Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 105 of 214
Found at i:31256612 original size:28 final size:28
Alignment explanation
Indices: 31256582--31256635 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
31256572 AAATCATTTA
*
31256582 AAAAT-AATAAAA-TTATAAATTATAAAT
1 AAAATAAATAAAAGTT-TAAAATATAAAT
31256609 AAAATAAATAAAAGTTTAAAATATAAA
1 AAAATAAATAAAAGTTTAAAATATAAA
31256636 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 17 0.71
29 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATAAATAAAAGTTTAAAATATAAAT
Found at i:31257760 original size:17 final size:17
Alignment explanation
Indices: 31257735--31257773 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31257725 TAATCCAATA
* *
31257735 GTTGTATAAGATAAATT
1 GTTGAATAAAATAAATT
31257752 GTTGAATAAAATAAATT
1 GTTGAATAAAATAAATT
*
31257769 TTTGA
1 GTTGA
31257774 GCGAGGCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
GTTGAATAAAATAAATT
Found at i:31261733 original size:25 final size:25
Alignment explanation
Indices: 31261699--31261749 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
31261689 ATTATCATTA
31261699 AATATGATTGCATGTAAAGTGTTAT
1 AATATGATTGCATGTAAAGTGTTAT
** *
31261724 AATATGATTGTGTTTAAAGTGTTAT
1 AATATGATTGCATGTAAAGTGTTAT
31261749 A
1 A
31261750 TGAATGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (25 bp):
AATATGATTGCATGTAAAGTGTTAT
Found at i:31269684 original size:192 final size:192
Alignment explanation
Indices: 31269353--31269743 Score: 547
Period size: 192 Copynumber: 2.0 Consensus size: 192
31269343 TGGCAGAGTG
* ** *
31269353 TGCTAATATGAGAAGATTAATGGATTAGGATGTGTATATTAATAAAATCAACCATTTTAGGTTGG
1 TGCTAATATGAGAAGATTAATGGATTAGGATGTGGATATTAATAAAATCAACCAACTTAGGCTGG
* *
31269418 TGGATTCTGACTGTGTTTATAATAGTGGATGAAGTTATAAAGAGAGCGAAAATTTTGGGATTTGT
66 TGGATTCTGACTGTGTTTATAAGAGTGGATGAAATTATAAAGAGAGCGAAAATTTTGGGATTTGT
** * *
31269483 TTACCATTGGGCACTGGTAATCTGTGATGGAAATAAGCATTTTTT-TGTATTCTAGTAGAGGA
131 CGACCATTGGGCACTGGTAATCTATGATGGAAATAAGC-TTTTTTAAGTATTCTAGTAGAGGA
* * * *
31269545 TGCTAATATGGGAAGATTAATGGATTAGGATGTGGATCTTAATAAGATTAACCAACTTAGGCTGG
1 TGCTAATATGAGAAGATTAATGGATTAGGATGTGGATATTAATAAAATCAACCAACTTAGGCTGG
*
31269610 TGGATTCTGACT-TTTCTTATAAGAGTGGATGAAATTATAAAGAGGGAG-GAAAA-TTTGGGATT
66 TGGATTCTGACTGTGT-TTATAAGAGTGGATGAAATTATAAAGA--GAGCGAAAATTTTGGGATT
* * *
31269672 TGTCGGCCATTGGGCACTGGTTATCTATGATGGAAATAAGCTTTTTTAAGTATTCTAGTAGGGGA
128 TGTCGACCATTGGGCACTGGTAATCTATGATGGAAATAAGCTTTTTTAAGTATTCTAGTAGAGGA
*
31269737 TACTAAT
1 TGCTAAT
31269744 GAACAAGTCA
Statistics
Matches: 176, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
191 8 0.05
192 160 0.91
193 5 0.03
194 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (192 bp):
TGCTAATATGAGAAGATTAATGGATTAGGATGTGGATATTAATAAAATCAACCAACTTAGGCTGG
TGGATTCTGACTGTGTTTATAAGAGTGGATGAAATTATAAAGAGAGCGAAAATTTTGGGATTTGT
CGACCATTGGGCACTGGTAATCTATGATGGAAATAAGCTTTTTTAAGTATTCTAGTAGAGGA
Found at i:31271315 original size:16 final size:16
Alignment explanation
Indices: 31271294--31271324 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31271284 TAATTGATTG
*
31271294 ATTTTTAGTTTAATTA
1 ATTTTTAGATTAATTA
31271310 ATTTTTAGATTAATT
1 ATTTTTAGATTAATT
31271325 GATGTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTTAGATTAATTA
Found at i:31275846 original size:12 final size:12
Alignment explanation
Indices: 31275829--31275853 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31275819 GTATATTTGA
31275829 ATTTTGGATTTT
1 ATTTTGGATTTT
31275841 ATTTTGGATTTT
1 ATTTTGGATTTT
31275853 A
1 A
31275854 ATTAGGATAG
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (12 bp):
ATTTTGGATTTT
Found at i:31290149 original size:17 final size:17
Alignment explanation
Indices: 31290127--31290163 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31290117 AAAAAACAAG
*
31290127 ATAACTCTTGACCTTTC
1 ATAACTCTTGACATTTC
*
31290144 ATAACTTTTGACATTTC
1 ATAACTCTTGACATTTC
31290161 ATA
1 ATA
31290164 TAACATAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (17 bp):
ATAACTCTTGACATTTC
Found at i:31302796 original size:16 final size:16
Alignment explanation
Indices: 31302777--31302809 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31302767 AAATTTTAAA
31302777 TTTAATTTATTTCATT
1 TTTAATTTATTTCATT
31302793 TTTAATTTATTTCATT
1 TTTAATTTATTTCATT
31302809 T
1 T
31302810 CAATTTTTTG
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:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAATTTATTTCATT
Found at i:31302799 original size:21 final size:22
Alignment explanation
Indices: 31302781--31303041 Score: 179
Period size: 22 Copynumber: 12.5 Consensus size: 22
31302771 TTTAAATTTA
31302781 ATTT-ATTTC-ATTTTTAATTT
1 ATTTCATTTCAATTTTTAATTT
31302801 ATTTCATTTCAA--TTT--TTT
1 ATTTCATTTCAATTTTTAATTT
*
31302819 GTTTCATTTCAATTTTT-ATTT
1 ATTTCATTTCAATTTTTAATTT
** *
31302840 ATTTCATTTCAATTTTTTGTTC
1 ATTTCATTTCAATTTTTAATTT
*
31302862 ATTTCATTTCAATTTTTAGTTT
1 ATTTCATTTCAATTTTTAATTT
*
31302884 CATTTCA-TT---TTTTTAGTTT
1 -ATTTCATTTCAATTTTTAATTT
*
31302903 ATTTCATTTC-A-TTTCAATTTTT
1 ATTTCATTTCAATTTTTAA--TTT
31302925 CATTTCATTTC-ATTTTTAATTT
1 -ATTTCATTTCAATTTTTAATTT
*
31302947 ATTTCAATTCAATTTTT-A---
1 ATTTCATTTCAATTTTTAATTT
*
31302965 GTTTCATTTC-ATTTTCTAATTT
1 ATTTCATTTCAATTTT-TAATTT
**
31302987 ATTTCATTT-AATTTCAAATTT
1 ATTTCATTTCAATTTTTAATTT
* *
31303008 CCATTACATTTC-CTTTTT-ATTT
1 --ATTTCATTTCAATTTTTAATTT
31303030 CATTTCATTTCA
1 -ATTTCATTTCA
31303042 TTTCATTTCA
Statistics
Matches: 196, Mismatches: 20, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
17 5 0.03
18 29 0.15
19 13 0.07
20 14 0.07
21 49 0.25
22 53 0.27
23 28 0.14
24 5 0.03
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTCATTTCAATTTTTAATTT
Found at i:31302825 original size:18 final size:18
Alignment explanation
Indices: 31302802--31302908 Score: 108
Period size: 18 Copynumber: 5.6 Consensus size: 18
31302792 TTTTAATTTA
31302802 TTTCATTTCAATTTTTTG
1 TTTCATTTCAATTTTTTG
*
31302820 TTTCATTTCAATTTTTATTTA
1 TTTCATTTCAA--TTT-TTTG
31302841 TTTCATTTCAATTTTTTG
1 TTTCATTTCAATTTTTTG
*
31302859 TTCATTTCATTTCAATTTTTAG
1 ----TTTCATTTCAATTTTTTG
*
31302881 TTTCATTTCATTTTTTTAG
1 TTTCATTTCAATTTTTT-G
31302900 TTT-ATTTCA
1 TTTCATTTCA
31302909 TTTCATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
18 35 0.46
19 7 0.09
20 3 0.04
21 14 0.18
22 17 0.22
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTCATTTCAATTTTTTG
Found at i:31302827 original size:23 final size:22
Alignment explanation
Indices: 31302741--31303113 Score: 149
Period size: 23 Copynumber: 16.8 Consensus size: 22
31302731 TTAAATAATA
31302741 AATTTATTTCATTTCATTTCAATTTT
1 AATTT-TTT-ATTTCATTTC-A-TTT
** *
31302767 AAATTTTAAATTTAATTT-ATTT
1 -AATTTTTTATTTCATTTCATTT
* *
31302789 CATTTTTAATTT-ATTTCATTT
1 AATTTTTTATTTCATTTCATTT
*
31302810 CAATTTTTTGTTTCATTTC----
1 -AATTTTTTATTTCATTTCATTT
31302829 AA-TTTTTATTT-ATTTCATTT
1 AATTTTTTATTTCATTTCATTT
*
31302849 CAATTTTTT-GTTCATTTCATTT
1 -AATTTTTTATTTCATTTCATTT
31302871 CAA-TTTTTAGTTTCATTTCATTT
1 -AATTTTTTA-TTTCATTTCATTT
*
31302894 -TTTTAGTTTATTTCATTTCATTT
1 AATTT--TTTATTTCATTTCATTT
*
31302917 CAATTTTTCATTTCATTTCATTT
1 -AATTTTTTATTTCATTTCATTT
* *
31302940 --TTAATTTATTTCA----ATTC
1 AATT-TTTTATTTCATTTCATTT
31302957 AATTTT-TAGTTTCATTTCATTT
1 AATTTTTTA-TTTCATTTCATTT
** ** *
31302979 TCTAATTTATTTCATTTAATTT
1 AATTTTTTATTTCATTTCATTT
* ** * *
31303001 CAAATTTCCATTACATTTCCTTTT
1 -AATTTTTTATTTCATTT-CATTT
*
31303025 TATTTCATTTCATTTCATTTCATTT
1 AATTT--TTT-ATTTCATTTCATTT
* *
31303050 CAA-TATTTAGTTTCACTTC-TTT
1 -AATTTTTTA-TTTCATTTCATTT
*
31303072 -TTTTATTTCATTTCATTTCATTT
1 AATTT-TTT-ATTTCATTTCATTT
*
31303095 CAATTTTTTGTTTCATTTC
1 -AATTTTTTATTTCATTTC
31303114 TTAATTATTA
Statistics
Matches: 259, Mismatches: 48, Indels: 82
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.02
17 13 0.05
18 8 0.03
19 2 0.01
20 6 0.02
21 32 0.12
22 63 0.24
23 85 0.33
24 10 0.04
25 20 0.08
26 10 0.04
27 5 0.02
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (22 bp):
AATTTTTTATTTCATTTCATTT
Found at i:31302992 original size:107 final size:105
Alignment explanation
Indices: 31302802--31303041 Score: 92
Period size: 107 Copynumber: 2.3 Consensus size: 105
31302792 TTTTAATTTA
* * * *
31302802 TTTCATTTCAA-TTTT--TTGTTTCATTTCAATTTTTA-TTTATTTCATTTCAATTTT-TTGTTC
1 TTTCATTTCAATTTTTATTTATTTCAATTCAATTTTTAGTTCATTTCATTTCAATTTTAGT-TTC
* * *
31302862 ATTTCATTTCAATTTTTAGTTTCATTTCATTT--TTTTAGTTTATTTCA
65 ATTT-AATT---TTTTTAGTTT-ATTT-ATTTCATTTCA-ATT-TTTCA
* * * * *
31302909 TTTCATTTCAA--TTT-TTCATTTCATTTC-ATTTTTAATTTATTTCAATTCAATTTTTAGTTTC
1 TTTCATTTCAATTTTTATTTATTTCAATTCAATTTTTAGTTCATTTCATTTCAA-TTTTAGTTTC
* * * * * *
31302970 ATTTCA-TTTTCTAATTTATTTCATTTAATTTCAAATTTCCA
65 ATTTAATTTTTTTAGTTTATTT-ATTTCATTTCAATTTTTCA
* * *
31303011 TTACATTTC-CTTTTTATTTCATTTCATTTCA
1 TTTCATTTCAATTTTTATTT-ATTTCAATTCA
31303042 TTTCATTTCA
Statistics
Matches: 107, Mismatches: 15, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
102 21 0.20
103 12 0.11
104 6 0.06
105 10 0.09
106 11 0.10
107 35 0.33
108 11 0.10
109 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.62
Consensus pattern (105 bp):
TTTCATTTCAATTTTTATTTATTTCAATTCAATTTTTAGTTCATTTCATTTCAATTTTAGTTTCA
TTTAATTTTTTTAGTTTATTTATTTCATTTCAATTTTTCA
Found at i:31303045 original size:44 final size:43
Alignment explanation
Indices: 31302747--31303113 Score: 213
Period size: 39 Copynumber: 8.3 Consensus size: 43
31302737 AATAAATTTA
* * *
31302747 TTTCATTTCATTTCAATTTTAAATTTTAAATTTAATTT-ATTTC-ATT
1 TTTCATTTCATTTC-ATTTT-TA-TTT--ATTTCATTTCATTTCAAAT
* ** *
31302793 TTTAATTT-ATTTCATTTCAATTT-TTT-GTTTCATTTC-AAT
1 TTTCATTTCATTTCATTTTTATTTATTTCATTTCATTTCAAAT
* ** *
31302832 TTTTATTT-ATTTCATTTCAATTTTTTGTTCATTTCATTTC-AAT
1 TTTCATTTCATTTCATTTTTA-TTTAT-TTCATTTCATTTCAAAT
* *
31302875 TTTTAGTTTCATTTCATTTTTTTAGTTTATTTCATTTCATTTCAATT
1 TTTCA-TTTCATTTCA--TTTTTA-TTTATTTCATTTCATTTCAAAT
*
31302922 TTTCATTTCATTTCATTTTTA---ATTT-ATTTCAATTC-AAT
1 TTTCATTTCATTTCATTTTTATTTATTTCATTTCATTTCAAAT
* *
31302960 TTTTAGTTTCATTTCATTTTCTAATTTATTTCATTTAATTTCAAAT
1 TTTCA-TTTCATTTCATTTT-T-ATTTATTTCATTTCATTTCAAAT
* * *
31303006 TTCCATTACATTTCCTTTTTATTTCATTTCATTTCATTTCATTTCAAT
1 TTTCATTTCATTTCATTTTTATTT-ATTTCATTTCATTTCA----AAT
* * *
31303054 ATTT-AGTTTCACTTCTTTTTTTATTTCATTTCATTTCATTTCAATT
1 -TTTCA-TTTCATTTC-ATTTTTATTT-ATTTCATTTCATTTCAAAT
**
31303100 TTTTGTTTCATTTC
1 TTTCATTTCATTTC
31303114 TTAATTATTA
Statistics
Matches: 265, Mismatches: 29, Indels: 55
0.76 0.08 0.16
Matches are distributed among these distances:
38 9 0.03
39 52 0.20
40 8 0.03
41 2 0.01
42 5 0.02
43 23 0.09
44 33 0.12
45 42 0.16
46 38 0.14
47 14 0.05
48 4 0.02
49 9 0.03
50 26 0.10
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.63
Consensus pattern (43 bp):
TTTCATTTCATTTCATTTTTATTTATTTCATTTCATTTCAAAT
Found at i:31303086 original size:84 final size:84
Alignment explanation
Indices: 31302840--31303101 Score: 203
Period size: 89 Copynumber: 3.0 Consensus size: 84
31302830 ATTTTTATTT
* *
31302840 ATTTCATTTCAATTTT-TTGTTCATTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTAGTTTA
1 ATTTCATTTC-ATTTTAAT-TTCATTTCATTTCAATTTTTAGTTTCACTTC-TTTTTTTA-TTTA
* *
31302904 TTTC-ATTTCATTTCAATTTTTC
62 TTTCAATTTCATTACAATTTTCC
* *
31302926 ATTTCATTTCATTTTTAATTT-ATTTCAATTCAATTTTTAGTTTCATTTCATTTTCTAATTTATT
1 ATTTCATTTCA-TTTTAATTTCATTTCATTTCAATTTTTAGTTTCACTTC--TTT-T--TTTATT
* *
31302990 TCATTT-AATTTCAAATTTCCATTACATTTCC
60 T-ATTTCAATTTC--A-TTACA--A-TTTTCC
* * * *
31303021 TTTTTATTTCA-TTTCATTTCATTTCATTTCAATATTTAGTTTCACTTCTTTTTTTATTTCATTT
1 ATTTCATTTCATTTTAATTTCATTTCATTTCAATTTTTAGTTTCACTTCTTTTTTTATTT-ATTT
*
31303085 C-ATTTCATTTCAATTTT
65 CAATTTCATTACAATTTT
31303102 TTGTTTCATT
Statistics
Matches: 146, Mismatches: 14, Indels: 35
0.75 0.07 0.18
Matches are distributed among these distances:
83 3 0.02
84 1 0.01
85 28 0.19
86 23 0.16
87 3 0.02
88 3 0.02
89 30 0.21
91 2 0.01
92 7 0.05
93 7 0.05
94 26 0.18
95 13 0.09
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (84 bp):
ATTTCATTTCATTTTAATTTCATTTCATTTCAATTTTTAGTTTCACTTCTTTTTTTATTTATTTC
AATTTCATTACAATTTTCC
Found at i:31303113 original size:5 final size:5
Alignment explanation
Indices: 31302820--31303096 Score: 126
Period size: 5 Copynumber: 53.0 Consensus size: 5
31302810 CAATTTTTTG
* **
31302820 TTTCA TTTCAA TTTTTA TTT-A TTTCA TTTCAA TTTTT TGTTCA TTTCA
1 TTTCA TTTC-A -TTTCA TTTCA TTTCA TTTC-A TTTCA T-TTCA TTTCA
* *
31302868 TTTCAA TTTTTA GTTTCA TTTCA TTT-- TTTTA GTTT-A TTTCA TTTCA
1 TTTC-A -TTTCA -TTTCA TTTCA TTTCA TTTCA -TTTCA TTTCA TTTCA
* * *
31302914 TTTCA ATT-- TTTCA TTTCA TTTCA TTTTTAA TTT-A TTTCA ATTCAA
1 TTTCA TTTCA TTTCA TTTCA TTTCA --TTTCA TTTCA TTTCA TTTC-A
* *
31302959 TTTTTA GTTTCA TTTCA TTTTCTAA TTT-A TTTCA TTTAA TTTCAAA TTTCCA
1 -TTTCA -TTTCA TTTCA -TTTC--A TTTCA TTTCA TTTCA TTTC--A TTT-CA
* * * *
31303011 TTACA TTTCCT TTTTA TTTCA TTTCA TTTCA TTTCA TTTCAA TATTTA
1 TTTCA TTT-CA TTTCA TTTCA TTTCA TTTCA TTTCA TTTC-A T-TTCA
* *
31303059 GTTTCA CTTC- TTT-- TTTTA TTTCA TTTCA TTTCA TTTCA
1 -TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
31303097 ATTTTTTGTT
Statistics
Matches: 212, Mismatches: 29, Indels: 62
0.70 0.10 0.20
Matches are distributed among these distances:
3 8 0.04
4 17 0.08
5 122 0.58
6 41 0.19
7 22 0.10
8 2 0.01
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:31303115 original size:45 final size:45
Alignment explanation
Indices: 31302820--31303113 Score: 290
Period size: 45 Copynumber: 6.6 Consensus size: 45
31302810 CAATTTTTTG
* *
31302820 TTTCATTTCAATTTTTA-TTT-ATTTCATTTCAATTT-TTT-GTTCA
1 TTTCATTTCAATTTTTAGTTTCATTTCATTT--TTTTATTTATTTCA
31302863 TTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTAGTTTATTTCA
1 TTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTA-TTTATTTCA
31302909 TTTCATTTCAATTTTTCA-TTTCATTTCA--TTTTTA---ATTT-A
1 TTTCATTTCAATTTTT-AGTTTCATTTCATTTTTTTATTTATTTCA
* * *
31302948 TTTCAATTCAATTTTTAGTTTCATTTCATTTTCTAATTTATTTCA
1 TTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTATTTATTTCA
* ** * *
31302993 TTTAATTTCAAATTTCCA-TTACATTTCCTTTTTATTTCATTTCATTTCA
1 TTTCATTTC-AATTTTTAGTTTCATTT-CATTTT-TTT-ATTT-ATTTCA
* *
31303042 TTTCATTTCAATATTTAGTTTCACTTC-TTTTTTTATTTCATTTCA
1 TTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTATTT-ATTTCA
*
31303087 TTTCATTTCAATTTTTTGTTTCATTTC
1 TTTCATTTCAATTTTTAGTTTCATTTC
31303114 TTAATTATTA
Statistics
Matches: 210, Mismatches: 22, Indels: 36
0.78 0.08 0.13
Matches are distributed among these distances:
38 1 0.00
39 26 0.12
40 4 0.02
41 4 0.02
43 20 0.10
44 13 0.06
45 62 0.30
46 44 0.21
47 6 0.03
48 10 0.05
49 20 0.10
ACGTcount: A:0.21, C:0.14, G:0.02, T:0.63
Consensus pattern (45 bp):
TTTCATTTCAATTTTTAGTTTCATTTCATTTTTTTATTTATTTCA
Found at i:31303253 original size:25 final size:26
Alignment explanation
Indices: 31303218--31303276 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
31303208 TTATTTACTT
31303218 AATTATTTTACACTATATAATAATCG
1 AATTATTTTACACTATATAATAATCG
*
31303244 AATT-TTTTACACTATATAATAATTG
1 AATTATTTTACACTATATAATAATCG
*
31303269 AATAATTT
1 AATTATTT
31303277 AAACAATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (26 bp):
AATTATTTTACACTATATAATAATCG
Found at i:31309415 original size:19 final size:20
Alignment explanation
Indices: 31309378--31309415 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
31309368 ATTCTAGTAA
* *
31309378 TAAAACTAATGACAGTAATC
1 TAAAACTAAAGACAATAATC
31309398 TAAAAC-AAAGACAATAAT
1 TAAAACTAAAGACAATAAT
31309416 ACTCATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (20 bp):
TAAAACTAAAGACAATAATC
Found at i:31311441 original size:50 final size:50
Alignment explanation
Indices: 31311368--31311560 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
31311358 ATTTGGGTAA
*
31311368 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACAAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
*
31311418 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
** * * * ** *
31311468 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
** *
31311518 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
31311561 TGTTATTATC
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 92 0.74
51 33 0.26
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
Found at i:31324743 original size:15 final size:15
Alignment explanation
Indices: 31324723--31324758 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
31324713 ATTAATTGTG
31324723 ATTAAAGTTTAATTA
1 ATTAAAGTTTAATTA
31324738 ATTAAAGTTTAATTA
1 ATTAAAGTTTAATTA
31324753 AGTTAA
1 A-TTAA
31324759 TTAAGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (15 bp):
ATTAAAGTTTAATTA
Found at i:31324792 original size:29 final size:28
Alignment explanation
Indices: 31324736--31324792 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
31324726 AAAGTTTAAT
* *
31324736 TAATTAAAGTTTAATTAAGTTAATTAAG
1 TAATTAAAATTTAATTAAGTTAAATAAG
31324764 TAATTAAATATTTAATTAAAG-TAAATAAG
1 TAATTAAA-ATTTAATT-AAGTTAAATAAG
31324793 GCAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 14 0.56
30 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
TAATTAAAATTTAATTAAGTTAAATAAG
Found at i:31328337 original size:3 final size:3
Alignment explanation
Indices: 31328329--31328353 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31328319 CAACTAAACA
31328329 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
31328354 CAGAAGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31338356 original size:21 final size:21
Alignment explanation
Indices: 31338330--31338373 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
31338320 AGAAAAAGGG
*
31338330 GTTGTTGCTGCTGCTGTTGTT
1 GTTGTTGCTGCTGCTGCTGTT
31338351 GTTGTTGCTGCTGCTGCTGTT
1 GTTGTTGCTGCTGCTGCTGTT
31338372 GT
1 GT
31338374 GGAAACTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.34, T:0.50
Consensus pattern (21 bp):
GTTGTTGCTGCTGCTGCTGTT
Found at i:31338812 original size:29 final size:29
Alignment explanation
Indices: 31338725--31338819 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
31338715 TATTATCATT
31338725 CAACTATCAATTTTTTTAATTTGATCACC
1 CAACTATCAATTTTTTTAATTTGATCACC
* * *** **
31338754 TAATTATTGTCTTTTTTTCCTTTTTG-TCACC
1 CAACTA-TCAATTTTTTT--AATTTGATCACC
31338785 CAACTATCAATTTTTTTAATTTGATCACC
1 CAACTATCAATTTTTTTAATTTGATCACC
31338814 CAACTA
1 CAACTA
31338820 AACGATATAG
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 4 0.08
29 15 0.31
30 16 0.33
31 9 0.19
32 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.48
Consensus pattern (29 bp):
CAACTATCAATTTTTTTAATTTGATCACC
Found at i:31338997 original size:18 final size:18
Alignment explanation
Indices: 31338953--31339013 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
31338943 ATTCTAACAA
* *
31338953 ATATATAAAAATTAAAAT
1 ATATATAATAATTTAAAT
* *
31338971 ACATA-AATACTTTAAAT
1 ATATATAATAATTTAAAT
31338988 ATATATAATAAATTTAAA-
1 ATATATAAT-AATTTAAAT
31339006 ATATATAA
1 ATATATAA
31339014 AAATACCCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 13 0.37
18 15 0.43
19 7 0.20
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATATAATAATTTAAAT
Found at i:31346019 original size:18 final size:18
Alignment explanation
Indices: 31345996--31346032 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31345986 TTAAAATTAT
*
31345996 AAAAATTCAAAACTATAA
1 AAAAATTCAAAAATATAA
*
31346014 AAAAATTTAAAAATATAA
1 AAAAATTCAAAAATATAA
31346032 A
1 A
31346033 TTATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATTCAAAAATATAA
Found at i:31346104 original size:14 final size:15
Alignment explanation
Indices: 31346085--31346124 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
31346075 AAAAAAATCA
*
31346085 AATTTTATATAT-TT
1 AATTTTATATATAAT
31346099 AATTTT-TAT-TAAT
1 AATTTTATATATAAT
31346112 AATTTTATATATA
1 AATTTTATATATA
31346125 TTCAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
12 1 0.05
13 10 0.45
14 9 0.41
15 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTTATATATAAT
Found at i:31348651 original size:15 final size:15
Alignment explanation
Indices: 31348631--31348684 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
31348621 TATTTAATGA
*
31348631 ATGTATTTAGAGTAG
1 ATGTATTTAGAATAG
* *
31348646 ATGTATCTAGTTTAATAA
1 ATGTATTTAG---AATAG
31348664 ATGTATTTAGAATAG
1 ATGTATTTAGAATAG
31348679 ATGTAT
1 ATGTAT
31348685 CTAGTAGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 19 0.61
18 12 0.39
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (15 bp):
ATGTATTTAGAATAG
Found at i:31348660 original size:33 final size:33
Alignment explanation
Indices: 31348623--31348689 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
31348613 TGTACTTTTA
* *
31348623 TTTAATGAATGTATTTAGAGTAGATGTATCTAG
1 TTTAATAAATGTATTTAGAATAGATGTATCTAG
31348656 TTTAATAAATGTATTTAGAATAGATGTATCTAG
1 TTTAATAAATGTATTTAGAATAGATGTATCTAG
31348689 T
1 T
31348690 AGTCATGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (33 bp):
TTTAATAAATGTATTTAGAATAGATGTATCTAG
Found at i:31354897 original size:87 final size:87
Alignment explanation
Indices: 31354737--31354912 Score: 271
Period size: 87 Copynumber: 2.0 Consensus size: 87
31354727 TTACAGAAAA
* * * * *
31354737 AGAATGTCTGGTTAGGACTACATAAAGCGAGAGAGACCATAGGGACTAGCAGATGAGGAAGTTTG
1 AGAATGTCTAGTTAGGACTACATAAAGCGAGAGAGACCATAGGGACTAGCAAACGAGAAAGTCTG
* *
31354802 CTGTGGACTACCTTAGGTAAAG
66 CTGAGGACTACCTTACGTAAAG
*
31354824 AGAATGTCTAGTTAGGACTACATAAAGCGAGAGAGACGATAGGGACTAGCAAACGAGAAAGTCTG
1 AGAATGTCTAGTTAGGACTACATAAAGCGAGAGAGACCATAGGGACTAGCAAACGAGAAAGTCTG
*
31354889 GTGAGGACTACCTTACGTAAAG
66 CTGAGGACTACCTTACGTAAAG
31354911 AG
1 AG
31354913 TCAGCTAGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (87 bp):
AGAATGTCTAGTTAGGACTACATAAAGCGAGAGAGACCATAGGGACTAGCAAACGAGAAAGTCTG
CTGAGGACTACCTTACGTAAAG
Found at i:31368079 original size:22 final size:23
Alignment explanation
Indices: 31368048--31368091 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31368038 TTCGAATGCC
*
31368048 CACACGGCCTGG-AACACGGGCT
1 CACACAGCCTGGCAACACGGGCT
*
31368070 CACACAGCCTGGCCACACGGGC
1 CACACAGCCTGGCAACACGGGC
31368092 ATGTGTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.23, C:0.41, G:0.30, T:0.07
Consensus pattern (23 bp):
CACACAGCCTGGCAACACGGGCT
Found at i:31370510 original size:67 final size:68
Alignment explanation
Indices: 31370346--31370561 Score: 251
Period size: 67 Copynumber: 3.2 Consensus size: 68
31370336 GGAAGTCTGT
* * * *
31370346 CAGGATAATAAACTTGGGGTTATATTGTGTAAGACCATAATTGGGCTATTG-CAACAAAATGAAT
1 CAGGACAATAAAC-AGGGGTTATATTGTGTAAGACCATAGTTGGGCTA-TGACAACAAAATGAAG
*
31370410 TCCTC
64 TCCAC
* * *
31370415 CAAGACAATAAACATGGGTTATATTGTGTAAGACCATAGTTGGGCTATGACAA-TAAATGAAGTC
1 CAGGACAATAAACAGGGGTTATATTGTGTAAGACCATAGTTGGGCTATGACAACAAAATGAAGTC
31370479 CAC
66 CAC
* * * *
31370482 TAGGACAATAAACAGGGGTTATATTGTGTAGGATCATAGTTGGGCTATGAC-AGAAAATGGAA-T
1 CAGGACAATAAACAGGGGTTATATTGTGTAAGACCATAGTTGGGCTATGACAACAAAAT-GAAGT
*
31370545 CCGC
65 CCAC
*
31370549 CAGGACAGTAAAC
1 CAGGACAATAAAC
31370562 CGAAAAGCCT
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
66 1 0.01
67 78 0.61
68 37 0.29
69 11 0.09
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (68 bp):
CAGGACAATAAACAGGGGTTATATTGTGTAAGACCATAGTTGGGCTATGACAACAAAATGAAGTC
CAC
Found at i:31373192 original size:32 final size:33
Alignment explanation
Indices: 31373131--31373193 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
31373121 TGTACTTGTA
* *
31373131 TTTAATGAATGTATTTAGAGTAGATGTATCTAG
1 TTTAATGAATGTATTTAAAGTAGACGTATCTAG
31373164 TTTAATGAATGT-TTTAAAGTAGACGTATCT
1 TTTAATGAATGTATTTAAAGTAGACGTATCT
31373194 TAGTCATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (33 bp):
TTTAATGAATGTATTTAAAGTAGACGTATCTAG
Found at i:31375939 original size:14 final size:15
Alignment explanation
Indices: 31375920--31375948 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31375910 ATTTTAAGAT
31375920 AAAAACAAAA-AAAA
1 AAAAACAAAACAAAA
31375934 AAAAACAAAACAAAA
1 AAAAACAAAACAAAA
31375949 TACTCATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAACAAAACAAAA
Found at i:31379908 original size:31 final size:30
Alignment explanation
Indices: 31379873--31379930 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
31379863 AACAACTAAG
*
31379873 TGACTTAAATAAAAACTTTCGAATAATTTAA
1 TGAC-TAAATAAAAACTTTCAAATAATTTAA
* * *
31379904 TGACTATATGAAAATTTTCAAATAATT
1 TGACTAAATAAAAACTTTCAAATAATT
31379931 CTATGCTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
TGACTAAATAAAAACTTTCAAATAATTTAA
Found at i:31380615 original size:17 final size:17
Alignment explanation
Indices: 31380593--31380627 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31380583 ATTACAAAAC
31380593 CAAATCTTACT-AGATTA
1 CAAATCTT-CTAAGATTA
31380610 CAAATCTTCTAAGATTA
1 CAAATCTTCTAAGATTA
31380627 C
1 C
31380628 TTTCCCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:31391377 original size:16 final size:16
Alignment explanation
Indices: 31391340--31391381 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31391330 TTAATCATAT
*
31391340 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
31391356 TT-AAATATATTATAA
1 TTAAAATATATTATAA
31391371 TTAAAATATAT
1 TTAAAATATAT
31391382 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:31391388 original size:14 final size:15
Alignment explanation
Indices: 31391349--31391390 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31391339 TTTAAACATA
*
31391349 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31391364 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31391378 A-TATAATTTAATA
1 ATTATAATTAAATA
31391391 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31391508 original size:14 final size:15
Alignment explanation
Indices: 31391459--31391510 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31391449 GTAAAATATA
31391459 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
31391474 TATTAAATATATTAT
1 AATTAAATATATTAT
31391489 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
31391502 AATTTAATA
1 AATTAAATA
31391511 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:31391556 original size:120 final size:121
Alignment explanation
Indices: 31391338--31391635 Score: 453
Period size: 120 Copynumber: 2.5 Consensus size: 121
31391328 TTTTAATCAT
*
31391338 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
31391403 ATTAATATTCTTATATGGATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
31391460 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
31391523 ATTAATATTCTTATATGAATTTACTCATATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * * * *
31391579 ATTTGAA-ATAATTAATA-TATCATATATTTTATTTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTA-AATATATTATAATTAAAATATATAATTTAATAAAATT
31391636 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
119 9 0.05
120 150 0.91
121 4 0.02
122 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:31391727 original size:92 final size:92
Alignment explanation
Indices: 31391631--31391859 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
31391621 TGATTTAATA
* * *
31391631 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTTTATAATTTAAAAT-ATTA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
31391693 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
31391723 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
31391788 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
31391813 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
31391860 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 79 0.66
93 11 0.09
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:31397519 original size:71 final size:72
Alignment explanation
Indices: 31397387--31397521 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 72
31397377 TAGGGTTTAT
* * *
31397387 GGTTTGGATTAATTAGTATTTTTTAATTTATATATTAATTAAGTTCTTATATAATTATAAAAGAG
1 GGTTTAGATTAATTAGTA-TTTTTAATTTATATATTAAATAAGTTATTATATAATTATAAAAGAG
31397452 GGGTTAGG
65 GGGTTAGG
* * *
31397460 GGTTTAGATTAATTGGTA-TTTTAATTTATATATTAAATAATTTATTATATAATTGTAAAAGA
1 GGTTTAGATTAATTAGTATTTTTAATTTATATATTAAATAAGTTATTATATAATTATAAAAGA
31397522 AATAATATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 40 0.71
73 16 0.29
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (72 bp):
GGTTTAGATTAATTAGTATTTTTAATTTATATATTAAATAAGTTATTATATAATTATAAAAGAGG
GGTTAGG
Found at i:31397786 original size:13 final size:13
Alignment explanation
Indices: 31397768--31397794 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31397758 ATTGATAAAT
31397768 AAATTAATGTAAC
1 AAATTAATGTAAC
31397781 AAATTAATGTAAC
1 AAATTAATGTAAC
31397794 A
1 A
31397795 GATTGACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:31401631 original size:43 final size:43
Alignment explanation
Indices: 31401557--31401743 Score: 198
Period size: 43 Copynumber: 4.3 Consensus size: 43
31401547 ATGTTATGTT
* * * *
31401557 TTTAGTGGCGTTTTTGCAAGAAGCGTCGCTAAAGGTCTTGATC
1 TTTAGTGGCGTTTGTGGAATAAGCGCCGCTAAAGGTCTTGATC
* * * *
31401600 TTCAGTGACGTTTGTGGAATAAGTGCCGCTAAAGGTCTTGATA
1 TTTAGTGGCGTTTGTGGAATAAGCGCCGCTAAAGGTCTTGATC
* * *
31401643 TTTAGCGGCGTTTGTGGGAA-AAGCGCCGCTGAAGGTCTTGATT
1 TTTAGTGGCGTTTGT-GGAATAAGCGCCGCTAAAGGTCTTGATC
* * *
31401686 TTTAGTGGCGTTAGTGGTAAT-AGCGCCGCTAAAGATCCTGATC
1 TTTAGTGGCGTTTGTGG-AATAAGCGCCGCTAAAGGTCTTGATC
* *
31401729 TATAGCGGCGTTTGT
1 TTTAGTGGCGTTTGT
31401744 AGAGCACCGC
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
42 2 0.02
43 112 0.95
44 4 0.03
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (43 bp):
TTTAGTGGCGTTTGTGGAATAAGCGCCGCTAAAGGTCTTGATC
Found at i:31401714 original size:86 final size:86
Alignment explanation
Indices: 31401577--31401743 Score: 219
Period size: 86 Copynumber: 1.9 Consensus size: 86
31401567 TTTTTGCAAG
* * * * *
31401577 AAGCGTCGCTAAAGGTCTTGATCTTCAGTGACGTTTGTGGAATAAGTGCCGCTAAAGGTCTTGAT
1 AAGCGCCGCTAAAGGTCTTGATCTTCAGTGACGTTAGTGGAATAAGCGCCGCTAAAGATCCTGAT
*
31401642 ATTTAGCGGCGTTTGTGGGAA
66 ATATAGCGGCGTTTGTGGGAA
* * * *
31401663 AAGCGCCGCTGAAGGTCTTGATTTTTAGTGGCGTTAGTGGTAAT-AGCGCCGCTAAAGATCCTGA
1 AAGCGCCGCTAAAGGTCTTGATCTTCAGTGACGTTAGTGG-AATAAGCGCCGCTAAAGATCCTGA
*
31401727 TCTATAGCGGCGTTTGT
65 TATATAGCGGCGTTTGT
31401744 AGAGCACCGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
86 66 0.96
87 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (86 bp):
AAGCGCCGCTAAAGGTCTTGATCTTCAGTGACGTTAGTGGAATAAGCGCCGCTAAAGATCCTGAT
ATATAGCGGCGTTTGTGGGAA
Found at i:31407099 original size:50 final size:50
Alignment explanation
Indices: 31406984--31407176 Score: 244
Period size: 50 Copynumber: 3.8 Consensus size: 50
31406974 GATAATAATA
* ** * *
31406984 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCAG
* * * ** *
31407035 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
31407085 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
31407135 TGCCAACGCCATGTCCCAGACATGGTCTTACAAT-GGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCT
31407177 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 87 0.72
51 34 0.28
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:31409310 original size:18 final size:18
Alignment explanation
Indices: 31409287--31409325 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
31409277 ATGGATCGCT
31409287 TTAGTGGCATGTTCTATC
1 TTAGTGGCATGTTCTATC
*
31409305 TTAGTGGCATGTTCTCTC
1 TTAGTGGCATGTTCTATC
31409323 TTA
1 TTA
31409326 AGAATCGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (18 bp):
TTAGTGGCATGTTCTATC
Found at i:31411643 original size:80 final size:80
Alignment explanation
Indices: 31411539--31411799 Score: 306
Period size: 80 Copynumber: 3.3 Consensus size: 80
31411529 GCTCCTCGTT
* *
31411539 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
31411604 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
31411619 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
31411682 GAATTAGTATCTCGCA
65 GATTTAGTAACTCGCA
* *
31411698 C-AATGCCTTCGGG-C-TAGCCCGG-AATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCC
* * * *
31411757 CGGATATGGTCACTTAGCA
63 CGGATTTAGTAAC-TCGCA
31411776 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
31411800 ACATCGTTCA
Statistics
Matches: 155, Mismatches: 16, Indels: 20
0.81 0.08 0.10
Matches are distributed among these distances:
75 3 0.02
76 27 0.17
77 15 0.10
78 26 0.17
79 26 0.17
80 56 0.36
81 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCGCA
Found at i:31411800 original size:40 final size:40
Alignment explanation
Indices: 31411539--31411800 Score: 278
Period size: 40 Copynumber: 6.7 Consensus size: 40
31411529 GCTCCTCGTT
* * *
31411539 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
31411579 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
* *
31411619 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
31411659 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
31411698 C-AATGCCTTCGGG-C-TAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
31411735 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
31411776 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31411801 CATCGTTCAA
Statistics
Matches: 199, Mismatches: 11, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
37 26 0.13
38 23 0.12
39 21 0.11
40 114 0.57
41 14 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:31412897 original size:13 final size:13
Alignment explanation
Indices: 31412879--31412903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31412869 AGGATGAGCA
31412879 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
31412892 TTTTTTTTCTTT
1 TTTTTTTTCTTT
31412904 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:31427009 original size:43 final size:42
Alignment explanation
Indices: 31426885--31427063 Score: 146
Period size: 43 Copynumber: 4.2 Consensus size: 42
31426875 AAAAAAAGCA
* * * * * *
31426885 GCTATAGAACGTGACCTTTAGCGGCGCTTCTCATAAAAATGCC
1 GCTAAAGAACATGACCTTTAGCGACGCTTTTC-TACAAACGCC
* * *
31426928 GCTATAGAACATGGCCTTTAGC-AGCGGTTTTCTCACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGA-CGCTTTTCT-ACAAACGCC
* *
31426971 GTTAAAGAACATGACCTTTAGCGACGCTTTTACTACAAACGCA
1 GCTAAAGAACATGACCTTTAGCGACGCTTTT-CTACAAACGCC
* * * * *
31427014 ACTAAAGAACATGACATTTAGCTG-CACTTTTCCCACAAACTCC
1 GCTAAAGAACATGACCTTTAGC-GACGCTTTT-CTACAAACGCC
31427057 GCTAAAG
1 GCTAAAG
31427064 GTCATGTTCT
Statistics
Matches: 110, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 105 0.95
44 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
GCTAAAGAACATGACCTTTAGCGACGCTTTTCTACAAACGCC
Found at i:31427077 original size:43 final size:43
Alignment explanation
Indices: 31427030--31427120 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
31427020 GAACATGACA
* * *
31427030 TTTAGCTGCACTTTTCCCACAAA-CTCCGCTAAAGGTCATGTTC
1 TTTAGCGGCACTTTTACCA-AAAGCCCCGCTAAAGGTCATGTTC
* **
31427073 TTTAGCGGCATTTTTAGTAAAAGCCCCGCTAAAGGTCATGTTC
1 TTTAGCGGCACTTTTACCAAAAGCCCCGCTAAAGGTCATGTTC
31427116 TTTAG
1 TTTAG
31427121 TGGTGTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.07
43 38 0.93
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCACTTTTACCAAAAGCCCCGCTAAAGGTCATGTTC
Found at i:31432791 original size:15 final size:15
Alignment explanation
Indices: 31432779--31432807 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31432769 TTTTGAAATG
31432779 CAAAATTTAGAAAAA
1 CAAAATTTAGAAAAA
31432794 CAAAATTTAGAAAA
1 CAAAATTTAGAAAA
31432808 GTTTGTACTC
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:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
CAAAATTTAGAAAAA
Found at i:31436779 original size:48 final size:48
Alignment explanation
Indices: 31436727--31436854 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 48
31436717 GTATATTTTT
* * ***
31436727 TTTCAAGCAACGAAAAGACTGAGAAAGAAAATGGATGGGAGTTTGGGA
1 TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAATGGACAAGAGTTTGGGA
* * * * * *
31436775 TTTCAAGTAAAGAGAAGTCT-AGGAAAAAAAAGGGACAAGATTTTGGGG
1 TTTCAAGCAAAGAAAAGTCTGA-GAAAGAAAATGGACAAGAGTTTGGGA
*
31436823 TTTCAGGCAAAGAAAAGTCTGAGAAAGAAAAT
1 TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAAT
31436855 AATTTGTGCG
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
47 1 0.02
48 60 0.97
49 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.28, T:0.20
Consensus pattern (48 bp):
TTTCAAGCAAAGAAAAGTCTGAGAAAGAAAATGGACAAGAGTTTGGGA
Found at i:31448466 original size:20 final size:20
Alignment explanation
Indices: 31448441--31448480 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31448431 TACTGCTGAG
31448441 CAGAGGAACC-GTGGTGCAAA
1 CAGAGGAACCAGT-GTGCAAA
*
31448461 CAGAGGCACCAGTGTGCAAA
1 CAGAGGAACCAGTGTGCAAA
31448481 AAGGGGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.35, C:0.23, G:0.33, T:0.10
Consensus pattern (20 bp):
CAGAGGAACCAGTGTGCAAA
Found at i:31448497 original size:20 final size:20
Alignment explanation
Indices: 31448454--31448539 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
31448444 AGGAACCGTG
* **
31448454 GTGCAAACAGAGGCACCAGT
1 GTGCAAAAAGAGGCACCAAA
*
31448474 GTGCAAAAAGGGGCACCAAA
1 GTGCAAAAAGAGGCACCAAA
** **
31448494 GTGCAATGAG-GGACACTGAA
1 GTGCAAAAAGAGG-CACCAAA
*
31448514 GTGCAAATAGAGGCACCAAA
1 GTGCAAAAAGAGGCACCAAA
31448534 GTGCAA
1 GTGCAA
31448540 TCTCGTACAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.04
20 48 0.92
21 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (20 bp):
GTGCAAAAAGAGGCACCAAA
Found at i:31450194 original size:40 final size:40
Alignment explanation
Indices: 31450164--31450427 Score: 313
Period size: 40 Copynumber: 6.7 Consensus size: 40
31450154 GCTCCTCGTT
* * *
31450164 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
31450204 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
31450244 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
31450284 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
31450323 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
31450362 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
31450403 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
31450428 CATCATTCAA
Statistics
Matches: 203, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.01
39 71 0.35
40 117 0.58
41 13 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:31458443 original size:40 final size:40
Alignment explanation
Indices: 31458181--31458443 Score: 276
Period size: 40 Copynumber: 6.7 Consensus size: 40
31458171 GCTCCTCGTT
* * *
31458181 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
31458221 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
* *
31458261 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
* * *
31458301 CAAATGCCTTCAGG-CTTAGCCCGAAT-TAGTA-TCTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACT-TCGCA
31458339 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
31458378 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
31458419 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31458444 CATCATTCAA
Statistics
Matches: 196, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.01
38 33 0.17
39 32 0.16
40 115 0.59
41 14 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:31473498 original size:40 final size:40
Alignment explanation
Indices: 31473454--31473717 Score: 292
Period size: 40 Copynumber: 6.7 Consensus size: 40
31473444 GCTCCTCGTT
*
31473454 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* * *
31473494 CAAATGCCTTCGGGACTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
31473534 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTT-GCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA-TTCGCA
* * * *
31473574 CAAATGCCTTCCGAACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
31473614 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAAT-TCGCA
* * * *
31473653 CAAATGCCTTC-GGATCTTAGTCCGGGTATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-AATTCGCA
31473694 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31473718 CAGCATTCAA
Statistics
Matches: 193, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
38 3 0.02
39 47 0.24
40 132 0.68
41 10 0.05
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:31481654 original size:39 final size:40
Alignment explanation
Indices: 31481453--31481714 Score: 299
Period size: 40 Copynumber: 6.7 Consensus size: 40
31481443 GCTCCTCGTT
*
31481453 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
31481493 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* *
31481533 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* * *
31481573 CAAATGCCTTCAGG-CTTAGCCC-GAATTAGTATCTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
31481611 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* * * *
31481650 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ATC-TCGCA
31481691 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31481715 CATCATTCAA
Statistics
Matches: 198, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
38 36 0.18
39 50 0.25
40 104 0.53
41 8 0.04
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:31481708 original size:117 final size:120
Alignment explanation
Indices: 31481453--31481712 Score: 318
Period size: 117 Copynumber: 2.2 Consensus size: 120
31481443 GCTCCTCGTT
* **
31481453 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
31481518 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 AATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* * *
31481573 CAAATGCCTTCAGG-CTTAGCCCGAAT-TAGT-ATCTCGCTCAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCG
* ** * *
31481634 GAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
65 GAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCA
31481691 C-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
31481713 GACATCATTC
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
116 11 0.09
117 61 0.50
118 27 0.22
119 9 0.07
120 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:31494592 original size:19 final size:19
Alignment explanation
Indices: 31494568--31494659 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
31494558 AATCATATCT
31494568 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
31494587 TCTAAGATTACATATGATA
1 TCTAAGATTGCATATCATA
31494606 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
31494625 TCTAAGAGTACATATCATA
1 TCTAAGATTGCATATCATA
31494644 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
31494660 CTTGAAGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:31494611 original size:38 final size:38
Alignment explanation
Indices: 31494561--31494659 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
31494551 ATTTCAAAAT
*
31494561 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
*
31494597 CATATGATATCTAAGATTGCATATCATATCTAAGAGTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
31494635 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
31494660 CTTGAAGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 5 0.09
37 1 0.02
38 52 0.90
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
Found at i:31496065 original size:16 final size:16
Alignment explanation
Indices: 31496046--31496099 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
31496036 TTTGGTTCGT
*
31496046 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGC
*
31496062 TGTAATTGAATAGAGC
1 TGTAATGGAATAGAGC
* *
31496078 TGTAATGAAATAAAGC
1 TGTAATGGAATAGAGC
31496094 TGTAAT
1 TGTAAT
31496100 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:31498065 original size:15 final size:15
Alignment explanation
Indices: 31498045--31498076 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31498035 ATTGCACAAC
31498045 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
31498060 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
31498075 TT
1 TT
31498077 TCCTCCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTAATAGTAAAGCAT
Found at i:31502860 original size:40 final size:40
Alignment explanation
Indices: 31502802--31503028 Score: 391
Period size: 40 Copynumber: 5.7 Consensus size: 40
31502792 AGCATTGGAT
31502802 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* **
31502842 TATATCCGGGCTATGACCCGAAGGCAATTATGCGAAATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
31502882 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
31502922 TATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
31502962 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
31503002 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
31503029 ATGTGTTTGC
Statistics
Matches: 175, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 175 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:31514160 original size:15 final size:15
Alignment explanation
Indices: 31514140--31514170 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31514130 TATTGAGGAG
31514140 CCAATTAATAATTAA
1 CCAATTAATAATTAA
31514155 CCAATTAATAATTAA
1 CCAATTAATAATTAA
31514170 C
1 C
31514171 AAATGGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (15 bp):
CCAATTAATAATTAA
Found at i:31514705 original size:59 final size:59
Alignment explanation
Indices: 31514639--31514808 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
31514629 TCAAGTTTGT
*
31514639 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
31514698 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
31514757 TTTACTAATCAAATGGTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
31514809 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:31514840 original size:16 final size:16
Alignment explanation
Indices: 31514819--31514860 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
31514809 AATAATTTGA
*
31514819 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
31514835 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
31514851 TAGTTTTAAT
1 TAATTTTAAT
31514861 TTTAATTAAA
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:31517851 original size:19 final size:19
Alignment explanation
Indices: 31517819--31517860 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31517809 AAAGCAACAT
* *
31517819 AACATTAGTTCAAGTAAAC
1 AACATGAGTCCAAGTAAAC
*
31517838 AACATGAGTCCAAGTGAAC
1 AACATGAGTCCAAGTAAAC
31517857 AACA
1 AACA
31517861 ACACAATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (19 bp):
AACATGAGTCCAAGTAAAC
Found at i:31526159 original size:16 final size:16
Alignment explanation
Indices: 31526138--31526171 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
31526128 TTGAGGAGTG
31526138 TTGAGAATCTTTGATA
1 TTGAGAATCTTTGATA
31526154 TTGAGAATCTTTGATA
1 TTGAGAATCTTTGATA
31526170 TT
1 TT
31526172 ATTAAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (16 bp):
TTGAGAATCTTTGATA
Found at i:31529475 original size:531 final size:531
Alignment explanation
Indices: 31528472--31530069 Score: 3043
Period size: 531 Copynumber: 3.0 Consensus size: 531
31528462 ACGAATATTC
31528472 GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
*
31528537 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTTCGTACATACCCAACGATAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
*
31528602 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAACAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
*
31528667 AAAAGAAAAAGAGAAGGAAAAAAAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
*
31528732 ATAAAATTGAAAAAAAAATTGAAGTAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
*
31528797 TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTGCTTTTCAGGTTCCCAAAATACCGAAAGA
326 TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
31528862 TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
*
31528927 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTAAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
31528992 CGTGCAGATTT
521 CGTGCAGATTT
31529003 GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
* *
31529068 GTGAAGTTTTCCAAGGGGATCATTGTTCATATACAAGTCATTCCGTACATACCCAACGATAGCTT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
31529133 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
*
31529198 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAGAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
31529263 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
*
31529328 TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATATCGAAAGA
326 TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
31529393 TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
31529458 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
31529523 CGTGCAGATTT
521 CGTGCAGATTT
*
31529534 GAAAAGAGATTCCTATGACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
1 GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
*
31529599 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGAGAGCCT
66 GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
31529664 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
131 TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
31529729 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
196 AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
* *
31529794 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGAGTAGTGAGAAATGTT
261 ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
* *
31529859 TCCACTAACCAAGATAGGAACTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
326 TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
*
31529924 TAACTTTCAACTTTAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
391 TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
31529989 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
456 AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
31530054 CGTGCAGATTT
521 CGTGCAGATTT
31530065 GAAAA
1 GAAAA
31530070 TTATTGATAA
Statistics
Matches: 1046, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
531 1046 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (531 bp):
GAAAAGAGATTCCTATAACTCCCATTCAATGAGGAATTCAAGGCGATGCAAAGCAAGTTTCGAGA
GTGAAGTTTTCCAAGGGGATCATTGTTCGTATACAAGTCATTCCGTACATACCCAACGATAGCCT
TTCCGTTCTAATTCATTTGTAACATCTCTATCTTGTAATGAAAGGAAGACACAAAAAGAAATCAA
AAAAGAAAAAGAGAAGGAAAAAGAGCAAAAAGAGATTGAAAGTGGAAAGGAATGTGAAACAAACA
ATAAAATTGAAAAAAAAATTGAAGAAACAAATGAAAAAGACGAGGAAAGGGTAGTGAGGAATGTT
TCCACTAACCAAGATAAGAATTTTTCTTCTGTTGCTACTTTTCAGGTTCCCAAAATACCGAAAGA
TAACTTTCAACTTCAATACCTTTCCGATGAAAGACGCTTTCATACGATCAACATAGGCAAGGTTG
AAGATGAAATCACACTACATGAGCCCGAAGGTAAGCGAGGTAAGGAAATTTTAGCCACTGAGTCC
CGTGCAGATTT
Found at i:31533476 original size:82 final size:82
Alignment explanation
Indices: 31533334--31533489 Score: 258
Period size: 82 Copynumber: 1.9 Consensus size: 82
31533324 CTCCGCCAAT
* * *
31533334 GATCACGAAGCAACTCAATTGTCTATTTATTACACCATTGGACATATTATTACCGAAAAATACAC
1 GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACAC
31533399 AAAAAGAAACCACTAGC
66 AAAAAGAAACCACTAGC
* * *
31533416 GATCACGAAGCAACTCAACTGTCTATTTATTCCACCATTGGAAATATCATTACCGGAAAATGCAC
1 GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACAC
31533481 AAAAAGAAA
66 AAAAAGAAA
31533490 ACATTCAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (82 bp):
GATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACAC
AAAAAGAAACCACTAGC
Found at i:31535857 original size:30 final size:30
Alignment explanation
Indices: 31535821--31535880 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
31535811 CACATGCGGA
31535821 TACTATTAATATTAAACATAAAATCTTTTT
1 TACTATTAATATTAAACATAAAATCTTTTT
31535851 TACTATTAATATTAAACATAAAATCTTTTT
1 TACTATTAATATTAAACATAAAATCTTTTT
31535881 AAAAGAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (30 bp):
TACTATTAATATTAAACATAAAATCTTTTT
Found at i:31542126 original size:26 final size:28
Alignment explanation
Indices: 31542092--31542147 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
31542082 GGTTTGCGAG
*
31542092 AAGTAAAAAT-TTTGGAG-GTAAAGTAA
1 AAGTAAAAATGTTTGGAGAGAAAAGTAA
*
31542118 AAGTAAAAATGTTTTGAGAGAAAAGTAA
1 AAGTAAAAATGTTTGGAGAGAAAAGTAA
31542146 AA
1 AA
31542148 AGGTCGGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 6 0.23
28 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (28 bp):
AAGTAAAAATGTTTGGAGAGAAAAGTAA
Found at i:31544111 original size:42 final size:42
Alignment explanation
Indices: 31544060--31544149 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
31544050 TTTTCATATT
*
31544060 TTTTTACTTCAAGTAAGTTTATTTCTTGTCATTTTCTTGAAA
1 TTTTTACTTCAAGTAAGTTTAGTTCTTGTCATTTTCTTGAAA
*
31544102 TTTTTACTTCAAGTGAGTTTAGTTCTTGTCATTTTCTTGAAA
1 TTTTTACTTCAAGTAAGTTTAGTTCTTGTCATTTTCTTGAAA
31544144 TTTTTA
1 TTTTTA
31544150 TGTTTTTAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (42 bp):
TTTTTACTTCAAGTAAGTTTAGTTCTTGTCATTTTCTTGAAA
Found at i:31544868 original size:23 final size:24
Alignment explanation
Indices: 31544838--31544945 Score: 141
Period size: 24 Copynumber: 4.6 Consensus size: 24
31544828 CATTATTGGG
* *
31544838 AAAGGATGAATTGACGG-AAATTT
1 AAAGGATGAATTGAAGGAAAATGT
31544861 AAAGGATGAATTGAAGGAAAATGT
1 AAAGGATGAATTGAAGGAAAATGT
* *
31544885 AAAGGA-GAAACTGACGGAAAATGT
1 AAAGGATG-AATTGAAGGAAAATGT
*
31544909 AAAGGATGAATTGAAGG-TAATGT
1 AAAGGATGAATTGAAGGAAAATGT
31544932 AAAGGATGAATTGA
1 AAAGGATGAATTGA
31544946 TGACAAATTG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 36 0.48
24 38 0.51
25 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.29, T:0.21
Consensus pattern (24 bp):
AAAGGATGAATTGAAGGAAAATGT
Found at i:31546511 original size:459 final size:459
Alignment explanation
Indices: 31545653--31546575 Score: 1810
Period size: 459 Copynumber: 2.0 Consensus size: 459
31545643 ATTAAGTATT
31545653 TGTGATGTTATGTCATGTTTAAAACATATGTTTAGCTTGTATTGATTGCTTGATTGGGATATATT
1 TGTGATGTTATGTCATGTTTAAAACATATGTTTAGCTTGTATTGATTGCTTGATTGGGATATATT
31545718 GAAGTATTGAAATGTTGTGTATAGGTTGATGTCAAAATGGGTGAGAAAGTGGTCTTAAAATGGTC
66 GAAGTATTGAAATGTTGTGTATAGGTTGATGTCAAAATGGGTGAGAAAGTGGTCTTAAAATGGTC
31545783 TATTTTCATCCACACTGGCAGAGACACGGGTGTGTGTCTCAACCGTGTGTGACACAAGGCCTGGC
131 TATTTTCATCCACACTGGCAGAGACACGGGTGTGTGTCTCAACCGTGTGTGACACAAGGCCTGGC
31545848 ACATGGGCATGTAGTCTGGTCATGAGTCCCCGCACCTACAATTTTGAAACAGAATGCCTAGGTTT
196 ACATGGGCATGTAGTCTGGTCATGAGTCCCCGCACCTACAATTTTGAAACAGAATGCCTAGGTTT
* *
31545913 TTGTACATGGCCTAACACACGGGCGTGTAGCTTGGCCGTGTGACCCCTGCACCTTACACATAGCC
261 TTGCACACGGCCTAACACACGGGCGTGTAGCTTGGCCGTGTGACCCCTGCACCTTACACATAGCC
*
31545978 TATCACACGGGCATGTGGTTGGCCGTGTGATCCAAGTTAGAGAGTTACACTGGTATGGACACAGG
326 TATCACACAGGCATGTGGTTGGCCGTGTGATCCAAGTTAGAGAGTTACACTGGTATGGACACAGG
31546043 CTGGGACATGGTCGTGTGCCTCACATCGAATGCCCACACGGCCTAAGACACGAGCGTGTCTTCTG
391 CTGGGACATGGTCGTGTGCCTCACATCGAATGCCCACACGGCCTAAGACACGAGCGTGTCTTCTG
31546108 GCCA
456 GCCA
31546112 TGTGATGTTATGTCATGTTTAAAACATATGTTTAGCTTGTATTGATTGCTTGATTGGGATATATT
1 TGTGATGTTATGTCATGTTTAAAACATATGTTTAGCTTGTATTGATTGCTTGATTGGGATATATT
31546177 GAAGTATTGAAATGTTGTGTATAGGTTGATGTCAAAATGGGTGAGAAAGTGGTCTTAAAATGGTC
66 GAAGTATTGAAATGTTGTGTATAGGTTGATGTCAAAATGGGTGAGAAAGTGGTCTTAAAATGGTC
31546242 TATTTTCATCCACACTGGCAGAGACACGGGTGTGTGTCTCAACCGTGTGTGACACAAGGCCTGGC
131 TATTTTCATCCACACTGGCAGAGACACGGGTGTGTGTCTCAACCGTGTGTGACACAAGGCCTGGC
31546307 ACATGGGCATGTAGTCTGGTCATGAGTCCCCGCACCTACAATTTTGAAACAGAATGCCTAGGTTT
196 ACATGGGCATGTAGTCTGGTCATGAGTCCCCGCACCTACAATTTTGAAACAGAATGCCTAGGTTT
*
31546372 TTGCACACGGCCTAACACACGGGCGTGTGGCTTGGCCGTGTGACCCCTGCACCTTACACATAGCC
261 TTGCACACGGCCTAACACACGGGCGTGTAGCTTGGCCGTGTGACCCCTGCACCTTACACATAGCC
31546437 TATCACACAGGCATGTGGTTGGCCGTGTGATCCAAGTTAGAGAGTTACACTGGTATGGACACAGG
326 TATCACACAGGCATGTGGTTGGCCGTGTGATCCAAGTTAGAGAGTTACACTGGTATGGACACAGG
31546502 CTGGGACATGGTCGTGTGCCTCACATCGAATGCCCACACGGCCTAAGACACGAGCGTGTCTTCTG
391 CTGGGACATGGTCGTGTGCCTCACATCGAATGCCCACACGGCCTAAGACACGAGCGTGTCTTCTG
31546567 GCCA
456 GCCA
31546571 TGTGA
1 TGTGA
31546576 GCCACACAAG
Statistics
Matches: 460, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
459 460 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (459 bp):
TGTGATGTTATGTCATGTTTAAAACATATGTTTAGCTTGTATTGATTGCTTGATTGGGATATATT
GAAGTATTGAAATGTTGTGTATAGGTTGATGTCAAAATGGGTGAGAAAGTGGTCTTAAAATGGTC
TATTTTCATCCACACTGGCAGAGACACGGGTGTGTGTCTCAACCGTGTGTGACACAAGGCCTGGC
ACATGGGCATGTAGTCTGGTCATGAGTCCCCGCACCTACAATTTTGAAACAGAATGCCTAGGTTT
TTGCACACGGCCTAACACACGGGCGTGTAGCTTGGCCGTGTGACCCCTGCACCTTACACATAGCC
TATCACACAGGCATGTGGTTGGCCGTGTGATCCAAGTTAGAGAGTTACACTGGTATGGACACAGG
CTGGGACATGGTCGTGTGCCTCACATCGAATGCCCACACGGCCTAAGACACGAGCGTGTCTTCTG
GCCA
Found at i:31550713 original size:13 final size:14
Alignment explanation
Indices: 31550697--31550726 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31550687 ATAATGAAGT
31550697 AATAAAT-AATAAA
1 AATAAATAAATAAA
31550710 AATAAATAAATAAA
1 AATAAATAAATAAA
31550724 AAT
1 AAT
31550727 TAGATTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:31554335 original size:21 final size:19
Alignment explanation
Indices: 31554310--31554356 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
31554300 TCATTTTTAG
31554310 CAACTTCCTCTTCTTCGGCAA
1 CAACTT-CTC-TCTTCGGCAA
*
31554331 CAACTT-TCTCTTCTGCAA
1 CAACTTCTCTCTTCGGCAA
31554349 CAACTTCT
1 CAACTTCT
31554357 GCTTTTGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 3 0.12
21 6 0.25
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (19 bp):
CAACTTCTCTCTTCGGCAA
Found at i:31567482 original size:41 final size:41
Alignment explanation
Indices: 31567419--31567769 Score: 486
Period size: 41 Copynumber: 8.6 Consensus size: 41
31567409 TATTTGAGTT
* * *
31567419 CTCGGGTCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATT
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* * *
31567460 CTCGGGTCTTTAGCGACGTTTTTGAAGAAGAGCCGCTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* **
31567501 CTTGGGTCTTTAGCGGTGTTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* *
31567542 CTCGGGTCTTTAGCGGCATTTTTGGAGAAGCGCCACTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
31567583 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* * * *
31567624 CTCGGGTCTTTAGCGGTATTTTTGAAGACGCACTGCTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* * *
31567665 CTCAGGTCTTTAGAGGCATTTTTGAAGAAGCGCTGCTAATG
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
* * * * *
31567706 CTCAGGTATTTAGCGGCGTTTTTGAAGAAGCACCGCTAATT
1 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
*
31567747 CTCGGGTCTTTAGCGGCGTTTTT
1 CTCGGGTCTTTAGCGGCATTTTT
31567770 AAAAAATCGC
Statistics
Matches: 276, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 276 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (41 bp):
CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
Found at i:31573550 original size:42 final size:42
Alignment explanation
Indices: 31573420--31573603 Score: 190
Period size: 42 Copynumber: 4.3 Consensus size: 42
31573410 AGCTCATGAC
* ** * *
31573420 CTTTAGCGACGTTTGGGGGAAAAGCGTTGCTGAAGGTCTTGTT
1 CTTTAGCGGCGTTT-GGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * * *
31573463 CTTTAGCAGCGTTTTTGGGAAAAGCGCCACTAAAAGTCTTGGT
1 CTTTAGCGGCG-TTTGGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * *
31573506 CTTTAGTGGCGTTTGCGGGAGAA-CGCCGCTAAAGGTCTTAGT
1 CTTTAGCGGCGTTTG-GGGAAAAGCGCCGCTAAAGGTCTTGGT
* * *
31573548 CTTTAGCGACGTTTGTGGAAAAGTGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
31573590 CTTTAACGGCGTTT
1 CTTTAGCGGCGTTT
31573604 TTTCTGGCGC
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
41 5 0.04
42 61 0.54
43 45 0.39
44 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:31574746 original size:10 final size:10
Alignment explanation
Indices: 31574731--31574846 Score: 52
Period size: 10 Copynumber: 12.3 Consensus size: 10
31574721 CATATGGTAA
31574731 AAAAAATTAT
1 AAAAAATTAT
31574741 -AAAAA--AT
1 AAAAAATTAT
*
31574748 AAAAAACT-T
1 AAAAAATTAT
31574757 -AAAAATTAT
1 AAAAAATTAT
* **
31574766 TAAATTTTAAT
1 AAAAAATT-AT
31574777 AAAAAA--AT
1 AAAAAATTAT
*
31574785 TAAAAATTA-
1 AAAAAATTAT
* *
31574794 CAAAAATCAT
1 AAAAAATTAT
*
31574804 AAAAAAACTAT
1 -AAAAAATTAT
**
31574815 AAAATTTTAT
1 AAAAAATTAT
*
31574825 -AAAAATCAT
1 AAAAAATTAT
31574834 AAAAAATTAT
1 AAAAAATTAT
31574844 AAA
1 AAA
31574847 CTTCACCAAA
Statistics
Matches: 76, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
7 2 0.03
8 18 0.24
9 20 0.26
10 24 0.32
11 12 0.16
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:31574831 original size:30 final size:27
Alignment explanation
Indices: 31574732--31574839 Score: 85
Period size: 29 Copynumber: 3.9 Consensus size: 27
31574722 ATATGGTAAA
* *
31574732 AAAAATTATAAAAA--ATAAAAAACTT
1 AAAAATTACAAAAATCATAAAAAAATT
* ** *
31574757 AAAAATTATTAAATTTTAATAAAAAAATT
1 AAAAATTA-CAAA-AATCATAAAAAAATT
31574786 AAAAATTACAAAAATCATAAAAAAACTAT
1 AAAAATTACAAAAATCATAAAAAAA-T-T
* *
31574815 AAAATTTTATAAAAATCATAAAAAA
1 AAAA-ATTACAAAAATCATAAAAAA
31574840 TTATAAACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
25 8 0.12
26 4 0.06
27 10 0.15
28 4 0.06
29 23 0.34
30 18 0.27
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAAATTACAAAAATCATAAAAAAATT
Found at i:31574858 original size:29 final size:28
Alignment explanation
Indices: 31574775--31574846 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
31574765 TTAAATTTTA
31574775 ATAAAAAAATTA-AAAATTACAAAAATC
1 ATAAAAAAATTATAAAATTACAAAAATC
* *
31574802 ATAAAAAAACTATAAAATTTTATAAAAATC
1 ATAAAAAAATTATAAAA--TTACAAAAATC
31574832 AT-AAAAAATTATAAA
1 ATAAAAAAATTATAAA
31574847 CTTCACCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 11 0.28
28 4 0.10
29 12 0.31
30 12 0.31
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (28 bp):
ATAAAAAAATTATAAAATTACAAAAATC
Found at i:31575086 original size:21 final size:22
Alignment explanation
Indices: 31575029--31575086 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
31575019 TTGGTACGAT
31575029 AATTTTTATAATTTAT-TTTACG
1 AATTTTTATAATTT-TCTTTACG
*
31575051 AA-TCTTAT-A-TTTCTTTAC-
1 AATTTTTATAATTTTCTTTACG
31575069 AATTTTTATAATTTTCTT
1 AATTTTTATAATTTTCTT
31575087 ATGACTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTTATAATTTTCTTTACG
Found at i:31575155 original size:96 final size:97
Alignment explanation
Indices: 31575033--31575209 Score: 220
Period size: 96 Copynumber: 1.8 Consensus size: 97
31575023 TACGATAATT
*
31575033 TTTATAATTTATTTTACGAATCTTATATTTCTTTACAATTTTTATA-ATTTTCT-TATGACTTTA
1 TTTATAATTTATTTTACGAATCTTATATTT-TTTACAATTCTTA-AGATTTT-TATAT-ACTTTA
31575096 -TAAAATTTAATAATTTTTTTCTATATTTCTATATA
62 TTAAAATTTAATAATTTTTTTCTATATTTCTATATA
* * * **
31575131 TTTATAA-TT-TTTTACGATTTTTATATTTTTTCCAATTCTTAAGTATTTTTATATTTTTTATTA
1 TTTATAATTTATTTTACGAATCTTATATTTTTTACAATTCTTAAG-ATTTTTATATACTTTATTA
31575194 AAATTTAATAATTTTT
65 AAATTTAATAATTTTT
31575210 ATAACTTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
94 1 0.01
95 16 0.23
96 43 0.62
97 2 0.03
98 7 0.10
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (97 bp):
TTTATAATTTATTTTACGAATCTTATATTTTTTACAATTCTTAAGATTTTTATATACTTTATTAA
AATTTAATAATTTTTTTCTATATTTCTATATA
Found at i:31577866 original size:140 final size:138
Alignment explanation
Indices: 31577646--31578342 Score: 1049
Period size: 138 Copynumber: 5.0 Consensus size: 138
31577636 TAGAAAAATA
* *
31577646 AATTATATTCTTTCCAAAA-ACTATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* **
31577710 TATAATTGTTTATATTAATAAATTTGGCAAAATATATACAATTAATATTTTAAATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
*
31577775 TATATATATT
130 T-CATATATT
* * *
31577785 AATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
31577850 TATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
31577915 CATATATT
131 CATATATT
* * *
31577923 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
31577988 TATAACTATTTATATTAATAAATTCGGTAAAATATATATACATTTAATATTTTGTATGAATCAAA
66 TATAATTGTTTATATTAATAAATTTGGT-AAA-ATATATACAATTAATATTTTGTATGAATCAAA
31578053 TTCATATATT
129 TTCATATATT
* * *
31578063 AATTATATTCTTTCCAAAAAAAATATTAGTTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
1 AATTATATTCTTTCC-AAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTA
*
31578128 ATATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTATGAATCAAAT
65 ATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
31578192 TCATATATT
130 TCATATATT
* * * *
31578201 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
31578266 TAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
66 TATAAT-TGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
31578330 TCATATATT
130 TCATATATT
31578339 AATT
1 AATT
31578343 TTATCTATGT
Statistics
Matches: 510, Mismatches: 42, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
136 2 0.00
137 51 0.10
138 208 0.41
139 26 0.05
140 173 0.34
141 50 0.10
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:31578146 original size:278 final size:276
Alignment explanation
Indices: 31577646--31578342 Score: 1035
Period size: 278 Copynumber: 2.5 Consensus size: 276
31577636 TAGAAAAATA
* *
31577646 AATTATATTCTTTCC-AAA-AACTATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAAC-ATTAATTTCCATGTCTTTTATATTTT-AACGAAATTAATTA
* * * **
31577709 ATATAATTGTTTATATTAATAAATTTGGCAAAATATATACA-ATTAATATTTTAAATGAATCAAA
64 ATATAACTGTTTATATTAATAAATTTGGTAAAATATATATACATTAATATTTTGTATGAATCAAA
* ** *
31577773 TTTATATATATTAATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACC
129 -TT-CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACC
*
31577838 GAAATTAATTAATATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAATATTTTGT
192 GAAATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGT
31577903 ATGAATCAAATTCATATATT
257 ATGAATCAAATTCATATATT
31577923 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTT-AACGAAATTAATTAA
* *
31577988 TATAACTATTTATATTAATAAATTCGGTAAAATATATATACATTTAATATTTTGTATGAATCAAA
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATATACA-TTAATATTTTGTATGAATCAAA
* * *
31578053 TTCATATATTAATTATATTCTTTCCAAAAAAAATATTAGTTTCCATGTCTTTTATATTTTGACTG
129 TTCATATATTAATTATATTCTTTCC-AAAAAAATATTAATTTCCATATCTTTTATATTTTGACCG
* * *
31578118 AAATTAATTAATATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTA
193 AAATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTA
31578182 TGAATCAAATTCATATATT
258 TGAATCAAATTCATATATT
* * * * *
31578201 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTAAC-GAAATTAATTAA
* * *
31578266 TATATCTGTTTATATTAATAAATTTGGTAAAATATATATA-ATTAATATTTTGTATGAACCACAT
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATATACATTAATATTTTGTATGAATCAAAT
31578330 TCATATATTAATT
130 TCATATATTAATT
31578343 TTATCTATGT
Statistics
Matches: 383, Mismatches: 31, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
276 34 0.09
277 18 0.05
278 254 0.66
279 57 0.15
280 20 0.05
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (276 bp):
AATTATATTCTTTCCAAAAGAACATTAATTTCCATGTCTTTTATATTTTAACGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTTGGTAAAATATATATACATTAATATTTTGTATGAATCAAATT
CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCGAAA
TTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGA
ATCAAATTCATATATT
Found at i:31585764 original size:27 final size:26
Alignment explanation
Indices: 31585710--31585774 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
31585700 TTTTATCCCA
*
31585710 GTAAAATTTTGACCATTTTACCAGTG
1 GTAAAATTTTGACCATTTTACCACTG
** *
31585736 GTAAAATTTTAGATGATTTTACCTCTG
1 GTAAAATTTT-GACCATTTTACCACTG
31585763 GTAAAATTTTGA
1 GTAAAATTTTGA
31585775 GAGAACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (26 bp):
GTAAAATTTTGACCATTTTACCACTG
Found at i:31589810 original size:23 final size:23
Alignment explanation
Indices: 31589780--31589828 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31589770 TACGGAAGGA
31589780 AAACTTGTATTAGTAAATAAACT
1 AAACTTGTATTAGTAAATAAACT
*
31589803 AAACTTGTATTAGTAGATAAACT
1 AAACTTGTATTAGTAAATAAACT
31589826 AAA
1 AAA
31589829 TAAGATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (23 bp):
AAACTTGTATTAGTAAATAAACT
Found at i:31591766 original size:24 final size:24
Alignment explanation
Indices: 31591731--31591778 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
31591721 AATTGATGTG
31591731 CAAATCAATGAGTTAAAGGGAGCT
1 CAAATCAATGAGTTAAAGGGAGCT
*
31591755 CAAATCAGTGAGTTAAAGGGAGCT
1 CAAATCAATGAGTTAAAGGGAGCT
31591779 GAGGTGGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (24 bp):
CAAATCAATGAGTTAAAGGGAGCT
Found at i:31592861 original size:33 final size:33
Alignment explanation
Indices: 31592824--31592913 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
31592814 ACGTTCATAG
* * *
31592824 TGCCATAACTCGGTTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAA
* *
31592857 TGCCATAGCCCAGCTATGGTCTTATCATCAGTA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAA
* *
31592890 TGCCATAGCCCAACTATGGTCTTA
1 TGCCATAACCCAGCTATGGTCTTA
31592914 CATATATACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (33 bp):
TGCCATAACCCAGCTATGGTCTTATCATCAGAA
Found at i:31596459 original size:42 final size:43
Alignment explanation
Indices: 31596348--31596459 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 43
31596338 CTCATACAAT
* * ** * *
31596348 GCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAATGAT
1 GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
* * * * *
31596391 GCCATTGTCCCAGATAGGGTTTTACACATAATCATAT-ACGAC
1 GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
*
31596433 GCCAATGTCTCAGACATGGTCTTACAC
1 GCCAATGTCCCAGACATGGTCTTACAC
31596460 GTAAATTTCA
Statistics
Matches: 53, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
42 25 0.47
43 28 0.53
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACATAATCAAATAACGAC
Found at i:31604355 original size:41 final size:41
Alignment explanation
Indices: 31604214--31604355 Score: 178
Period size: 41 Copynumber: 3.5 Consensus size: 41
31604204 TTTAAAATGA
* * * *
31604214 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGA-TAGAAGTAAAGTCTGAATTAT
* * *
31604255 TACACCAGCATTAAGCCTGCTAGAAGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGAAGTAAAGTCTGAATTAT
* **
31604296 TTCACTGGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGAAGTAAAGTCTGAATTAT
31604337 TTCACTAGCATTAAGCCTG
1 TTCACTAGCATTAAGCCTG
31604356 CTAAGTACAG
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
TTCACTAGCATTAAGCCTGATAGAAGTAAAGTCTGAATTAT
Found at i:31604373 original size:82 final size:81
Alignment explanation
Indices: 31604214--31604374 Score: 209
Period size: 82 Copynumber: 2.0 Consensus size: 81
31604204 TTTAAAATGA
31604214 TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAGA
1 TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTA-A
*
31604279 AGTAAAGTCTGAATTAT
65 AGTAAAGCCTGAATTAT
** * * * *
31604296 TTCACTGGCATTAAGCCTGA-TAGGTGTAAAGTCTGAATTATTTCACTAGCATTAAGCCTGCT-A
1 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAA
31604359 AGTACAGAGCCTGAAT
65 AGTA-A-AGCCTGAAT
31604375 AACTCAGATA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 5 0.07
81 1 0.01
82 62 0.90
83 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (81 bp):
TTCACTGGCATTAAGCCTACTAGACGTAAAGTCTAAAATATTACACCAGCATTAAGCCTGCTAAA
GTAAAGCCTGAATTAT
Found at i:31606544 original size:29 final size:29
Alignment explanation
Indices: 31606502--31606570 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
31606492 CACAAATAAA
31606502 TTGTACA-AGTAGACCGAATTCTACTAATC
1 TTGTACACA-TAGACCGAATTCTACTAATC
31606531 TTGTACACATAGACCGAATTCTACTAATC
1 TTGTACACATAGACCGAATTCTACTAATC
31606560 TTGTACACATA
1 TTGTACACATA
31606571 CATATACTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (29 bp):
TTGTACACATAGACCGAATTCTACTAATC
Found at i:31610051 original size:24 final size:24
Alignment explanation
Indices: 31610017--31610065 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
31610007 GCCGCTATAG
31610017 AACATGACCTTTAGCGGCACTTTT
1 AACATGACCTTTAGCGGCACTTTT
* * *
31610041 AACATGGCCTTTAGTGGCATTTTT
1 AACATGACCTTTAGCGGCACTTTT
31610065 A
1 A
31610066 TCACAAACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
AACATGACCTTTAGCGGCACTTTT
Found at i:31610108 original size:43 final size:43
Alignment explanation
Indices: 31610041--31610220 Score: 236
Period size: 43 Copynumber: 4.2 Consensus size: 43
31610031 CGGCACTTTT
* * ** *
31610041 AACATGGCCTTTAGTGGCATTTTTATCACAAACGCCGTTAAAG
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
** *
31610084 AACATGATATTTAGCGGCGCTTTTATCACAAACGCCGCTAAAT
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
* * *
31610127 AACATGCCCTTTAGCGGCACTTTTATCACAAATGCCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
*
31610170 AACATGACCTTTAGCGGCGCTTCTT-TCACAAATGCCGCTAAAG
1 AACATGACCTTTAGCGGCGCTT-TTATCACAAACGCCGCTAAAG
31610213 AACATGAC
1 AACATGAC
31610221 TTGACTCTCC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 118 0.98
44 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAG
Found at i:31610185 original size:86 final size:86
Alignment explanation
Indices: 31610040--31610218 Score: 261
Period size: 86 Copynumber: 2.1 Consensus size: 86
31610030 GCGGCACTTT
* * * * *
31610040 TAACATGGCCTTTAGTGGCATTTTTATCACAAACGCCGTTAAAGAACATGATATTTAGCGGCGCT
1 TAACATGCCCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAGAACATGACATTTAGCGGCGCT
31610105 T-TTATCACAAACGCCGCTAAA
66 TCTT-TCACAAACGCCGCTAAA
* *
31610126 TAACATGCCCTTTAGCGGCACTTTTATCACAAATGCCGCTAAAGAACATGACCTTTAGCGGCGCT
1 TAACATGCCCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAGAACATGACATTTAGCGGCGCT
*
31610191 TCTTTCACAAATGCCGCTAAA
66 TCTTTCACAAACGCCGCTAAA
*
31610212 GAACATG
1 TAACATG
31610219 ACTTGACTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 81 0.98
87 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (86 bp):
TAACATGCCCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAGAACATGACATTTAGCGGCGCT
TCTTTCACAAACGCCGCTAAA
Found at i:31614696 original size:21 final size:21
Alignment explanation
Indices: 31614672--31614719 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
31614662 AATTGAAGTA
*
31614672 ACAAATGATGTAGAGGCAGAG
1 ACAAATGATGCAGAGGCAGAG
*
31614693 ACAAATGATGCAGAGGTAGAG
1 ACAAATGATGCAGAGGCAGAG
31614714 ACAAAT
1 ACAAAT
31614720 TTGATGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.29, T:0.15
Consensus pattern (21 bp):
ACAAATGATGCAGAGGCAGAG
Found at i:31614830 original size:19 final size:19
Alignment explanation
Indices: 31614802--31614839 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31614792 CCGAAAACTA
31614802 GAAGGCAGGAGACAACTTG
1 GAAGGCAGGAGACAACTTG
*
31614821 GAAGGTAGGAGACAACTTG
1 GAAGGCAGGAGACAACTTG
31614840 CAACAGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.37, T:0.13
Consensus pattern (19 bp):
GAAGGCAGGAGACAACTTG
Found at i:31616508 original size:7 final size:7
Alignment explanation
Indices: 31616498--31616610 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 7
31616488 TAATAAAACA
31616498 TAAACCC
1 TAAACCC
31616505 TAAACCCC
1 TAAA-CCC
31616513 T-AACCC
1 TAAACCC
*
31616519 TTAACCC
1 TAAACCC
*
31616526 ATAAACCA
1 -TAAACCC
*
31616534 TAATCCC
1 TAAACCC
31616541 TAAACCC
1 TAAACCC
* *
31616548 ATAATCCA
1 -TAAACCC
*
31616556 TAAACCT
1 TAAACCC
*
31616563 TAAA--A
1 TAAACCC
*
31616568 TAGGAACTCT
1 TA--AAC-CC
*
31616578 TAAACCT
1 TAAACCC
31616585 TAAACCC
1 TAAACCC
*
31616592 TAAACCA
1 TAAACCC
*
31616599 TAAACCT
1 TAAACCC
31616606 TAAAC
1 TAAAC
31616611 TATATGGATA
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.02
6 4 0.05
7 58 0.70
8 17 0.20
10 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:31616546 original size:29 final size:29
Alignment explanation
Indices: 31616496--31616566 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
31616486 AATAATAAAA
* *
31616496 CATAAACCCTAAACCCCTAACCCTTAACC
1 CATAAACCATAAACCCCTAACCCATAACC
* *
31616525 CATAAACCAT-AATCCCTAAACCCATAATC
1 CATAAACCATAAACCCCT-AACCCATAACC
*
31616554 CATAAACCTTAAA
1 CATAAACCATAAA
31616567 ATAGGAACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.17
29 27 0.77
30 2 0.06
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.20
Consensus pattern (29 bp):
CATAAACCATAAACCCCTAACCCATAACC
Found at i:31616549 original size:15 final size:15
Alignment explanation
Indices: 31616510--31616561 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31616500 AACCCTAAAC
*
31616510 CCCT-AACCCTTAA-
1 CCCTAAACCCATAAT
31616523 CCCATAAA-CCATAAT
1 CCC-TAAACCCATAAT
31616538 CCCTAAACCCATAAT
1 CCCTAAACCCATAAT
*
31616553 CCATAAACC
1 CCCTAAACC
31616562 TTAAAATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 3 0.09
14 10 0.30
15 20 0.61
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCTAAACCCATAAT
Found at i:31616566 original size:22 final size:22
Alignment explanation
Indices: 31616498--31616610 Score: 94
Period size: 22 Copynumber: 5.2 Consensus size: 22
31616488 TAATAAAACA
* *
31616498 TAAACCC-TAAACCCCTAACCCT
1 TAAACCCATAAA-CCATAAACCT
* *
31616520 T-AACCCATAAACCATAATCCC
1 TAAACCCATAAACCATAAACCT
*
31616541 TAAACCCATAATCCATAAACCT
1 TAAACCCATAAACCATAAACCT
*
31616563 TAAA---ATAGGAACTCTTAAACCT
1 TAAACCCATA--AAC-CATAAACCT
31616585 TAAACCC-TAAACCATAAACCT
1 TAAACCCATAAACCATAAACCT
31616606 TAAAC
1 TAAAC
31616611 TATATGGATA
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.04
21 28 0.38
22 41 0.55
24 2 0.03
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.21
Consensus pattern (22 bp):
TAAACCCATAAACCATAAACCT
Found at i:31616597 original size:14 final size:14
Alignment explanation
Indices: 31616491--31616610 Score: 66
Period size: 14 Copynumber: 8.4 Consensus size: 14
31616481 CCTTGAATAA
*
31616491 TAAAACATAAACCC
1 TAAACCATAAACCC
*
31616505 TAAACCCCT-AACCC
1 TAAA-CCATAAACCC
* *
31616519 TTAACCCATAAACCA
1 -TAAACCATAAACCC
* *
31616534 TAATCCCTAAACCC
1 TAAACCATAAACCC
* *
31616548 ATAATCCATAAACCT
1 -TAAACCATAAACCC
*
31616563 TAAA--ATAGGAACTCT
1 TAAACCATA--AAC-CC
*
31616578 TAAACCTTAAACCC
1 TAAACCATAAACCC
*
31616592 TAAACCATAAACCT
1 TAAACCATAAACCC
31616606 TAAAC
1 TAAAC
31616611 TATATGGATA
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
12 3 0.04
14 47 0.57
15 30 0.37
17 2 0.02
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:31616750 original size:7 final size:7
Alignment explanation
Indices: 31616730--31616806 Score: 84
Period size: 7 Copynumber: 11.0 Consensus size: 7
31616720 AACCCCTATC
31616730 CCATAAA
1 CCATAAA
*
31616737 CCCTAAA
1 CCATAAA
*
31616744 TCATAAA
1 CCATAAA
*
31616751 ACATAAA
1 CCATAAA
*
31616758 CCCTAAA
1 CCATAAA
31616765 CCATAAA
1 CCATAAA
*
31616772 CC-TCAAC
1 CCAT-AAA
*
31616779 CCTTAAA
1 CCATAAA
31616786 CCATAAA
1 CCATAAA
31616793 CCATAAA
1 CCATAAA
31616800 CCATAAA
1 CCATAAA
31616807 GCTCGATCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
6 1 0.02
7 56 0.97
8 1 0.02
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (7 bp):
CCATAAA
Found at i:31617019 original size:40 final size:40
Alignment explanation
Indices: 31616917--31617459 Score: 175
Period size: 40 Copynumber: 13.8 Consensus size: 40
31616907 TTTTGCGACG
* * * * *
31616917 TTTTTCAAAAAGCGCCACTAATGGTTGACCTATAGTGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* * * *
31616957 TTTTGCAAAACGCACCGGTAATGCTCGATCTATAGTGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* **
31616997 TTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGCAGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* * *
31617037 TTTTTCAAAAAGTGCTGCTAATGC-C-A-CTAAAGCT--CA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG-TGGCA
*** * ** ** ** * * * *
31617073 -ACAT-AAAATGACGGTG-TTGTGCTTAATTTTTTGCGGCA
1 TTTTTCAAAAAG-CGCCGCTAATGCTCGATCTATAGTGGCA
** * * * * * * *
31617111 TTTTTTGAAAAGTGCTGCTAATGGTCAACCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* * * *
31617151 TTTTTCAAGAAGCGCCGCTAGTGCTCTATCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
** * * ** *
31617191 TTTTTCATGAAGCGCCGCTAATTCTCGATTTATAACGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* * *
31617231 TTTTCCAAAAAACGCCGCTAATGC-C-A-CTAAAGCT--CA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG-TGGCA
*** * * ** ** * * * * **
31617267 -ACAT-AAAATAGGGGCG-TTGTGCTTAATTTTTTTGCGGTG
1 TTTTTCAAAA-AGCGCCGCTAATGCTCGA-TCTATAGTGGCA
* * * * *
31617306 TTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* * **
31617346 TTTTTCAAGAAGCGCCG-TGAATGCTCGATCTATAGAGGTG
1 TTTTTCAAAAAGCGCCGCT-AATGCTCGATCTATAGTGGCA
* * * *
31617386 TTTTTCAAAAGGCGCCACTAATGCTCGATCTATAGCGGTA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
* *
31617426 TTTTTTAAAAAGCGTCGCTAATGCTCGATCTATA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
31617460 ACGGCGTTTT
Statistics
Matches: 356, Mismatches: 124, Indels: 46
0.68 0.24 0.09
Matches are distributed among these distances:
34 17 0.05
35 8 0.02
36 5 0.01
37 10 0.03
38 6 0.02
39 7 0.02
40 293 0.82
41 10 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCA
Found at i:31617196 original size:194 final size:194
Alignment explanation
Indices: 31616835--31617449 Score: 772
Period size: 195 Copynumber: 3.2 Consensus size: 194
31616825 TTTTTCGAAA
* * * *
31616835 AGCGGCA-TTTTCTGAAAAGCGACGCTAATGCCACTAAAGCTCAACATAAAATGATGGTGTTATG
1 AGCGGCATTTTTC-AAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTG
* * * * * *
31616899 CTTAATTTTTTTGCGACGTTTTTCAAAAAGCGCCACTAATGGTTGACCTATAGTGGCGTTTTGCA
65 CTTAATTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCA
* *
31616964 A-AACGCACCGGTAATGCTCGATCTATAGTGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCT
130 AGAA-GCGCC-GTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCT
31617028 AT
193 AT
* * *
31617030 AGCAGCATTTTTCAAAAAGTGCTGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGC
1 AGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGC
* ** * * *
31617095 TTAA-TTTTTTGCGGCATTTTTTGAAAAGTGCTGCTAATGGTCAACCTATAGCGGCGTTTTTCAA
66 TTAATTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAA
* * * * * *
31617159 GAAGCGCCGCTAGTGCTCTATCTATAGCGGCATTTTTCATGAA-GCGCCGCTAATTCTCGATTTA
131 GAAGCGCCG-TAATGCTCGATCTATAGAGGCATTTTTCA-AAAGGCGCCGCTAATGCTCGATCTA
31617223 T
194 T
* * * * * *
31617224 AACGGCGTTTTCCAAAAAACGCCGCTAATGCCACTAAAGCTCAACATAAAAT-AGGGGCGTTGTG
1 AGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGA-CGGTGTTGTG
*
31617288 CTTAATTTTTTTGCGGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCA
65 CTTAATTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCA
** *
31617353 AGAAGCGCCGTGAATGCTCGATCTATAGAGGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTA
130 AGAAGCGCCGT-AATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTA
31617418 T
194 T
* * *
31617419 AGCGGTATTTTTTAAAAAGCGTCGCTAATGC
1 AGCGGCATTTTTCAAAAAGCGCCGCTAATGC
31617450 TCGATCTATA
Statistics
Matches: 355, Mismatches: 57, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
193 2 0.01
194 160 0.45
195 188 0.53
196 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (194 bp):
AGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGC
TTAATTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAA
GAAGCGCCGTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTAT
Found at i:31617439 original size:80 final size:80
Alignment explanation
Indices: 31617302--31617459 Score: 210
Period size: 80 Copynumber: 2.0 Consensus size: 80
31617292 ATTTTTTTGC
* * * *
31617302 GGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAAGCGCCG-TGA
1 GGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCT-A
31617366 ATGCTCGATCTATAGA
65 ATGCTCGATCTATAGA
* * * * * *
31617382 GGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAGCGGTATTTTTTAAAAAGCGTCGCTAA
1 GGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCTAA
31617447 TGCTCGATCTATA
66 TGCTCGATCTATA
31617460 ACGGCGTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
80 66 0.99
81 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (80 bp):
GGTGTTTTTCAAAAAGAGCCACTAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCTAA
TGCTCGATCTATAGA
Found at i:31617472 original size:40 final size:40
Alignment explanation
Indices: 31617305--31617470 Score: 183
Period size: 40 Copynumber: 4.2 Consensus size: 40
31617295 TTTTTGCGGT
* * * *
31617305 GTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAACGGC
* *
31617345 GTTTTTCAAGAAGCGCCG-TGAATGCTCGATCTATAGA-GGT
1 GTTTTTCAAAAAGCGCCGCT-AATGCTCGATCTATA-ACGGC
* * * *
31617385 GTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAGCGGT
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAACGGC
* * *
31617425 ATTTTTTAAAAAGCGTCGCTAATGCTCGATCTATAACGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAACGGC
31617465 GTTTTT
1 GTTTTT
31617471 TATCCAAACA
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 102 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAACGGC
Found at i:31620068 original size:11 final size:11
Alignment explanation
Indices: 31620054--31620092 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31620044 CCACCCTATC
31620054 ACCACCATACA
1 ACCACCATACA
* *
31620065 ACCACCACACC
1 ACCACCATACA
*
31620076 ACCACCATTCA
1 ACCACCATACA
31620087 ACCACC
1 ACCACC
31620093 GTAGCACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.54, G:0.00, T:0.08
Consensus pattern (11 bp):
ACCACCATACA
Found at i:31622536 original size:13 final size:14
Alignment explanation
Indices: 31622520--31622548 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31622510 CATGTTAGCC
31622520 AAATAAACA-TATA
1 AAATAAACATTATA
31622533 AAATAAACATTATA
1 AAATAAACATTATA
31622547 AA
1 AA
31622549 CATGGATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAACATTATA
Found at i:31623499 original size:11 final size:11
Alignment explanation
Indices: 31623485--31623518 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
31623475 GGTAAATTCA
31623485 TAAAAAATACT
1 TAAAAAATACT
31623496 TAAAAAATACT
1 TAAAAAATACT
31623507 TAAAAAATACT
1 TAAAAAATACT
31623518 T
1 T
31623519 TTAATTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAAATACT
Found at i:31632574 original size:33 final size:31
Alignment explanation
Indices: 31632520--31632588 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
31632510 CAATTCAATA
31632520 ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
1 ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
*
31632551 ACAGTCTCAGTGTCAG-TGTGGCCTTATCCCATT
1 ACAGT-TCAGT-TCAGTTG-GGCCTTAGCCCATT
31632584 ACAGT
1 ACAGT
31632589 GACAGTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 22 0.65
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (31 bp):
ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
Found at i:31635782 original size:24 final size:24
Alignment explanation
Indices: 31635746--31635791 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31635736 GTAATTTTAA
*
31635746 AAAATATATAATTATA-CCAATATT
1 AAAATATAAAATT-TACCCAATATT
*
31635770 AAAATTTAAAATTTACCCAATA
1 AAAATATAAAATTTACCCAATA
31635792 GTCAAAGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATATAAAATTTACCCAATATT
Found at i:31641961 original size:37 final size:37
Alignment explanation
Indices: 31641920--31641996 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
31641910 TCCGAACATG
31641920 AATGCCAAATTGAGGAATGATATTACGTCCTTTGGGC
1 AATGCCAAATTGAGGAATGATATTACGTCCTTTGGGC
31641957 AATGCCAAATTGAGGAATGATATTACGTCCTTTGGGC
1 AATGCCAAATTGAGGAATGATATTACGTCCTTTGGGC
31641994 AAT
1 AAT
31641997 CTGAGAGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (37 bp):
AATGCCAAATTGAGGAATGATATTACGTCCTTTGGGC
Found at i:31651023 original size:25 final size:24
Alignment explanation
Indices: 31650985--31651051 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
31650975 CTATGATCGA
*
31650985 TAAGCTCATTTCGAGCTGAAGAACGG
1 TAAGCTCATATCGAGCTG-A-AACGG
*
31651011 TAAGCTC-TATCGAGTTGAAACGG
1 TAAGCTCATATCGAGCTGAAACGG
*
31651034 TAAGCTCATA-AGAGCTGA
1 TAAGCTCATATCGAGCTGA
31651052 TATATTGGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 18 0.50
24 3 0.08
25 8 0.22
26 7 0.19
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (24 bp):
TAAGCTCATATCGAGCTGAAACGG
Found at i:31656194 original size:40 final size:40
Alignment explanation
Indices: 31656133--31656378 Score: 318
Period size: 40 Copynumber: 6.2 Consensus size: 40
31656123 CGGAATTTAG
* * * *
31656133 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
31656173 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
31656213 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
31656253 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
*
31656293 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
31656333 CCGGATAAAATCACTAGCACAAATGCCTTC-GGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
31656372 CCGGATA
1 CCGGATA
31656379 TCATTCAAAT
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
39 16 0.09
40 167 0.89
41 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Done.