Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 150 of 168
Found at i:44238813 original size:20 final size:20
Alignment explanation
Indices: 44238790--44238868 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
44238780 TTACAAAAAC
*
44238790 TTCTATGAGTTTACCAATAT
1 TTCTATGAATTTACCAATAT
44238810 TTCTAAT-AATTTTACCAA-ATT
1 TTCT-ATGAA-TTTACCAATA-T
*
44238831 TTATATGAATTTACCAATAT
1 TTCTATGAATTTACCAATAT
*
44238851 TTCTATCAATTTACCAAT
1 TTCTATGAATTTACCAAT
44238869 TTTTATATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 33 0.66
21 17 0.34
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (20 bp):
TTCTATGAATTTACCAATAT
Found at i:44238838 original size:41 final size:40
Alignment explanation
Indices: 44238761--44238877 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
44238751 TTTTTGACTG
* * * * ** * *
44238761 TACCAAAATTTCTAACTATTTACAAAAACTTCTATGAGTT
1 TACCAATATTTCTATCAATTTACCAAATTTTATATGAATT
44238801 TACCAATATTTCTAAT-AATTTTACCAAATTTTATATGAATT
1 TACCAATATTTCT-ATCAA-TTTACCAAATTTTATATGAATT
*
44238842 TACCAATATTTCTATCAATTTACCAATTTTTATATG
1 TACCAATATTTCTATCAATTTACCAAATTTTATATG
44238878 GATATTTTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.49
41 33 0.51
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (40 bp):
TACCAATATTTCTATCAATTTACCAAATTTTATATGAATT
Found at i:44238980 original size:20 final size:20
Alignment explanation
Indices: 44238955--44239008 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
44238945 TTGATTTATT
44238955 AAATATCTAAAATTTTACCA
1 AAATATCTAAAATTTTACCA
** *
44238975 AAATATCTAGTATATTACCA
1 AAATATCTAAAATTTTACCA
44238995 AAAT-TCTTAAAATT
1 AAATATC-TAAAATT
44239009 AAACCCAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATCTAAAATTTTACCA
Found at i:44239205 original size:24 final size:24
Alignment explanation
Indices: 44239173--44239219 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
44239163 GACGTCCTTG
44239173 TCAATGAAATCCTAACAGTTTTAT
1 TCAATGAAATCCTAACAGTTTTAT
*
44239197 TCAATGAAATCCTAACGGTTTTA
1 TCAATGAAATCCTAACAGTTTTA
44239220 CCTTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (24 bp):
TCAATGAAATCCTAACAGTTTTAT
Found at i:44244378 original size:20 final size:22
Alignment explanation
Indices: 44244339--44244381 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
44244329 CCCGACTCGA
44244339 ATTTTAATAAACACAAAAAAAT
1 ATTTTAATAAACACAAAAAAAT
*
44244361 ATTTTAA-AAATA-AAAAAAAT
1 ATTTTAATAAACACAAAAAAAT
44244381 A
1 A
44244382 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTTTAATAAACACAAAAAAAT
Found at i:44244863 original size:18 final size:18
Alignment explanation
Indices: 44244840--44244901 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
44244830 CGTCCATATT
44244840 ATTTTTTAATTTTTTTTA
1 ATTTTTTAATTTTTTTTA
*
44244858 ATTTTTT-ATATTATTTTA
1 ATTTTTTAAT-TTTTTTTA
* * *
44244876 ATATTTAATAATTTTATATA
1 AT-TTT-TTAATTTTTTTTA
44244896 ATTTTT
1 ATTTTT
44244902 ATTTATTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.06
18 16 0.47
19 6 0.18
20 8 0.24
21 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTAATTTTTTTTA
Found at i:44244874 original size:28 final size:27
Alignment explanation
Indices: 44244839--44244925 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
44244829 CCGTCCATAT
* ** *
44244839 TATTTTTTAATTTTTTTTAATTTTTTA
1 TATTTTTTAATATTTAATAATTTTATA
44244866 TATTATTTTAATATTTAATAATTTTATA
1 TATT-TTTTAATATTTAATAATTTTATA
* * *
44244894 TAATTTTTATTTATTGAA-AATTTTTATA
1 TATTTTTTA-ATATTTAATAA-TTTTATA
44244922 TATT
1 TATT
44244926 CATCTTAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 11 0.22
28 38 0.78
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (27 bp):
TATTTTTTAATATTTAATAATTTTATA
Found at i:44249379 original size:27 final size:27
Alignment explanation
Indices: 44249341--44249431 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
44249331 GGAGGGTTTT
*
44249341 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCGGCACCAATGGTGCCAT-AC
*
44249368 TGATTGGCGGCACCGATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
*
44249395 TGGTTGGCGGCACCAATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
44249422 TGATTGGCGG
1 TGATTGGCGG
44249432 GACTACTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.22
Consensus pattern (27 bp):
TGATTGGCGGCACCAATGGTGCCATAC
Found at i:44252627 original size:41 final size:43
Alignment explanation
Indices: 44252508--44252640 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 43
44252498 ACGATTTTCG
* *
44252508 ATATGTGTTCTCGTGTAAGACCAC-GTCTGGGACGATGGTATCGAT
1 ATATGTGAT-TCGTGTAAGACC-CTGTCTGGGAC-ATGGCATCGAT
* *
44252553 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T
1 ATATGTGATT-CGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
*
44252597 AT-T-TGATTCGTGTAAGACCCTGTCCGGGACAGTGGCATCGAT
1 ATATGTGATTCGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
44252639 AT
1 AT
44252641 GAGATAGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
41 28 0.37
42 8 0.11
43 1 0.01
44 5 0.07
45 34 0.45
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCCTGTCTGGGACATGGCATCGAT
Found at i:44256323 original size:11 final size:11
Alignment explanation
Indices: 44256307--44256331 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44256297 GCTTATGCTT
44256307 AAATTGTATCC
1 AAATTGTATCC
44256318 AAATTGTATCC
1 AAATTGTATCC
44256329 AAA
1 AAA
44256332 CTAAGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:44259211 original size:319 final size:319
Alignment explanation
Indices: 44258543--44259319 Score: 1281
Period size: 319 Copynumber: 2.4 Consensus size: 319
44258533 GCAAGTTGAA
* *
44258543 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTCTCTCCGTATTTTATTA
1 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCT-CGCATTTTATTA
*
44258608 TTTTAGAAAATATTATAATTTTTTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
65 TTTTAGAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
* *
44258673 TTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAAACCATTATCCCTGCCCT
130 TTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAG-AAAAAAACCATTATCACTGCCCT
* * *
44258738 TTGCTCGTATTATTTTATCGATTTTTATTACTTTAAATAAAAATATTTTATTTTCGTATTTTATT
194 TTGCTCATATTATTTTATCAATTTTTATTACTTTAAATAAAAACATTTTATTTTCGTATTTTATT
44258803 ATTTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
259 ATTTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
*
44258864 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCATATTTTTTTCTCTGCATTTTATTA
1 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTC-GCATTTTATTA
* *
44258929 TTTTAGAAAATATTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
65 TTTTAGAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
*
44258994 TTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAG-AAAAAACCCTTATCACTGCCCTT
130 TTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCATTATCACTGCCCTT
* **
44259058 TGCTCATATTATTTT-CCTAATTTTTATTACTTTCGATAAAAACATTTTATTTTCGTATTTTATT
195 TGCTCATATTATTTTATC-AATTTTTATTACTTTAAATAAAAACATTTTATTTTCGTATTTTATT
*
44259122 ATTTTATATTATTTCAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
259 ATTTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
*
44259183 AAAAAAGTTAGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTATC-CGCATTTTATTA
1 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTT-TCTCGCATTTTATTA
* ** * * *
44259247 TTTTAAAAAATATCGTAATTTTTAATTTTATTATTTTACATTATTTCAGTGTATTATGTTTGAAA
65 TTTTAGAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
44259312 TTTATTAA
130 TTTATTAA
44259320 ATATACAAAT
Statistics
Matches: 427, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
318 77 0.18
319 185 0.43
320 3 0.01
321 162 0.38
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (319 bp):
AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGCATTTTATTAT
TTTAGAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
TTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCATTATCACTGCCCTTT
GCTCATATTATTTTATCAATTTTTATTACTTTAAATAAAAACATTTTATTTTCGTATTTTATTAT
TTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
Found at i:44259707 original size:5 final size:5
Alignment explanation
Indices: 44259681--44259899 Score: 86
Period size: 5 Copynumber: 44.2 Consensus size: 5
44259671 TCCTTCCCTC
*
44259681 TTCTT CTTC-T TTCTT TTTTT TTCTT TTCTCAT TTCCTT TTC-T TTCTT
1 TTCTT -TTCTT TTCTT TTCTT TTCTT TTCT--T TT-CTT TTCTT TTCTT
* * *
44259728 TCCTT CT-TT TTCTT TTCTTT TTCTT TTCTCCT TTCCTT TTCTT TCCTT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTCT--T TT-CTT TTCTT TTCTT
* * * * *
44259776 CT-TT TTC-T TTCTT TT-TT GTTCTT CTCATT TCCTT TTCTT TCCTT CT-TT
1 TTCTT TTCTT TTCTT TTCTT -TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT
* * * * * * * * *
44259824 TTC-T TTCTT TCCTC TCCTC TCCTT TTC-T TTCTT TCCTC TCCTT TCCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
44259872 TTC-T TTC-T TTC-T TTC-T TTCTT CTTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT T
44259900 CCCTCTCCTT
Statistics
Matches: 167, Mismatches: 26, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
4 46 0.28
5 87 0.52
6 24 0.14
7 6 0.04
8 4 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (5 bp):
TTCTT
Found at i:44259722 original size:18 final size:16
Alignment explanation
Indices: 44259681--44259901 Score: 83
Period size: 14 Copynumber: 13.9 Consensus size: 16
44259671 TCCTTCCCTC
*
44259681 TTCTTCTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
*
44259696 TT-TTTTTCTTTTCTCAT
1 TTCTTTTTC-TTTC-CTT
*
44259713 TTCCTTTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
* *
44259728 TCCTTCTT-TTT-CTT
1 TTCTTTTTCTTTCCTT
*
44259742 TTCTTTTTCTTTTCTCCT
1 TTCTTTTTC-TTTC-CTT
*
44259760 TTCCTTTTCTTTCC--
1 TTCTTTTTCTTTCCTT
44259774 TTCTTTTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
* *
44259789 TT-TTGTTC-TTCTCAT
1 TTCTTTTTCTTTC-CTT
*
44259804 TTCCTTTTCTTTCCTT
1 TTCTTTTTCTTTCCTT
*
44259820 CTTTTTCTTTCTTTCCTCT
1 -TTCTT-TTTCTTTCCT-T
*
44259839 CCTCTCCTTTTCTTT-C-T
1 --T-TCTTTTTCTTTCCTT
* * *
44259856 TTCCTCTCCTTTCCTT
1 TTCTTTTTCTTTCCTT
44259872 TTCTTTCTTTCTTT-C-T
1 TTC-TT-TTTCTTTCCTT
*
44259888 TTCTTCTTCTTTCC
1 TTCTTTTTCTTTCC
44259902 CTCTCCTTCT
Statistics
Matches: 155, Mismatches: 27, Indels: 48
0.67 0.12 0.21
Matches are distributed among these distances:
13 3 0.02
14 48 0.31
15 23 0.15
16 18 0.12
17 20 0.13
18 30 0.19
19 2 0.01
20 9 0.06
21 2 0.01
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTTTCTTTCCTT
Found at i:44259727 original size:36 final size:35
Alignment explanation
Indices: 44259647--44259745 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 35
44259637 TTAATAAAAA
* *
44259647 TTTCTTTTTTTCTTTTTTTTTC-CTTC-CTTCCCT
1 TTTCTTTCTTTCTTTTTTTTTCTTTTCTCTTCCCT
* *
44259680 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCT
1 TTTC-T-TTCTTTCTTTTTTTTTCTTTTCTC-TTCCCT
* *
44259718 TTTCTTTCTTTCCTTCTTTTTCTTTTCT
1 TTTCTTTCTTTCTTTTTTTTTCTTTTCT
44259746 TTTTCTTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
33 3 0.06
34 1 0.02
35 16 0.30
36 24 0.44
37 2 0.04
38 8 0.15
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTCTTTCTTTCTTTTTTTTTCTTTTCTCTTCCCT
Found at i:44259734 original size:44 final size:43
Alignment explanation
Indices: 44259683--44259881 Score: 199
Period size: 44 Copynumber: 4.6 Consensus size: 43
44259673 CTTCCCTCTT
44259683 CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
44259726 TTTCCTTCTTTTTCTTTTCTTTTTCTTTTCTCCTTTCCTTTTCTTTC
1 CTT-CTTC--TTTCTTTT-TTTTTCTTTTCTCATTTCCTTTTCTTTC
*
44259773 CTTCTT-TTTCTTTCTTTTTTGTTCTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTTCTTT-TTTTTTCTT-TTCTCATTTCCTTTTCTTTC
** ** * *
44259817 CTTCTT-TTTCTTTCTTTCCTCTCCTCTCCTTTTC-TTTCTTTC
1 CTTCTTCTTTCTTT-TTTTTTCTTTTCTCATTTCCTTTTCTTTC
* * *
44259859 C-TCTCCTTTCCTTTTCTTTCTTT
1 CTTCTTCTTTCTTTTTTTTTCTTT
44259882 CTTTCTTTCT
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
41 8 0.06
42 15 0.12
43 24 0.18
44 43 0.33
46 11 0.08
47 29 0.22
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (43 bp):
CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
Found at i:44259734 original size:47 final size:46
Alignment explanation
Indices: 44259680--44259833 Score: 224
Period size: 47 Copynumber: 3.4 Consensus size: 46
44259670 TTCCTTCCCT
44259680 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
44259726 TTTCCTTCTT-TTTCTTTTCTTTTTCTTTTCTCCTTTCCTTTTCTTTC
1 CTT-CTTCTTCTTTCTTTT-TTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
44259773 CTTCTTTTTCTTTCTTTTTTGTTC--TTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
*
44259817 CTTCTTTTTCTTTCTTT
1 CTTCTTCTTCTTTCTTT
44259834 CCTCTCCTCT
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
44 36 0.36
46 20 0.20
47 43 0.43
ACGTcount: A:0.01, C:0.26, G:0.01, T:0.72
Consensus pattern (46 bp):
CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
Found at i:44259825 original size:87 final size:89
Alignment explanation
Indices: 44259680--44259860 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 89
44259670 TTCCTTCCCT
*
44259680 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTCTTTCCTTCTTTTTCTTTTC
1 CTTCTTCTTCTTTCTTTTTTGTTC-TTTCTCATTTCC--TTCTTTCTTTCCTTCTTTTTC-TTTC
* **
44259745 TTT-TTCTTTTCTCCTTTCCTTTTCTTTC
62 TTTCCTCTCCTCTCCTTTCC-TTTCTTTC
*
44259773 CTTCTTTTTCTTTCTTTTTTGTTC-TTCTCATTTCC-T-TTTCTTTCCTTCTTTTTCTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTGTTCTTTCTCATTTCCTTCTTTCTTTCCTTCTTTTTCTTTCTTTC
*
44259835 CTCTCCTCTCCTTTTCTTTCTTTC
66 CTCTCCTCTCCTTTCCTTTCTTTC
44259859 CT
1 CT
44259861 CTCCTTTCCT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
86 17 0.21
87 30 0.37
88 1 0.01
91 11 0.14
93 22 0.27
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (89 bp):
CTTCTTCTTCTTTCTTTTTTGTTCTTTCTCATTTCCTTCTTTCTTTCCTTCTTTTTCTTTCTTTC
CTCTCCTCTCCTTTCCTTTCTTTC
Found at i:44259830 original size:24 final size:23
Alignment explanation
Indices: 44259680--44259900 Score: 140
Period size: 24 Copynumber: 9.6 Consensus size: 23
44259670 TTCCTTCCCT
*
44259680 CTTCTTCTTCTTTCTTTT-TTT-
1 CTTCTTTTTCTTTCTTTTCTTTC
44259701 -TTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTTT-TC-TTT-CTTTTCTTTC
* *
44259726 TTTCCTTCTT-TTTCTTTTCTTT-
1 CTT-CTTTTTCTTTCTTTTCTTTC
*
44259748 -TTCTTTTCTCCTTTCCTTTTCTTTC
1 CTTC-TTT-TTCTTT-CTTTTCTTTC
44259773 CTTCTTTTTCTTTC-TTT-TTT-
1 CTTCTTTTTCTTTCTTTTCTTTC
* *
44259793 GTTC-TTCTCATTTCCTTTTCTTTC
1 CTTCTTTTTC-TTT-CTTTTCTTTC
* *
44259817 CTTCTTTTTCTTTCTTTCCTCTC
1 CTTCTTTTTCTTTCTTTTCTTTC
* * *
44259840 CTCTCCTTTTCTTTCTTTCCTCTC
1 CT-TCTTTTTCTTTCTTTTCTTTC
*
44259864 CTTTCCTTTTCTTTC-TTTCTTTC
1 C-TTCTTTTTCTTTCTTTTCTTTC
* *
44259887 TTTCTTCTTCTTTC
1 CTTCTTTTTCTTTC
44259901 CCTCTCCTTC
Statistics
Matches: 162, Mismatches: 17, Indels: 41
0.74 0.08 0.19
Matches are distributed among these distances:
19 4 0.02
20 13 0.08
21 10 0.06
22 21 0.13
23 37 0.23
24 59 0.36
25 8 0.05
26 6 0.04
27 4 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (23 bp):
CTTCTTTTTCTTTCTTTTCTTTC
Found at i:44259995 original size:27 final size:26
Alignment explanation
Indices: 44259949--44260016 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
44259939 TATAAGGGCA
44259949 GTGCCGCCAACCTCA-TTGGCACCATCG
1 GTGCCGCCAA--TCAGTTGGCACCATCG
* *
44259976 GTGCCGCCAATCAGTATGGCACCTTTG
1 GTGCCGCCAATCAGT-TGGCACCATCG
44260003 GTGCCGCCAATCAG
1 GTGCCGCCAATCAG
44260017 AAACCCTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 33 0.89
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (26 bp):
GTGCCGCCAATCAGTTGGCACCATCG
Found at i:44285512 original size:24 final size:25
Alignment explanation
Indices: 44285485--44285532 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
44285475 AGAAGAAAGT
44285485 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
44285509 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
44285533 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:44285945 original size:19 final size:19
Alignment explanation
Indices: 44285923--44285967 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44285913 AGTTTTTAAG
*
44285923 TTTTAAATATTTTTTGGAT
1 TTTTAAATATTTTTTGAAT
*
44285942 TTTTAAATATTTTTTTAAT
1 TTTTAAATATTTTTTGAAT
44285961 TTTTAAA
1 TTTTAAA
44285968 CGAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTAAATATTTTTTGAAT
Found at i:44286638 original size:26 final size:26
Alignment explanation
Indices: 44286609--44286658 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
44286599 CTTAAACTAA
44286609 ACTTTTTAAAAATATTTCTCAAAATC
1 ACTTTTTAAAAATATTTCTCAAAATC
*
44286635 ACTTTTTAAAAGTATTTCTCAAAA
1 ACTTTTTAAAAATATTTCTCAAAA
44286659 GTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (26 bp):
ACTTTTTAAAAATATTTCTCAAAATC
Found at i:44289241 original size:21 final size:21
Alignment explanation
Indices: 44289215--44289265 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
44289205 CTCATTCTTT
**
44289215 CTTGGCAGTAGATTTAGTGGC
1 CTTGGCACCAGATTTAGTGGC
*
44289236 CTTGGCACCCGATTTAGTGGC
1 CTTGGCACCAGATTTAGTGGC
44289257 CTTGGCACC
1 CTTGGCACC
44289266 GTTGGATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTGGCACCAGATTTAGTGGC
Found at i:44289675 original size:8 final size:8
Alignment explanation
Indices: 44289665--44289711 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
44289655 TATATACATT
*
44289665 TTTTTATT
1 TTTTTATA
44289673 TTTTTATA
1 TTTTTATA
44289681 TTTTTATA
1 TTTTTATA
44289689 TTTTTAATA
1 TTTTT-ATA
* *
44289698 ATTTTAAA
1 TTTTTATA
44289706 TTTTTA
1 TTTTTA
44289712 ATTAATTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTATA
Found at i:44289692 original size:17 final size:17
Alignment explanation
Indices: 44289665--44289713 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
44289655 TATATACATT
*
44289665 TTTTTAT-TTTTTTATA
1 TTTTTATATTTTTAATA
44289681 TTTTTATATTTTTAATA
1 TTTTTATATTTTTAATA
* *
44289698 ATTTTAAATTTTTAAT
1 TTTTTATATTTTTAAT
44289714 TAATTGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATATTTTTAATA
Found at i:44296837 original size:2 final size:2
Alignment explanation
Indices: 44296830--44296860 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44296820 CGCATTAACA
44296830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44296861 AAGAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44297173 original size:6 final size:6
Alignment explanation
Indices: 44297154--44297192 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
44297144 CCGCATTTGC
* *
44297154 TCAT-G TCATAG TCATGG TCATGG TCATGG TCTTGG TCAT
1 TCATGG TCATGG TCATGG TCATGG TCATGG TCATGG TCAT
44297193 ACAAGGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (6 bp):
TCATGG
Found at i:44299218 original size:2 final size:2
Alignment explanation
Indices: 44299211--44299259 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
44299201 ATAATTATTT
44299211 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
44299253 TA CTA TA
1 TA -TA TA
44299260 AAATCAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44301659 original size:24 final size:24
Alignment explanation
Indices: 44301626--44301706 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
44301616 ATGCTGAGGA
*
44301626 TGCTCATCTACCTTGGTTGGAAAC
1 TGCTCCTCTACCTTGGTTGGAAAC
* *
44301650 TGCTCCTCTACTTTGGTAGGAAGA-
1 TGCTCCTCTACCTTGGTTGGAA-AC
* *
44301674 TCCT-CTGCTACCTTGGTTGGAACC
1 TGCTCCT-CTACCTTGGTTGGAAAC
44301698 TGCTCCTCT
1 TGCTCCTCT
44301707 TTCTTAGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.04
24 40 0.89
25 3 0.07
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (24 bp):
TGCTCCTCTACCTTGGTTGGAAAC
Found at i:44312061 original size:19 final size:18
Alignment explanation
Indices: 44312032--44312077 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
44312022 ATATTGAATA
44312032 TTTAT-ATTATTTATT-T
1 TTTATAATTATTTATTCT
44312048 TTAATATAATTA-TTATTCT
1 TT--TATAATTATTTATTCT
44312067 TTTATAATTAT
1 TTTATAATTAT
44312078 CCATTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 8 0.32
19 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATAATTATTTATTCT
Found at i:44316810 original size:16 final size:17
Alignment explanation
Indices: 44316778--44316813 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
44316768 ATTATGTTAA
44316778 TAATTTATTTAAAATTT
1 TAATTTATTTAAAATTT
*
44316795 TAATTT-TTTTAAATTT
1 TAATTTATTTAAAATTT
44316811 TAA
1 TAA
44316814 AAAAATTAAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTATTTAAAATTT
Found at i:44317763 original size:6 final size:6
Alignment explanation
Indices: 44317752--44317778 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44317742 ATTAAGAAGC
44317752 AAAAGG AAAAGG AAAAGG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAA
44317779 CAAACTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:44321243 original size:46 final size:46
Alignment explanation
Indices: 44321129--44321247 Score: 118
Period size: 46 Copynumber: 2.6 Consensus size: 46
44321119 ACTGCTACAT
* * *
44321129 TGCTCTTAAACACAAACTT-AATCTGTTTA-CACAAAATAAATGATGA
1 TGCTCTTAAGCACAAGCTTAAAT-TGTTCATC-CAAAATAAATGATGA
** *
44321175 TGCTCTTAAGCATGAGCTTAAATTGTTCATCCAAAATAAATGATGT
1 TGCTCTTAAGCACAAGCTTAAATTGTTCATCCAAAATAAATGATGA
* *
44321221 TGTTCTTAAGTACAAG-TATAAATTGTT
1 TGCTCTTAAGCACAAGCT-TAAATTGTT
44321248 TATATATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.02
46 55 0.92
47 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (46 bp):
TGCTCTTAAGCACAAGCTTAAATTGTTCATCCAAAATAAATGATGA
Found at i:44322625 original size:21 final size:21
Alignment explanation
Indices: 44322592--44322636 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
44322582 TACCTAATTT
44322592 TATATTATAAAATT-ATTTGA
1 TATATTATAAAATTAATTTGA
44322612 TATATTACTAAAATTAGATTTGA
1 TATATTA-TAAAATTA-ATTTGA
44322635 TA
1 TA
44322637 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
23 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TATATTATAAAATTAATTTGA
Found at i:44322684 original size:26 final size:25
Alignment explanation
Indices: 44322627--44322695 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
44322617 TACTAAAATT
* *
44322627 AGATTTGATAACATTTTTTTAAGTA
1 AGATTTGATAATACTTTTTTAAGTA
* *
44322652 AGTTTTGGTAATACATTTTTTAAGGTA
1 AGATTTGATAATAC-TTTTTTAA-GTA
44322679 A-ATTTGATAATACTTTT
1 AGATTTGATAATACTTTT
44322696 AATTATACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 14 0.39
26 18 0.50
27 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (25 bp):
AGATTTGATAATACTTTTTTAAGTA
Found at i:44323245 original size:25 final size:25
Alignment explanation
Indices: 44323215--44323268 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
44323205 ATAAAAAAAA
44323215 TTAAAATTAATTCCATATATTTTAG
1 TTAAAATTAATTCCATATATTTTAG
* *
44323240 TTAAAATTGATTTCATATATTTTAG
1 TTAAAATTAATTCCATATATTTTAG
44323265 TTAA
1 TTAA
44323269 TATGAGGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (25 bp):
TTAAAATTAATTCCATATATTTTAG
Found at i:44325920 original size:3 final size:3
Alignment explanation
Indices: 44325912--44325948 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44325902 TTTAAATGAA
44325912 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
44325949 TCAACTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44340177 original size:104 final size:104
Alignment explanation
Indices: 44339997--44340204 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
44339987 CTAATTGATG
44339997 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
1 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
44340062 TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
66 TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
44340101 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
1 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
44340166 TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
66 TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
44340205 CAAACATAAC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (104 bp):
ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
Found at i:44343221 original size:58 final size:58
Alignment explanation
Indices: 44343148--44343271 Score: 221
Period size: 58 Copynumber: 2.1 Consensus size: 58
44343138 CCAAATTTGT
*
44343148 TCAGTAAAGGCTGAAGGGGTATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
1 TCAG-AAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
*
44343207 TCAGAAAGGCTGAAGGGGGATTAGGTATGAAGGAATCGGAGAGCTGGAATAGAGCTCA
1 TCAGAAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
44343265 TCAGAAA
1 TCAGAAA
44343272 CATACTTGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 59 0.94
59 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.35, T:0.19
Consensus pattern (58 bp):
TCAGAAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
Found at i:44347768 original size:31 final size:29
Alignment explanation
Indices: 44347703--44347771 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
44347693 TTGTCCAAGA
***
44347703 GTAAATACTCAAAATTTGAAGGGTTAAAGT
1 GTAAATA-TCAAAATTTGAAGGACCAAAGT
44347733 GTAAATATCAAAAATTTGAAGGACCAATAGT
1 GTAAATATC-AAAATTTGAAGGACCAA-AGT
44347764 GTAAATAT
1 GTAAATAT
44347772 TTTAAGGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 21 0.62
31 11 0.32
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (29 bp):
GTAAATATCAAAATTTGAAGGACCAAAGT
Found at i:44350001 original size:90 final size:90
Alignment explanation
Indices: 44349841--44350056 Score: 256
Period size: 90 Copynumber: 2.4 Consensus size: 90
44349831 CTCCTTGGTT
* * * * * * *
44349841 TTAATGAGTTCATAGCCTAAAGTTTGGGTGGTCCTGCTAAGATGGACTTGATGAATTCATCGAAT
1 TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTCATCAAAT
* *
44349906 ATATAGGATGAACTACTAGATGCTC
66 ATATAGGATGAACCACTAAATGCTC
* *
44349931 TTAATGAGTTCATAACCTAGAGTTTGGGTGATCCTATTAAGACGAACTTGATGAAC-CTATCAAA
1 TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTC-ATCAAA
* *
44349995 TTTATAGGATGAGCCACTAAATGCTC
65 TATATAGGATGAACCACTAAATGCTC
* * *
44350021 TTAATGAATTCATATCCCAG-GTTTTGGGTGGTCCTA
1 TTAATGAGTTCATAACCTAGAG-TTTGGGTGGTCCTA
44350057 GTGAGATGGG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
89 2 0.02
90 105 0.98
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (90 bp):
TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTCATCAAAT
ATATAGGATGAACCACTAAATGCTC
Found at i:44350087 original size:90 final size:89
Alignment explanation
Indices: 44349841--44350087 Score: 250
Period size: 90 Copynumber: 2.7 Consensus size: 89
44349831 CTCCTTGGTT
* * * *
44349841 TTAATGAGTTCATAGCCTAAAGTTTGGGTGGTCCT-GCTAAGATGGACTTGATGAATTCATCGAA
1 TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAG-TAAGATGGACTTGATGAATTCAT-GAA
* * *
44349905 TATATAGGATGAACTACTAGATGCTC
64 TTTATAGGATGAACCACTAAATGCTC
* * * * * *
44349931 TTAATGAGTTCATAACCTAGAGTTTGGGTGATCCTATTAAGACGAACTTGATGAACCTATCA--A
1 TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAGTAAGATGGACTTGATGAA--T-TCATGA
*
44349994 ATTTATAGGATGAGCCACTAAATGCTC
63 ATTTATAGGATGAACCACTAAATGCTC
* * *
44350021 TTAATGAATTCATATCCCAG-GTTTTGGGTGGTCCTAGTGAGATGGGCTTGATGAATTCACTGAA
1 TTAATGAATTCATAACCCAGAG-TTTGGGTGGTCCTAGTAAGATGGACTTGATGAATTCA-TGAA
44350085 TTT
64 TTT
44350088 TTAAACTGAA
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
87 3 0.02
88 1 0.01
89 1 0.01
90 121 0.93
92 1 0.01
93 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (89 bp):
TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAGTAAGATGGACTTGATGAATTCATGAATT
TATAGGATGAACCACTAAATGCTC
Found at i:44350724 original size:14 final size:14
Alignment explanation
Indices: 44350707--44350735 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44350697 TTACTAAAAT
44350707 TACATTAGATGAAA
1 TACATTAGATGAAA
44350721 TACATTAGATGAAA
1 TACATTAGATGAAA
44350735 T
1 T
44350736 TTTGTCTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (14 bp):
TACATTAGATGAAA
Found at i:44351973 original size:27 final size:28
Alignment explanation
Indices: 44351929--44351988 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
44351919 AATAATTCAA
*
44351929 AAAAATTTATAAAAAATACT-TAAAATTT
1 AAAAATTTATAAAAAATA-TATAAAATTG
* *
44351957 AAAAATTTA-GAATAATATATAAAATTG
1 AAAAATTTATAAAAAATATATAAAATTG
44351984 AAAAA
1 AAAAA
44351989 AGTATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTTATAAAAAATATATAAAATTG
Found at i:44352008 original size:28 final size:29
Alignment explanation
Indices: 44351977--44352031 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
44351967 AATAATATAT
*
44351977 AAAATTG-AAAAAAGTA-TTTAAATTTTAG
1 AAAATTGTAAAAAA-AACTTTAAATTTTAG
44352005 AAAATTGTAAAAAAAACTTTAAATTTT
1 AAAATTGTAAAAAAAACTTTAAATTTT
44352032 CAAAAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAATTGTAAAAAAAACTTTAAATTTTAG
Found at i:44352218 original size:21 final size:21
Alignment explanation
Indices: 44352194--44352234 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44352184 AAAAAAGTCA
44352194 AAATATA-TAGATTTTTTAAAT
1 AAATATAGTA-ATTTTTTAAAT
*
44352215 AAATTTAGTAATTTTTTAAA
1 AAATATAGTAATTTTTTAAA
44352235 GAATTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATATAGTAATTTTTTAAAT
Found at i:44367813 original size:16 final size:15
Alignment explanation
Indices: 44367783--44367811 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44367773 TCTCTTAATT
44367783 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
44367798 TTTTTAAAATATTT
1 TTTTTAAAATATTT
44367812 TACAATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:44368548 original size:15 final size:13
Alignment explanation
Indices: 44368511--44368545 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
44368501 TTTCTTTTTT
44368511 ATTTTATTTAATA
1 ATTTTATTTAATA
44368524 A-TTTATTTAATA
1 ATTTTATTTAATA
44368536 ATTTTTATTT
1 A-TTTTATTT
44368546 TAAATAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 1 0.05
14 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTATTTAATA
Found at i:44377431 original size:4 final size:4
Alignment explanation
Indices: 44377424--44377461 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
44377414 TTATATATAT
44377424 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
44377462 TATTTAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:44385298 original size:29 final size:29
Alignment explanation
Indices: 44385256--44385313 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
44385246 CAAAGAATAG
44385256 TTACATTATAGCCAGTTTAGCTCCCCACA
1 TTACATTATAGCCAGTTTAGCTCCCCACA
44385285 TTACATTATAGCCAGTTTAGCTCCCCACA
1 TTACATTATAGCCAGTTTAGCTCCCCACA
44385314 ATATATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (29 bp):
TTACATTATAGCCAGTTTAGCTCCCCACA
Found at i:44385321 original size:29 final size:29
Alignment explanation
Indices: 44385257--44385321 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
44385247 AAAGAATAGT
*
44385257 TACATTATAGCCAGTTTAGCTCCCCACAT
1 TACATTATAGCCAGTTTAGCTCCCCACAA
44385286 TACATTATAGCCAGTTTAGCTCCCCACAA
1 TACATTATAGCCAGTTTAGCTCCCCACAA
*
44385315 TATATTA
1 TACATTA
44385322 CTGCTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (29 bp):
TACATTATAGCCAGTTTAGCTCCCCACAA
Found at i:44402626 original size:22 final size:24
Alignment explanation
Indices: 44402600--44402643 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44402590 GAAAAATATT
44402600 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
44402622 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
44402644 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:44402754 original size:9 final size:9
Alignment explanation
Indices: 44402740--44402767 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
44402730 TTTTGTTACA
44402740 ACAATTAAT
1 ACAATTAAT
44402749 ACAATTAAT
1 ACAATTAAT
44402758 ACAATTAAT
1 ACAATTAAT
44402767 A
1 A
44402768 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:44402789 original size:68 final size:68
Alignment explanation
Indices: 44402710--44402919 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
44402700 TCAAGTTTGT
*
44402710 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
44402775 AAA
66 AAA
44402778 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
44402843 AAA
66 AAA
*
44402846 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGGT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
44402909 AAT
66 AAA
44402912 TTTACTAA
1 TTTACTAA
44402920 CAATTAATTT
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
67 1 0.01
68 112 0.81
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:44402820 original size:9 final size:9
Alignment explanation
Indices: 44402808--44402835 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
44402798 TTTTATTACA
44402808 ACAATTAAT
1 ACAATTAAT
44402817 ACAATTAAT
1 ACAATTAAT
44402826 ACAATTAAT
1 ACAATTAAT
44402835 A
1 A
44402836 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:44402929 original size:16 final size:16
Alignment explanation
Indices: 44402908--44402949 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
44402898 AATAATTTGG
*
44402908 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
44402924 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
44402940 TAGTTTTAAT
1 TAATTTTAAT
44402950 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:44402933 original size:22 final size:23
Alignment explanation
Indices: 44402923--44402978 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
44402913 TTACTAACAA
* * *
44402923 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
44402945 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
44402968 TTAATTTTAAT
1 TTAATTTTAAT
44402979 TTTAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:44412698 original size:28 final size:28
Alignment explanation
Indices: 44412644--44412713 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
44412634 TTTGATATAT
* *
44412644 TTTTAT-AATTTTTACATTATTTGTAAG
1 TTTTATGAATTTTTAAATTATTTATAAG
44412671 TTTTATGAATTTTTAAATCT-TTTATAAG
1 TTTTATGAATTTTTAAAT-TATTTATAAG
*
44412699 ATTT-TGAATGTTTTA
1 TTTTATGAAT-TTTTA
44412714 GTAATTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.30
28 25 0.68
29 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.59
Consensus pattern (28 bp):
TTTTATGAATTTTTAAATTATTTATAAG
Found at i:44413232 original size:3 final size:3
Alignment explanation
Indices: 44413224--44413260 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44413214 TATAATTAAA
44413224 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44413261 TTCCCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44425028 original size:24 final size:24
Alignment explanation
Indices: 44424968--44425028 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
44424958 TGCTGCAGTC
* *
44424968 GATGGTGAGGATGGTAATGGTGAT
1 GATGGTGACGATGGTAATGATGAT
* * *
44424992 GACGGTGATGATGGTATTGATGAT
1 GATGGTGACGATGGTAATGATGAT
*
44425016 GATGATGACGATG
1 GATGGTGACGATG
44425029 ACGATGAAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.41, T:0.30
Consensus pattern (24 bp):
GATGGTGACGATGGTAATGATGAT
Found at i:44437737 original size:16 final size:17
Alignment explanation
Indices: 44437707--44437738 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44437697 TATTTTAAAA
44437707 TTTCTTTTACAATTTTT
1 TTTCTTTTACAATTTTT
44437724 TTTCTTTT-CAATTTT
1 TTTCTTTTACAATTTT
44437739 AGAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTTTACAATTTTT
Found at i:44439364 original size:25 final size:27
Alignment explanation
Indices: 44439293--44439357 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
44439283 CCTATCAGGT
*
44439293 AGGCGCCAATGAAGGTGCCTGATAGAG
1 AGGCGCCAATGAATGTGCCTGATAGAG
44439320 AGGCGCCAATGAATGTGCCTGATAGAG
1 AGGCGCCAATGAATGTGCCTGATAGAG
44439347 AGGCGCCAATG
1 AGGCGCCAATG
44439358 GTGGCCTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.35, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTGATAGAG
Found at i:44439503 original size:3 final size:3
Alignment explanation
Indices: 44439497--44439549 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
44439487 GAGAGAAAGG
*
44439497 AGA AGA AG- AGA AGG AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
44439543 AGA AGA A
1 AGA AGA A
44439550 AAAAAGGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44439523 original size:23 final size:23
Alignment explanation
Indices: 44439497--44439549 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
44439487 GAGAGAAAGG
*
44439497 AGAAGAAGAGAAGGAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
44439520 AGAAGAAGAGAAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
44439543 AGAAGAA
1 AGAAGAA
44439550 AAAAAGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAGAAGAAGAAGAAGA
Found at i:44439634 original size:12 final size:12
Alignment explanation
Indices: 44439617--44439642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44439607 GTTTGTGAAT
44439617 TTTTAGAAGATA
1 TTTTAGAAGATA
44439629 TTTTAGAAGATA
1 TTTTAGAAGATA
44439641 TT
1 TT
44439643 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:44439737 original size:22 final size:21
Alignment explanation
Indices: 44439711--44439896 Score: 100
Period size: 22 Copynumber: 9.0 Consensus size: 21
44439701 TAGATTAGAA
44439711 TTTTGTATGAATATTCTAACTT
1 TTTTGTATGAATATTCTAA-TT
*
44439733 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTCTAATT
* *
44439754 TTTTTTATGAATATTGTAA--
1 TTTTGTATGAATATTCTAATT
* * *
44439773 TGTTGTCTGAATATTGTAATT
1 TTTTGTATGAATATTCTAATT
* * *
44439794 ATTTTATAATTAA-ATT-TGTATT
1 -TTTTGT-ATGAATATTCT-AATT
* * * * **
44439816 TATAGTTTTGGAT-TAGTAA--
1 TTTTG-TATGAATATTCTAATT
*
44439835 -TTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTCTAATT
*
44439855 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTCTAA-TT
*
44439877 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTCTAAT
44439897 ATTATAGTTT
Statistics
Matches: 128, Mismatches: 23, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
17 5 0.04
18 7 0.05
19 16 0.12
21 46 0.36
22 51 0.40
23 3 0.02
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTCTAATT
Found at i:44439909 original size:27 final size:26
Alignment explanation
Indices: 44439855--44440026 Score: 216
Period size: 27 Copynumber: 6.8 Consensus size: 26
44439845 TATTGTAATT
44439855 TTTTGTATGAATATTGT-A-ATTT--
1 TTTTGTATGAATATTGTAATATTTAA
*
44439877 TTTTGTATGAATATTGTAATATTATAG
1 TTTTGTATGAATATTGTAATATT-TAA
*
44439904 TTTTGTATGAATATTGTATTATTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
44439931 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATT-TAA
*
44439958 TTTTGTATGAATATTG-CA-ATTT--
1 TTTTGTATGAATATTGTAATATTTAA
*
44439980 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
44440007 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
44440027 GTCGGGATAT
Statistics
Matches: 132, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
22 33 0.25
23 2 0.02
24 6 0.05
25 5 0.04
26 1 0.01
27 85 0.64
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (26 bp):
TTTTGTATGAATATTGTAATATTTAA
Found at i:44439945 original size:19 final size:19
Alignment explanation
Indices: 44439923--44440005 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 19
44439913 AATATTGTAT
44439923 TATTGTAATTTTGTATGAA
1 TATTGTAATTTTGTATGAA
44439942 TATTGTAATATTATAATTTTGTATGAA
1 TATTG---TA--AT--T-TTGTATGAA
*
44439969 TATTGCAATTTTTTTGTATGAA
1 TATTGTAA---TTTTGTATGAA
44439991 TATTGTAATTTTGTA
1 TATTGTAATTTTGTA
44440006 ATTTTGTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 22
0.68 0.03 0.29
Matches are distributed among these distances:
19 12 0.24
22 19 0.37
23 1 0.02
24 3 0.06
25 1 0.02
26 1 0.02
27 14 0.27
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (19 bp):
TATTGTAATTTTGTATGAA
Found at i:44439984 original size:76 final size:78
Alignment explanation
Indices: 44439845--44440026 Score: 245
Period size: 76 Copynumber: 2.4 Consensus size: 78
44439835 TTTGTATGAA
44439845 TATTGTAATTTTTTGTATGAATATTGT-A-ATTTTTTTGTATGAATATTGTAATATTATAGTTTT
1 TATTGTAA--TTTTGTATGAATATTGTAATATTTTTTTGTATGAATATTGTAATATTATA-TTTT
44439908 GTATGAATATTGT-AT
63 GTATGAATATTGTAAT
*
44439923 TATTGTAATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTG-CA-ATT-T-TTTT
1 TATTGTAATTTTGTATGAATATTGTAATATT-T--TTTTGTATGAATATTGTAATATTATATTTT
44439984 GTATGAATATTGTAAT
63 GTATGAATATTGTAAT
44440000 T-TTGTAATTTTGTATGAATATTGTAAT
1 TATTGTAATTTTGTATGAATATTGTAAT
44440027 GTCGGGATAT
Statistics
Matches: 97, Mismatches: 1, Indels: 14
0.87 0.01 0.12
Matches are distributed among these distances:
76 60 0.62
77 4 0.04
78 12 0.12
79 4 0.04
80 1 0.01
81 16 0.16
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (78 bp):
TATTGTAATTTTGTATGAATATTGTAATATTTTTTTGTATGAATATTGTAATATTATATTTTGTA
TGAATATTGTAAT
Found at i:44440057 original size:76 final size:76
Alignment explanation
Indices: 44439845--44440077 Score: 236
Period size: 76 Copynumber: 3.1 Consensus size: 76
44439835 TTTGTATGAA
*
44439845 TATTGTAATTTTTTGTATGAATATTGTAAT-T--T--TTTTGTATGAATATTGTAATATTATAGT
1 TATTGTAA--TTTTGTATGAATATTGTAATATGATAATATTG-ATGAATATTGT-A-ATT-T--T
44439905 TTTGTATGAATATTGT-AT
58 TTTGTATGAATATTGTAAT
* * *
44439923 TATTGTAATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTAT
1 TATTGTAATTTTGTATGAATATTGTAATATGATAATATTG-ATGAATATTGTAATTTTTTTGTAT
44439988 GAATATTGTAAT
65 GAATATTGTAAT
*
44440000 T-TTGTAATTTTGTATGAATATTGTAATGTCGGGAT-ATATTG-T-AATATTGTAA-TTTTTTGT
1 TATTGTAATTTTGTATGAATATTGTAATAT---GATAATATTGATGAATATTGTAATTTTTTTGT
44440060 ATGAATATTGTAAT
63 ATGAATATTGTAAT
44440074 TATT
1 TATT
44440078 TTATAATTAA
Statistics
Matches: 140, Mismatches: 5, Indels: 23
0.83 0.03 0.14
Matches are distributed among these distances:
74 23 0.16
75 11 0.08
76 65 0.46
77 4 0.03
78 14 0.10
79 6 0.04
80 1 0.01
81 16 0.11
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (76 bp):
TATTGTAATTTTGTATGAATATTGTAATATGATAATATTGATGAATATTGTAATTTTTTTGTATG
AATATTGTAAT
Found at i:44440067 original size:123 final size:117
Alignment explanation
Indices: 44439704--44440073 Score: 331
Period size: 123 Copynumber: 3.0 Consensus size: 117
44439694 TATAGTTTAG
*
44439704 ATTAGAATTTTGTATGAATATT-CTAACTTTTTTGTATGAATATTGTAATTTTTTT-TATGAATA
1 ATTATAATTTTGTATGAATATTGC-AA-TTTTTTGTATGAATATTGTAATTTTTTTGTATGAATA
* * * ** ***
44439767 TTGTAATGTTGTCTGA-ATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT-TTGG
64 TTGTAATGTTG--GGATATATTGTAA-TA--TTGTAATT--TTTTGTATGAATA-TTGTAAT
*
44439827 ATTAGTAA-TTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATAT
1 ATTA-TAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATAT
* * *
44439891 TGTAATATTATAGTTTTGTATGAATATTGTATTATTGTAA--TTTTGTATGAATATTGTAAT
65 TG---TA--AT-G-TTGGGAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAAT
44439951 ATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATG
1 ATTATAATTTTGTATGAATATTGCAA-TTTTTTGTATGAATATTGTAA--TT-T--TTTTGTATG
*
44440016 AATATTGTAATGTCGGGATATATTGTAATATTGTAATTTTTTGTATGAATATTGTAAT
60 AATATTGTAATGTTGGGATATATTGTAATATTGTAATTTTTTGTATGAATATTGTAAT
44440074 TATTTTATAA
Statistics
Matches: 206, Mismatches: 18, Indels: 46
0.76 0.07 0.17
Matches are distributed among these distances:
121 16 0.08
122 28 0.14
123 60 0.29
124 35 0.17
125 23 0.11
126 2 0.01
127 4 0.02
128 9 0.04
129 1 0.00
130 20 0.10
131 8 0.04
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (117 bp):
ATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATT
GTAATGTTGGGATATATTGTAATATTGTAATTTTTTGTATGAATATTGTAAT
Found at i:44440156 original size:60 final size:60
Alignment explanation
Indices: 44440067--44440188 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
44440057 TGTATGAATA
* * * * *
44440067 TTGTAATTATTTTATAATTAAATTTTTAGTAACTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAAATTTTTAGTAACTTAGGATTAAGCTATAAATTGTTGTGT
* * *
44440127 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAATTAAATTT-TTAGTAACTTAGGATTAAGCTATAAATTGTTGTGT
44440187 TT
1 TT
44440189 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 13 0.25
60 40 0.75
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAAATTTTTAGTAACTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:44440280 original size:38 final size:38
Alignment explanation
Indices: 44440228--44440305 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
44440218 AAGTTTATAA
* * *
44440228 AAAAAAATTCAAAATCATTTCATTAAAAGTTTAATTAT
1 AAAAAAATTAAAAATCATTTCATTAAAAGCTTAACTAT
* *
44440266 AAAAAAATTAAAAATTATTTTATTAAAAGCTTAACTAT
1 AAAAAAATTAAAAATCATTTCATTAAAAGCTTAACTAT
44440304 AA
1 AA
44440306 CTGACTGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (38 bp):
AAAAAAATTAAAAATCATTTCATTAAAAGCTTAACTAT
Found at i:44440466 original size:15 final size:16
Alignment explanation
Indices: 44440430--44440466 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44440420 NNNNNNNNNT
*
44440430 TTTTATATAATGTAAC
1 TTTTATATAATGTAAA
44440446 TTTTATATAAT-TAAA
1 TTTTATATAATGTAAA
44440461 TTTTAT
1 TTTTAT
44440467 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTTATATAATGTAAA
Found at i:44442089 original size:6 final size:6
Alignment explanation
Indices: 44442078--44442118 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
44442068 GCATCATGCA
* * *
44442078 CCAGAG CCAGAG CCTGAG CCAGAG CTAGAG CCAGAG ACAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
44442119 ACTATATTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.32, T:0.05
Consensus pattern (6 bp):
CCAGAG
Found at i:44445582 original size:21 final size:21
Alignment explanation
Indices: 44445556--44445607 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
44445546 AATACCTTAT
*
44445556 TTTTTTCTTCT-TTTCCTTCC
1 TTTTTTCTTCTGCTTCCTTCC
44445576 TTCTTTTCTTCTGCTTCCTTCC
1 TT-TTTTCTTCTGCTTCCTTCC
*
44445598 TTATTTCTTC
1 TTTTTTCTTC
44445608 CGTTTCTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 10 0.36
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTTCTTCTGCTTCCTTCC
Found at i:44447690 original size:11 final size:11
Alignment explanation
Indices: 44447676--44447715 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
44447666 TGTTTTCTCC
44447676 CTATTTTGCTA
1 CTATTTTGCTA
*
44447687 CTATTTTACTA
1 CTATTTTGCTA
* *
44447698 TTATGTTGCTA
1 CTATTTTGCTA
44447709 CTATTTT
1 CTATTTT
44447716 TGTTGGTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:44447816 original size:30 final size:30
Alignment explanation
Indices: 44447757--44447816 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
44447747 TATTTTATTA
*
44447757 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGAATTTG
44447787 TTAATTTTGTTATTATTTTAGAA-GAATTTG
1 TTAATTTTGTTATTATTTTA-AAGGAATTTG
44447817 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGAATTTG
Found at i:44451178 original size:7 final size:7
Alignment explanation
Indices: 44451166--44451198 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
44451156 TCCAGCAAAA
44451166 ATGAAAT
1 ATGAAAT
44451173 ATGAAAT
1 ATGAAAT
44451180 ATGAAAT
1 ATGAAAT
44451187 ATGAAAT
1 ATGAAAT
*
44451194 GTGAA
1 ATGAA
44451199 TGGTATGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (7 bp):
ATGAAAT
Found at i:44465675 original size:12 final size:12
Alignment explanation
Indices: 44465637--44465676 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
44465627 ATTATTTATG
44465637 TCTTTT-ATAAA
1 TCTTTTAATAAA
44465648 T-TTTTAAT-AA
1 TCTTTTAATAAA
*
44465658 TATTTTAATAAA
1 TCTTTTAATAAA
44465670 TCTTTTA
1 TCTTTTA
44465677 TATCATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.28
11 10 0.40
12 8 0.32
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (12 bp):
TCTTTTAATAAA
Found at i:44465735 original size:18 final size:18
Alignment explanation
Indices: 44465712--44465748 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44465702 AATCTTAAAT
44465712 ATTGAAACTTGAATCTTC
1 ATTGAAACTTGAATCTTC
44465730 ATTGAAACTTGAATCTTC
1 ATTGAAACTTGAATCTTC
44465748 A
1 A
44465749 GAGTTCGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTGAAACTTGAATCTTC
Found at i:44473696 original size:14 final size:14
Alignment explanation
Indices: 44473677--44473704 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44473667 ACTCGGCATA
44473677 AGACTTGGCAAAAT
1 AGACTTGGCAAAAT
44473691 AGACTTGGCAAAAT
1 AGACTTGGCAAAAT
44473705 TCAGACATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGACTTGGCAAAAT
Found at i:44474993 original size:22 final size:22
Alignment explanation
Indices: 44474964--44475016 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
44474954 ATATATATAT
* * *
44474964 AATT-AATAGAATTGATTTTAA
1 AATTAAATAAAATTAATTTCAA
*
44474985 AGTTAAATAAAATTAATTTCAA
1 AATTAAATAAAATTAATTTCAA
44475007 AATTAAATAA
1 AATTAAATAA
44475017 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTAAATAAAATTAATTTCAA
Found at i:44483744 original size:71 final size:73
Alignment explanation
Indices: 44483603--44483752 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 73
44483593 ACTTTTGGTT
* **
44483603 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTTATGTCACTTGGC
1 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
*
44483668 CATTAACC
66 CATTAACA
* * * * * *
44483676 AAGAGTTGTCAC-ATTTATAGTGATGAGTTATGTCTCTTG-TTACCAAAAGTCATGTCATTTAAT
1 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
*
44483739 TATTAACA
66 CATTAACA
44483747 AAGAGT
1 AAGAGT
44483753 CATAATTATT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
71 30 0.45
72 24 0.36
73 12 0.18
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (73 bp):
AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
CATTAACA
Found at i:44489292 original size:22 final size:21
Alignment explanation
Indices: 44489249--44489292 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
44489239 TACGCGTGTG
*
44489249 TTTTTAGATATTATCTTCTAA
1 TTTTTAGATATTATATTCTAA
* *
44489270 TTTTTATATATTTATATTTTAA
1 TTTTTAGATA-TTATATTCTAA
44489292 T
1 T
44489293 GCGGATTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAGATATTATATTCTAA
Found at i:44500914 original size:27 final size:27
Alignment explanation
Indices: 44500876--44500931 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
44500866 ATTATAATAT
44500876 AAAATACTAATAGAATAG-AAGAAGAAG
1 AAAATACTAATAGAATAGAAAGAA-AAG
*
44500903 AAAATACTAATATAATAGAAAGAAAAG
1 AAAATACTAATAGAATAGAAAGAAAAG
44500930 AA
1 AA
44500932 TTGTCTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATACTAATAGAATAGAAAGAAAAG
Found at i:44502108 original size:12 final size:12
Alignment explanation
Indices: 44502093--44502117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44502083 TCTCTCTCTC
44502093 TCTCTCGTTCTA
1 TCTCTCGTTCTA
44502105 TCTCTCGTTCTA
1 TCTCTCGTTCTA
44502117 T
1 T
44502118 GGATGGAAAG
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:0.08, C:0.32, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTCTCGTTCTA
Found at i:44509913 original size:22 final size:22
Alignment explanation
Indices: 44509870--44509914 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44509860 TGTAACAAGA
***
44509870 TTTTAATTTAACACGTTTAATT
1 TTTTAATTTAACACGAACAATT
*
44509892 TTTTAATTTAACTCGAACAATT
1 TTTTAATTTAACACGAACAATT
44509914 T
1 T
44509915 CACTCGATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTAATTTAACACGAACAATT
Found at i:44514498 original size:16 final size:16
Alignment explanation
Indices: 44514461--44514500 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
44514451 TTGATAAAAT
* *
44514461 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
44514477 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
44514493 TAAAATTA
1 TAAAATTA
44514501 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:44514561 original size:66 final size:68
Alignment explanation
Indices: 44514489--44514634 Score: 206
Period size: 75 Copynumber: 2.1 Consensus size: 68
44514479 AAATTAATTG
*
44514489 TTAGTAAAATTATCAAATTATTAATTG-TTAATTG-TATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAACATT
44514552 TGA
66 TGA
44514555 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTAATTATATTAATTGTTGTAACAAAATC
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTG-----T-TATTAATTGTTGTAACAAAATC
44514620 TAACATTTGA
59 TAACATTTGA
44514630 TTAGT
1 TTAGT
44514635 TTACATTTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
66 27 0.39
68 7 0.10
75 36 0.51
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAACATT
TGA
Found at i:44514594 original size:16 final size:16
Alignment explanation
Indices: 44514570--44514608 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
44514560 AAAATTATCA
* *
44514570 AATTATTAATTGTATT
1 AATTGTTAATTATATT
44514586 AATTGTTAATTATATT
1 AATTGTTAATTATATT
44514602 AATTGTT
1 AATTGTT
44514609 GTAACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTGTTAATTATATT
Found at i:44514925 original size:20 final size:20
Alignment explanation
Indices: 44514900--44514950 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
44514890 NNNNNNNNNC
44514900 TAAAAATAAAATTGAAAACA
1 TAAAAATAAAATTGAAAACA
*
44514920 TAAAAATAAAATTGAAAACT
1 TAAAAATAAAATTGAAAACA
*
44514940 TAAACATAAAA
1 TAAAAATAAAA
44514951 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAAAATAAAATTGAAAACA
Found at i:44515021 original size:20 final size:20
Alignment explanation
Indices: 44514993--44515033 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44514983 ATGTCGGGGG
*
44514993 AAATGAAATTGAAAACATAA
1 AAATAAAATTGAAAACATAA
*
44515013 AAATAAAATTGAAAACTTAA
1 AAATAAAATTGAAAACATAA
44515033 A
1 A
44515034 CTGTCAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATAAAATTGAAAACATAA
Found at i:44515130 original size:16 final size:16
Alignment explanation
Indices: 44515109--44515141 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44515099 TATATATATT
44515109 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
44515125 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
44515141 A
1 A
44515142 TATATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:44523414 original size:2 final size:2
Alignment explanation
Indices: 44523407--44523442 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
44523397 TTATTAAATC
*
44523407 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
44523443 TTAATAAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44523831 original size:5 final size:5
Alignment explanation
Indices: 44523821--44523846 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44523811 TGAGCATTCG
44523821 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
44523847 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:44524896 original size:9 final size:9
Alignment explanation
Indices: 44524882--44524918 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44524872 TATAGTTTGA
44524882 TATTCGAAT
1 TATTCGAAT
44524891 TATTCGAAT
1 TATTCGAAT
*
44524900 TATTCGAGT
1 TATTCGAAT
44524909 TATTCGAAT
1 TATTCGAAT
44524918 T
1 T
44524919 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44525200 original size:41 final size:41
Alignment explanation
Indices: 44525155--44525252 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
44525145 GGCTTTGTAC
*
44525155 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
44525196 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
*
44525237 CTAGCAGGTTTAATGC
1 CTAGCAGGCTTAATGC
44525253 TAGTGTATTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
Found at i:44530717 original size:14 final size:14
Alignment explanation
Indices: 44530698--44530726 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44530688 ATCACTTGAT
44530698 TGTCTCTGGTGAAC
1 TGTCTCTGGTGAAC
44530712 TGTCTCTGGTGAAC
1 TGTCTCTGGTGAAC
44530726 T
1 T
44530727 TAGACACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (14 bp):
TGTCTCTGGTGAAC
Found at i:44532238 original size:19 final size:20
Alignment explanation
Indices: 44532214--44532260 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
44532204 GTAACTTCCT
*
44532214 TAACTAACTAAC-TGCTCAC
1 TAACTAACTAACTTGATCAC
* *
44532233 TAACT-ACTGACTTGATGAC
1 TAACTAACTAACTTGATCAC
44532252 TAACTAACT
1 TAACTAACT
44532261 TCCTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 15 0.65
20 3 0.13
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
TAACTAACTAACTTGATCAC
Found at i:44534138 original size:14 final size:14
Alignment explanation
Indices: 44534121--44534147 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44534111 ATTTGGTGAG
44534121 AGAAAAAATTTTAA
1 AGAAAAAATTTTAA
44534135 AGAAAAAATTTTA
1 AGAAAAAATTTTA
44534148 TGTTAAAATT
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AGAAAAAATTTTAA
Found at i:44534155 original size:13 final size:13
Alignment explanation
Indices: 44534139--44534181 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
44534129 TTTTAAAGAA
44534139 AAAATTTTATGTT
1 AAAATTTTATGTT
44534152 AAAATTTTA----
1 AAAATTTTATGTT
44534161 AAAATTTTATGTT
1 AAAATTTTATGTT
44534174 AAAATTTT
1 AAAATTTT
44534182 TTTGAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.35
13 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
AAAATTTTATGTT
Found at i:44534164 original size:22 final size:22
Alignment explanation
Indices: 44534138--44534181 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
44534128 ATTTTAAAGA
44534138 AAAAATTTTATGTTAAAATTTT
1 AAAAATTTTATGTTAAAATTTT
44534160 AAAAATTTTATGTTAAAATTTT
1 AAAAATTTTATGTTAAAATTTT
44534182 TTTGAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAAATTTTATGTTAAAATTTT
Found at i:44538699 original size:28 final size:28
Alignment explanation
Indices: 44538647--44538700 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
44538637 ATTAAGATTC
* **
44538647 AATTGATGGTACATATTTACCTTTAAAA
1 AATTGATGATACATATTTAAATTTAAAA
*
44538675 AATTGATTATACATATTTAAATTTAA
1 AATTGATGATACATATTTAAATTTAA
44538701 CTGAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (28 bp):
AATTGATGATACATATTTAAATTTAAAA
Found at i:44549451 original size:13 final size:13
Alignment explanation
Indices: 44549433--44549457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44549423 AGTTCTTTAT
44549433 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
44549446 TGCTTTTGAGAA
1 TGCTTTTGAGAA
44549458 ATTTGAGTGT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:44550709 original size:11 final size:11
Alignment explanation
Indices: 44550693--44550718 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44550683 CAAGAAATAC
44550693 CAGCAAATCAA
1 CAGCAAATCAA
44550704 CAGCAAATCAA
1 CAGCAAATCAA
44550715 CAGC
1 CAGC
44550719 TTCAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.31, G:0.12, T:0.08
Consensus pattern (11 bp):
CAGCAAATCAA
Found at i:44550769 original size:19 final size:19
Alignment explanation
Indices: 44550723--44550771 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
44550713 AACAGCTTCA
* *
44550723 AAATATTAAACAGAAGAGG
1 AAATATAAAACAGAAGAAG
*
44550742 AACTAATAAAACAGAAGAAG
1 AAAT-ATAAAACAGAAGAAG
44550762 AAATATAAAA
1 AAATATAAAA
44550772 GAAACTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.14
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:44559197 original size:13 final size:13
Alignment explanation
Indices: 44559179--44559206 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44559169 GCAATCGTTA
44559179 TAGAATACATGGT
1 TAGAATACATGGT
44559192 TAGAATACATGGT
1 TAGAATACATGGT
44559205 TA
1 TA
44559207 ATGGTTCTTT
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:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (13 bp):
TAGAATACATGGT
Found at i:44562124 original size:3 final size:3
Alignment explanation
Indices: 44562116--44562141 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44562106 TTCTTTTCGT
44562116 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
44562142 TTCATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:44577301 original size:18 final size:18
Alignment explanation
Indices: 44577278--44577314 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44577268 AAGTGGCATG
44577278 CTGCTTTGACAAAGTTTC
1 CTGCTTTGACAAAGTTTC
44577296 CTGCTTTGACAAAGTTTC
1 CTGCTTTGACAAAGTTTC
44577314 C
1 C
44577315 AACTTCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (18 bp):
CTGCTTTGACAAAGTTTC
Found at i:44581782 original size:17 final size:18
Alignment explanation
Indices: 44581760--44581794 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44581750 ATGTTTTGGA
44581760 TCCTTATT-TATTTATGT
1 TCCTTATTATATTTATGT
*
44581777 TCCTTATTATTTTTATGT
1 TCCTTATTATATTTATGT
44581795 ACAATGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TCCTTATTATATTTATGT
Found at i:44594170 original size:13 final size:13
Alignment explanation
Indices: 44594148--44594183 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
44594138 GGGTATAGTT
*
44594148 ATATATTAAAAAA
1 ATATAGTAAAAAA
44594161 ATATAGT-AAAAA
1 ATATAGTAAAAAA
44594173 ATATAGTAAAA
1 ATATAGTAAAA
44594184 TATTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (13 bp):
ATATAGTAAAAAA
Found at i:44594288 original size:3 final size:3
Alignment explanation
Indices: 44594280--44594328 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
44594270 AATATTAACC
*
44594280 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44594328 T
1 T
44594329 GTTTGTCAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:44602818 original size:3 final size:3
Alignment explanation
Indices: 44602798--44602861 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
44602788 GTCTGTTAAT
* * *
44602798 TAA TAA TGA TGA TGA TAA TAA 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
*
44602846 TAA TAA TGA TAA -AA TA
1 TAA TAA TAA TAA TAA TA
44602862 GCTGTAAGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44603869 original size:27 final size:28
Alignment explanation
Indices: 44603839--44603893 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
44603829 CAAAAAAGTT
*
44603839 TTTTAAAAA-ATTAAAAA-ATTCATAAAA
1 TTTTAAAAAGATAAAAAATATTC-TAAAA
44603866 TTTTAAAAAGATAAAAAATATTCTAAAA
1 TTTTAAAAAGATAAAAAATATTCTAAAA
44603894 AATTAGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
TTTTAAAAAGATAAAAAATATTCTAAAA
Found at i:44620130 original size:16 final size:17
Alignment explanation
Indices: 44620097--44620132 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
44620087 GTGTATAATT
44620097 AAATTAATACTACAAATC
1 AAATTAATAC-ACAAATC
44620115 AAATTAATAC-CAAATC
1 AAATTAATACACAAATC
44620131 AA
1 AA
44620133 TCAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATTAATACACAAATC
Found at i:44620397 original size:22 final size:21
Alignment explanation
Indices: 44620365--44620408 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
44620355 AACAAGACTT
* *
44620365 TATTTTTATTTTAAAATATAA
1 TATTTTTATTTAAAAAAATAA
44620386 TATTTTTAATTTAAAAAAATAA
1 TATTTTT-ATTTAAAAAAATAA
44620408 T
1 T
44620409 TTTCAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTTATTTAAAAAAATAA
Found at i:44626630 original size:2 final size:2
Alignment explanation
Indices: 44626623--44626673 Score: 93
Period size: 2 Copynumber: 25.0 Consensus size: 2
44626613 TGACAAGAGA
44626623 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
44626665 AT AT GAT AT
1 AT AT -AT AT
44626674 TAGATCAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44628622 original size:6 final size:6
Alignment explanation
Indices: 44628611--44628654 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
44628601 TGAGAAGAGG
*
44628611 AGAAAA AGAAAA AGAAAA AGAAAA TA-AAGAA ATAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA -AGAA-AA AGAAAA AGAAAA A
44628655 TTAAATTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:44633084 original size:20 final size:20
Alignment explanation
Indices: 44633059--44633115 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
44633049 TACCTTTTGT
* * *
44633059 AAATTATCAAATTTCTTACA
1 AAATTACCAAATATCTTAAA
*
44633079 AAATTACCGAATATCTTAAA
1 AAATTACCAAATATCTTAAA
*
44633099 AAATTACTAAAT-TCTTA
1 AAATTACCAAATATCTTA
44633116 TAATATTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTACCAAATATCTTAAA
Done.