Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 137 of 210
Found at i:41667793 original size:2 final size:2
Alignment explanation
Indices: 41667786--41667824 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41667776 CAAAATAAGG
41667786 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
41667825 GATGGTATGA
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:41671287 original size:12 final size:14
Alignment explanation
Indices: 41671255--41671291 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
41671245 TTTTACATTG
*
41671255 CAATTCATCATATT
1 CAATTTATCATATT
41671269 CAATTTATCA-ATT
1 CAATTTATCATATT
41671282 -AATTTATCAT
1 CAATTTATCAT
41671292 TTTCTTCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 9 0.43
13 3 0.14
14 9 0.43
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (14 bp):
CAATTTATCATATT
Found at i:41679969 original size:138 final size:137
Alignment explanation
Indices: 41679560--41679970 Score: 495
Period size: 138 Copynumber: 3.0 Consensus size: 137
41679550 ATGTCATTAG
* * *
41679560 GGTTACCATGTTTTGGATGCTAGTCTTGAATGTCCTATC-AGTGGCTGA-GTTTCAG-ATGTGTT
1 GGTTACCATGTTTCGGATGCTGGTCTTGAATGTCCTATCGA-TGGCTGAGGTCT-AGAAT-TGTT
* *
41679622 GCGGATACTTGACAGCTTGTGTGAGTAACATCGTGTAGCTTACATTCCGATCGACAGCTTGTGTG
63 GCGGATACTTGACAGCTTGTGTGAGCAACATCGTGTAGCTTACATTCCGACCGACAGCTTGTGTG
* *
41679687 AGTAGAACTA
128 AGCAGACCTA
* * * * * * * * **
41679697 GGTTATCATGTTTCGGGTGTTGGTCTTGAATGTCCTATCGGTGGCTAAGTTTCAATACGTGTTGC
1 GGTTACCATGTTTCGGATGCTGGTCTTGAATGTCCTATCGATGGCTGAG-GTCTAGAATTGTTGC
* *
41679762 AGATACTTGACAGCTTGTGTGAGCAACACCGTGTAGCTTACATTCCGACCGACAGCTTGTGTGAG
65 GGATACTTGACAGCTTGTGTGAGCAACATCGTGTAGCTTACATTCCGACCGACAGCTTGTGTGAG
41679827 CAGACCTA
130 CAGACCTA
* * * *
41679835 GGTTACCATGTTTCGGATGCTGGTCTTGAATGTCTTACCGATGGATGAGGTCTAGAATTAGTTGT
1 GGTTACCATGTTTCGGATGCTGGTCTTGAATGTCCTATCGATGGCTGAGGTCTAGAATT-GTTGC
* * * * * *
41679900 GGATACTCGATAGCTTGTGTGAGCAACATCGTCTAGCTTACATTTCAACCGATAGCTTGTGTGAG
65 GGATACTTGACAGCTTGTGTGAGCAACATCGTGTAGCTTACATTCCGACCGACAGCTTGTGTGAG
41679965 CAGACC
130 CAGACC
41679971 CATTTTACAG
Statistics
Matches: 228, Mismatches: 41, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
137 45 0.20
138 182 0.80
139 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (137 bp):
GGTTACCATGTTTCGGATGCTGGTCTTGAATGTCCTATCGATGGCTGAGGTCTAGAATTGTTGCG
GATACTTGACAGCTTGTGTGAGCAACATCGTGTAGCTTACATTCCGACCGACAGCTTGTGTGAGC
AGACCTA
Found at i:41685883 original size:14 final size:14
Alignment explanation
Indices: 41685864--41685893 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41685854 CCTCCCTTGG
41685864 GTACGATCCTCGGA
1 GTACGATCCTCGGA
41685878 GTACGATCCTCGGA
1 GTACGATCCTCGGA
41685892 GT
1 GT
41685894 TGTAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (14 bp):
GTACGATCCTCGGA
Found at i:41708092 original size:21 final size:21
Alignment explanation
Indices: 41708068--41708124 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
41708058 TGAATAGTGT
* *
41708068 TGTGGTTGCATCTGATTTTGA
1 TGTGGATGCATCTGACTTTGA
* *
41708089 TGTGGATGCATCTGGCTTTGT
1 TGTGGATGCATCTGACTTTGA
41708110 TGTGGATGCATCTGA
1 TGTGGATGCATCTGA
41708125 GTATGCTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.14, C:0.12, G:0.32, T:0.42
Consensus pattern (21 bp):
TGTGGATGCATCTGACTTTGA
Found at i:41728600 original size:50 final size:50
Alignment explanation
Indices: 41728492--41728622 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 50
41728482 GAGGTTCAGT
* * * ** *
41728492 GTAACACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * *
41728542 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * *
41728592 GTAGGACCATATCTGGGATATGGCATTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
41728623 GTACTAGAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
Found at i:41728651 original size:49 final size:49
Alignment explanation
Indices: 41728491--41728662 Score: 143
Period size: 50 Copynumber: 3.5 Consensus size: 49
41728481 AGAGGTTCAG
* * * * * * ** *
41728491 TGTAACACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATATCTGGGACATGGCATGGGCA-CGATATGAGAACTCCCA
* *
41728541 CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCA
1 TGTAAGACCATATCTGGGACATGGCATGGGCA-CGATATGAGAACTCCCA
* * *
41728591 TGTAGGACCATATCTGGGATATGGCATTGGCA-G-TACT-AGAAACATCCCA
1 TGTAAGACCATATCTGGGACATGGCATGGGCACGATA-TGAG-AAC-TCCCA
*
41728640 TGTAAGACCATATATGGGACATG
1 TGTAAGACCATATCTGGGACATG
41728663 ACTTTGGCAT
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
47 4 0.04
48 5 0.05
49 25 0.25
50 68 0.67
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (49 bp):
TGTAAGACCATATCTGGGACATGGCATGGGCACGATATGAGAACTCCCA
Found at i:41736460 original size:42 final size:42
Alignment explanation
Indices: 41736409--41736649 Score: 270
Period size: 43 Copynumber: 5.7 Consensus size: 42
41736399 TTATATGGAA
* * * *
41736409 AAACGCCGCTATAGAACATGACTTTTAGCGGTGCTTCCTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCCCCAC
* * * * *
41736451 AAATGCCGCTATAGAACATGACCTTTACCGGTGCTGCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCCCCAC
*
41736493 AAA-GACCTCTAAAGAACATGACCTTTAGCGGCGCTTACCCCAC
1 AAACG-CCGCTAAAGAACATGACCTTTAGCGGCGCTT-CCCCAC
* * * *
41736536 AAACGCTGCTAGAA-AACATGACATTTATCAGCGCTTTCCCCAC
1 AAACGCCGCTA-AAGAACATGACCTTTAGCGGCGC-TTCCCCAC
* * *
41736579 AAATGCCGCTAAAAAACATGACCTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTCCCCAC
41736622 AAACGCCGCTAAAGAACATGACCTTTAG
1 AAACGCCGCTAAAGAACATGACCTTTAG
41736650 TGAAATTTCC
Statistics
Matches: 170, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.40
43 96 0.56
44 5 0.03
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCCCCAC
Found at i:41736672 original size:42 final size:43
Alignment explanation
Indices: 41736407--41736677 Score: 165
Period size: 43 Copynumber: 6.4 Consensus size: 43
41736397 GTTTATATGG
* * *** *
41736407 AAAAACGCCGCTATAGAACATGACTTTTAGCGG-TGCTTCCTC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
* * * * *** *
41736449 ACAAATGCCGCTATAGAACATGACCTTTACCGG-TGCTGCCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
* * *** *
41736491 ACAAA-GACCTCTAAAGAACATGACCTTTAGCGGCGCTTACCCC
1 AAAAACG-CCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
* * * * * ***
41736534 ACAAACGCTGCTAGAA-AACATGACATTTATCAGCGCTTTCCCC
1 AAAAACGCCGCTA-AAGAACATGACCTTTAGCGGAAATTTCCCC
* * * * *
41736577 ACAAATGCCGCTAAAAAACATGACCTTTAGCGGCACTTTCCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
* * *
41736620 ACAAACGCCGCTAAAGAACATGACCTTTAG-TGAAATTTCCTC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
41736662 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
41736678 GTCATGTTCT
Statistics
Matches: 192, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 89 0.46
43 99 0.52
44 3 0.02
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGAAATTTCCCC
Found at i:41746006 original size:9 final size:9
Alignment explanation
Indices: 41745989--41746020 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
41745979 TATTTATGTA
*
41745989 TTATATAAG
1 TTATGTAAG
41745998 TTATGTAAG
1 TTATGTAAG
41746007 TTATGTAAG
1 TTATGTAAG
41746016 TTATG
1 TTATG
41746021 ATCCAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41746091 original size:13 final size:13
Alignment explanation
Indices: 41746073--41746098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41746063 GATTATCATT
41746073 TTTAAATTTTAAC
1 TTTAAATTTTAAC
41746086 TTTAAATTTTAAC
1 TTTAAATTTTAAC
41746099 CCTTTAATTA
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTTTAAC
Found at i:41746755 original size:20 final size:21
Alignment explanation
Indices: 41746730--41746773 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
41746720 AAGTTATCTT
41746730 AAATTTTAAAAT-AAAAATAA
1 AAATTTTAAAATCAAAAATAA
* *
41746750 AAA-TTTAGAATCAAAACTAA
1 AAATTTTAAAATCAAAAATAA
41746770 AAAT
1 AAAT
41746774 AAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTTTAAAATCAAAAATAA
Found at i:41746785 original size:20 final size:19
Alignment explanation
Indices: 41746739--41746786 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
41746729 TAAATTTTAA
**
41746739 AATAAAAATAAAAATTTAG
1 AATAAAAATAAAAATAAAG
* *
41746758 AATCAAAACTAAAAATAAAT
1 AAT-AAAAATAAAAATAAAG
41746778 AATAAAAAT
1 AATAAAAAT
41746787 TGGATTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:41748455 original size:26 final size:26
Alignment explanation
Indices: 41748408--41748462 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
41748398 AACACACCAA
* *
41748408 TATCGCAGCAAAGCTGCAAGTAATAG
1 TATCGCAGCAAAGCTACAAGTAACAG
* *
41748434 TATCGCAGCAAAGTTACCAGTAACAG
1 TATCGCAGCAAAGCTACAAGTAACAG
41748460 TAT
1 TAT
41748463 ATGTGGTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACAAGTAACAG
Found at i:41748620 original size:27 final size:27
Alignment explanation
Indices: 41748603--41748826 Score: 258
Period size: 27 Copynumber: 8.3 Consensus size: 27
41748593 GGGTATAACA
*
41748603 GTCATTTTACCCTATAGGGGAATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
41748630 GTCATTTTACTCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
41748657 ATCATTTTACCCTAT-GGGGTTATTTTG
1 GTCATTTTACCCTATAGGGG-TATTTCG
* *
41748684 GTCATTTTACCCTA-CGAGGGTATTTTG
1 GTCATTTTACCCTATAG-GGGTATTTCG
* * *
41748711 ATCATTTTACCCTACAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
41748738 GTCATTTTATCCTA-CGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCG
*
41748764 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
41748791 GTCATTTTACCCTAT-GAGGGTATTTTG
1 GTCATTTTACCCTATAG-GGGTATTTCG
41748818 GTCATTTTA
1 GTCATTTTA
41748827 TTAACCTCAC
Statistics
Matches: 173, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
26 27 0.16
27 142 0.82
28 4 0.02
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:41748650 original size:54 final size:55
Alignment explanation
Indices: 41748604--41748815 Score: 290
Period size: 54 Copynumber: 3.9 Consensus size: 55
41748594 GGTATAACAG
* * *
41748604 TCATTTTACCCTATAGGGGAATTTCGGTCATTTTACTCTATGGGGGTATTTC-GA
1 TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAGA
* * *
41748658 TCATTTTACCCTAT-GGGGTTATTTTGGTCATTTTACCCTACGAGGGTATTT-TGA
1 TCATTTTACCCTATAGGGG-TATTTTGGTCATTTTACCCTATGGGGGTATTTCAGA
* * *
41748712 TCATTTTACCCTACAGGGGTATTTTGGTCATTTTATCCTA-CGGGGTATTTCAG-
1 TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAGA
*
41748765 TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
1 TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTT
41748816 TGGTCATTTT
Statistics
Matches: 139, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
53 50 0.36
54 85 0.61
55 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (55 bp):
TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAGA
Found at i:41748796 original size:80 final size:78
Alignment explanation
Indices: 41748587--41748827 Score: 286
Period size: 80 Copynumber: 3.0 Consensus size: 78
41748577 TTATTTAATC
** * * * *
41748587 TCCTAGGGGTATAACAGTCATTTTACCCTATAGGGGAATTTCGGTCATTTTACTCTATGGGGGTA
1 TCCTAGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTA-AGGGGTA
* *
41748652 TTTCGATCATTTTA
65 TTTTGGTCATTTTA
* ** * *
41748666 CCCTATGGGGTTATTTTGGTCATTTTACCCTA-CGAGGGTATTTTGATCATTTTACCCTACAGGG
1 TCCTA-GGGG-TATTTCAGTCATTTTACCCTATAG-GGGTATTTTGGTCATTTTACCCTA-AGGG
41748730 GTATTTTGGTCATTTTA
62 GTATTTTGGTCATTTTA
*
41748747 TCCTACGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGAGGGT
1 TCCTA-GGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTAAG-GGGT
41748812 ATTTTGGTCATTTTA
64 ATTTTGGTCATTTTA
41748827 T
1 T
41748828 TAACCTCACG
Statistics
Matches: 136, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
79 5 0.04
80 67 0.49
81 64 0.47
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (78 bp):
TCCTAGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTAAGGGGTAT
TTTGGTCATTTTA
Found at i:41748798 original size:107 final size:108
Alignment explanation
Indices: 41748604--41748826 Score: 337
Period size: 107 Copynumber: 2.1 Consensus size: 108
41748594 GGTATAACAG
* *
41748604 TCATTTTACCCTATAGGGGAATTTCGGTCATTTTACTCTATGGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTACAGGGGAATTTCGGTCATTTTACTCTATCGGGGTATTTCGATCATTTTACCC
41748669 TATGGGGTTATTTTGGTCATTTTACCCTACGAGGGTATTTTGA
66 TATGGGGTTATTTTGGTCATTTTACCCTACGAGGGTATTTTGA
* *
41748712 TCATTTTACCCTACAGGGGTATTTTGGTCATTTTA-TCCTA-CGGGGTATTTC-AGTCATTTTAC
1 TCATTTTACCCTACAGGGGAATTTCGGTCATTTTACT-CTATCGGGGTATTTCGA-TCATTTTAC
* *
41748774 CCTATAGGGG-TATTTTGGTCATTTTACCCTATGAGGGTATTTTGG
64 CCTAT-GGGGTTATTTTGGTCATTTTACCCTACGAGGGTATTTTGA
41748819 TCATTTTA
1 TCATTTTA
41748827 TTAACCTCAC
Statistics
Matches: 106, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
106 1 0.01
107 66 0.62
108 39 0.37
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (108 bp):
TCATTTTACCCTACAGGGGAATTTCGGTCATTTTACTCTATCGGGGTATTTCGATCATTTTACCC
TATGGGGTTATTTTGGTCATTTTACCCTACGAGGGTATTTTGA
Found at i:41756159 original size:16 final size:17
Alignment explanation
Indices: 41756123--41756160 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
41756113 AGTATTTCAT
*
41756123 GTCATAAATCATATACA
1 GTCATAAATCAAATACA
41756140 -TCATAAATCAAAT-CA
1 GTCATAAATCAAATACA
41756155 GTCATA
1 GTCATA
41756161 CATAACATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (17 bp):
GTCATAAATCAAATACA
Found at i:41756327 original size:81 final size:82
Alignment explanation
Indices: 41756211--41756431 Score: 331
Period size: 81 Copynumber: 2.7 Consensus size: 82
41756201 TATAATAGTC
* * * *
41756211 ATTTTACCCTATAAGGGTATTTCGATCATTTTACCCTATGAGGGTATTTCGGTCATTTTAAC-CT
1 ATTTTACCCTACAGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTAACGCT
41756275 ATGGGGGTATTTTGGTT
66 ATGGGGGTATTTTGGTT
* * * * *
41756292 ATTTTACCCTACAGGGGTATTTCGGTCAATCTACCCTACAAGGGTATTTTGGTCATTTT-ACGTT
1 ATTTTACCCTACAGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTAACGCT
41756356 ATGGGGGTATTTTGGTT
66 ATGGGGGTATTTTGGTT
*
41756373 ATTTTACCCTAC-GGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTA
1 ATTTTACCCTACAGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTA
41756432 TTGACTTCAC
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 43 0.35
81 81 0.65
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (82 bp):
ATTTTACCCTACAGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTAACGCT
ATGGGGGTATTTTGGTT
Found at i:41756425 original size:27 final size:27
Alignment explanation
Indices: 41756208--41756431 Score: 243
Period size: 27 Copynumber: 8.3 Consensus size: 27
41756198 GGGTATAATA
41756208 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* *
41756235 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* ** *
41756262 GTCATTTTAACCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTCG
* * *
41756289 GTTATTTTACCCTACAGGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
* * * *
41756316 GTCAATCTACCCTACAAGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTCG
** ** *
41756343 GTCATTTTACGTTATGGGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTCG
* ** *
41756370 GTTATTTTACCCTA-CGGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTCG
41756396 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATAAGGGTATTTCG
41756423 GTCATTTTA
1 GTCATTTTA
41756432 TTGACTTCAC
Statistics
Matches: 165, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 24 0.15
27 141 0.85
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATAAGGGTATTTCG
Found at i:41757086 original size:35 final size:35
Alignment explanation
Indices: 41757040--41757109 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
41757030 CTTCATCCCT
41757040 TTGAAAAGTTCCTAGGCACCAACCGAAACTGGGTA
1 TTGAAAAGTTCCTAGGCACCAACCGAAACTGGGTA
41757075 TTGAAAAGTTCCTAGGCACCAACCGAAACTGGGTA
1 TTGAAAAGTTCCTAGGCACCAACCGAAACTGGGTA
41757110 AGCACTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (35 bp):
TTGAAAAGTTCCTAGGCACCAACCGAAACTGGGTA
Found at i:41766048 original size:19 final size:19
Alignment explanation
Indices: 41766019--41766062 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41766009 TGGGGCACAC
* *
41766019 GACCATGTGAAATCATGCA
1 GACCGTGTGAAATCAGGCA
*
41766038 GGCCGTGTGAAATCAGGCA
1 GACCGTGTGAAATCAGGCA
41766057 GACCGT
1 GACCGT
41766063 ATGGGTAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (19 bp):
GACCGTGTGAAATCAGGCA
Found at i:41769542 original size:27 final size:28
Alignment explanation
Indices: 41769482--41769542 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
41769472 TAATATTGAA
*
41769482 TAGTAAATTTTAATTAAAAATTCAAAGT
1 TAGTAAAATTTAATTAAAAATTCAAAGT
* *
41769510 TGGTAAAATTTAA-T-AAAATTCAAAATT
1 TAGTAAAATTTAATTAAAAATTC-AAAGT
41769537 TAGTAA
1 TAGTAA
41769543 TAAAAATCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.25
27 10 0.36
28 11 0.39
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (28 bp):
TAGTAAAATTTAATTAAAAATTCAAAGT
Found at i:41771856 original size:16 final size:18
Alignment explanation
Indices: 41771830--41771862 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41771820 TAAATGTAAA
41771830 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
41771847 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
41771863 CACAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:41785418 original size:9 final size:9
Alignment explanation
Indices: 41785404--41785440 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
41785394 TCAGTTTAAT
41785404 ATGTGTTTA
1 ATGTGTTTA
41785413 ATGTGTTTA
1 ATGTGTTTA
41785422 ATGTGTTTTTA
1 ATGTG--TTTA
41785433 ATGTGTTT
1 ATGTGTTT
41785441 TGATTGTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 17 0.65
11 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:41785422 original size:20 final size:20
Alignment explanation
Indices: 41785397--41785440 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41785387 TGCTTATTCA
41785397 GTTTAATATGTGTTTAATGT
1 GTTTAATATGTGTTTAATGT
* *
41785417 GTTTAATGTGTTTTTAATGT
1 GTTTAATATGTGTTTAATGT
41785437 GTTT
1 GTTT
41785441 TGATTGTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (20 bp):
GTTTAATATGTGTTTAATGT
Found at i:41785435 original size:11 final size:11
Alignment explanation
Indices: 41785398--41785441 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
41785388 GCTTATTCAG
* *
41785398 TTTAATATGTG
1 TTTAATGTGTT
41785409 TTTAATGTG--
1 TTTAATGTGTT
41785418 TTTAATGTGTT
1 TTTAATGTGTT
41785429 TTTAATGTGTT
1 TTTAATGTGTT
41785440 TT
1 TT
41785442 GATTGTACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (11 bp):
TTTAATGTGTT
Found at i:41785588 original size:24 final size:23
Alignment explanation
Indices: 41785552--41785634 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 23
41785542 CAAAGGGCTA
*
41785552 TTACATCAATTAAATGAGAGCATT
1 TTACATCATTTAAA-GAGAGCATT
41785576 TTACATCATTTAAAG-GAG--TT
1 TTACATCATTTAAAGAGAGCATT
*
41785596 GTTACGTCATTTAAAAGAGAGCATT
1 -TTACATCATTT-AAAGAGAGCATT
* *
41785621 ATACATCCTTTAAA
1 TTACATCATTTAAA
41785635 ATTCGGCAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 7 0.14
23 7 0.14
24 21 0.43
25 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
TTACATCATTTAAAGAGAGCATT
Found at i:41792277 original size:50 final size:50
Alignment explanation
Indices: 41792180--41792296 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
41792170 GTTATCAGAG
* * * *
41792180 GTCCCACGTAAGACCATTTCTGAGACATGGCATTGGTACCGAGATGAGAT
1 GTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAAATGAGAT
* * *
41792230 GTCCCCCGTAAGACCATGTCTG-GCACATGGCATGGGCACGGAAATGAGAA
1 GTCCCACGTAAGACCATGTCTGAG-ACATGGCATGGGCACCGAAATGAGAT
* * *
41792280 CTCTCATGTAAGACCAT
1 GTCCCACGTAAGACCAT
41792297 ATCTAGGATA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 1 0.02
50 54 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (50 bp):
GTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAAATGAGAT
Found at i:41797500 original size:12 final size:12
Alignment explanation
Indices: 41797475--41797513 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41797465 CTTTGCTTCT
* *
41797475 TTACTTACTCAC
1 TTACTTGCTTAC
*
41797487 TTACTTGTTTAC
1 TTACTTGCTTAC
41797499 TTACTTGCTTAC
1 TTACTTGCTTAC
41797511 TTA
1 TTA
41797514 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:41797838 original size:50 final size:50
Alignment explanation
Indices: 41797763--41797955 Score: 179
Period size: 50 Copynumber: 3.7 Consensus size: 50
41797753 TTTTCTGTAT
* * * ** *
41797763 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCAG
* * * *
41797813 TGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCAG
* * * * *
41797863 TACCAACGCCATGTCCCAGACATGGTCTCACGTGGGACCTCTTATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT-A--TC---AG
* *
41797919 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
41797956 TCTCATCCCT
Statistics
Matches: 113, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
50 78 0.69
53 2 0.02
56 33 0.29
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCAG
Found at i:41798657 original size:69 final size:69
Alignment explanation
Indices: 41798546--41798685 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
41798536 TAATTTCAAG
41798546 CTTCATATTATACCATAAAACATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATG
1 CTTCATATTATACCATAAAACATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATG
*
41798611 ATCT
66 AACT
*
41798615 CTTCATATTCTACCATAAAACATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATG
1 CTTCATATTATACCATAAAACATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATG
41798680 AACT
66 AACT
41798684 CT
1 CT
41798686 AACATGAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (69 bp):
CTTCATATTATACCATAAAACATCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATG
AACT
Found at i:41802915 original size:50 final size:48
Alignment explanation
Indices: 41802835--41802956 Score: 138
Period size: 50 Copynumber: 2.5 Consensus size: 48
41802825 TCCCAAATAC
* *
41802835 GACCATGTCTGGGACATGGCGTTGGTACCGAGATGAGAGGTCTCCC-GTAA
1 GACCATGTCTGGGACATGGC-ATGGCACCGAGATGAGA--TCTCCCAGTAA
* *
41802885 GACCATGTCTGGCACATGGCATGGCCACCGATATGAGATCTCCCATGTAA
1 GACCATGTCTGGGACATGGCATGG-CACCGAGATGAGATCTCCCA-GTAA
* *
41802935 GACCATATCTGGGATATGGCAT
1 GACCATGTCTGGGACATGGCAT
41802957 TTGCAGTACC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 6 0.10
49 3 0.05
50 53 0.85
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (48 bp):
GACCATGTCTGGGACATGGCATGGCACCGAGATGAGATCTCCCAGTAA
Found at i:41805006 original size:11 final size:11
Alignment explanation
Indices: 41804960--41805024 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
41804950 GCTTATTAAA
*
41804960 TTTAATATGTGT
1 TTTAATGTGT-T
*
41804972 TTAAATGTG--
1 TTTAATGTGTT
41804981 TTTAATGTG--
1 TTTAATGTGTT
41804990 TTTAATGTGTT
1 TTTAATGTGTT
41805001 TTTAATGTGTT
1 TTTAATGTGTT
41805012 TTTAATGTGTT
1 TTTAATGTGTT
41805023 TT
1 TT
41805025 GATTATAGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
9 17 0.35
11 24 0.50
12 7 0.15
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (11 bp):
TTTAATGTGTT
Found at i:41815071 original size:22 final size:22
Alignment explanation
Indices: 41815033--41815076 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41815023 AAAGTCTAAA
*
41815033 TATTTATTTATTCATTTGTTTT
1 TATTTATTTATTCATTTATTTT
*
41815055 TATTTATTT-TTAGATTTATTTT
1 TATTTATTTATT-CATTTATTTT
41815077 CTTTTGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (22 bp):
TATTTATTTATTCATTTATTTT
Found at i:41815888 original size:19 final size:20
Alignment explanation
Indices: 41815864--41815902 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
41815854 GTGTAGACCC
41815864 CCACACGGCC-TAGGCACTT
1 CCACACGGCCGTAGGCACTT
*
41815883 CCACACGGCCGTAGGGACTT
1 CCACACGGCCGTAGGCACTT
41815903 ATGTTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
CCACACGGCCGTAGGCACTT
Found at i:41816418 original size:38 final size:38
Alignment explanation
Indices: 41816342--41816420 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
41816332 TGGTGTGTAG
* *
41816342 GGTTGGATGGGCCTTCCAAAGTCATATGTGGTATGCAT
1 GGTTGGATGGGCCTTCCAAAGTCATATGTGGGACGCAT
* *
41816380 GGTTGGATGGG-CTT-GAATAGCTCATATGTGGGGCGCAT
1 GGTTGGATGGGCCTTCCAA-AG-TCATATGTGGGACGCAT
41816418 GGT
1 GGT
41816421 GATCAGAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 2 0.06
37 5 0.14
38 28 0.80
ACGTcount: A:0.19, C:0.14, G:0.37, T:0.30
Consensus pattern (38 bp):
GGTTGGATGGGCCTTCCAAAGTCATATGTGGGACGCAT
Found at i:41834514 original size:39 final size:39
Alignment explanation
Indices: 41834471--41834585 Score: 196
Period size: 39 Copynumber: 2.9 Consensus size: 39
41834461 AACATGTTTT
*
41834471 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
41834510 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
41834549 TGAGTATTGTGATATATGCCTAAAAT-TTATGTGATTA
1 TGAGTATTGTGATATATG-CTTAAATGTTATGTGATTA
41834586 ATGTGGACAT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
39 67 0.92
40 6 0.08
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:41837080 original size:12 final size:12
Alignment explanation
Indices: 41837060--41837089 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41837050 CTAATTTGCC
*
41837060 ATCAATTATCCA
1 ATCACTTATCCA
41837072 ATCACTTATCCA
1 ATCACTTATCCA
41837084 ATCACT
1 ATCACT
41837090 GAAAACAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (12 bp):
ATCACTTATCCA
Found at i:41841492 original size:182 final size:182
Alignment explanation
Indices: 41841185--41841554 Score: 659
Period size: 182 Copynumber: 2.0 Consensus size: 182
41841175 ATGTTTTCTT
*
41841185 TCTTTAACACATCCATCATAATAAGGTTCAGTCTCTATTGTCTATCAATCATCCATTTCTGACCA
1 TCTTTAACACATCCATCATAATAAGGTTCAGTCACTATTGTCTATCAATCATCCATTTCTGACCA
*
41841250 TATTCTAAGATGATCTTGTGCATGTACATGAATAGACTAATACCAAGAATATCAACTATGGTCCA
66 TATTCTAAGATGATCTTGTGCATGTACACGAATAGACTAATACCAAGAATATCAACTATGGTCCA
* *
41841315 TCTGGTAGCCTTCTTGAATTGTTTCAGCACTAAAATAAGTTTATCTTCTTGA
131 TCTAGTAGCCTTCTTGAATTGTTTCAGCACTAAAATAAGTTTATCTTATTGA
* *
41841367 TCTTTAACACATCCATCATAATAGGGTTCAGTCACTATTGTCTATCAATCATCCATTTCTTACCA
1 TCTTTAACACATCCATCATAATAAGGTTCAGTCACTATTGTCTATCAATCATCCATTTCTGACCA
* *
41841432 TATTCTAAGATGATCTTGTGCATGTACACGGATGGACTAATACCAAGAATATCAACTATGGTCCA
66 TATTCTAAGATGATCTTGTGCATGTACACGAATAGACTAATACCAAGAATATCAACTATGGTCCA
41841497 TCTAGTAGCCTTCTTGAATTGTTTCAGCACTAAAATAAGTTTATCTTATTGA
131 TCTAGTAGCCTTCTTGAATTGTTTCAGCACTAAAATAAGTTTATCTTATTGA
*
41841549 CCTTTA
1 TCTTTA
41841555 GTTAAATCTA
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 179 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (182 bp):
TCTTTAACACATCCATCATAATAAGGTTCAGTCACTATTGTCTATCAATCATCCATTTCTGACCA
TATTCTAAGATGATCTTGTGCATGTACACGAATAGACTAATACCAAGAATATCAACTATGGTCCA
TCTAGTAGCCTTCTTGAATTGTTTCAGCACTAAAATAAGTTTATCTTATTGA
Found at i:41850626 original size:15 final size:16
Alignment explanation
Indices: 41850606--41850635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41850596 AGTACTAATA
41850606 ATAAAA-GAAAATAAC
1 ATAAAAGGAAAATAAC
41850621 ATAAAAGGAAAATAA
1 ATAAAAGGAAAATAA
41850636 GTTTCAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (16 bp):
ATAAAAGGAAAATAAC
Found at i:41855676 original size:29 final size:29
Alignment explanation
Indices: 41855630--41855687 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41855620 TTTCAAATGT
41855630 AGTTTATATCCTCGATTTGTTGATACTTA
1 AGTTTATATCCTCGATTTGTTGATACTTA
*
41855659 AGTTTATATCCTCTATTTGTTGATACTTA
1 AGTTTATATCCTCGATTTGTTGATACTTA
41855688 TCATCCTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (29 bp):
AGTTTATATCCTCGATTTGTTGATACTTA
Found at i:41869993 original size:26 final size:26
Alignment explanation
Indices: 41869964--41870034 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
41869954 CACCAATATC
* *
41869964 GCAGCAAAACTGCTAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAATAGTGAT
41869990 GCAGCAAAGCTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAATAGTGAT
41870016 GCAGCAAAGCTGCCAGTAA
1 GCAGCAAAGCTGCCAGTAA
41870035 CAGTATATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTGAT
Found at i:41870527 original size:27 final size:27
Alignment explanation
Indices: 41870182--41870539 Score: 422
Period size: 27 Copynumber: 13.3 Consensus size: 27
41870172 GGTGTAACAG
* *
41870182 TCATTTTACCCTTCGCGGGTATTT-TA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870208 GTCATTTTACCCTTCAAGGGTATTTCAA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870236 TCATTTTATCCTTCGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * * *
41870263 ACATTTTACCATTTGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870290 TCATTTTACCTTTCG-GGGCTAATTTTG-
1 TCATTTTACCCTTCGAGGG-T-ATTTCGA
41870317 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870344 TCATTTTA-CCTGTCTAGGGTATTTCGG
1 TCATTTTACCCT-TCGAGGGTATTTCGA
*
41870371 TCATTTTACCCTTC-ATGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCGA
*
41870398 TCAATTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
41870425 TCATTTTACCCTTCAAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870452 TCATTTTACCCTTCGGGGGT-TTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
41870478 TCAGTTTACCCTTCGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
41870505 TCATTTTACCCGTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
41870532 TTATTTTA
1 TCATTTTA
41870540 GGCCCATTAC
Statistics
Matches: 287, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
26 35 0.12
27 239 0.83
28 13 0.05
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:41877404 original size:28 final size:28
Alignment explanation
Indices: 41877373--41877467 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
41877363 CCTAAGCCTT
* * *
41877373 ATACAGCAATAGTGTGGGCCATAACTCA
1 ATACAGTAACAGTGTGGGCCATAACCCA
* * *
41877401 ATACAGTAACAGTGTAGGCCTTAGCCCA
1 ATACAGTAACAGTGTGGGCCATAACCCA
* * **
41877429 ATACAGTAACAGCGTGGGCCTTAGTCCA
1 ATACAGTAACAGTGTGGGCCATAACCCA
*
41877457 ATACATTAACA
1 ATACAGTAACA
41877468 ATACAATGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (28 bp):
ATACAGTAACAGTGTGGGCCATAACCCA
Found at i:41877605 original size:26 final size:26
Alignment explanation
Indices: 41877576--41877640 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
41877566 CACCAATATC
* *
41877576 GCAGCAAAGTTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAATAATAGTGAT
*
41877602 GCAGTAAAGCTGCCAATAATAGTGAT
1 GCAGCAAAGCTGCCAATAATAGTGAT
*
41877628 GCAGCAAAACTGC
1 GCAGCAAAGCTGC
41877641 TAGTAACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAATAATAGTGAT
Found at i:41877848 original size:27 final size:27
Alignment explanation
Indices: 41877824--41878238 Score: 491
Period size: 27 Copynumber: 15.4 Consensus size: 27
41877814 AGGGGTATAA
41877824 CAGTCATTTTACCCTTC-AGGCGTATTT
1 CAGTCATTTTACCCTTCGAGG-GTATTT
* *
41877851 CAATCATTTTACCCTTCGAGGTTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
41877878 CAATCATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * *
41877905 CAATTATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
41877932 CAATTATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
**
41877959 CAGTCATTTTA-CCTTTTAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
**
41877985 CAGTCATTTTACCCTTCGAGGAAATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
41878012 -TGATCATTTTACCCTTCTG-GGGTATTT
1 CAG-TCATTTTACCCTTC-GAGGGTATTT
* * *
41878039 CGGTCATTTTACCGTTCGAGGGTACGTT
1 CAGTCATTTTACCCTTCGAGGGTA-TTT
*
41878067 -GGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
41878093 CAGTCATTTTACCCTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
41878120 CGGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
41878147 CAGTCATTTTACCCTTTGAGAGG-ATTT
1 CAGTCATTTTACCCTTCGAG-GGTATTT
*
41878174 CGGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * * *
41878201 CGGTTAGTTTACCCTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
**
41878228 TGGTCATTTTA
1 CAGTCATTTTA
41878239 GGCCCATTAC
Statistics
Matches: 342, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
26 30 0.09
27 303 0.89
28 9 0.03
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:41881361 original size:29 final size:29
Alignment explanation
Indices: 41881324--41881399 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
41881314 TAAACGCCGG
* * *
41881324 TACAAAGTACCTGATAATGTAATCACTGA
1 TACATAGTACCTGATAATATAAACACTGA
*
41881353 TACATAGTACCTGATAATATAAACACTGG
1 TACATAGTACCTGATAATATAAACACTGA
* * *
41881382 CACATAGTGCCTAATAAT
1 TACATAGTACCTGATAAT
41881400 CCCTAATGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (29 bp):
TACATAGTACCTGATAATATAAACACTGA
Found at i:41885599 original size:16 final size:15
Alignment explanation
Indices: 41885580--41885621 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
41885570 CTAAATATAA
41885580 GTTGTTCAAAACAATG
1 GTTGTTCAAAAC-ATG
*
41885596 GTTGTTCTAAACATG
1 GTTGTTCAAAACATG
*
41885611 GTTATTCAAAA
1 GTTGTTCAAAA
41885622 AATTCCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (15 bp):
GTTGTTCAAAACATG
Found at i:41885613 original size:15 final size:15
Alignment explanation
Indices: 41885566--41885613 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
41885556 AAAAAACAGA
* *
41885566 TGTTCTAAATATAAGT
1 TGTTCTAAACAT-GGT
*
41885582 TGTTCAAAACAATGGT
1 TGTTCTAAAC-ATGGT
41885598 TGTTCTAAACATGGT
1 TGTTCTAAACATGGT
41885613 T
1 T
41885614 ATTCAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.22
16 19 0.70
17 2 0.07
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (15 bp):
TGTTCTAAACATGGT
Found at i:41887059 original size:10 final size:10
Alignment explanation
Indices: 41887046--41887070 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41887036 TAATGAAAGT
41887046 TTAAACAAAA
1 TTAAACAAAA
41887056 TTAAACAAAA
1 TTAAACAAAA
41887066 TTAAA
1 TTAAA
41887071 GAATGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAACAAAA
Found at i:41888049 original size:21 final size:21
Alignment explanation
Indices: 41888023--41888064 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41888013 TCGGGTGGAC
*
41888023 CAGCTCTTATGAGCTTCTGTT
1 CAGCTCTTATGAGCATCTGTT
*
41888044 CAGCTCTTTTGAGCATCTGTT
1 CAGCTCTTATGAGCATCTGTT
41888065 GGCTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
CAGCTCTTATGAGCATCTGTT
Found at i:41888102 original size:39 final size:40
Alignment explanation
Indices: 41888043--41888140 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
41888033 GAGCTTCTGT
* * * * *
41888043 TCAGCTCTTTTGAGCATCTG-TTGGCTTGTTTTGGGTGGA
1 TCAGCTCTTATGAGCTTCTGTTTGGCGTATTTCGGGTGGA
*
41888082 -CTAGCTCTTATGAGCTTCTGTTTGGCGTATTTCGGTTGGA
1 TC-AGCTCTTATGAGCTTCTGTTTGGCGTATTTCGGGTGGA
41888122 TCAGCTCTTATGAGCTTCT
1 TCAGCTCTTATGAGCTTCT
41888141 CTCTGGTGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.02
39 16 0.32
40 32 0.64
41 1 0.02
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (40 bp):
TCAGCTCTTATGAGCTTCTGTTTGGCGTATTTCGGGTGGA
Found at i:41890759 original size:16 final size:19
Alignment explanation
Indices: 41890733--41890770 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
41890723 TTAAATTAAC
41890733 TAAATTAA-TTTCTCAA-T
1 TAAATTAATTTTCTCAACT
41890750 TAAA-TAATTTTCTCAACT
1 TAAATTAATTTTCTCAACT
41890768 TAA
1 TAA
41890771 TTCTAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 12 0.63
18 4 0.21
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTAATTTTCTCAACT
Found at i:41890908 original size:14 final size:13
Alignment explanation
Indices: 41890863--41890914 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
41890853 CATAATAACT
*
41890863 AATTAATTTAATTA
1 AATT-ATTTAATTC
41890877 AATT-TTTAAAATTC
1 AATTATTT--AATTC
41890891 AATTATTTAATTC
1 AATTATTTAATTC
41890904 TAATTATTTAA
1 -AATTATTTAA
41890915 ATAATAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 22 0.67
15 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATTTAATTC
Found at i:41891821 original size:263 final size:262
Alignment explanation
Indices: 41891354--41891882 Score: 959
Period size: 263 Copynumber: 2.0 Consensus size: 262
41891344 GTATTGTTTT
* *
41891354 AAAATGTATGGATCGACGTCGCGACTTCATCTAGTTCTCTTCACGTTGTTGCCATCACAATATGT
1 AAAATGTATGGATCGACGTCGCGACTTCATCTAGTTCTATTCACGTTGTGGCCATCACAATATGT
** *
41891419 CATGTCATAGTGACAAGCCCTAGCTCATCACGACGTCACTCACTGTAATTACAACATTGTGACAT
66 CATGTCATAACGACAAGCCCTAGCTCATCACGACGTCACTCACTGTAATGACAACATTGTGACAT
41891484 CCAAAATCTGAGGTTGTGACGTGGCCCTTACTTTTGGTAAAAATGAACCATTTAGTGACTATTTC
131 CCAAAATCTGAGGTTGTGACGTGGCCCTTACTTTTGGTAAAAATGAACCATTTAGTGACTATTTC
*
41891549 ATAATCTCCAACCAAACCATACAACATATACAGCCAAAAACCAATTTTAATTGAATCAAAACATG
196 ATAATCTCCAACCAAACCATACAACATATACAG-CAAAAACCAATTTTAATTGAATCAAAACATA
41891614 CCA
260 CCA
*
41891617 AAAATGTATGGATCGACGTCGTGACTTCATCTAGTTCTATTCACGTTGTGGCCATCACAATATGT
1 AAAATGTATGGATCGACGTCGCGACTTCATCTAGTTCTATTCACGTTGTGGCCATCACAATATGT
*
41891682 CATGTCATAACGACAAGCCCTAGCTCGTCACGACGTCACTCACTGTAATGACAACATTGTGACAT
66 CATGTCATAACGACAAGCCCTAGCTCATCACGACGTCACTCACTGTAATGACAACATTGTGACAT
* *
41891747 CCAAAATCTGAGGTTGTGATGTGGCCCTTACTTTTGGTAAAAATGAACCATTTTGTGACTATTTC
131 CCAAAATCTGAGGTTGTGACGTGGCCCTTACTTTTGGTAAAAATGAACCATTTAGTGACTATTTC
41891812 ATAATCTCCAACCAAACCATACAACATATACAGCAAAAACCAATTTTAATTGAATCAAAACATAC
196 ATAATCTCCAACCAAACCATACAACATATACAGCAAAAACCAATTTTAATTGAATCAAAACATAC
41891877 CA
261 CA
41891879 AAAA
1 AAAA
41891883 CATGCCAAAT
Statistics
Matches: 256, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
262 37 0.14
263 219 0.86
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (262 bp):
AAAATGTATGGATCGACGTCGCGACTTCATCTAGTTCTATTCACGTTGTGGCCATCACAATATGT
CATGTCATAACGACAAGCCCTAGCTCATCACGACGTCACTCACTGTAATGACAACATTGTGACAT
CCAAAATCTGAGGTTGTGACGTGGCCCTTACTTTTGGTAAAAATGAACCATTTAGTGACTATTTC
ATAATCTCCAACCAAACCATACAACATATACAGCAAAAACCAATTTTAATTGAATCAAAACATAC
CA
Found at i:41906549 original size:24 final size:26
Alignment explanation
Indices: 41906511--41906558 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
41906501 TCCTTTTCAT
*
41906511 GTTTATTTCCTA-TT-TTTAGTTTTA
1 GTTTATTTCCGATTTATTTAGTTTTA
*
41906535 GTTTATTTTCGATTTATTTAGTTT
1 GTTTATTTCCGATTTATTTAGTTT
41906559 GCTTGAGGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 2 0.10
26 8 0.40
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.67
Consensus pattern (26 bp):
GTTTATTTCCGATTTATTTAGTTTTA
Found at i:41918491 original size:16 final size:18
Alignment explanation
Indices: 41918465--41918497 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41918455 TTAAATTAAC
41918465 TAAATTAATTT-CTCAAT
1 TAAATTAATTTCCTCAAT
41918482 TAAA-TAATTTCCTCAA
1 TAAATTAATTTCCTCAA
41918498 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTAATTTCCTCAAT
Found at i:41932111 original size:95 final size:95
Alignment explanation
Indices: 41932001--41932184 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 95
41931991 TAAATGGCGG
41932001 GAATAAATCCCGAAACAGATTTTATTTT-A-TTTAATTTC-TCGTTTTTGGTAACA-AAATC-AA
1 GAATAAATCCCGAAACAGATTTTATTTTAACTTTAATTTCAT-G--TTTGG-AA-ATAAATCAAA
* *
41932061 AATGTAATAACTCCATTGAACGGCGAGATTTACGA
61 AATGGAATAAATCCATTGAACGGCGAGATTTACGA
*
41932096 GAATAAATCCTGAAACAGATTTTATTTTAACTTTAATTTCATGTTTGGAAATAAATCAAAAAATG
1 GAATAAATCCCGAAACAGATTTTATTTTAACTTTAATTTCATGTTTGGAAATAAATC-AAAAATG
41932161 GAATAAATCCATTGAACGGCGAGA
65 GAATAAATCCATTGAACGGCGAGA
41932185 ATAAATCCCG
Statistics
Matches: 80, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
93 1 0.01
94 7 0.09
95 32 0.40
96 29 0.36
97 10 0.12
98 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (95 bp):
GAATAAATCCCGAAACAGATTTTATTTTAACTTTAATTTCATGTTTGGAAATAAATCAAAAATGG
AATAAATCCATTGAACGGCGAGATTTACGA
Found at i:41939831 original size:48 final size:48
Alignment explanation
Indices: 41939772--41940016 Score: 292
Period size: 48 Copynumber: 5.1 Consensus size: 48
41939762 TACTATGCTT
* * * * * *
41939772 ACCGATGTTCTGTCATGACACAAGAGTGGCACGGACTATGTGTAGGCC
1 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
* *
41939820 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTATGCAGGTC
1 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
*
41939868 ATCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
1 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * *
41939916 TCCAATAATCTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCC
1 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * * * * *
41939964 ACTGAAAATCTGTTATTACACAAAGGAGGTACGGACTGTGTGCAGGCC
1 ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
41940012 ACCGA
1 ACCGA
41940017 GAAATCTGTT
Statistics
Matches: 168, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 168 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
ACCGATATTCTGTTATGATACAAGGGTGGCACGGACTGTGTGCAGGCC
Found at i:41950479 original size:48 final size:48
Alignment explanation
Indices: 41950408--41950503 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
41950398 GAGTATGTGA
* *
41950408 GGTTGAGTTGAAGAATGAATAGATGAAAGATGGGTAGAATTGTTTGTC
1 GGTTGAGTTAAAGAACGAATAGATGAAAGATGGGTAGAATTGTTTGTC
41950456 GGTTGAGTTAAAGAACGAATAGATGAAAGATGGGTAGAATTGTTTGTC
1 GGTTGAGTTAAAGAACGAATAGATGAAAGATGGGTAGAATTGTTTGTC
41950504 ATGTGGTCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.30
Consensus pattern (48 bp):
GGTTGAGTTAAAGAACGAATAGATGAAAGATGGGTAGAATTGTTTGTC
Found at i:41952382 original size:28 final size:27
Alignment explanation
Indices: 41952338--41952400 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
41952328 ATATAAAATA
* * *
41952338 ATTTTTATGTATTTTTAAAATTTGTAT
1 ATTTTTAAGGATTTTTAAAATTTATAT
* *
41952365 ATTTTTAAGGATTCTTTAGATTTTATAT
1 ATTTTTAAGGATT-TTTAAAATTTATAT
41952393 ATTCTTTA
1 ATT-TTTA
41952401 TTTTTAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 11 0.38
28 14 0.48
29 4 0.14
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (27 bp):
ATTTTTAAGGATTTTTAAAATTTATAT
Found at i:41952944 original size:42 final size:42
Alignment explanation
Indices: 41952868--41953219 Score: 480
Period size: 42 Copynumber: 8.3 Consensus size: 42
41952858 ACGTCGCTAA
* * *
41952868 CTTTTGCGGCGCTTACAGAAAAAAACACCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
*
41952912 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
41952954 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* *
41952996 CTTTAGCGGCGCTTA-AAAAAAACGCCGCAAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
41953037 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
41953079 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * *
41953121 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* **
41953164 CTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-GAAAAAACGCCGCTAAAGA-TCA-TGTT
41953206 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
41953220 GTTTCACAAA
Statistics
Matches: 282, Mismatches: 21, Indels: 12
0.90 0.07 0.04
Matches are distributed among these distances:
41 40 0.14
42 196 0.70
43 33 0.12
44 13 0.05
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:41953035 original size:125 final size:126
Alignment explanation
Indices: 41952868--41953219 Score: 487
Period size: 125 Copynumber: 2.8 Consensus size: 126
41952858 ACGTCGCTAA
* * *
41952868 CTTTTGCGGCGCTTACAGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAA
1 CTTTAGCGGCGCTTA-A-AAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAA
*
41952933 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
64 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
41952996 CTTTAGCGGCGCTT-AAAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAAAAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
**
41953060 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
** * * * * **
41953121 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAAAG-TAATGTTCTATAGCGGCGCTT-GTTCAA
1 CTTTAGCGGCGC-TTAAAAAAAAACGCCGC-AAAAGATCATGTTCTTTAGCGGCGCTTAG-GAAA
*
41953184 AAACGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTT
63 AAACGCCGCTAAAGGTCA-TGTTCTTTAGCGGCGCTT
41953220 GTTTCACAAA
Statistics
Matches: 203, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
125 117 0.58
126 5 0.02
127 63 0.31
128 18 0.09
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (126 bp):
CTTTAGCGGCGCTTAAAAAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
CGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:41953673 original size:12 final size:12
Alignment explanation
Indices: 41953642--41953676 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
41953632 TTTGAACCTT
*
41953642 TGCTTCTATCGC
1 TGCTTCTCTCGC
41953654 TGCTTCTCTCGC
1 TGCTTCTCTCGC
41953666 TGCTTCTCTCG
1 TGCTTCTCTCG
41953677 TTGCGGCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.37, G:0.17, T:0.43
Consensus pattern (12 bp):
TGCTTCTCTCGC
Found at i:41953709 original size:21 final size:21
Alignment explanation
Indices: 41953665--41953709 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41953655 GCTTCTCTCG
* * *
41953665 CTGCTTCTCTCGTTGCGGCAT
1 CTGCTTCCCTCGCTGCCGCAT
*
41953686 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCCGCAT
41953707 CTG
1 CTG
41953710 ATATAAGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.42, G:0.22, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCCGCAT
Found at i:41955760 original size:53 final size:54
Alignment explanation
Indices: 41955691--41955802 Score: 181
Period size: 53 Copynumber: 2.1 Consensus size: 54
41955681 TTTATAGCGG
* *
41955691 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAAT
1 GTAATGTATCTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTAAGTAAT
* *
41955745 -TAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTAAGTAAT
1 GTAATGTATCTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTAAGTAAT
41955798 GTAAT
1 GTAAT
41955803 ATATAAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 49 0.92
54 4 0.08
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (54 bp):
GTAATGTATCTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTAAGTAAT
Found at i:41955918 original size:46 final size:42
Alignment explanation
Indices: 41955868--41955959 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 42
41955858 TTAAATTGTA
*
41955868 AAAATATTAACATATATATATTTTTTTAATATTAATAAGTTATAAT
1 AAAATA-TAACA-ATATATA-CTTTTTAATATTAATAAGTTA-AAT
**
41955914 AAAATATATGAATATATACTTTTTAATATTAATAAGTTAAAT
1 AAAATATAACAATATATACTTTTTAATATTAATAAGTTAAAT
41955956 AAAA
1 AAAA
41955960 ACTAAAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 7 0.16
43 20 0.47
44 7 0.16
45 3 0.07
46 6 0.14
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (42 bp):
AAAATATAACAATATATACTTTTTAATATTAATAAGTTAAAT
Found at i:41956318 original size:21 final size:21
Alignment explanation
Indices: 41956289--41956406 Score: 128
Period size: 21 Copynumber: 5.5 Consensus size: 21
41956279 CACTTCATTC
*
41956289 AACAGAAAATAGCAAGACAGAA
1 AACAGAAAATAG-AAAACAGAA
*
41956311 AACAAAAAATAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
* *
41956332 AATAGAAAGTAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
* *
41956353 AACAGAAAAATATAAAATAGAA
1 AACAG-AAAATAGAAAACAGAA
* * *
41956375 AACAGAAAACAAAAAACAAAA
1 AACAGAAAATAGAAAACAGAA
*
41956396 AACAAAAAATA
1 AACAGAAAATA
41956407 AAGAAACATA
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
21 51 0.64
22 29 0.36
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.07
Consensus pattern (21 bp):
AACAGAAAATAGAAAACAGAA
Found at i:41956326 original size:7 final size:7
Alignment explanation
Indices: 41956289--41956403 Score: 97
Period size: 7 Copynumber: 16.3 Consensus size: 7
41956279 CACTTCATTC
41956289 AACAGAA
1 AACAGAA
*
41956296 AATAGCAA
1 AACAG-AA
*
41956304 GACAGAA
1 AACAGAA
*
41956311 AACAAAA
1 AACAGAA
*
41956318 AATAGAA
1 AACAGAA
41956325 AACAGAA
1 AACAGAA
*
41956332 AATAGAA
1 AACAGAA
**
41956339 AGTAGAA
1 AACAGAA
41956346 AACAGAA
1 AACAGAA
41956353 AACAGAAA
1 AACAG-AA
* *
41956361 AATATAA
1 AACAGAA
*
41956368 AATAGAA
1 AACAGAA
41956375 AACAGAA
1 AACAGAA
*
41956382 AACAAAA
1 AACAGAA
*
41956389 AACAAAA
1 AACAGAA
41956396 AACA-AA
1 AACAGAA
41956402 AA
1 AA
41956404 ATAAAGAAAC
Statistics
Matches: 89, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
6 4 0.04
7 75 0.84
8 10 0.11
ACGTcount: A:0.73, C:0.10, G:0.11, T:0.06
Consensus pattern (7 bp):
AACAGAA
Found at i:41956326 original size:14 final size:14
Alignment explanation
Indices: 41956307--41956421 Score: 95
Period size: 14 Copynumber: 8.0 Consensus size: 14
41956297 ATAGCAAGAC
41956307 AGAAAACAAAAAAT
1 AGAAAACAAAAAAT
*
41956321 AGAAAACAGAAAAT
1 AGAAAACAAAAAAT
** * *
41956335 AGAAAGTAGAAAAC
1 AGAAAACAAAAAAT
41956349 AGAAAACAGAAAAAT
1 AGAAAACA-AAAAAT
* * * *
41956364 ATAAAATAGAAAAC
1 AGAAAACAAAAAAT
*
41956378 AGAAAACAAAAAAC
1 AGAAAACAAAAAAT
*
41956392 AAAAAACAAAAAAT
1 AGAAAACAAAAAAT
*
41956406 AAAGAAACATAAAAAT
1 AGA-AAACA-AAAAAT
41956422 GGTACAGAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
14 60 0.74
15 15 0.19
16 6 0.07
ACGTcount: A:0.75, C:0.08, G:0.10, T:0.08
Consensus pattern (14 bp):
AGAAAACAAAAAAT
Found at i:41956329 original size:36 final size:35
Alignment explanation
Indices: 41956289--41956410 Score: 131
Period size: 36 Copynumber: 3.5 Consensus size: 35
41956279 CACTTCATTC
*
41956289 AACAGAAAATAGCAAGACAGAAAACAAAAAATAGAA
1 AACAGAAAATAG-AAGACAGAAAACAAAAAACAGAA
* *
41956325 AACAGAAAATAGAA-AGTAGAAAACAGAAAACAGAAA
1 AACAGAAAATAGAAGA-CAGAAAACAAAAAACAG-AA
* * * *
41956361 AATATAAAATAGAAAACAGAAAACAAAAAACAAAA
1 AACAGAAAATAGAAGACAGAAAACAAAAAACAGAA
*
41956396 AACAAAAAATA-AAGA
1 AACAGAAAATAGAAGA
41956411 AACATAAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.06
35 27 0.38
36 40 0.56
37 1 0.01
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.07
Consensus pattern (35 bp):
AACAGAAAATAGAAGACAGAAAACAAAAAACAGAA
Found at i:41956347 original size:29 final size:28
Alignment explanation
Indices: 41956289--41956390 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 28
41956279 CACTTCATTC
* * * * *
41956289 AACAGAAAATAGCAAGACAGAAAACAAAA
1 AACAGAAAACAG-AAAATAGAAAATAGAA
* *
41956318 AATAGAAAACAGAAAATAGAAAGTAGAA
1 AACAGAAAACAGAAAATAGAAAATAGAA
*
41956346 AACAGAAAACAGAAAAATATAAAATAGAA
1 AACAGAAAACAG-AAAATAGAAAATAGAA
*
41956375 AACAGAAAACAAAAAA
1 AACAGAAAACAGAAAA
41956391 CAAAAAACAA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 26 0.43
29 35 0.57
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.07
Consensus pattern (28 bp):
AACAGAAAACAGAAAATAGAAAATAGAA
Found at i:41956404 original size:7 final size:7
Alignment explanation
Indices: 41956344--41956420 Score: 64
Period size: 7 Copynumber: 10.6 Consensus size: 7
41956334 TAGAAAGTAG
*
41956344 AAAACAG
1 AAAACAA
41956351 AAAACAGA
1 AAAACA-A
* *
41956359 AAAATAT
1 AAAACAA
* *
41956366 AAAATAG
1 AAAACAA
*
41956373 AAAACAG
1 AAAACAA
41956380 AAAACAA
1 AAAACAA
41956387 AAAACAA
1 AAAACAA
41956394 AAAACAA
1 AAAACAA
*
41956401 AAAATAA
1 AAAACAA
41956408 AGAAACATA
1 A-AAACA-A
41956417 AAAA
1 AAAA
41956421 TGGTACAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
7 45 0.76
8 12 0.20
9 2 0.03
ACGTcount: A:0.78, C:0.09, G:0.06, T:0.06
Consensus pattern (7 bp):
AAAACAA
Found at i:41956450 original size:18 final size:19
Alignment explanation
Indices: 41956408--41956451 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
41956398 CAAAAAATAA
*
41956408 AGAAACATAAAAATGGTAC
1 AGAAACATAAAAATGCTAC
* *
41956427 AGAAACAT-AACATGCTAG
1 AGAAACATAAAAATGCTAC
41956445 AGAAACA
1 AGAAACA
41956452 GAAATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (19 bp):
AGAAACATAAAAATGCTAC
Found at i:41965131 original size:23 final size:22
Alignment explanation
Indices: 41965100--41965156 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
41965090 CAATAGTGTA
*
41965100 TCCTCTGAGGAAGGGATAAAATG
1 TCCTTTGAGGAAGGGA-AAAATG
*
41965123 TCCTTTGA-GAAGGGAAAATTG
1 TCCTTTGAGGAAGGGAAAAATG
41965144 TACCTTATGAGGA
1 T-CCTT-TGAGGA
41965157 GATAATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 11 0.38
23 10 0.34
24 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (22 bp):
TCCTTTGAGGAAGGGAAAAATG
Found at i:41970591 original size:2 final size:2
Alignment explanation
Indices: 41970584--41970617 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41970574 NNNNNNNNNG
*
41970584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41970618 CCAAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41972118 original size:36 final size:36
Alignment explanation
Indices: 41972078--41972151 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
41972068 TTGGGAGTCC
*
41972078 ATCCAACTCCTATAGCTAAGACAAGATATCTCCTTA
1 ATCCAACTCCGATAGCTAAGACAAGATATCTCCTTA
41972114 ATCCAACTCCGATAGCTAAGACAAGATATCTCCTTA
1 ATCCAACTCCGATAGCTAAGACAAGATATCTCCTTA
41972150 AT
1 AT
41972152 TGGACTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (36 bp):
ATCCAACTCCGATAGCTAAGACAAGATATCTCCTTA
Found at i:41973942 original size:29 final size:28
Alignment explanation
Indices: 41973891--41973949 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
41973881 AAAATATATA
41973891 TTAAAAATTTAAAAAATTGAATTAAATT
1 TTAAAAATTTAAAAAATTGAATTAAATT
* *
41973919 TTAAAAA-TTAAACACAATTTAATTTAATT
1 TTAAAAATTTAAA-A-AATTGAATTAAATT
41973948 TT
1 TT
41973950 TGTAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 8 0.30
29 14 0.52
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
TTAAAAATTTAAAAAATTGAATTAAATT
Found at i:41973986 original size:16 final size:17
Alignment explanation
Indices: 41973965--41974000 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41973955 CTTTAAAACT
41973965 TTTATAATATTTT-TTA
1 TTTATAATATTTTATTA
*
41973981 TTTATAATTTTTTATTA
1 TTTATAATATTTTATTA
41973998 TTT
1 TTT
41974001 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATAATATTTTATTA
Found at i:41976081 original size:7 final size:7
Alignment explanation
Indices: 41976065--41976094 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41976055 CATAAATAAC
*
41976065 TATTTGT
1 TATTTTT
41976072 TATTTTT
1 TATTTTT
41976079 TATTTTT
1 TATTTTT
41976086 TATTTTT
1 TATTTTT
41976093 TA
1 TA
41976095 ATTGAGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:41978896 original size:19 final size:20
Alignment explanation
Indices: 41978868--41978921 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
41978858 GATGGTGTTG
*
41978868 ATAA-ATACATGTGTA-ATA
1 ATAATATACATATGTATATA
*
41978886 ATAATATACATATGTATTTA
1 ATAATATACATATGTATATA
*
41978906 ATAATA-AAATATGTAT
1 ATAATATACATATGTAT
41978922 TGCTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 19 0.61
20 8 0.26
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (20 bp):
ATAATATACATATGTATATA
Found at i:41978922 original size:19 final size:20
Alignment explanation
Indices: 41978884--41978922 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
41978874 ACATGTGTAA
*
41978884 TAATAATATACATATGTATT
1 TAATAATATAAATATGTATT
41978904 TAATAATA-AAATATGTATT
1 TAATAATATAAATATGTATT
41978923 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TAATAATATAAATATGTATT
Found at i:41979026 original size:14 final size:15
Alignment explanation
Indices: 41978967--41979035 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 15
41978957 ATTATAATTA
* *
41978967 AAACAAAACAAATA-
1 AAACAAAAGAAAAAG
* *
41978981 AAAGAAAAGAAAATG
1 AAACAAAAGAAAAAG
* *
41978996 AAATGAAATATAAAAAG
1 AAA-CAAA-AGAAAAAG
41979013 AAA-AAAAGAAAAAG
1 AAACAAAAGAAAAAG
41979027 AAACAAAAG
1 AAACAAAAG
41979036 GGGAAAAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
14 20 0.45
15 11 0.25
16 4 0.09
17 9 0.20
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.07
Consensus pattern (15 bp):
AAACAAAAGAAAAAG
Found at i:41979090 original size:5 final size:6
Alignment explanation
Indices: 41979073--41979097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41979063 AGGGGAAAGG
41979073 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
41979098 CTAGAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:41979487 original size:17 final size:18
Alignment explanation
Indices: 41979465--41979498 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41979455 TAAATGAGTT
41979465 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
41979482 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
41979499 AAAAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:41979984 original size:23 final size:22
Alignment explanation
Indices: 41979953--41980006 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
41979943 GCTTTGTCGG
41979953 TCAAGCACTTTACGTGTCGT-ATT
1 TCAAGCACTTT-CGTGT-GTCATT
*
41979976 TCAGGCAC-TTCGTGTGTCATT
1 TCAAGCACTTTCGTGTGTCATT
41979997 TCAAGCACTT
1 TCAAGCACTT
41980007 ATGTGTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 3 0.11
23 7 0.26
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (22 bp):
TCAAGCACTTTCGTGTGTCATT
Found at i:41993177 original size:31 final size:30
Alignment explanation
Indices: 41993135--41993202 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
41993125 GATTAAAACA
*
41993135 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCAAGTATATAATTGAACC
* * * *
41993165 ACAATTAGAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAAGTATATAATTGAACC
41993196 AAATTAA
1 AAATTAA
41993203 TCAAAATTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATAATTGAACC
Found at i:42005099 original size:16 final size:16
Alignment explanation
Indices: 42005074--42005109 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42005064 ATAACCAATT
*
42005074 TTCATATCATTATTAA
1 TTCATATCATTATCAA
*
42005090 TTCATTTCATTATCAA
1 TTCATATCATTATCAA
42005106 TTCA
1 TTCA
42005110 CAAATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (16 bp):
TTCATATCATTATCAA
Found at i:42007611 original size:8 final size:8
Alignment explanation
Indices: 42007600--42007629 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
42007590 TCAAATTTAC
42007600 AAAAATAT
1 AAAAATAT
42007608 AAAAATAT
1 AAAAATAT
42007616 AAAAATAT
1 AAAAATAT
42007624 AAAAAT
1 AAAAAT
42007630 CTATGATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:42009863 original size:3 final size:3
Alignment explanation
Indices: 42009855--42009895 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42009845 TTCTTAATTA
42009855 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42009896 ATCCCCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42020521 original size:15 final size:16
Alignment explanation
Indices: 42020501--42020530 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42020491 TTATCTTATT
42020501 TATTTAATAA-AAATC
1 TATTTAATAACAAATC
42020516 TATTTAATAACAAAT
1 TATTTAATAACAAAT
42020531 AATAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTTAATAACAAATC
Found at i:42020774 original size:3 final size:3
Alignment explanation
Indices: 42020766--42020817 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
42020756 ATTTCATAAC
42020766 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42020814 ATA A
1 ATA A
42020818 AATTTATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42023341 original size:25 final size:26
Alignment explanation
Indices: 42023284--42023341 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
42023274 TATATATATG
**
42023284 TATATAAAAAGTTAGGAAGTAAAATA
1 TATATAAAAACATAGGAAGTAAAATA
* * *
42023310 AAAATAAAAACATAGGTA-TAAAATA
1 TATATAAAAACATAGGAAGTAAAATA
42023335 TATATAA
1 TATATAA
42023342 GCATACGTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (26 bp):
TATATAAAAACATAGGAAGTAAAATA
Found at i:42023932 original size:19 final size:19
Alignment explanation
Indices: 42023908--42023980 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
42023898 AATCATATCT
42023908 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42023927 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42023946 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
42023965 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
42023981 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42025065 original size:136 final size:136
Alignment explanation
Indices: 42024821--42025079 Score: 367
Period size: 136 Copynumber: 1.9 Consensus size: 136
42024811 TTACATATAC
* * *
42024821 GCTCACACGAGTTGTCGGTCAGAACGTAGCTACACGGTGCTACTCCACAAGCTGTCGAGTATCCA
1 GCTCACACAAGCTGTCGGTCAGAACGTAGCTACAAGGTGCTACTCCACAAGCTGTCGAGTATCCA
* * * * *
42024886 CAACAAATACTGGAACTCAGCCACCGGTAGGACATTCAAGACCAGTACCTGAAACATGGTAACCT
66 CAACAAATACTAGAACTCAGCCACCAGTAAGACATTCAAGACCAGCACCCGAAACATGGTAACCT
42024951 GGGTCT
131 GGGTCT
** * * *
42024957 GCTCACACAAGCTGTCGGTTGGAACGTAGCTACAAGGTGTTGCTCCACAAGCTGTCGAGTATCCG
1 GCTCACACAAGCTGTCGGTCAGAACGTAGCTACAAGGTGCTACTCCACAAGCTGTCGAGTATCCA
* *
42025022 CAACAAAT-GTCAGAACTCAGCCATCAGTAAGACATTCAAGACCAGCACCCGAAACATG
66 CAACAAATACT-AGAACTCAGCCACCAGTAAGACATTCAAGACCAGCACCCGAAACATG
42025080 TAAACCCTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
135 1 0.01
136 106 0.99
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (136 bp):
GCTCACACAAGCTGTCGGTCAGAACGTAGCTACAAGGTGCTACTCCACAAGCTGTCGAGTATCCA
CAACAAATACTAGAACTCAGCCACCAGTAAGACATTCAAGACCAGCACCCGAAACATGGTAACCT
GGGTCT
Found at i:42025424 original size:13 final size:13
Alignment explanation
Indices: 42025406--42025433 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42025396 TTAATTTAGA
42025406 TAGTGAAACAACT
1 TAGTGAAACAACT
42025419 TAGTGAAACAACT
1 TAGTGAAACAACT
42025432 TA
1 TA
42025434 TTTTATGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (13 bp):
TAGTGAAACAACT
Found at i:42027469 original size:9 final size:9
Alignment explanation
Indices: 42027457--42027533 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
42027447 AAATAAAAAA
42027457 AATTCGGGT
1 AATTCGGGT
42027466 AATTCGGGT
1 AATTCGGGT
* **
42027475 ATTTTATGGT
1 A-ATTCGGGT
*
42027485 AATTCGGTT
1 AATTCGGGT
42027494 AATTCGGGT
1 AATTCGGGT
42027503 AATTCGGGT
1 AATTCGGGT
42027512 AATTCGGGT
1 AATTCGGGT
42027521 AATTCGGGT
1 AATTCGGGT
42027530 AATT
1 AATT
42027534 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
9 53 0.90
10 6 0.10
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:42036633 original size:33 final size:33
Alignment explanation
Indices: 42036571--42036641 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
42036561 AATTCAGTTA
*
42036571 ATTTTAATTTTTTCAGAATTTTTTCTTTTTTAT
1 ATTTTAATTTTTTCAGAATTTTATCTTTTTTAT
*
42036604 ATTTTAATTTTATTTA-AATTCTTAT-TTTTTTAT
1 ATTTTAATTTT-TTCAGAATT-TTATCTTTTTTAT
*
42036637 TTTTT
1 ATTTT
42036642 GCTTTCGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (33 bp):
ATTTTAATTTTTTCAGAATTTTATCTTTTTTAT
Found at i:42036877 original size:19 final size:18
Alignment explanation
Indices: 42036847--42036882 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42036837 TTTAATGACC
42036847 AATTAATTAATCAATTAA
1 AATTAATTAATCAATTAA
*
42036865 AATTAATTTAATCGATTA
1 AATTAA-TTAATCAATTA
42036883 TTTCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTAATTAATCAATTAA
Found at i:42039015 original size:11 final size:11
Alignment explanation
Indices: 42038999--42039041 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
42038989 ATTTAAAAAA
42038999 ATAAAAAATAT
1 ATAAAAAATAT
*
42039010 ATAAAAAAGAT
1 ATAAAAAATAT
42039021 AT-AAAAAT-T
1 ATAAAAAATAT
42039030 ATAAAGAAATAT
1 ATAAA-AAATAT
42039042 TTTTTAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 3 0.11
10 7 0.26
11 16 0.59
12 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:42039016 original size:20 final size:20
Alignment explanation
Indices: 42038954--42039034 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
42038944 TAAATTTTTT
*
42038954 AAAATTTAAAAATTCA-AAAA
1 AAAATATAAAAATT-ATAAAA
* * *
42038974 AAAATTATGAAGATTATTTAAA
1 AAAA-TATAAAAATTA-TAAAA
42038996 AAAATA-AAAAATATATAAAA
1 AAAATATAAAAAT-TATAAAA
*
42039016 AAGATATAAAAATTATAAA
1 AAAATATAAAAATTATAAA
42039035 GAAATATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 24 0.50
21 17 0.35
22 7 0.15
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATATAAAAATTATAAAA
Found at i:42040101 original size:21 final size:20
Alignment explanation
Indices: 42040083--42040135 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
42040073 AACATTTAAT
42040083 TAATTTTT-AATAATTTTTA
1 TAATTTTTAAATAATTTTTA
*
42040102 TGATTTTTAAAATAATTTTTA
1 TAATTTTT-AAATAATTTTTA
42040123 TAATTTTTTAAAT
1 TAA-TTTTTAAAT
42040136 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
21 17 0.59
22 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATTTTTAAATAATTTTTA
Found at i:42040130 original size:9 final size:10
Alignment explanation
Indices: 42040077--42040130 Score: 58
Period size: 9 Copynumber: 5.3 Consensus size: 10
42040067 CATGTCAACA
42040077 TTTAATTAATT
1 TTTAA-TAATT
42040088 TTTAATAATT
1 TTTAATAATT
*
42040098 TTT-ATGATT
1 TTTAATAATT
42040107 TTTAAAATAATT
1 TTT--AATAATT
42040119 TTT-ATAATT
1 TTTAATAATT
42040128 TTT
1 TTT
42040131 TAAATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 17 0.45
10 8 0.21
11 5 0.13
12 8 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTAATAATT
Found at i:42044145 original size:25 final size:24
Alignment explanation
Indices: 42044084--42044145 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
42044074 GTACATGTAT
*
42044084 GCTCATACGAGCTATAAACGGTAA
1 GCTCATACGAGCTAAAAACGGTAA
** * * *
42044108 GCTTTTCCAAGCTAAATAATGGTAA
1 GCTCATACGAGCTAAA-AACGGTAA
42044133 GCTCATACGAGCT
1 GCTCATACGAGCT
42044146 GAGTATCGGT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (24 bp):
GCTCATACGAGCTAAAAACGGTAA
Found at i:42050276 original size:43 final size:43
Alignment explanation
Indices: 42050224--42050434 Score: 251
Period size: 43 Copynumber: 4.9 Consensus size: 43
42050214 CCAACACAAT
* * * * * *
42050224 TATATTGGCACATAAAGTGCATCATCAGATATACCAAAGCAAC
1 TATACTGGCACATACAGTGCATCATCAGATAAACCGAAGTATC
*
42050267 TATACTGGCACATACAGTGCATCATCGGATAAACCGAAGTATC
1 TATACTGGCACATACAGTGCATCATCAGATAAACCGAAGTATC
* * * *
42050310 TATACTGGTACATATAGTGCATCATCGGATAAACTGAAGTATC
1 TATACTGGCACATACAGTGCATCATCAGATAAACCGAAGTATC
* * * *
42050353 TATACTGGTACATACAGTGCATCATCAAATAAGCTGAAGTATC
1 TATACTGGCACATACAGTGCATCATCAGATAAACCGAAGTATC
* ** *
42050396 TATACTAGCATTTACAGTGCATCATCAGATATACCGAAG
1 TATACTGGCACATACAGTGCATCATCAGATAAACCGAAG
42050435 GACAACCTGT
Statistics
Matches: 146, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 146 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (43 bp):
TATACTGGCACATACAGTGCATCATCAGATAAACCGAAGTATC
Found at i:42050291 original size:86 final size:86
Alignment explanation
Indices: 42050201--42050426 Score: 211
Period size: 86 Copynumber: 2.6 Consensus size: 86
42050191 ACATAAATGT
* * *
42050201 ATCATCGAATGAACCAACACAAT-TATATTGGCACATAAAGTGCATCATCAGATATACCAAAGCA
1 ATCATCGAATAAACCAA-ACAATCTATACTGGCACATAAAGTGCATCATCAGATAAACCAAAGCA
42050265 ACTATACTGGCACATACAGTGC
65 ACTATACTGGCACATACAGTGC
* * ** * * * ** * *
42050287 ATCATCGGATAAACCGAAGTATCTATACTGGTACATATAGTGCATCATCGGATAAACTGAAGTAT
1 ATCATCGAATAAACCAAACAATCTATACTGGCACATAAAGTGCATCATCAGATAAACCAAAGCAA
*
42050352 CTATACTGGTACATACAGTGC
66 CTATACTGGCACATACAGTGC
* * ** ** * ** *
42050373 ATCATCAAATAAGCTGAAGTATCTATACTAGCATTTACAGTGCATCATCAGATA
1 ATCATCGAATAAACCAAACAATCTATACTGGCACATAAAGTGCATCATCAGATA
42050427 TACCGAAGGA
Statistics
Matches: 114, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
85 3 0.03
86 111 0.97
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (86 bp):
ATCATCGAATAAACCAAACAATCTATACTGGCACATAAAGTGCATCATCAGATAAACCAAAGCAA
CTATACTGGCACATACAGTGC
Found at i:42050843 original size:17 final size:17
Alignment explanation
Indices: 42050821--42050856 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42050811 TTTGGCCAAG
* *
42050821 TATCGATATTTTTGAAA
1 TATCGATATCTTTCAAA
42050838 TATCGATATCTTTCAAA
1 TATCGATATCTTTCAAA
42050855 TA
1 TA
42050857 AATGATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (17 bp):
TATCGATATCTTTCAAA
Found at i:42053376 original size:16 final size:17
Alignment explanation
Indices: 42053355--42053388 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42053345 ATGACGTTTT
42053355 CGAAAAT-AGATATAAA
1 CGAAAATGAGATATAAA
*
42053371 CGAAAATGAGTTATAAA
1 CGAAAATGAGATATAAA
42053388 C
1 C
42053389 TAGAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.21
Consensus pattern (17 bp):
CGAAAATGAGATATAAA
Found at i:42065958 original size:24 final size:24
Alignment explanation
Indices: 42065921--42066017 Score: 160
Period size: 24 Copynumber: 4.0 Consensus size: 24
42065911 GGTAAGACAT
*
42065921 TTTCCACAGCTCCTCTCTTCACCT
1 TTTCCACAGCTCCTCTCTTCACCC
*
42065945 TTTCCACTA-TTCCTCTCTTCACCC
1 TTTCCAC-AGCTCCTCTCTTCACCC
42065969 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
42065993 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
42066017 T
1 T
42066018 ATCGATTGCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 1 0.01
24 66 0.97
25 1 0.01
ACGTcount: A:0.12, C:0.47, G:0.03, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:42066826 original size:8 final size:8
Alignment explanation
Indices: 42066805--42066845 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
42066795 AAAAGATTAG
42066805 TGTTGTTCC
1 TGTTGTT-C
42066814 TGTTGTTC
1 TGTTGTTC
42066822 TGTTGTTC
1 TGTTGTTC
42066830 TGTTGTTC
1 TGTTGTTC
42066838 TGTTGTTC
1 TGTTGTTC
42066846 CTGGTAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.00, C:0.15, G:0.24, T:0.61
Consensus pattern (8 bp):
TGTTGTTC
Found at i:42071250 original size:14 final size:14
Alignment explanation
Indices: 42071227--42071266 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42071217 ACAGAAAAGT
*
42071227 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42071241 AAATCATTTTACGG
1 AAAACATTTTACAG
42071255 AAAACATTTTAC
1 AAAACATTTTAC
42071267 TGCCAATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42071252 original size:34 final size:35
Alignment explanation
Indices: 42071192--42071258 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42071182 CAAACACCAG
* *
42071192 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42071227 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42071259 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42072747 original size:11 final size:11
Alignment explanation
Indices: 42072731--42072757 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42072721 AGATAAATGT
42072731 TATTTAATTAA
1 TATTTAATTAA
42072742 TATTTAATTAA
1 TATTTAATTAA
42072753 TATTT
1 TATTT
42072758 TTAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAATTAA
Found at i:42075561 original size:43 final size:42
Alignment explanation
Indices: 42075485--42075609 Score: 135
Period size: 43 Copynumber: 3.0 Consensus size: 42
42075475 GAAACACATA
* * *
42075485 TATCACATA-CAATGCCATATCCCAGATATGGTCTTACATGT
1 TATCACATATCGATGCCATGTCCCAGATATGGTCTTACACGT
* *
42075526 TATCACATATCGATGCCACTGTCCTAGATAGGGTCTTACACGT
1 TATCACATATCGATGCCA-TGTCCCAGATATGGTCTTACACGT
* ** * *
42075569 AATCGTATATCGATGACAATGTCCCAGACATGGTCTTACAC
1 TATCACATATCGATG-CCATGTCCCAGATATGGTCTTACAC
42075610 AAAATCACAC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 9 0.13
42 7 0.10
43 51 0.74
44 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
TATCACATATCGATGCCATGTCCCAGATATGGTCTTACACGT
Found at i:42081467 original size:43 final size:43
Alignment explanation
Indices: 42081356--42081476 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
42081346 ATCTCATACA
* * * *
42081356 ATGCC-ATATCCCAGATATGGTCTTAAATGTTATCACATATAG
1 ATGCCAATGTCCCAGATATGGTCTTACACGTAATCACATATAG
* * *
42081398 ATGCCACTGTCCCAGATAGGGTCTTACACGTAATCACATATCG
1 ATGCCAATGTCCCAGATATGGTCTTACACGTAATCACATATAG
* * *
42081441 ATGCCAATGTCCCAGACATGGTCTTACTCGAAATCA
1 ATGCCAATGTCCCAGATATGGTCTTACACGTAATCA
42081477 TGCCTCGGGA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 5 0.08
43 61 0.92
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATATGGTCTTACACGTAATCACATATAG
Found at i:42084454 original size:22 final size:22
Alignment explanation
Indices: 42084411--42084454 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42084401 AAGAATCACA
*
42084411 TTTACATGCCCTTAAGAGAATC
1 TTTACATGCCCTTAAGACAATC
*
42084433 TTTAGATG-CCTTAGAGACAATC
1 TTTACATGCCCTTA-AGACAATC
42084455 CTAATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (22 bp):
TTTACATGCCCTTAAGACAATC
Found at i:42085142 original size:19 final size:20
Alignment explanation
Indices: 42085107--42085144 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42085097 TTTCATGTGG
*
42085107 TTATTTGATCTATTTTGACC
1 TTATTTGATCTAGTTTGACC
42085127 TTATTTG-TCTAGTTTGAC
1 TTATTTGATCTAGTTTGAC
42085145 TTGTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (20 bp):
TTATTTGATCTAGTTTGACC
Found at i:42096655 original size:27 final size:27
Alignment explanation
Indices: 42096617--42096693 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
42096607 AACACGTCAG
* * *
42096617 GAAAGAACAGCCCTTGTGGTGAACTCT
1 GAAAGAATAGCCCTCGTGGCGAACTCT
* *
42096644 GAAATAATAGCCGTCGTGGCGAACTCT
1 GAAAGAATAGCCCTCGTGGCGAACTCT
* * *
42096671 GGAAGAATAGCCTTAGTGGCGAA
1 GAAAGAATAGCCCTCGTGGCGAA
42096694 TTATGAAGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (27 bp):
GAAAGAATAGCCCTCGTGGCGAACTCT
Done.