Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold143
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: 1221646
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:162211 original size:21 final size:22
Alignment explanation
Indices: 162182--162224 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
162172 AAGAGAGCAT
162182 AAAATATTTTATTAAGAGGGAG
1 AAAATATTTTATTAAGAGGGAG
*
162204 AAAA-ATTTTATTAAGGGGGAG
1 AAAATATTTTATTAAGAGGGAG
162225 TTATATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (22 bp):
AAAATATTTTATTAAGAGGGAG
Found at i:162265 original size:101 final size:101
Alignment explanation
Indices: 162059--162265 Score: 299
Period size: 102 Copynumber: 2.0 Consensus size: 101
162049 TTTGTTTTAG
*
162059 AAATCTTATTAAAAAAGAGCATAAAAATTTTATTAAGGGGGAGAAAAATTTTATTAAGGAGGAGT
1 AAATCTTATTAAAAAAGAGCATAAAAATTTTATTAAGAGGGAGAAAAATTTTATTAAGGAGGAGT
* * ** *
162124 TATATATTGAAAATTTGCATTAAAAATTTGTTTTAG
66 TATATATTGAAAATTTACATTAAAAATCTGTAATAA
* *
162160 AAATCTTATTAAAAGAGAGCATAAAATATTTTATTAAGAGGGAGAAAAATTTTATTAAGGGGGAG
1 AAATCTTATTAAAAAAGAGCATAAAA-ATTTTATTAAGAGGGAGAAAAATTTTATTAAGGAGGAG
* **
162225 TTATATATTGAAAATTTACCTTAAACCTCT-TAATAA
65 TTATATATTGAAAATTTACATTAAAAATCTGTAATAA
162261 AAATC
1 AAATC
162266 CGTTTTTAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 33 0.35
102 61 0.65
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.34
Consensus pattern (101 bp):
AAATCTTATTAAAAAAGAGCATAAAAATTTTATTAAGAGGGAGAAAAATTTTATTAAGGAGGAGT
TATATATTGAAAATTTACATTAAAAATCTGTAATAA
Found at i:164677 original size:50 final size:50
Alignment explanation
Indices: 164546--164679 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 50
164536 TTCCATAATT
* * * *
164546 TGTATCAATACA-TTCTTCATTGTATCGATACATTTTGGTTTTTACCCATA
1 TGTATCGATACATTTC-TCATTGTATCGATACATTCTGGGTTTTACCCAGA
* *
164596 TGTATCGATACATTAT-TAATTATATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATT-TCTCATTGTATCGATACATTCTGGGTTTTACCCAGA
*
164646 TGTATCGATACATTTCTCATTGTATCAATACATT
1 TGTATCGATACATTTCTCATTGTATCGATACATT
164680 AAGGCATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 69 0.96
51 1 0.01
52 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTTCTCATTGTATCGATACATTCTGGGTTTTACCCAGA
Found at i:176306 original size:22 final size:22
Alignment explanation
Indices: 176281--176324 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
176271 ATTATCATCA
176281 TCACGCAAATCTTACTTACATT
1 TCACGCAAATCTTACTTACATT
176303 TCACGCAAATCTTACTTACATT
1 TCACGCAAATCTTACTTACATT
176325 AATCCCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (22 bp):
TCACGCAAATCTTACTTACATT
Found at i:176461 original size:62 final size:62
Alignment explanation
Indices: 176383--177273 Score: 891
Period size: 62 Copynumber: 14.3 Consensus size: 62
176373 CTTTTATCCT
* * ** * * *
176383 TTTTAGTCCTTAAAGAGTAGGACACCTTCTTCTTTTTAAAGCCCATACAAGTTGGTGGCACCC
1 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * *
176446 TTTTGTCCTCGAAGAGCAGGATACCTTTTTCTTTTCAAAGCCGACACAAGCTGGTAGCACCTC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACC-C
* * ** * *
176509 TTTAGTACTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGACTTGGTGGCACTC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
176571 TTTAGTCCTCAAAGACCAGGATGGCTTTTTCTTTTCAAAGCCCAGACGAGTTGGTGGCGCCC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * * *
176633 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCCTTTTGAAAGCTCACACAAGTTGGTGGCACCC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * * * *
176696 TTTAGTCCTCAAAGAGTAGGATACCTTTTT-TTTTTCAAAGCCCACACTAGTTGGTGGCACCA
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTT-AAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
176758 TTTAGTCCTTAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCATCA
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* ** * * *
176820 TTTTGTTCTTGAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCGCACGAGCTGGTGGCACCC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * *
176882 TTTTAGTCCTCAAAAAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
1 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
176945 TTTTGTCCTCGAAGAGCAGGATGCCTTTTTCATTTCAAAGCCCATACAAGCTGGTGGCAACCC
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGC-ACCC
* * * * *
177008 TTTAGTACTCAAAGAGCAAGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA-CT
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * ** **
177069 TTTTAGTCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTCT-AAGCTTACACGAGTTAATGGCA-
1 TTTT-GTCCTCAAAGAGCAGGATGCC---TTTTTCTTTT-TAAAGCCCACACGAGTTGGTGGCAC
*
177132 CT
61 CC
* ** *
177134 TTTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTTTAAGCCCACACGAGTTGGTGGCA-CC
1 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
* * **
177196 TTTTAGTTCTCAAAGAGCAGGACGCC--TTTCCATTTAAAGCCCGA-ACGAGTTGGTGGCA-CC
1 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCC-ACACGAGTTGGTGGCACCC
*
177256 TTTTATTCCTCAAAGAGC
1 TTTT-GTCCTCAAAGAGC
177274 TGTGTAGACA
Statistics
Matches: 711, Mismatches: 104, Indels: 29
0.84 0.12 0.03
Matches are distributed among these distances:
60 45 0.06
61 10 0.01
62 379 0.53
63 221 0.31
65 55 0.08
66 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (62 bp):
TTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
Found at i:176606 original size:125 final size:124
Alignment explanation
Indices: 176384--177273 Score: 1003
Period size: 125 Copynumber: 7.1 Consensus size: 124
176374 TTTTATCCTT
* * * * * *
176384 TTTAGTCCTTAAAGAGTAGGACACCTTCTTCTTTTTAAAGCCCATACAAGTTGGTGGCACCCTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * * * *
176449 TGTCCTCGAAGAGCAGGATACCTTTTTCTTTTCAAAGCCGACACAAGCTGGTAGCACCTC
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACC-C
* * * *
176509 TTTAGTACTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGACTTGGTGGCACTCTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * * *
176574 AGTCCTCAAAGACCAGGATGGCTTTTTCTTTTCAAAGCCCAGACGAGTTGGTGGCGCCC
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCC
* * * *
176633 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCCTTTTGAAAGCTCACACAAGTTGGTGGCACCCTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCCTT
* * * * * *
176698 TAGTCCTCAAAGAGTAGGATACCTTTTTTTTTTCAAAGCCCACACTAGTTGGTGGCACCA
65 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCC
* * * * * *
176758 TTTAGTCCTTAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCATCATTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
* * ** *
176823 TGTTCTTGAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCGCACGAGCTGGTGGCACCC
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCC
* * * *
176882 TTTTAGTCCTCAAAAAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTT
1 -TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTT
* * * * *
176947 TTGTCCTCGAAGAGCAGGATGCCTTTTTCATTTCAAAGCCCATACAAGCTGGTGGCAACCC
65 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGC-ACCC
* * **
177008 TTTAGTACTCAAAGAGCAAGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACTTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * ** * ** **
177073 AGTCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTCTAAGCTTACACGAGTTAATGGCACTT
66 AGTCCTCAAAGAGCAGGATGCC---TTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCC
* * * *
177135 TTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTTTAAGCCCACACGAGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * * * *
177200 AGTTCTCAAAGAGCAGGACGCC-TTTCCATTT-AAAGCCCGA-ACGAGTTGGTGGCACCT
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCC-ACACGAGCTGGTGGCACCC
*
177257 TTTATTCCTCAAAGAGC
1 TTTAGTCCTCAAAGAGC
177274 TGTGTAGACA
Statistics
Matches: 656, Mismatches: 102, Indels: 17
0.85 0.13 0.02
Matches are distributed among these distances:
122 34 0.05
123 8 0.01
124 107 0.16
125 396 0.60
126 4 0.01
127 83 0.13
128 24 0.04
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (124 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTT
AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCC
Found at i:176701 original size:187 final size:186
Alignment explanation
Indices: 176384--177273 Score: 973
Period size: 187 Copynumber: 4.8 Consensus size: 186
176374 TTTTATCCTT
* * ** * * * *
176384 TTTAGTCCTTAAAGAGTAGGACACCTTCTTCTTTTTAAAGCCCATACAAGTTGGTGGCACCCTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * * * * *
176449 TGTCCTCGAAGAGCAGGATACCTTTTTCTTTTCAAAGCCGACACAAGCTGGTAGCACCTCTTTAG
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-CTTTAG
* *
176514 TACTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGACTTGGTGGCACTC
130 TCCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACTC
* * * *
176571 TTTAGTCCTCAAAGACCAGGATGGCTTTTTCTTTTCAAAGCCCAGACGAGTTGGTGGCGCCCTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
* * *
176636 AGTCCTCAAAGAGCAGGATGCCTTTTTCCTTTTGAAAGCTCACACAAGTTGGTGGCACCCTTTAG
66 AGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAG
* * *
176701 TCCTCAAAGAGTAGGATACCTTTTT-TTTTTCAAAGCCCACACTAGTTGGTGGCAC-C
130 TCCTCAAAGAGCAGGACACCTTTTTCTTTTT-AAAGCCCACACGAGTTGGTGGCACTC
* * * *
176757 ATTTAGTCCTTAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCATCATT
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTT
* * ** * *
176822 TTGTTCTTGAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCGCACGAGCTGGTGGCACCCTTTTA
65 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC-TTTA
* * ** * *
176887 GTCCTCAAAAAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
129 GTCCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACTC
* * * * * *
176945 TTTTGTCCTCGAAGAGCAGGATGCCTTTTTCATTTCAAAGCCCATACAAGCTGGTGGCAACCCTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGC-ACCCTT
* * * * **
177010 TAGTACTCAAAGAGCAAGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACTTTTTAG
65 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAG
* * ** ** *
177075 TCCTCAAAGAGCAAGACGCCTTTTTTTTCTTTTCT-AAGCTTACACGAGTTAATGGCACTT
130 TCCTCAAAGAGCAGGACACC---TTTTTCTTTT-TAAAGCCCACACGAGTTGGTGGCACTC
* ** ** *
177135 TTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTTTAAGCCCACACGAGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * * * *
177200 AGTTCTCAAAGAGCAGGACGCC-TTTCCATTT-AAAGCCCGA-ACGAGTTGGTGGCACCTTTTAT
66 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCC-ACACGAGTTGGTGGCACCCTTTAG
177262 TCCTCAAAGAGC
130 TCCTCAAAGAGC
177274 TGTGTAGACA
Statistics
Matches: 596, Mismatches: 95, Indels: 24
0.83 0.13 0.03
Matches are distributed among these distances:
186 33 0.06
187 369 0.62
188 92 0.15
189 26 0.04
190 76 0.13
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (186 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGT
CCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACTC
Found at i:177580 original size:13 final size:13
Alignment explanation
Indices: 177562--177586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177552 TTCAACAATT
177562 TGTATCGATACAA
1 TGTATCGATACAA
177575 TGTATCGATACA
1 TGTATCGATACA
177587 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:177658 original size:20 final size:20
Alignment explanation
Indices: 177633--177670 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
177623 TACTGCCAAG
177633 GAAATGTATCGATACATTAC
1 GAAATGTATCGATACATTAC
177653 GAAATGTATCGATACATT
1 GAAATGTATCGATACATT
177671 GTATCGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAATGTATCGATACATTAC
Found at i:177675 original size:13 final size:13
Alignment explanation
Indices: 177657--177682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177647 CATTACGAAA
177657 TGTATCGATACAT
1 TGTATCGATACAT
177670 TGTATCGATACAT
1 TGTATCGATACAT
177683 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:177694 original size:20 final size:20
Alignment explanation
Indices: 177669--177735 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
177659 TATCGATACA
177669 TTGTATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
*
177689 TTGTATC---A-AT--A-CA
1 TTGTATCGATACATGGATCT
*
177702 TTATATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
177722 TTGTATCGATACAT
1 TTGTATCGATACAT
177736 TTGGGAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
13 7 0.19
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 21 0.58
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATGGATCT
Found at i:177694 original size:33 final size:33
Alignment explanation
Indices: 177657--177736 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
177647 CATTACGAAA
*
177657 TGTATCGATACATTGTATCGATACATGGATCTT
1 TGTATCGATACATTATATCGATACATGGATCTT
*
177690 TGTATCAATACATTATATCGATACATGGATCTT
1 TGTATCGATACATTATATCGATACATGGATCTT
177723 TGTATCGATACATT
1 TGTATCGATACATT
177737 TGGGAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTATATCGATACATGGATCTT
Found at i:181773 original size:13 final size:13
Alignment explanation
Indices: 181755--181779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
181745 ATAATGCACA
181755 GTATCGATACATT
1 GTATCGATACATT
181768 GTATCGATACAT
1 GTATCGATACAT
181780 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:181792 original size:20 final size:21
Alignment explanation
Indices: 181767--181819 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
181757 ATCGATACAT
*
181767 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
* *
181787 TGTATCAATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
181808 TGTATCGATACA
1 TGTATCGATACA
181820 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:181898 original size:13 final size:13
Alignment explanation
Indices: 181880--181904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
181870 ACATACAAGA
181880 TGTATCGATACAG
1 TGTATCGATACAG
181893 TGTATCGATACA
1 TGTATCGATACA
181905 TGACCAAATT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:181923 original size:34 final size:32
Alignment explanation
Indices: 181861--181925 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
181851 CTTAATTGTT
181861 TGTATCGATACATACAAGATGTATCGATACAG
1 TGTATCGATACATACAAGATGTATCGATACAG
181893 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
181926 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAG
Found at i:187855 original size:8 final size:8
Alignment explanation
Indices: 187842--187872 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
187832 ATTTGATTAA
187842 ATTTTGTG
1 ATTTTGTG
187850 ATTTTGTG
1 ATTTTGTG
187858 ATTTTGTG
1 ATTTTGTG
187866 ATGTTTG
1 AT-TTTG
187873 ATGTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:188077 original size:13 final size:13
Alignment explanation
Indices: 188059--188096 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
188049 CAGCATTCTC
*
188059 TGTATCGATACAT
1 TGTATCGATACAG
188072 TGTATCGATACAG
1 TGTATCGATACAG
188085 TGTATCGATACA
1 TGTATCGATACA
188097 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:188564 original size:20 final size:22
Alignment explanation
Indices: 188539--188583 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
188529 GGCACACTCA
*
188539 CCAGGTCGCGACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
188559 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
188581 CCA
1 CCA
188584 CACTCACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.18, C:0.49, G:0.29, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:189962 original size:29 final size:29
Alignment explanation
Indices: 189920--189978 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
189910 AATAAATTTA
189920 TGATTAAGGGGGAGAAAGAAACATGTGAT
1 TGATTAAGGGGGAGAAAGAAACATGTGAT
*
189949 TGATTAAGGGGGAGTAAGAAACATGTGAT
1 TGATTAAGGGGGAGAAAGAAACATGTGAT
189978 T
1 T
189979 AAAGGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.34, T:0.24
Consensus pattern (29 bp):
TGATTAAGGGGGAGAAAGAAACATGTGAT
Found at i:190024 original size:21 final size:22
Alignment explanation
Indices: 189983--190024 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
189973 GTGATTAAAG
189983 GAAATTGTTTTATTAAGGGGGA
1 GAAATTGTTTTATTAAGGGGGA
190005 GAAATT-TTTTGATTAAGGGG
1 GAAATTGTTTT-ATTAAGGGG
190025 TAGAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (22 bp):
GAAATTGTTTTATTAAGGGGGA
Found at i:190602 original size:13 final size:13
Alignment explanation
Indices: 190584--190608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190574 ATAATGCACA
190584 GTATCGATACATT
1 GTATCGATACATT
190597 GTATCGATACAT
1 GTATCGATACAT
190609 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:190621 original size:20 final size:20
Alignment explanation
Indices: 190596--190646 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
190586 ATCGATACAT
190596 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
190616 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
190636 TGTATCGATAC
1 TGTATCGATAC
190647 TTGCAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:190751 original size:32 final size:34
Alignment explanation
Indices: 190710--190772 Score: 96
Period size: 32 Copynumber: 1.9 Consensus size: 34
190700 CTTAACTGTT
190710 TGTATCGATACAT-A-CAAGA-TGTATCGATATAG
1 TGTATCGATACATGACCAA-ATTGTATCGATATAG
190742 TGTATCGATACATGACCAAATTGTATCGATA
1 TGTATCGATACATGACCAAATTGTATCGATA
190773 CATTGGCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.46
33 2 0.07
34 13 0.46
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (34 bp):
TGTATCGATACATGACCAAATTGTATCGATATAG
Found at i:201566 original size:19 final size:20
Alignment explanation
Indices: 201542--201592 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
201532 TAGCTAAACT
**
201542 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
201561 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
201581 TGTATCGATACA
1 TGTATCGATACA
201593 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:207785 original size:13 final size:13
Alignment explanation
Indices: 207767--207805 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
207757 ACAGTATTCT
207767 TTGTATCGATACA
1 TTGTATCGATACA
207780 TTGTATCGATACA
1 TTGTATCGATACA
* *
207793 CTGTATTGATACA
1 TTGTATCGATACA
207806 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:209468 original size:22 final size:20
Alignment explanation
Indices: 209425--209468 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
209415 GTAATTAATG
**
209425 TATTTGCTTGACTTTGTGTT
1 TATTTGCTTGACTTTGACTT
209445 TATTTGCATTGTACTTTGACTT
1 TATTTGC-TTG-ACTTTGACTT
209467 TA
1 TA
209469 ATCTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (20 bp):
TATTTGCTTGACTTTGACTT
Found at i:209880 original size:169 final size:169
Alignment explanation
Indices: 209601--209909 Score: 609
Period size: 169 Copynumber: 1.8 Consensus size: 169
209591 GCAAATAAAT
*
209601 TTTTGATTAAGGGGGAGAATGCGAATTTATTAAAATTGCTTTATTAAGGGGGAGAAATTTTTTGA
1 TTTTGATGAAGGGGGAGAATGCGAATTTATTAAAATTGCTTTATTAAGGGGGAGAAATTTTTTGA
209666 TTAAGGGGGAGAGATAAGAAAAATGAAAAATCTTGATTTTTGAAATCTACTAATGTGTTTCTTGA
66 TTAAGGGGGAGAGATAAGAAAAATGAAAAATCTTGATTTTTGAAATCTACTAATGTGTTTCTTGA
209731 AGCTATGAAATTGATTAAGGGGGAGAAAGAGATAAGTGC
131 AGCTATGAAATTGATTAAGGGGGAGAAAGAGATAAGTGC
209770 TTTTGATGAAGGGGGAGAATGCGAATTTATTAAAATTGCTTTATTAAGGGGGAGAAATTTTTTGA
1 TTTTGATGAAGGGGGAGAATGCGAATTTATTAAAATTGCTTTATTAAGGGGGAGAAATTTTTTGA
209835 TTAAGGGGGAGAGATAAGAAAAATGAAAAATCTTGATTTTTGAAATCTACTAATGTGTTTCTTGA
66 TTAAGGGGGAGAGATAAGAAAAATGAAAAATCTTGATTTTTGAAATCTACTAATGTGTTTCTTGA
209900 AGCTATGAAA
131 AGCTATGAAA
209910 GTCAGATCAC
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 139 1.00
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (169 bp):
TTTTGATGAAGGGGGAGAATGCGAATTTATTAAAATTGCTTTATTAAGGGGGAGAAATTTTTTGA
TTAAGGGGGAGAGATAAGAAAAATGAAAAATCTTGATTTTTGAAATCTACTAATGTGTTTCTTGA
AGCTATGAAATTGATTAAGGGGGAGAAAGAGATAAGTGC
Found at i:210503 original size:13 final size:13
Alignment explanation
Indices: 210485--210509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210475 ACACACAGTA
210485 TGTATCGATACAT
1 TGTATCGATACAT
210498 TGTATCGATACA
1 TGTATCGATACA
210510 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:210506 original size:32 final size:33
Alignment explanation
Indices: 210465--210532 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
210455 GTAGCTAAAC
**
210465 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
210497 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
210530 TTG
1 TTG
210533 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:213608 original size:52 final size:51
Alignment explanation
Indices: 213530--213657 Score: 229
Period size: 52 Copynumber: 2.5 Consensus size: 51
213520 CGAAATATGA
213530 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTG-GC
*
213582 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGG
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGC
*
213633 AAAATTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
213658 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 25 0.34
52 49 0.66
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGC
Found at i:213684 original size:13 final size:13
Alignment explanation
Indices: 213666--213690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213656 CAAAGATCAG
213666 TGTATCGATACAA
1 TGTATCGATACAA
213679 TGTATCGATACA
1 TGTATCGATACA
213691 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:213768 original size:33 final size:33
Alignment explanation
Indices: 213731--213797 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
213721 AGTAGCTTAA
213731 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
213764 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
213797 A
1 A
213798 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:213771 original size:13 final size:13
Alignment explanation
Indices: 213753--213777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213743 CAAAAAAATA
213753 TGTATCGATACAT
1 TGTATCGATACAT
213766 TGTATCGATACA
1 TGTATCGATACA
213778 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:214767 original size:49 final size:50
Alignment explanation
Indices: 214588--214790 Score: 221
Period size: 49 Copynumber: 3.9 Consensus size: 50
214578 GAAAAGTGAT
* * * * * *
214588 AAAGATGCCAATATGTTGATTCACA-GCCAACGATATTGGGCTTAAAGATGAG
1 AAAGGTGCCAATGTGCTGATTCA-AGGCCAGCTATATTGGACTTAAAGAT--G
* * *
214640 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 --AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
* *
214694 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTCAAGAT-
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
214744 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
214791 GTGCCAAAAT
Statistics
Matches: 130, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 45 0.35
52 39 0.30
53 6 0.05
54 6 0.05
55 34 0.26
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (50 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
Found at i:216292 original size:1 final size:1
Alignment explanation
Indices: 216286--216413 Score: 112
Period size: 1 Copynumber: 128.0 Consensus size: 1
216276 GCGTCCTCCG
* * * * * * * *
216286 AAAAAAAAAAAAAAACAAAAAACAAAAAAAGAGAGAAAAAAACAAAACAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
216351 AAGAGAGAAAAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAACAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
216414 GGTCCGGATG
Statistics
Matches: 95, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:216324 original size:35 final size:33
Alignment explanation
Indices: 216285--216412 Score: 157
Period size: 35 Copynumber: 3.7 Consensus size: 33
216275 GGCGTCCTCC
216285 GAAAAAAAAAAAAAAACAAAAAACAAAAAAAGAGA
1 GAAAAAAAAAAAAAAA-AAAAAACAAAAAAA-AGA
*
216320 GAAAAAAACAAAACAAAAAAAAACAAAAAAAAAGA
1 GAAAAAAA-AAAAAAAAAAAAAAC-AAAAAAAAGA
* *
216355 GAGAAAAAAAAACAAAAAAAAAACAAAAAAAACA
1 GA-AAAAAAAAAAAAAAAAAAAACAAAAAAAAGA
*
216389 AAAAAAACAAAAAGAAAAAAAAAA
1 GAAAAAA-AAAAA-AAAAAAAAAA
216413 AGGTCCGGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 5 0.06
34 14 0.17
35 43 0.52
36 20 0.24
ACGTcount: A:0.87, C:0.07, G:0.06, T:0.00
Consensus pattern (33 bp):
GAAAAAAAAAAAAAAAAAAAAACAAAAAAAAGA
Found at i:216372 original size:45 final size:45
Alignment explanation
Indices: 216286--216411 Score: 147
Period size: 44 Copynumber: 2.9 Consensus size: 45
216276 GCGTCCTCCG
* * *
216286 AAAAAAA-AAAAAAAAC--AAAAAACAAAAA-AAGAGAGAA-AAA
1 AAAAAAACAAAAAAAACAAAAAAAACAAAAAGAAAAAAAAACAAA
* * *
216326 AACAAAACAAAAAAAAACAAAAAAAA-AGAGAGAAAAAAAAACAAA
1 AAAAAAAC-AAAAAAAACAAAAAAAACAAAAAGAAAAAAAAACAAA
216371 AAAAAAACAAAAAAAACAAAAAAAACAAAAAGAAAAAAAAA
1 AAAAAAACAAAAAAAACAAAAAAAACAAAAAGAAAAAAAAA
216412 AAGGTCCGGA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
40 6 0.09
42 9 0.13
43 3 0.04
44 29 0.41
45 23 0.33
ACGTcount: A:0.87, C:0.07, G:0.06, T:0.00
Consensus pattern (45 bp):
AAAAAAACAAAAAAAACAAAAAAAACAAAAAGAAAAAAAAACAAA
Found at i:216384 original size:59 final size:58
Alignment explanation
Indices: 216286--216413 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 58
216276 GCGTCCTCCG
* *
216286 AAAAAAAAAAAAAAACAAAAAACAAAAAAAGAGAGAAAAAAACAAAACAAAA-AAAAAC
1 AAAAAAAAAAAAAAACAAAAAACAAAAAAAGAAAAAAAAAAACAAAA-AAAACAAAAAC
* *
216344 AAAAAAAAAGAGAGAAA-AAAAAACAAAAAAA-AAACAAAAAAAACAAAAAAAACAAAAAG
1 AAAAAAAAA-A-AAAAACAAAAAACAAAAAAAGAAA-AAAAAAAACAAAAAAAACAAAAAC
216403 AAAAAAAAAAA
1 AAAAAAAAAAA
216414 GGTCCGGATG
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.02
58 16 0.26
59 41 0.66
60 4 0.06
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (58 bp):
AAAAAAAAAAAAAAACAAAAAACAAAAAAAGAAAAAAAAAAACAAAAAAAACAAAAAC
Found at i:217955 original size:49 final size:49
Alignment explanation
Indices: 217895--218891 Score: 1077
Period size: 49 Copynumber: 20.8 Consensus size: 49
217885 GGCATCTTCT
* * * * * **
217895 TTTAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTTGTC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * **
217944 TTTAAGACCAATGTCGCTCGCTGGCCTTAAATTAGCATATTGGCACCTTTGTC
1 TTTAAGACCAA--T-G-TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
217997 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * **
218046 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
218095 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
218138 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * **
218187 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
218236 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
218279 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * **
218328 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
218377 TTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCACC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * **
218426 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
218475 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
218518 TTTAAGACCAATATGGCAGGCTTTGAATCAGCACATTGGCA----C--C
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
218561 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACGTTGGCA----C--C
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
218604 TTTAA-ATCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
1 TTTAAGA-CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
218653 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * ** * * *
218702 TTTAAGACCGATGTCGTTGGCCTTGAATCAATACATCGACACCTCAACCATC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT---TCATC
* * * *
218754 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CGTCATC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
218802 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCCTCTCATC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCATC
* * * * *
218854 TTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTG
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
218892 ACATTCTTTA
Statistics
Matches: 821, Mismatches: 96, Indels: 59
0.84 0.10 0.06
Matches are distributed among these distances:
43 200 0.24
47 2 0.00
48 42 0.05
49 452 0.55
50 1 0.00
51 4 0.00
52 75 0.09
53 45 0.05
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:218161 original size:22 final size:22
Alignment explanation
Indices: 218094--218161 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
218084 GCACCTTTGT
218094 CTTTAAGACCAATGTCGCTGGC
1 CTTTAAGACCAATGTCGCTGGC
* * * * *
218116 CTTGAATCAGCACAT-TGGC--AC
1 CTTTAA-GACCA-ATGTCGCTGGC
218137 CTTTAAGACCAATGTCGCTGGC
1 CTTTAAGACCAATGTCGCTGGC
218159 CTT
1 CTT
218162 GAATCAGCAC
Statistics
Matches: 31, Mismatches: 10, Indels: 10
0.61 0.20 0.20
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 6 0.19
22 9 0.29
23 6 0.19
24 2 0.06
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (22 bp):
CTTTAAGACCAATGTCGCTGGC
Found at i:218204 original size:92 final size:92
Alignment explanation
Indices: 218042--218891 Score: 862
Period size: 92 Copynumber: 9.0 Consensus size: 92
218032 TTGGCACCTT
* * **
218042 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAAT
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAAT
218107 GTCGCTGGCCTTGAATCAGCACATTGG
66 GTCGCTGGCCTTGAATCAGCACATTGG
* * *
218134 CACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAAT
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAAT
* *
218199 ATCGCTGGCCTTGAATCAGCATATTGG
66 GTCGCTGGCCTTGAATCAGCACATTGG
*
218226 CACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAG
1 CA-C-----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG
218285 ACCAATGTCGCTGGCCTTGAATCAGCACATTGG
60 ACCAATGTCGCTGGCCTTGAATCAGCACATTGG
* * **
218318 CACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAG
1 ------CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG
*
218383 ACCAATGTCACTGGCCTTGAATCAGCACATTGG
60 ACCAATGTCGCTGGCCTTGAATCAGCACATTGG
* * * **
218416 CACCTTCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAG
1 ------CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG
218481 ACCAATGTCGCTGGCCTTGAATCAGCACATTGG
60 ACCAATGTCGCTGGCCTTGAATCAGCACATTGG
* * * *
218514 CACCTTTAAGACCAATATGGCAGGCTTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAAT
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAAT
* *
218573 ATCGCTGGCCTTGAATCAGCACGTTGG
66 GTCGCTGGCCTTGAATCAGCACATTGG
* *
218600 CACCTTTAA-ATCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAA
1 CACCTTTAAGA-CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAA
*
218664 TGTCGTTGGCCTTGAATCAGCACATTGG
65 TGTCGCTGGCCTTGAATCAGCACATTGG
* * * ** * * *
218692 CACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAATACATCGACACCTCAACCATCTTT
1 CA----C--CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT---TCATCTTT
* * *
218757 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGG
57 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG
* * *
218793 CACGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCCTCTCATCTTCA
1 CA---C--CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTA
* * * *
218858 AGTCTAATGTCGCTGACCGTGAATCAGCACATTG
58 AGACCAATGTCGCTGGCCTTGAATCAGCACATTG
218892 ACATTCTTTA
Statistics
Matches: 655, Mismatches: 66, Indels: 66
0.83 0.08 0.08
Matches are distributed among these distances:
85 1 0.00
86 77 0.12
92 239 0.36
93 1 0.00
94 1 0.00
96 1 0.00
97 1 0.00
98 215 0.33
99 1 0.00
100 75 0.11
101 40 0.06
102 3 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAAT
GTCGCTGGCCTTGAATCAGCACATTGG
Found at i:218221 original size:141 final size:141
Alignment explanation
Indices: 217895--218842 Score: 1213
Period size: 141 Copynumber: 6.6 Consensus size: 141
217885 GGCATCTTCT
* *
217895 TTTAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAA--T-G
* * *
217960 CTCGCTGGCCTTAAATTAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAAT
63 -TCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGACCAATGTCGCTGGCCTTGAAT
218025 CAGCACATTGGCACCTTCACC
121 CAGCACATTGGCACCTTCACC
218046 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
218111 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
218176 GCACCTTCACC
131 GCACCTTCACC
218187 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
218252 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
218317 GCACCTTCACC
131 GCACCTTCACC
*
218328 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
* * *
218393 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGG------CACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
* ***
218458 ATATTGGCACCTTTGTC
125 ACATTGGCACCTTCACC
* * * * *
218475 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGACCAATATGG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
* * * * *
218534 CAGGCTTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACGTTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
218599 G------CACC
131 GCACCTTCACC
* * * *
218604 TTTAAATCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
* * * **
218669 TTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAAT
66 CTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
* *
218734 ACATCGACACC-TCAACCATC
125 ACATTGGCACCTTC-A-C--C
* * ** *
218754 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CGTCATCTTTAAGTCCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
218818 CTGGCCTTGAATCAGCACATTGGCA
66 CTGGCCTTGAATCAGCACATTGGCA
218843 TTCCTCTCAT
Statistics
Matches: 719, Mismatches: 51, Indels: 56
0.87 0.06 0.07
Matches are distributed among these distances:
129 39 0.05
130 1 0.00
135 76 0.11
139 1 0.00
141 344 0.48
146 3 0.00
147 110 0.15
148 2 0.00
149 46 0.06
150 39 0.05
151 58 0.08
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (141 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
GCACCTTCACC
Found at i:218302 original size:22 final size:22
Alignment explanation
Indices: 218235--218302 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
218225 GCACCTTTGT
218235 CTTTAAGACCAATGTCGCTGGC
1 CTTTAAGACCAATGTCGCTGGC
* * * * *
218257 CTTGAATCAGCACAT-TGGC--AC
1 CTTTAA-GACCA-ATGTCGCTGGC
218278 CTTTAAGACCAATGTCGCTGGC
1 CTTTAAGACCAATGTCGCTGGC
218300 CTT
1 CTT
218303 GAATCAGCAC
Statistics
Matches: 31, Mismatches: 10, Indels: 10
0.61 0.20 0.20
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 6 0.19
22 9 0.29
23 6 0.19
24 2 0.06
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (22 bp):
CTTTAAGACCAATGTCGCTGGC
Found at i:218519 original size:21 final size:21
Alignment explanation
Indices: 218495--218562 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
218485 ATGTCGCTGG
218495 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
218516 CCTTTAA-GACCA-ATATGGCA
1 CCTTGAATCAGCACAT-TGGCA
*
218536 GGCTTTGAATCAGCACATTGGCA
1 --CCTTGAATCAGCACATTGGCA
218559 CCTT
1 CCTT
218563 TAAGTCCAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 2 0.06
20 8 0.24
21 9 0.26
22 5 0.15
23 8 0.24
24 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:218581 original size:24 final size:23
Alignment explanation
Indices: 218554--218624 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
218544 ATCAGCACAT
218554 TGGCACCTTTAAGTCCAATATCGC
1 TGGCACCTTTAA-TCCAATATCGC
* ** *
218578 TGG--CCTTGAAT-CAGCA-CGT
1 TGGCACCTTTAATCCAATATCGC
218597 TGGCACCTTTAAATCCAATATCGC
1 TGGCACCTTT-AATCCAATATCGC
218621 TGGC
1 TGGC
218625 CTTGAATCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 5 0.15
22 9 0.26
23 3 0.09
24 9 0.26
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (23 bp):
TGGCACCTTTAATCCAATATCGC
Found at i:218584 original size:22 final size:21
Alignment explanation
Indices: 218559--218632 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
218549 CACATTGGCA
218559 CCTTTAAGTCCAATATCGCTGG
1 CCTTTAA-TCCAATATCGCTGG
* ** *
218581 CCTTGAAT-CAGCA-CGTTGG
1 CCTTTAATCCAATATCGCTGG
218600 CACCTTTAAATCCAATATCGCTGG
1 --CCTTT-AATCCAATATCGCTGG
*
218624 CCTTGAATC
1 CCTTTAATC
218633 AGCACATTGG
Statistics
Matches: 38, Mismatches: 9, Indels: 11
0.66 0.16 0.19
Matches are distributed among these distances:
19 5 0.13
20 3 0.08
21 9 0.24
22 13 0.34
23 3 0.08
24 5 0.13
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (21 bp):
CCTTTAATCCAATATCGCTGG
Found at i:218605 original size:21 final size:21
Alignment explanation
Indices: 218581--218648 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
218571 ATATCGCTGG
218581 CCTTGAATCAGCACGTTGGCA
1 CCTTGAATCAGCACGTTGGCA
* ** *
218602 CCTTTAAATCCAATATCGCTGG--
1 CC-TTGAAT-CAGCA-CGTTGGCA
*
218624 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACGTTGGCA
218645 CCTT
1 CCTT
218649 TATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACGTTGGCA
Found at i:218907 original size:52 final size:52
Alignment explanation
Indices: 218610--218897 Score: 177
Period size: 52 Copynumber: 5.7 Consensus size: 52
218600 CACCTTTAAA
* * * * * *
218610 TCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TTATCTTTAAG
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTCTCATCTTCAAG
* * * * *
218659 TCCAATGTCGTTGGCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTAAG
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTCTCATCTTCAAG
* * * * * ** * * *
218708 ACCGATGTCGTTGGCCTTGAATCAATACATCGACA--CCTCAACCATCTTTAAG
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTC--TCATCTTCAAG
* * * * * * * *
218760 CCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---C-GTCATCTTTAAG
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTCTCATCTTCAAG
* * *
218808 TCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCCTCTCATCTTCAAG
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTCTCATCTTCAAG
*
218860 TCTAATGTCGCTGACCGTGAATCAGCACATTGACATTC
1 TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTC
218898 TTTACATCTT
Statistics
Matches: 202, Mismatches: 30, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
48 42 0.21
49 78 0.39
51 2 0.01
52 80 0.40
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (52 bp):
TCCAATGTCGCTGACCGTGAATCAGCACATTGACATTCCTCTCATCTTCAAG
Found at i:219700 original size:20 final size:20
Alignment explanation
Indices: 219675--219741 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
219665 TTACGAAATG
219675 TTGTATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
219695 TTGTATCGATAC----A---
1 TTGTATCGATACATGGATCT
219708 TTGTATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
219728 TTGTATCGATACAT
1 TTGTATCGATACAT
219742 TTAGGAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.30
16 1 0.03
17 1 0.03
20 26 0.65
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATGGATCT
Found at i:219713 original size:13 final size:13
Alignment explanation
Indices: 219695--219721 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
219685 ACATGGATCT
219695 TTGTATCGATACA
1 TTGTATCGATACA
219708 TTGTATCGATACA
1 TTGTATCGATACA
219721 T
1 T
219722 GGATCTTTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:219717 original size:33 final size:33
Alignment explanation
Indices: 219675--219742 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
219665 TTACGAAATG
219675 TTGTATCGATACATGGATCTTTGTATCGATACA
1 TTGTATCGATACATGGATCTTTGTATCGATACA
219708 TTGTATCGATACATGGATCTTTGTATCGATACA
1 TTGTATCGATACATGGATCTTTGTATCGATACA
219741 TT
1 TT
219743 TAGGAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (33 bp):
TTGTATCGATACATGGATCTTTGTATCGATACA
Found at i:223058 original size:63 final size:62
Alignment explanation
Indices: 222885--223804 Score: 970
Period size: 62 Copynumber: 14.8 Consensus size: 62
222875 AAGCTAGACA
* * * ** * * * *
222885 CCTTTTTCTTTTCAAAGCCCAGACGAGTTGGTGGCATCCTTTTGTCCTTGAATAGCACGAAG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * * * * * ** * *
222947 CCTTTTT-TTTTTAAAGCTCACACAAGCTGTTGGTATCTTTTTAATCCTCAAAGAGTAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCCTTTAGTCCTCAAAGAGTAGGACG
* * * *
223009 CCTTTTTCCTTTTAAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAAAGTAGGATG
1 CCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * * * *
223072 CCTTTTTCTTTTCAAAGCCCATACAAGTTGGTGGTACCCTTTAGTCCTCAAAGAGCAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * * *
223134 CCTTTTTCTTTTCTAAGCCCACACGAGTTGGTGGTACCCTTTAGTCCTCAAAGAGCAAGACG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * ** * * *
223196 CC-TTTTCATTT-AAAGCCCACAGGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCATGACA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * * * *
223256 TCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * * * *
223318 CCTTTTTCTTTTCAAAGCCCACAC-AATTGGTGGCATCCTTTTGTCCTCGAAGAGTAGGACA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* ** * * * * *
223379 CCTTTTTATTTTCAAAGCCCACATAAGCTGGTGGCACCTTTTTGGTCTTCAAAAAGTAGGACG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-CTTTAGTCCTCAAAGAGTAGGACG
* * * * * *
223442 GCTTTATCTTTTCGAAGCCCACACGAGTTGGTGGCACTCTTTTGTCTTCAAAGAGTAGGACG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
* * *
223504 CC-TTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCCCTTTAGTCCTCAAAGAGTAGGATG
1 CCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCA-CCCTTTAGTCCTCAAAGAGTAGGACG
* * **
223567 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTTGTCCTCAAAGAGCAGGATT
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
** * * *
223629 CCTTTTTATCTTTTTGAAGCCCATATGAGTTGGTGGCACCCTTTAGTCCTTAAAGAGTAGGACG
1 CC-TTTT-TCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
** * * *
223693 TTTTTTTCTTTTCAAATCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
** * * *
223755 CCTTTTTCTTTT-AAAGCATACATGAGTTGGTGGCACCTTTTAGTCTTCAA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAA
223805 GAAGCATGAC
Statistics
Matches: 720, Mismatches: 126, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.06
61 126 0.17
62 343 0.48
63 135 0.19
64 73 0.10
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (62 bp):
CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACG
Found at i:223120 original size:125 final size:124
Alignment explanation
Indices: 222885--223804 Score: 988
Period size: 125 Copynumber: 7.4 Consensus size: 124
222875 AAGCTAGACA
* * * ** * * * *
222885 CCTTTTTCTTTTCAAAGCCCAGACGAGTTGGTGGCATCCTTTTGTCCTTGAATAGCACGAAGCCT
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCT
* * * * * * ** * *
222950 TTTT-TTTTTAAAGCTCACACAAGCTGTTGGTATCTTTTTAATCCTCAAAGAGTAGGATG
66 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCCTTTAGTCCTCAAAGAGCAGGATG
* * * *
223009 CCTTTTTCCTTTTAAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAAAGTAGGATGCC
1 CCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCC
* * *
223074 TTTTTCTTTTCAAAGCCCATACAAGTTGGTGGTACCCTTTAGTCCTCAAAGAGCAGGATG
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
* * * *
223134 CCTTTTTCTTTTCTAAGCCCACACGAGTTGGTGGTACCCTTTAGTCCTCAAAGAGCAAGACGCC-
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCT
* * ** * **
223198 TTTTCATTT-AAAGCCCACAGGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCATGACA
66 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
* * * * *
223256 TCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCT
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCT
* * * * * **
223321 TTTTCTTTTCAAAGCCCACAC-AATTGGTGGCATCCTTTTGTCCTCGAAGAGTAGGACA
66 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
* ** * * * * * *
223379 CCTTTTTATTTTCAAAGCCCACATAAGCTGGTGGCACCTTTTTGGTCTTCAAAAAGTAGGACGGC
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-CTTTAGTCCTCAAAGAGTAGGACGCC
* * * * * * *
223444 TTTATCTTTTCGAAGCCCACACGAGTTGGTGGCACTCTTTTGTCTTCAAAGAGTAGGACG
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
* * *
223504 CC-TTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCCCTTTAGTCCTCAAAGAGTAGGATGC
1 CCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCA-CCCTTTAGTCCTCAAAGAGTAGGACGC
* *
223568 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTTGTCCTCAAAGAGCAGGATT
64 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
** * * * *
223629 CCTTTTTATCTTTTTGAAGCCCATATGAGTTGGTGGCACCCTTTAGTCCTTAAAGAGTAGGACGT
1 CC-TTTT-TCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGC
* *
223694 TTTTTTCTTTTCAAATCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
64 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
** * * *
223755 CCTTTTTCTTTT-AAAGCATACATGAGTTGGTGGCACCTTTTAGTCTTCAA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAA
223805 GAAGCATGAC
Statistics
Matches: 675, Mismatches: 110, Indels: 23
0.84 0.14 0.03
Matches are distributed among these distances:
122 97 0.14
123 108 0.16
124 116 0.17
125 219 0.32
126 108 0.16
127 25 0.04
128 2 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (124 bp):
CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCT
TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGATG
Found at i:223857 original size:44 final size:43
Alignment explanation
Indices: 223807--224187 Score: 217
Period size: 41 Copynumber: 9.0 Consensus size: 43
223797 GTCTTCAAGA
*
223807 AGCATGACACTTTCCTCATTTCCTTTTTTCCTTTGTCCTTAAAG
1 AGCATGACAC-TTCCTCATTTCCTTTTTTCCTTTGTCCTCAAAG
*
223851 AGCATGATGCACTT--T-ATTTTC-TTTTTCCTTTGTCCTCAAAG
1 AGCATGA--CACTTCCTCATTTCCTTTTTTCCTTTGTCCTCAAAG
* * *
223892 AGCAAGGCAC-ACCTCATTTCCTTTTTTTCCTTTAGTCCTCAAAG
1 AGCATGACACTTCCTCATTTCC-TTTTTTCCTTT-GTCCTCAAAG
* * * * *
223936 AGCTTG--AC-GCCT--TTTCCTTTTCTCTTTTGTCCTCAAAA
1 AGCATGACACTTCCTCATTTCCTTTTTTCCTTTGTCCTCAAAG
* * * *
223974 AGCAAGACAC-GCTTCATTTCCTTCTTTTCCCTTTTCTCCTCAAAG
1 AGCATGACACTTCCTCATTTCCTT-TTTT-CC-TTTGTCCTCAAAG
* *
224019 AGCAAGATGCACTT-GT--TTTCC-TTTTTCCTTTGTCCTCAAAG
1 AGCATGA--CACTTCCTCATTTCCTTTTTTCCTTTGTCCTCAAAG
* * * *
224060 AGCAGGGC-GTACCTCATTTCCTTATTTTCCCTTTGTCCTCAAAG
1 AGCATGACACTTCCTCATTTCCTT-TTTT-CCTTTGTCCTCAAAG
* * * * * *
224104 AGTAGGACGC-ACTTCATTTCTTTTTTTTCTCTTTTGTCCTCAAAG
1 AGCATGACACTTCCTCATTTC-CTTTTTTC-C-TTTGTCCTCAAAG
* * *
224149 AGCAAGACGCATT--TTATTTCC-TTTTTCCTTTGTCCTCAA
1 AGCATGACAC-TTCCTCATTTCCTTTTTTCCTTTGTCCTCAA
224188 CAAGTAGGGT
Statistics
Matches: 270, Mismatches: 37, Indels: 63
0.73 0.10 0.17
Matches are distributed among these distances:
38 14 0.05
39 14 0.05
40 11 0.04
41 62 0.23
42 21 0.08
43 29 0.11
44 58 0.21
45 54 0.20
46 3 0.01
47 4 0.01
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (43 bp):
AGCATGACACTTCCTCATTTCCTTTTTTCCTTTGTCCTCAAAG
Found at i:223937 original size:85 final size:84
Alignment explanation
Indices: 223820--224317 Score: 408
Period size: 86 Copynumber: 5.9 Consensus size: 84
223810 ATGACACTTT
* * *
223820 CCTCATTTCC-TTTTTTCCTTTGTCCTTAAAGAGCATGATGCACTTTATTTTCTTTTTCCTTTGT
1 CCTCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTGT
*
223884 CCTCAAAGAGCAAGGCACA
66 CCTCAAAGAGCAAGGCGCA
** * *
223903 CCTCATTTCCTTTTTTTCCTTTAGTCCTCAAAGAGCTTGACGC-C--T-TTTCCTTTTCTCTTTT
1 CCTCATTTCCTTTTTTTCCTTT-GTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTT-TCCTTT
* * * *
223964 GTCCTCAAAAAGCAAGACACG
64 GTCCTCAAAGAGCAAGGCGCA
* * * *
223985 CTTCATTTCCTTCTTTTCCCTTTTCTCCTCAAAGAGCAAGATGCACTTGT-TTTCCTTTTTCCTT
1 CCTCATTTCCTT-TTTTTCC-TTTGTCCTCAAAGAGCAGGATGCACTT-TATTTCCTTTTTCCTT
* *
224049 TGTCCTCAAAGAGCAGGGCGTA
63 TGTCCTCAAAGAGCAAGGCGCA
* * * * *
224071 CCTCATTTCCTTATTTTCCCTTTGTCCTCAAAGAGTAGGACGCACTTCATTTCTTTTTTTTCTCT
1 CCTCATTTCCTT-TTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTC--CTTTTTC-C-
*
224136 TTTGTCCTCAAAGAGCAAGACGCA
61 TTTGTCCTCAAAGAGCAAGGCGCA
** * * * *
224160 TTTTATTTCC--TTTTTCCTTTGTCCTCAACA-AGTAGGGTGCACCTTATTTCCTTCTTTTCCCT
1 CCTCATTTCCTTTTTTTCCTTTGTCCTCAA-AGAGCAGGATGCACTTTATTTCC-T-TTTT-CCT
* *
224222 TTCTCCTTAAAGAGC-AGGACGCA
62 TTGTCCTCAAAGAGCAAGG-CGCA
* * * * * *
224245 CTTTATTT-CTTTTTCTCCTTTGTCTTTAAAGAGCAGGACT-CACTTAATTTCCTTCTTTTCCTT
1 CCTCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGA-TGCACTTTATTTCC-T-TTTTCCTT
224308 TGTCCTCAAA
63 TGTCCTCAAA
224318 AAGTAGGATG
Statistics
Matches: 338, Mismatches: 54, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
81 8 0.02
82 35 0.10
83 32 0.09
84 19 0.06
85 83 0.25
86 113 0.33
87 19 0.06
88 1 0.00
89 28 0.08
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (84 bp):
CCTCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTGT
CCTCAAAGAGCAAGGCGCA
Found at i:224132 original size:130 final size:127
Alignment explanation
Indices: 223820--224317 Score: 453
Period size: 130 Copynumber: 3.9 Consensus size: 127
223810 ATGACACTTT
* * * * *
223820 CCTCATTTCCTTTTTTCCTTTGTCCTTAAAGAGCATGATGCACTTTA-TT-TTCTTTTTCC-TTT
1 CCTCATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTTCCTTTT
* * * * * ** *
223882 GTCCTCAAAGAGCAAGGCACACCTCATTTCCTTTTTTTCCTTTAGTCCTCAAAGAGCTTGACG-
66 CTCCTCAAAGAGCAAGACGCACTTAATTTCC-TTTTTTCCTTT-GTCCTCAAAGAGCAGGGCGA
* * * * * * * *
223945 CCT--TTTCCTTTTCTCTTTTGTCCTCAAAAAGCAAGACACGCTTCATTTCCTTCTTTTCCCTTT
1 CCTCATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTT-CTTTTTTTTCCTTT
* **
224008 TCTCCTCAAAGAGCAAGATGCACTTGTTTTCC-TTTTTCCTTTGTCCTCAAAGAGCAGGGCGTA
65 TCTCCTCAAAGAGCAAGACGCACTTAATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGGCG-A
*
224071 CCTCATTTCCTTATTTTCCCTTTGTCCTCAAAGAGTAGGACGCACTTCATTTCTTTTTTTTCTCT
1 CCTCATTTCCTT-TTTT-CCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTTC-CT
* * * * *
224136 TTTGTCCTCAAAGAGCAAGACGCATTTTATTTCC-TTTTTCCTTTGTCCTCAACA-AGTAGGGTG
63 TTTCTCCTCAAAGAGCAAGACGCACTTAATTTCCTTTTTTCCTTTGTCCTCAA-AGAGCAGGGCG
224199 CA
127 -A
* * * * *
224201 CCTTATTTCCTTCTTTTCCCTTTCTCCTTAAAGAGCAGGACGCACTTTATTTC-TTTTTCTCCTT
1 CCTCATTTCCTT-TTTT-CCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTTCCTT
* * *
224265 TGTCT--TTAAAGAGCAGGACTCACTTAATTTCCTTCTTTTCCTTTGTCCTCAAA
64 T-TCTCCTCAAAGAGCAAGACGCACTTAATTTCCTT-TTTTCCTTTGTCCTCAAA
224318 AAGTAGGATG
Statistics
Matches: 308, Mismatches: 50, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
123 33 0.11
124 18 0.06
125 13 0.04
126 12 0.04
127 49 0.16
128 13 0.04
129 37 0.12
130 132 0.43
131 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (127 bp):
CCTCATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTTCCTTTT
CTCCTCAAAGAGCAAGACGCACTTAATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGGCGA
Found at i:224217 original size:44 final size:43
Alignment explanation
Indices: 223831--224317 Score: 341
Period size: 44 Copynumber: 11.4 Consensus size: 43
223821 CTCATTTCCT
* * * *
223831 TTTTTCCTTTGTCCTTAAAGAGCATGATGCACTTTA-TT-TTC
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
* *
223872 TTTTTCCTTTGTCCTCAAAGAGCAAGG-CACACCTCATTTCCTT-
1 TTTTTCCTTTGTCCTCAAAGAGC-AGGACGCACCTTATTT-CTTC
**
223915 TTTTTCCTTTAGTCCTCAAAGAGCTTGACG--CC-T-TTTC--C
1 TTTTTCCTTT-GTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
* * *
223953 TTTTCTCTTTTGTCCTCAAAAAGCAAGA--CACGCTTCATTTCCTTC
1 TTTT-TCCTTTGTCCTCAAAGAGCAGGACGCAC-CTT-ATTT-CTTC
* * * * * *
223998 TTTTCCCTTTTCTCCTCAAAGAGCAAGATGCA-CTTGTTT-TCC
1 TTTTTCC-TTTGTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
* * * *
224040 TTTTTCCTTTGTCCTCAAAGAGCAGGGCGTACCTCATTTCCTTA
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTTATTT-CTTC
* * *
224084 TTTTCCCTTTGTCCTCAAAGAGTAGGACGCA-CTTCATTTCTTT
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTT-ATTTCTTC
* **
224127 TTTTTCTCTTTTGTCCTCAAAGAGCAAGACGCATTTTATTTC--C
1 TTTTTC-C-TTTGTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
* **
224170 TTTTTCCTTTGTCCTCAACA-AGTAGGGTGCACCTTATTTCCTTC
1 TTTTTCCTTTGTCCTCAA-AGAGCAGGACGCACCTTATTT-CTTC
* * * *
224214 TTTTCCCTTTCTCCTTAAAGAGCAGGACGCACTTTATTTCTT-
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
* * * *
224256 TTTCTCCTTTGTCTTTAAAGAGCAGGACTCA-CTTAATTTCCTTC
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTT-ATTT-CTTC
224300 -TTTTCCTTTGTCCTCAAA
1 TTTTTCCTTTGTCCTCAAA
224318 AAGTAGGATG
Statistics
Matches: 348, Mismatches: 63, Indels: 68
0.73 0.13 0.14
Matches are distributed among these distances:
38 19 0.05
39 7 0.02
40 4 0.01
41 72 0.21
42 55 0.16
43 50 0.14
44 84 0.24
45 53 0.15
46 2 0.01
47 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.42
Consensus pattern (43 bp):
TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACCTTATTTCTTC
Found at i:224978 original size:30 final size:30
Alignment explanation
Indices: 224942--225065 Score: 106
Period size: 30 Copynumber: 4.5 Consensus size: 30
224932 TATTCTTCAT
*
224942 TGTATCGATACATTCTAGGTTTTACCCAGA
1 TGTATCGATACATTCTAGGTTTTACCTAGA
224972 TGTATCGATACA-T-TA---TTTA--T---
1 TGTATCGATACATTCTAGGTTTTACCTAGA
* *
224992 TGTATCGATACATTCTGGGGTTTACCTAGA
1 TGTATCGATACATTCTAGGTTTTACCTAGA
* * ** *
225022 TGTATCGATACATTCTGGGTTGTATATGGA
1 TGTATCGATACATTCTAGGTTTTACCTAGA
225052 TGTATCGATACATT
1 TGTATCGATACATT
225066 TCTCAATGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
20 12 0.16
21 1 0.01
22 1 0.01
25 8 0.10
27 1 0.01
28 2 0.03
29 1 0.01
30 51 0.66
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (30 bp):
TGTATCGATACATTCTAGGTTTTACCTAGA
Found at i:224998 original size:50 final size:50
Alignment explanation
Indices: 224922--225035 Score: 165
Period size: 50 Copynumber: 2.3 Consensus size: 50
224912 TTCCACAATT
* * * *
224922 TGTATCAATATATTCTTCATTGTATCGATACATTCTAGGTTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTAGGGTTTACCCAGA
* * *
224972 TGTATCGATACATTATTTATTGTATCGATACATTCTGGGGTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTAGGGTTTACCCAGA
225022 TGTATCGATACATT
1 TGTATCGATACATT
225036 CTGGGTTGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (50 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTAGGGTTTACCCAGA
Found at i:225045 original size:50 final size:50
Alignment explanation
Indices: 224940--225046 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
224930 TATATTCTTC
* **
224940 ATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTATTT
1 ATTGTATCGATACATTCTAGGGTTTACCCAGATGTATCGATACATTATGG
* * *
224990 ATTGTATCGATACATTCTGGGGTTTACCTAGATGTATCGATACATTCTGG
1 ATTGTATCGATACATTCTAGGGTTTACCCAGATGTATCGATACATTATGG
*
225040 GTTGTAT
1 ATTGTAT
225047 ATGGATGTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (50 bp):
ATTGTATCGATACATTCTAGGGTTTACCCAGATGTATCGATACATTATGG
Found at i:225076 original size:30 final size:30
Alignment explanation
Indices: 225020--225076 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
225010 GGTTTACCTA
***
225020 GATGTATCGATACATTCTGGGTTGTATATG
1 GATGTATCGATACATTCTGCAATGTATATG
225050 GATGTATCGATACATTTCT-CAATGTAT
1 GATGTATCGATACA-TTCTGCAATGTAT
225077 CGATACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (30 bp):
GATGTATCGATACATTCTGCAATGTATATG
Found at i:226054 original size:13 final size:13
Alignment explanation
Indices: 226036--226060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
226026 ACACAAAGTA
226036 TGTATCGATACAT
1 TGTATCGATACAT
226049 TGTATCGATACA
1 TGTATCGATACA
226061 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:232261 original size:13 final size:13
Alignment explanation
Indices: 232243--232280 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
232233 CATCATTCTT
232243 TGTATCGATACAA
1 TGTATCGATACAA
*
232256 TGTATCGATACAT
1 TGTATCGATACAA
*
232269 TGTATCGTTACA
1 TGTATCGATACA
232281 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234844 original size:13 final size:13
Alignment explanation
Indices: 234826--234850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234816 ACACAAAGTA
234826 TGTATCGATACAT
1 TGTATCGATACAT
234839 TGTATCGATACA
1 TGTATCGATACA
234851 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234847 original size:32 final size:33
Alignment explanation
Indices: 234806--234873 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
234796 GTAGCCAAAC
*
234806 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
234838 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
234871 TTG
1 TTG
234874 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:237660 original size:79 final size:77
Alignment explanation
Indices: 237410--237662 Score: 267
Period size: 79 Copynumber: 3.2 Consensus size: 77
237400 TTTTCATCGA
* * * * *
237410 TGTTTTTATTTTCAAAATAT-AATTTCCCACCATCAGGGACACTCTAACCCCGTTATCTTCAAGG
1 TGTTTTTA-TTCCAAAACATCAATTTTCCACCATCAGGGAAACTCTAACCCCGTTATTTTC-AGG
237474 GGATACTCCAACCC
64 GGATACTCCAACCC
* ** * * ** *
237488 CGGCTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCTAACCCCGTTATTTTCATGG
1 TGTTTTTA-TTCCAAAACATCAATTTTCCACCATCAGGGAAACTCTAACCCCGTTATTTTCA-GG
237553 GGATACTCCAA-CC
64 GGATACTCCAACCC
* * * *
237566 TCGATTTTCATTCCAAAACATCGATTTTCCACCATCGGGGAAACTCCAACCCCGTTATTTTCGAG
1 T-G-TTTTTATTCCAAAACATCAATTTTCCACCATCAGGGAAACTCTAACCCCGTTATTTTC-AG
237631 GGGATACTCCAACCC
63 GGGATACTCCAACCC
237646 TGTTTTTATCTCCAAAA
1 TGTTTTTAT-TCCAAAA
237663 TATTAAACTT
Statistics
Matches: 143, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
78 23 0.16
79 113 0.79
80 7 0.05
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (77 bp):
TGTTTTTATTCCAAAACATCAATTTTCCACCATCAGGGAAACTCTAACCCCGTTATTTTCAGGGG
ATACTCCAACCC
Found at i:245651 original size:15 final size:15
Alignment explanation
Indices: 245613--245669 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
245603 TAACATGAAT
* *
245613 AATAAAAAAACAAAA
1 AATAAATAAATAAAA
245628 AA-AAATAAATAAAA
1 AATAAATAAATAAAA
*
245642 AATAATTAAATAAAA
1 AATAAATAAATAAAA
* *
245657 CATAAAAAAATAA
1 AATAAATAAATAA
245670 TAATTAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAATAAATAAAA
Found at i:245662 original size:26 final size:26
Alignment explanation
Indices: 245627--245676 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
245617 AAAAAACAAA
245627 AAAAAATAAATAAAA-AATAATTAAAT
1 AAAAAATAAA-AAAATAATAATTAAAT
*
245653 AAAACATAAAAAAATAATAATTAA
1 AAAAAATAAAAAAATAATAATTAA
245677 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAAAATAAAAAAATAATAATTAAAT
Found at i:245672 original size:11 final size:11
Alignment explanation
Indices: 245610--245672 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
245600 ATTTAACATG
245610 AATAATAAAAA
1 AATAATAAAAA
*
245621 AACAA-AAAAA
1 AATAATAAAAA
245631 AATAA-ATAAAA
1 AATAATA-AAAA
245642 AATAATTAAATAA
1 AATAA-TAAA-AA
*
245655 AA-CATAAAAA
1 AATAATAAAAA
245665 AATAATAA
1 AATAATAA
245673 TTAATTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 14 0.33
11 21 0.49
12 3 0.07
13 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAATAAAAA
Found at i:245678 original size:30 final size:31
Alignment explanation
Indices: 245629--245686 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
245619 AAAACAAAAA
245629 AAAATAAATAAAAAATAATTAAATAAAACAT
1 AAAATAAATAAAAAATAATTAAATAAAACAT
* * *
245660 AAAA-AAATAATAATTAATTAATTAAAA
1 AAAATAAATAAAAAATAATTAAATAAAA
245687 GAAAAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (31 bp):
AAAATAAATAAAAAATAATTAAATAAAACAT
Found at i:245682 original size:34 final size:33
Alignment explanation
Indices: 245610--245686 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
245600 ATTTAACATG
245610 AATAA-TAAAAAAACAAAAAAAAATAAATAAAA
1 AATAATTAAAAAAACAAAAAAAAATAAATAAAA
* *
245642 AATAATTAAATAAAACATAAAAAAAT-AATAATTA
1 AATAATTAAA-AAAACAAAAAAAAATAAATAA-AA
*
245676 ATTAATTAAAA
1 AATAATTAAAA
245687 GAAAAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 5 0.13
33 10 0.26
34 24 0.62
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (33 bp):
AATAATTAAAAAAACAAAAAAAAATAAATAAAA
Found at i:245807 original size:17 final size:17
Alignment explanation
Indices: 245785--245846 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
245775 GTGGCGTTTT
245785 ATGCATACTTTTATTTC
1 ATGCATACTTTTATTTC
* *
245802 ATGCATGCTTTTACTTC
1 ATGCATACTTTTATTTC
*
245819 ATGCATACTTTCATTTC
1 ATGCATACTTTTATTTC
*
245836 ATGCATGCTTT
1 ATGCATACTTT
245847 CATGCAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (17 bp):
ATGCATACTTTTATTTC
Found at i:246014 original size:12 final size:12
Alignment explanation
Indices: 245997--246026 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
245987 AATGAAGATG
245997 TTTCATCCATGC
1 TTTCATCCATGC
*
246009 TTTCATGCATGC
1 TTTCATCCATGC
246021 TTTCAT
1 TTTCAT
246027 ACTAACATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (12 bp):
TTTCATCCATGC
Found at i:248466 original size:10 final size:10
Alignment explanation
Indices: 248447--248477 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
248437 ATCTCATTTT
248447 TCACTGTTCA
1 TCACTGTTCA
*
248457 TCACTATTCA
1 TCACTGTTCA
248467 TCACTGTTCA
1 TCACTGTTCA
248477 T
1 T
248478 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:249079 original size:34 final size:35
Alignment explanation
Indices: 249016--249082 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
249006 CTAAGTGATT
249016 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
249052 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
249083 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:249404 original size:35 final size:34
Alignment explanation
Indices: 249337--249454 Score: 109
Period size: 36 Copynumber: 3.5 Consensus size: 34
249327 GCTCACAGTG
* *
249337 AGGTTCTATCTTTGCCTTTGAAAAAGATAGAGAGAA
1 AGGTTCTATCTTAGCCCTTG-AAAAGATAGAGAG-A
*
249373 AGGTTCTATCTTAGCCCGTGAAAAGATAGAGAG-
1 AGGTTCTATCTTAGCCCTTGAAAAGATAGAGAGA
* * *
249406 -GTTTCTATCTTAG-CCTTG-AAAGATAGTGCTGTA
1 AGGTTCTATCTTAGCCCTTGAAAAGATAGAG-AG-A
*
249439 AGGTTATATCTTAGCC
1 AGGTTCTATCTTAGCC
249455 TCAAAGGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
30 9 0.13
31 5 0.07
32 12 0.18
34 11 0.16
35 14 0.21
36 17 0.25
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (34 bp):
AGGTTCTATCTTAGCCCTTGAAAAGATAGAGAGA
Found at i:253775 original size:20 final size:20
Alignment explanation
Indices: 253750--253800 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
253740 ACCCAGATGC
*
253750 ATCGATACATTAT-TCACTGT
1 ATCGATACATT-TCTCAATGT
253770 ATCGATACATTTCTCAATGT
1 ATCGATACATTTCTCAATGT
*
253790 ATCAATACATT
1 ATCGATACATT
253801 CAGGCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCGATACATTTCTCAATGT
Found at i:256274 original size:79 final size:79
Alignment explanation
Indices: 256143--256456 Score: 354
Period size: 79 Copynumber: 4.0 Consensus size: 79
256133 TCATTGATGT
** * * *
256143 TTTTATTTCCGAAACATCGATTTTCCACCATCGGGGATACTCCAACCTCGTTA-TTTCTAAGGGG
1 TTTTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTCCAACCTCGTTATTTTC-AAGGGG
256207 ATACTCCAACCCTGA
65 ATACTCCAACCCTGA
* *
256222 TTTTATTTCTAAAACATCGATTTTCCACAATCGAAGATACTCCAATCC-CGTTATTTT-ATAGGG
1 TTTTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTCCAA-CCTCGTTATTTTCA-AGGG
256285 GATACTCCAAGCCC-GA
64 GATACTCCAA-CCCTGA
* * * *
256301 CTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAATCC-CGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTCCAA-CCTCGTTATTTTCAAGGGG
256365 ATACTCCAACCCT-A
65 ATACTCCAACCCTGA
** * *
256379 GTTTTATTTCTAAAACATCAATTTTTTACCATC-AGGGATACTCCAACCTCGTTATTTCTGAAGG
1 -TTTTATTTCTAAAACATCAATTTTCCACAATCGA-GGATACTCCAACCTCGTTATTT-TCAAGG
* *
256443 GGGTACTCCGACCC
63 GGATACTCCAACCC
256457 CATTTTTATC
Statistics
Matches: 206, Mismatches: 19, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
78 8 0.04
79 174 0.84
80 24 0.12
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTCCAACCTCGTTATTTTCAAGGGGA
TACTCCAACCCTGA
Found at i:273006 original size:42 final size:42
Alignment explanation
Indices: 272951--273030 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
272941 TTCTTCTCTC
* * *
272951 CTCCTCCTGTCATCCATCATCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCATCATATCTCTACTATCTCTCCTGTCT
* * *
272993 CTCCTCCTATCATCCCTCCTATCTCTCCTATCTCTCCT
1 CTCCTCCTATCATCCATCATATCTCTACTATCTCTCCT
273031 CCTATCATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.11, C:0.45, G:0.03, T:0.41
Consensus pattern (42 bp):
CTCCTCCTATCATCCATCATATCTCTACTATCTCTCCTGTCT
Found at i:273010 original size:12 final size:11
Alignment explanation
Indices: 272984--273050 Score: 66
Period size: 12 Copynumber: 5.9 Consensus size: 11
272974 TCTATTATCT
*
272984 CTCCTGTCTCTC
1 CTCCTATCTC-C
272996 CTCCTATCATCC
1 CTCCTATC-TCC
273008 CTCCTATCT--
1 CTCCTATCTCC
273017 CTCCTATCTCTC
1 CTCCTATCTC-C
273029 CTCCTATCATCC
1 CTCCTATC-TCC
*
273041 CTCCTCTCTC
1 CTCCTATCTC
273051 TTCTTTCTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 9 0.19
11 3 0.06
12 32 0.67
13 4 0.08
ACGTcount: A:0.09, C:0.51, G:0.01, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:273011 original size:24 final size:24
Alignment explanation
Indices: 272975--273021 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
272965 CATCATCTCT
* * *
272975 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTATCTCTCCTC
272999 CTATCATCCCTCCTATCTCTCCT
1 CTATCATCCCTCCTATCTCTCCT
273022 ATCTCTCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.45, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTATCTCTCCTC
Found at i:273016 original size:33 final size:33
Alignment explanation
Indices: 272979--273060 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
272969 ATCTCTCTAT
*
272979 TATCTCTCCTGTCTCTCCTCCTATCATCCCTCC
1 TATCTCTCCTATCTCTCCTCCTATCATCCCTCC
273012 TATCTCTCCTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTCCTATCTCTCCTCCTATCATCCCTCC
* * *
273045 TCTCTCTTCTTTCTCT
1 TATCTCTCCTATCTCT
273061 TTGAGGGCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (33 bp):
TATCTCTCCTATCTCTCCTCCTATCATCCCTCC
Found at i:273020 original size:21 final size:21
Alignment explanation
Indices: 272979--273036 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
272969 ATCTCTCTAT
* *
272979 TATCTCTCCT-GTCTCTCCTCC
1 TATCTCTCCTCCTATCT-CTCC
273000 TATCATC-CCTCCTATCTCTCC
1 TATC-TCTCCTCCTATCTCTCC
273021 TATCTCTCCTCCTATC
1 TATCTCTCCTCCTATC
273037 ATCCCTCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 24 0.75
22 6 0.19
ACGTcount: A:0.10, C:0.47, G:0.02, T:0.41
Consensus pattern (21 bp):
TATCTCTCCTCCTATCTCTCC
Found at i:274918 original size:13 final size:13
Alignment explanation
Indices: 274900--274925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
274890 AAAAAAATCC
274900 ATGTATCGATACA
1 ATGTATCGATACA
274913 ATGTATCGATACA
1 ATGTATCGATACA
274926 TTTCGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:274937 original size:20 final size:20
Alignment explanation
Indices: 274912--274949 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
274902 GTATCGATAC
274912 AATGTATCGATACATTTCGT
1 AATGTATCGATACATTTCGT
274932 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
274950 CTTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCGT
Found at i:274987 original size:13 final size:13
Alignment explanation
Indices: 274969--275020 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
274959 AGCTTCGTAG
274969 CGATACATTGTAT
1 CGATACATTGTAT
274982 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
275001 CGATACATTGTAT
1 CGATACATTGTAT
275014 CGATACA
1 CGATACA
275021 AATTGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:280712 original size:61 final size:61
Alignment explanation
Indices: 280609--281057 Score: 584
Period size: 61 Copynumber: 7.4 Consensus size: 61
280599 AACCTTTTAT
* * *
280609 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTCT-CTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * *
280670 CTTTTTAGTCTTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
280731 CTTTCTAGTCCTCAAAGAGTAGGACACATTTTCCTTTTAAAGCCCACACAAATTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
280792 CTTTCCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** * *
280853 CCTT-TCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACATAAGTTGGCGGCA
1 CCTTCT-AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
280914 CATTCTAGTCCTCAAAGAGCAGGGCA-C-TTTCCTTTCAAAGCCCACCCAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
280973 CCTTCTAGTCCTCAAAGAGCAGGACACTTTTTCCTTGCAAAGCCCATACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
281034 CCTTCTAGTCC-CTAAAGAGCAGGA
1 CCTTCTAGTCCTC-AAAGAGCAGGA
281058 TTTCCTTTTC
Statistics
Matches: 346, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
59 52 0.15
60 2 0.01
61 286 0.83
62 6 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:281119 original size:42 final size:41
Alignment explanation
Indices: 281057--281287 Score: 185
Period size: 42 Copynumber: 5.8 Consensus size: 41
281047 AAAGAGCAGG
* * *
281057 ATTTCCTTTTCCCTTTGTCCTCAAAGAGCAGGATGCATTTT
1 ATTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTT
* * *
281098 ATTTCTTTTTCTCCTTTGTCCTCAAAGAGTAGGACACATTTA
1 ATTTCTTTTT-TCCTTTGTCCTCAAAGAGCAGGACGCATTTT
* *
281140 ATTTCCTCATTTTCCTTTGTCCTCAAAGAGCAGTACGCATTTT
1 ATTT-CT-TTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTT
* *
281183 A--T-TTTTTTCCTTTGTCCTCGAAGAGCA-G--G-A-TGT
1 ATTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTT
* * * * *
281216 A-CTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTC
1 ATTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTT
* * * * *
281256 A-TTCTCTTTTACTTTATCCTCGACGAGCAGGA
1 ATTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGA
281288 TGTGCTCCTT
Statistics
Matches: 152, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
33 3 0.02
34 2 0.01
35 23 0.15
36 1 0.01
38 22 0.14
39 2 0.01
40 26 0.17
41 10 0.07
42 30 0.20
43 30 0.20
44 3 0.02
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (41 bp):
ATTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTT
Found at i:281232 original size:35 final size:35
Alignment explanation
Indices: 281186--281323 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 35
281176 GCATTTTATT
281186 TTTTTCCTTTGTCCTCGAAGAGCAGGATGTACTCC
1 TTTTTCCTTTGTCCTCGAAGAGCAGGATGTACTCC
* *
281221 TTTTTCCTTTGTCCTC-AAGGAGCAGGACCCAT-TTCATTC
1 TTTTTCCTTTGTCCTCGAA-GAGCAGG----ATGTAC-TCC
* * * *
281260 TCTTTTACTTTATCCTCGACGAGCAGGATGTGCTCC
1 T-TTTTCCTTTGTCCTCGAAGAGCAGGATGTACTCC
* *
281296 -TTTTCCTTTGTCCTCAAATAGCAGGATG
1 TTTTTCCTTTGTCCTCGAAGAGCAGGATG
281324 CCCCTTCCTT
Statistics
Matches: 82, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
34 25 0.30
35 23 0.28
36 4 0.05
37 2 0.02
38 2 0.02
39 5 0.06
40 20 0.24
41 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (35 bp):
TTTTTCCTTTGTCCTCGAAGAGCAGGATGTACTCC
Found at i:281319 original size:34 final size:34
Alignment explanation
Indices: 281187--281323 Score: 121
Period size: 35 Copynumber: 3.8 Consensus size: 34
281177 CATTTTATTT
*
281187 TTTTCCTTTGTCCTCGAAGAGCAGGATGTACTCC
1 TTTTCCTTTGTCCTCAAAGAGCAGGATGTACTCC
* * *
281221 TTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCTC
1 -TTTTCCTTTGTCCTCAAAGAGCAGG----ATGT-ACTC-C
* * * * *
281262 TTTTACTTTATCCTCGACGAGCAGGATGTGCTCC
1 TTTTCCTTTGTCCTCAAAGAGCAGGATGTACTCC
*
281296 TTTTCCTTTGTCCTCAAATAGCAGGATG
1 TTTTCCTTTGTCCTCAAAGAGCAGGATG
281324 CCCCTTCCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
34 24 0.30
35 25 0.31
36 3 0.04
39 3 0.04
40 24 0.30
41 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (34 bp):
TTTTCCTTTGTCCTCAAAGAGCAGGATGTACTCC
Found at i:281339 original size:75 final size:75
Alignment explanation
Indices: 281149--281321 Score: 226
Period size: 73 Copynumber: 2.3 Consensus size: 75
281139 AATTTCCTCA
* * * * * *
281149 TTTTCCTTTGTCCTCAAAGAGCAGTACGCATTTTATT-T-TTTTCCTTTGTCCTCGAAGAGCAGG
1 TTTTCCTTTGTCCTCAAAGAGCAGGACCCACTTCATTCTCTTTTACTTTATCCTCGAAGAGCAGG
281212 ATGTACTCCT
66 ATGTACTCCT
* * *
281222 TTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCTCTTTTACTTTATCCTCGACGAGCAGG
1 TTTTCCTTTGTCCTCAAAGAGCAGGACCCACTTCATTCTCTTTTACTTTATCCTCGAAGAGCAGG
*
281287 ATGTGCTCC-
66 ATGTACTCCT
*
281296 TTTTCCTTTGTCCTCAAATAGCAGGA
1 TTTTCCTTTGTCCTCAAAGAGCAGGA
281322 TGCCCCTTCC
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
73 33 0.38
74 25 0.28
75 30 0.34
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (75 bp):
TTTTCCTTTGTCCTCAAAGAGCAGGACCCACTTCATTCTCTTTTACTTTATCCTCGAAGAGCAGG
ATGTACTCCT
Found at i:281960 original size:49 final size:49
Alignment explanation
Indices: 281907--282041 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 49
281897 TTTCACAATT
*
281907 TGTATCGATATATTCTTCATTGTATCGATAC-TTCTGGGTTTTACCCAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGGGTTTTACCCAGA
* * * *
281956 TGTATCAACACATTATTCATTGTATCGATACATTTTGGGTTTTACCTAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGGGTTTTACCCAGA
*
282006 TGTATCGATACATTTCTCAATGTATCGATACATTCT
1 TGTATCGATACATTT-TCATTGTATCGATACATTCT
282042 AGCATTTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
49 28 0.38
50 46 0.62
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (49 bp):
TGTATCGATACATTTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
Found at i:284520 original size:79 final size:79
Alignment explanation
Indices: 284414--284673 Score: 367
Period size: 79 Copynumber: 3.3 Consensus size: 79
284404 ATTTTCCACC
* *
284414 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAC
284479 ATCAATTTTTCATA
66 ATCAATTTTTCATA
* * *
284493 ATCGGGGATACTCCAACCTCGTGATTTTTGAGGGGATACTCCAAGCCTGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAC
* *
284558 ATCGATTTTCCATA
66 ATCAATTTTTCATA
* * * * * * *
284572 ATCGGGGACACTCCAACCCCGTTATTTTTAAGGAGATACTCCAACCTTAGTTTTATTTCCAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAC
**
284637 ATCAATTTTTCACC
66 ATCAATTTTTCATA
*
284651 ATCGGAGATACTCCAACCCCGTT
1 ATCGGGGATACTCCAACCCCGTT
284674 TTTATCTCCA
Statistics
Matches: 158, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 158 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAC
ATCAATTTTTCATA
Found at i:284677 original size:51 final size:52
Alignment explanation
Indices: 284603--284700 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 52
284593 TTATTTTTAA
* * *
284603 GGAGATACTCCAACCTTAGTTTTATTTCCAAAACA-TCAATTTTTCACCATC
1 GGAGATACTCCAACCTCAGTTTTATCTCCAAAACATTAAATTTTTCACCATC
* *
284654 GGAGATACTCCAACC-CCGTTTTTATCTCCAAAATATTAAATTTTTCA
1 GGAGATACTCCAACCTCAG-TTTTATCTCCAAAACATTAAATTTTTCA
284701 TCGAGAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 1 0.03
51 29 0.73
52 10 0.25
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (52 bp):
GGAGATACTCCAACCTCAGTTTTATCTCCAAAACATTAAATTTTTCACCATC
Found at i:297209 original size:8 final size:8
Alignment explanation
Indices: 297196--297235 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
297186 ATTCTTTTTT
297196 AAAAAACA
1 AAAAAACA
297204 AAAAAACA
1 AAAAAACA
*
297212 AAAAAAAA
1 AAAAAACA
297220 AACAAAACA
1 AA-AAAACA
297229 AAGAAAA
1 AA-AAAA
297236 AAGAGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 17 0.61
9 11 0.39
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:297218 original size:17 final size:17
Alignment explanation
Indices: 297196--297237 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
297186 ATTCTTTTTT
*
297196 AAAAAACAAA-AAAACA
1 AAAAAAAAAACAAAACA
297212 AAAAAAAAAACAAAACA
1 AAAAAAAAAACAAAACA
297229 AAGAAAAAA
1 AA-AAAAAA
297238 GAGAGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAACA
Found at i:297221 original size:20 final size:21
Alignment explanation
Indices: 297196--297237 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
297186 ATTCTTTTTT
297196 AAAAAACAAAA-AAACAAAAA
1 AAAAAACAAAACAAACAAAAA
*
297216 AAAAAACAAAACAAAGAAAAA
1 AAAAAACAAAACAAACAAAAA
297237 A
1 A
297238 GAGAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAACAAAACAAACAAAAA
Found at i:298340 original size:55 final size:56
Alignment explanation
Indices: 298256--298483 Score: 302
Period size: 55 Copynumber: 4.0 Consensus size: 56
298246 CCTTTTCCTT
298256 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC-CTC
1 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCTCTC
*
298311 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC-CT-
1 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCTCTC
* * * *
298365 TTCAAAGACCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGTAGGATGCTTTCTCC
1 TT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC--TCT-C
* *
298425 TTCTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGTAGGACGCTCTC
1 -T-TAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGCTCTC
298483 T
1 T
298484 CTTTTCGCCC
Statistics
Matches: 154, Mismatches: 10, Indels: 16
0.86 0.06 0.09
Matches are distributed among these distances:
54 2 0.01
55 98 0.64
57 1 0.01
58 3 0.02
59 3 0.02
60 4 0.03
61 42 0.27
62 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (56 bp):
TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCTCTC
Found at i:298690 original size:61 final size:60
Alignment explanation
Indices: 298517--298698 Score: 191
Period size: 61 Copynumber: 3.1 Consensus size: 60
298507 GAGCAGGACA
* *
298517 CCTT-TAAAGCCTACACAAGTTGGTGGCAC--CCTTCAGTCCTCAAAGAGCAGGACGC--CT
1 CCTTCTAAAGCCCACACAAGTTGGTGGCACTTCC-T-AGTCCTCAAAGAGCAGGATGCTTCT
* * **
298574 --TTC-AAAGCCCACACAAGCTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGGATGCTTTCT
1 CCTTCTAAAGCCCACACAAGTTGGTGGCA--CTTCCTAGTCCTCAAAGAGCAGGATGC-TTCT
*
298634 CCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGATGCTCTCT
1 CCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCT-TCT
298695 CCTT
1 CCTT
298699 TCGCCCTTTA
Statistics
Matches: 102, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
55 23 0.23
57 20 0.20
58 1 0.01
60 3 0.03
61 30 0.29
62 3 0.03
63 22 0.22
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (60 bp):
CCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATGCTTCT
Found at i:298785 original size:54 final size:55
Alignment explanation
Indices: 298702--298810 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 55
298692 TCTCCTTTCG
* *
298702 CCCTTTAGTCCTCAAAGAGCAGGACGCCTTT-AAAGCCCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGACCACACAAGTTGGTGGCA
* *
298756 CCCTTCAGTCCTTAAAGAGCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGACCACACAAGTTGGTGGCA
298811 TTTTTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 28 0.56
55 22 0.44
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (55 bp):
CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGACCACACAAGTTGGTGGCA
Found at i:298919 original size:212 final size:211
Alignment explanation
Indices: 298287--299358 Score: 1516
Period size: 212 Copynumber: 5.1 Consensus size: 211
298277 GGCATTTTCC
**
298287 AGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCT-TTAAAGCCCACACAAGTTGGTGGCACCCTT-CAGTCCTCAA
* * ** * *
298351 AGAGCAGGACACCTTTCAAAGACCACACAAGTTGGTGGCA--TTTTCCAGTCCTTAAAGAGTAGG
64 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGG
298414 ATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGC
129 ATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGC
*
298479 TCTCTCTTTTCGCCCTTT
194 TCTCTCCTTTCGCCCTTT
* * *
298497 AATCCTCAAAGAGCAGGACACCTTTAAAGCCTACACAAGTTGGTGGCACCCTTCAGTCCTCAAAG
1 AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAG
*
298562 AGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGGAT
66 AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGGAT
*
298627 GCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGATGCTC
131 GCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTC
298692 TCTCCTTTCGCCCTTT
196 TCTCCTTTCGCCCTTT
*
298708 AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTTAAAG
1 AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAG
* *
298773 AGCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCATTTTTTTTTAGTCCTCAAAGAGCAGGA
66 AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTTTTAGTCCTCAAAGAGCAGGA
*
298838 TGCTTTCTCCTTCTAAAGCCCACACTAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCT
130 TGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCT
298903 CTCTCCTTTCGCCCTTT
195 CTCTCCTTTCGCCCTTT
298920 AGTCCTCAAAGAGCAGGAC-CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCC-TTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAA
*
298984 GAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTTAGTCCTCAAAGAGTAGG
65 GAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTTTTAGTCCTCAAAGAGCAGG
*
299049 ATGC---CT--TTC-AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
129 ATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGC
299108 TCTCTCCTTTCGCCCTTT
194 TCTCTCCTTTCGCCCTTT
* * * *
299126 AGTCCTCAAAGAGCAGGATGCCTTTTGAAGCCCACATAAGTTGGTGGCA--CTTCCCGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCC-TTTAAAGCCCACACAAGTTGGTGGCACCCTT-CAGTCCTCAA
* ** **
299189 AGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA-CCTTCCT-GTCCTCAAAG
64 AGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAG
* * * **
299252 AGCAGGACGCCTTT-T-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAG
123 AGCAGGATG-CTTTCTCCTTCT-AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
* * * *
299315 CAGGATGC-CTTTTCCTTTTC-TCCTTT
186 TAGGACGCTC-TCTCC-TTTCGCCCTTT
299341 -GTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
299359 ACACTTCATT
Statistics
Matches: 792, Mismatches: 48, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
205 3 0.00
206 102 0.13
207 30 0.04
208 1 0.00
209 90 0.11
210 28 0.04
211 202 0.26
212 257 0.32
213 2 0.00
214 18 0.02
215 55 0.07
216 4 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (211 bp):
AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAG
AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGGAT
GCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTC
TCTCCTTTCGCCCTTT
Found at i:298958 original size:423 final size:414
Alignment explanation
Indices: 298287--299360 Score: 1563
Period size: 423 Copynumber: 2.6 Consensus size: 414
298277 GGCATTTTCC
*
298287 AGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCT-TTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAA
** * * *
298352 GAGCAGGACACCTTTCAAAGACCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGTAGGATG
64 GAGCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATG
298417 CTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCT
129 CTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCT
* * *
298482 CTCTTTTCGCCCTTTAATCCTCAAAGAGCAGGACACCTTTAAAGCCTACACAAGTTGGTGGCACC
194 CTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACC
298547 CTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCA-TTTTTTTTAGT
259 CTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCATTTTTTTTTAGT
298611 CCTCAAAGAGCAGGATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTC
324 CCTCAAAGAGCAGGATGC---CT--TTC-AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTC
* *
298676 AAAGAGTAGGATGCTCTCTCCTTTCGCCCTTT
383 AAAGAGCAGGACGCTCTCTCCTTTCGCCCTTT
*
298708 AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTT-CAGTCCTTAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCA--CTTCCAGTCCTCAAA
*
298772 GAGCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCATTTTTTTTTAGTCCTCAAAGAGCAGG
64 GAGCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCA---TTTTCTAGTCCTCAAAGAGCAGG
*
298837 ATGCTTTCTCCTTCTAAAGCCCACACTAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGC
126 ATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGC
298902 TCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGAC-CCTTTTAAAGCCCACACAAGTTGGTGG
191 TCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACACC-TTTAAAGCCCACACAAGTTGGTGG
*
298966 CACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTT
255 CACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCATTTTTTTT
*
299031 TAGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
320 TAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
299096 AGAGCAGGACGCTCTCTCCTTTCGCCCTTT
385 AGAGCAGGACGCTCTCTCCTTTCGCCCTTT
* * * *
299126 AGTCCTCAAAGAGCAGGATGCCTTTTGAAGCCCACATAAGTTGGTGGCACTTCCCGTCCTCAAAG
1 AGTCCTCAAAGAGCAGGACGCC-TTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAG
* * *
299191 AGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCT-GTCCTCAAAGAGC
65 AGCAGGATG----C-CTTT-CAAAGACCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGC
* * * ** *
299255 AGGACGCCTTT-T-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAG
123 AGGATG-CTTTCTCCTTCT-AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAG
* * *
299318 GATGC-CTTTTCCTTTTC-TCCTTT-GTCCTCAAAGAGCAGGACAC
186 GACGCTC-TCTCC-TTTCGCCCTTTAGTCCTCAAAGAGCAGGACAC
299361 ACTTCATTCC
Statistics
Matches: 598, Mismatches: 36, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
417 3 0.01
418 106 0.18
419 27 0.05
420 95 0.16
421 101 0.17
422 14 0.02
423 201 0.34
424 51 0.09
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (414 bp):
AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGA
GCAGGATGCCTTTCAAAGACCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCT
TTCTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCTCT
CCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCCT
TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCATTTTTTTTTAGTCC
TCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCA
GGACGCTCTCTCCTTTCGCCCTTT
Found at i:299018 original size:55 final size:55
Alignment explanation
Indices: 298914--299107 Score: 250
Period size: 58 Copynumber: 3.5 Consensus size: 55
298904 TCTCCTTTCG
* *
298914 CCCTTTAGTCCTCAAAGAGCAGGAC-CCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
298968 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*** * * *
299023 TTTTTTTTTAGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 ---CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
299081 --CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCCTT-C-AGTCCTCAAAGAGCAGGACGC
299108 TCTCTCCTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.02
54 24 0.20
55 47 0.39
58 49 0.40
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:299142 original size:152 final size:151
Alignment explanation
Indices: 298968--299261 Score: 398
Period size: 152 Copynumber: 1.9 Consensus size: 151
298958 GTTGGTGGCA
* **
298968 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTTA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA----CTTCCA
*
299033 GTCCTCAAAGAGTAGGATG-C-CTTT-CAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTC
62 GTCCTCAAAGAGCAGGATGTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCT-GTCCTC
299094 AAAGAGCAGGACGCTCTCTCCTTTCG
126 AAAGAGCAGGACGCTCTCTCCTTTCG
* * ** * *
299120 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTGAAGCCCACATAAGTTGGTGGCACTTCCCGTCC
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCC
299185 TCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCTGTCCTCAA
66 TCAAAGAGCAGGATG---TCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCTGTCCTCAA
299250 AGAGCAGGACGC
128 AGAGCAGGACGC
299262 CTTTTCTTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
148 20 0.16
152 51 0.41
153 4 0.03
154 44 0.35
155 6 0.05
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (151 bp):
CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCC
TCAAAGAGCAGGATGTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCTGTCCTCAAAGA
GCAGGACGCTCTCTCCTTTCG
Found at i:299159 original size:94 final size:93
Alignment explanation
Indices: 299029--299206 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 93
299019 GGCATTTTTT
*
299029 TTTAGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCC-AGTCCTC
299094 AAAGAGCAGGACGCTCTCTCCTTTCGCCC
65 AAAGAGCAGGACGCTCTCTCCTTTCGCCC
** * *
299123 TTTAGTCCTCAAAGAGCAGGATGCCTTTTGAAGCCCACATAAGTTGGTGGCACTTCCCGTCCTCA
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCA
* *
299188 AAGAGCAGGATGCTTTCTC
66 AAGAGCAGGACGCTCTCTC
299207 TTTGCAAAGC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 24 0.31
94 53 0.69
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (93 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCA
AAGAGCAGGACGCTCTCTCCTTTCGCCC
Found at i:299258 original size:61 final size:60
Alignment explanation
Indices: 299127--299322 Score: 253
Period size: 61 Copynumber: 3.3 Consensus size: 60
299117 TCGCCCTTTA
* *
299127 GTCCTCAAAGAGCAGGATGC---CT-TTTG--AAGCCCACATAAGTTGGTGGCACTTCCC
1 GTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACTTCCT
299181 GTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCT
1 GTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA-CTTCCT
* * * **
299242 GTCCTCAAAGAGCAGGACGCCTTT-TCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 GTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACTTCCT
299302 AGTCCTCAAAGAGCAGGATGC
1 -GTCCTCAAAGAGCAGGATGC
299323 CTTTTCCTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
54 20 0.16
57 2 0.02
58 4 0.03
60 26 0.21
61 69 0.55
62 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (60 bp):
GTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACTTCCT
Found at i:299393 original size:45 final size:43
Alignment explanation
Indices: 299303--299498 Score: 185
Period size: 42 Copynumber: 4.7 Consensus size: 43
299293 GCACTTTTTA
* *
299303 GTCCTCAAAGAGCAGGATG--C--CTTTTCCTT-TTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTCTTTTCCTTCTTTTCCTTT
* * *
299341 GTCCTCAAAGAGCAGGACACACTTCATTCCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTCTTTTCCTTCTTTT-CC-TTT
* *
299386 GTCCTCAAAGAGCAGGACGCACTTTGTTTTCC-TC-TTTCTTTT
1 GTCCTCAAAGAGCAGGACGCAC-TTCTTTTCCTTCTTTTCCTTT
* *
299428 GTCGTCAAAGAGCAGGACGCATTTCGTTTTCCTT-TTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTC-TTTTCCTTCTTTTCCTTT
* * *
299471 ATCCTCAAAAAGCAGGACGTAC-TCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTCTTTT
299499 TCATTTTGCC
Statistics
Matches: 128, Mismatches: 19, Indels: 19
0.77 0.11 0.11
Matches are distributed among these distances:
38 17 0.13
40 1 0.01
41 6 0.05
42 38 0.30
43 29 0.23
44 5 0.04
45 26 0.20
46 6 0.05
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTCTTTTCCTTCTTTTCCTTT
Found at i:299442 original size:87 final size:85
Alignment explanation
Indices: 299324--299489 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 85
299314 GCAGGATGCC
*
299324 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTC-ATTCCCTTCTTTTCCCTTTTGT
1 TTTTCCTTTTCT-CTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTT-TTTT-CC-TTTAT
*
299388 CCTCAAAGAGCAGGACGCACTTTG
62 CCTCAAAAAGCAGGACGCACTTTG
* * * * *
299412 TTTTCCTCTTTCT-TTTGTCGTCAAAGAGCAGGACGCATTTCGTTTTCCTTTTTTCCTTTATCCT
1 TTTTCCT-TTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTTTTTTCCTTTATCCT
299476 CAAAAAGCAGGACG
65 CAAAAAGCAGGACG
299490 TACTCTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
85 20 0.29
86 2 0.03
87 29 0.42
88 13 0.19
89 5 0.07
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (85 bp):
TTTTCCTTTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTTTTTTCCTTTATCCTC
AAAAAGCAGGACGCACTTTG
Found at i:300148 original size:20 final size:20
Alignment explanation
Indices: 300123--300299 Score: 120
Period size: 20 Copynumber: 8.8 Consensus size: 20
300113 TTTTCACAAT
300123 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
300143 TTGTATCGATACATTCTAGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
*
300171 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
* *
300192 TTGTATCGATACATTGCTCC
1 TTGTATCGATACATTGTTCA
* *
300212 TTGTATCGATACATTGCTCC
1 TTGTATCGATACATTGTTCA
300232 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
**
300245 TTGTATCGATACATTACTCA
1 TTGTATCGATACATTGTTCA
300265 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
300285 ATGTATCGATACATT
1 TTGTATCGATACATT
300300 CAGGCATTTT
Statistics
Matches: 131, Mismatches: 8, Indels: 36
0.75 0.05 0.21
Matches are distributed among these distances:
13 11 0.08
15 1 0.01
18 1 0.01
19 1 0.01
20 91 0.69
21 4 0.03
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.02
29 12 0.09
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:300249 original size:33 final size:33
Alignment explanation
Indices: 300212--300279 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
300202 ACATTGCTCC
* *
300212 TTGTATCGATACATTGCTCCTTGTATCGATACA
1 TTGTATCGATACATTACTCATTGTATCGATACA
300245 TTGTATCGATACATTACTCATTGTATCGATACA
1 TTGTATCGATACATTACTCATTGTATCGATACA
300278 TT
1 TT
300280 TTACAATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
TTGTATCGATACATTACTCATTGTATCGATACA
Found at i:300250 original size:13 final size:13
Alignment explanation
Indices: 300232--300259 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
300222 ACATTGCTCC
300232 TTGTATCGATACA
1 TTGTATCGATACA
300245 TTGTATCGATACA
1 TTGTATCGATACA
300258 TT
1 TT
300260 ACTCATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:300290 original size:53 final size:53
Alignment explanation
Indices: 300190--300299 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
300180 ATACATTTTG
* * **
300190 CATTGTATCGATACATTGCTCCTTGTATCGATACATTGCTCCTTGTATCGATA
1 CATTGTATCGATACATTACTCATTGTATCGATACATTGCTCAATGTATCGATA
*
300243 CATTGTATCGATACATTACTCATTGTATCGATACATT-TTACAATGTATCGATA
1 CATTGTATCGATACATTACTCATTGTATCGATACATTGCT-CAATGTATCGATA
300296 CATT
1 CATT
300300 CAGGCATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.02
53 50 0.98
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (53 bp):
CATTGTATCGATACATTACTCATTGTATCGATACATTGCTCAATGTATCGATA
Found at i:302655 original size:51 final size:50
Alignment explanation
Indices: 302590--302709 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 50
302580 ATTTTTCATC
* * * **
302590 TCGGGGATACTCCAATCCCGGTTTCATTTCCAAAATATCAATTTTTCTTAA
1 TCGGGGATACTCCAA-CCCGATTTCATTTCCAAAACACCAATTTTTCACAA
* * *
302641 TCGGGGTTACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAAC-CCGATTTCATTTCCAAAACACCAATTTTTCACAA
*
302692 TTGGGGATACTCCAACCC
1 TCGGGGATACTCCAACCC
302710 CGTTATTTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 3 0.05
51 55 0.95
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (50 bp):
TCGGGGATACTCCAACCCGATTTCATTTCCAAAACACCAATTTTTCACAA
Found at i:302726 original size:28 final size:28
Alignment explanation
Indices: 302694--302767 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
302684 TTTCACAATT
*
302694 GGGGATACTCCAACCCCGTTATTT-CATC
1 GGGGATACTCCAACCCCGTTATTTCCA-A
*
302722 GGGGATACTCCAACCCTGTTATTTCCAA
1 GGGGATACTCCAACCCCGTTATTTCCAA
302750 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
302768 GCTTTATATC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 40 0.95
29 2 0.05
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:302840 original size:28 final size:28
Alignment explanation
Indices: 302801--302877 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
302791 TTTTTTCATA
*
302801 ATCGGGGGTACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
302829 ATCGGGGATACTCTAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
302857 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
302878 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:302930 original size:51 final size:51
Alignment explanation
Indices: 302862--302979 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
302852 ATTTCCGAGG
* *
302862 GGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGA
* * *
302913 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGA
302964 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
302980 TTATTTCATT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGA
Found at i:302938 original size:110 final size:107
Alignment explanation
Indices: 302643--302924 Score: 386
Period size: 110 Copynumber: 2.6 Consensus size: 107
302633 TTTCTTAATC
* * * *
302643 GGGGTTACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
302708 CCCGTTATTTCATCGGGGATACTCCAACCCTGTTATTTCCAA
66 CCCGTTATTTCATCGGGGATACTCCAACCCTGTTATTTCCAA
** * ** * * *
302750 GGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGATTTTTTTCATAATCGGGGGTACTCC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAATA-CCA-ATTTTTCACAATCGGGGATACTCC
* *
302815 AACCCCGTTATTTCATCGGGGATACTCTAATCCC-GTTATTTCCGA
63 AACCCCGTTATTTCATCGGGGATACTCCAA-CCCTGTTATTTCCAA
*
302860 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
302925 TCCGATTTTA
Statistics
Matches: 148, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
107 47 0.32
108 6 0.04
109 7 0.05
110 85 0.57
111 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCATCGGGGATACTCCAACCCTGTTATTTCCAA
Found at i:302995 original size:28 final size:27
Alignment explanation
Indices: 302963--303035 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 27
302953 TTCACAATTG
302963 GGGATACTCCAACCCCGTTATTTCATT-A
1 GGGATACTCCAACCCCGTTATTT--TTGA
*
302991 GGGATACTCCAACCCCGTTATTTTTGT
1 GGGATACTCCAACCCCGTTATTTTTGA
303018 GGTGATACTCCAACCCCG
1 GG-GATACTCCAACCCCG
303036 ACCTTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 2 0.05
27 2 0.05
28 38 0.90
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTTTGA
Found at i:303030 original size:107 final size:107
Alignment explanation
Indices: 302914--303114 Score: 262
Period size: 107 Copynumber: 1.9 Consensus size: 107
302904 CACAATCGAG
* ** ** **
302914 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGGGGATACTCCAACCCC
1 GATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTCCCACAATCAGGGATACTCCAACCCC
302979 GTTA-TTTC-ATTAGGGATACTCCAACCCCGTTATTTTTGTGGT
66 GTTATTTTCGA--AGGGATACTCCAACCCCGTTATTTTTGTGGT
* * **
303021 GATACTCCAACCCCGACCTTATTTCTAAAGCATTAATTTCCCACAATCAGGGATACTCCAACCCC
1 GATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTCCCACAATCAGGGATACTCCAACCCC
*
303086 GTTATTTTCGAGGGGATACTCCAACCCCG
66 GTTATTTTCGAAGGGATACTCCAACCCCG
303115 ATTTTATTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
107 75 0.94
108 4 0.05
109 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.30
Consensus pattern (107 bp):
GATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTCCCACAATCAGGGATACTCCAACCCC
GTTATTTTCGAAGGGATACTCCAACCCCGTTATTTTTGTGGT
Done.