 TCTTCCTATTGATCTCCCTCTCCTT
1 TCTTCCTATTGATCTCCCTCTCCTT
28345329 TCTTCCTATTGATCTCCCTCTCCTT
1 TCTTCCTATTGATCTCCCTCTCCTT
28345354 TCT
1 TCT
28345357 CCATTTCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.08, C:0.40, G:0.04, T:0.49
Consensus pattern (25 bp):
TCTTCCTATTGATCTCCCTCTCCTT
Found at i:28346479 original size:2 final size:2
Alignment explanation
Indices: 28346472--28346513 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
28346462 ATCTACATCT
*
28346472 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28346514 AAGGTTCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28349898 original size:22 final size:22
Alignment explanation
Indices: 28349879--28349930 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
28349869 TTCTCGCTAG
28349879 AGCGAGAATTCTTCTTCGCTGC
1 AGCGAGAATTCTTCTTCGCTGC
28349901 AGCGAGAATTCTTCTTCGCTGC
1 AGCGAGAATTCTTCTTCGCTGC
28349923 AGCGAGAA
1 AGCGAGAA
28349931 ACGGGGCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
AGCGAGAATTCTTCTTCGCTGC
Found at i:28349914 original size:19 final size:20
Alignment explanation
Indices: 28349862--28349930 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 20
28349852 CGGGTCTACT
*
28349862 CGAGAGTTTC-TCGCTAG-AG
1 CGAGAATTTCTTCGCT-GCAG
28349881 CGAGAATTCTTCTTCGCTGCAG
1 CGAGAA-T-TTCTTCGCTGCAG
28349903 CGAGAATTCTTCTTCGCTGCAG
1 CGAGAA-T-TTCTTCGCTGCAG
28349925 CGAGAA
1 CGAGAA
28349931 ACGGGGCTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 5 0.11
20 1 0.02
21 4 0.09
22 35 0.78
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (20 bp):
CGAGAATTTCTTCGCTGCAG
Found at i:28350238 original size:43 final size:43
Alignment explanation
Indices: 28350191--28350308 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 43
28350181 ACTTATGCAA
* * * *
28350191 ACTCCCCATTCACACATAGCCTGGTCATCATCGGTTTATGGGC
1 ACTCCCCATTCGCACATAGCCTGGTCATCATCAGCTCATGGGC
* * *
28350234 ACTCCCTACTT-GCACATAGTCCGGGTCATCATCAGCTCATGTGC
1 ACTCCCCA-TTCGCACATAG-CCTGGTCATCATCAGCTCATGGGC
28350278 ACTCCCACA-TCGCACATAG-CTGGGTCATCAT
1 ACTCCC-CATTCGCACATAGCCT-GGTCATCAT
28350309 TATCACACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
42 1 0.02
43 24 0.39
44 35 0.57
45 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (43 bp):
ACTCCCCATTCGCACATAGCCTGGTCATCATCAGCTCATGGGC
Found at i:28350280 original size:44 final size:43
Alignment explanation
Indices: 28350203--28350308 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
28350193 TCCCCATTCA
* * * * *
28350203 CACATAGCCTGGTCATCATCGGTTTATGGGCACTCCCTAC-TTG
1 CACATAGCCGGGTCATCATCAGCTCATGGGCACTCCC-ACATCG
*
28350246 CACATAGTCCGGGTCATCATCAGCTCATGTGCACTCCCACATCG
1 CACATAG-CCGGGTCATCATCAGCTCATGGGCACTCCCACATCG
*
28350290 CACATAGCTGGGTCATCAT
1 CACATAGCCGGGTCATCAT
28350309 TATCACACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 20 0.37
44 34 0.63
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (43 bp):
CACATAGCCGGGTCATCATCAGCTCATGGGCACTCCCACATCG
Found at i:28352268 original size:2 final size:2
Alignment explanation
Indices: 28352261--28352289 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28352251 ATGTAACTTA
28352261 AT AT 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 AT AT A
28352290 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28360395 original size:54 final size:54
Alignment explanation
Indices: 28360319--28360477 Score: 273
Period size: 54 Copynumber: 2.9 Consensus size: 54
28360309 TCATCATGTA
*
28360319 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
28360373 CATCTTACCCAGCTCATGTGCATCCCACTACATCGTGCACATAGCCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
28360427 CATCTCACCCAACTCATGTGCATTCCACCACATCGTGCACATAGCCGGACA
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
28360478 GTATCACCAT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:28360590 original size:2 final size:2
Alignment explanation
Indices: 28360583--28360609 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28360573 TATGACATAG
28360583 TA 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 TA T
28360610 CAACATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28363461 original size:43 final size:43
Alignment explanation
Indices: 28363405--28363539 Score: 148
Period size: 43 Copynumber: 3.1 Consensus size: 43
28363395 AGTCGGCTCA
* *
28363405 TCATCATCATCTTATGCGCACTCCCTACTTGCACATAGCC-ATG
1 TCATCACCATCTTATGCGCACTCCCTACTCGCACATAGCCGA-G
* *
28363448 TCATCACCGTCTTATGCGCACTCCCTTCTCGCACATAGCCGAG
1 TCATCACCATCTTATGCGCACTCCCTACTCGCACATAGCCGAG
* * * * * *
28363491 TCATCATCAGCTCATGTGCACTCCC-ACATCGCACATAGCTGGG
1 TCATCACCATCTTATGCGCACTCCCTAC-TCGCACATAGCCGAG
28363534 TCATCA
1 TCATCA
28363540 TTATCACACA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 76 0.97
44 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (43 bp):
TCATCACCATCTTATGCGCACTCCCTACTCGCACATAGCCGAG
Found at i:28365290 original size:18 final size:18
Alignment explanation
Indices: 28365263--28365302 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28365253 AATAGTTAAT
**
28365263 TTATGAGTTATTTATGAA
1 TTATGAGTTACCTATGAA
*
28365281 TTATGTGTTACCTATGAA
1 TTATGAGTTACCTATGAA
28365299 TTAT
1 TTAT
28365303 TTGTGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGAGTTACCTATGAA
Found at i:28368910 original size:21 final size:20
Alignment explanation
Indices: 28368885--28368925 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28368875 GCATTTGTAG
* *
28368885 ATATTTATTGTTACTTATTAT
1 ATATTTACTCTTA-TTATTAT
28368906 ATATTTACTCTTATTATTAT
1 ATATTTACTCTTATTATTAT
28368926 CATTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTACTCTTATTATTAT
Found at i:28369890 original size:40 final size:40
Alignment explanation
Indices: 28369782--28369912 Score: 205
Period size: 40 Copynumber: 3.4 Consensus size: 40
28369772 CGAGAGGAAC
*
28369782 AAGCATAACC--TCACAAAGTCATTGCCTTTTCAAGGTTA
1 AAGCATAACCTTTCACAAAGTCTTTGCCTTTTCAAGGTTA
* *
28369820 AAGCACAACCTTTCA-AAAGTCTCTGCCTTTTCAAGGTTA
1 AAGCATAACCTTTCACAAAGTCTTTGCCTTTTCAAGGTTA
*
28369859 AAGCATAACCTTTCACAAAGTTTTTGCCTTTTCAAGGTTA
1 AAGCATAACCTTTCACAAAGTCTTTGCCTTTTCAAGGTTA
28369899 AAGCATAACCTTTC
1 AAGCATAACCTTTC
28369913 TACCTTTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
38 9 0.11
39 36 0.43
40 39 0.46
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (40 bp):
AAGCATAACCTTTCACAAAGTCTTTGCCTTTTCAAGGTTA
Found at i:28379168 original size:26 final size:26
Alignment explanation
Indices: 28379139--28379199 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
28379129 ACCATATACC
28379139 CATCATCATCAAGCACACCATCCCAT
1 CATCATCATCAAGCACACCATCCCAT
*
28379165 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCAAGCACACCATCCCAT
28379191 CATCATCAT
1 CATCATCAT
28379200 TCCCAGCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.33, C:0.41, G:0.03, T:0.23
Consensus pattern (26 bp):
CATCATCATCAAGCACACCATCCCAT
Found at i:28379261 original size:43 final size:43
Alignment explanation
Indices: 28379213--28379361 Score: 181
Period size: 43 Copynumber: 3.5 Consensus size: 43
28379203 CAGCTCATGC
** *
28379213 GCACTCCCTACTCGCACATGGCTAGGTCATCACCGGGTTATGT
1 GCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGT
* **
28379256 GCACTCCCTACTCTCACATAACCAGGTCATCACCAAGTTATGT
1 GCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGT
* * * * *
28379299 GCACTCCCTACTAGCACATAACCGGGTCATCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGT
* *
28379342 GCACTTCCTACTCGTACATA
1 GCACTCCCTACTCGCACATA
28379362 GCCGAGTCAA
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGT
Found at i:28392446 original size:2 final size:2
Alignment explanation
Indices: 28392439--28392463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28392429 GCTTGACATC
28392439 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
28392464 TTGCAATAGA
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:28393052 original size:155 final size:155
Alignment explanation
Indices: 28392770--28393079 Score: 611
Period size: 155 Copynumber: 2.0 Consensus size: 155
28392760 AGAATGAATT
*
28392770 CTCGCTGCAGCGAGAAACCTTCTGTCGTGCTTGCTACCTTGTTTGGTTTCTGTCATATTTTCCAC
1 CTCGCTGCAGCGAGAAACCTTCTGTCGTGCTTGCTACCTTGTTTGGTTTCTGCCATATTTTCCAC
28392835 TTCTTTAACATCATAGTTGATCATGGACTTCCAACATCAAGGAATTAATTAATTAAGTTTGAAAT
66 TTCTTTAACATCATAGTTGATCATGGACTTCCAACATCAAGGAATTAATTAATTAAGTTTGAAAT
28392900 GAGGGGTTTTAGTGAGAAACCCTCG
131 GAGGGGTTTTAGTGAGAAACCCTCG
28392925 CTCGCTGCAGCGAGAAACCTTCTGTCGTGCTTGCTACCTTGTTTGGTTTCTGCCATATTTTCCAC
1 CTCGCTGCAGCGAGAAACCTTCTGTCGTGCTTGCTACCTTGTTTGGTTTCTGCCATATTTTCCAC
28392990 TTCTTTAACATCATAGTTGATCATGGACTTCCAACATCAAGGAATTAATTAATTAAGTTTGAAAT
66 TTCTTTAACATCATAGTTGATCATGGACTTCCAACATCAAGGAATTAATTAATTAAGTTTGAAAT
28393055 GAGGGGTTTTAGTGAGAAACCCTCG
131 GAGGGGTTTTAGTGAGAAACCCTCG
28393080 GCCAGCTTAT
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 154 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (155 bp):
CTCGCTGCAGCGAGAAACCTTCTGTCGTGCTTGCTACCTTGTTTGGTTTCTGCCATATTTTCCAC
TTCTTTAACATCATAGTTGATCATGGACTTCCAACATCAAGGAATTAATTAATTAAGTTTGAAAT
GAGGGGTTTTAGTGAGAAACCCTCG
Found at i:28394967 original size:101 final size:100
Alignment explanation
Indices: 28394814--28395016 Score: 352
Period size: 101 Copynumber: 2.0 Consensus size: 100
28394804 CAACTATGTG
*
28394814 AAATTCTTGAAAGACATCTTGAGTAAAAGAGGAAATTAGGTGAGTTTAAGACTATTGCACTTATT
1 AAATTCTTGAAAGACATCTTGAGTAAAAGAGGAAATTAAGTGAGTTTAAGACTATTGCACTTATT
*
28394879 GAAGAGTGCAATGCCATAATTCAAAATAAGCTTCC
66 GAAGAGTGCAATGCCATAATGCAAAATAAGCTTCC
*
28394914 AAATTCTTGAAAGACATCTTGAGTAAAAAGAGGAAATTAAGTGAGTTTAAGACTGTTGCACTTAT
1 AAATTCTTGAAAGACATCTTGAGT-AAAAGAGGAAATTAAGTGAGTTTAAGACTATTGCACTTAT
* *
28394979 TGAAGAGTGTAGTGCCATAATGCAAAATAAGCTTCC
65 TGAAGAGTGCAATGCCATAATGCAAAATAAGCTTCC
28395015 AA
1 AA
28395017 CAAAGCTTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 24 0.25
101 73 0.75
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (100 bp):
AAATTCTTGAAAGACATCTTGAGTAAAAGAGGAAATTAAGTGAGTTTAAGACTATTGCACTTATT
GAAGAGTGCAATGCCATAATGCAAAATAAGCTTCC
Found at i:28398357 original size:19 final size:20
Alignment explanation
Indices: 28398315--28398357 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
28398305 AAATCAAGAT
*
28398315 TTTTCATTTTCTTTTCCTTG
1 TTTTCATTTTCTTTTCCTTC
* *
28398335 TTTTCCTTTT-TTTTCTTTC
1 TTTTCATTTTCTTTTCCTTC
28398354 TTTT
1 TTTT
28398358 TCTTACTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCATTTTCTTTTCCTTC
Found at i:28398998 original size:35 final size:35
Alignment explanation
Indices: 28398967--28399037 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
28398957 AAAGTGCGTG
*
28398967 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
28399002 TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
28399037 T
1 T
28399038 AAGCTGGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (35 bp):
TGATGATATTGAAATGTACGTGTAGGGAGTGCACA
Found at i:28401106 original size:17 final size:17
Alignment explanation
Indices: 28401084--28401117 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28401074 TAGCATGGAG
28401084 TGTAACAACTCAGGGCA
1 TGTAACAACTCAGGGCA
28401101 TGTAACAACTCAGGGCA
1 TGTAACAACTCAGGGCA
28401118 GTGTTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
TGTAACAACTCAGGGCA
Found at i:28401713 original size:27 final size:27
Alignment explanation
Indices: 28401659--28401719 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
28401649 AAATATATTA
*
28401659 AAAAATTAAAATAAAATATACAAAATT
1 AAAAATAAAAATAAAATATACAAAATT
* ** *
28401686 ATAAATAAAAATAAAATATATGATATT
1 AAAAATAAAAATAAAATATACAAAATT
28401713 AAAAATA
1 AAAAATA
28401720 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAATAAAAATAAAATATACAAAATT
Found at i:28401730 original size:14 final size:15
Alignment explanation
Indices: 28401698--28401747 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
28401688 AAATAAAAAT
**
28401698 AAAATATATGATATTA
1 AAAATATATTTTA-TA
28401714 AAAATATATTTTA-A
1 AAAATATATTTTATA
*
28401728 AAAAGATATTTTATA
1 AAAATATATTTTATA
28401743 AAAAT
1 AAAAT
28401748 TAATAATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.45
15 5 0.17
16 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (15 bp):
AAAATATATTTTATA
Found at i:28402356 original size:34 final size:32
Alignment explanation
Indices: 28402290--28402360 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
28402280 AAATTTAAAT
*
28402290 TTAAATAATAAAAAAATATCTCAAATATCAAC
1 TTAAATAATAAAAAAATATCTCAAATAACAAC
28402322 TTAAATAATTAGAAACAAATAT-TCAAATAACAAC
1 TTAAATAA-TA-AAA-AAATATCTCAAATAACAAC
28402356 TTAAA
1 TTAAA
28402361 CACTACAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 8 0.23
33 2 0.06
34 19 0.54
35 6 0.17
ACGTcount: A:0.59, C:0.11, G:0.01, T:0.28
Consensus pattern (32 bp):
TTAAATAATAAAAAAATATCTCAAATAACAAC
Found at i:28402630 original size:40 final size:39
Alignment explanation
Indices: 28402583--28402673 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
28402573 TATATACTAA
* ** *
28402583 AATATATATAATAGTA-ATTATATTTTTTATAAATTAATAT
1 AATATATATAATA-TATATTAAAGATATTATAAATTAAT-T
*
28402623 AATATATAAAATATATATTAAAGATATTATAAATTAATT
1 AATATATATAATATATATTAAAGATATTATAAATTAATT
28402662 AATA-ATTATAAT
1 AATATA-TATAAT
28402674 TTTATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.02
39 12 0.28
40 30 0.70
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (39 bp):
AATATATATAATATATATTAAAGATATTATAAATTAATT
Found at i:28402695 original size:22 final size:24
Alignment explanation
Indices: 28402646--28402700 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
28402636 TATATTAAAG
28402646 ATATTATAAATTAATTAATAATTATA
1 ATATTATAAATTAATT--TAATTATA
*
28402672 ATTTTATAAATTAATTTAATTAATA
1 ATATTATAAATTAATTTAATT-ATA
28402697 ATAT
1 ATAT
28402701 AAATTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTATAAATTAATTTAATTATA
Found at i:28402701 original size:22 final size:22
Alignment explanation
Indices: 28402650--28402728 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
28402640 TTAAAGATAT
28402650 TATAAATTAATTAATAATT-ATAA
1 TATAAATTAATT--TAATTAATAA
28402673 TTTTATAAATTAATTTAATTAATAA
1 ---TATAAATTAATTTAATTAATAA
* *
28402698 TATAAATTTATTT--TTAATCA
1 TATAAATTAATTTAATTAATAA
28402718 TATAAAATTAA
1 TAT-AAATTAA
28402729 AAAAATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 9 0.19
21 6 0.12
22 12 0.25
24 5 0.10
25 4 0.08
26 12 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAATTAATTTAATTAATAA
Found at i:28402707 original size:18 final size:17
Alignment explanation
Indices: 28402610--28402705 Score: 51
Period size: 17 Copynumber: 5.5 Consensus size: 17
28402600 TTATATTTTT
28402610 TATAAATTAATATAAT-A
1 TATAAATTAAT-TAATAA
*
28402627 TATAAAATATATATTAAAGATAT
1 TAT-AAAT-TA-ATT--A-ATAA
28402650 TATAAATTAATTAATAA
1 TATAAATTAATTAATAA
28402667 T-TATAATT--TT-ATAA
1 TATA-AATTAATTAATAA
*
28402681 -ATTAATTTAATTAATAA
1 TA-TAAATTAATTAATAA
28402698 TATAAATT
1 TATAAATT
28402706 TATTTTTAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
14 7 0.11
15 4 0.07
16 4 0.07
17 20 0.33
18 6 0.10
19 3 0.05
20 5 0.08
21 3 0.05
22 6 0.10
23 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
TATAAATTAATTAATAA
Found at i:28403041 original size:34 final size:34
Alignment explanation
Indices: 28403001--28403076 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
28402991 CAGCCGTCTT
*
28403001 CCTCTCTCTCACGAGCTTCACATTTGCTCCGCTG
1 CCTCTCTCTAACGAGCTTCACATTTGCTCCGCTG
* *
28403035 CCTCTCTCTAACGAGCTTCACATTTGGTCCGCTT
1 CCTCTCTCTAACGAGCTTCACATTTGCTCCGCTG
28403069 CCTCTCTC
1 CCTCTCTC
28403077 GAGCTTCCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.12, C:0.41, G:0.13, T:0.34
Consensus pattern (34 bp):
CCTCTCTCTAACGAGCTTCACATTTGCTCCGCTG
Found at i:28409040 original size:53 final size:53
Alignment explanation
Indices: 28408960--28409065 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
28408950 AAAAAAAACC
*
28408960 TTTAAATTATTCAAGAAAATTCAAATCTTTATTCTTTTGTTGTGTTCAAATAA
1 TTTAAATTATTCAAGAAAATTCAAATCTTTATTCTTTTATTGTGTTCAAATAA
*
28409013 TTTAAATTATTCAAGAAAATTCAAATCTTTATTTTTTTATTGTGTTCAAATAA
1 TTTAAATTATTCAAGAAAATTCAAATCTTTATTCTTTTATTGTGTTCAAATAA
28409066 ATTCTTATAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (53 bp):
TTTAAATTATTCAAGAAAATTCAAATCTTTATTCTTTTATTGTGTTCAAATAA
Found at i:28409081 original size:18 final size:18
Alignment explanation
Indices: 28409058--28409092 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28409048 TTTATTGTGT
28409058 TCAAATAAATTCTTATAG
1 TCAAATAAATTCTTATAG
*
28409076 TCAAATAAATTTTTATA
1 TCAAATAAATTCTTATA
28409093 ATTAATGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (18 bp):
TCAAATAAATTCTTATAG
Found at i:28410094 original size:79 final size:80
Alignment explanation
Indices: 28409891--28410098 Score: 212
Period size: 80 Copynumber: 2.6 Consensus size: 80
28409881 GGTACGATGC
* * * *
28409891 CCAA-CTTAACCCTATGGTATTCTTACCCCCACACC-AAGACTAGAGCCAACATACAAAAAAGGA
1 CCAAGCTTAACCTTGTGGTATTCTTACCTCAACACCGAA-ACTAGAGCCAACATACAAAAAAGGA
28409954 AAATGTAACACGTTGG
65 AAATGTAACACGTTGG
* * * ** *
28409970 CCAAGCTTAACCTTGTGGTATTCTTACTCCTACAATA--G-GATTAGAGTTAACATACAAAAAGG
1 CCAAGCTTAACCTTGTGGTATTCTTA--CCT-CAACACCGAAACTAGAGCCAACATACAAAAAAG
* **
28410032 GAAGATGTGGCAC-TTGG
63 GAAAATGTAACACGTTGG
*
28410049 CCAAGTTTAACCTTGTGGTATTCTTACCTCAACACCGAAACTAGAGCCAA
1 CCAAGCTTAACCTTGTGGTATTCTTACCTCAACACCGAAACTAGAGCCAA
28410099 TATATATAAG
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
76 4 0.04
77 3 0.03
78 1 0.01
79 41 0.40
80 48 0.47
82 2 0.02
83 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (80 bp):
CCAAGCTTAACCTTGTGGTATTCTTACCTCAACACCGAAACTAGAGCCAACATACAAAAAAGGAA
AATGTAACACGTTGG
Found at i:28413492 original size:21 final size:21
Alignment explanation
Indices: 28413454--28413494 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28413444 AAGTAAGTTA
*
28413454 TTTTAATTTTATATTTATTTC
1 TTTTAATTTGATATTTATTTC
28413475 TTTTAATTTGACTA-TTATTT
1 TTTTAATTTGA-TATTTATTT
28413495 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTAATTTGATATTTATTTC
Found at i:28416390 original size:9 final size:9
Alignment explanation
Indices: 28416372--28416412 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
28416362 AAGAAGGCTG
28416372 AATG-ATAC
1 AATGAATAC
28416380 AATGAATAC
1 AATGAATAC
28416389 AATGAATAC
1 AATGAATAC
*
28416398 AATGAATAT
1 AATGAATAC
28416407 AATGAA
1 AATGAA
28416413 AGAATAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 4 0.13
9 27 0.87
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (9 bp):
AATGAATAC
Found at i:28417718 original size:15 final size:15
Alignment explanation
Indices: 28417700--28417747 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
28417690 TTTGTATCCC
28417700 AAATATCAACATTCA
1 AAATATCAACATTCA
* *
28417715 AAATATGAACATCCA
1 AAATATCAACATTCA
* *
28417730 AAGTATTAACATTCA
1 AAATATCAACATTCA
28417745 AAA
1 AAA
28417748 GTGTTAGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (15 bp):
AAATATCAACATTCA
Found at i:28423914 original size:54 final size:54
Alignment explanation
Indices: 28423850--28424082 Score: 367
Period size: 54 Copynumber: 4.3 Consensus size: 54
28423840 AAAACATTTT
* * *
28423850 ATCTCACCCAGCTCATGTGCATCCCACCACATGGTGCACATAGCTGAACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
* *
28423904 ATCTCACCCAGCTCACGTGCATCCCACCACATGGTGCACATAGCCGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
*
28423958 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
* ** * *
28424012 ACCTCACTTAGCTCATGTGCAGCCCACCACATCGTGCACATAGCTGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
28424066 ATCTCACCCAGCTCATG
1 ATCTCACCCAGCTCATG
28424083 CACAGTTACA
Statistics
Matches: 164, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 164 1.00
ACGTcount: A:0.26, C:0.40, G:0.15, T:0.18
Consensus pattern (54 bp):
ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
Found at i:28423933 original size:30 final size:30
Alignment explanation
Indices: 28423898--28423990 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
28423888 CATAGCTGAA
28423898 CACCACATCTCACCCAGCTCACGTGCATCC
1 CACCACATCTCACCCAGCTCACGTGCATCC
* **
28423928 CACCACATGGTGCACATAG--C-CG-G-A---
1 CACCACAT-CT-CACCCAGCTCACGTGCATCC
*
28423952 CACCACATCTCACCCAGCTCATGTGCATCC
1 CACCACATCTCACCCAGCTCACGTGCATCC
28423982 CACCACATC
1 CACCACATC
28423991 GTGCACATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 20
0.63 0.10 0.27
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
24 9 0.20
25 1 0.02
26 1 0.02
27 2 0.04
28 1 0.02
29 2 0.04
30 18 0.39
31 1 0.02
32 5 0.11
ACGTcount: A:0.26, C:0.45, G:0.13, T:0.16
Consensus pattern (30 bp):
CACCACATCTCACCCAGCTCACGTGCATCC
Found at i:28438249 original size:21 final size:21
Alignment explanation
Indices: 28438210--28438249 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28438200 ACAGAATGTT
*
28438210 TCTCGCTACAACGAGATTGAA
1 TCTCGCTACAACGAAATTGAA
* *
28438231 TCTCGCTATAGCGAAATTG
1 TCTCGCTACAACGAAATTG
28438250 TAACCCAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TCTCGCTACAACGAAATTGAA
Found at i:28438264 original size:60 final size:58
Alignment explanation
Indices: 28438139--28438292 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 58
28438129 TAAGAGGCAA
* * * *
28438139 AAACAGAAGATTTTTCGCTGCAGCGAGATTGAATTTGCTGCAGCGAAATTATGACCCAG
1 AAACAGAAG-TTTCTCGCTGCAGCGAGATTGAATTCGCTACAGCGAAATTATAACCCAG
* * * *
28438198 AAACAGAATGTTTCTCGCTACAACGAGATTGAATCTCGCTATAGCGAAATTGTAACCCAG
1 AAACAGAA-GTTTCTCGCTGCAGCGAGATTGAAT-TCGCTACAGCGAAATTATAACCCAG
*
28438258 AAACAGAAAGTTTCTCGCTGCAGCGAGAATGAATT
1 AAACAG-AAGTTTCTCGCTGCAGCGAGATTGAATT
28438293 TTGCTGCTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 30 0.37
60 49 0.60
61 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (58 bp):
AAACAGAAGTTTCTCGCTGCAGCGAGATTGAATTCGCTACAGCGAAATTATAACCCAG
Found at i:28438720 original size:43 final size:43
Alignment explanation
Indices: 28438672--28438790 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 43
28438662 TCACCAGCTC
**** *
28438672 ATGCGCACTCCCTACTCTCACATGGTTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCTCACATAACCGGGTCATC-CTCGGCTT
28438715 ATGCGCACTCCCTACT-TGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCT-CACATAACCGGGTCATCCTCGGCTT
* * * *
28438758 ATGCTCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCTCACATAACCGGGTCA
28438791 ATATAATTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.03
43 62 0.97
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCTCACATAACCGGGTCATCCTCGGCTT
Found at i:28442088 original size:17 final size:17
Alignment explanation
Indices: 28442063--28442096 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28442053 GTTCAACTGT
* *
28442063 GAAAGTAAAAATAACAG
1 GAAAATAAAAAAAACAG
28442080 GAAAATAAAAAAAACAG
1 GAAAATAAAAAAAACAG
28442097 TCAATATGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.09
Consensus pattern (17 bp):
GAAAATAAAAAAAACAG
Found at i:28443697 original size:43 final size:43
Alignment explanation
Indices: 28443622--28443709 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
28443612 TGATAATAAG
* * * * * * *
28443622 GACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGTTGATGAT
1 GACCAAGCTATATGCAGTGTGGGACTACACATGAGCTAATGAT
*
28443665 GACCAAGCTATATGCAGTGTGGGACTATACATGAGCTAATGAT
1 GACCAAGCTATATGCAGTGTGGGACTACACATGAGCTAATGAT
28443708 GA
1 GA
28443710 TGATATTGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (43 bp):
GACCAAGCTATATGCAGTGTGGGACTACACATGAGCTAATGAT
Found at i:28444822 original size:2 final size:2
Alignment explanation
Indices: 28444815--28444862 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28444805 CAAACAATAG
28444815 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
28444857 AT AT AT
1 AT AT AT
28444863 GATGATGCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28447209 original size:21 final size:21
Alignment explanation
Indices: 28447185--28447226 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28447175 AGACAGAATG
*
28447185 CTCTTAGTTGACTAAGTGCCT
1 CTCTTAGTAGACTAAGTGCCT
28447206 CTCTTAGTAGACTAAGTGCCT
1 CTCTTAGTAGACTAAGTGCCT
28447227 ACTGTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (21 bp):
CTCTTAGTAGACTAAGTGCCT
Found at i:28454267 original size:30 final size:28
Alignment explanation
Indices: 28454222--28454423 Score: 163
Period size: 30 Copynumber: 6.9 Consensus size: 28
28454212 TCAGCTTTAC
*
28454222 CATGTTTGTTTTAATTTAGACAAAAAAA
1 CATGTTTGTCTTAATTTAGACAAAAAAA
* *
28454250 CATTGTTTAGTCATAATTTAGACAAGAAAA
1 CA-TGTTT-GTCTTAATTTAGACAAAAAAA
*
28454280 TATGTTTGTCTTAATTTAAGACAAGAAAAA
1 CATGTTTGTCTTAATTT-AGACAA-AAAAA
* * * *
28454310 TACTTTTTGTCTTAATGTAGACAAGAAAA
1 CA-TGTTTGTCTTAATTTAGACAAAAAAA
* *
28454339 CATATTTGTCTCAATTTAGACAAGATAAAA
1 CATGTTTGTCTTAATTTAGACAA-A-AAAA
* * * *
28454369 TATTTTTGTCTTAATTAAGGACAAGACAAA
1 CATGTTTGTCTTAATTTA-GACAA-AAAAA
* *
28454399 -ATATTTGTCTTAATTAAAGACAAAA
1 CATGTTTGTCTTAATT-TAGACAAAA
28454424 GTTGTCTTAA
Statistics
Matches: 144, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
28 30 0.21
29 40 0.28
30 54 0.38
31 20 0.14
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (28 bp):
CATGTTTGTCTTAATTTAGACAAAAAAA
Found at i:28454336 original size:59 final size:55
Alignment explanation
Indices: 28454226--28454413 Score: 216
Period size: 59 Copynumber: 3.2 Consensus size: 55
28454216 CTTTACCATG
* * * *
28454226 TTTGTTTTAATTTAGACAA-AAAAACATTGTTTAGTCATAATTTAGACAAGAAAATATG
1 TTTGTCTTAATTTAGACAAGAAAAATATT-TTT-GTCTTAA-TTAGACAAGAAAA-ATA
28454284 TTTGTCTTAATTTAAGACAAGAAAAATACTTTTTGTCTTAATGTAGACAAGAAAACATA
1 TTTGTCTTAATTT-AGACAAGAAAAATA-TTTTTGTCTTAAT-TAGACAAGAAAA-ATA
*
28454343 TTTGTCTCAATTTAGACAAGATAAAATATTTTTGTCTTAATTAAGGACAAGACAAAATA
1 TTTGTCTTAATTTAGACAAGA-AAAATATTTTTGTCTTAATT-A-GACAAGA-AAAATA
28454402 TTTGTCTTAATT
1 TTTGTCTTAATT
28454414 AAAGACAAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
57 1 0.01
58 35 0.30
59 65 0.57
60 12 0.10
61 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (55 bp):
TTTGTCTTAATTTAGACAAGAAAAATATTTTTGTCTTAATTAGACAAGAAAAATA
Found at i:28454377 original size:89 final size:87
Alignment explanation
Indices: 28454226--28454412 Score: 231
Period size: 89 Copynumber: 2.1 Consensus size: 87
28454216 CTTTACCATG
* * *
28454226 TTTGTTTTAATTTAGACAAAAAAACATTGTTTAGTCATAATTTAGACAAGAAAATATGTTTGTCT
1 TTTGTCTTAATGTAGACAAAAAAACATTATTTAGTCATAATTTAGACAAGAAAATATGTTTGTCT
28454291 TAATTTAA-GACAAGA-AAAATA
66 TAA-TTAAGGACAAGACAAAATA
* *
28454312 CTTTTTGTCTTAATGTAGACAAGAAAACA-TATTT-GTC-TCAATTTAGACAAGATAAAATATTT
1 ---TTTGTCTTAATGTAGACAAAAAAACATTATTTAGTCAT-AATTTAGACAAG--AAAATATGT
28454374 TTGTCTTAATTAAGGACAAGACAAAATA
60 TTGTCTTAATTAAGGACAAGACAAAATA
28454402 TTTGTCTTAAT
1 TTTGTCTTAAT
28454413 TAAAGACAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
86 1 0.01
87 26 0.30
88 8 0.09
89 47 0.53
90 6 0.07
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (87 bp):
TTTGTCTTAATGTAGACAAAAAAACATTATTTAGTCATAATTTAGACAAGAAAATATGTTTGTCT
TAATTAAGGACAAGACAAAATA
Found at i:28454576 original size:17 final size:17
Alignment explanation
Indices: 28454554--28454586 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28454544 ATAATAATAA
28454554 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
28454571 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
28454587 TTATCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:28459952 original size:42 final size:42
Alignment explanation
Indices: 28459892--28460068 Score: 257
Period size: 42 Copynumber: 4.2 Consensus size: 42
28459882 TTTTATGTGA
*
28459892 TAATGATGACCTAACTATGTGCGTGTGGGAGTGCACATGAGC
1 TAATGATGACCTAGCTATGTGCGTGTGGGAGTGCACATGAGC
* * *
28459934 TGATGATGACCTAGCTATGTGTGTGTGGGAGTGGACATGAGC
1 TAATGATGACCTAGCTATGTGCGTGTGGGAGTGCACATGAGC
28459976 TAATGATGACCTAGCTATGTGCG-GTGTGGAGTGCACATGAGC
1 TAATGATGACCTAGCTATGTGCGTGTG-GGAGTGCACATGAGC
* * * *
28460018 TGATGATGACCGAGCTATGTGCGAGTAGGGAGTACACATGAGC
1 TAATGATGACCTAGCTATGTGCGTGT-GGGAGTGCACATGAGC
28460061 TAATGATG
1 TAATGATG
28460069 GTGGGATGGT
Statistics
Matches: 121, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
41 3 0.02
42 94 0.78
43 23 0.19
44 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (42 bp):
TAATGATGACCTAGCTATGTGCGTGTGGGAGTGCACATGAGC
Found at i:28460101 original size:2 final size:2
Alignment explanation
Indices: 28460094--28460137 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28460084 TGATGATGTG
28460094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28460136 TA
1 TA
28460138 GATAAATATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28460486 original size:40 final size:40
Alignment explanation
Indices: 28460388--28460486 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
28460378 GCTAAAGCTC
* * * *
28460388 CTCGCTGCAACGAGAAACATTCTGTTTTTGATGCCTGCAA
1 CTCGCTGCAACGAGAAACTTTCTATTTTGGATACCTGCAA
* * *
28460428 CTCGCTGCAGCGAGAAACTTTTTATTTTGGCTACCTG-AA
1 CTCGCTGCAACGAGAAACTTTCTATTTTGGATACCTGCAA
28460467 TCTCGCTGCAACGAGAAACT
1 -CTCGCTGCAACGAGAAACT
28460487 CTCCATCCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
39 2 0.04
40 48 0.96
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
CTCGCTGCAACGAGAAACTTTCTATTTTGGATACCTGCAA
Found at i:28461664 original size:15 final size:15
Alignment explanation
Indices: 28461644--28461675 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28461634 TTCTCTATGA
28461644 CTTCT-TTCTT-TTC
1 CTTCTCTTCTTCTTC
28461657 CTTCTCTTCTTCTTC
1 CTTCTCTTCTTCTTC
28461672 CTTC
1 CTTC
28461676 ATTTCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 5 0.29
15 7 0.41
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTCTCTTCTTCTTC
Found at i:28467914 original size:15 final size:13
Alignment explanation
Indices: 28467876--28467918 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 13
28467866 AACAAACATA
28467876 AAAATAACATAAAAT
1 AAAATAAC-T-AAAT
28467891 AAAATAACTAAAT
1 AAAATAACTAAAT
28467904 AAACATAAACTAAAT
1 AAA-AT-AACTAAAT
28467919 CTTTATCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 16 0.62
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAACTAAAT
Found at i:28469858 original size:2 final size:2
Alignment explanation
Indices: 28469851--28469955 Score: 126
Period size: 2 Copynumber: 53.5 Consensus size: 2
28469841 ACTTATAAAC
* *
28469851 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AG GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * *
28469892 -T AT GG AA AT -T NT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
28469933 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
28469956 GGTTAGTAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
1 3 0.03
2 85 0.94
3 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28478541 original size:34 final size:33
Alignment explanation
Indices: 28478485--28478555 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
28478475 ATATTTTATT
* * *
28478485 TTTATATGGTAATGTAATATGCTTATATGTTTA
1 TTTATATGGTAATGCAATATGCTTATACGTATA
*
28478518 TTTATATGTTAAATGCAATATGCTTATACGTATA
1 TTTATATGGT-AATGCAATATGCTTATACGTATA
28478552 TTTA
1 TTTA
28478556 AATAGATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 9 0.27
34 24 0.73
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (33 bp):
TTTATATGGTAATGCAATATGCTTATACGTATA
Found at i:28479799 original size:40 final size:38
Alignment explanation
Indices: 28479737--28479842 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 38
28479727 ATCCTTGTAA
* *
28479737 AGGTTATACTTTATC-CTTGAAAAGGTAGAGTGTTTAGAGT
1 AGGTTATACCTTAACTCTTGAAAAGGTAGAGTG-TT-GA-T
28479777 -GGTTATACCTTAACTCTTGAAAAGGT--AGTGTTGAT
1 AGGTTATACCTTAACTCTTGAAAAGGTAGAGTGTTGAT
*
28479812 AGGTTATACCTTAGCT-TGTGAAAAGGTAGAG
1 AGGTTATACCTTAACTCT-TGAAAAGGTAGAG
28479843 AAATTGTGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
35 2 0.03
36 25 0.43
37 2 0.03
38 6 0.10
39 12 0.21
40 11 0.19
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (38 bp):
AGGTTATACCTTAACTCTTGAAAAGGTAGAGTGTTGAT
Found at i:28479938 original size:33 final size:33
Alignment explanation
Indices: 28479896--28479969 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 33
28479886 TACTTTCATG
28479896 AAAAGGCATTGTATG-GGTTATGCTTAAGCCCAA
1 AAAAGGCATTGT-TGAGGTTATGCTTAAGCCCAA
*
28479929 AAAAGGCATTGTTGTAAAGGTTATGCTTAAGCCTAA
1 AAAAGGCATTGTTG---AGGTTATGCTTAAGCCCAA
28479965 AAAAG
1 AAAAG
28479970 TATTTTCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 2 0.06
33 12 0.33
36 22 0.61
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (33 bp):
AAAAGGCATTGTTGAGGTTATGCTTAAGCCCAA
Found at i:28485847 original size:36 final size:35
Alignment explanation
Indices: 28485807--28485901 Score: 115
Period size: 36 Copynumber: 2.8 Consensus size: 35
28485797 ATTAGGCTTG
*
28485807 ATGACTTAATTAAACAATTTTAATCAACCAGGCCC
1 ATGACTTAATTAAACAATTTTAATCAACCAGGCAC
* * **
28485842 AATGACTTAATTGAACAA-TTTAATTAATTAGGCAC
1 -ATGACTTAATTAAACAATTTTAATCAACCAGGCAC
28485877 A--ACTTAATTAAACAATTTTAATCAA
1 ATGACTTAATTAAACAATTTTAATCAA
28485902 GTGCTTGAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 13 0.25
33 8 0.16
34 1 0.02
35 13 0.25
36 16 0.31
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (35 bp):
ATGACTTAATTAAACAATTTTAATCAACCAGGCAC
Found at i:28492169 original size:19 final size:19
Alignment explanation
Indices: 28492145--28492182 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28492135 CCATTTGACT
28492145 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28492164 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28492183 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:28493431 original size:13 final size:13
Alignment explanation
Indices: 28493413--28493437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28493403 GGAGAAATTG
28493413 TGATTTTATAAAA
1 TGATTTTATAAAA
28493426 TGATTTTATAAA
1 TGATTTTATAAA
28493438 TTTTCTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:28498701 original size:30 final size:30
Alignment explanation
Indices: 28498661--28498730 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
28498651 CAAGAAGTTA
*
28498661 ATGAAGAGATTCAAAATGATCATAAAAATC
1 ATGAAAAGATTCAAAATGATCATAAAAATC
* *
28498691 ATGAAAAGATTCAAAATGATTATAGAAATC
1 ATGAAAAGATTCAAAATGATCATAAAAATC
28498721 ATGATAAAGA
1 ATGA-AAAGA
28498731 GGATCAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.24
Consensus pattern (30 bp):
ATGAAAAGATTCAAAATGATCATAAAAATC
Found at i:28507913 original size:14 final size:14
Alignment explanation
Indices: 28507889--28507931 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
28507879 AATAAAGGGG
28507889 AAGAGAAAGAGAAGA
1 AAGA-AAAGAGAAGA
*
28507904 AAGCAAAGAG-AGA
1 AAGAAAAGAGAAGA
*
28507917 AGGAAAAGAGAAGA
1 AAGAAAAGAGAAGA
28507931 A
1 A
28507932 GAGAGAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.46
14 10 0.42
15 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAGAAGA
Found at i:28507932 original size:14 final size:14
Alignment explanation
Indices: 28507894--28507932 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
28507884 AGGGGAAGAG
* *
28507894 AAAGAGAAGAAAGC
1 AAAGAGAAGAAGGA
28507908 AAAGAG-AGAAGGA
1 AAAGAGAAGAAGGA
28507921 AAAGAGAAGAAG
1 AAAGAGAAGAAG
28507933 AGAGAGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAGAGAAGAAGGA
Found at i:28508679 original size:21 final size:19
Alignment explanation
Indices: 28508655--28508702 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
28508645 ACGACACGAT
28508655 ATGATTAATAGCACGTTTAAC
1 ATGATTAA-A-CACGTTTAAC
28508676 ATGATT-AACACGTTTAAC
1 ATGATTAAACACGTTTAAC
*
28508694 ATAATTAAA
1 ATGATTAAA
28508703 TAAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 15 0.60
19 3 0.12
20 1 0.04
21 6 0.24
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (19 bp):
ATGATTAAACACGTTTAAC
Found at i:28508689 original size:18 final size:18
Alignment explanation
Indices: 28508666--28508701 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28508656 TGATTAATAG
*
28508666 CACGTTTAACATGATTAA
1 CACGTTTAACATAATTAA
28508684 CACGTTTAACATAATTAA
1 CACGTTTAACATAATTAA
28508702 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (18 bp):
CACGTTTAACATAATTAA
Found at i:28510094 original size:16 final size:17
Alignment explanation
Indices: 28510041--28510095 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
28510031 ATCGAAATTT
*
28510041 AAAACATATGAACAAATA
1 AAAACAAATG-ACAAATA
* *
28510059 GAAAAGAAATGA-AAAAA
1 -AAAACAAATGACAAATA
28510076 AAAACAAAT-ACAAATA
1 AAAACAAATGACAAATA
28510092 AAAA
1 AAAA
28510096 TAATTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 16 0.53
17 4 0.13
18 1 0.03
19 8 0.27
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.11
Consensus pattern (17 bp):
AAAACAAATGACAAATA
Found at i:28514006 original size:19 final size:19
Alignment explanation
Indices: 28513982--28514019 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28513972 CTATCTAACT
28513982 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28514001 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28514020 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:28518813 original size:56 final size:54
Alignment explanation
Indices: 28518671--28518826 Score: 181
Period size: 55 Copynumber: 2.8 Consensus size: 54
28518661 CTGACGGTGG
* *
28518671 TGATTCCAACTATGTGCGATGTGGGGGGACACATAAGCTGATGAACGGTGGTTGA
1 TGATTCCAACTATGTGCGATGTGGGGGGACACATAGGCTGA-GGACGGTGGTTGA
* * * *
28518726 TGATTCCAA-TCGTGTGCGATGTGGGAGGACACATGGGCTGAGGACTGGTGG-TGG
1 TGATTCCAACT-ATGTGCGATGTGGGGGGACACATAGGCTGAGGAC-GGTGGTTGA
* *
28518780 TCTATATCCAACTATGTGTGATGTGGGGGGACACATAGGCTGAGGAC
1 T-GAT-TCCAACTATGTGCGATGTGGGGGGACACATAGGCTGAGGAC
28518827 CGTTGGGCGT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
54 7 0.08
55 42 0.49
56 35 0.41
57 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (54 bp):
TGATTCCAACTATGTGCGATGTGGGGGGACACATAGGCTGAGGACGGTGGTTGA
Found at i:28529641 original size:66 final size:66
Alignment explanation
Indices: 28529500--28529645 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 66
28529490 TATGCAATTG
* ** * * *
28529500 TCAATTAA-TCCAACAACTTAATAAAACAATTTAATTAAGTTCTTAAGAAGCTTATAAGTTCTTA
1 TCAATGAAGTCCAACAACTTAATAAAACAATTTAATTAAGCCCTTAAGAAGCTTAGAACTTCTAA
28529564 T
66 T
* * * * * *
28529565 TCAATTAAGTCCAATAACTTAATTAAACAATTTAGTTAAGCCCTTGAGAAGCTTGGAACTTCTAA
1 TCAATGAAGTCCAACAACTTAATAAAACAATTTAATTAAGCCCTTAAGAAGCTTAGAACTTCTAA
28529630 T
66 T
**
28529631 TTGATGAAGTCCAAC
1 TCAATGAAGTCCAAC
28529646 TTAATCACCT
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
65 8 0.12
66 58 0.88
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (66 bp):
TCAATGAAGTCCAACAACTTAATAAAACAATTTAATTAAGCCCTTAAGAAGCTTAGAACTTCTAA
T
Found at i:28535298 original size:12 final size:12
Alignment explanation
Indices: 28535281--28535316 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
28535271 AACTCGGGTT
28535281 TGCTTTGTTTTA
1 TGCTTTGTTTTA
28535293 TGCTTTGTTTTA
1 TGCTTTGTTTTA
28535305 TGCTTTGTTTTA
1 TGCTTTGTTTTA
28535317 GAATCATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.67
Consensus pattern (12 bp):
TGCTTTGTTTTA
Found at i:28541161 original size:20 final size:19
Alignment explanation
Indices: 28541117--28541161 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
28541107 AGAATGATGC
* *
28541117 CATCATTCAAAGTTAATAG
1 CATCATTCAAAGTCAAGAG
28541136 CTATCATTCAAAGTCAAGAGG
1 C-ATCATTCAAAGTCAAGA-G
28541157 CATCA
1 CATCA
28541162 ATTAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.86
21 2 0.09
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (19 bp):
CATCATTCAAAGTCAAGAG
Found at i:28541389 original size:18 final size:17
Alignment explanation
Indices: 28541366--28541400 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28541356 AAAAGAAGTT
*
28541366 GAAATTGTTGTTGAAAAA
1 GAAATTGTGGTT-AAAAA
28541384 GAAATTGTGGTTAAAAA
1 GAAATTGTGGTTAAAAA
28541401 TTCTGGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (17 bp):
GAAATTGTGGTTAAAAA
Found at i:28547821 original size:68 final size:68
Alignment explanation
Indices: 28547667--28547936 Score: 278
Period size: 68 Copynumber: 4.0 Consensus size: 68
28547657 GCATTTTAGA
* * * * *
28547667 CATGTAC-CATTACTTATGTCATATAGCATGTGGAATCATCATCACATAAATCT-CACACATAGC
1 CATGTACTCATT-CTTATCTCATATAGTATGTGGAACCAACATCACATACAT-TACA-ACATAGC
*
28547730 ATTCAT
63 ATACAT
* * * * * *
28547736 CATGTTCTCATTTTTATCTCATATAGTATGTGGAAGCAACCTCACATGCA-TAGCAACATATCAT
1 CATGTACTCATTCTTATCTCATATAGTATGTGGAACCAACATCACATACATTA-CAACATAGCAT
28547800 ACAT
65 ACAT
* * * *
28547804 CATGTGCTCATTCTTATCTCATATAGTATGTGGGACCAACATCATATACATTACAACATGGCATA
1 CATGTACTCATTCTTATCTCATATAGTATGTGGAACCAACATCACATACATTACAACATAGCATA
28547869 CAT
66 CAT
* * * * *
28547872 TATGTACTCTTTCTTATTTCATATAGTATGTGGGAA-TAACATCACATACATTACAACTTAGCAT
1 CATGTACTCATTCTTATCTCATATAGTATGT-GGAACCAACATCACATACATTACAACATAGCAT
28547936 A
65 A
28547937 TTTCATACAA
Statistics
Matches: 167, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
67 1 0.01
68 119 0.71
69 43 0.26
70 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (68 bp):
CATGTACTCATTCTTATCTCATATAGTATGTGGAACCAACATCACATACATTACAACATAGCATA
CAT
Found at i:28550186 original size:16 final size:16
Alignment explanation
Indices: 28550165--28550212 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
28550155 CTTATAAATA
*
28550165 AAATATTAATATTTTT
1 AAATATTAATATTTTC
*
28550181 AAATATTAATGATTATC
1 AAATATTAAT-ATTTTC
28550198 AAATATTAATATTTT
1 AAATATTAATATTTT
28550213 ATATAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
AAATATTAATATTTTC
Found at i:28550201 original size:17 final size:16
Alignment explanation
Indices: 28550165--28550210 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
28550155 CTTATAAATA
* *
28550165 AAATATTAATATTTTT
1 AAATATTAATATTATC
28550181 AAATATTAATGATTATC
1 AAATATTAAT-ATTATC
28550198 AAATATTAATATT
1 AAATATTAATATT
28550211 TTATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AAATATTAATATTATC
Found at i:28550210 original size:112 final size:113
Alignment explanation
Indices: 28550083--28550308 Score: 323
Period size: 112 Copynumber: 2.0 Consensus size: 113
28550073 TATTTAAATG
* *
28550083 ATCAATTATTAATATTTTAAAAAAATTATAAATGATTAATATTTAAAAATTAATAATCATAATAT
1 ATCAAATATTAATATTTTAAAAAAATTATAAATGATTAATATTTAAAAATAAATAATCATAAT-T
* * *
28550148 -CCTTTAACTTATAAATAAAATATTAATA-TTTTTAA-ATATTAATGATT
65 GCATTTAAATTATAAATAAAATATTAAGATTTTTTAAGA-ATTAATGATT
* * *
28550195 ATCAAATATTAATATTTTATATAAATTATAAATTATTAATATTTAAAAATAAATAATCATAATTG
1 ATCAAATATTAATATTTTAAAAAAATTATAAATGATTAATATTTAAAAATAAATAATCATAATTG
* *
28550260 TATTTAAATTATAAATAAATTATTAAGATTTTTTAAGAATTAATGATT
66 CATTTAAATTATAAATAAAATATTAAGATTTTTTAAGAATTAATGATT
28550308 A
1 A
28550309 AATTATAATA
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
111 1 0.01
112 81 0.80
113 18 0.18
114 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (113 bp):
ATCAAATATTAATATTTTAAAAAAATTATAAATGATTAATATTTAAAAATAAATAATCATAATTG
CATTTAAATTATAAATAAAATATTAAGATTTTTTAAGAATTAATGATT
Found at i:28550222 original size:27 final size:29
Alignment explanation
Indices: 28550165--28550238 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 29
28550155 CTTATAAATA
28550165 AAATATTAATATTTTTAAATATTAATGATTAT
1 AAATATTAATA-TTTT-AATATTAA-GATTAT
28550197 CAAATATTAATATTTT-ATA-TAA-ATTAT
1 -AAATATTAATATTTTAATATTAAGATTAT
28550224 AAATTATTAATATTT
1 AAA-TATTAATATTT
28550239 AAAAATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 3 0.08
27 16 0.40
29 3 0.08
30 3 0.08
32 4 0.10
33 11 0.28
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
AAATATTAATATTTTAATATTAAGATTAT
Found at i:28550272 original size:48 final size:46
Alignment explanation
Indices: 28550198--28550418 Score: 130
Period size: 48 Copynumber: 4.6 Consensus size: 46
28550188 AATGATTATC
* * *
28550198 AAATATTAATATTTTATATAAATTATAAATTATTAATATTTAAAAAT
1 AAATAATAATAATTGAT-TAAATTATAAATTATTAATATTTAAAAAT
* * *
28550245 AAATAATCATAATTGTATTTAAATTATAAA-TA--AAT-TATTAAGATT
1 AAATAATAATAATTG-A-TTAAATTATAAATTATTAATAT-TTAAAAAT
*** * * * *
28550290 TTTTAAGAATTAA-TGATTAAATTATAATAAAATAGTAATATTTAAATTAT
1 AAATAATAA-TAATTGATTAAA-T-T-ATAAATTATTAATATTTAAA-AAT
* *
28550340 CAATTAGTAATATATTGATTAAATTATAAATTATTAATATTTAAAAAT
1 -AAATAATAATA-ATTGATTAAATTATAAATTATTAATATTTAAAAAT
*
28550388 AAATAATCATAATAAT-ATTTAAATTATAAAT
1 AAATAATAATAAT--TGA-TTAAATTATAAAT
28550419 AAAATATTAA
Statistics
Matches: 132, Mismatches: 24, Indels: 35
0.69 0.13 0.18
Matches are distributed among these distances:
43 5 0.04
44 3 0.02
45 16 0.12
46 10 0.08
47 24 0.18
48 28 0.21
49 26 0.20
50 5 0.04
51 7 0.05
52 8 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (46 bp):
AAATAATAATAATTGATTAAATTATAAATTATTAATATTTAAAAAT
Found at i:28550285 original size:52 final size:49
Alignment explanation
Indices: 28550222--28550435 Score: 153
Period size: 52 Copynumber: 4.4 Consensus size: 49
28550212 TATATAAATT
28550222 ATAAATTATTAATATTTAAAAATAAATAATCATAATTGTATTTAAATTATAA
1 ATAAATTATTAATATTTAAAAATAAATAATCATAATTG-A-TTAAATTAT-A
* * * *
28550274 ATAAATTATTAAGATTT----TTTAAGAAT--TAA-TGATTAAATTATA
1 ATAAATTATTAATATTTAAAAATAAATAATCATAATTGATTAAATTATA
* * * * * *
28550316 ATAAAATAGTAATATTTAAATTATCAATTAGTAATATATTGATTAAA-T-T-
1 ATAAATTATTAATATTTAAA-AAT-AAATAATCATA-ATTGATTAAATTATA
28550365 ATAAATTATTAATATTTAAAAATAAATAATCATAATAAT-ATTTAAATTATAA
1 ATAAATTATTAATATTTAAAAATAAATAATCATAAT--TGA-TTAAATTAT-A
*
28550417 ATAAAATATTAATACTTTA
1 ATAAATTATTAATA-TTTA
28550436 TAATGTTAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 35
0.70 0.11 0.20
Matches are distributed among these distances:
42 15 0.12
43 9 0.07
44 1 0.01
45 2 0.02
46 5 0.04
47 10 0.08
48 17 0.14
49 19 0.15
50 4 0.03
51 2 0.02
52 37 0.30
53 4 0.03
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (49 bp):
ATAAATTATTAATATTTAAAAATAAATAATCATAATTGATTAAATTATA
Found at i:28550350 original size:22 final size:22
Alignment explanation
Indices: 28550316--28550418 Score: 71
Period size: 27 Copynumber: 4.3 Consensus size: 22
28550306 TTAAATTATA
*
28550316 ATAAAATAGTAATATTTAAATT
1 ATAAATTAGTAATATTTAAATT
*
28550338 ATCAATTAGTAATATATTGATTAAATT
1 ATAAATTAGT-A-ATA-T--TTAAATT
* *
28550365 ATAAATTATTAATATTTAAAAAT
1 ATAAATTAGTAATATTT-AAATT
* *
28550388 AAATAATCATAATAATATTTAAATT
1 ATA-AAT--TAGTAATATTTAAATT
28550413 ATAAAT
1 ATAAAT
28550419 AAAATATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
22 10 0.16
23 7 0.11
24 10 0.16
25 10 0.16
26 11 0.17
27 15 0.24
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAAATTAGTAATATTTAAATT
Done.