Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008982.1 Hibiscus syriacus cultivar Beakdansim tig00112344_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2253222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:1717534 original size:31 final size:31
Alignment explanation
Indices: 1717488--1717553 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1717478 ATATAAAAAA
* *
1717488 GGTGTCCAACGTATGTCTGTTTTTTTAGTTT
1 GGTGCCCAACGTATGTCCGTTTTTTTAGTTT
*
1717519 GGTGCCCAATGTATGTCCGTTTTTTTAGTTT
1 GGTGCCCAACGTATGTCCGTTTTTTTAGTTT
1717550 GGTG
1 GGTG
1717554 TCTAACATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.48
Consensus pattern (31 bp):
GGTGCCCAACGTATGTCCGTTTTTTTAGTTT
Found at i:1717581 original size:23 final size:23
Alignment explanation
Indices: 1717538--1717589 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1717528 TGTATGTCCG
* **
1717538 TTTTTTTAGTTTGGTGTCTAACA
1 TTTTTTTAGTTTGATACCTAACA
*
1717561 TTTTTTTAGTTTGATACCTAACG
1 TTTTTTTAGTTTGATACCTAACA
1717584 TTTTTT
1 TTTTTT
1717590 ACGTTCTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.10, G:0.13, T:0.60
Consensus pattern (23 bp):
TTTTTTTAGTTTGATACCTAACA
Found at i:1717725 original size:21 final size:21
Alignment explanation
Indices: 1717684--1717732 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1717674 TGAGTATAAT
* **
1717684 ATTAAAA-AATGAATTTTTTA
1 ATTAAAATAATAAATTAATTA
1717704 ATTAAAATAATAAATTAATTA
1 ATTAAAATAATAAATTAATTA
*
1717725 ATTGAAAT
1 ATTAAAAT
1717733 TGAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
ATTAAAATAATAAATTAATTA
Found at i:1719708 original size:86 final size:86
Alignment explanation
Indices: 1719512--1719918 Score: 667
Period size: 86 Copynumber: 4.9 Consensus size: 86
1719502 CCCAGTTCTA
* *
1719512 AGCTTCATCCCTTCTATCCTCAACTTTACTAGTTCCTCAATTTGTTTAATCAACTCCCCT--A--
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
*
1719573 --CAGTGGCAGTGACAGTGAC
66 GGCAGTGGCAGTGACAGTGGC
* *
1719592 AACTTCATCCCTTCTATCCTCAACTTTACCAATTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1719657 GGCAGTGGCAGTGACAGTGGC
66 GGCAGTGGCAGTGACAGTGGC
*
1719678 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCTTACAGG
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1719743 GGCAGTGGCAGTGACAGTGGC
66 GGCAGTGGCAGTGACAGTGGC
1719764 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCT--A--
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
*
1719825 --CAGTGGCAGTGGCAGTGGC
66 GGCAGTGGCAGTGACAGTGGC
1719844 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1719909 GGCAGTGGCA
66 GGCAGTGGCA
1719919 CCTCAAAGAT
Statistics
Matches: 305, Mismatches: 10, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
80 134 0.44
82 2 0.01
84 1 0.00
86 168 0.55
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (86 bp):
AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
GGCAGTGGCAGTGACAGTGGC
Found at i:1719831 original size:166 final size:168
Alignment explanation
Indices: 1719512--1719918 Score: 659
Period size: 166 Copynumber: 2.4 Consensus size: 168
1719502 CCCAGTTCTA
* *
1719512 AGCTTCATCCCTTCTATCCTCAACTTTACTAGTTCCTCAATTTGTTTAATCAACTCCCCT--A--
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1719573 --CAGTGGCAGTGACAGTGACAACTTCATCCCTTCTATCCTCAACTTTACCAATTCCTCCATTTG
66 GGCAGTGGCAGTGACAGTGACAACTTCATCCCTTCTATCCTCAACTTTACCAATTCCTCCATTTG
1719636 TTTAATCAACTCCCCTACAGGGGCAGTGGCAGTGACAGTGGC
131 TTTAATCAACTCCCCTA-A---GCAGTGGCAGTGACAGTGGC
*
1719678 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCTTACAGG
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
* * *
1719743 GGCAGTGGCAGTGACAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTG
66 GGCAGTGGCAGTGACAGTGACAACTTCATCCCTTCTATCCTCAACTTTACCAATTCCTCCATTTG
*
1719808 TTTAATCAACTCCCCT-A-CAGTGGCAGTGGCAGTGGC
131 TTTAATCAACTCCCCTAAGCAGTGGCAGTGACAGTGGC
1719844 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1 AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
1719909 GGCAGTGGCA
66 GGCAGTGGCA
1719919 CCTCAAAGAT
Statistics
Matches: 227, Mismatches: 8, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
166 149 0.66
168 1 0.00
170 1 0.00
172 76 0.33
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (168 bp):
AGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATCAACTCCCCTACAGG
GGCAGTGGCAGTGACAGTGACAACTTCATCCCTTCTATCCTCAACTTTACCAATTCCTCCATTTG
TTTAATCAACTCCCCTAAGCAGTGGCAGTGACAGTGGC
Found at i:1719836 original size:74 final size:76
Alignment explanation
Indices: 1719750--1719918 Score: 270
Period size: 80 Copynumber: 2.2 Consensus size: 76
1719740 AGGGGCAGTG
*
1719750 GCAGTGACAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATC
1 GCAGTGGCAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATC
1719815 AACTCCCCTACA
66 AACTCCCCTA-A
1719827 GTGGCAGTGGCAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTA
1 ---GCAGTGGCAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTA
1719892 ATCAACTCCCCT-A
63 ATCAACTCCCCTAA
*
1719905 -CAGGGGCAGTGGCA
1 GCAGTGGCAGTGGCA
1719919 CCTCAAAGAT
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
74 13 0.15
78 1 0.01
80 73 0.84
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.31
Consensus pattern (76 bp):
GCAGTGGCAGTGGCAGCTTCATCCCTTCTATCCTCAACTTTACCAGTTCCTCCATTTGTTTAATC
AACTCCCCTAA
Found at i:1725403 original size:14 final size:14
Alignment explanation
Indices: 1725384--1725410 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1725374 CTTCTTTCTG
1725384 TCTCTCTGTTTTTT
1 TCTCTCTGTTTTTT
1725398 TCTCTCTGTTTTT
1 TCTCTCTGTTTTT
1725411 CTGTCCCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.07, T:0.70
Consensus pattern (14 bp):
TCTCTCTGTTTTTT
Found at i:1725893 original size:3 final size:3
Alignment explanation
Indices: 1725885--1725992 Score: 166
Period size: 3 Copynumber: 36.7 Consensus size: 3
1725875 TTAATATATT
*
1725885 TAA TAA TAA TAG TAA -AA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1725931 TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1725979 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1725993 TGGATAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
2 4 0.04
3 92 0.96
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1726841 original size:113 final size:113
Alignment explanation
Indices: 1726283--1726810 Score: 878
Period size: 113 Copynumber: 4.7 Consensus size: 113
1726273 AGATAATATC
* * * *
1726283 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1726347 TCATTCATGAACTTTCTCTAGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
1726396 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1726461 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
1726509 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTATTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1726574 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
1726622 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
1726687 TCATTATGAACCTTCTCTGGTAATGATGATCCACCAAATGATGGATTC
66 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*** * * *
1726735 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1726800 TCATTATGAAC
66 TCATTATGAAC
1726811 TCTACCTTGC
Statistics
Matches: 395, Mismatches: 19, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
113 334 0.85
114 61 0.15
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
Found at i:1727601 original size:84 final size:84
Alignment explanation
Indices: 1727423--1728735 Score: 2547
Period size: 84 Copynumber: 15.6 Consensus size: 84
1727413 GGTTCTGTAA
* *
1727423 GTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATT-GGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727487 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1727506 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727571 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1727590 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727655 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1727674 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727739 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1727758 GTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727823 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1727842 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACACTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727907 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1727926 GTTCTGCCAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1727991 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1728010 GTTCTGCCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728075 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728094 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728159 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1728178 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728243 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728262 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728327 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728346 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728411 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728430 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728495 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728514 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728579 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
*
1728598 GTTCTGCCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1728663 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
1728682 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1728736 AGCATATATA
Statistics
Matches: 1215, Mismatches: 14, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
83 51 0.04
84 1164 0.96
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (84 bp):
GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
CTTCTAAATTCAATGATTG
Found at i:1729701 original size:16 final size:16
Alignment explanation
Indices: 1729669--1729717 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1729659 CACCTTGACC
*
1729669 CTCTTTCTTTTTCTTCT
1 CTCTTT-TTTTTTTTCT
1729686 CTCTTTTTTTTTTTCT
1 CTCTTTTTTTTTTTCT
*
1729702 -TTTTTTTTTCTTTTCT
1 CTCTTTTTTT-TTTTCT
1729718 TTATTCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.28
16 15 0.52
17 6 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
CTCTTTTTTTTTTTCT
Found at i:1729705 original size:13 final size:13
Alignment explanation
Indices: 1729674--1729771 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 13
1729664 TGACCCTCTT
* *
1729674 TCTTTTTCTTCTC
1 TCTTTTTTTTTTC
1729687 TCTTTTTTTTTT-
1 TCTTTTTTTTTTC
1729699 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
* *
1729712 T-TTTCTTTATTC
1 TCTTTTTTTTTTC
*
1729724 ATCATTTTTTTTTC
1 -TCTTTTTTTTTTC
* *
1729738 T-TTTCTTTATTC
1 TCTTTTTTTTTTC
*
1729750 ATC--ATTTTTTTC
1 -TCTTTTTTTTTTC
1729762 T-TTTTTTTTT
1 TCTTTTTTTTT
1729772 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
11 1 0.02
12 41 0.64
13 14 0.22
14 8 0.12
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:1729767 original size:26 final size:26
Alignment explanation
Indices: 1729702--1729760 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
1729692 TTTTTTTTCT
1729702 TTTTTTTTTCTTTTCTTTATTCATCA
1 TTTTTTTTTCTTTTCTTTATTCATCA
1729728 TTTTTTTTTCTTTTCTTTATTCATCA
1 TTTTTTTTTCTTTTCTTTATTCATCA
1729754 TTTTTTT
1 TTTTTTT
1729761 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTTTTCTTTATTCATCA
Found at i:1729776 original size:26 final size:25
Alignment explanation
Indices: 1729701--1729776 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 25
1729691 TTTTTTTTTC
1729701 TTTTTTTTTTCTTTTCTTTATTCATCA
1 TTTTTTTTTT-TTTT-TTTATTCATCA
*
1729728 TTTTTTTTTCTTTTCTTTATTCATCA
1 TTTTTTTTT-TTTTTTTTATTCATCA
*
1729754 TTTTTTTCTTTTTTTTTTCTTCA
1 TTTTTTT-TTTTTTTTTTATTCA
1729777 AGCATAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
26 29 0.66
27 14 0.32
28 1 0.02
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTTATTCATCA
Found at i:1740385 original size:17 final size:17
Alignment explanation
Indices: 1740345--1740387 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1740335 ATACTTGCAA
*
1740345 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
1740363 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
1740380 ATAAAAAT
1 ATAAAAAT
1740388 TTTGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:1742074 original size:21 final size:19
Alignment explanation
Indices: 1742040--1742088 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
1742030 TTTTTTTCGT
1742040 TTTCTGTTTCTGTTTCTTC
1 TTTCTGTTTCTGTTTCTTC
*
1742059 TTTCTGTCTCTCTGTTTTTTC
1 TTTCTGT-T-TCTGTTTCTTC
*
1742080 TCTCTGTTT
1 TTTCTGTTT
1742089 TTCTGTCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.31
20 2 0.08
21 16 0.62
ACGTcount: A:0.00, C:0.22, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTCTGTTTCTGTTTCTTC
Found at i:1742081 original size:13 final size:13
Alignment explanation
Indices: 1742065--1742090 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1742055 CTTCTTTCTG
1742065 TCTCTCTGTTTTT
1 TCTCTCTGTTTTT
1742078 TCTCTCTGTTTTT
1 TCTCTCTGTTTTT
1742091 CTGTCCCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (13 bp):
TCTCTCTGTTTTT
Found at i:1742093 original size:21 final size:21
Alignment explanation
Indices: 1742046--1742094 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1742036 TCGTTTTCTG
*
1742046 TTTCTGTTTCTTCTTTCTGTC
1 TTTCTGTTTCTTCTCTCTGTC
* * *
1742067 TCTCTGTTTTTTCTCTCTGTT
1 TTTCTGTTTCTTCTCTCTGTC
1742088 TTTCTGT
1 TTTCTGT
1742095 CCCCTTTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTCTGTTTCTTCTCTCTGTC
Found at i:1742573 original size:3 final size:3
Alignment explanation
Indices: 1742565--1742668 Score: 154
Period size: 3 Copynumber: 34.7 Consensus size: 3
1742555 TTAATATATT
* * *
1742565 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1742613 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1742661 TAA TAA TA
1 TAA TAA TA
1742669 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1744358 original size:27 final size:27
Alignment explanation
Indices: 1744304--1744360 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1744294 GTTGGGTATT
**
1744304 TGGGGGAGGATAAGGAGCAGTGGAAGA
1 TGGGGGAGGATAAGGAGCAGCAGAAGA
*
1744331 TGGGGGAGGATAAGGAGCAGCAGTAGA
1 TGGGGGAGGATAAGGAGCAGCAGAAGA
1744358 TGG
1 TGG
1744361 TGGAACATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.12
Consensus pattern (27 bp):
TGGGGGAGGATAAGGAGCAGCAGAAGA
Found at i:1745177 original size:3 final size:3
Alignment explanation
Indices: 1745169--1745195 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1745159 ACTCAAAAAG
1745169 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1745196 TAGATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1749459 original size:12 final size:12
Alignment explanation
Indices: 1749444--1749468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1749434 CGATACGGAT
1749444 ACGGGGACGGGA
1 ACGGGGACGGGA
1749456 ACGGGGACGGGA
1 ACGGGGACGGGA
1749468 A
1 A
1749469 ACGGCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.56, T:0.00
Consensus pattern (12 bp):
ACGGGGACGGGA
Found at i:1749556 original size:20 final size:20
Alignment explanation
Indices: 1749531--1749583 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1749521 AAATAATTTT
1749531 AAAATTATAAATATATGTAA
1 AAAATTATAAATATATGTAA
1749551 AAAATTATAAATATATGTAA
1 AAAATTATAAATATATGTAA
1749571 AAAATTATAAATA
1 AAAATTATAAATA
1749584 AAGTCAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATTATAAATATATGTAA
Found at i:1755555 original size:8 final size:8
Alignment explanation
Indices: 1755542--1755582 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1755532 CTCATTTTCA
1755542 GAGAATTT
1 GAGAATTT
1755550 GAGAATTT
1 GAGAATTT
*
1755558 -AGAGTTT
1 GAGAATTT
*
1755565 GGGAATTT
1 GAGAATTT
1755573 GAGAATTT
1 GAGAATTT
1755581 GA
1 GA
1755583 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1755814 original size:14 final size:14
Alignment explanation
Indices: 1755795--1755830 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1755785 GGGACATGAA
*
1755795 GGCGCGTTCCCGGG
1 GGCGCGTCCCCGGG
1755809 GGCGCGTCCCCGGG
1 GGCGCGTCCCCGGG
1755823 GGCGCGTC
1 GGCGCGTC
1755831 TTACATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.50, T:0.11
Consensus pattern (14 bp):
GGCGCGTCCCCGGG
Found at i:1756037 original size:128 final size:128
Alignment explanation
Indices: 1755809--1756295 Score: 893
Period size: 128 Copynumber: 3.8 Consensus size: 128
1755799 CGTTCCCGGG
* * * **
1755809 GGCGCGTCCCCGGGGGCGCGTCTTACATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
1755874 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
66 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
*
1755937 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
1756002 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
66 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
1756065 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
*
1756130 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTCACTATTCACATGAA
66 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
* *
1756193 TGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
1 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
1756258 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1756296 AATCAGGTAA
Statistics
Matches: 351, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 351 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
GTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAA
Found at i:1756756 original size:33 final size:34
Alignment explanation
Indices: 1756695--1756794 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1756685 AAATTTAATG
*
1756695 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1756729 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1756762 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1756795 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1757402 original size:21 final size:21
Alignment explanation
Indices: 1757314--1757407 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1757304 TATGGTATAA
*
1757314 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1757335 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1757356 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1757377 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1757398 AACCCTGCGG
1 AACCCTGCGG
1757408 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1757437 original size:21 final size:21
Alignment explanation
Indices: 1757411--1757458 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1757401 CCTGCGGAGA
*
1757411 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1757432 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1757453 GGGCAT
1 TGGCAT
1757459 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1759191 original size:16 final size:16
Alignment explanation
Indices: 1759172--1759258 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 16
1759162 GCAAAAAAAT
*
1759172 TAATAATTCTAATAAA
1 TAATAATTATAATAAA
1759188 TAATAATTAT-ATAAA
1 TAATAATTATAATAAA
* *
1759203 T-ATTATTTTAATAAAA
1 TAATAATTATAAT-AAA
*
1759219 AAATATATT-TACATAAA
1 TAATA-ATTATA-ATAAA
*
1759236 TATATTAA-TATAAAAAA
1 TA-A-TAATTATAATAAA
1759253 TAATAA
1 TAATAA
1759259 CTATTTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
14 6 0.11
15 11 0.20
16 13 0.23
17 15 0.27
18 9 0.16
19 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATTATAATAAA
Found at i:1760783 original size:15 final size:15
Alignment explanation
Indices: 1760763--1760806 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1760753 ATATTTAGTT
* *
1760763 GGGCGGGCGAATGTG
1 GGGCGGGCGGATGTA
*
1760778 GGGCGGGCGGATGCA
1 GGGCGGGCGGATGTA
1760793 GGGCGGGCGGATGT
1 GGGCGGGCGGATGT
1760807 CTTAAACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.61, T:0.11
Consensus pattern (15 bp):
GGGCGGGCGGATGTA
Found at i:1763500 original size:19 final size:18
Alignment explanation
Indices: 1763478--1763531 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
1763468 AATTAAATTG
1763478 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
*
1763497 ATTA-TT-TTTAAATTAT
1 ATTATTTATTTAAATAAT
1763513 -TTATTTAATTTTAAATAAT
1 ATTATTT-A-TTTAAATAAT
1763532 TTAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 8 0.28
17 3 0.10
18 2 0.07
19 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:1763542 original size:35 final size:34
Alignment explanation
Indices: 1763470--1763542 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
1763460 ATTTTTAAAA
*
1763470 TTAAATTGATTATTTATTTGAAATAATATTATTT
1 TTAAATTGATTATTTATTTGAAATAATATTATAT
*
1763504 TTAAATT-ATTTATTTAATTTTAAATAAT-TTAATAT
1 TTAAATTGA-TTATTT-ATTTGAAATAATATT-ATAT
1763539 TTAA
1 TTAA
1763543 GTTAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 1 0.03
34 15 0.44
35 18 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (34 bp):
TTAAATTGATTATTTATTTGAAATAATATTATAT
Found at i:1763750 original size:2 final size:2
Alignment explanation
Indices: 1763743--1763777 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1763733 AATATAAACT
1763743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1763778 GAATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1764969 original size:2 final size:2
Alignment explanation
Indices: 1764962--1765000 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1764952 ATTTTAACCG
1764962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1765001 AACTCAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1774073 original size:2 final size:2
Alignment explanation
Indices: 1774066--1774119 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1774056 TAATAATTTC
1774066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1774108 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1774120 CATTAAATTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1789253 original size:15 final size:15
Alignment explanation
Indices: 1789233--1789287 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 15
1789223 ATATTAATTA
1789233 ATTATTTTAAATAAT
1 ATTATTTTAAATAAT
*
1789248 ATTATTTTAAAATTATCT
1 ATTATTTT-AAA-TA-AT
1789266 ATTTAATTTTAAATAAT
1 A-TT-ATTTTAAATAAT
1789283 ATTAT
1 ATTAT
1789288 ACATGAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 10 0.30
16 5 0.15
17 4 0.12
18 4 0.12
19 5 0.15
20 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTTTAAATAAT
Found at i:1789263 original size:26 final size:23
Alignment explanation
Indices: 1789206--1789251 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1789196 TTAAAATCAT
*
1789206 ATTATTTATTTGAAATAATATTA
1 ATTAATTATTTGAAATAATATTA
*
1789229 ATTAATTATTTTAAATAATATTA
1 ATTAATTATTTGAAATAATATTA
1789252 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTAATTATTTGAAATAATATTA
Found at i:1789350 original size:22 final size:22
Alignment explanation
Indices: 1789324--1789379 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
1789314 TAATTTACCC
*
1789324 TAAATTTTAAATTATTTAAAAA
1 TAAATTTTAAATAATTTAAAAA
1789346 TAAA---TAAATAATTTAAAAA
1 TAAATTTTAAATAATTTAAAAA
*
1789365 TAATATTTCAAATAA
1 TAA-ATTTTAAATAA
1789380 ATAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 17 0.61
20 1 0.04
22 4 0.14
23 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTTAAATAATTTAAAAA
Found at i:1789369 original size:18 final size:19
Alignment explanation
Indices: 1789331--1789367 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1789321 CCCTAAATTT
*
1789331 TAAATTATTTAAAAATAAA
1 TAAATAATTTAAAAATAAA
1789350 TAAATAATTTAAAAATAA
1 TAAATAATTTAAAAATAA
1789368 TATTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAATTTAAAAATAAA
Found at i:1796804 original size:20 final size:21
Alignment explanation
Indices: 1796761--1796804 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1796751 ACGGAACGTT
* *
1796761 AAATTATCATAATGATAGATA
1 AAATTATCATAATAATAGAAA
*
1796782 AAATTGTCATAA-AATAGAAA
1 AAATTATCATAATAATAGAAA
1796802 AAA
1 AAA
1796805 ATATGTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (21 bp):
AAATTATCATAATAATAGAAA
Found at i:1800565 original size:2 final size:2
Alignment explanation
Indices: 1800553--1800613 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1800543 CATTATAATT
*
1800553 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1800595 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1800614 TACATATGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1801573 original size:138 final size:138
Alignment explanation
Indices: 1801240--1801581 Score: 625
Period size: 137 Copynumber: 2.5 Consensus size: 138
1801230 TTTTTTTTTT
*
1801240 TTTTTTTTTGAAAAACAAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAGCAAAA
1 TTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAGCAAAA
1801305 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
66 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
1801370 CCGAGGCC
131 CCGAGGCC
*
1801378 -TTTTTTTTGAAGAAA-CAACTTGATTTTCAAAACAAGGAGAAGAAAAGCATTCGGAAAAGCAAA
1 TTTTTTTTTGAA-AAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAGCAAA
1801441 AAAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAA
65 AAAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAA
1801506 CCCGAGGCC
130 CCCGAGGCC
* *
1801515 TTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAAAGTAAAA
1 TTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAGCAAAA
1801580 AA
66 AA
1801582 TCTTTTGATT
Statistics
Matches: 196, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
137 134 0.68
138 62 0.32
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (138 bp):
TTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAGCAAAA
AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
CCGAGGCC
Found at i:1802157 original size:168 final size:171
Alignment explanation
Indices: 1801863--1802202 Score: 557
Period size: 168 Copynumber: 2.0 Consensus size: 171
1801853 GCGAGAGATT
1801863 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
1 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
** *
1801928 AATCCTTGTAAATTGACCCTTGAGTTTATTTTGTTTTCAATTAATCCCTACTATATTATATAC--
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTAATCCCTACTATATTATATACTA
1801991 TA-TTTCATTATTATTATATTTTACTCCCTTATT-TATATATA
131 TATTTTCATTATTA-T-TATTTTACTCCCTTATTATATATATA
* * *
1802032 TGCGTTTTGGTTCTCCAGTTTCAAAAACGTTTAA-TTGGTCCTCTGAATCGATTATTGAACCTGA
1 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
1802096 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTTAATCCCTACTAT-TTATATACT
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAA-TTAATCCCTACTATATTATATACT
1802160 ATATTTTCATTATTATTATTTTACTCCCTTATTATATATATA
130 ATATTTTCATTATTATTATTTTACTCCCTTATTATATATATA
1802202 T
1 T
1802203 ATCTTATGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 9
0.91 0.03 0.05
Matches are distributed among these distances:
168 74 0.46
169 63 0.39
170 12 0.08
171 11 0.07
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.46
Consensus pattern (171 bp):
TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTAATCCCTACTATATTATATACTA
TATTTTCATTATTATTATTTTACTCCCTTATTATATATATA
Found at i:1802228 original size:10 final size:10
Alignment explanation
Indices: 1802188--1802238 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1802178 TTTTACTCCC
1802188 TTATTATA-T
1 TTATTATATT
* *
1802197 ATA-TATATC
1 TTATTATATT
1802206 TTATGTATATT
1 TTAT-TATATT
*
1802217 TTATTTTATT
1 TTATTATATT
1802227 TTATTATATT
1 TTATTATATT
1802237 TT
1 TT
1802239 TATATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 4 0.12
9 4 0.12
10 16 0.48
11 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATTATATT
Found at i:1813881 original size:105 final size:105
Alignment explanation
Indices: 1813699--1814562 Score: 1387
Period size: 105 Copynumber: 8.2 Consensus size: 105
1813689 AGGTTTTACC
1813699 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1813764 ACGAAGGGACCGCTGGTTGTCTACAAGCGTTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1813804 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAGCGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1813869 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1813909 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1813974 ACGAAGGGACCGCTGGTTGTCTACAAGCGTTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1814014 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1814079 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1814119 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1814184 ACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1814224 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1814289 ACGAAGGGACCGCTGGTTGTCAATAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1814329 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1814394 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTC-AATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
* * * * * * *
1814434 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1814499 ACGAAGGGA-CGACTGGCTGTCAACGAATA-ATTTCTC-AATT
66 ACGAAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCAAATT
*
1814539 CCATAGCC-ATTTCCAACTTCACAA
1 -CAGAGCCAATTT-CAACTTCACAA
1814563 ACAGATTGAC
Statistics
Matches: 710, Mismatches: 43, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
104 4 0.01
105 678 0.95
106 27 0.04
107 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:1814942 original size:2 final size:2
Alignment explanation
Indices: 1814935--1814999 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1814925 CATTATAATT
1814935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1814977 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1815000 TACATATGGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1815904 original size:138 final size:138
Alignment explanation
Indices: 1815544--1815966 Score: 715
Period size: 137 Copynumber: 3.0 Consensus size: 138
1815534 AGTTGAAAGT
1815544 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
1 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
1815609 CGAGGCCCTTTTTTTTTTTTTTTGAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCAT
66 CGAGG-CC-----TTTTTTTTTTG-AAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCAT
1815674 TCGGAAAAGCAAAAAA
124 TCGGAAAAGC-AAAAA
1815690 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
1 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
*
1815755 CGAGGCC--TTTTTTTTGAAGAAACAACTTGATTTTCAAAACAAGGAGAAGAAAAGCATTCGGAA
66 CGAGGCCTTTTTTTTTTGAA-AAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAA
1815818 AAGCAAAAA
130 AAGCAAAAA
1815827 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
1 AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
*
1815892 CGAGGCCTTTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAA
66 CGAGGCCTTTTTTTTTTGAAAAA-CAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAA
*
1815957 AAGTAAAAA
130 AAGCAAAAA
1815966 A
1 A
1815967 TCTTTTGATT
Statistics
Matches: 269, Mismatches: 4, Indels: 15
0.93 0.01 0.05
Matches are distributed among these distances:
137 79 0.29
138 59 0.22
139 59 0.22
145 2 0.01
146 70 0.26
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (138 bp):
AAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAACC
CGAGGCCTTTTTTTTTTGAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAA
AGCAAAAA
Found at i:1816544 original size:174 final size:174
Alignment explanation
Indices: 1816249--1816597 Score: 644
Period size: 174 Copynumber: 2.0 Consensus size: 174
1816239 GCGAGAGATT
1816249 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
1 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
** *
1816314 AATCCTTGTAAATTGACCCTTGAGTTTATTTTGTTTTCAATTTAATCCCTACTATTATTATATAC
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTTAATCCCTACTATTATTATATAC
1816379 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
131 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
* * *
1816423 TGCGTTTTGGTTCTCCAGTTTCAAAAACGTTTAATTTGGTCCTCTGAATCGATTATTGAACCTGA
1 TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
1816488 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTTAATCCCTACTATTATTATATAC
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTTAATCCCTACTATTATTATATAC
1816553 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
131 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
1816597 T
1 T
1816598 ATATATCTTA
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 169 1.00
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (174 bp):
TGCGATTTGGTTCTCCAGTTTCAAAAACATTTAATTTGGTCCTCTGAATCGATTATCGAACCTGA
AATCCTTGTAAATTGACCCTTGAGTTTATTTCATTCTCAATTTAATCCCTACTATTATTATATAC
TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
Found at i:1818285 original size:309 final size:306
Alignment explanation
Indices: 1817712--1818557 Score: 1034
Period size: 309 Copynumber: 2.7 Consensus size: 306
1817702 TCATGCTTGT
* * * *
1817712 TATGATAACTCGATA-TTTTTAATAAATTATTACAATATACGATTTCAATGAGGATTAAACCTAA
1 TATGATAACTCGTTATTTTTTAATAAATTATTACAATGTACGATTTCAATGAGGATTAAAACTAG
* *
1817776 AACTTTAAGGGGGAGTGCAACTCCTATCACTAGAATAAGTAAGGAATTTGTTAAG--TTTTCAAA
66 AACTTTAA-GGGGAGTGCAACGCCTATCACTAG-A-AAGTAAGGAATTTGTTAAGTTTTTTAAAA
1817839 AAAAAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAAGGGGAACTCATTAAGTAGCTTC
128 AAAAAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAA-GGGAACTCATTAAGTAGCTTC
* * * *
1817904 AATAGTGAAATAGAGTATTGTTC-TTCTTTGAGGTCTTGAGTTCGAACAGTGAACTCATTGAGTA
192 AATAGTTAAAT-GAATATTGTTCTTTC-TTGAGGTCCTGAGTTCGAACAGTGAACTCATTCAGTA
*
1817968 ATCTCAGTAATTAAAT-GAAGTATTATTCTTCCTTGTATCATATTTGATCTCA
255 ACCTCAGTAATTAAATAG-AGTATTATTCTTCCTTGTATCATATTTGATCTCA
* * * *
1818020 TATGATGACTCGTTATTTTTTAATAAATTATTAAAATGTACGATTTCCATGAAGATTAAAACTAG
1 TATGATAACTCGTTATTTTTTAATAAATTATTACAATGTACGATTTCAATGAGGATTAAAACTAG
*
1818085 AACTTTAAGGGGAGTGTAACGCCTATCACTAG-AA-TAAGGAATTTGTTAAGGTTTTTTTTTATA
66 AACTTTAAGGGGAGTGCAACGCCTATCACTAGAAAGTAAGGAATTTGTTAA-G---TTTTTTA-A
*
1818148 AAAAAAAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAAGGGAACTCATTGAGTAG-TT
126 AAAAAAAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAAGGGAACTCATTAAGTAGCTT
*
1818212 CAAT-GATTAAATGGAATATTGTTCTTTCTTGAGTTCCTGAGTTC-AAGCAGTGAACTCATTCAG
191 CAATAG-TTAAAT-GAATATTGTTCTTTCTTGAGGTCCTGAGTTCGAA-CAGTGAACTCATTCAG
* * *
1818275 TAGCCTCAGTAGTTAAATAGAGTATTGTTCTTCCTTGTATCATATTTGATCTCA
253 TAACCTCAGTAATTAAATAGAGTATTATTCTTCCTTGTATCATATTTGATCTCA
* * * * *
1818329 TATGATAACTCATTATATTTTAATAAACTATTACAATGTACAATTTCAATGAGGAAT-AAACATA
1 TATGATAACTCGTTATTTTTTAATAAATTATTACAATGTACGATTTCAATGAGGATTAAAAC-TA
* ** ** * * *
1818393 GATCTTGGAGGGAGAGCACAACGCCTATCCCTAGAATAAGTAAGGACTTTGTTAAATTTTTTAAA
65 GAACTTTAAGGG-GAGTGCAACGCCTATCACTAG-A-AAGTAAGGAATTTGTTAAGTTTTTTAAA
* ** *
1818458 TAAAAAAACAATGCTTTTAATTTGTTTAA-GAATCGATTTTCGAAGGAGAACTCATTCAA-TAGC
127 -AAAAAAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAAGG-GAACTCATT-AAGTAGC
* *
1818521 CTCAATAGTTAAATGAAGTATTTTTCTTTCTTGAGGT
189 TTCAATAGTTAAATGAA-TATTGTTCTTTCTTGAGGT
1818558 TCTGTGTTTG
Statistics
Matches: 466, Mismatches: 48, Indels: 45
0.83 0.09 0.08
Matches are distributed among these distances:
304 15 0.03
305 3 0.01
308 42 0.09
309 226 0.48
310 88 0.19
311 75 0.16
312 1 0.00
313 2 0.00
314 14 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (306 bp):
TATGATAACTCGTTATTTTTTAATAAATTATTACAATGTACGATTTCAATGAGGATTAAAACTAG
AACTTTAAGGGGAGTGCAACGCCTATCACTAGAAAGTAAGGAATTTGTTAAGTTTTTTAAAAAAA
AAACAGTGCTTTTAATTTGAGTAACGAATCAATTTTCGAAGGGAACTCATTAAGTAGCTTCAATA
GTTAAATGAATATTGTTCTTTCTTGAGGTCCTGAGTTCGAACAGTGAACTCATTCAGTAACCTCA
GTAATTAAATAGAGTATTATTCTTCCTTGTATCATATTTGATCTCA
Found at i:1821481 original size:19 final size:21
Alignment explanation
Indices: 1821457--1821502 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1821447 ATATATGTTT
*
1821457 TATGAACAGT-AA-AATATGG
1 TATGAACAGTGAACAATATCG
1821476 TATGAACAGTGAACAATATCG
1 TATGAACAGTGAACAATATCG
1821497 TATGAA
1 TATGAA
1821503 TAATAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 12 0.50
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (21 bp):
TATGAACAGTGAACAATATCG
Found at i:1822188 original size:31 final size:31
Alignment explanation
Indices: 1822164--1822326 Score: 209
Period size: 31 Copynumber: 5.3 Consensus size: 31
1822154 TGAAAAACCA
*
1822164 AGGTAATCAGTTCATATGTCCTGAAGAACAT
1 AGGTAAACAGTTCATATGTCCTGAAGAACAT
* * *
1822195 AGGTAAACAGTCCATATATCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCTGAAGAACAT
*
1822226 AGGTAAACAGTTCATATGTCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCTGAAGAACAT
* * * * *
1822257 AGGTAAATAATCCATATATCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCTGAAGAACAT
* * *
1822288 AGGTAAATAGTCCATATGTCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCTGAAGAACAT
1822319 AGGTAAAC
1 AGGTAAAC
1822327 CCTCGATCCT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 119 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (31 bp):
AGGTAAACAGTTCATATGTCCTGAAGAACAT
Found at i:1822237 original size:62 final size:62
Alignment explanation
Indices: 1822164--1822326 Score: 272
Period size: 62 Copynumber: 2.6 Consensus size: 62
1822154 TGAAAAACCA
* * *
1822164 AGGTAATCAGTTCATATGTCCTGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCCGAAGAACATAGGTAAACAATCCATATATCCCGAAGAACAT
*
1822226 AGGTAAACAGTTCATATGTCCCGAAGAACATAGGTAAATAATCCATATATCCCGAAGAACAT
1 AGGTAAACAGTTCATATGTCCCGAAGAACATAGGTAAACAATCCATATATCCCGAAGAACAT
* *
1822288 AGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 AGGTAAACAGTTCATATGTCCCGAAGAACATAGGTAAAC
1822327 CCTCGATCCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 94 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (62 bp):
AGGTAAACAGTTCATATGTCCCGAAGAACATAGGTAAACAATCCATATATCCCGAAGAACAT
Found at i:1825790 original size:22 final size:22
Alignment explanation
Indices: 1825738--1825791 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1825728 GGAACGGGAA
*
1825738 GTATCGATA-TCCTAAACTAGG
1 GTATCGATACTCATAAACTAGG
* * *
1825759 GTACCAATACTCATATACTAGG
1 GTATCGATACTCATAAACTAGG
1825781 GTATCGATACT
1 GTATCGATACT
1825792 ATCTTGAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (22 bp):
GTATCGATACTCATAAACTAGG
Found at i:1828801 original size:69 final size:67
Alignment explanation
Indices: 1828637--1828844 Score: 233
Period size: 69 Copynumber: 3.0 Consensus size: 67
1828627 AGTCATTAAC
* * *
1828637 ATCCAATTACTAAACTATCAAAACTTAATCTAATTATGATATTAAATTATAATCACA-ACTCAT-
1 ATCCAATTACTAAACTATCAAAACTTAATCCAATTAT-A-ATTCAATTAAAAT-A-ATA-TCATA
1828700 TTATATA
61 TTATATA
** * * *
1828707 ATTTAATTACCTAGACTATCAAAACTTAATCCAGTTATAATCCAATTAAAATAATATCATATTAA
1 ATCCAATTA-CTAAACTATCAAAACTTAATCCAATTATAATTCAATTAAAATAATATCATATT-A
1828772 TCATA
64 T-ATA
1828777 ATCCAATTACTAAACTATCAAAACTTAATCCAATTATAATTCAATTACAAATAATATCAATATT-
1 ATCCAATTACTAAACTATCAAAACTTAATCCAATTATAATTCAATTA-AAATAATATC-ATATTA
1828841 TATA
64 TATA
1828845 CAAATTATCA
Statistics
Matches: 118, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
67 5 0.04
68 7 0.06
69 48 0.41
70 28 0.24
71 30 0.25
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (67 bp):
ATCCAATTACTAAACTATCAAAACTTAATCCAATTATAATTCAATTAAAATAATATCATATTATA
TA
Found at i:1828885 original size:2 final size:2
Alignment explanation
Indices: 1828878--1828915 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1828868 GTAATTGGAT
1828878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1828916 AACTAACTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1836284 original size:23 final size:24
Alignment explanation
Indices: 1836233--1836277 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1836223 AGGATCGTGC
*
1836233 CACAAGAGTAGAGAAAACGTGTAA
1 CACAAGAGCAGAGAAAACGTGTAA
*
1836257 CACAAGAGCATAGAAAA-GTGT
1 CACAAGAGCAGAGAAAACGTGT
1836278 GTCACAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.49, C:0.13, G:0.24, T:0.13
Consensus pattern (24 bp):
CACAAGAGCAGAGAAAACGTGTAA
Found at i:1836799 original size:13 final size:13
Alignment explanation
Indices: 1836781--1836805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1836771 AAGGAAAAAC
1836781 AAATGAAGAATGG
1 AAATGAAGAATGG
1836794 AAATGAAGAATG
1 AAATGAAGAATG
1836806 TTTTCTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (13 bp):
AAATGAAGAATGG
Found at i:1839304 original size:31 final size:31
Alignment explanation
Indices: 1839233--1839418 Score: 261
Period size: 31 Copynumber: 6.0 Consensus size: 31
1839223 GAGTCAAGGG
*
1839233 TTTACCTATGTTCTTTGGGACATATGGACAGGA
1 TTTACCTATGTTCTTCGGGACATATGGACA--A
*
1839266 -TTACCTATGTTCTTCGGGACATATGAACAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
* *
1839296 TTTACCTATGTTCTTCGGGATATATGGATAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
* *
1839327 TTTACCTATGTTTTTCGGGACATATAGG-CAG
1 TTTACCTATGTTCTTCGGGACATAT-GGACAA
1839358 TTTACCTATGTTCTTCGGGACATATGGACAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
1839389 TTTACCTATGTTC-TCTGGGACATATGGACA
1 TTTACCTATGTTCTTC-GGGACATATGGACA
1839419 GATTATTATA
Statistics
Matches: 138, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
30 5 0.04
31 104 0.75
32 29 0.21
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACAA
Found at i:1840216 original size:19 final size:19
Alignment explanation
Indices: 1840192--1840240 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1840182 CTGTTCACAG
1840192 TATTGTTCATACAATATAA
1 TATTGTTCATACAATATAA
** *
1840211 TATTGTTCATACCGTATAT
1 TATTGTTCATACAATATAA
1840230 TATTGTTCATA
1 TATTGTTCATA
1840241 AAAATCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (19 bp):
TATTGTTCATACAATATAA
Found at i:1842020 original size:14 final size:15
Alignment explanation
Indices: 1842001--1842029 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1841991 TATAATTTAC
1842001 CATTTAT-TTTAAAT
1 CATTTATCTTTAAAT
1842015 CATTTATCTTTAAAT
1 CATTTATCTTTAAAT
1842030 TTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
CATTTATCTTTAAAT
Found at i:1856567 original size:323 final size:322
Alignment explanation
Indices: 1855973--1856735 Score: 1305
Period size: 323 Copynumber: 2.4 Consensus size: 322
1855963 ATGCAACACT
*
1855973 TACTTGGAATTGGCGTGCTTATATGCTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
1 TACTGGGAATTGGCGTGCTTATATGCTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
1856038 CATTTTAAGCCTTTATGGTCTCTTTCGATGCTTCTTTGTTTTTGGAGTCTTTTTGATATGCTTCA
66 CATTTTAAGCCTTTATGGTCTCTTTCGATGCTTCTTTGTTTTTGGAGTCTTTTTGATATGCTTCA
1856103 CTTGCTCTTTGATATGCCAAAAACGGGGTGAATAAAAGAAATTTTGCATTTGCTCATATTGTCTA
131 CTTGCTCTTTGATATGCCAAAAACGGGGTGAATAAAAGAAATTTTGCATTTGCTCATATTGTCTA
*
1856168 TGTATTGATATGCAACACTTTATAAATTGATCATGCAAGTGTGCTTATTATCGTATAATCGATGC
196 TGTATTGATATGCAACACTTAATAAATTGATCATGCAAGTGTGCTTATTATCGTATAATCGATGC
*
1856233 TAAGGTGCTTATTCTGTATGCATTGGCAAGGACAGCTTTTTATAGGACTTGTCTGTCTGTTACC
261 TAAGGTGCTTATTCTGTATGCATTGGCAAGGACAGCTTTTTATAGGAATTGTC--TCTGTTACC
* *
1856297 TACTGGGAATTGGCGTGCTTCTATGTTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
1 TACTGGGAATTGGCGTGCTTATATGCTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
* *
1856362 CATTTTAAGCCTTTATGGTC-CCTTCGATGCTTCTTTGTTTTTGGAGTCTTTTTTATATGCTTCA
66 CATTTTAAGCCTTTATGGTCTCTTTCGATGCTTCTTTGTTTTTGGAGTCTTTTTGATATGCTTCA
* *
1856426 CTTGTTCTTTGATATGCCAAAAACTGGGTGAATAAAAGAAATTTTGCATTTGCTCATATTGTCTA
131 CTTGCTCTTTGATATGCCAAAAACGGGGTGAATAAAAGAAATTTTGCATTTGCTCATATTGTCTA
* * *
1856491 TGTATTGATATTCAACACTTAATAAATTGATCGTGCAAGTGTGTTTATTATCGTATAATCGATGC
196 TGTATTGATATGCAACACTTAATAAATTGATCATGCAAGTGTGCTTATTATCGTATAATCGATGC
* * *
1856556 TAAGGTGCTTATTGTGTATGCATTGGCAAGGACAGGTTTTTATAGGAATTGTCTCTGTTGCC
261 TAAGGTGCTTATTCTGTATGCATTGGCAAGGACAGCTTTTTATAGGAATTGTCTCTGTTACC
* * * * *
1856618 TAGTGGGAATTAGCGTGCTTTTATGCTTTATTACAGTGGCATTTCGTGG-ATTCATATTGTTTTG
1 TACTGGGAATTGGCGTGCTTATATGCTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
*
1856682 CATTTTAAGCCTTTATGGTCTCTTTTGATGCTTCTTTGTTTTTGGAGTCTTTTT
66 CATTTTAAGCCTTTATGGTCTCTTTCGATGCTTCTTTGTTTTTGGAGTCTTTTT
1856736 ATCAAGAACA
Statistics
Matches: 415, Mismatches: 23, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
320 35 0.08
321 82 0.20
323 216 0.52
324 82 0.20
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (322 bp):
TACTGGGAATTGGCGTGCTTATATGCTTTCTTACAGTGGCTTTTCGTGGAATTCATATTGTTTTG
CATTTTAAGCCTTTATGGTCTCTTTCGATGCTTCTTTGTTTTTGGAGTCTTTTTGATATGCTTCA
CTTGCTCTTTGATATGCCAAAAACGGGGTGAATAAAAGAAATTTTGCATTTGCTCATATTGTCTA
TGTATTGATATGCAACACTTAATAAATTGATCATGCAAGTGTGCTTATTATCGTATAATCGATGC
TAAGGTGCTTATTCTGTATGCATTGGCAAGGACAGCTTTTTATAGGAATTGTCTCTGTTACC
Found at i:1859483 original size:19 final size:20
Alignment explanation
Indices: 1859452--1859508 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
1859442 ATTTTTTAAG
1859452 TAAATAATTAATAAA-ATTT
1 TAAATAATTAATAAATATTT
1859471 TAAA-AATTAAATAAATATTTT
1 TAAATAATT-AATAAATA-TTT
1859492 TATAAT-ATT-ATAAATAT
1 TA-AATAATTAATAAATAT
1859509 GCTTTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 8 0.24
21 5 0.15
22 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATAATTAATAAATATTT
Found at i:1859504 original size:20 final size:21
Alignment explanation
Indices: 1859481--1859520 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1859471 TAAAAATTAA
1859481 ATAAATAT-TTTTATAATATT
1 ATAAATATCTTTTATAATATT
1859501 ATAAATATGCTTTTATAATA
1 ATAAATAT-CTTTTATAATA
1859521 ATTTCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
ATAAATATCTTTTATAATATT
Found at i:1860954 original size:20 final size:20
Alignment explanation
Indices: 1860880--1860955 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
1860870 ATTTCAAAAT
* *
1860880 GGGTATCGGTACCCTA-GGTA
1 GGGTATCGATACCCTATAG-A
*
1860900 GGGTATCGATA-CCTCAGTTAGG
1 GGGTATCGATACCCT-A--TAGA
*
1860922 GGTGTATCAATACCCTATAGA
1 GG-GTATCGATACCCTATAGA
1860943 GGGTATCGATACC
1 GGGTATCGATACC
1860956 TACTTTAAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.07
20 21 0.48
21 5 0.11
22 2 0.05
23 10 0.23
24 3 0.07
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCCTATAGA
Found at i:1861541 original size:22 final size:22
Alignment explanation
Indices: 1861511--1861593 Score: 139
Period size: 22 Copynumber: 3.8 Consensus size: 22
1861501 AGGTCTACGC
* * *
1861511 GGTCCTTCGGGACATATACAGA
1 GGTCTTTCGGGACAAATACATA
1861533 GGTCTTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
1861555 GGTCTTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
1861577 GGTCTTTCGGGACAAAT
1 GGTCTTTCGGGACAAAT
1861594 TTCACATGCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (22 bp):
GGTCTTTCGGGACAAATACATA
Found at i:1862162 original size:22 final size:23
Alignment explanation
Indices: 1862134--1862184 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1862124 CCGAAATTAT
*
1862134 TGTAGCAAGGGTATC-AGTACA-C
1 TGTAGCAAGGATATCGA-TACACC
1862156 TGTAGC-AGGATATCGATACACC
1 TGTAGCAAGGATATCGATACACC
1862178 TGTAGCA
1 TGTAGCA
1862185 TTTTGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (23 bp):
TGTAGCAAGGATATCGATACACC
Found at i:1863347 original size:38 final size:38
Alignment explanation
Indices: 1863305--1863395 Score: 155
Period size: 38 Copynumber: 2.4 Consensus size: 38
1863295 TATTTCATTA
*
1863305 ATACTACTTTACACAATGAGTATAGTCAAGGAGTATTG
1 ATACTACTTTACACAAGGAGTATAGTCAAGGAGTATTG
* *
1863343 ATACTACTTTACATAAGGAGTATAGTCAAGGAGTATTT
1 ATACTACTTTACACAAGGAGTATAGTCAAGGAGTATTG
1863381 ATACTACTTTACACA
1 ATACTACTTTACACA
1863396 GTAATATCGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (38 bp):
ATACTACTTTACACAAGGAGTATAGTCAAGGAGTATTG
Found at i:1865525 original size:28 final size:28
Alignment explanation
Indices: 1865483--1865548 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
1865473 TCCTTAAGGA
*
1865483 GTGGTCCTTCGGGACATATGTGTTATAT
1 GTGGTCCTTCAGGACATATGTGTTATAT
1865511 GTGGTCCTTCAGGACATATGTGTTATAT
1 GTGGTCCTTCAGGACATATGTGTTATAT
1865539 GTGGTCCTTC
1 GTGGTCCTTC
1865549 GGGGCAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (28 bp):
GTGGTCCTTCAGGACATATGTGTTATAT
Found at i:1867034 original size:17 final size:17
Alignment explanation
Indices: 1867012--1867054 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1867002 GAGGTGACTC
1867012 ATGAAGGAA-CAAGCTAA
1 ATGAA-GAATCAAGCTAA
*
1867029 ATGAAGAATTAAGCTAA
1 ATGAAGAATCAAGCTAA
*
1867046 ATAAAGAAT
1 ATGAAGAAT
1867055 TCAAAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (17 bp):
ATGAAGAATCAAGCTAA
Found at i:1867055 original size:17 final size:17
Alignment explanation
Indices: 1867022--1867055 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1867012 ATGAAGGAAC
*
1867022 AAGCTAAATGAAGAATT
1 AAGCTAAATAAAGAATT
1867039 AAGCTAAATAAAGAATT
1 AAGCTAAATAAAGAATT
1867056 CAAAGATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
AAGCTAAATAAAGAATT
Found at i:1868638 original size:2 final size:2
Alignment explanation
Indices: 1868631--1868655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1868621 CCATAATTGT
1868631 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1868656 TGAAGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1874180 original size:31 final size:31
Alignment explanation
Indices: 1874142--1874264 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
1874132 CCCGAAGGAC
* *
1874142 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1874173 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1874204 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1874235 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1874265 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1878524 original size:31 final size:31
Alignment explanation
Indices: 1878486--1878639 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
1878476 CCCGAAGGAC
* *
1878486 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1878517 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1878548 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1878579 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1878610 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1878640 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1886321 original size:31 final size:31
Alignment explanation
Indices: 1886283--1886434 Score: 238
Period size: 31 Copynumber: 5.0 Consensus size: 31
1886273 CCCGAAGGAC
* *
1886283 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1886314 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1886345 CAGTCCATATGTTCCGAAGAACATAGG-AAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1886375 CAGTCCATATGTT-CGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1886405 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
1886435 CCCTCGACCC
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
29 13 0.12
30 32 0.29
31 66 0.59
32 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1886408 original size:60 final size:62
Alignment explanation
Indices: 1886283--1886434 Score: 238
Period size: 60 Copynumber: 2.5 Consensus size: 62
1886273 CCCGAAGGAC
* * *
1886283 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1886345 CAGTCCATATGTTCCGAAGAACATAGG-AAACAGTCCATATGT-TCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
1886405 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
1886435 CCCTCGACCC
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
60 43 0.51
61 16 0.19
62 24 0.29
63 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1887324 original size:21 final size:21
Alignment explanation
Indices: 1887294--1887338 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1887284 ATTCTGTCGT
* *
1887294 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1887315 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1887336 TTG
1 TTG
1887339 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1890324 original size:31 final size:31
Alignment explanation
Indices: 1890286--1890439 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
1890276 CCCGAAGGAC
* *
1890286 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1890317 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1890348 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1890379 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1890410 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
1890440 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1891336 original size:21 final size:21
Alignment explanation
Indices: 1891306--1891350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1891296 ATTCTGTCGT
* *
1891306 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1891327 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1891348 TTG
1 TTG
1891351 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1892308 original size:21 final size:20
Alignment explanation
Indices: 1892275--1892322 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
1892265 CTTTAAAGCG
* *
1892275 TGAAAAAGATCGAGTATGTTT
1 TGAAAAAGATCGACTAAG-TT
* *
1892296 TGAAAAGGTTCGACTAAGTT
1 TGAAAAAGATCGACTAAGTT
1892316 TGAAAAA
1 TGAAAAA
1892323 CATTTAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (20 bp):
TGAAAAAGATCGACTAAGTT
Found at i:1894813 original size:21 final size:21
Alignment explanation
Indices: 1894776--1894829 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1894766 TGTTATACCA
*
1894776 AAGGGATTGA-CCATTTTCCTC
1 AAGGGATAGATCCATTTT-CTC
*
1894797 AAGGGATAGATCC-TTTTGTC
1 AAGGGATAGATCCATTTTCTC
*
1894817 AAGGGATCGATCC
1 AAGGGATAGATCC
1894830 CAAACTCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 13 0.45
22 2 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (21 bp):
AAGGGATAGATCCATTTTCTC
Found at i:1894899 original size:21 final size:21
Alignment explanation
Indices: 1894851--1894925 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
1894841 TTGTCCAAGA
* * *
1894851 GATCGATCCTTT-TTTAAGGG
1 GATCGATCCTTTGGTCAAAGG
*
1894871 GATTGATCCTTTGGTCAAAGG
1 GATCGATCCTTTGGTCAAAGG
1894892 GATCGATCCTTTGGTCAAAGG
1 GATCGATCCTTTGGTCAAAGG
1894913 GATCGATCCTTTG
1 GATCGATCCTTTG
1894926 AGCTAGAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 11 0.22
21 38 0.78
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
GATCGATCCTTTGGTCAAAGG
Found at i:1896621 original size:24 final size:24
Alignment explanation
Indices: 1896584--1896640 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1896574 ATAATTTGCT
* *
1896584 TATTAAA-TAAAATTAATTTTTAAA
1 TATTAAATTAAATTTAA-TATTAAA
*
1896608 TATTAAATTTAATTTAATATTAAA
1 TATTAAATTAAATTTAATATTAAA
*
1896632 GATTAAATT
1 TATTAAATT
1896641 CTGTAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTAAATTAAATTTAATATTAAA
Found at i:1898049 original size:17 final size:16
Alignment explanation
Indices: 1898027--1898061 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1898017 TTCGGTTTGA
1898027 AAAAAAACCGGATTTTT
1 AAAAAAACCGG-TTTTT
1898044 AAAAAAACCGGTTTTT
1 AAAAAAACCGGTTTTT
1898060 AA
1 AA
1898062 TCCGATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (16 bp):
AAAAAAACCGGTTTTT
Found at i:1898111 original size:20 final size:21
Alignment explanation
Indices: 1898086--1898132 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
1898076 CGGTCATTCA
1898086 ATTTTTTAAACC-CAGACCGG
1 ATTTTTTAAACCTCAGACCGG
*
1898106 A-TTTTTAAACCTCAGACTGG
1 ATTTTTTAAACCTCAGACCGG
1898126 ATTTTTT
1 ATTTTTT
1898133 TCTGGATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 5 0.21
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (21 bp):
ATTTTTTAAACCTCAGACCGG
Found at i:1898112 original size:19 final size:20
Alignment explanation
Indices: 1898088--1898131 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1898078 GTCATTCAAT
1898088 TTTTTAAACC-CAGACCGGA
1 TTTTTAAACCTCAGACCGGA
*
1898107 TTTTTAAACCTCAGACTGGA
1 TTTTTAAACCTCAGACCGGA
1898127 TTTTT
1 TTTTT
1898132 TTCTGGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (20 bp):
TTTTTAAACCTCAGACCGGA
Found at i:1903488 original size:29 final size:28
Alignment explanation
Indices: 1903367--1903492 Score: 96
Period size: 29 Copynumber: 4.4 Consensus size: 28
1903357 TTAAAAATAT
* * *
1903367 TTTTTATTTTAAATTATGAAATCTATTTTA
1 TTTTTATCTTAACTTA--AAATATATTTTA
* *
1903397 TTATTT-TCTTAACCTAAAAATATTTTTTA
1 TT-TTTATCTTAA-CTTAAAATATATTTTA
*
1903426 TTTTTATTTTAACTT--AATATATTTTA
1 TTTTTATCTTAACTTAAAATATATTTTA
* ** *
1903452 ATACTATCATAACTTAAAATTATATTTTA
1 TTTTTATCTTAACTTAAAA-TATATTTTA
1903481 TTTTTATCTTAA
1 TTTTTATCTTAA
1903493 TTTTTAAAAA
Statistics
Matches: 73, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
26 20 0.27
28 7 0.10
29 34 0.47
30 7 0.10
31 5 0.07
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTTATCTTAACTTAAAATATATTTTA
Found at i:1903566 original size:30 final size:30
Alignment explanation
Indices: 1903527--1903596 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1903517 ATTTTATCTG
* *
1903527 ATTACATATATTATA-TTCTTAAATTAAATT
1 ATTAAATATATTATAGCT-TTAAATTAAATT
* **
1903557 ATTAAATATATTCTAGCTTTACCTTAAATT
1 ATTAAATATATTATAGCTTTAAATTAAATT
1903587 ATTAAATATA
1 ATTAAATATA
1903597 ATTTATCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (30 bp):
ATTAAATATATTATAGCTTTAAATTAAATT
Found at i:1903728 original size:29 final size:29
Alignment explanation
Indices: 1903653--1903764 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 29
1903643 TATATTTTAT
1903653 TTTTTAAGTTAATAA-AATAATAAAATATA
1 TTTTTAAGTTAA-AATAATAATAAAATATA
*
1903682 TATTTTAAGTTAAAATAATAATAAAATATG
1 T-TTTTAAGTTAAAATAATAATAAAATATA
* * *
1903712 TTTTTAAATTAAGATAAGAATAAAATATATA
1 TTTTTAAGTTAAAATAATAAT-AAA-ATATA
* *
1903743 TTTTTAATGTTAAGATATTAAT
1 TTTTTAA-GTTAAAATAATAAT
1903765 TTAATTTAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
29 20 0.29
30 28 0.40
31 11 0.16
32 11 0.16
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTTTAAGTTAAAATAATAATAAAATATA
Found at i:1912476 original size:55 final size:55
Alignment explanation
Indices: 1912421--1913919 Score: 1224
Period size: 55 Copynumber: 27.5 Consensus size: 55
1912411 GTATCGCTTT
* * ** * *
1912421 AGGGAGTATAGAACTTGAACAATCTTCTACAAATAGGTTCACTCCCTCTTTCTTT
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
** **
1912476 AGGGAGTATAGAACTCGAA-AATCTTCTTAAAATAGGTTCGCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* *
1912530 AGGGAGTATAGAACTCGAA-AATCGTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * *
1912584 AGGGAGTATAGAAATCAAAC-ATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * * ** *
1912638 AGGGAGTATGGAACTCAAAAAATCTTATAAAAATGGGTTCGCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * *
1912693 AGGGATTATAGATCTCGAA-AATCTTCTGCAAACGGGTTCGCTCCATTTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * *
1912747 AGAGAGTATAAAACTCGAAC-ATCTTCTGCAAACGGGTTCGCTCCCTATTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* ** * ** ** * *
1912801 AGGGAGTATGGAACTAAAAAAATCTTCTAAAAACGGGTTTTCTCACTCTTTCTTT
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * *
1912856 AGGGAGTATAGAACTCGAAC-ATCTTCTGCAAACGGGTTTGCTCCATTTTTCTTT
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
*
1912910 AGGGAGTATAGAACTCGAA-AATCTTCTGCAAAC--G-TCACTCCCT-TTTCCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTT-CTTC
* * * **
1912961 AGGGAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* ** * *
1913016 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCACTTTCACATTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * * * ** *
1913071 AGGGAGTCTGGAACTCGAACAATCTTCTGAAAATGAGTTCGCTCCCAATTTTTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * * ** *
1913126 AGAGAGTATAGAACTCAAAAAATCTTCTTCTTAGGGGTTCGCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * **
1913181 AGGGAGTATATAACTCGAACAATCTTTTGCAAACGTGTTCGCTTACTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * * * *
1913236 AGGGAGTCTGGAACTCGAACAGTCTTCTGAAAACGGGTTCGTTCCCTCTTTATTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
** *
1913291 AGATAGTATAGAACTCGAAC-ATCTTCTGCAAACAGGTTCGCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * *
1913345 AGGGAGTATAGAACTCGAA-AATCTTCTGCAAACGGGTTCGTTCTCTTTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* * * *
1913399 AGGGAGTATGGAACTCAAAAAATCTTCTGCAAACGGGTTCTCTCCCTCTTTCTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* ** * * * *
1913454 AGAGAGTATAGAACTCGAA-AATCTTCAACAATCGTG-TCTACTCCCT-ATTCTTTC
1 AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTC-TTC
* ** * * * * *
1913508 AGAGAGTATA-AGACTCGAACAATCTTCAACGATCGTG-TCTGCTCCCTATTCCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTCTTC
** * * * *
1913563 AGGGAGTATA-AGACTCGAACAATCTTCAACAATCGTG-TCAGCTCCCTATTCCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTCTTC
* *** * * * * *
1913618 AGAGAGTATA-AGACTCGAACAATCTTCAATAATCGTG-TCTGCTCCCTATTCCTTG
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTCTTC
* * ** * * *
1913673 AGAGAGTATA-AGACTCAAACAATCTTCAACAATCGTG-TCTGCTCCCTAC-TCCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCT-CTTTCTTC
* * ** * * * * * *
1913728 AGAGAGTATA-AGACTTGAACAATCTTCAACAATCGTG-TCTGCTCTCTATTCCTTT
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTCTTC
* ** * * * * * *
1913783 AGAGAGTATA-AGACTCGAACAATCTTCAACAATCGTGTTTGCTCCATATTCCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
* ** * * * * *
1913838 AGAGAGTATA-ATACTCGAACAATCTTCAACAATCGTGTGT-GCTCTCTATTCCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGT-TCGCTCCCTCTTTCTTC
*
1913893 AGAGAGTATA-AGACTCGAACAATCTTC
1 AGGGAGTATAGA-ACTCGAACAATCTTC
1913920 AACAATCGTG
Statistics
Matches: 1235, Mismatches: 187, Indels: 44
0.84 0.13 0.03
Matches are distributed among these distances:
50 3 0.00
51 27 0.02
52 12 0.01
53 6 0.00
54 429 0.35
55 751 0.61
56 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (55 bp):
AGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTC
Found at i:1912679 original size:163 final size:163
Alignment explanation
Indices: 1912421--1913479 Score: 1250
Period size: 163 Copynumber: 6.5 Consensus size: 163
1912411 GTATCGCTTT
* * ** * *
1912421 AGGGAGTATAGAACTTGAACAATCTTCTACAAATAGGTTCACTCCCTCTTTCTTTAGGGAGTATA
1 AGGGAGTATAGAACTCGAAC-ATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATA
* **
1912486 GAACTC-GAAAATCTTCTTAAAATAGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAA
65 GAACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAA
*
1912550 ATCGTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
130 ATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* * * *
1912584 AGGGAGTATAGAAATCAAACATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTCAGGGAGTATGG
1 AGGGAGTATAGAACTCGAACATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAG
* * * * *
1912649 AACTCAAAAAATCTTATAAAAATGGGTTCGCTCCCTCTTTCTTCAGGGATTATAGATCTCGAAAA
66 AACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAA
*
1912714 TCTTCTGCAAACGGGTTCGCTCCATTTTTCTTC
131 TCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* * * *
1912747 AGAGAGTATAAAACTCGAACATCTTCTGCAAACGGGTTCGCTCCCTATTTCTTCAGGGAGTATGG
1 AGGGAGTATAGAACTCGAACATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAG
* * ** * * *
1912812 AACTAAAAAAATCTTCTAAAAACGGGTTTTCTCACTCTTTCTTTAGGGAGTATAGAACTCGAACA
66 AACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAA
* * *
1912877 TCTTCTGCAAACGGGTTTGCTCCATTTTTCTTT
131 TCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* *
1912910 AGGGAGTATAGAACTCGAAAATCTTCTGCAAAC--G-TCACTCCCT-TTTCCTTCAGGGAGTATA
1 AGGGAGTATAGAACTCGAACATCTTCTGCAAACGGGTTCGCTCCCTCTTT-CTTCAGGGAGTATA
***
1912971 GAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAC
65 GAACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-
* ** ***
1913036 AATCTTCTGCAAACGGGTTCACTTTCACATTCTTC
129 AATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* * * * * ** * *
1913071 AGGGAGTCTGGAACTCGAACAATCTTCTGAAAATGAGTTCGCTCCCAATTTTTTCAGAGAGTATA
1 AGGGAGTATAGAACTCGAAC-ATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATA
*** * *
1913136 GAACTCAAAAAATCTTCTTCTTAGGGGTTCGCTCCCTCTTTCTTCAGGGAGTATATAACTCGAAC
65 GAACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-
* * ** *
1913201 AATCTTTTGCAAACGTGTTCGCTTACTCTTTCTTC
129 AATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* * * * * **
1913236 AGGGAGTCTGGAACTCGAACAGTCTTCTGAAAACGGGTTCGTTCCCTCTTTATTCAGATAGTATA
1 AGGGAGTATAGAACTCGAACA-TCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATA
* * ** *
1913301 GAACTC-GAACATCTTCTGCAAACAGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAA
65 GAACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAA
* *
1913365 ATCTTCTGCAAACGGGTTCGTTCTCTTTTTCTTC
130 ATCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
* * * * *
1913399 AGGGAGTATGGAACTCAAAAAATCTTCTGCAAACGGGTTCTCTCCCTCTTTCTTCAGAGAGTATA
1 AGGGAGTATAGAACTC-GAACATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATA
*
1913464 GAACTC-GAAAATCTTC
65 GAACTCAAAAAATCTTC
1913480 AACAATCGTG
Statistics
Matches: 780, Mismatches: 106, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
159 3 0.00
160 76 0.10
161 43 0.06
162 54 0.07
163 374 0.48
164 54 0.07
165 173 0.22
166 3 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (163 bp):
AGGGAGTATAGAACTCGAACATCTTCTGCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAG
AACTCAAAAAATCTTCTTAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAA
TCTTCTGCAAACGGGTTCGCTCCCTTTTTCTTC
Found at i:1913920 original size:55 final size:55
Alignment explanation
Indices: 1913440--1914083 Score: 1022
Period size: 55 Copynumber: 11.7 Consensus size: 55
1913430 AACGGGTTCT
* * *
1913440 CTCCCTCTTTCTTCAGAGAGTAT-AGAACTCGAA-AATCTTCAACAATCGTGTCTA
1 CTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTG
* *
1913494 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
1913549 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCAG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
*
1913604 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
1913659 CTCCCTATTCCTTGAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
1913714 CTCCCTACTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* * *
1913769 CTCTCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* * *
1913824 CTCCATATTCCTTCAGAGAGTATAATACTCGAACAATCTTCAACAATCGTGTGTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
1913879 CTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* * * * *
1913934 TTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTTAATAATCGTGTATG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
*
1913989 CTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
*
1914044 CTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTT
1 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTT
1914084 GATGCTTCAA
Statistics
Matches: 542, Mismatches: 46, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
54 27 0.05
55 515 0.95
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
Found at i:1915142 original size:13 final size:13
Alignment explanation
Indices: 1915126--1915194 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 13
1915116 TTTTGCTTCA
1915126 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
*
1915139 TTTTTTTATTCATTC
1 TTTTTTTCTT--TTC
*
1915154 TTTTCTTCCTTTTTC
1 TTTT-TTTC-TTTTC
1915169 TTCTTTTT-TTTTC
1 TT-TTTTTCTTTTC
1915182 TTTTTTTCATTTT
1 TTTTTTTC-TTTT
1915195 TTCATTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
12 5 0.11
13 16 0.36
14 4 0.09
15 14 0.31
16 4 0.09
17 2 0.04
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:1915145 original size:8 final size:8
Alignment explanation
Indices: 1915126--1915206 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 8
1915116 TTTTGCTTCA
1915126 TTTTTTTC
1 TTTTTTTC
*
1915134 TTTTCTTTT
1 TTTT-TTTC
1915143 TTTATTCATTC
1 TTT-TT--TTC
*
1915154 TTTTCTTCC
1 TTTT-TTTC
1915163 TTTTTCTTC
1 TTTTT-TTC
1915172 TTTTTTTTTC
1 --TTTTTTTC
1915182 TTTTTTTC
1 TTTTTTTC
*
1915190 ATTTTTTC
1 TTTTTTTC
1915198 ATTTTTTTC
1 -TTTTTTTC
1915207 ATCTTCAAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
8 20 0.34
9 22 0.38
10 5 0.09
11 11 0.19
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1915165 original size:48 final size:47
Alignment explanation
Indices: 1915112--1915206 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 47
1915102 TCTTGAACCC
1915112 TCCTTTTTGCTTC-ATTTTTTTCTTTTCTTT-TTTTATTCATTCTTTTCT
1 TCCTTTTT-CTTCTATTTTTTTCTTTT-TTTATTTT-TTCATTCTTTTCT
* *
1915160 TCCTTTTTCTTCTTTTTTTTTCTTTTTTTCATTTTTTCATTTTTTTC
1 TCCTTTTTCTTCTATTTTTTTCTTTTTTT-ATTTTTTCATTCTTTTC
1915207 ATCTTCAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 7 0.17
48 31 0.74
49 4 0.10
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (47 bp):
TCCTTTTTCTTCTATTTTTTTCTTTTTTTATTTTTTCATTCTTTTCT
Found at i:1915186 original size:10 final size:10
Alignment explanation
Indices: 1915128--1915188 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
1915118 TTGCTTCATT
1915128 TTTTTCTTTTC
1 TTTTT-TTTTC
1915139 TTTTTTTATTC
1 TTTTTTT-TTC
*
1915150 ATTCTTTTCTTC
1 -TT-TTTTTTTC
* *
1915162 CTTTTTCTTC
1 TTTTTTTTTC
1915172 TTTTTTTTTC
1 TTTTTTTTTC
1915182 TTTTTTT
1 TTTTTTT
1915189 CATTTTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 25 0.58
11 9 0.21
12 5 0.12
13 4 0.09
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1915195 original size:10 final size:10
Alignment explanation
Indices: 1915129--1915205 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
1915119 TGCTTCATTT
*
1915129 TTTTCTTTTCT
1 TTTT-TTTTCA
1915140 TTTTTTATTCA
1 TTTTTT-TTCA
*
1915151 TTCTTTTCTTCC
1 TT-TTTT-TTCA
* *
1915163 TTTTTCTTCT
1 TTTTTTTTCA
1915173 TTTTTTTTC-
1 TTTTTTTTCA
1915182 -TTTTTTTCA
1 TTTTTTTTCA
1915191 --TTTTTTCA
1 TTTTTTTTCA
1915199 TTTTTTT
1 TTTTTTT
1915206 CATCTTCAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
8 16 0.29
10 18 0.33
11 12 0.22
12 9 0.16
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:1915196 original size:9 final size:9
Alignment explanation
Indices: 1915122--1915208 Score: 58
Period size: 8 Copynumber: 9.6 Consensus size: 9
1915112 TCCTTTTTGC
1915122 TTCATTTTT
1 TTCATTTTT
1915131 TTC-TTTTCT
1 TTCATTTT-T
*
1915140 TT--TTTTA
1 TTCATTTTT
1915147 TTCATTCTTTT
1 TTCA-T-TTTT
*
1915158 CTTCCTTTTT
1 -TTCATTTTT
*
1915168 CTTCTTTTTTT
1 -TTC-ATTTTT
1915179 TTC-TTTTT
1 TTCATTTTT
1915187 TTCA-TTTT
1 TTCATTTTT
1915195 TTCATTTTT
1 TTCATTTTT
1915204 TTCAT
1 TTCAT
1915209 CTTCAAGCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
7 2 0.03
8 24 0.37
9 15 0.23
10 12 0.18
11 9 0.14
12 3 0.05
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCATTTTT
Found at i:1915207 original size:17 final size:16
Alignment explanation
Indices: 1915134--1915208 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 16
1915124 CATTTTTTTC
1915134 TTTTCTTTTTTT-ATT
1 TTTTCTTTTTTTCATT
** * *
1915149 CATTCTTTTCTTC-CT
1 TTTTCTTTTTTTCATT
*
1915164 TTTTC-TTCTTT--TT
1 TTTTCTTTTTTTCATT
1915177 TTTTCTTTTTTTCATT
1 TTTTCTTTTTTTCATT
1915193 TTTTCATTTTTTTCAT
1 TTTTC-TTTTTTTCAT
1915209 CTTCAAGCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
13 6 0.13
14 9 0.20
15 13 0.29
16 7 0.16
17 10 0.22
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTTCATT
Found at i:1936678 original size:39 final size:39
Alignment explanation
Indices: 1936619--1936698 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1936609 GTTGAAATTA
* *
1936619 TTGAATGAGTTCTATTTAATTATACTATTAAACAAAATG
1 TTGAATAAGTTCTATGTAATTATACTATTAAACAAAATG
1936658 TTGAATAAGTTCTATGTAATTATACTATTAAACAAAATG
1 TTGAATAAGTTCTATGTAATTATACTATTAAACAAAATG
1936697 TT
1 TT
1936699 TTAATTACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (39 bp):
TTGAATAAGTTCTATGTAATTATACTATTAAACAAAATG
Found at i:1936728 original size:2 final size:2
Alignment explanation
Indices: 1936721--1936747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1936711 GCTCAAACTC
1936721 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
1936748 ACCCATTAAC
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:1937704 original size:20 final size:20
Alignment explanation
Indices: 1937660--1937704 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1937650 CTGAATATTT
* * *
1937660 ATCCCGAATGACCACTGTTT
1 ATCCCGAAGGACCACTGATA
*
1937680 GTCCCGAAGGACCACTGATA
1 ATCCCGAAGGACCACTGATA
1937700 ATCCC
1 ATCCC
1937705 TCGACTCTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCCCGAAGGACCACTGATA
Found at i:1939347 original size:21 final size:21
Alignment explanation
Indices: 1939323--1939380 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1939313 TTTACCCTTG
*
1939323 ATGCATCGGTGCACATTGAAT
1 ATGCATCGATGCACATTGAAT
1939344 ATGCATCGATGCACATTGAAT
1 ATGCATCGATGCACATTGAAT
1939365 ATGCATCGATGCACAT
1 ATGCATCGATGCACAT
1939381 AGCCCAGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACATTGAAT
Found at i:1939855 original size:10 final size:10
Alignment explanation
Indices: 1939840--1939871 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1939830 ACGGAAGGAG
1939840 AGGAAGAAGA
1 AGGAAGAAGA
1939850 AGGAAGAAGA
1 AGGAAGAAGA
1939860 AGGAAGAAGA
1 AGGAAGAAGA
1939870 AG
1 AG
1939872 AAGTTCTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AGGAAGAAGA
Found at i:1939860 original size:13 final size:13
Alignment explanation
Indices: 1939833--1939874 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1939823 TGGAGATACG
*
1939833 GAAGG-AGAGGAA
1 GAAGGAAGAAGAA
1939845 GAA-GAAGGAAGAA
1 GAAGGAA-GAAGAA
1939858 GAAGGAAGAAGAA
1 GAAGGAAGAAGAA
1939871 GAAG
1 GAAG
1939875 TTCTGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 4 0.15
13 18 0.69
14 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (13 bp):
GAAGGAAGAAGAA
Found at i:1949653 original size:25 final size:25
Alignment explanation
Indices: 1949606--1949657 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1949596 TAGGTCCACC
** *
1949606 AATAATGCATGTGCGGGTCGTTTAT
1 AATAATGCATGCACGAGTCGTTTAT
*
1949631 AATAATGCATGCACGAGTTGTTTAT
1 AATAATGCATGCACGAGTCGTTTAT
1949656 AA
1 AA
1949658 GAGGGCTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (25 bp):
AATAATGCATGCACGAGTCGTTTAT
Found at i:1949976 original size:30 final size:30
Alignment explanation
Indices: 1949936--1950036 Score: 166
Period size: 30 Copynumber: 3.4 Consensus size: 30
1949926 AATAAGCTTT
*
1949936 GGACCATTTTGGAACATTGTAAAGTTATAG
1 GGACCATTTTGGAACATTGTAATGTTATAG
*
1949966 GGATCATTTTGGAACATTGTAATGTTATAG
1 GGACCATTTTGGAACATTGTAATGTTATAG
*
1949996 GGACCATTTTGGAATATTGTAATGTTATAG
1 GGACCATTTTGGAACATTGTAATGTTATAG
*
1950026 GGACCTTTTTG
1 GGACCATTTTG
1950037 AAAATTTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.39
Consensus pattern (30 bp):
GGACCATTTTGGAACATTGTAATGTTATAG
Found at i:1952668 original size:13 final size:13
Alignment explanation
Indices: 1952650--1952689 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1952640 TTTACTATTA
1952650 AATAATTATTAGT
1 AATAATTATTAGT
1952663 AATAATTATTA--
1 AATAATTATTAGT
*
1952674 AATCATTATTAGT
1 AATAATTATTAGT
1952687 AAT
1 AAT
1952690 TTTTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (13 bp):
AATAATTATTAGT
Found at i:1952683 original size:11 final size:11
Alignment explanation
Indices: 1952645--1952684 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1952635 AGTTTTTTAC
1952645 TATTAAATAAT
1 TATTAAATAAT
1952656 TATTAGTAATAAT
1 TATTA--AATAAT
*
1952669 TATTAAATCAT
1 TATTAAATAAT
1952680 TATTA
1 TATTA
1952685 GTAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTAAATAAT
Found at i:1952703 original size:24 final size:24
Alignment explanation
Indices: 1952645--1952930 Score: 109
Period size: 24 Copynumber: 11.5 Consensus size: 24
1952635 AGTTTTTTAC
*
1952645 TATTAAATAATTATTAGTAATAAT
1 TATTAAATCATTATTAGTAATAAT
**
1952669 TATTAAATCATTATTAGTAATTTT
1 TATTAAATCATTATTAGTAATAAT
* ***
1952693 TA-TAATTTCATTATTTCAAATAAT
1 TATTAA-ATCATTATTAGTAATAAT
* *
1952717 TACTAAATCATT-TGTA-TCA-AAT
1 TATTAAATCATTAT-TAGTAATAAT
* * *
1952739 CATTAAAT-ATTAATAATAA-AACGT
1 TATTAAATCATTATTAGTAATAA--T
* * *
1952763 TATTACTAATCATTACTAAATCATATCAT
1 TATTA--AATCATTA-TTAGT-A-ATAAT
* *
1952792 TACTAAATCATTAAATTAATAATAAT
1 TATTAAATCATT--ATTAGTAATAAT
* * *
1952818 TAGTAAATCATGATTAGTAATTAT
1 TATTAAATCATTATTAGTAATAAT
* * *
1952842 TA-TAATTTCATTAGTAGTAATCAT
1 TATTAA-ATCATTATTAGTAATAAT
* *
1952866 TACTAAATCATTATCATATTAATAAT
1 TATTAAATCATTAT--TAGTAATAAT
* * * *
1952892 TAATAATTCATTATTAAATTTATAAT
1 TATTAAATCATTATT--AGTAATAAT
*
1952918 TAATAAATCATTA
1 TATTAAATCATTA
1952931 AAGTTAAATC
Statistics
Matches: 200, Mismatches: 40, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
21 5 0.03
22 13 0.06
23 8 0.04
24 83 0.41
25 6 0.03
26 57 0.28
27 12 0.06
28 7 0.04
29 7 0.04
30 1 0.00
31 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (24 bp):
TATTAAATCATTATTAGTAATAAT
Found at i:1952792 original size:16 final size:16
Alignment explanation
Indices: 1952771--1952802 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1952761 GTTATTACTA
1952771 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1952787 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1952803 TAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:1952819 original size:26 final size:24
Alignment explanation
Indices: 1952790--1952930 Score: 95
Period size: 26 Copynumber: 5.6 Consensus size: 24
1952780 AAATCATATC
*
1952790 ATTACTAAATCATTAAATTAATAATA
1 ATTAATAAATCATT--ATTAATAATA
* * * *
1952816 ATTAGTAAATCATGATTAGTAATT
1 ATTAATAAATCATTATTAATAATA
* * * *
1952840 ATT-ATAATTTCATTAGTAGTAATC
1 ATTAATAA-ATCATTATTAATAATA
* *
1952864 ATTACTAAATCATTATCATATTAATA
1 ATTAATAAATCATTAT--TAATAATA
* *
1952890 ATTAATAATTCATTATTAAATTTATA
1 ATTAATAAATCATTATT-AA-TAATA
1952916 ATTAATAAATCATTA
1 ATTAATAAATCATTA
1952931 AAGTTAAATC
Statistics
Matches: 90, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
23 3 0.03
24 33 0.37
25 4 0.04
26 50 0.56
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTAATAAATCATTATTAATAATA
Found at i:1960892 original size:65 final size:64
Alignment explanation
Indices: 1960774--1960983 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
1960764 TATTCAAAGG
* * * ** *
1960774 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGC-T
1 CATGCATCGATGCA-CAATCCATGCATCGATGCA-CCA-GAATATTTTTCAAACATCGAATGCAT
1960836 TT
63 TT
* ** * *
1960838 CCATGCACCGATGCACTCTCTATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCAT
1 -CATGCATCGATGCACAATCCATGCATCGATGCAC-CAGAATATTTTTC-AAACATCGAATGCAT
1960902 TT
63 TT
* **
1960904 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
1960968 CATGCATCGATGCACA
1 CATGCATCGATGCACA
1960984 CTTGGTGCAC
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.43
65 60 0.49
66 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:1960998 original size:64 final size:64
Alignment explanation
Indices: 1960823--1961000 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 64
1960813 GAATTAATTG
* * *
1960823 AACATCGAATGC-TTTCCATGCACCGATGCACTCTCTATGCATCGATGCACTCTGAATATTTTCA
1 AACATCGAATGCATTT-CATGCATCGATGCACACT-TATGCATCGATGCACTCAGAATATTTTCA
1960887 A
64 A
* * * **
1960888 AACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCATCGATGCACTCAGAATA-TTTTCA
1960951 A
64 A
* *
1960952 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCATCGATGCA
1961001 TCAAGTGTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
64 48 0.49
65 46 0.47
66 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1966779 original size:20 final size:21
Alignment explanation
Indices: 1966750--1966805 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1966740 TTTGTGCTTC
*
1966750 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1966770 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1966792 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1966806 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1968377 original size:21 final size:21
Alignment explanation
Indices: 1968335--1968378 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1968325 ACCCCGGGAG
*
1968335 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1968356 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1968377 CT
1 CT
1968379 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1969010 original size:31 final size:31
Alignment explanation
Indices: 1968957--1969036 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
1968947 ATTTAACAAA
* * **
1968957 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
**
1968988 GCGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1969019 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
1969037 CAAAATCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:1969483 original size:65 final size:64
Alignment explanation
Indices: 1969365--1969574 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
1969355 TATTCAAAGG
* * * ** *
1969365 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCAT
1 CATGCATCGATGCA-CAATCCATGCATCGATGCA-CCA-GAATATTTTTCAAACATCGAATGCAT
*
1969428 TC
63 TT
* ** * *
1969430 CATGCACCGATGCACTCTCTATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATT
1 CATGCATCGATGCACAATCCATGCATCGATGCAC-CAGAATATTTTTC-AAACATCGAATGCATT
1969494 T
64 T
* **
1969495 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
1969559 CATGCATCGATGCACA
1 CATGCATCGATGCACA
1969575 CTTGGTGCAC
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 7 0.06
64 52 0.43
65 63 0.52
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:1976578 original size:61 final size:60
Alignment explanation
Indices: 1976452--1976612 Score: 150
Period size: 61 Copynumber: 2.6 Consensus size: 60
1976442 ATGGTTTATT
* * * * * **
1976452 TTAAAATAAATACCTAAAATATGTCAATTTTTTTTATCTA-AGTATCTAAAATATTTGTTGG
1 TTAAAGTAAATACTTAAAGTATAT-AA-TTTTTTTATCTAGAGTATCCAAAATATTTGTTAA
*
1976513 TTAAAGTAAATATTTAAAAGTAT-TCATATTTTTTTATCTAGA-TATCCAAAATATTT-TGTAA
1 TTAAAGTAAATACTT-AAAGTATAT-A-ATTTTTTTATCTAGAGTATCCAAAATATTTGT-TAA
**
1976574 TTAAAGTATGTACTTAAAGTATATAATTTTTTTATCTAG
1 TTAAAGTAAATACTTAAAGTATATAATTTTTTTATCTAG
1976613 TACCTAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
59 14 0.16
60 9 0.11
61 54 0.64
62 8 0.09
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (60 bp):
TTAAAGTAAATACTTAAAGTATATAATTTTTTTATCTAGAGTATCCAAAATATTTGTTAA
Found at i:1979084 original size:42 final size:42
Alignment explanation
Indices: 1979033--1979172 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 42
1979023 AAAATCATAC
*
1979033 TTTAGCAGCGTTTTTTAAACAAACGCCGTAATAGAGTTGTAA
1 TTTAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTTGTAA
** * * *
1979075 TTTAGCAGCG-TTTTTAGCTCAAACGTCGCAATTGAGTTGT--
1 TTTAGCAGCGTTTTTTA-AACAAACGCCGAAATAGAGTTGTAA
** * * *
1979115 TTATAGTGGCGTTTTTTCAACAAACACCGAAATAGAGTGGTAA
1 TT-TAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTTGTAA
* *
1979158 TGTAGCGGCGTTTTT
1 TTTAGCAGCGTTTTT
1979173 GTACAAACGC
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
40 2 0.03
41 28 0.37
42 45 0.59
43 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (42 bp):
TTTAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTTGTAA
Done.