Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 125 of 171
Found at i:39780961 original size:94 final size:93
Alignment explanation
Indices: 39780836--39781007 Score: 245
Period size: 94 Copynumber: 1.8 Consensus size: 93
39780826 TAGCTTCGAT
* *** *
39780836 CTTTCCCGTCATGCTTCTAAGGTACTAGGTTCACCGTTGTGGCCTTAACCTTTCCCATCACATCT
1 CTTTCCCGTCATGCTTCTAAGGTACCAGGTTCACCGTTGCAACCGTAACCTTTCCCATCACATCT
39780901 TCTAAGGTATCGGATTCACGGTCGTAAC
66 TCTAAGGTATCGGATTCACGGTCGTAAC
* * * * *
39780929 CTTTCCCTTCATGTTTTCTAAGGTACCGGGTTCGCCGTTGCAACCGTAACCTTTCCCATCACATT
1 CTTTCCCGTCATG-CTTCTAAGGTACCAGGTTCACCGTTGCAACCGTAACCTTTCCCATCACATC
39780994 TTCTAAGGTATCGG
65 TTCTAAGGTATCGG
39781008 GTTCCCCTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 12 0.18
94 56 0.82
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (93 bp):
CTTTCCCGTCATGCTTCTAAGGTACCAGGTTCACCGTTGCAACCGTAACCTTTCCCATCACATCT
TCTAAGGTATCGGATTCACGGTCGTAAC
Found at i:39781079 original size:49 final size:49
Alignment explanation
Indices: 39780923--39781341 Score: 367
Period size: 50 Copynumber: 8.5 Consensus size: 49
39780913 GATTCACGGT
** * **
39780923 CGTAACCTTTCCCTTCATGTTTTCTAAGGTACCGGGTTCGCCGTTGCAAC
1 CGTAACCTTTCCCTTCAAATCTTC-AAGGTACCGGGTTCGCCGTTGCGGC
* * * * *
39780973 CGTAACCTTTCCCATCACATTTTCTAAGGTATCGGGTTC-CCCTTCGCGGC
1 CGTAACCTTTCCCTTCAAATCTTC-AAGGTACCGGGTTCGCCGTT-GCGGC
* * * * *
39781023 TGTAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGTCGTTGCGGT
1 CGTAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCGTTGCGGC
* * ** *** *
39781072 CGTAACCTTT-CTTTCAAATCTTCATGGTACCAAGTTTATCGTTGCGAC
1 CGTAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCGTTGCGGC
* * * *
39781120 CGTAACCTTTCCCATCAAATCTTCTAAGGTACCAGGTTCACCGTTGTGGC
1 CGTAACCTTTCCCTTCAAATCTTC-AAGGTACCGGGTTCGCCGTTGCGGC
* * * *
39781170 CGTAACCTTTCCCTTCAAATCTTCACGGTACCGGGTTCACCGTTGTGGT
1 CGTAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCGTTGCGGC
* * * * *
39781219 CGTAACCTTTCCCTTCAAATCTTCATGGTATCGGATTCGTCGTTGCGAC
1 CGTAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCGTTGCGGC
* * * * * * *
39781268 CGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTTGCCGTTACGGT
1 CGTAACCTTTCCCTTCAAATC-TTCAAGGTACCGGGTTCGCCGTTGCGGC
*
39781318 C-TCAACCTTTCCCTTCATATCTTC
1 CGT-AACCTTTCCCTTCAAATCTTC
39781342 GTGGTAATGA
Statistics
Matches: 306, Mismatches: 57, Indels: 13
0.81 0.15 0.03
Matches are distributed among these distances:
48 42 0.14
49 124 0.41
50 140 0.46
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (49 bp):
CGTAACCTTTCCCTTCAAATCTTCAAGGTACCGGGTTCGCCGTTGCGGC
Found at i:39781145 original size:147 final size:148
Alignment explanation
Indices: 39780919--39781341 Score: 485
Period size: 147 Copynumber: 2.9 Consensus size: 148
39780909 ATCGGATTCA
** * * * * ** *
39780919 CGGTCGTAACCTTTCCCTTCATGTTTTCTAAGGTACCGGGTTCGCCGTTGCAACCGTAACCTTTC
1 CGGTCGTAACCTTTCCCTTCAAATCTTC-ATGGTACCAGATTCATCGTTGCGACCGTAACCTTTC
* *
39780984 CCATCACATTTTCTAAGGTATCGGGTTC-CCCTTCGCGGCTGTAACCTTTCCCTTCAAATCTTCA
65 CCATCACATCTTCTAAGGTATCGGGTTCACCCTT-GCGGCCGTAACCTTTCCCTTCAAATCTTCA
* **
39781048 TGGTACCAGGTTCGTCGTTG
129 CGGTACCAGGTTCACCGTTG
* *
39781068 CGGTCGTAACCTTT-CTTTCAAATCTTCATGGTACCA-AGTTTATCGTTGCGACCGTAACCTTTC
1 CGGTCGTAACCTTTCCCTTCAAATCTTCATGGTACCAGA-TTCATCGTTGCGACCGTAACCTTTC
* * * * *
39781131 CCATCAAATCTTCTAAGGTACCAGGTTCACCGTTGTGGCCGTAACCTTTCCCTTCAAATCTTCAC
65 CCATCACATCTTCTAAGGTATCGGGTTCACCCTTGCGGCCGTAACCTTTCCCTTCAAATCTTCAC
*
39781196 GGTACCGGGTTCACCGTTG
130 GGTACCAGGTTCACCGTTG
* * * *
39781215 TGGTCGTAACCTTTCCCTTCAAATCTTCATGGTATCGGATTCGTCGTTGCGACCGTAACCTTTCC
1 CGGTCGTAACCTTTCCCTTCAAATCTTCATGGTACCAGATTCATCGTTGCGACCGTAACCTTTCC
* ** * * * *
39781280 CATCACATCTTTTAAGGTATCGGGTTTGCCGTTACGGTC-TCAACCTTTCCCTTCATATCTTC
66 CATCACATCTTCTAAGGTATCGGGTTCACCCTTGCGGCCGT-AACCTTTCCCTTCAAATCTTC
39781342 GTGGTAATGA
Statistics
Matches: 231, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
147 110 0.48
148 106 0.46
149 15 0.06
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (148 bp):
CGGTCGTAACCTTTCCCTTCAAATCTTCATGGTACCAGATTCATCGTTGCGACCGTAACCTTTCC
CATCACATCTTCTAAGGTATCGGGTTCACCCTTGCGGCCGTAACCTTTCCCTTCAAATCTTCACG
GTACCAGGTTCACCGTTG
Found at i:39781304 original size:99 final size:99
Alignment explanation
Indices: 39780856--39781347 Score: 400
Period size: 99 Copynumber: 5.0 Consensus size: 99
39780846 ATGCTTCTAA
* * * * * * *
39780856 GGTACTAGGTTCACCGTTGTGGCCTTAACCTTTCCCATCACATCTTCTAAGGTATCGGATTCA--
1 GGTACCAGGTTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTCACC
** * *
39780919 ----CGGTCGTAACCTTTCCCTTCATGTTTTCTAA
66 GTTGCGGTCGTAACCTTTCCCTTCAAATCTTC-AT
* *
39780950 GGTACCGGGTTCGCCGTTGCAACCGTAACCTTTCCCATCACAT-TTTCTAAGGTATCGGGTTC-C
1 GGTACCAGGTTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTT-TAAGGTATCGGGTTCAC
*
39781013 CCTTCGCGG-CTGTAACCTTTCCCTTCAAATCTTCAT
65 CGTT-GCGGTC-GTAACCTTTCCCTTCAAATCTTCAT
* ** ** * * * * ** * *
39781049 GGTACCAGGTTCGTCGTTGCGGTCGTAACCTTT-CTTTCAAATC-TTCATGGTACCAAGTTTATC
1 GGTACCAGGTTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTCACC
** * *
39781112 GTTGCGACCGTAACCTTTCCCATCAAATCTTCTAA
66 GTTGCGGTCGTAACCTTTCCCTTCAAATCTTC-AT
* * * * * * * *
39781147 GGTACCAGGTTCACCGTTGTGGCCGTAACCTTTCCCTTCAAATC-TTCACGGTACCGGGTTCACC
1 GGTACCAGGTTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTCACC
*
39781211 GTTGTGGTCGTAACCTTTCCCTTCAAATCTTCAT
66 GTTGCGGTCGTAACCTTTCCCTTCAAATCTTCAT
* * **
39781245 GGTATC-GGATTCGTCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTTGC
1 GGTACCAGG-TTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTCAC
* * *
39781309 CGTTACGGTC-TCAACCTTTCCCTTCATATCTTCGT
65 CGTTGCGGTCGT-AACCTTTCCCTTCAAATCTTCAT
39781344 GGTA
1 GGTA
39781348 ATGAAACCTT
Statistics
Matches: 318, Mismatches: 63, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
93 2 0.01
94 50 0.16
97 36 0.11
98 78 0.25
99 129 0.41
100 23 0.07
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.34
Consensus pattern (99 bp):
GGTACCAGGTTCGCCGTTGCGACCGTAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTCACC
GTTGCGGTCGTAACCTTTCCCTTCAAATCTTCAT
Found at i:39788608 original size:66 final size:68
Alignment explanation
Indices: 39788536--39788732 Score: 161
Period size: 64 Copynumber: 2.9 Consensus size: 68
39788526 AAAATAGTAA
* * * ** *
39788536 AAAATCAGTATGTATATCTATTTATATATATATGTACGTACATGTGTATATGTATA-AAATAAA-
1 AAAATCAGTATGTATATCTATTTATATATATATGTACATACATATATATATAAAAATAAATAAAG
39788599 AAT
66 AAT
* * * * *
39788602 GAAATCAATAT-T-TATGT-TTGCATATATATATGTACATACGTATATATATAAAAATAAATAAA
1 AAAATCAGTATGTATATCTATT-TATATATATATGTACATACATATATATATAAAAATAAATAAA
39788664 GAAT
65 GAAT
* * * * *
39788668 AAAATCAGAATGTATGTCTATGTATATATATATATATATGCCTACGTATATATATAAAAAATAAA
1 AAAATCAGTATGTATATCTAT-T-TATATATATATGTA--CATACATATATATAT-AAAAATAAA
39788733 ACAAATACAT
Statistics
Matches: 101, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
63 2 0.02
64 30 0.30
65 8 0.08
66 20 0.20
67 1 0.01
68 3 0.03
69 1 0.01
70 13 0.13
72 14 0.14
73 9 0.09
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (68 bp):
AAAATCAGTATGTATATCTATTTATATATATATGTACATACATATATATATAAAAATAAATAAAG
AAT
Found at i:39792622 original size:58 final size:59
Alignment explanation
Indices: 39792553--39792890 Score: 250
Period size: 59 Copynumber: 5.8 Consensus size: 59
39792543 GCTCGAGGGT
** * *
39792553 AAAATGATAATTTTTGGAGGTTCGAGG-GTAAAACGGTAATTTTTGGATGCTCAGGGACA
1 AAAATG-TAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGGATGTTCAGGGACA
* * * * *
39792612 AAAATGTAATTTTTAGACATCCG-GGTGTAAAATGGTAATCTTTGGAAAGTTCAAGGTA-A
1 AAAATGTAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGG-ATGTTC-AGGGACA
* * * * * * * *
39792671 AAAATGTAATTTTTGAACATTC-AGGGGTAAAAGGGTAACTTTT-GAGGTTCGGGGTCC
1 AAAATGTAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGGATGTTCAGGGACA
* ** *
39792728 AAAATGAAATTTTTGGACATTC-AGGCATAAAATGGTAATTTTTGGAAAT-TTCTGGGACA
1 AAAATGTAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGG--ATGTTCAGGGACA
* *** * * *
39792787 AAAATGGAATTTTCAAACATTCGAGG-GTCAAATGGTAATTTTTGGAAGTTC-GAGGTCA
1 AAAATGTAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGGATGTTCAG-GGACA
* *
39792845 AAAAGGGAATTTTTGGA-AGTTCG-GGTGTGAAAAT-GTAATTTTTGGA
1 AAAATGTAATTTTTGGACA-TTCGAGGTGT-AAAATGGTAATTTTTGGA
39792891 AAGTTTGGGG
Statistics
Matches: 221, Mismatches: 44, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
56 2 0.01
57 49 0.22
58 70 0.32
59 92 0.42
60 8 0.04
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAATGTAATTTTTGGACATTCGAGGTGTAAAATGGTAATTTTTGGATGTTCAGGGACA
Found at i:39792747 original size:116 final size:117
Alignment explanation
Indices: 39792573--39792895 Score: 325
Period size: 116 Copynumber: 2.8 Consensus size: 117
39792563 TTTTTGGAGG
* * * * * * * *
39792573 TTCGAGGGTAAAACGGTAATTTTTGGATGCTC-AGGGACAAAAATGTAATTTTTAGACATCCGGG
1 TTCGAGGGTAAAAGGGTAACTTTTGGAAGTTCGA-GGTCAAAAATGAAATTTTTGGACATTCGGG
* * * **
39792637 TGTAAAATGGTAATCTTTGGAAAGTTCAAGGTA-AAAAATGTAATTTTTGAACA
65 TGTAAAATGGTAATTTTTGGAAAGTTC-AGGGACAAAAATGGAATTTTCAAACA
* * * *
39792690 TTC-AGGGGTAAAAGGGTAACTTTT-GAGGTTCGGGGTCCAAAATGAAATTTTTGGACATTCAGG
1 TTCGA-GGGTAAAAGGGTAACTTTTGGAAGTTCGAGGTCAAAAATGAAATTTTTGGACATTCGGG
** * *
39792753 CATAAAATGGTAATTTTTGGAAATTTCTGGGACAAAAATGGAATTTTCAAACA
65 TGTAAAATGGTAATTTTTGGAAAGTTCAGGGACAAAAATGGAATTTTCAAACA
* * * * *
39792806 TTCGAGGGTCAAATGGTAATTTTTGGAAGTTCGAGGTCAAAAAGGGAATTTTTGGA-AGTTCGGG
1 TTCGAGGGTAAAAGGGTAACTTTTGGAAGTTCGAGGTCAAAAATGAAATTTTTGGACA-TTCGGG
39792870 TGTGAAAAT-GTAATTTTTGGAAAGTT
65 TGT-AAAATGGTAATTTTTGGAAAGTT
39792896 TGGGGTCAAA
Statistics
Matches: 167, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
115 3 0.02
116 90 0.54
117 69 0.41
118 5 0.03
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (117 bp):
TTCGAGGGTAAAAGGGTAACTTTTGGAAGTTCGAGGTCAAAAATGAAATTTTTGGACATTCGGGT
GTAAAATGGTAATTTTTGGAAAGTTCAGGGACAAAAATGGAATTTTCAAACA
Found at i:39792838 original size:29 final size:29
Alignment explanation
Indices: 39792533--39792993 Score: 142
Period size: 29 Copynumber: 15.8 Consensus size: 29
39792523 TAAAAATACG
* * * *
39792533 ATTTTTGGATGCTCGAGGGTAAAATGATA
1 ATTTTTGGAAGTTCGAGGGTCAAATGGTA
* * *
39792562 ATTTTTGGAGGTTCGAGGGTAAAACGGTA
1 ATTTTTGGAAGTTCGAGGGTCAAATGGTA
* * *
39792591 ATTTTTGGATGCTC-AGGGACAAAAAT-GTA
1 ATTTTTGGAAGTTCGAGGGTC--AAATGGTA
* * *
39792620 ATTTTTAGACA-TCCG-GGTGTAAAATGGTA
1 ATTTTTGGA-AGTTCGAGG-GTCAAATGGTA
* * *
39792649 ATCTTTGGAAAGTTC-AAGGTAAAAAAT-GTA
1 ATTTTTGG-AAGTTCGAGGGT--CAAATGGTA
* * *
39792679 ATTTTT-GAACATTC-AGGGGTAAAAGGGTA
1 ATTTTTGGAA-GTTCGA-GGGTCAAATGGTA
* * *
39792708 ACTTTT-GAGGTTCG-GGGTCCAAAAT-GAA
1 ATTTTTGGAAGTTCGAGGGT-C-AAATGGTA
* *
39792736 ATTTTTGGACA-TTC-AGGCATAAAATGGTA
1 ATTTTTGGA-AGTTCGAGG-GTCAAATGGTA
* * *
39792765 ATTTTTGGAAATTTC-TGGGACAAAAATGG-A
1 ATTTTTGG-AAGTTCGAGGGTC--AAATGGTA
** *
39792795 A-TTTTCAAACATTCGAGGGTCAAATGGTA
1 ATTTTTGGAA-GTTCGAGGGTCAAATGGTA
* *
39792824 ATTTTTGGAAGTTCGA-GGTCAAAAAGGGA
1 ATTTTTGGAAGTTCGAGGGTC-AAATGGTA
*
39792853 ATTTTTGGAAGTTCG-GGTGTGAAAAT-GTA
1 ATTTTTGGAAGTTCGAGG-GT-CAAATGGTA
* *
39792882 ATTTTTGGAAAGTTTG-GGGTCAAAAT-GTG
1 ATTTTTGG-AAGTTCGAGGGTC-AAATGGTA
* *
39792911 ATTTTTGGAAGTTAG-GGGGCAAAAAT-GTA
1 ATTTTTGGAAGTTCGAGGGTC--AAATGGTA
* ***
39792940 ATTTTTGTGAAGTTCGGGGGTCAAAACATA
1 ATTTTTG-GAAGTTCGAGGGTCAAATGGTA
*
39792970 ATTTTTGGAAAGTT-TAGGGTCAAA
1 ATTTTTGG-AAGTTCGAGGGTCAAA
39792994 ATGTTATTTT
Statistics
Matches: 328, Mismatches: 63, Indels: 82
0.69 0.13 0.17
Matches are distributed among these distances:
27 4 0.01
28 50 0.15
29 187 0.57
30 72 0.22
31 15 0.05
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGTCAAATGGTA
Found at i:39792891 original size:58 final size:57
Alignment explanation
Indices: 39792816--39792965 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 57
39792806 TTCGAGGGTC
* * * **
39792816 AAATGGTAATTTTTGGAAGTTCGAGGTCAAAAAGGGAATTTTTGGAAGTTCGGGTGTGA
1 AAAT-GTAATTTTTGGAAGTTCGGGGTCAAAAAGGG-ATTTTTGGAAGTTAGGGGGCAA
* * *
39792875 AAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGTGATTTTTGGAAGTTAGGGGGCAA
1 AAATGTAATTTTTGG-AAGTTCGGGGTCAAAAAGGGATTTTTGGAAGTTAGGGGGCAA
39792933 AAATGTAATTTTTGTGAAGTTCGGGGGTCAAAA
1 AAATGTAATTTTTG-GAAGTTC-GGGGTCAAAA
39792966 CATAATTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 48 0.61
59 31 0.39
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (57 bp):
AAATGTAATTTTTGGAAGTTCGGGGTCAAAAAGGGATTTTTGGAAGTTAGGGGGCAA
Found at i:39792908 original size:88 final size:88
Alignment explanation
Indices: 39792810--39793004 Score: 259
Period size: 88 Copynumber: 2.2 Consensus size: 88
39792800 CAAACATTCG
* * *
39792810 AGGGTC-AAATGGTAATTTTTGGAAGTTCGAGGTCAAAAAGGGAATTTTTG-GAAGTTCGGGTGT
1 AGGGTCAAAAT-GTAATTTTTGGAAGTTAGAGGGCAAAAAGGGAATTTTTGTGAAGTTCGGGGGT
* **
39792873 GAAAATGTAATTTTTGGAAAGTTT
65 CAAAACATAATTTTTGGAAAGTTT
* * * * *
39792897 GGGGTCAAAATGTGATTTTTGGAAGTTAGGGGGCAAAAATGTAATTTTTGTGAAGTTCGGGGGTC
1 AGGGTCAAAATGTAATTTTTGGAAGTTAGAGGGCAAAAAGGGAATTTTTGTGAAGTTCGGGGGTC
39792962 AAAACATAATTTTTGGAAAGTTT
66 AAAACATAATTTTTGGAAAGTTT
*
39792985 AGGGTCAAAATGTTATTTTT
1 AGGGTCAAAATGTAATTTTT
39793005 AGAAAGTTTA
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 38 0.41
88 55 0.59
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (88 bp):
AGGGTCAAAATGTAATTTTTGGAAGTTAGAGGGCAAAAAGGGAATTTTTGTGAAGTTCGGGGGTC
AAAACATAATTTTTGGAAAGTTT
Found at i:39792994 original size:29 final size:29
Alignment explanation
Indices: 39792852--39793042 Score: 147
Period size: 29 Copynumber: 6.5 Consensus size: 29
39792842 TCAAAAAGGG
** * *
39792852 AATTTTTGG-AAGTTCGGGTGTGAAAATGT
1 AATTTTTGGAAAGTTTAGG-GTCAAAATAT
* *
39792881 AATTTTTGGAAAGTTTGGGGTCAAAATGT
1 AATTTTTGGAAAGTTTAGGGTCAAAATAT
* * *
39792910 GATTTTTGG-AAG-TTAGGGGGCAAAAATGT
1 AATTTTTGGAAAGTTTA-GGGTC-AAAATAT
** *
39792939 AATTTTTGTG-AAGTTCGGGGGTCAAAACAT
1 AATTTTTG-GAAAGTT-TAGGGTCAAAATAT
*
39792969 AATTTTTGGAAAGTTTAGGGTCAAAATGT
1 AATTTTTGGAAAGTTTAGGGTCAAAATAT
* * *
39792998 TATTTTTAGAAAGTTTAGGATCAAAAATAT
1 AATTTTTGGAAAGTTTAGGGTC-AAAATAT
*
39793028 AATTTTTGGATAGTT
1 AATTTTTGGAAAGTT
39793043 CAGAGACCTG
Statistics
Matches: 132, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.02
28 7 0.05
29 70 0.53
30 48 0.36
31 5 0.04
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAAGTTTAGGGTCAAAATAT
Found at i:39794545 original size:6 final size:6
Alignment explanation
Indices: 39794534--39794608 Score: 66
Period size: 6 Copynumber: 13.0 Consensus size: 6
39794524 AATGGGACTT
** * *
39794534 TTTAAA TTTAAA AGTAAA TTTAAA CTT-AA TTTAAA TTTTAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
39794581 -ACAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39794609 AAGGGGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
5 11 0.21
6 41 0.79
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:39794570 original size:17 final size:17
Alignment explanation
Indices: 39794534--39794608 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
39794524 AATGGGACTT
39794534 TTTAAATTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
39794552 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
* *
39794569 TTTTAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
39794586 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
39794603 TTTAAA
1 TTTAAA
39794609 AAGGGGTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 37 0.79
18 10 0.21
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:39794602 original size:11 final size:11
Alignment explanation
Indices: 39794536--39794609 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
39794526 TGGGACTTTT
39794536 TAAATTTAAAA
1 TAAATTTAAAA
*
39794547 GTAAATTTAAAC
1 -TAAATTTAAAA
* *
39794559 TTAATTTAAATT
1 TAAATTTAAA-A
*
39794571 TTAATTTAAAA
1 TAAATTTAAAA
*
39794582 CAAA-TT----
1 TAAATTTAAAA
39794588 TAAATTTAAAA
1 TAAATTTAAAA
39794599 TAAATTTAAAA
1 TAAATTTAAAA
39794610 AGGGGTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
10 2 0.04
11 22 0.45
12 20 0.41
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:39795057 original size:86 final size:86
Alignment explanation
Indices: 39794912--39795117 Score: 351
Period size: 86 Copynumber: 2.4 Consensus size: 86
39794902 TGGTGTTATT
*
39794912 GATTTGG-TCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTC
1 GATTTGGTTC-ACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTC
*
39794976 TCTATGTCTCATCAAGAAGACG
65 TCTATGTCTCATCAAGAAGACA
*
39794998 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTGATCCACTTCT
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCT
39795063 CTATGTCTCATCAAGAAGACA
66 CTATGTCTCATCAAGAAGACA
* *
39795084 GATTTGGTTCACTTCTCTGTATTTCATCAAGAAG
1 GATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
39795118 GTAACCGCTT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 112 0.98
87 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (86 bp):
GATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCT
CTATGTCTCATCAAGAAGACA
Found at i:39795422 original size:209 final size:208
Alignment explanation
Indices: 39795009--39795612 Score: 800
Period size: 209 Copynumber: 2.9 Consensus size: 208
39794999 ATTTGGTTCA
* * ** * * *
39795009 CTTCTCTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTGATCCACTTCTCTATGTCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACAGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * * * * **
39795074 CAAGAAGACAGATTTGGT-TCACTTCTCTGTATTTCATCAAGAAGGTAACC-GCTTATTGCTTCG
66 CAAGAAGAGA-ATTTGGTCT-ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* * * *
39795137 ACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTCGAAGATTCACTCACTTTAAGCCTAGCTT
129 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTGAAGCCTAGCTT
39795202 CATTAATTTGGTCTT
194 CATTAATTTGGTCTT
* * * *
39795217 CTTCTCAGTACCTTATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACAGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
39795282 CAAGAAGAGGAATGTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGA
66 CAAGAAGA-GAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* ** * * * *
39795347 CCTACTTCTCAGTATCTCATCAGGTCGCTGGGGTTCGAAGATTTGCTCACTTGGAG-CTTGGTTC
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTGAAGCCTAGCTT-
*
39795411 CATTGATTTGGTCTT
194 CATTAATTTGGTCTT
*
39795426 CTTCTCAGTATCTCATCAGGAAGATGACAGTATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACAGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
39795491 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAAGAAGA-GAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
39795556 CCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTTGAAGATTCGCTCACTTTAAGC
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTGAAGC
39795613 TTTGAGTTGG
Statistics
Matches: 342, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
208 100 0.29
209 242 0.71
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (208 bp):
CTTCTCAGTATCTCATCAGGAAGATGACAGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAAGAAGAGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTGAAGCCTAGCTTCA
TTAATTTGGTCTT
Found at i:39806241 original size:16 final size:17
Alignment explanation
Indices: 39806209--39806241 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39806199 ATAAATCTTT
*
39806209 AATTTTTCAATAGTTAA
1 AATTTTTAAATAGTTAA
39806226 AATTTTTAAATA-TTAA
1 AATTTTTAAATAGTTAA
39806242 TATAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTTTTAAATAGTTAA
Found at i:39806270 original size:15 final size:16
Alignment explanation
Indices: 39806247--39806277 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39806237 ATTAATATAA
39806247 AATTATTTAAAATTAT
1 AATTATTTAAAATTAT
39806263 AATT-TTTAAAATTAT
1 AATTATTTAAAATTAT
39806278 TAAATATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTAAAATTAT
Found at i:39806917 original size:17 final size:18
Alignment explanation
Indices: 39806880--39806917 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
39806870 ATTTACTGTC
*
39806880 ATTAATGATTTAAGATAT
1 ATTAATGATTTAACATAT
*
39806898 ATTAAT-ATTTAACATTT
1 ATTAATGATTTAACATAT
39806915 ATT
1 ATT
39806918 TGTGTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTAATGATTTAACATAT
Found at i:39807414 original size:35 final size:34
Alignment explanation
Indices: 39807348--39807416 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
39807338 ATTTTACTTA
*
39807348 CTTGATTGTTTATGATTATGAATGAATTGAAATT
1 CTTGATTGTTTATGAATATGAATGAATTGAAATT
*
39807382 CTTGATTGTTTAT-AATATGTAAATGAGTTGAAATT
1 CTTGATTGTTTATGAATATG--AATGAATTGAAATT
39807417 TCTAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 5 0.16
34 13 0.42
35 13 0.42
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.46
Consensus pattern (34 bp):
CTTGATTGTTTATGAATATGAATGAATTGAAATT
Found at i:39808410 original size:29 final size:28
Alignment explanation
Indices: 39808378--39808550 Score: 100
Period size: 29 Copynumber: 6.1 Consensus size: 28
39808368 TTGTAACTGT
39808378 TTTTCTAAATTTTACAATTTTGCCATTGA
1 TTTTCTAAATTTTACAATTTTGCCATT-A
* * * * * * *
39808407 TTTTATAGATTTTATAATTCTACCACTG
1 TTTTCTAAATTTTACAATTTTGCCATTA
* * *
39808435 TTTTCCAAAATTTTATAGTTTTGCCATTAA
1 TTTT-CTAAATTTTACAATTTTGCCATT-A
* * *
39808465 TTTT-TCAAATTTTACAGTTTTACCACTA
1 TTTTCT-AAATTTTACAATTTTGCCATTA
***
39808493 TTTTCCGTA-TTTAGCAATTTTGCCATTA
1 TTTTCTAAATTTTA-CAATTTTGCCATTA
* * *
39808521 TTTT-TCAAATTTTATAATTTTTCCACTA
1 TTTTCT-AAATTTTACAATTTTGCCATTA
39808549 TT
1 TT
39808551 CTTCAAAAAA
Statistics
Matches: 106, Mismatches: 31, Indels: 15
0.70 0.20 0.10
Matches are distributed among these distances:
27 4 0.04
28 39 0.37
29 59 0.56
30 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTTCTAAATTTTACAATTTTGCCATTA
Found at i:39808419 original size:58 final size:58
Alignment explanation
Indices: 39808349--39808541 Score: 162
Period size: 58 Copynumber: 3.4 Consensus size: 58
39808339 TGTACTACCG
** * * *
39808349 TTTTATAGATTTTATAGTTTTGTAACTGTTTTTCTAAATTTTACAATTTTGCCATTGA
1 TTTTATAGATTTTATAGTTTTACAACTGTTTTCCAAAATTTTACAATTTTGCCATTAA
* * * * *
39808407 TTTTATAGATTTTATAATTCTACCACTGTTTTCCAAAATTTTATAGTTTTGCCATTAA
1 TTTTATAGATTTTATAGTTTTACAACTGTTTTCCAAAATTTTACAATTTTGCCATTAA
* * * * **
39808465 TTTT-TCAAATTTTACAGTTTTACCACTATTTTCC-GTA-TTTAGCAATTTTGCCATT-A
1 TTTTAT-AGATTTTATAGTTTTACAACTGTTTTCCAAAATTTTA-CAATTTTGCCATTAA
* *
39808521 TTTT-TCAAATTTTATAATTTT
1 TTTTAT-AGATTTTATAGTTTT
39808542 TCCACTATTC
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
56 24 0.21
57 13 0.12
58 75 0.67
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.53
Consensus pattern (58 bp):
TTTTATAGATTTTATAGTTTTACAACTGTTTTCCAAAATTTTACAATTTTGCCATTAA
Found at i:39809030 original size:52 final size:52
Alignment explanation
Indices: 39808952--39809051 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
39808942 AGTTCTAACA
**
39808952 GTTTTACTGCATTTCGATAAGCCATCGTTGCTGGGCAAC-CTGGGGTGGGAGG
1 GTTTTACTGCATTTCGATAAGCCATCGTTGCCAGGCAACTC-GGGGTGGGAGG
* *
39809004 GTTTTACTGTATTTCGATAAGTCATCGTTGCCAGGCAACTCGGGGTGG
1 GTTTTACTGCATTTCGATAAGCCATCGTTGCCAGGCAACTCGGGGTGG
39809052 CGGGTCATCG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 42 0.98
53 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (52 bp):
GTTTTACTGCATTTCGATAAGCCATCGTTGCCAGGCAACTCGGGGTGGGAGG
Found at i:39809411 original size:37 final size:37
Alignment explanation
Indices: 39809354--39809459 Score: 97
Period size: 37 Copynumber: 2.9 Consensus size: 37
39809344 TACCGTATTG
* ** **
39809354 AATTGATTGATGTGCCAAACTGTTTGTTATTATGTTA
1 AATTGATTGATATGTGAAACTGTTTGTTATTATACTA
* * * *
39809391 AATTGATTGATATGTGAAACTGGTTATCATTGTACTA
1 AATTGATTGATATGTGAAACTGTTTGTTATTATACTA
* *
39809428 AACTT-ATTGATATGTGAAATTGTTTGATATTA
1 AA-TTGATTGATATGTGAAACTGTTTGTTATTA
39809460 CTGTACAGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
37 51 0.96
38 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (37 bp):
AATTGATTGATATGTGAAACTGTTTGTTATTATACTA
Found at i:39809623 original size:3 final size:3
Alignment explanation
Indices: 39809615--39809651 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39809605 CACCAATGAT
39809615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39809652 CATTTTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39814470 original size:29 final size:30
Alignment explanation
Indices: 39814428--39814696 Score: 145
Period size: 29 Copynumber: 9.1 Consensus size: 30
39814418 ACCCGAGGGC
39814428 AAAATGGTAATTTTGGTAAAATCGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
* *
39814458 AAAATGG-AATTTT--AAAAGATTCGGGGGT-
1 AAAATGGTAATTTTGGTAAA-A-TCGGGGTTA
* * *
39814486 AAAATGGTATTTTTGGTGAAATTGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
* ** *
39814516 AAAATGG-AATTTTAG-AAGCTTCGGGGGT-
1 AAAATGGTAATTTTGGTAA-AATCGGGGTTA
* *
39814544 AAAATGGTAATTTTCGATGAAATCGGGGTTA
1 AAAATGGTAATTTT-GGTAAAATCGGGGTTA
* * **
39814575 AAAACGG-AATTTTAG-AAGCTTCGAGGG-T-
1 AAAATGGTAATTTTGGTAA-AATCG-GGGTTA
*
39814603 AAAATGGTAATTTTTGGTAAAATCAGGGTTA
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTTA
* * **
39814634 AAAATGG-GATTTTCG-AAGCTTCGAGGG-T-
1 AAAATGGTAATTTTGGTAA-AATCG-GGGTTA
*
39814662 AAAATGGTAATTTTTGGTGAAAATCGAGGTTA
1 AAAATGGTAA-TTTTGGT-AAAATCGGGGTTA
39814694 AAA
1 AAA
39814697 TGGGATTTAG
Statistics
Matches: 172, Mismatches: 41, Indels: 50
0.65 0.16 0.19
Matches are distributed among these distances:
27 3 0.02
28 32 0.19
29 60 0.35
30 50 0.29
31 22 0.13
32 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCGGGGTTA
Found at i:39814586 original size:59 final size:59
Alignment explanation
Indices: 39814421--39814736 Score: 408
Period size: 59 Copynumber: 5.4 Consensus size: 59
39814411 TATGGATACC
* * * *
39814421 CGAGGGCAAAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
39814479 CGGGGGTAAAATGGT-ATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * *
39814537 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * *
39814596 CGAGGGTAAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGGATTTTCGAAGCTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * *
39814655 CGAGGGTAAAATGGTAATTTTTGGTGAAAATCGAGGTT-AAAATGGGA-TTTAGGAAAGTTT
1 CGAGGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGAATTTTA-G-AAGCTT
*
39814715 CGAGGTTAAAAT-GTAATTTTTG
1 CGAGGGTAAAATGGTAATTTTTG
39814737 AAAGTTTTGG
Statistics
Matches: 229, Mismatches: 24, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
57 1 0.00
58 68 0.30
59 135 0.59
60 25 0.11
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:39814696 original size:31 final size:31
Alignment explanation
Indices: 39814595--39814699 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
39814585 TTTAGAAGCT
39814595 TCGAGGGTAAAATGGTAATTTTTGGT-AAAA
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAAA
* * **
39814625 TC-AGGGTTAAAAATGG-GA-TTTT--CGAAGCT
1 TCGAGGG-T-AAAATGGTAATTTTTGGTGAA-AA
39814654 TCGAGGGTAAAATGGTAATTTTTGGTGAAAA
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAAA
*
39814685 TCGAGGTTAAAATGG
1 TCGAGGGTAAAATGG
39814700 GATTTAGGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
28 9 0.16
29 12 0.21
30 12 0.21
31 21 0.37
32 3 0.05
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (31 bp):
TCGAGGGTAAAATGGTAATTTTTGGTGAAAA
Found at i:39814773 original size:30 final size:30
Alignment explanation
Indices: 39814708--39814946 Score: 374
Period size: 30 Copynumber: 8.0 Consensus size: 30
39814698 GGGATTTAGG
* * * *
39814708 AAAGTTTCGAGGTTAAAATGTAATTTTTG-
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
39814737 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
39814767 AAAGTTTT-GGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
39814796 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
39814826 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
39814856 AAAGCTTTGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
**
39814886 AAAGTTTCAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
39814916 AAAGTTTTGGGGTCAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
39814947 TAATTTATGG
Statistics
Matches: 193, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
29 53 0.27
30 136 0.70
31 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:39814824 original size:19 final size:19
Alignment explanation
Indices: 39814800--39814854 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
39814790 TTTGGAAAAG
39814800 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
39814819 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
39814830 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
39814849 TTTTGG
1 TTTTGG
39814855 AAAAGCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:39815246 original size:162 final size:161
Alignment explanation
Indices: 39815044--39815353 Score: 489
Period size: 162 Copynumber: 1.9 Consensus size: 161
39815034 AAAATCTTGA
* *
39815044 AAAATTTTTGGACCAAATTTGTAATTAAATAAAAGTTGATTTGTGGATTAAATTAAAACAAATTA
1 AAAATTTTTGGACCAAATTTGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAACAAATCA
39815109 AAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAG-CTCCTGGTACAGT
66 AAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCT-CTGGTACAGT
39815173 CAAACAGTCAAAGGACTAATTTATAAACCATG
130 CAAACAGTCAAAGGACTAATTTATAAACCATG
* *
39815205 AAAATTTCTTGGGCC-AATTTCGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAATAAAT
1 AAAATTT-TTGGACCAAATTT-GTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAACAAAT
*** * * *
39815269 CAAAAATGTCAGGGACTAAATGCATAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTACAG
64 CAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACAG
39815334 TCAAACAGTCAAAGGACTAA
129 TCAAACAGTCAAAGGACTAA
39815354 ATTGAAAAGA
Statistics
Matches: 136, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
161 12 0.09
162 122 0.90
163 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (161 bp):
AAAATTTTTGGACCAAATTTGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAACAAATCA
AAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACAGTC
AAACAGTCAAAGGACTAATTTATAAACCATG
Found at i:39815819 original size:21 final size:22
Alignment explanation
Indices: 39815794--39815841 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
39815784 CTTATTCTTC
39815794 TTCTTC-TATTTT-GTTCTTTTA
1 TTCTTCAT-TTTTCGTTCTTTTA
39815815 TTCTTCATTTTTCGTTC-TTTA
1 TTCTTCATTTTTCGTTCTTTTA
39815836 TT-TTCA
1 TTCTTCA
39815842 AAATCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.10, C:0.17, G:0.04, T:0.69
Consensus pattern (22 bp):
TTCTTCATTTTTCGTTCTTTTA
Found at i:39816721 original size:16 final size:17
Alignment explanation
Indices: 39816693--39816724 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39816683 CAGGGCATGG
39816693 TGGAGCTTGGTGGTGGA
1 TGGAGCTTGGTGGTGGA
39816710 TGGAGC-TGGTGGTGG
1 TGGAGCTTGGTGGTGG
39816725 CAGCAGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.56, T:0.28
Consensus pattern (17 bp):
TGGAGCTTGGTGGTGGA
Found at i:39816910 original size:6 final size:6
Alignment explanation
Indices: 39816899--39816965 Score: 68
Period size: 6 Copynumber: 11.7 Consensus size: 6
39816889 GAATTTATAA
* * *
39816899 TAAATT TAAATT TAAA-T TAAATC CAAAAT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
39816945 TAAA-A TAAATT TAATTT TAAA
1 TAAATT TAAATT TAAATT TAAA
39816966 ACAAATTCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 14 0.29
6 35 0.71
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:39816916 original size:23 final size:23
Alignment explanation
Indices: 39816890--39816965 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
39816880 TTGGACTTTG
*
39816890 AATTTATAATAAATTTAAATTTA
1 AATTTAAAATAAATTTAAATTTA
39816913 AATTAAATCCAAAATTAAA-TTAAATTTA
1 AATT---T--AAAA-TAAATTTAAATTTA
*
39816941 AATTTAAAATAAATTTAATTTTA
1 AATTTAAAATAAATTTAAATTTA
39816964 AA
1 AA
39816966 ACAAATTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
22 4 0.09
23 18 0.41
25 1 0.02
26 1 0.02
28 16 0.36
29 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTAAAATAAATTTAAATTTA
Found at i:39816918 original size:11 final size:11
Alignment explanation
Indices: 39816899--39816958 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
39816889 GAATTTATAA
39816899 TAAATTTAAATT
1 TAAA-TTAAATT
*
39816911 TAAATTAAATCC
1 TAAATTAAAT-T
*
39816923 AAAATTAAA-T
1 TAAATTAAATT
39816933 TAAATTTAAATT
1 TAAA-TTAAATT
*
39816945 TAAAATAAATT
1 TAAATTAAATT
39816956 TAA
1 TAA
39816959 TTTTAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 3 0.08
11 20 0.50
12 17 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:39816966 original size:17 final size:17
Alignment explanation
Indices: 39816890--39816972 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
39816880 TTGGACTTTG
*
39816890 AATTTATAATAAATTTA
1 AATTTAAAATAAATTTA
* **
39816907 AATTTAAATTAAATCCA
1 AATTTAAAATAAATTTA
* *
39816924 AAATTAAATTAAATTTA
1 AATTTAAAATAAATTTA
39816941 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
39816958 ATTTTAAAACAAATT
1 AATTTAAAATAAATT
39816973 CAAAATGGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:39817467 original size:76 final size:76
Alignment explanation
Indices: 39817286--39817608 Score: 493
Period size: 76 Copynumber: 4.2 Consensus size: 76
39817276 TTGGTGCTTT
* * * * *
39817286 ATCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTCATTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTCAGA--GATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAG
39817351 AGGATAGGAAAATG
64 AGGATAGG-AAATG
* * *
39817365 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
39817430 GATAGGAAATG
66 GATAGGAAATG
* * *
39817441 ATCTTCCTCTTACTTCAATTTTAGAGATGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
39817506 GATAGGAAGTG
66 GATAGGAAATG
* *
39817517 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
39817582 GATAGGAAATG
66 GATAGGAAATG
39817593 ATCTTGCTCTTACTTC
1 ATCTTGCTCTTACTTC
39817609 GTGTTATCCA
Statistics
Matches: 223, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
76 160 0.72
77 39 0.17
79 24 0.11
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:39817607 original size:38 final size:38
Alignment explanation
Indices: 39817339--39817608 Score: 207
Period size: 38 Copynumber: 7.1 Consensus size: 38
39817329 CCAGCTTCAT
39817339 TTCAATTTCAAGAGGATAGGAAAATGATCTTGCTCTTAC
1 TTCAATTTCAAGAGGATAGG-AAATGATCTTGCTCTTAC
* ** * * *
39817378 TTCAATTTC-AGA-GATAAAGACTTGAT-ATCCAGTTTTAC
1 TTCAATTTCAAGAGGAT-AGGAAATGATCTTGC--TCTTAC
*
39817416 TTCAATTTCAAGAGGATAGGAAATGATCTTCCTCTTAC
1 TTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTAC
* * ** **
39817454 TTCAATTTTAGAGATGA-AGG-CTTGTTATCCAGCT-TTAC
1 TTCAATTTCA-AGAGGATAGGAAATG--ATCTTGCTCTTAC
*
39817492 TTCAATTTCAAGAGGATAGGAAGTGATCTTGCTCTTAC
1 TTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTAC
* ** ***
39817530 TTCAATTTC-AGA-GATGAAGACTTGTTATCCAACTC-TAC
1 TTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCTCTTAC
39817568 TTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTAC
1 TTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTAC
39817606 TTC
1 TTC
39817609 GTGTTATCCA
Statistics
Matches: 177, Mismatches: 36, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
36 5 0.03
37 35 0.20
38 83 0.47
39 45 0.25
40 9 0.05
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (38 bp):
TTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTAC
Found at i:39817728 original size:68 final size:68
Alignment explanation
Indices: 39817608--39818532 Score: 1496
Period size: 68 Copynumber: 13.6 Consensus size: 68
39817598 GCTCTTACTT
** * * * * *
39817608 CGTGTTATCCACTCTACTTTGATTTCGATGGGATGATGTCGCTCTTATTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
39817673 AAA
66 AGA
* *
39817676 CGTGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTTTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39817741 AGA
66 AGA
* * *
39817744 CGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTTTTACTTCGATTTCAGAGAT-A
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39817808 ATGA
66 A-GA
* *
39817812 CGTGTTATCCACTCTACTTCAATTCCGAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39817877 AGA
66 AGA
* *
39817880 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATTACGTTGCTCTTACTTCAATTTCAGAGATAA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39817945 AGA
66 AGA
* *
39817948 CGTGTTATACACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818013 AGA
66 AGA
*
39818016 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATAA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818081 AGA
66 AGA
* *
39818084 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTTTTACTTCGATTTCAGAGAT-A
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818148 ATGA
66 A-GA
* * *
39818152 CGTGTTATGCACTCTACTTCAATTCCGAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818217 AGA
66 AGA
*
39818220 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATAA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818285 AGA
66 AGA
* *
39818288 CGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCGATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818353 AGA
66 AGA
* *
39818356 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTATTTCAATTTCAGAGATAA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
39818421 AGA
66 AGA
*
39818424 CGTGTTATCCACTCTACTTTAATTTCGAA-GGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
1 CGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
*
39818488 AAAA
65 AAGA
* *
39818492 CGTGTTATCCACTCTATTTCAATTTCAAGAGGATGACGTTG
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
39818533 AGACCTGCAG
Statistics
Matches: 799, Mismatches: 52, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
67 6 0.01
68 787 0.98
69 6 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (68 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGA
Found at i:39830555 original size:59 final size:59
Alignment explanation
Indices: 39830455--39830680 Score: 337
Period size: 59 Copynumber: 3.8 Consensus size: 59
39830445 TATGGATACC
* * * *
39830455 CGGGGGTAAAATGGTAATTTT-GGTGAAATTGGGGTTAAAAATAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*
39830513 CGGGGGTAAAATGGTAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
** * * *
39830572 CGGGGGTAAAATGGTAATTTTCAATAAAATCGAGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
39830631 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTT
39830681 AGGAAAGTTT
Statistics
Matches: 151, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
58 21 0.14
59 130 0.86
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:39830562 original size:30 final size:30
Alignment explanation
Indices: 39830462--39830675 Score: 110
Period size: 30 Copynumber: 7.2 Consensus size: 30
39830452 ACCCGGGGGT
39830462 AAAATGGTAATTTTGGTGAAATTGGGGTTA
1 AAAATGGTAATTTTGGTGAAATTGGGGTTA
* ** *
39830492 AAAATAG-AATTTT--AAAAGATTCGGGGGT-
1 AAAATGGTAATTTTGGTGAA-ATT-GGGGTTA
39830520 AAAATGGTAATTTTCGGTGAAATTGGGGTTA
1 AAAATGGTAATTTT-GGTGAAATTGGGGTTA
* * *
39830551 AAAATGG-AATTTT--AGAAGCTTCGGGGGT-
1 AAAATGGTAATTTTGGTGAA-ATT-GGGGTTA
** * * *
39830579 AAAATGGTAATTTTCAATAAAATCGAGGTTA
1 AAAATGGTAATTTT-GGTGAAATTGGGGTTA
* * * *
39830610 AAAACGG-AATTTT--AGAAGCTTCGGGGGT-
1 AAAATGGTAATTTTGGTGAA-ATT-GGGGTTA
*
39830638 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTTA
39830669 AAAATGG
1 AAAATGG
39830676 GATTTAGGAA
Statistics
Matches: 134, Mismatches: 29, Indels: 41
0.66 0.14 0.20
Matches are distributed among these distances:
27 7 0.05
28 25 0.19
29 34 0.25
30 36 0.27
31 25 0.19
32 7 0.05
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATTGGGGTTA
Found at i:39830649 original size:29 final size:30
Alignment explanation
Indices: 39830455--39830651 Score: 128
Period size: 29 Copynumber: 6.7 Consensus size: 30
39830445 TATGGATACC
*
39830455 CGGGGGTAAAATGGTAATTTTGGTGAA-ATT
1 CGGGGGTAAAATGGTAATTTT-GAGAAGATT
* * *
39830485 -GGGGTTAAAAATAG-AATTTT-AAAAGATT
1 CGGGGGT-AAAATGGTAATTTTGAGAAGATT
*
39830513 CGGGGGTAAAATGGTAATTTTCGGTGAA-ATT
1 CGGGGGTAAAATGGTAATTTT--GAGAAGATT
* *
39830544 -GGGGTTAAAAATGG-AATTTT-AGAAGCTT
1 CGGGGGT-AAAATGGTAATTTTGAGAAGATT
* * *
39830572 CGGGGGTAAAATGGTAATTTTCA-ATAAAAT
1 CGGGGGTAAAATGGTAATTTTGAGA-AGATT
* * * *
39830602 CGAGGTTAAAAACGG-AATTTT-AGAAGCTT
1 CGGGGGT-AAAATGGTAATTTTGAGAAGATT
39830631 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
39830652 TGGTGAAATC
Statistics
Matches: 127, Mismatches: 24, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.04
28 24 0.19
29 48 0.38
30 32 0.25
31 16 0.13
32 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTGAGAAGATT
Found at i:39830707 original size:118 final size:118
Alignment explanation
Indices: 39830459--39830710 Score: 323
Period size: 118 Copynumber: 2.1 Consensus size: 118
39830449 GATACCCGGG
** * * * *
39830459 GGTAAAATGGTAATTTT-GGTGAAATTGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGGTAAA
1 GGTAAAATGGTAATTTTCAATAAAATCGAGGTTAAAAACAGAATTTTAAAAGATTCGGGGGTAAA
* *
39830523 ATGGTAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGCTTCGGG
66 ATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGA
* * *
39830576 GGTAAAATGGTAATTTTCAATAAAATCGAGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTAAA
1 GGTAAAATGGTAATTTTCAATAAAATCGAGGTTAAAAACAGAATTTTAAAAGATTCGGGGGTAAA
* * *
39830641 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGA-TTTAGGAAAGTTTC-GA
66 ATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA-G-AAGCTTCGGA
39830694 GGTCAAAAT-GTAATTTT
1 GGT-AAAATGGTAATTTT
39830711 TGAAAGTTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
117 21 0.18
118 85 0.73
119 11 0.09
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (118 bp):
GGTAAAATGGTAATTTTCAATAAAATCGAGGTTAAAAACAGAATTTTAAAAGATTCGGGGGTAAA
ATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGA
Found at i:39830749 original size:30 final size:29
Alignment explanation
Indices: 39830677--39830769 Score: 141
Period size: 29 Copynumber: 3.2 Consensus size: 29
39830667 TAAAAATGGG
* * *
39830677 ATTTAGGAAAGTTTCGAGGTCAAAATGTA
1 ATTTTGGAAAGTTTTGGGGTCAAAATGTA
*
39830706 ATTTTTGAAAGTTTTGGGGTCAAAATGTA
1 ATTTTGGAAAGTTTTGGGGTCAAAATGTA
39830735 ATTTTGGAAAAGTTTTGGGGTCAAAATGTA
1 ATTTTGG-AAAGTTTTGGGGTCAAAATGTA
39830765 ATTTT
1 ATTTT
39830770 TGGACAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 31 0.53
30 27 0.47
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (29 bp):
ATTTTGGAAAGTTTTGGGGTCAAAATGTA
Found at i:39831060 original size:162 final size:162
Alignment explanation
Indices: 39830878--39831180 Score: 473
Period size: 162 Copynumber: 1.9 Consensus size: 162
39830868 TGAAAAAATT
** * * *
39830878 TTGGACCAATTTTGTAATTAAATAAAAGTTGATTTGTGGATTAAATTAAAACAAATTAAAAATAA
1 TTGGACCAATTTCATAATTAAATAAAAGTTAATTTGAGGATTAAATTAAAACAAATCAAAAATAA
39830943 AAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAG-CTCCTGGTACAGTCAAACAG
66 AAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCT-CTGGTACAGTCAAACAG
39831007 TCAAAAGACTAATTTATAAACCATGAAAATTTC
130 TCAAAAGACTAATTTATAAACCATGAAAATTTC
* * **
39831040 TTGGGCCAATTTCATAATTAAATAAAAGTTAATTTGAGGATTAAATTAAAATAAATCAAAAATGT
1 TTGGACCAATTTCATAATTAAATAAAAGTTAATTTGAGGATTAAATTAAAACAAATCAAAAATAA
* * *
39831105 CAGGGACTAAATGCATAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTACAGTCAAACAGT
66 AAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACAGTCAAACAGT
*
39831170 CAAAGGACTAA
131 CAAAAGACTAA
39831181 ATTGAAAAGA
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
162 125 0.98
163 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (162 bp):
TTGGACCAATTTCATAATTAAATAAAAGTTAATTTGAGGATTAAATTAAAACAAATCAAAAATAA
AAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACAGTCAAACAGT
CAAAAGACTAATTTATAAACCATGAAAATTTC
Found at i:39831642 original size:21 final size:22
Alignment explanation
Indices: 39831617--39831658 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39831607 CTTATTCTTC
39831617 TTCTTCTA-TTTT-GTTCTTTTA
1 TTCTTC-ACTTTTCGTTCTTTTA
39831638 TTCTTCACTTTTCGTTCTTTT
1 TTCTTCACTTTTCGTTCTTTT
39831659 TTTTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.69
Consensus pattern (22 bp):
TTCTTCACTTTTCGTTCTTTTA
Found at i:39832546 original size:16 final size:17
Alignment explanation
Indices: 39832518--39832549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39832508 CAGGGCATGG
39832518 TGGAGCTTGGTGGTGGA
1 TGGAGCTTGGTGGTGGA
39832535 TGGAGC-TGGTGGTGG
1 TGGAGCTTGGTGGTGG
39832550 CAGCAGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.56, T:0.28
Consensus pattern (17 bp):
TGGAGCTTGGTGGTGGA
Found at i:39832735 original size:6 final size:6
Alignment explanation
Indices: 39832724--39832790 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
39832714 GAATTTATAA
* *
39832724 TAAATT TAAATT TAAA-T TAAATC CAAATT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
39832770 TAAA-A TAAATT TAATTT TAAA
1 TAAATT TAAATT TAAATT TAAA
39832791 ACAAATTCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 14 0.28
6 36 0.72
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:39832743 original size:11 final size:11
Alignment explanation
Indices: 39832715--39832769 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
39832705 TTGGACTTTG
39832715 AATTTATAA-TA
1 AATTTA-AATTA
39832726 AATTTAAATTTA
1 AATTTAAA-TTA
*
39832738 AA-TTAAATCCA
1 AATTTAAAT-TA
39832749 AATTTAAATTA
1 AATTTAAATTA
39832760 AATTTAAATT
1 AATTTAAATT
39832770 TAAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 3 0.08
11 25 0.66
12 10 0.26
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:39832791 original size:17 final size:17
Alignment explanation
Indices: 39832715--39832797 Score: 103
Period size: 17 Copynumber: 4.9 Consensus size: 17
39832705 TTGGACTTTG
*
39832715 AATTTATAATAAATTTA
1 AATTTAAAATAAATTTA
* **
39832732 AATTTAAATTAAATCCA
1 AATTTAAAATAAATTTA
*
39832749 AATTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
39832766 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
39832783 ATTTTAAAACAAATT
1 AATTTAAAATAAATT
39832798 CAAAATGGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:39836599 original size:35 final size:35
Alignment explanation
Indices: 39836559--39836672 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 35
39836549 TTAAAATATA
39836559 TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATG
1 TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATG
* * * **
39836594 TTAAATGAAAAAAGTATTGTTGTTGTGGCGATATG
1 TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATG
* * *
39836629 TTAAAAGAATGAAGTATCAATGTTGTGGCGGGATG
1 TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATG
39836664 TTAAATGAA
1 TTAAATGAA
39836673 CAAAGTGTCC
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (35 bp):
TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATG
Found at i:39836700 original size:70 final size:70
Alignment explanation
Indices: 39836559--39836702 Score: 173
Period size: 70 Copynumber: 2.1 Consensus size: 70
39836549 TTAAAATATA
* * * * *
39836559 TTAAATGAAAGAAGTATCGATGTTGTGGCGGGATGTTAAATGAAAAAAGTATTGTTGTTGTGGCG
1 TTAAAAGAAAGAAGTATCAATGTTGTGGCGGGATGTTAAATGAAAAAAGTATCGTTGTTATGACG
*
39836624 ATATG
66 AGATG
* * * *
39836629 TTAAAAGAATGAAGTATCAATGTTGTGGCGGGATGTTAAATGAACAAAGTGTCCG-TGTTATGAT
1 TTAAAAGAAAGAAGTATCAATGTTGTGGCGGGATGTTAAATGAAAAAAGTAT-CGTTGTTATGAC
*
39836693 GGGATG
65 GAGATG
39836699 TTAA
1 TTAA
39836703 GTGAATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
70 61 0.98
71 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (70 bp):
TTAAAAGAAAGAAGTATCAATGTTGTGGCGGGATGTTAAATGAAAAAAGTATCGTTGTTATGACG
AGATG
Found at i:39845952 original size:22 final size:25
Alignment explanation
Indices: 39845910--39845961 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
39845900 GTTTTTTGGA
*
39845910 TTTTCAATCAAAGGATCA-TTTC-T
1 TTTTCAATCAAAGGATAATTTTCAT
*
39845933 TTTTCAA-CAAAGGTTAATTTTCAT
1 TTTTCAATCAAAGGATAATTTTCAT
39845957 TTTTC
1 TTTTC
39845962 TATTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.32
23 11 0.44
24 6 0.24
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (25 bp):
TTTTCAATCAAAGGATAATTTTCAT
Found at i:39848940 original size:12 final size:13
Alignment explanation
Indices: 39848912--39848952 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
39848902 ATCTAAGAAT
39848912 TTTTTAATTATTA
1 TTTTTAATTATTA
39848925 -TTTTAATT-TTA
1 TTTTTAATTATTA
39848936 TTTTTGAAATTATTA
1 TTTTT--AATTATTA
39848951 TT
1 TT
39848953 ACATTAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.12
12 12 0.50
14 4 0.17
15 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTTTAATTATTA
Found at i:39849662 original size:2 final size:2
Alignment explanation
Indices: 39849655--39849681 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39849645 AAAAACAATA
39849655 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 A
39849682 ATGGATAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39858488 original size:29 final size:29
Alignment explanation
Indices: 39858432--39858593 Score: 198
Period size: 29 Copynumber: 5.6 Consensus size: 29
39858422 AGACAATCAT
* ** *
39858432 TTCACATATAATCAATTCGTGTACAATAT
1 TTCACATATAATCAGTTCGCATACAATAG
* * *
39858461 TTAACATATAATTAGTTCGCATATAATAG
1 TTCACATATAATCAGTTCGCATACAATAG
* *
39858490 TTCACAAATAATCTGTTCGCATACAATAG
1 TTCACATATAATCAGTTCGCATACAATAG
* *
39858519 TTCACATATAATCAGTTTGCATACTATAG
1 TTCACATATAATCAGTTCGCATACAATAG
* **
39858548 TTTACATATAATCAGTTTACATACAATAG
1 TTCACATATAATCAGTTCGCATACAATAG
39858577 TTCACATATAATCAGTT
1 TTCACATATAATCAGTT
39858594 TAAGCTCACA
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 113 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (29 bp):
TTCACATATAATCAGTTCGCATACAATAG
Found at i:39860570 original size:21 final size:21
Alignment explanation
Indices: 39860546--39860609 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
39860536 GAGCTCACAC
* * *
39860546 AACATCTAAAGGAGTTTGTAT
1 AACATATAAAAGAGTTTGCAT
**
39860567 AACATATAAAAGAGTTCACAT
1 AACATATAAAAGAGTTTGCAT
*
39860588 AACATTTAAAAGAGTTTGCAT
1 AACATATAAAAGAGTTTGCAT
39860609 A
1 A
39860610 TGCATGTAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (21 bp):
AACATATAAAAGAGTTTGCAT
Found at i:39866698 original size:12 final size:13
Alignment explanation
Indices: 39866672--39866711 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
39866662 GGTTTTCTCC
* *
39866672 AAAATAAAATTGA
1 AAAAGAAAAATGA
39866685 AAAAGAAAAA-GA
1 AAAAGAAAAATGA
39866697 AAAAGAAAAATGA
1 AAAAGAAAAATGA
39866710 AA
1 AA
39866712 TTGACATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (13 bp):
AAAAGAAAAATGA
Found at i:39868374 original size:16 final size:16
Alignment explanation
Indices: 39868348--39868391 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
39868338 TATAATATAA
39868348 TATATAAATTTTAATTT
1 TATA-AAATTTTAATTT
39868365 TATAAAATTTTAATTT
1 TATAAAATTTTAATTT
* *
39868381 AATTAAATTTT
1 TATAAAATTTT
39868392 CGTAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAAAATTTTAATTT
Found at i:39868570 original size:29 final size:30
Alignment explanation
Indices: 39868513--39868570 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
39868503 TTTTTTTTCA
* *
39868513 AAATTTTTATATATATAATTCAATCAAAATC
1 AAATTTTCATATATATAATT-AATAAAAATC
*
39868544 AAATTTTCATATATATTATT-ATAAAAA
1 AAATTTTCATATATATAATTAATAAAAA
39868571 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
31 18 0.75
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATTTTCATATATATAATTAATAAAAATC
Found at i:39879145 original size:40 final size:40
Alignment explanation
Indices: 39879057--39879145 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
39879047 TTATGTTGCA
* * *
39879057 ACCAACCCCTTATGTCGCAACATAGGAATGTCTATGTCGCG
1 ACCAACCCCCTATGTCACAACATA-GAATGTCTATGTCACG
* *
39879098 ACAAACCCCCTATGTCATAACATA-ACATGTCTATGTCACG
1 ACCAACCCCCTATGTCACAACATAGA-ATGTCTATGTCACG
39879138 ACCAACCC
1 ACCAACCC
39879146 TAAAGATGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 20 0.49
41 20 0.49
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.22
Consensus pattern (40 bp):
ACCAACCCCCTATGTCACAACATAGAATGTCTATGTCACG
Found at i:39908163 original size:15 final size:15
Alignment explanation
Indices: 39908140--39908180 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
39908130 AGAATAAGAA
39908140 AAAAGAGAAGAGGAA-G
1 AAAA-AGAAGA-GAAGG
39908156 AAAAAGAAGAGAAGG
1 AAAAAGAAGAGAAGG
39908171 AAAAAGAAGA
1 AAAAAGAAGA
39908181 AGTTATCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 17 0.71
16 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAGAAGG
Found at i:39915512 original size:24 final size:24
Alignment explanation
Indices: 39915468--39915513 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39915458 TTGACACAAA
* *
39915468 TTAATTATTTTTAGTAATAATTAT
1 TTAATTATCTTTAGAAATAATTAT
39915492 TTAATTA-CTTTAGAAATTAATT
1 TTAATTATCTTTAGAAA-TAATT
39915514 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TTAATTATCTTTAGAAATAATTAT
Found at i:39924471 original size:16 final size:16
Alignment explanation
Indices: 39924450--39924484 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39924440 ACATTATATT
* *
39924450 TACAACCTGTCCTGTA
1 TACAACCTGACCCGTA
39924466 TACAACCTGACCCGTA
1 TACAACCTGACCCGTA
39924482 TAC
1 TAC
39924485 TTGCAGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (16 bp):
TACAACCTGACCCGTA
Found at i:39925230 original size:16 final size:15
Alignment explanation
Indices: 39925209--39925242 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39925199 AGTTGTCACA
39925209 TGAATTAAATTAATAT
1 TGAATTAAATTAAT-T
*
39925225 TGAATTAATTTAATT
1 TGAATTAAATTAATT
39925240 TGA
1 TGA
39925243 TAGTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (15 bp):
TGAATTAAATTAATT
Found at i:39925475 original size:49 final size:49
Alignment explanation
Indices: 39925416--39925516 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 49
39925406 AAACATGGTA
*
39925416 GTTATAATTCTTTTTCGAAAGAATATAA-CATTTTAAATACTTTCCAAAT
1 GTTATAATTCTTTTTCGAAAGAATATAATAATTTT-AATACTTTCCAAAT
* * *
39925465 GTTATAATTCTTTTTGGAAAGAATATAATAATTTTAATGCTTTCCATAT
1 GTTATAATTCTTTTTCGAAAGAATATAATAATTTTAATACTTTCCAAAT
39925514 GTT
1 GTT
39925517 CTCTATAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
49 42 0.89
50 5 0.11
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.46
Consensus pattern (49 bp):
GTTATAATTCTTTTTCGAAAGAATATAATAATTTTAATACTTTCCAAAT
Found at i:39927124 original size:18 final size:20
Alignment explanation
Indices: 39927101--39927138 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
39927091 GAGTGTTAGC
39927101 TATATGCTTC-ACT-TATGA
1 TATATGCTTCGACTCTATGA
*
39927119 TATATGTTTCGACTCTATGA
1 TATATGCTTCGACTCTATGA
39927139 GTCCAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (20 bp):
TATATGCTTCGACTCTATGA
Found at i:39932502 original size:43 final size:43
Alignment explanation
Indices: 39932449--39932536 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
39932439 ATGAGTTGAT
39932449 TTTCCGAAAAATTTTAAAACGATTTAATAGATGAAATTTACAC
1 TTTCCGAAAAATTTTAAAACGATTTAATAGATGAAATTTACAC
39932492 TTTCCGAAAAATTTTAAAACGATTTAATAGATGAAATTTACAC
1 TTTCCGAAAAATTTTAAAACGATTTAATAGATGAAATTTACAC
39932535 TT
1 TT
39932537 AGCTTTTATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTCCGAAAAATTTTAAAACGATTTAATAGATGAAATTTACAC
Found at i:39940983 original size:19 final size:19
Alignment explanation
Indices: 39940947--39940985 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39940937 TAAAAATCGG
*
39940947 TAAATAATATTTCGGAAAA
1 TAAATAATATTTCAGAAAA
39940966 TAAA-AATATTTCTAGAAAA
1 TAAATAATATTTC-AGAAAA
39940985 T
1 T
39940986 TTAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (19 bp):
TAAATAATATTTCAGAAAA
Found at i:39951521 original size:24 final size:24
Alignment explanation
Indices: 39951494--39951568 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
39951484 AGTTTGACTC
39951494 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
39951518 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
39951542 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
39951566 AAA
1 AAA
39951569 GATTATTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:39953518 original size:24 final size:24
Alignment explanation
Indices: 39953491--39953555 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
39953481 TGACTCAAAT
39953491 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAATTGAAAC
*
39953515 AAATAAACAAAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAATTGAAAC
*
39953539 AATTAAACAGAGTTTAA
1 AAATAAACAGAGTTTAA
39953556 CTAAAAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (24 bp):
AAATAAACAGAGTTTAATTGAAAC
Found at i:39961518 original size:25 final size:23
Alignment explanation
Indices: 39961473--39961518 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
39961463 TCCAATTAGG
39961473 AATTATTGTTTAGATTTAATTAT
1 AATTATTGTTTAGATTTAATTAT
*
39961496 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
39961519 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTAT
Found at i:39964275 original size:51 final size:51
Alignment explanation
Indices: 39964150--39964337 Score: 189
Period size: 51 Copynumber: 3.6 Consensus size: 51
39964140 TTTCATTTAA
** ** *** * *
39964150 TACTCACGATGACATATAGTCATCGGACCTCTTGTTTTGTATAGGAATTCATA
1 TACTCACGATGACACCTAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * *
39964203 TACTCACGATAACA-CTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACCT-AGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
39964254 TACTCATGATGACACCTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
39964305 TACTCACGATGACACTTAGTCATCGGATCCTTT
1 TACTCACGATGACACCTAGTCATCGGA-CCTTT
39964338 CTTTTATAGC
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
51 72 0.64
52 14 0.12
53 26 0.23
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACCTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:39970554 original size:14 final size:14
Alignment explanation
Indices: 39970521--39970560 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
39970511 AAATTAGTAT
*
39970521 ATTTATATTTATTTTC
1 ATTT-TATTT-TTTTA
39970537 ATTTTATTTTTTTA
1 ATTTTATTTTTTTA
39970551 ATTTTATTTT
1 ATTTTATTTT
39970561 AATTATGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 5 0.22
16 4 0.17
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTATTTTTTTA
Found at i:39972592 original size:23 final size:25
Alignment explanation
Indices: 39972566--39972611 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39972556 CCAATTAGGG
39972566 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
39972589 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
39972612 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:39978299 original size:15 final size:16
Alignment explanation
Indices: 39978279--39978319 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
39978269 CTATGACGAC
39978279 ATCTATGAAGAT-GAT
1 ATCTATGAAGATGGAT
*
39978294 ATCTATGAATATGGAT
1 ATCTATGAAGATGGAT
39978310 A-CTATGAAGA
1 ATCTATGAAGA
39978320 CTGGGAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (16 bp):
ATCTATGAAGATGGAT
Found at i:39986401 original size:24 final size:24
Alignment explanation
Indices: 39986372--39986452 Score: 144
Period size: 24 Copynumber: 3.4 Consensus size: 24
39986362 TAAAGTAATA
*
39986372 AAAGTTTGATTGAAACAAATAAAC
1 AAAGTTTAATTGAAACAAATAAAC
39986396 AAAGTTTAATTGAAACAAATAAAC
1 AAAGTTTAATTGAAACAAATAAAC
*
39986420 AAAGTTTTATTGAAACAAATAAAC
1 AAAGTTTAATTGAAACAAATAAAC
39986444 AAAGTTTAA
1 AAAGTTTAA
39986453 CTAGAAGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (24 bp):
AAAGTTTAATTGAAACAAATAAAC
Found at i:39989826 original size:20 final size:19
Alignment explanation
Indices: 39989790--39989844 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
39989780 CTTTAGCCAT
**
39989790 TTTTTAT-TTTTGTTTTAA
1 TTTTTATATTTTAATTTAA
39989808 TATTTTCAT-TTTTAATTTAA
1 T-TTTT-ATATTTTAATTTAA
39989828 TTTTTATATTTTAATTT
1 TTTTTATATTTTAATTT
39989845 TTCCCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.09
19 17 0.53
20 12 0.38
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATATTTTAATTTAA
Found at i:39989846 original size:14 final size:14
Alignment explanation
Indices: 39989788--39989846 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
39989778 TACTTTAGCC
*
39989788 ATTTTT-TATTTTT
1 ATTTTTATATTTTA
* * *
39989801 GTTTTAATATTTTC
1 ATTTTTATATTTTA
39989815 ATTTTTA-A-TTTA
1 ATTTTTATATTTTA
39989827 ATTTTTATATTTTA
1 ATTTTTATATTTTA
39989841 ATTTTT
1 ATTTTT
39989847 CCCTTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 10 0.27
13 6 0.16
14 21 0.57
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (14 bp):
ATTTTTATATTTTA
Found at i:39992187 original size:18 final size:18
Alignment explanation
Indices: 39992164--39992378 Score: 207
Period size: 18 Copynumber: 11.4 Consensus size: 18
39992154 AATTAGTATG
* *
39992164 TTTATTTTTATTTTTGTT
1 TTTATTTTCATTTTTATT
*
39992182 TTTATTTTCATTTTCATTTT
1 TTTATTTTCATTTT--TATT
39992202 TTTATTTTCATTTTTAATT
1 TTTATTTTCATTTTT-ATT
39992221 TTTAATTTTTCATTTTTCATT
1 TTT-A-TTTTCATTTTT-ATT
*
39992242 TTTCATTTTTCATTTTCATT
1 TTT-A-TTTTCATTTTTATT
* *
39992262 TTCATTTTCATTTTCATT
1 TTTATTTTCATTTTTATT
* *
39992280 TTCATTTTCATTTTCATT
1 TTTATTTTCATTTTTATT
* *
39992298 TTCATTTTCATTTTCATT
1 TTTATTTTCATTTTTATT
* *
39992316 TTCATTTTCATTTTCATT
1 TTTATTTTCATTTTTATT
*
39992334 TTCATTTTCATTTTTATT
1 TTTATTTTCATTTTTATT
*
39992352 TTCTTTTTTGC-TTTTTATT
1 TT-TATTTT-CATTTTTATT
39992371 TTTATTTT
1 TTTATTTT
39992379 TTTTATTATG
Statistics
Matches: 179, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
18 106 0.59
19 20 0.11
20 24 0.13
21 29 0.16
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTATTTTCATTTTTATT
Found at i:39992223 original size:8 final size:7
Alignment explanation
Indices: 39992206--39992257 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
39992196 CATTTTTTTA
*
39992206 TTTTCAT
1 TTTTAAT
39992213 TTTTAAT
1 TTTTAAT
39992220 TTTTAAT
1 TTTTAAT
*
39992227 TTTTCAT
1 TTTTAAT
*
39992234 TTTTCAT
1 TTTTAAT
*
39992241 TTTTCAT
1 TTTTAAT
*
39992248 TTTTCAT
1 TTTTAAT
39992255 TTT
1 TTT
39992258 CATTTTCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:39992360 original size:12 final size:12
Alignment explanation
Indices: 39992180--39992358 Score: 234
Period size: 12 Copynumber: 14.3 Consensus size: 12
39992170 TTTATTTTTG
*
39992180 TTTTTATTTTCA
1 TTTTCATTTTCA
*
39992192 TTTTCATTTTTTTA
1 TTTTCA--TTTTCA
*
39992206 TTTTCATTTTTAA
1 TTTTCA-TTTTCA
*
39992219 TTTTTAATTTTTCA
1 -TTTTCA-TTTTCA
39992233 TTTTTCATTTTTCA
1 -TTTTCA-TTTTCA
39992247 TTTTTCATTTTCA
1 -TTTTCATTTTCA
39992260 TTTTCATTTTCA
1 TTTTCATTTTCA
39992272 TTTTCATTTTCA
1 TTTTCATTTTCA
39992284 TTTTCATTTTCA
1 TTTTCATTTTCA
39992296 TTTTCATTTTCA
1 TTTTCATTTTCA
39992308 TTTTCATTTTCA
1 TTTTCATTTTCA
39992320 TTTTCATTTTCA
1 TTTTCATTTTCA
39992332 TTTTCATTTTCA
1 TTTTCATTTTCA
*
39992344 TTTTTATTTTC-
1 TTTTCATTTTCA
39992355 TTTT
1 TTTT
39992359 TTGCTTTTTA
Statistics
Matches: 157, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.03
12 99 0.63
13 12 0.08
14 42 0.27
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:39992379 original size:12 final size:12
Alignment explanation
Indices: 39992164--39992378 Score: 202
Period size: 12 Copynumber: 17.7 Consensus size: 12
39992154 AATTAGTATG
*
39992164 TTTATTTTTATT
1 TTTATTTTCATT
* *
39992176 TTTGTTTTTATT
1 TTTATTTTCATT
*
39992188 TTCATTTTCATTTT
1 TTTATTTTCA--TT
39992202 TTTATTTTCATT
1 TTTATTTTCATT
*
39992214 TTTAATTT--TT
1 TTTATTTTCATT
**
39992224 AAT-TTTTCATT
1 TTTATTTTCATT
39992235 TTTCATTTTTCATT
1 TTT-A-TTTTCATT
39992249 TTTCATTTTCATT
1 TTT-ATTTTCATT
*
39992262 TTCATTTTCATT
1 TTTATTTTCATT
*
39992274 TTCATTTTCATT
1 TTTATTTTCATT
*
39992286 TTCATTTTCATT
1 TTTATTTTCATT
*
39992298 TTCATTTTCATT
1 TTTATTTTCATT
*
39992310 TTCATTTTCATT
1 TTTATTTTCATT
*
39992322 TTCATTTTCATT
1 TTTATTTTCATT
*
39992334 TTCATTTTCATT
1 TTTATTTTCATT
*
39992346 TTTATTTTCTTT
1 TTTATTTTCATT
* *
39992358 TTTGCTTTTTATT
1 TTT-ATTTTCATT
39992371 TTTATTTT
1 TTTATTTT
39992379 TTTTATTATG
Statistics
Matches: 177, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
9 3 0.02
10 3 0.02
11 3 0.02
12 125 0.71
13 19 0.11
14 24 0.14
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.73
Consensus pattern (12 bp):
TTTATTTTCATT
Found at i:39992380 original size:7 final size:6
Alignment explanation
Indices: 39992164--39992379 Score: 155
Period size: 6 Copynumber: 34.5 Consensus size: 6
39992154 AATTAGTATG
* * * *
39992164 TTTATT TTTATT TTTGTT TTTATT TTCATT TTCATTTT TTTATT TTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT--TATT TTTATT TTTATT
*
39992214 TTTAATT TTTAATT TTTCATT TTTCATT TTTCATT TTTCATT TTCATT
1 TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTTATT
* * * * * * * *
39992262 TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * * * * *
39992310 TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTTATT TTCT-TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT-TATT
*
39992358 TTTGCTT TTTATT TTTATT TTT
1 TTT-ATT TTTATT TTTATT TTT
39992380 TTTATTATGC
Statistics
Matches: 192, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
5 1 0.01
6 142 0.74
7 45 0.23
8 4 0.02
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTATT
Found at i:39998779 original size:87 final size:86
Alignment explanation
Indices: 39998670--39998831 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 86
39998660 TAAGTTCAGT
* *
39998670 GAATTCATCAAGTCCGTCTCAATAGGACCACCCAAA-CTTTGGGATATGAATTCATTAAGAGTAA
1 GAATTCATCAAGTCCGTCTCAATAGGACCACCCAAATC-TTGGGATATGAACTCATTAAAAGTAA
39998734 TAAACTCAACCTCTCATGTCGGC
65 -AAACTCAACCTCTCATGTCGGC
* *
39998757 GAATTGATCAAGTCTC-TCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAAAGTGA
1 GAATTCATCAAGTC-CGTCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAAAGTAA
*
39998821 GAACTCAACCT
65 AAACTCAACCT
39998832 TATGCATGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
86 10 0.15
87 56 0.82
88 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (86 bp):
GAATTCATCAAGTCCGTCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAAAGTAAA
AACTCAACCTCTCATGTCGGC
Found at i:40002949 original size:24 final size:23
Alignment explanation
Indices: 40002891--40002951 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
40002881 AAAGGTGTTA
*
40002891 TAAGAAAATGAAAGGTGAAAAGT
1 TAAGAAAATAAAAGGTGAAAAGT
*
40002914 TAAGGAAGATAAAAGGTGAAATA-T
1 TAA-GAAAATAAAAGGTGAAA-AGT
40002938 TGAAGAAAATAAAA
1 T-AAGAAAATAAAA
40002952 AGTTGAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.09
24 26 0.81
25 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (23 bp):
TAAGAAAATAAAAGGTGAAAAGT
Found at i:40003491 original size:18 final size:19
Alignment explanation
Indices: 40003463--40003501 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40003453 ATGAAAATTT
*
40003463 TTTTATTTAAACTCTTAAA
1 TTTTATTTAAAATCTTAAA
*
40003482 TTTT-TTTAAAATTTTAAA
1 TTTTATTTAAAATCTTAAA
40003500 TT
1 TT
40003502 AGTAAAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATTTAAAATCTTAAA
Found at i:40005614 original size:6 final size:5
Alignment explanation
Indices: 40005562--40005633 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
40005552 ATTTTAGACC
* * * *
40005562 TTTAT CTTAT TTT-T ATTA- TTTGT TTTA- TTTCT TTTAT TTTAT GTTTACT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTA-T
*
40005611 TTTAT TTTTT ATTTAT TTTAT TT
1 TTTAT TTTAT -TTTAT TTTAT TT
40005634 ATCTTTAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 8 0.16
5 30 0.59
6 12 0.24
7 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:40005614 original size:17 final size:17
Alignment explanation
Indices: 40005587--40005633 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
40005577 TTATTTGTTT
40005587 TATTT-CTTTTATTTTA
1 TATTTACTTTTATTTTA
* *
40005603 TGTTTACTTTTATTTTT
1 TATTTACTTTTATTTTA
40005620 TATTTA-TTTTATTT
1 TATTTACTTTTATTT
40005634 ATCTTTAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
TATTTACTTTTATTTTA
Found at i:40009928 original size:16 final size:15
Alignment explanation
Indices: 40009907--40009958 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
40009897 ACTTCACCAA
*
40009907 AAAAAAGAAAAGAAAT
1 AAAAAAGAAAA-AAAG
*
40009923 AAAAAAGGGAAAAAAG
1 AAAAAA-GAAAAAAAG
40009939 AAAAAAGAAGAAAAAG
1 AAAAAAGAA-AAAAAG
40009955 AAAA
1 AAAA
40009959 GGAGATGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 2 0.06
16 25 0.81
17 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:40010989 original size:100 final size:101
Alignment explanation
Indices: 40010796--40011342 Score: 478
Period size: 100 Copynumber: 5.4 Consensus size: 101
40010786 AGATAAATAC
* * * * * * * * *
40010796 GACATCAAATCCTATATCCCTAAAGTTACAGTGAATCAAATTGAAACCACA-AAAGCAAATCTTT
1 GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAAT-ATT
** * *
40010860 ATCTCTCTAAAGTTATAGTAGAACAAGATGAAGCTAC
65 ATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
* * * * * *
40010897 AACATCGAATCTTATACCCCTGAAGTTGCAGTGGGTCAGATTCAAGCTAAAG-AGGCAAATATTA
1 GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAATATTA
* * *
40010961 TCTCTCTAAAGATGCAGTGGAGCAAGATGAAGTTAT
66 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
* * * ** * * * *
40010997 GGCATCAAAT-TCGATATCCTTGAAGTTGCAG-GGATTGGATTAAAGCTATAG-TAGCAAATCTT
1 GACATCAAATCT-TATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAAT-AT
*
40011059 TATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAC
64 TATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
* * * * * * * * *
40011097 CAAATCAAATCTGATACCCCTGAAGTTGTAGTGGGTCGGATTGAAGCTACA-AAAGCAAATCTTA
1 GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAATATTA
* * * * * *
40011161 TCCCACTGAAGATGCAATGGAGCAAGATGAAGCTAT
66 TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
* * * **
40011197 GACATCAAATCCTATATCCTTAAACCTGCAGTGGATCAGATTGAAGCT-AAGAAAGCAAATATTT
1 GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAATA-TT
* * ** *
40011261 ATCTCTCTGAAGTTGAAACAGAGCAAGATGAAGTTAT
65 ATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
* *
40011298 GACATCAAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAA
1 GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAA
40011343 ACTACAAGTC
Statistics
Matches: 354, Mismatches: 84, Indels: 16
0.78 0.19 0.04
Matches are distributed among these distances:
99 23 0.06
100 190 0.54
101 141 0.40
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (101 bp):
GACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTAAAGAAAGCAAATATTA
TCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTAT
Found at i:40011123 original size:50 final size:49
Alignment explanation
Indices: 40011069--40011195 Score: 123
Period size: 50 Copynumber: 2.5 Consensus size: 49
40011059 TATCTCTCTA
* *
40011069 AAGTTGCAGTAGAGCAAGATGAAGCTACCAAATCAAATCTGATACCC-CTG
1 AAGTTGCAGT-GAGCAAGATGAAGCTACAAAAGCAAATCTGAT-CCCACTG
* * * *
40011119 AAGTTGTAGTGGGTC-GGATTGAAGCTACAAAAGCAAATCTTATCCCACTG
1 AAGTTGCAGTGAG-CAAGA-TGAAGCTACAAAAGCAAATCTGATCCCACTG
* *
40011169 AAGATGCAATGGAGCAAGATGAAGCTA
1 AAGTTGCAGT-GAGCAAGATGAAGCTA
40011196 TGACATCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
49 7 0.11
50 50 0.82
51 4 0.07
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (49 bp):
AAGTTGCAGTGAGCAAGATGAAGCTACAAAAGCAAATCTGATCCCACTG
Found at i:40011192 original size:200 final size:200
Alignment explanation
Indices: 40010847--40011350 Score: 595
Period size: 200 Copynumber: 2.5 Consensus size: 200
40010837 TGAAACCACA
* *
40010847 AAAGCAAATCTTTATCTCTCTAAAGTT-ATAGTAGAACAAGATGAAGCTACAACATCGAATCTTA
1 AAAGCAAATCTTTATCTCTCTAAAGTTGA-AGTAGAGCAAGATGAAGCTACAA-ATCAAATC-TA
* * * *
40010911 TACCCCTGAAGTTGCAGTGGGTCAGATTCAAGCTA-AAGAGGCAAATATTATCTCTCTAAAGATG
63 TACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAGAAGCAAATATTATCCCACTAAAGATG
* * * * * ** **
40010975 CAGTGGAGCAAGATGAAGTTATGGCATCAAATTCGATATCCTTGAAGTTGCAG-GGATTGGATTA
128 CAATGGAGCAAGATGAAGCTATGACATCAAATCCGATATCCTTAAACCTGCAGTGGATCAGATTA
40011039 AAGCTATAG
193 AAGCTA-AG
* *
40011048 -TAGCAAATCTTTATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAGCTACCAAATCAAATCTGAT
1 AAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATGAAGCTA-CAAATCAAATCT-AT
* * * *
40011112 ACCCCTGAAGTTGTAGTGGGTCGGATTGAAGCTACAA-AAGCAAATCTTATCCCACTGAAGATGC
64 ACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAGAAGCAAATATTATCCCACTAAAGATGC
* *
40011176 AATGGAGCAAGATGAAGCTATGACATCAAATCCTATATCCTTAAACCTGCAGTGGATCAGATTGA
129 AATGGAGCAAGATGAAGCTATGACATCAAATCCGATATCCTTAAACCTGCAGTGGATCAGATTAA
40011241 AGCTAAG
194 AGCTAAG
* * ** * * *
40011248 AAAGCAAATATTTATCTCTCTGAAGTTGAAACAGAGCAAGATGAAGTTATGACATCAAATCCTAT
1 AAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATGAAGCTA-CAAATCAAAT-CTAT
* * * *
40011313 ATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAAG
64 ACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAG
40011351 TCTTATCTCC
Statistics
Matches: 256, Mismatches: 39, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
199 1 0.00
200 152 0.59
201 101 0.39
202 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (200 bp):
AAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATGAAGCTACAAATCAAATCTATAC
CCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAGAAGCAAATATTATCCCACTAAAGATGCAA
TGGAGCAAGATGAAGCTATGACATCAAATCCGATATCCTTAAACCTGCAGTGGATCAGATTAAAG
CTAAG
Found at i:40011729 original size:101 final size:100
Alignment explanation
Indices: 40011589--40012041 Score: 274
Period size: 97 Copynumber: 4.6 Consensus size: 100
40011579 CTACAGTGGT
* * * * * * * * * *
40011589 AAATCTTATCTCCTTGAAGTTACAATGGAGCAAAATGAAGCTATAATAAC-AATTCAAGTCCCCT
1 AAATCTTATCTCCTCGAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCCAA-TACCCT
* * * *
40011653 TGAGGTTACAGTGGGTTGGAATGAAATTACAAACAGA
65 TGAAGTTACAATGGGTCGGAATGAAACTACAAA-AGA
* * * *
40011690 AAATCTTATCTCCTCGAAGATGTAGTGGAGTAAGATGAAGCTACAACATCAAATCCTATACCTTT
1 AAATCTTATCTCCTCGAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCCAATACCCTT
* * * * *
40011755 GAAGTTGCAATTGGTCGGATTGAAGCTACAAAAGC
66 GAAGTTACAATGGGTCGGAATGAAACTACAAAAGA
* * * * * * *
40011790 AAATCTTATCTCCTCGGATATGCAGTGGAGTAAGATGAAGTTGCAAC-ATAAAT-TATATACCCC
1 AAATCTTATCTCCTCGAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCCA-ATACCCT
** * * * *
40011853 TGAAGTCGCAGTGGGTCGGATTGAAGCTACAAAAGC
65 TGAAGTTACAATGGGTCGGAATGAAACTACAAAAGA
* * * * * * * *
40011889 AAATCTTATCTCC-CTGAAGTTACAATGGAGCAAGTTGAAG---CAACATCAAATCCTATACCCC
1 AAATCTTATCTCCTC-GAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCCAATACCCT
* * * * * * * * *
40011950 TAAAGTTGCAGTGGTTTGGATTGAAGCTACAGAAGC
65 TGAAGTTACAATGGGTCGGAATGAAACTACAAAAGA
* * * * * *
40011986 AAATCTTATCTACCT-AAAGATGCAATGGAGCAAGATGAAGTTACGACATCAAATCC
1 AAATCTTATCT-CCTCGAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCC
40012042 TGTATCCCTG
Statistics
Matches: 284, Mismatches: 58, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
96 4 0.01
97 74 0.26
98 3 0.01
99 73 0.26
100 56 0.20
101 69 0.24
102 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (100 bp):
AAATCTTATCTCCTCGAAGATGCAGTGGAGTAAGATGAAGCTACAACAACAAATCCAATACCCTT
GAAGTTACAATGGGTCGGAATGAAACTACAAAAGA
Found at i:40011829 original size:50 final size:49
Alignment explanation
Indices: 40011680--40011901 Score: 116
Period size: 50 Copynumber: 4.4 Consensus size: 49
40011670 GGAATGAAAT
* * *
40011680 TACAAACAGAAAATCTTATCTCCTCGAAGATGTAGTGGAGTAAGATGAAGC
1 TACAAA-AGCAAATCTTATCTCCTCGGA-ATGCAGTGGAGTAAGATGAAGC
* * * * ** * * **
40011731 TACAACATCAAATCCTAT-ACCTTTGAAGTTGCAATTG-GTCGGATTGAAGC
1 TACAAAAGCAAATCTTATCTCCTCGGAA--TGCAGTGGAGTAAGA-TGAAGC
*
40011781 TACAAAAGCAAATCTTATCTCCTCGGATATGCAGTGGAGTAAGATGAAGT
1 TACAAAAGCAAATCTTATCTCCTCGGA-ATGCAGTGGAGTAAGATGAAGC
* * * * **
40011831 TGCAACA-TAAAT-TATATAC-CC-CTGAAGTCGCAGTGG-GTCGGATTGAAGC
1 TACAAAAGCAAATCT-TAT-CTCCTCGGAA-T-GCAGTGGAGTAAGA-TGAAGC
40011880 TACAAAAGCAAATCTTATCTCC
1 TACAAAAGCAAATCTTATCTCC
40011902 CTGAAGTTAC
Statistics
Matches: 123, Mismatches: 34, Indels: 29
0.66 0.18 0.16
Matches are distributed among these distances:
47 1 0.01
48 10 0.08
49 35 0.28
50 61 0.50
51 15 0.12
52 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (49 bp):
TACAAAAGCAAATCTTATCTCCTCGGAATGCAGTGGAGTAAGATGAAGC
Found at i:40012087 original size:100 final size:98
Alignment explanation
Indices: 40011516--40012162 Score: 464
Period size: 100 Copynumber: 6.5 Consensus size: 98
40011506 AGTTATAGTT
* * * **** * * *
40011516 GAGCAAGATGAAGCTACAACACCAAATCTTATATTATTGAAGTTGTAGTGGATCGGATTAAAACT
1 GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGG-TCGGATTGAAGCT
*** * * *
40011581 ACAGTGGTAAATCTTATCTCCTTGAAGTTACAATG
65 ACAAAAGCAAATCTTATCTCC-TGAAGATGCAATG
* * * * * * * * * * * *
40011616 GAGCAAAATGAAGCTATAATAAC-AATTCAAGT-CCCCTTGAGGTTACAGTGGGTTGGAATGAAA
1 GAGCAAGATGAAGTTACAACATCAAATCCTA-TACCCC-TGAAGTTGCAGT-GGTCGGATTGAAG
* * * *
40011679 TTACAAACAGAAAATCTTATCTCCTCGAAGATGTAGTG
63 CTACAAA-AGCAAATCTTATCTCCT-GAAGATGCAATG
* * ** *
40011717 GAGTAAGATGAAGCTACAACATCAAATCCTATACCTTTGAAGTTGCAATTGGTCGGATTGAAGCT
1 GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGC-AGTGGTCGGATTGAAGCT
* * *
40011782 ACAAAAGCAAATCTTATCTCCTCGGATATGCAGTG
65 ACAAAAGCAAATCTTATCTCCT-GAAGATGCAATG
* * ** *
40011817 GAGTAAGATGAAGTTGCAACAT-AAATTATATACCCCTGAAGTCGCAGTGGGTCGGATTGAAGCT
1 GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGCAGT-GGTCGGATTGAAGCT
* *
40011881 ACAAAAGCAAATCTTATCTCCCTGAAGTTACAATG
65 ACAAAAGCAAATCTTATCT-CCTGAAGATGCAATG
* * *
40011916 GAGCAAGTTGAAG---CAACATCAAATCCTATACCCCTAAAGTTGCAGTGGTTTGGATTGAAGCT
1 GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGG-TCGGATTGAAGCT
* *
40011978 ACAGAAGCAAATCTTATCTACCTAAAGATGCAATG
65 ACAAAAGCAAATCTTATCT-CCTGAAGATGCAATG
* * * * * * *
40012013 GAGCAAGATGAAGTTACGACATCAAATCCTGTATCCCTGAAGTTGTAGTGGATCGAATTAAAACT
1 GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGG-TCGGATTGAAGCT
** * * *
40012078 ACATTAGCAAGTCCTATCTCCCTAAAGATGCAGA-G
65 ACAAAAGCAAATCTTATCT-CCTGAAGATGCA-ATG
* * * * *
40012113 GAGCAAGATGAAGTTATAATATCAAATCATGT-CTTCCTGAAGTTGCAGTG
1 GAGCAAGATGAAGTTACAACATCAAATCCTATAC-CCCTGAAGTTGCAGTG
40012163 AAGTGGATAA
Statistics
Matches: 436, Mismatches: 94, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
96 8 0.02
97 76 0.17
98 2 0.00
99 74 0.17
100 200 0.46
101 67 0.15
102 9 0.02
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (98 bp):
GAGCAAGATGAAGTTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGGTCGGATTGAAGCTA
CAAAAGCAAATCTTATCTCCTGAAGATGCAATG
Found at i:40013291 original size:5 final size:5
Alignment explanation
Indices: 40013281--40013307 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40013271 GATTTAACCC
40013281 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
40013308 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:40013647 original size:26 final size:27
Alignment explanation
Indices: 40013607--40013669 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
40013597 TTTTATTGCT
*
40013607 TTTATTTTACGTTTA-CTTTTACTTTTTA
1 TTTATTTTAC-TTTATC-TTTAATTTTTA
*
40013635 TTTATTTTA-TTTATCTTTAATTTTTT
1 TTTATTTTACTTTATCTTTAATTTTTA
40013661 TTTATTTTA
1 TTTATTTTA
40013670 AGCTATTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 9 0.28
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTATTTTACTTTATCTTTAATTTTTA
Found at i:40015133 original size:5 final size:5
Alignment explanation
Indices: 40015123--40015147 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40015113 GATTTAGTCT
40015123 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
40015148 AGTTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:40020461 original size:17 final size:17
Alignment explanation
Indices: 40020438--40020566 Score: 152
Period size: 17 Copynumber: 7.4 Consensus size: 17
40020428 CTAAACCCAT
40020438 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
40020456 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
40020472 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
**
40020490 TTTAAATTTGCTTTAGAA
1 TTTAAATTTATTTTA-AA
* * *
40020508 TTTAAATTTAATCTAAG
1 TTTAAATTTATTTTAAA
40020525 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
40020543 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
40020560 TTTAAAT
1 TTTAAAT
40020567 GAATAAAAGT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.01
17 50 0.53
18 44 0.46
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40020475 original size:6 final size:6
Alignment explanation
Indices: 40020438--40020566 Score: 92
Period size: 6 Copynumber: 22.2 Consensus size: 6
40020428 CTAAACCCAT
* * **
40020438 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTTATT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
40020484 TTTAAA TTTAAA TTT-GC TTTAGAA TTTAAA TTT-AA TCTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40020531 TTTATA TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
40020567 GAATAAAAGT
Statistics
Matches: 93, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
4 2 0.02
5 17 0.18
6 67 0.72
7 7 0.08
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:40020495 original size:35 final size:34
Alignment explanation
Indices: 40020438--40020566 Score: 152
Period size: 35 Copynumber: 3.7 Consensus size: 34
40020428 CTAAACCCAT
*
40020438 TTTAAATTTATTTTAAGA-TTAAATTTATTTTAAA
1 TTTAAATTTATTCTAA-ATTTAAATTTATTTTAAA
* **
40020472 TTTAAATTTATTTTTAAATTTAAATTTGCTTTAGAA
1 TTTAAATTTA-TTCTAAATTTAAATTTATTTTA-AA
* *
40020508 TTTAAATTTAATCTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTATTCTAAATTTAAATTTAT-TTTAAA
*
40020543 TTTAAAATTATTCTAAATTTAAAT
1 TTTAAATTTATTCTAAATTTAAAT
40020567 GAATAAAAGT
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
34 11 0.14
35 54 0.67
36 16 0.20
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTCTAAATTTAAATTTATTTTAAA
Found at i:40022315 original size:30 final size:29
Alignment explanation
Indices: 40022281--40022549 Score: 246
Period size: 30 Copynumber: 9.1 Consensus size: 29
40022271 CCCTGAAGGT
* *
40022281 CCCTAAACTATCCAAAAATTACATTTTGAC
1 CCCTAAACTTTCCAAAAATTACATTTT-AA
*
40022311 CCCTAAACTTTCCAAAAATTACATTTCAA
1 CCCTAAACTTTCCAAAAATTACATTTTAA
*
40022340 CCCTCAAACTTTCCAAAAATTACATTTCAA
1 CCCT-AAACTTTCCAAAAATTACATTTTAA
*
40022370 CCCTCAAACTTTCCTAAAATTACATTTTAA
1 CCCT-AAACTTTCCAAAAATTACATTTTAA
* *
40022400 CCCTAAACTTT-CTAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAAATTA-CATTTTAA
* *
40022429 CCCTAAAC-TTCCAAAAATTCCATTTTTCA
1 CCCTAAACTTTCCAAAAATTACA-TTTTAA
** *
40022458 CCCTAATTTTTCCAAAATTTACAATTTT-A
1 CCCTAAACTTTCCAAAAATTAC-ATTTTAA
* *
40022487 CCTTTAAA-TTTCCAAAAA-TACCATTTTTGA
1 CC-CTAAACTTTCCAAAAATTA-CA-TTTTAA
* *
40022517 -CCTCGAACTTTTCAAAAATTACTATTTT-A
1 CCCT-AAACTTTCCAAAAATTAC-ATTTTAA
40022546 CCCT
1 CCCT
40022550 CGGATGTTTA
Statistics
Matches: 204, Mismatches: 20, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
28 17 0.08
29 65 0.32
30 118 0.58
31 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTAA
Found at i:40022500 original size:59 final size:58
Alignment explanation
Indices: 40022281--40022548 Score: 260
Period size: 59 Copynumber: 4.5 Consensus size: 58
40022271 CCCTGAAGGT
*
40022281 CCCTAAACTATCCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTACA-TTTCAA
1 CCCTAAACTTTCCAAAAATTACATTTT-ACCCCTAAACTTTCCAAAAATTACATTTTC-A
* * * *
40022340 CCCTCAAACTTTCCAAAAATTACATTTCAACCCTCAAACTTTCCTAAAATTACATTTTAA
1 CCCT-AAACTTTCCAAAAATTACATTTTACCCCT-AAACTTTCCAAAAATTACATTTTCA
* *
40022400 CCCTAAACTTT-CTAAAATTACCATTTTACCCCTAAAC-TTCCAAAAATTCCATTTTTCA
1 CCCTAAACTTTCCAAAAATTA-CATTTTACCCCTAAACTTTCCAAAAATTACA-TTTTCA
** * ** *
40022458 CCCTAATTTTTCCAAAATTTACAATTTTACCTTTAAA-TTTCCAAAAA-TACCATTTTTGA
1 CCCTAAACTTTCCAAAAATTAC-ATTTTACCCCTAAACTTTCCAAAAATTA-CA-TTTTCA
* *
40022517 -CCTCGAACTTTTCAAAAATTACTATTTTACCC
1 CCCT-AAACTTTCCAAAAATTAC-ATTTTACCC
40022549 TCGGATGTTT
Statistics
Matches: 173, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
57 12 0.07
58 31 0.18
59 83 0.48
60 44 0.25
61 3 0.02
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAAATTACATTTTACCCCTAAACTTTCCAAAAATTACATTTTCA
Found at i:40022593 original size:30 final size:29
Alignment explanation
Indices: 40022291--40022602 Score: 113
Period size: 30 Copynumber: 10.6 Consensus size: 29
40022281 CCCTAAACTA
* * *
40022291 TCCAAAAATTACATTTTGACCCCT-AAACTT
1 TCCAAAAATTCCATTTTTA-CCTTGAAA-TT
* ** * *
40022321 TCCAAAAATTACATTTCAACCCTCAAACTT
1 TCCAAAAATTCCATTTTTACCTTGAAA-TT
* ** * *
40022351 TCCAAAAATTACATTTCAACCCTCAAACTT
1 TCCAAAAATTCCATTTTTACCTTGAAA-TT
* * * *
40022381 TCCTAAAATTACATTTTAACCCT-AAACTT
1 TCCAAAAATTCCATTTTTACCTTGAAA-TT
* * *
40022410 T-CTAAAATTACCA-TTTTACCCCT-AAACT
1 TCCAAAAATT-CCATTTTTA-CCTTGAAATT
* *
40022438 TCCAAAAATTCCATTTTTCACCCT-AATTTT
1 TCCAAAAATTCCATTTTT-ACCTTGAA-ATT
* * * *
40022468 TCCAAAATTTACAATTTTACCTTTAAATT
1 TCCAAAAATTCCATTTTTACCTTGAAATT
* * *
40022497 TCCAAAAATACCATTTTTGACCTCGAACTT
1 TCCAAAAATTCCATTTTT-ACCTTGAAATT
* * * *
40022527 TTCAAAAATTAC-TATTTTACCCTCG-GATGT
1 TCCAAAAATTCCAT-TTTTA-CCTTGAAAT-T
*
40022557 T--TAAAATTCCATTTTTGACCTTGAAATT
1 TCCAAAAATTCCATTTTT-ACCTTGAAATT
40022585 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
40022603 CCCCAAAATG
Statistics
Matches: 232, Mismatches: 32, Indels: 35
0.78 0.11 0.12
Matches are distributed among these distances:
28 34 0.15
29 64 0.28
30 127 0.55
31 7 0.03
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCTTGAAATT
Found at i:40023032 original size:98 final size:97
Alignment explanation
Indices: 40022864--40023039 Score: 253
Period size: 98 Copynumber: 1.8 Consensus size: 97
40022854 TAAACCTTTA
* * *
40022864 AAATCGAGGCAATATTCCTTTATTTCGAATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTCCTTTATCTCGAATTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAC
40022929 TTTTCTTCAAATCAAAATAATCTAATACCCAT
66 TTTTCTTCAAATCAAAATAATCTAATACCCAT
* * ** ***
40022961 AAATCGAGGCAATGTTTCTTTATCTCTGTTTTTTGAAAATTTGTGCCTTAACTTACTAGGTGTAA
1 AAATCGAGGCAATATTCCTTTATCTC-GAATTTTGAAAATTTGTGCCTTAACTTACTAGGCACAA
40023026 CTTTTCTTCAAATC
65 CTTTTCTTCAAATC
40023040 GCGATAATCG
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
97 23 0.34
98 45 0.66
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCGAATTTTGAAAATTTGTGCCTTAACTTACTAGGCACAAC
TTTTCTTCAAATCAAAATAATCTAATACCCAT
Found at i:40024113 original size:18 final size:18
Alignment explanation
Indices: 40024090--40024137 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
40024080 TACATTTACA
40024090 AGCTCACCTAAAGATT-CG
1 AGCTCACC-AAAGATTGCG
*
40024108 AGCTCATCAAAGATTGCG
1 AGCTCACCAAAGATTGCG
*
40024126 AGCTCATCAAAG
1 AGCTCACCAAAG
40024138 TGTAAGCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (18 bp):
AGCTCACCAAAGATTGCG
Found at i:40024121 original size:17 final size:18
Alignment explanation
Indices: 40024099--40024137 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40024089 AAGCTCACCT
40024099 AAAGATT-CGAGCTCATC
1 AAAGATTGCGAGCTCATC
40024116 AAAGATTGCGAGCTCATC
1 AAAGATTGCGAGCTCATC
40024134 AAAG
1 AAAG
40024138 TGTAAGCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (18 bp):
AAAGATTGCGAGCTCATC
Found at i:40033607 original size:31 final size:31
Alignment explanation
Indices: 40033572--40033635 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
40033562 CTCAACCGGT
40033572 GACTTTGACAAGGTAAATTGCACGTTTGACA
1 GACTTTGACAAGGTAAATTGCACGTTTGACA
40033603 GACTTTGACAAGGTAAATTGCACGTTTGACA
1 GACTTTGACAAGGTAAATTGCACGTTTGACA
40033634 GA
1 GA
40033636 AGCGTGACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (31 bp):
GACTTTGACAAGGTAAATTGCACGTTTGACA
Found at i:40033762 original size:30 final size:31
Alignment explanation
Indices: 40033712--40033783 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
40033702 TTGGTAGGGT
* * *
40033712 GGAAAGAAAATTGAAAAGATGAAAAATTGAA
1 GGAAAAAAAATAGAAAAGATGAAAAATAGAA
*
40033743 GGAAAAAAAATAG-AAAGATGGAAAATAGAA
1 GGAAAAAAAATAGAAAAGATGAAAAATAGAA
*
40033773 AGAAAATAAAA
1 GGAAAA-AAAA
40033784 AAATTTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 20 0.57
31 15 0.43
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (31 bp):
GGAAAAAAAATAGAAAAGATGAAAAATAGAA
Found at i:40035262 original size:30 final size:29
Alignment explanation
Indices: 40035228--40035288 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
40035218 CTTAATAAAT
*
40035228 AAATGCCTCTAAAATAGTAACAAAATTAAC
1 AAATGCCTCTAAAATAAT-ACAAAATTAAC
*
40035258 AAATGCCTCTAAAATAATAGAAAATTAAC
1 AAATGCCTCTAAAATAATACAAAATTAAC
40035287 AA
1 AA
40035289 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.23
Consensus pattern (29 bp):
AAATGCCTCTAAAATAATACAAAATTAAC
Found at i:40039432 original size:34 final size:34
Alignment explanation
Indices: 40039393--40039460 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
40039383 CCTGTATTAG
40039393 TATGATGGTTAGGGTATTTATCGTCCTAAATGTA
1 TATGATGGTTAGGGTATTTATCGTCCTAAATGTA
*
40039427 TATGATGGTTAGGGTATTTATCGTCCTCAATGTA
1 TATGATGGTTAGGGTATTTATCGTCCTAAATGTA
40039461 GCATGAGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (34 bp):
TATGATGGTTAGGGTATTTATCGTCCTAAATGTA
Found at i:40044432 original size:210 final size:210
Alignment explanation
Indices: 40044035--40044455 Score: 790
Period size: 210 Copynumber: 2.0 Consensus size: 210
40044025 GTCAATTGCA
*
40044035 TTGCTGTTAGGGCTTTGTCATCCCCTTTGTAATTCACCAAAAAAATTTTTACTCTCCTTTTTATA
1 TTGCTGTTAGGGCTTTGTCATCCCCTTTGTAATTCACCAAAAAAAATTTTACTCTCCTTTTTATA
*
40044100 CCTTAAAGATCATATCATGGTCATGTATAATTAATATAATAAGATGGACATTTTTTTCTAGTGTG
66 CCCTAAAGATCATATCATGGTCATGTATAATTAATATAATAAGATGGACATTTTTTTCTAGTGTG
40044165 GTGCTTATATTATTTTTAGGTTCAATATTATATTTGTATTTGATAAAAGTTCATATTTTGGTACC
131 GTGCTTATATTATTTTTAGGTTCAATATTATATTTGTATTTGATAAAAGTTCATATTTTGGTACC
40044230 TAAAGGTAATGGTGT
196 TAAAGGTAATGGTGT
*
40044245 TTGCTGTTAGGGCTTTGTCATCCCCTTTGTAATTCACCAAAAAAAATTTTACTCTCTTTTTTATA
1 TTGCTGTTAGGGCTTTGTCATCCCCTTTGTAATTCACCAAAAAAAATTTTACTCTCCTTTTTATA
40044310 CCCTAAAGATCATATCATGGTCATGTATAATTAATATAATAAGATGGAC-TTTTTTTCTAGTGTG
66 CCCTAAAGATCATATCATGGTCATGTATAATTAATATAATAAGATGGACATTTTTTTCTAGTGTG
40044374 GTGCTTATATTATTTTTAGGTTCAATATTATATTTGTATTTGATAAAAGTTACATATTTTGGTAC
131 GTGCTTATATTATTTTTAGGTTCAATATTATATTTGTATTTGATAAAAGTT-CATATTTTGGTAC
*
40044439 CTGAAGGTAATGGTGT
195 CTAAAGGTAATGGTGT
40044455 T
1 T
40044456 AACTTTTTAG
Statistics
Matches: 206, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
209 66 0.32
210 140 0.68
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (210 bp):
TTGCTGTTAGGGCTTTGTCATCCCCTTTGTAATTCACCAAAAAAAATTTTACTCTCCTTTTTATA
CCCTAAAGATCATATCATGGTCATGTATAATTAATATAATAAGATGGACATTTTTTTCTAGTGTG
GTGCTTATATTATTTTTAGGTTCAATATTATATTTGTATTTGATAAAAGTTCATATTTTGGTACC
TAAAGGTAATGGTGT
Found at i:40054529 original size:43 final size:45
Alignment explanation
Indices: 40054430--40054554 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 45
40054420 TCATGCTTTC
* *
40054430 AATCAATCACATACTATCAATATTAGGAAATAATGTTCCAATCAT
1 AATCAATCACATACTTTCAATATTAGGAAACAATGTTCCAATCAT
** * *
40054475 TTTC--TCACATACTTTCAATAATAGGAAACAGTGTTCC-A-CAT
1 AATCAATCACATACTTTCAATATTAGGAAACAATGTTCCAATCAT
* *
40054516 AATCAATCTCATACTTTCAATTTTAGGAAACAATGTTCC
1 AATCAATCACATACTTTCAATATTAGGAAACAATGTTCC
40054555 TCTCAATGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 5 0.08
42 1 0.02
43 58 0.88
45 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (45 bp):
AATCAATCACATACTTTCAATATTAGGAAACAATGTTCCAATCAT
Found at i:40064679 original size:17 final size:17
Alignment explanation
Indices: 40064631--40064670 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
40064621 CTGTAGGATA
40064631 ATTGTC-CTGCATTTTTT
1 ATTGTCACTGCA-TTTTT
40064648 ATTGTCACTGCATTTTT
1 ATTGTCACTGCATTTTT
40064665 ATTGTC
1 ATTGTC
40064671 GTTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:40064696 original size:17 final size:17
Alignment explanation
Indices: 40064648--40064696 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
40064638 TGCATTTTTT
* **
40064648 ATTGTCACTGCATTTTT
1 ATTGTCATTGCATTTAC
* *
40064665 ATTGTCGTTGTATTTAC
1 ATTGTCATTGCATTTAC
40064682 ATTGTCATTGCATTT
1 ATTGTCATTGCATTT
40064697 CCATATATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.53
Consensus pattern (17 bp):
ATTGTCATTGCATTTAC
Found at i:40066729 original size:16 final size:16
Alignment explanation
Indices: 40066708--40066738 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40066698 TTGTGGATCC
40066708 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
40066724 CATTTTATCTTTATT
1 CATTTTACCTTTATT
40066739 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:40066977 original size:24 final size:24
Alignment explanation
Indices: 40066950--40067023 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
40066940 GTAAGCAAGC
40066950 ATGTGTGCACCGTAT-CT-GTAAAGT
1 ATGTGTGCA-C-TATACTCGTAAAGT
40066974 ATGTGTGCACTATACTCGTAAAGT
1 ATGTGTGCACTATACTCGTAAAGT
* * * *
40066998 ATGTGTACATTATCCTTGTAAAGT
1 ATGTGTGCACTATACTCGTAAAGT
40067022 AT
1 AT
40067024 ACGTGAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 38 0.86
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (24 bp):
ATGTGTGCACTATACTCGTAAAGT
Found at i:40068937 original size:23 final size:22
Alignment explanation
Indices: 40068885--40068940 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
40068875 ACTGTAATAT
* *
40068885 TACTTATTTACACATTATTCAA
1 TACTCATTTACACATTAATCAA
* *
40068907 TAGTTCATTTACATATTAATCACA
1 TA-CTCATTTACACATTAATCA-A
40068931 TACTCATTTA
1 TACTCATTTA
40068941 GGCATATATC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.45
Consensus pattern (22 bp):
TACTCATTTACACATTAATCAA
Done.