Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold198
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1589021
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.28
Warning! 220217 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1317772 original size:4 final size:4
Alignment explanation
Indices: 1317763--1317812 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
1317753 ATGTTCATNT
* * * *
1317763 ACGG ACGG ACGG ACAG ACAG ACGG ACAG ACAG ACGG ACGG ACGG ACGG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG
1317811 AC
1 AC
1317813 AGACAGACAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:1317787 original size:12 final size:12
Alignment explanation
Indices: 1317770--1317825 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
1317760 TNTACGGACG
1317770 GACGGACAGACA
1 GACGGACAGACA
1317782 GACGGACAGACA
1 GACGGACAGACA
* *
1317794 GACGGACGGACG
1 GACGGACAGACA
1317806 GACGGACAGACA
1 GACGGACAGACA
*
1317818 GACAGACA
1 GACGGACA
1317826 CACAAGGGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00
Consensus pattern (12 bp):
GACGGACAGACA
Found at i:1317817 original size:4 final size:4
Alignment explanation
Indices: 1317774--1317825 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1317764 CGGACGGACG
* * * * *
1317774 GACA GACA GACG GACA GACA GACG GACG GACG GACG GACA GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1317822 GACA
1 GACA
1317826 CACAAGGGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1320380 original size:29 final size:28
Alignment explanation
Indices: 1320332--1320389 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
1320322 ATTTTTAAAT
1320332 CGGATAAAAACGAAATTTTAACAAAAAAA
1 CGGATAAAAACGAAATTTT-ACAAAAAAA
*
1320361 CGGATAAAAACAGAAA-TTTACGAAAAAA
1 CGGATAAAAAC-GAAATTTTACAAAAAAA
1320389 C
1 C
1320390 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 14 0.52
30 4 0.15
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (28 bp):
CGGATAAAAACGAAATTTTACAAAAAAA
Found at i:1330259 original size:159 final size:160
Alignment explanation
Indices: 1329940--1330280 Score: 526
Period size: 159 Copynumber: 2.1 Consensus size: 160
1329930 AAACATCCAC
* * * *
1329940 AAAGAAAATGAACGTAAACTTCAAATAACTGGAATTTTACTAAGTCCAAGGGCCATAACTCTGTC
1 AAAGAAAATGAACGGAAACTGCAAAAAAC-GGAATTTTACTAACTCCAAGGGCCATAACTCTGTC
*
1330005 GAAAATTGCTCTATCATACCCAAATCAAACTTGACCCAGATATTAATATGATAAACCTGTATACC
65 GAAAATTGCTCGATCATACCCAAATCAAACTTGACCCAGATATTAATATGATAAACCTGTATACC
1330070 AAATTTCATTTCAATATGTTCATCCTCTGCG
130 AAATTTCATTTCAATATGTTCATCCTCTGCG
* * *
1330101 -AAGAAAATGAGCGGAAACTGCAAAAAAC-GAATTTTTCTACCTCCAAGGGCCATAACTCTGTCG
1 AAAGAAAATGAACGGAAACTGCAAAAAACGGAATTTTACTAACTCCAAGGGCCATAACTCTGTCG
* ** *
1330164 AAAATTGCTCGATCGTACCCAATATTGAACTTGACCTAGATATT-ATCATGATAAACCTGTATAC
66 AAAATTGCTCGATCATACCCAA-ATCAAACTTGACCCAGATATTAAT-ATGATAAACCTGTATAC
1330228 CAAATTTCATTTCAATATGTTCATCCTCTGCG
129 CAAATTTCATTTCAATATGTTCATCCTCTGCG
1330260 AAAGAAAATGAACGGAAACTG
1 AAAGAAAATGAACGGAAACTG
1330281 TTAATGGAGT
Statistics
Matches: 164, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
158 54 0.33
159 67 0.41
160 43 0.26
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (160 bp):
AAAGAAAATGAACGGAAACTGCAAAAAACGGAATTTTACTAACTCCAAGGGCCATAACTCTGTCG
AAAATTGCTCGATCATACCCAAATCAAACTTGACCCAGATATTAATATGATAAACCTGTATACCA
AATTTCATTTCAATATGTTCATCCTCTGCG
Found at i:1331696 original size:15 final size:16
Alignment explanation
Indices: 1331676--1331705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1331666 ATGTATCCAG
1331676 CAGTG-AAACAAAATC
1 CAGTGAAAACAAAATC
1331691 CAGTGAAAACAAAAT
1 CAGTGAAAACAAAAT
1331706 TATGCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (16 bp):
CAGTGAAAACAAAATC
Found at i:1339642 original size:22 final size:22
Alignment explanation
Indices: 1339617--1339664 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1339607 TATATTAAAT
1339617 ATACAGTGACATGAACACGTTA
1 ATACAGTGACATGAACACGTTA
*
1339639 ATACAGTGACATGTACACGTTA
1 ATACAGTGACATGAACACGTTA
1339661 ATAC
1 ATAC
1339665 TGCTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (22 bp):
ATACAGTGACATGAACACGTTA
Found at i:1340146 original size:9 final size:9
Alignment explanation
Indices: 1340132--1340181 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
1340122 ATAATACATT
1340132 TTAAATACA
1 TTAAATACA
*
1340141 TTAAATTAGA
1 TTAAA-TACA
1340151 TTAAATACA
1 TTAAATACA
*
1340160 TTAAAAACA
1 TTAAATACA
1340169 TTCAAAATACA
1 TT--AAATACA
1340180 TT
1 TT
1340182 TTAAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 18 0.53
10 8 0.24
11 8 0.24
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (9 bp):
TTAAATACA
Found at i:1340935 original size:19 final size:19
Alignment explanation
Indices: 1340911--1340948 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1340901 AAGTTAAGTC
1340911 GTTAAGTGACATAGGCAAA
1 GTTAAGTGACATAGGCAAA
1340930 GTTAAGTGACATAGGCAAA
1 GTTAAGTGACATAGGCAAA
1340949 ATACATACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (19 bp):
GTTAAGTGACATAGGCAAA
Found at i:1353225 original size:53 final size:53
Alignment explanation
Indices: 1353149--1353761 Score: 552
Period size: 53 Copynumber: 12.1 Consensus size: 53
1353139 TTGTATGTTT
* * * ** *
1353149 GTGTTTGTGAGCGCGTGTATAACAAAACTTATTTATCATACCTGTCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* * * *
1353202 GTGTGTGTGAGTGTGTGTGTAACAATACTTACTTATCATACCTGTCAATGACAGT
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTC--C
* * * * *
1353257 GTGTGTGTGAGTGCGTGTGTTACAGTACTTACATATTATACCTATCAAAGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* *
1353310 --GTGTGT--GT--GTGT-TAA-AGTACTT-CTTTTTATACCTGTCAATGT-C
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* *
1353353 --G-GTGT--GTGCCTGT-TATACAGTACTTTCTTATCATACCTGTCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTA-ACAGTACTTACTTATCATACCTGTCAATGTCC
* * **
1353401 GTGTGTGTGAGTGCGTGTG-ATACAGTACTTACTTATCATACCTGTCACTTTTT
1 GTGTGTGTGAGTGCGTGTGTA-ACAGTACTTACTTATCATACCTGTCAATGTCC
* * * * **
1353454 GTGTGTGTAAGTGTGTGTGTAACAGTACTTACATATCATACCTATCGTTGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
*
1353507 GTGTGTGTGAGTGCGTGTGTTACAGTACTTACTTATCATACCTGTCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* * * *
1353560 GTGTGTGTGAGTGCGTGTTTTACAGTATTTACATATCATACCTGTCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* * * * *
1353613 GTGTGTGCGAGTGTGTGTGTGTTACAGTACTTACATATCATACCTGTCAAAGTCC
1 GTGTGTGTGA--GTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* * *
1353668 GTATGTG-G-GTGC---T-T-A-AGTACTT-CTTTTTATACCTGTCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
* *
1353712 GTGTGTGT--GT--GTG-AT-ACAGTACTTACTTATCATACCTATCAATGTCC
1 GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
1353759 GTG
1 GTG
1353762 CTTCCTGTAG
Statistics
Matches: 471, Mismatches: 65, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
42 6 0.01
43 2 0.00
44 47 0.10
45 17 0.04
46 17 0.04
47 45 0.10
48 2 0.00
49 2 0.00
50 1 0.00
51 13 0.03
53 228 0.48
54 2 0.00
55 89 0.19
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (53 bp):
GTGTGTGTGAGTGCGTGTGTAACAGTACTTACTTATCATACCTGTCAATGTCC
Found at i:1353758 original size:47 final size:47
Alignment explanation
Indices: 1353623--1353761 Score: 178
Period size: 47 Copynumber: 3.0 Consensus size: 47
1353613 GTGTGTGCGA
* *
1353623 GTGTGTGTGTGTTACAGTACTTACATATCATACCTGTCAAAGTCCGT
1 GTGTGTGTGTGTTACAGTACTTACTTATCATACCTGTCAATGTCCGT
* * *
1353670 ATGTG-G-GTGCTTA-AGTACTT-CTTTTTATACCTGTCAATGTCCGT
1 GTGTGTGTGTG-TTACAGTACTTACTTATCATACCTGTCAATGTCCGT
* *
1353714 GTGTGTGTGTGATACAGTACTTACTTATCATACCTATCAATGTCCGT
1 GTGTGTGTGTGTTACAGTACTTACTTATCATACCTGTCAATGTCCGT
1353761 G
1 G
1353762 CTTCCTGTAG
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
44 24 0.31
45 13 0.17
46 14 0.18
47 26 0.34
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (47 bp):
GTGTGTGTGTGTTACAGTACTTACTTATCATACCTGTCAATGTCCGT
Found at i:1353847 original size:20 final size:20
Alignment explanation
Indices: 1353822--1353938 Score: 216
Period size: 20 Copynumber: 5.8 Consensus size: 20
1353812 ACAACATGAA
1353822 ACACGCCACTAATTGTACTT
1 ACACGCCACTAATTGTACTT
1353842 ACACGCCACTAATTGTACTT
1 ACACGCCACTAATTGTACTT
*
1353862 ACATGCCACTAATTGTACTT
1 ACACGCCACTAATTGTACTT
1353882 ACACGCCACTAATTGTACTT
1 ACACGCCACTAATTGTACTT
*
1353902 ACACGCCACTAATTATACTT
1 ACACGCCACTAATTGTACTT
1353922 ACACGCCACTAATTGTA
1 ACACGCCACTAATTGTA
1353939 ATTGTGTAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (20 bp):
ACACGCCACTAATTGTACTT
Found at i:1363061 original size:1 final size:1
Alignment explanation
Indices: 1363057--1363082 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1363047 TGGGGGCCAG
1363057 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
1363083 GATGCTACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1363659 original size:167 final size:166
Alignment explanation
Indices: 1363290--1363755 Score: 770
Period size: 167 Copynumber: 2.8 Consensus size: 166
1363280 AAACTTATAC
* * *
1363290 AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTCCACCAGAAATGTCAACATTTACACAACAG
1 AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAG
1363355 CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCC
66 CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCC
* *
1363420 AGGCGGGGTTCAAAATTTAACATAGATATCCATAGG
131 AGGCGGGGTTCAAAATTTAACATAGAAATACATAGG
* * *
1363456 AAAAATGTTTAGAAATCATCTTCTCAAGACCCACTGCACCAGAAATGCCAACATTTACACAAAAG
1 AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAG
* * * *
1363521 CTTTTATATATAGTGAAGATTCTAAATTATAAAAATCGTGACTCCCGGGCCAAAAACTGGGGCCC
66 CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACC-AAAACTGGGGCCC
* * * *
1363586 CAGGCGGGGTTCAAAGTTTAACATTGAAATAGATTGG
130 CAGGCGGGGTTCAAAATTTAACATAGAAATACATAGG
1363623 AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAG
1 AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAG
*
1363688 CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATTGTGACCCCCGGACCAAAACTGGGGCCCC
66 CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCC
1363753 AGG
131 AGG
1363756 TGGTCCGGGC
Statistics
Matches: 275, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
166 123 0.45
167 152 0.55
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (166 bp):
AAAAATGTTTAAAAATCGTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAG
CTTGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCC
AGGCGGGGTTCAAAATTTAACATAGAAATACATAGG
Found at i:1364677 original size:28 final size:28
Alignment explanation
Indices: 1364645--1364701 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1364635 GTAAAATCGT
* * *
1364645 GACCCCCGGACTAATACTGGGGCCCCAA
1 GACCCCCAGACCAATACTGAGGCCCCAA
1364673 GACCCCCAGACCAATACTGAGGCCCCAA
1 GACCCCCAGACCAATACTGAGGCCCCAA
1364701 G
1 G
1364702 TGGGGTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.40, G:0.23, T:0.09
Consensus pattern (28 bp):
GACCCCCAGACCAATACTGAGGCCCCAA
Found at i:1391608 original size:28 final size:28
Alignment explanation
Indices: 1391568--1392002 Score: 701
Period size: 28 Copynumber: 15.5 Consensus size: 28
1391558 NNNNNNNNNN
1391568 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
1391596 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
*
1391624 ATTGTATACACTGTTAGTTAGGCCAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
* *
1391652 TTTGTATACACTGTTAGTTAGACTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
*
1391680 ATTGTATACACTGTTAGTTAAGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
1391708 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
* * *
1391736 TTTGTATACACTGTTATTTAGGCCAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
* *
1391764 TTTGTATACACTGTTAGTTAGGCCA-GG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
* *
1391791 ATGTGTATACACTATTAGTTAGGCTAGGA
1 AT-TGTATACACTGTTAGTTAGGCTAGGG
1391820 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
1391848 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
1391876 ATTGTATACACTGTTAGTTAGGCTAGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
* *
1391904 TTTGTATACACTGTTAGTTAGGCTGGGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
*
1391932 TTTTGTATACACTGTTAGTTAGGCTAGGG
1 -ATTGTATACACTGTTAGTTAGGCTAGGG
* *
1391961 TTTGTATACACTGTTAGTTAGGCTATGG
1 ATTGTATACACTGTTAGTTAGGCTAGGG
1391989 ATTGTATACACTGT
1 ATTGTATACACTGT
1392003 GGACTGTTGC
Statistics
Matches: 381, Mismatches: 23, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
27 3 0.01
28 348 0.91
29 30 0.08
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.37
Consensus pattern (28 bp):
ATTGTATACACTGTTAGTTAGGCTAGGG
Found at i:1393318 original size:24 final size:23
Alignment explanation
Indices: 1393270--1393340 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
1393260 GATAGTAGGC
1393270 CTATGCCTATTTTATATTAAAAA
1 CTATGCCTATTTTATATTAAAAA
1393293 CTATGCCTATTTTATATTTAAAAA
1 CTATGCCTATTTTATA-TTAAAAA
*
1393317 CTATGCCT-TTTTAAATTAAAAA
1 CTATGCCTATTTTATATTAAAAA
1393339 CT
1 CT
1393341 CTTTGGGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
22 9 0.20
23 22 0.48
24 15 0.33
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (23 bp):
CTATGCCTATTTTATATTAAAAA
Found at i:1397150 original size:2 final size:2
Alignment explanation
Indices: 1397143--1397181 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1397133 ATGAGCATGA
1397143 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1397182 TATTGATACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1398746 original size:15 final size:15
Alignment explanation
Indices: 1398726--1398768 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1398716 AGGTCATAGA
1398726 AGAATATTAGCAATC
1 AGAATATTAGCAATC
* *
1398741 AGAATATTTGCAGTC
1 AGAATATTAGCAATC
*
1398756 AGCA-ATTAGCAAT
1 AGAATATTAGCAAT
1398769 TAGCTAGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (15 bp):
AGAATATTAGCAATC
Found at i:1399387 original size:2 final size:2
Alignment explanation
Indices: 1399380--1399424 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1399370 AAAAGATTTT
* * *
1399380 GA GA GA GA GA GA GA GA GA GA GA GA AA CA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1399422 GA G
1 GA G
1399425 GGGGAAGACG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.53, C:0.02, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1402802 original size:25 final size:25
Alignment explanation
Indices: 1402768--1402823 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1402758 CTCAATGTTT
1402768 TAAATCTGTATAAAACTGTACCATC
1 TAAATCTGTATAAAACTGTACCATC
1402793 TAAATCTGTATAAAACTGTACCATC
1 TAAATCTGTATAAAACTGTACCATC
1402818 TAAATC
1 TAAATC
1402824 ATGCTGCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (25 bp):
TAAATCTGTATAAAACTGTACCATC
Found at i:1409636 original size:2 final size:2
Alignment explanation
Indices: 1409629--1409680 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1409619 AACCCTGCAA
1409629 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1409671 TC TC TC TC TC
1 TC TC TC TC TC
1409681 AAAAGTTGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1411572 original size:26 final size:26
Alignment explanation
Indices: 1411542--1411753 Score: 204
Period size: 26 Copynumber: 8.2 Consensus size: 26
1411532 CGCCAAAAAT
*
1411542 ATACGCGGTAAGTGAGCGCCACCAAC
1 ATACGCGGTAACTGAGCGCCACCAAC
*
1411568 GTACGCGGTAACTGCA-CGCCACCAAC
1 ATACGCGGTAACTG-AGCGCCACCAAC
1411594 ATACGCGGTAACTGCA-CGCCACCAAC
1 ATACGCGGTAACTG-AGCGCCACCAAC
*
1411620 ATACGCGGTAACTGCA-CGCCACTAAC
1 ATACGCGGTAACTG-AGCGCCACCAAC
* * * *
1411646 ACACGCGGTAACT-ACACGCCACTAAT
1 ATACGCGGTAACTGA-GCGCCACCAAC
* * *
1411672 GTACGCGGTTTAA--GAGAGCCTCCAAC
1 ATACGCGG--TAACTGAGCGCCACCAAC
* *
1411698 ATACGCGGTAAGTGAGCGCCA-CAGAT
1 ATACGCGGTAACTGAGCGCCACCA-AC
1411724 ATACGCGGTAACTGAGCGCCACCAAC
1 ATACGCGGTAACTGAGCGCCACCAAC
1411750 ATAC
1 ATAC
1411754 ATGTACGTGT
Statistics
Matches: 157, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.03
25 2 0.01
26 144 0.92
27 4 0.03
28 3 0.02
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.14
Consensus pattern (26 bp):
ATACGCGGTAACTGAGCGCCACCAAC
Found at i:1420196 original size:15 final size:15
Alignment explanation
Indices: 1420173--1420283 Score: 177
Period size: 15 Copynumber: 7.4 Consensus size: 15
1420163 CTTGCCATTC
1420173 ACAACAGCTGCACCG
1 ACAACAGCTGCACCG
*
1420188 ACCACAGCTGCACCG
1 ACAACAGCTGCACCG
*
1420203 ACAACAGCTGCACCT
1 ACAACAGCTGCACCG
1420218 ACAACAGCTGCACCG
1 ACAACAGCTGCACCG
*
1420233 ACAACATCTGCACCG
1 ACAACAGCTGCACCG
*
1420248 ACAACAACTGCACCG
1 ACAACAGCTGCACCG
*
1420263 ACAACAACTGCACCG
1 ACAACAGCTGCACCG
1420278 ACAACA
1 ACAACA
1420284 TTAGCTGCTA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 90 1.00
ACGTcount: A:0.36, C:0.41, G:0.15, T:0.08
Consensus pattern (15 bp):
ACAACAGCTGCACCG
Found at i:1420725 original size:33 final size:33
Alignment explanation
Indices: 1420669--1420735 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1420659 GAAACAAGAC
* * *
1420669 CACCGACAACAACAACGGTAATACCGACAACAA
1 CACCAACAACAACAACAGCAATACCGACAACAA
*
1420702 CACCAACAACAACGACAGCAATACCGACAACAA
1 CACCAACAACAACAACAGCAATACCGACAACAA
1420735 C
1 C
1420736 TACAGTGATA
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:0.49, C:0.36, G:0.10, T:0.04
Consensus pattern (33 bp):
CACCAACAACAACAACAGCAATACCGACAACAA
Found at i:1420740 original size:21 final size:21
Alignment explanation
Indices: 1420693--1420778 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
1420683 ACGGTAATAC
* * *
1420693 CGACAACAACACCAACAACAA
1 CGACAGCAATACCGACAACAA
1420714 CGACAGCAATACCGACAACAA
1 CGACAGCAATACCGACAACAA
* ** * *
1420735 CTACAGTGATACCTACAATAA
1 CGACAGCAATACCGACAACAA
*
1420756 CGACTA-CAAAACCGACAACAA
1 CGAC-AGCAATACCGACAACAA
1420777 CG
1 CG
1420779 GTGGGGACAA
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
21 49 0.98
22 1 0.02
ACGTcount: A:0.49, C:0.33, G:0.10, T:0.08
Consensus pattern (21 bp):
CGACAGCAATACCGACAACAA
Found at i:1422072 original size:30 final size:30
Alignment explanation
Indices: 1422023--1422392 Score: 435
Period size: 30 Copynumber: 12.3 Consensus size: 30
1422013 CATTGGCCAA
*
1422023 TACAAC-CCAGCATGTGACAACAGAATCCAT
1 TACAACACCA-CATGTGACAACAGAGTCCAT
* * * * *
1422053 TACTACACTAAAAGTGACAACAGAATCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
* * * *
1422083 TACAACACCGCACGTGACAACTGAGTTCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
* *
1422113 TACAACACCACGTGTGACAACAGAAT-CAGT
1 TACAACACCACATGTGACAACAGAGTCCA-T
*
1422143 TACAACACCACGTGTGACAACAGAGTCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
* *
1422173 TACAACACCACGTGTGACAACAGAAT-CAGT
1 TACAACACCACATGTGACAACAGAGTCCA-T
* *
1422203 TACAACCCCACGTGTGACAACAGAGTCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
*
1422233 TACAACACCA-ATTGTGACAACAGAAT-CAGT
1 TACAACACCACA-TGTGACAACAGAGTCCA-T
* *
1422263 TACAACACCACGTGTGACAACAGAGTCAAT
1 TACAACACCACATGTGACAACAGAGTCCAT
* *
1422293 TACAACACCGCACGTGACAACAGAGTCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
*
1422323 TACAACACCACACGTGACAACAGAGTCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
* *
1422353 TACAACACCGCACGTGACAACAGAGTCCAT
1 TACAACACCACATGTGACAACAGAGTCCAT
1422383 TACAACACCA
1 TACAACACCA
1422393 ATTTTAACAA
Statistics
Matches: 297, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
29 6 0.02
30 284 0.96
31 7 0.02
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.16
Consensus pattern (30 bp):
TACAACACCACATGTGACAACAGAGTCCAT
Found at i:1422132 original size:15 final size:15
Alignment explanation
Indices: 1422114--1422224 Score: 54
Period size: 15 Copynumber: 7.4 Consensus size: 15
1422104 TGAGTTCATT
1422114 ACAACACCACGTGTG
1 ACAACACCACGTGTG
**
1422129 ACAACAGAATCAGT-T-
1 ACAACACCA-C-GTGTG
1422144 ACAACACCACGTGTG
1 ACAACACCACGTGTG
* * *
1422159 ACAACA-GA-GTCCATT
1 ACAACACCACGT--GTG
1422174 ACAACACCACGTGTG
1 ACAACACCACGTGTG
**
1422189 ACAACAGAATCAGT-T-
1 ACAACACCA-C-GTGTG
*
1422204 ACAACCCCACGTGTG
1 ACAACACCACGTGTG
1422219 ACAACA
1 ACAACA
1422225 GAGTCCATTA
Statistics
Matches: 68, Mismatches: 16, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
13 6 0.09
14 5 0.07
15 46 0.68
16 5 0.07
17 6 0.09
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (15 bp):
ACAACACCACGTGTG
Found at i:1422387 original size:15 final size:15
Alignment explanation
Indices: 1422309--1422389 Score: 51
Period size: 15 Copynumber: 5.4 Consensus size: 15
1422299 ACCGCACGTG
1422309 ACAACAGAGTCCATT
1 ACAACAGAGTCCATT
* * *
1422324 ACAACACCA--CACGTG
1 ACAACA-GAGTC-CATT
1422339 ACAACAGAGTCCATT
1 ACAACAGAGTCCATT
** * *
1422354 ACAACACCG-CACGTG
1 ACAACAGAGTC-CATT
1422369 ACAACAGAGTCCATT
1 ACAACAGAGTCCATT
1422384 ACAACA
1 ACAACA
1422390 CCAATTTTAA
Statistics
Matches: 46, Mismatches: 14, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
14 3 0.07
15 40 0.87
16 3 0.07
ACGTcount: A:0.41, C:0.32, G:0.14, T:0.14
Consensus pattern (15 bp):
ACAACAGAGTCCATT
Found at i:1423629 original size:18 final size:18
Alignment explanation
Indices: 1423606--1424575 Score: 531
Period size: 18 Copynumber: 53.7 Consensus size: 18
1423596 TCAACGCCTA
* *
1423606 AAGCTCTAACGACAACTC
1 AAGCTCCAACAACAACTC
*
1423624 AAGCTCCAACAACCACTC
1 AAGCTCCAACAACAACTC
* *
1423642 AATCAT-CAACAACCACTC
1 AAGC-TCCAACAACAACTC
* ***
1423660 AAGTTCCAATTTCAA-T-
1 AAGCTCCAACAACAACTC
* **
1423676 AACGCTAACTTCAACAACTC
1 AA-GCT-CCAACAACAACTC
* * *
1423696 AAACTTCGACAACAACTC
1 AAGCTCCAACAACAACTC
* * * *
1423714 AAGCTTCAACACCCACAC
1 AAGCTCCAACAACAACTC
* *
1423732 AAGCTCCAACAAAAACTG
1 AAGCTCCAACAACAACTC
* ** ** *
1423750 AAGCACTTACAACCCCTG
1 AAGCTCCAACAACAACTC
* * *
1423768 GAGCTCCAACGACAACAC
1 AAGCTCCAACAACAACTC
* *
1423786 AAGCTCAAACAACTACTC
1 AAGCTCCAACAACAACTC
* * *
1423804 AAGATCCATCAACAACAAC
1 AAGCTCCAACAACAAC-TC
*
1423823 AA-CAT-CAACAACAACTG
1 AAGC-TCCAACAACAACTC
* **
1423840 AGGCTCCAATTACAACTC
1 AAGCTCCAACAACAACTC
* * *
1423858 AA-CCCCTAACAACCACTA
1 AAGCTCC-AACAACAACTC
*
1423876 AAGCTGCATCAACCACAACT-
1 AAGCT-C--CAACAACAACTC
*
1423896 AA-CATGCCAACAACAACTG
1 AAGC-T-CCAACAACAACTC
** *
1423915 GGGCTCTAACAACAACTC
1 AAGCTCCAACAACAACTC
*
1423933 AAGCTCCTACAACGAA-TC
1 AAGCTCCAACAAC-AACTC
*
1423951 AA-CGTTCAACAAC--CTC
1 AAGC-TCCAACAACAACTC
*
1423967 AGAAGC-CCTACCAACAACTC
1 --AAGCTCC-AACAACAACTC
* * * *
1423987 AACCTTCAACAACCACAC
1 AAGCTCCAACAACAACTC
* * * *
1424005 AAGCTCCTATAACCACAC
1 AAGCTCCAACAACAACTC
*
1424023 AAGCTCCAACAACAAATC
1 AAGCTCCAACAACAACTC
1424041 AA-CTTCCAACAACAACT-
1 AAGC-TCCAACAACAACTC
* *
1424058 AACGCTCCAACAACCACAC
1 AA-GCTCCAACAACAACTC
*
1424077 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424095 AGGCTCCAACAACTACAC
1 AAGCTCCAACAACAACTC
1424113 AAG-TACCAACAACAACTC
1 AAGCT-CCAACAACAACTC
* * *
1424131 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
*
1424149 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424167 AGGCTCCAACAACTACAC
1 AAGCTCCAACAACAACTC
1424185 AAG-TACCAACAACAACTC
1 AAGCT-CCAACAACAACTC
* * *
1424203 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
* *
1424221 AAGCACAAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424239 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
*
1424257 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * * *
1424275 AGGCTCAAACAACTACAC
1 AAGCTCCAACAACAACTC
*
1424293 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* *
1424311 AGGCTCCAACAACCAA-AC
1 AAGCTCCAACAA-CAACTC
*
1424329 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * * *
1424347 AGGATCCAACAACTACAC
1 AAGCTCCAACAACAACTC
*
1424365 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424383 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
*
1424401 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424419 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
1424437 AAG-TACCAACAACAACTC
1 AAGCT-CCAACAACAACTC
* * **
1424455 AGGCTCCAACAACTACAA
1 AAGCTCCAACAACAACTC
*
1424473 AAGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* *
1424491 AA-CTTCCAACAACCACAC
1 AAGC-TCCAACAACAACTC
***
1424509 AAGCAAAAACAACAACTC
1 AAGCTCCAACAACAACTC
* * *
1424527 AGGCTCCAACAACCACAC
1 AAGCTCCAACAACAACTC
* *
1424545 ACGCACCAACAACAACTC
1 AAGCTCCAACAACAACTC
* *
1424563 AACCTCCATCAAC
1 AAGCTCCAACAAC
1424576 GACAGGAGCC
Statistics
Matches: 693, Mismatches: 217, Indels: 84
0.70 0.22 0.08
Matches are distributed among these distances:
16 4 0.01
17 21 0.03
18 622 0.90
19 25 0.04
20 12 0.02
21 8 0.01
22 1 0.00
ACGTcount: A:0.44, C:0.38, G:0.07, T:0.11
Consensus pattern (18 bp):
AAGCTCCAACAACAACTC
Found at i:1423846 original size:72 final size:73
Alignment explanation
Indices: 1423770--1424563 Score: 832
Period size: 72 Copynumber: 11.0 Consensus size: 73
1423760 AACCCCTGGA
* * * * * * * * * *
1423770 GCTCCAACGACAACACAAGCTCAAACAACTACTCAAGATCCATCAACAACAACAA-CATCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
*
1423834 CAACTGAG
66 CAACTCAG
** * * * * * * * *
1423842 GCTCCAATTACAACTCAA-CCCCTAACAACCACTAAAGCTGCATCAACCACAACTAA-CATGCCA
1 GCTCCAACAACCACACAAGCACC-AACAACAACTCAGGCTCCAACAACCACAAC-AAGCA--CCA
**
1423905 ACAACAACTGGG
62 ACAACAACTCAG
* * * * * * * * * *
1423917 GCTCTAACAACAACTCAAGCTCCTACAACGAA-TCA-ACGTTCAACAACCTC-AGAAGC-CCTAC
1 GCTCCAACAACCACACAAGCACCAACAAC-AACTCAGGC-TCCAACAACCACAACAAGCACC-AA
*
1423978 CAACAACTCAA
63 CAACAACTCAG
* * * * * * * * *
1423989 CCTTCAACAACCACACAAGCTCCTATAACCACACAAGCTCCAACAA-CA-AATCAA-CTTCCAAC
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAA-CAAGC-ACCAAC
* *
1424051 AACAACTAAC
64 AACAACTCAG
* *
1424061 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACTAC-ACAAGTACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424125 CAACTCAG
66 CAACTCAG
* *
1424133 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACTAC-ACAAGTACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424197 CAACTCAG
66 CAACTCAG
*
1424205 GCTCCAACAACCACACAAGCACAAACAACAACTCAGGCTCCAACAACCAC-ACAAGCACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424269 CAACTCAG
66 CAACTCAG
* *
1424277 GCTCAAACAACTACACAAGCACCAACAACAACTCAGGCTCCAACAACCA-AACAAGCACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424341 CAACTCAG
66 CAACTCAG
* *
1424349 GATCCAACAACTACACAAGCACCAACAACAACTCAGGCTCCAACAACCAC-ACAAGCACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424413 CAACTCAG
66 CAACTCAG
* *
1424421 GCTCCAACAACCACACAAGTACCAACAACAACTCAGGCTCCAACAACTACAA-AAGCACCAACAA
1 GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
1424485 CAACTCA-
66 CAACTCAG
* ** *
1424492 ACTTCCAACAACCACACAAGCAAAAACAACAACTCAGGCTCCAACAACCAC-ACACGCACCAACA
1 GC-TCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACA
1424556 ACAACTCA
65 ACAACTCA
1424564 ACCTCCATCA
Statistics
Matches: 625, Mismatches: 74, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
71 10 0.02
72 552 0.88
73 12 0.02
74 3 0.00
75 44 0.07
76 4 0.01
ACGTcount: A:0.45, C:0.38, G:0.08, T:0.10
Consensus pattern (73 bp):
GCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACCACAACAAGCACCAACAA
CAACTCAG
Found at i:1424137 original size:108 final size:107
Alignment explanation
Indices: 1423902--1424563 Score: 787
Period size: 108 Copynumber: 6.1 Consensus size: 107
1423892 AACTAACATG
** * * * * *
1423902 CCAACAACAACTGGGGCTCTAACAACAACTCAAGCTCCTACAACGAA-TCAACG-TTCAACAACC
1 CCAACAACAACTCAGGCTCCAACAACAA-ACAAGCACCAACAAC-AACT-AACGCTCCAACAACC
* * * ** * *
1423965 TCAGAAGC-CCTACCAACAACTCAACCTTCAACAACCACACAAGCT
63 ACACAAGCACC-AACAACAACTCAGGCTCCAACAACCACACAAGCA
* * * * * *
1424010 CCTATAACCACACAAGCTCCAACAACAAATCAA-CTTCCAACAACAACTAACGCTCCAACAACCA
1 CCAACAACAACTCAGGCTCCAACAACAAA-CAAGC-ACCAACAACAACTAACGCTCCAACAACCA
* *
1424074 CACAAGCACCAACAACAACTCAGGCTCCAACAACTACACAAGTA
64 CACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
* * * *
1424118 CCAACAACAACTCAGGCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCCAACAACTAC
1 CCAACAACAACTCAGGCTCCAACAA-CAAACAAGCACCAACAACAACTAACGCTCCAACAACCAC
*
1424183 ACAAGTACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
65 ACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
* * * * * *
1424226 CAAACAACAACTCAGGCTCCAACAACCACACAAGCACCAACAACAACTCAGGCTCAAACAACTAC
1 CCAACAACAACTCAGGCTCCAACAA-CAAACAAGCACCAACAACAACTAACGCTCCAACAACCAC
*
1424291 ACAAGCACCAACAACAACTCAGGCTCCAACAACCAAACAAGCA
65 ACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
* * * *
1424334 CCAACAACAACTCAGGATCCAACAACTACACAAGCACCAACAACAACTCAGGCTCCAACAACCAC
1 CCAACAACAACTCAGGCTCCAACAAC-AAACAAGCACCAACAACAACTAACGCTCCAACAACCAC
*
1424399 ACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGTA
65 ACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
*
1424442 CCAACAACAACTCAGGCTCCAACAACTACAA-AAGCACCAACAACAACTCAAC-TTCCAACAACC
1 CCAACAACAACTCAGGCTCCAACAAC-A-AACAAGCACCAACAACAACT-AACGCTCCAACAACC
** *
1424505 ACACAAGCAAAAACAACAACTCAGGCTCCAACAACCACACACGCA
63 ACACAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
1424550 CCAACAACAACTCA
1 CCAACAACAACTCA
1424564 ACCTCCATCA
Statistics
Matches: 492, Mismatches: 52, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
107 8 0.02
108 476 0.97
109 8 0.02
ACGTcount: A:0.45, C:0.39, G:0.08, T:0.09
Consensus pattern (107 bp):
CCAACAACAACTCAGGCTCCAACAACAAACAAGCACCAACAACAACTAACGCTCCAACAACCACA
CAAGCACCAACAACAACTCAGGCTCCAACAACCACACAAGCA
Found at i:1424593 original size:36 final size:36
Alignment explanation
Indices: 1423978--1424563 Score: 854
Period size: 36 Copynumber: 16.3 Consensus size: 36
1423968 GAAGCCCTAC
** * * *
1423978 CAACAACTCAACCTTCAACAACCACACAAGCTCCTA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* * * * * *
1424014 TAACCACACAAGCTCCAACAA-CAAATCAA-CTTCCAA
1 CAACAACTCAGGCTCCAACAACCACA-CAAGC-ACCAA
* *
1424050 CAACAACTAACGCTCCAACAACCACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* *
1424086 CAACAACTCAGGCTCCAACAACTACACAAGTACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1424122 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* *
1424158 CAACAACTCAGGCTCCAACAACTACACAAGTACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
*
1424194 CAACAACTCAGGCTCCAACAACCACACAAGCACAAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1424230 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* *
1424266 CAACAACTCAGGCTCAAACAACTACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
*
1424302 CAACAACTCAGGCTCCAACAACCAAACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* *
1424338 CAACAACTCAGGATCCAACAACTACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1424374 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
*
1424410 CAACAACTCAGGCTCCAACAACCACACAAGTACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* *
1424446 CAACAACTCAGGCTCCAACAACTACAAAAGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
* **
1424482 CAACAACTCA-ACTTCCAACAACCACACAAGCAAAAA
1 CAACAACTCAGGC-TCCAACAACCACACAAGCACCAA
*
1424518 CAACAACTCAGGCTCCAACAACCACACACGCACCAA
1 CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
1424554 CAACAACTCA
1 CAACAACTCA
1424564 ACCTCCATCA
Statistics
Matches: 495, Mismatches: 49, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
35 5 0.01
36 485 0.98
37 5 0.01
ACGTcount: A:0.46, C:0.39, G:0.07, T:0.08
Consensus pattern (36 bp):
CAACAACTCAGGCTCCAACAACCACACAAGCACCAA
Found at i:1426690 original size:15 final size:15
Alignment explanation
Indices: 1426670--1426711 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
1426660 CTATATATAT
1426670 TGAATGTTACGTTAC
1 TGAATGTTACGTTAC
1426685 TGAATGTTACGTTAC
1 TGAATGTTACGTTAC
1426700 TGAATGTTACGT
1 TGAATGTTACGT
1426712 CTGTGCTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (15 bp):
TGAATGTTACGTTAC
Found at i:1431585 original size:2 final size:2
Alignment explanation
Indices: 1431578--1431628 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1431568 TCTGCTGAGA
1431578 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1431620 CT CT CT CT C
1 CT CT CT CT C
1431629 GTGTAATGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1432620 original size:21 final size:21
Alignment explanation
Indices: 1432596--1432635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1432586 TAAATGAACA
*
1432596 AACATTATGTCAAGATGCAGG
1 AACATTATGTCAACATGCAGG
*
1432617 AACATTATGTTAACATGCA
1 AACATTATGTCAACATGCA
1432636 AGATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
AACATTATGTCAACATGCAGG
Found at i:1432789 original size:21 final size:21
Alignment explanation
Indices: 1432759--1432798 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1432749 AATAATGACA
*
1432759 ACATGTGACTTATTTATGTTG
1 ACATGCGACTTATTTATGTTG
1432780 ACATGCGACTTATTTATGT
1 ACATGCGACTTATTTATGT
1432799 GAACTTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (21 bp):
ACATGCGACTTATTTATGTTG
Found at i:1433451 original size:21 final size:21
Alignment explanation
Indices: 1433429--1433512 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
1433419 CATAACTAAG
* * *
1433429 TTGCATGTCTACTTAGATAAG
1 TTGCATGTCGACATAGATAAA
1433450 TTGCATGTCGACATAGATAAA
1 TTGCATGTCGACATAGATAAA
1433471 TTGCATGTCGACATAGATAAA
1 TTGCATGTCGACATAGATAAA
1433492 TTGCATGTCGACATAGATAAA
1 TTGCATGTCGACATAGATAAA
1433513 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (21 bp):
TTGCATGTCGACATAGATAAA
Found at i:1434421 original size:2 final size:2
Alignment explanation
Indices: 1434414--1434446 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1434404 NNNNNNNNNN
1434414 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1434447 GTGTAATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1435438 original size:21 final size:21
Alignment explanation
Indices: 1435414--1435453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1435404 TAAATGAACA
*
1435414 AACATTATGTCAAGATGCAGG
1 AACATTATGTCAACATGCAGG
*
1435435 AACATTATGTTAACATGCA
1 AACATTATGTCAACATGCA
1435454 AGATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
AACATTATGTCAACATGCAGG
Found at i:1435607 original size:21 final size:21
Alignment explanation
Indices: 1435577--1435616 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1435567 AATAATGACA
*
1435577 ACATGTGACTTATTTATGTTG
1 ACATGCGACTTATTTATGTTG
1435598 ACATGCGACTTATTTATGT
1 ACATGCGACTTATTTATGT
1435617 GAACTTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (21 bp):
ACATGCGACTTATTTATGTTG
Found at i:1436516 original size:21 final size:21
Alignment explanation
Indices: 1436243--1436514 Score: 287
Period size: 21 Copynumber: 12.9 Consensus size: 21
1436233 TTGACATAAC
* *
1436243 TAAGTTGCATGTCTACTTAGA
1 TAAGTTGCATGTCGACATAGA
1436264 TAAGTTGCATGTCGACATAGA
1 TAAGTTGCATGTCGACATAGA
*
1436285 TAAATTGCATGTCGACATAGA
1 TAAGTTGCATGTCGACATAGA
*
1436306 TAAATTGCATGTCGACATAGA
1 TAAGTTGCATGTCGACATAGA
** * * *
1436327 TAAACTGCATATCAACAAAGA
1 TAAGTTGCATGTCGACATAGA
1436348 TAAGTTGCATGTCGACATAGA
1 TAAGTTGCATGTCGACATAGA
1436369 TAAGTTGCATGTCGACATAGA
1 TAAGTTGCATGTCGACATAGA
* *
1436390 TAAGTTGCATGTTGACGTAGA
1 TAAGTTGCATGTCGACATAGA
*
1436411 TAAGTTGCATGTCGACATAAA
1 TAAGTTGCATGTCGACATAGA
* * * * *
1436432 GAAGCTGCATTTTGACATAAAA
1 TAAGTTGCATGTCGACAT-AGA
* * *
1436454 TAAGTAGCATGTCAACAT-GT
1 TAAGTTGCATGTCGACATAGA
* ** *
1436474 TTA-TCTCGCATGTTAACATAAA
1 TAAGT-T-GCATGTCGACATAGA
1436496 TAAGTTGCATGTCGACATA
1 TAAGTTGCATGTCGACATA
1436515 AAAAGGTAGC
Statistics
Matches: 209, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.00
20 2 0.01
21 187 0.89
22 18 0.09
23 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (21 bp):
TAAGTTGCATGTCGACATAGA
Found at i:1436673 original size:42 final size:42
Alignment explanation
Indices: 1436594--1436673 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1436584 TATGCAACTT
* * **
1436594 TCTTGCATGTCAACATAGTTATGTTGGATGTTGACATAATAA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCAACATAATAA
*
1436636 TCTTGCATGTCAACATATTTATCTTGCATGTCAACATA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCAACATA
1436674 TTTGATAGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATCTTGCATGTCAACATAATAA
Found at i:1436674 original size:21 final size:21
Alignment explanation
Indices: 1436594--1436676 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
1436584 TATGCAACTT
*
1436594 TCTTGCATGTCAACATAGTTA
1 TCTTGCATGTCAACATATTTA
* * ** * *
1436615 TGTTGGATGTTGACATAATAA
1 TCTTGCATGTCAACATATTTA
1436636 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATATTTA
1436657 TCTTGCATGTCAACATATTT
1 TCTTGCATGTCAACATATTT
1436677 GATAGACAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TCTTGCATGTCAACATATTTA
Found at i:1440305 original size:32 final size:32
Alignment explanation
Indices: 1440269--1440329 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1440259 ATATTCCTGG
* * *
1440269 AATGATAGTACATATACTTTAACCTATGCTGC
1 AATGATAGCACATAAACTTTAACATATGCTGC
* *
1440301 AATGATGGCATATAAACTTTAACATATGC
1 AATGATAGCACATAAACTTTAACATATGC
1440330 CTGGAACCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
AATGATAGCACATAAACTTTAACATATGCTGC
Found at i:1441777 original size:32 final size:30
Alignment explanation
Indices: 1441741--1441819 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1441731 ATTTATTGGC
*
1441741 TGACGGTGTATTATAATGATGTAAGTATGTAG
1 TGACGTTGTATTATAATGAT-T-AGTATGTAG
* * *
1441773 TGACGTTTTATTGTAATGATTAGTATGTTG
1 TGACGTTGTATTATAATGATTAGTATGTAG
* *
1441803 TGAAGTTGCATTATAAT
1 TGACGTTGTATTATAAT
1441820 CATCGGTTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 21 0.54
31 1 0.03
32 17 0.44
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (30 bp):
TGACGTTGTATTATAATGATTAGTATGTAG
Found at i:1442439 original size:32 final size:32
Alignment explanation
Indices: 1442403--1442498 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 32
1442393 GTAGTGGTGC
*
1442403 TTTGCTGTTTTAGTAACAAATTGAAGTGGTAA
1 TTTGCTGTTTTAGTAACAAATGGAAGTGGTAA
** * *
1442435 TTTGCTGTCATAGGTAAAAAATGGGAGT-GTAA
1 TTTGCTGTTTTA-GTAACAAATGGAAGTGGTAA
* *
1442467 TTTGCTGTTATAAGTAACAAGTGGAAGTGGTA
1 TTTGCTGTT-TTAGTAACAAATGGAAGTGGTA
1442499 CTCTGTTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
32 34 0.68
33 16 0.32
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (32 bp):
TTTGCTGTTTTAGTAACAAATGGAAGTGGTAA
Found at i:1442634 original size:33 final size:33
Alignment explanation
Indices: 1442565--1442638 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1442555 TGGTAGAGAC
* * *
1442565 AGTGGGAGTGGTACTTTGCTTGTGAAAGTAACA
1 AGTGGTAGTGGTACTTTGCTTGCGAAAGTAAAA
**
1442598 AGTGGTAGTGGTACTTTGC-TGCGGTAGATAAAA
1 AGTGGTAGTGGTACTTTGCTTGCGAAAG-TAAAA
1442631 AGTGGTAG
1 AGTGGTAG
1442639 CATTGTAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.30
Consensus pattern (33 bp):
AGTGGTAGTGGTACTTTGCTTGCGAAAGTAAAA
Found at i:1442938 original size:174 final size:174
Alignment explanation
Indices: 1442738--1443078 Score: 481
Period size: 174 Copynumber: 2.0 Consensus size: 174
1442728 AGGTACCTGG
* * * *
1442738 TAAGTAACTAAAGGGAGTAGTACTTTGCTTTGGTAATTAACAAGTTGTATCGATACTTTGTTGTG
1 TAAGTAACAAAAGGGAGTAGTACTTTGCTTTGGTAAGTAACAAGTTGTATCGATACTTTGCTATG
* * * *
1442803 TTAAGT-AACAATTGGGAGTGGTACT-TTTCTGTTGTAAGAAACAAGTGGGAGTGGTACTTTAAA
66 GTAA-TAAACAATTGAGAGTGGTACTGTGT-TGTCGTAAGAAACAAGTGGGAGTGGTACTTTAAA
* *
1442866 CTCAATA-TTGAACAAAACTTACAATGTACCTAGTACTTTGCAGTGA
129 CTCAATACTT-AAAAAAACTTACAAAGTACCTAGTACTTTGCAGTGA
* * *
1442912 TAAGTAACAAAAGGGAGTAGTACTTTGCTTTGGTAAGTAACAAGTTGTTTTGGTACTTTGCTATG
1 TAAGTAACAAAAGGGAGTAGTACTTTGCTTTGGTAAGTAACAAGTTGTATCGATACTTTGCTATG
** *
1442977 GTAATAAACAATTGAGAGTGGTACTGTGTTGTCGTAAGTTACAGGTGGGAGTGGTACTTTAAACT
66 GTAATAAACAATTGAGAGTGGTACTGTGTTGTCGTAAGAAACAAGTGGGAGTGGTACTTTAAACT
*
1443042 CAATACTTAAAAAAACTTACAAAGTACCTGGTACTTT
131 CAATACTTAAAAAAACTTACAAAGTACCTAGTACTTT
1443079 AATTTCTCAC
Statistics
Matches: 147, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
173 1 0.01
174 142 0.97
175 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (174 bp):
TAAGTAACAAAAGGGAGTAGTACTTTGCTTTGGTAAGTAACAAGTTGTATCGATACTTTGCTATG
GTAATAAACAATTGAGAGTGGTACTGTGTTGTCGTAAGAAACAAGTGGGAGTGGTACTTTAAACT
CAATACTTAAAAAAACTTACAAAGTACCTAGTACTTTGCAGTGA
Found at i:1444131 original size:51 final size:51
Alignment explanation
Indices: 1444049--1448200 Score: 5340
Period size: 51 Copynumber: 81.7 Consensus size: 51
1444039 TTTGTCTGTC
* *
1444049 TCTGTCTGAATGTT-TCGTCAATGTCTGTACCTGACTCTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * ** *
1444099 CCTGTCTGAAAGTTGTAGTCAATACCTTTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* ** * **
1444150 TCTGTCTGAATGTTGTAGTCAATATCAATACCTGACTGTTAAAAGCGAAG-G
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCG-AGTG
* * *
1444201 TCTGTCTGAATGTTGTTAGTCATTGTCTGTACCTGACTGTGAGTAGCAACTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444253 TCTGTCTTAATGTTGTTAGTCAATGTTTGTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444305 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1444356 CCTTTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCAACTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1444407 TATGTTTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444458 GCTGTCTGAATGTTGTAGTCAATGTCTGTCCCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
** *
1444509 TCTGTGGGAATGTTGTAGTCAATGTCTGTCCCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
** *
1444560 TCTGTGGGAATGTTGTAGTCAATGTCTGTCCCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
** * * *
1444611 TCTGTGGGAATGTTGTAGTCAACGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * **
1444662 TCTGTCTGAATGTTGTGGTCAATATCTATACCTGACTGTTAAAAGCGAAG-G
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCG-AGTG
* * *
1444713 TCTGTCTGAATGTTGTTAGTCAATGTTTATACCTGACTGTGAGTAGCGACTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444765 TCTGTCTGAATGTTGTTAGTCAATGTTTGTACCTGACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1444817 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444868 CCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1444919 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1444970 -CTTGTCTGAATGTTGTTAGTCAATGTCTATACCTGACTGTGAGTAGCGACTG
1 TC-TGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445022 TCTGTCTGAATGTTGTTAGTCAATGTTTGTACCTAACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445074 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * *
1445125 TCTGTCTGAATGTTGTAGTCAATGCCTGTACCTGACTCTGGGTATCGAATG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1445176 TCTGTCTGAATGTTG-ATGTCAATGTCTGTGCCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTA-GTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * * * *
1445227 TCTGTTTGAATGTTTTAGTCAATGCCT-AAACAGACTGTTAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1445277 --TGTCTTAATTTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCAACTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445326 TATGTTTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1445377 CCTTTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCAACTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1445428 TATGTTTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1445479 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * **
1445530 TCTGTCTGAATGTTGTGGTCAATATCTATACCTGACTGTTAAAAGCGAAG-G
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCG-AGTG
* * *
1445581 TCTGTCTGAATGTTGTTAGTCAATGTTTATACCTGACTGTGAGTAGCGACTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1445633 TCTGTCTGAATGTTGTTAGTCAATGTTTGTACCTGACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1445685 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445736 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAACGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1445787 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445838 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1445889 -CTTGTCTGAATGTTGTTAGTCAATGTCTATACCTGACTGTGAGTAGCGACTG
1 TC-TGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445941 TCTGTCTGAATGTTGTTAGTCAATGTTTGTACCTAACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1445993 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * *
1446044 TCTGTCTGAATGTTGTAGTCAATGCCTGTACCTGACTCTGGGTATCGAATG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1446095 TCTGTCTGAATGTTG-ATGTCAATGTCTGTGCCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTA-GTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * * * *
1446146 TCTGTTTGAATGTTTTAGTCAATGCCT-AAACAGACTGTTAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1446196 --TGTCTTAATTTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * * *
1446245 TCTGTCTGAATGTTGGAGTCAATATCTATACCTGACTGTTAGAAGCAAAG-G
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGC-GAGTG
* * * * *
1446296 TCTGTTTGAATGTTGTTTGTC-A--T-TGT--CTGACTGTGAGTTGTGACTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1446342 TCTGTCTGAATGTTATTA-TCCATGTCTGTACCTGACTGTGAGTAGCGAGGG
1 TCTGTCTGAATGTT-GTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1446393 TCTGTCTGAATGTTATAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1446444 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1446495 CCTGTCTGAATGTTGTTA-TCAATGTCTGTATCTGACTGTGAGTAGCAACTG
1 TCTGTCTGAATGTTG-TAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
1446546 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * ** *
1446597 CCTGTCTGAATGTTATAGTCAATGTATGTACCTCACTGCAAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * *
1446648 TCTGTGTGAATGTTGTAGTCAATGCCTATACGTGACTGTGAGTAGC-A-AG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1446697 TC--CCAGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1446746 CCTGTGTGAATGTTGTAGTCAATGTCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1446797 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1446848 TCTGTTTGAATGTTATAGTCAATGTCTGTACCTGACTGCGAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* **
1446899 TCTGTTTGAATGTTGTAGTCAATGTCTGTACCTGACTGCCAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1446950 TCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGA-TCAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGT-AGCGAGTG
* *
1447001 TCTGTTTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGAAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
** * * * *
1447052 TCTGTCTGAATGTTGTTTTCAGTGTCTGTACCTCACTGTAAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1447103 TCTGTGTGAATGTTGTAGTCAATGTCTGTACCTGACTG-GAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1447153 CCTGTCTGAATGTTATAGTCAATGTCTGTACCTGATTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * **
1447204 CCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGAGTAGCGAAAG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1447255 CCTGTCTGAATGTTGTAGTCAATGTCTATACCTGACTGTGAGTAGTGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1447306 CCTGTCTGAATGTTGTAGTCAATG-CTCATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCT-GTACCTGACTGTGAGTAGCGAGTG
* * ** *
1447357 TCTGTTTGAATGTTATAGTCAATGTCTGTACCTGACTGCAAGTAGCAAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* ** *
1447408 TCTGTCTGAATGTTGTAATCAATGTC--TAAATAGACTGTTAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCT-GACTGTGAGTAGCGAGTG
* * *
1447458 TCTGTCTGAATGTTGTAGTCAATGCCTATACCTGACTGTGATTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1447509 TCTGTTTGAATATTATAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1447560 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*** * * *
1447611 TCTGTCTGAATGTTGTAGTCAAT-TCCCAAACAGACTGCGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * ** *
1447661 CCTGTCTGAATGTTGTAGTTAATGTCTGTACAGGACGGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1447712 CCTGTCTGAATGTTGTAGTTAATGTCTGTA-CTGGACGGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCT-GACTGTGAGTAGCGAGTG
* *
1447763 CCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGATTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * *
1447814 CCTGTCTGAATGTTGTAGTCATTGCCTATACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1447865 TC--TCTGAATGTTGTTGTCAATGTCTGTACCTGGCTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * * * *
1447914 TCTGTCTTAATTTTGTTGTCGATGTCTGTACCTGGCTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1447965 TCTGTCTTAATTTTGTTGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1448016 TCTGTCTGATTGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* * *
1448067 TCTGTCCT-AATTTTGTTGTCAATGTCTGTACCTGGCTGTGAGTAGCGAGTG
1 TCTGT-CTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
* *
1448118 TCTGTCTGATTGTTGTAGTCAATGTCTGTACCTGACTGCGAGTAGCGAGTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
*
1448169 TC--TCTGAATGTTGTTGTCAATGTCTGTACCTG
1 TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTG
1448201 GCTGACAACT
Statistics
Matches: 3601, Mismatches: 443, Indels: 117
0.87 0.11 0.03
Matches are distributed among these distances:
45 3 0.00
46 27 0.01
47 36 0.01
48 44 0.01
49 119 0.03
50 188 0.05
51 2707 0.75
52 475 0.13
53 2 0.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.35
Consensus pattern (51 bp):
TCTGTCTGAATGTTGTAGTCAATGTCTGTACCTGACTGTGAGTAGCGAGTG
Found at i:1446448 original size:27 final size:26
Alignment explanation
Indices: 1446418--1446499 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
1446408 TAGTCAATGT
1446418 CTGTACCTGACTGCGAGTAGCGAGTGC
1 CTGTACCTGACTG-GAGTAGCGAGTGC
* ** *
1446445 CTGT--CTGAATGTTGTAGTC-AATGC
1 CTGTACCTGACTGGAGTAG-CGAGTGC
*
1446469 CTATACCTGACTGTGAGTAGCGAGTGC
1 CTGTACCTGACTG-GAGTAGCGAGTGC
1446496 CTGT
1 CTGT
1446500 CTGAATGTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
24 11 0.28
25 7 0.17
26 7 0.17
27 15 0.38
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (26 bp):
CTGTACCTGACTGGAGTAGCGAGTGC
Found at i:1446548 original size:27 final size:26
Alignment explanation
Indices: 1446363--1447615 Score: 164
Period size: 24 Copynumber: 49.3 Consensus size: 26
1446353 GTTATTATCC
*
1446363 ATGTCTGTACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
** * *
1446390 GGGTCTG--TCTGAATGTTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1446414 ATGTCTGTACCTGACTGCGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1446441 GTGCCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * *
1446465 ATGCCTATACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * * *
1446492 GTGCCTG--TCTGAATGTTG-TTATCA
1 ATGTCTGTATCTGACTG-TGAGTAGCA
1446516 ATGTCTGTATCTGACTGTGAGTAGCA
1 ATGTCTGTATCTGACTGTGAGTAGCA
* *
1446542 ACTGTCTG--TCTGAATGT-TGTAGTCA
1 A-TGTCTGTATCTGACTGTGAGTAG-CA
*
1446567 ATGTCTGTACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1446594 GTGCCTG--TCTGAATGTTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * * **
1446618 ATGTATGTACCTCACTGCAAGTAGCA
1 ATGTCTGTATCTGACTGTGAGTAGCA
* * *
1446644 AGTGTCTG--TGTGAATGT-TGTAGTCA
1 A-TGTCTGTATCTGACTGTGAGTAG-CA
* *
1446669 ATGCCTATA-CGTGACTGTGAGTAGCA
1 ATGTCTGTATC-TGACTGTGAGTAGCA
* * * *
1446695 A-GTC----CCAGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
*
1446716 ATGTCTGTACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * * *
1446743 GTGCCTG--TGTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1446767 ATGTCTATACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1446794 GTGCCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * *
1446818 ATGCCTATACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * *
1446845 GTGTCTGT-T-TGAATGTTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1446869 ATGTCTGTACCTGACTGCGAGTAGCA
1 ATGTCTGTATCTGACTGTGAGTAGCA
* *
1446895 AGTGTCTGT-T-TGAATGT-TGTAGTCA
1 A-TGTCTGTATCTGACTGTGAGTAG-CA
* **
1446920 ATGTCTGTACCTGACTGCCAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * *
1446947 GTGTCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * *
1446971 ATGCCTATACCTGACTGTGA-TCAGCGA
1 ATGTCTGTATCTGACTGTGAGT-AGC-A
* * *
1446998 GTGTCTGT-T-TGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1447022 ATGTCTGTACCTGACTGTGAGAAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * **
1447049 GTGTCTG--TCTGAATGTTG-TTTTCA
1 ATGTCTGTATCTGACTG-TGAGTAGCA
* * * *
1447073 GTGTCTGTACCTCACTGTAAGTAGCA
1 ATGTCTGTATCTGACTGTGAGTAGCA
* * *
1447099 AGTGTCTG--TGTGAATGT-TGTAGTCA
1 A-TGTCTGTATCTGACTGTGAGTAG-CA
*
1447124 ATGTCTGTACCTGACTG-GAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1447150 GTGCCTG--TCTGAATGTTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1447174 ATGTCTGTACCTGATTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1447201 GTGCCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * *
1447225 ATGCCTATACCTGACTGTGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1447252 AAGCCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * *
1447276 ATGTCTATACCTGACTGTGAGTAGTGA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * * *
1447303 GTGCCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1447327 ATG-CTCATACCTGACTGTGAGTAGCGA
1 ATGTCT-GTATCTGACTGTGAGTAGC-A
* * *
1447354 GTGTCTGT-T-TGAATGTTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* **
1447378 ATGTCTGTACCTGACTGCAAGTAGCA
1 ATGTCTGTATCTGACTGTGAGTAGCA
* * *
1447404 AGTGTCTG--TCTGAATGT-TGTAATCA
1 A-TGTCTGTATCTGACTGTGAGT-AGCA
** * *
1447429 ATGTCTAAAT-AGACTGTTAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * *
1447455 GTGTCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* * * *
1447479 ATGCCTATACCTGACTGTGATTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * * *
1447506 GTGTCTGT-T-TGAATATTA-TAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1447530 ATGTCTGTACCTGACTGCGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
* * *
1447557 GTGTCTG--TCTGAATGT-TGTAGTCA
1 ATGTCTGTATCTGACTGTGAGTAG-CA
* *
1447581 ATGTCTGTACCTGACTGCGAGTAGCGA
1 ATGTCTGTATCTGACTGTGAGTAGC-A
*
1447608 GTGTCTGT
1 ATGTCTGT
1447616 CTGAATGTTG
Statistics
Matches: 839, Mismatches: 259, Indels: 256
0.62 0.19 0.19
Matches are distributed among these distances:
20 4 0.00
21 8 0.01
22 4 0.00
23 2 0.00
24 221 0.26
25 189 0.23
26 206 0.25
27 203 0.24
28 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (26 bp):
ATGTCTGTATCTGACTGTGAGTAGCA
Found at i:1447716 original size:27 final size:26
Alignment explanation
Indices: 1447686--1447767 Score: 60
Period size: 27 Copynumber: 3.2 Consensus size: 26
1447676 TAGTTAATGT
1447686 CTGTACAGGACGGTGAGTAGCGAGTGC
1 CTGTAC-GGACGGTGAGTAGCGAGTGC
* ** * ** * *
1447713 CTGT-CTGAATGT-TGTAGTTAATGT
1 CTGTACGGACGGTGAGTAGCGAGTGC
1447737 CTGTACTGGACGGTGAGTAGCGAGTGC
1 CTGTAC-GGACGGTGAGTAGCGAGTGC
1447764 CTGT
1 CTGT
1447768 CTGAATGTTG
Statistics
Matches: 36, Mismatches: 16, Indels: 6
0.62 0.28 0.10
Matches are distributed among these distances:
24 11 0.31
25 5 0.14
26 5 0.14
27 15 0.42
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (26 bp):
CTGTACGGACGGTGAGTAGCGAGTGC
Found at i:1449030 original size:33 final size:33
Alignment explanation
Indices: 1448980--1449046 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1448970 AGTTGGACAC
*
1448980 TAGTGTAGCGATCTTCGTGAGCGGATCAAAGGA
1 TAGTATAGCGATCTTCGTGAGCGGATCAAAGGA
*
1449013 TAGTATAGCGATTTTCGTGAGCGGATCAAAGGA
1 TAGTATAGCGATCTTCGTGAGCGGATCAAAGGA
1449046 T
1 T
1449047 CTGATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.27
Consensus pattern (33 bp):
TAGTATAGCGATCTTCGTGAGCGGATCAAAGGA
Found at i:1450821 original size:13 final size:13
Alignment explanation
Indices: 1450790--1450826 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1450780 AAAGACCCTC
*
1450790 TTTTTTCTTCTTTT
1 TTTTTTGTT-TTTT
1450804 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
1450817 TTTTTTGTTT
1 TTTTTTGTTT
1450827 AAGTTTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:1463410 original size:12 final size:12
Alignment explanation
Indices: 1463393--1463429 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1463383 CGAGCGATCT
1463393 CGGACGGACAGA
1 CGGACGGACAGA
1463405 CGGACGGA-AGGA
1 CGGACGGACA-GA
1463417 CGGACGGACAGA
1 CGGACGGACAGA
1463429 C
1 C
1463430 TGATAGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.32, C:0.24, G:0.43, T:0.00
Consensus pattern (12 bp):
CGGACGGACAGA
Found at i:1471555 original size:46 final size:46
Alignment explanation
Indices: 1471449--1471556 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
1471439 TAATCGAATC
* * *
1471449 CCCTGACCGGTATATAAAAGACGTAACATTTATCATTTATAAATAA
1 CCCTGACCGGTAGATAAAAGACGGAACATTTATCATTTAAAAATAA
** * * * *
1471495 CCCTGACCTATAGATAAAGGACGGGACTTTTATCATTTAAAAATAT
1 CCCTGACCGGTAGATAAAAGACGGAACATTTATCATTTAAAAATAA
*
1471541 CCCTCACCGGTAGATA
1 CCCTGACCGGTAGATA
1471557 GGGGACGGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (46 bp):
CCCTGACCGGTAGATAAAAGACGGAACATTTATCATTTAAAAATAA
Found at i:1472972 original size:95 final size:96
Alignment explanation
Indices: 1472824--1473000 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 96
1472814 TTTCTTATAA
* *
1472824 TGTACAGTGTACGCACAATATACAAATTGATGAAGATATGACACAAAAACCTTGTATCCTGCATT
1 TGTACAATGTACGCAAAATATACAAATTGATGAAGATATGACACAAAAACCTTGTATCCTGCATT
*
1472889 TGCTAGTTTATAAGCTTCTTATAATATACAG
66 GGCTAGTTTATAAGCTTCTTATAATATACAG
* * * * *
1472920 TGTACAATGTACGTAAAATAT-CAAGTTGATGAGGCTATGACACACAAACCTTGTATCCTGCATT
1 TGTACAATGTACGCAAAATATACAAATTGATGAAGATATGACACAAAAACCTTGTATCCTGCATT
*
1472984 GGCTAGTTTATAGGCTT
66 GGCTAGTTTATAAGCTT
1473001 TGTCCCCGTG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 54 0.75
96 18 0.25
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (96 bp):
TGTACAATGTACGCAAAATATACAAATTGATGAAGATATGACACAAAAACCTTGTATCCTGCATT
GGCTAGTTTATAAGCTTCTTATAATATACAG
Found at i:1484788 original size:21 final size:21
Alignment explanation
Indices: 1484762--1484852 Score: 146
Period size: 21 Copynumber: 4.3 Consensus size: 21
1484752 GTGCGAGAAA
1484762 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
1484783 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
* * **
1484804 CGTTTCGTGTGAATCGTGAAG
1 CGTTTCGTGTAAACCGTTTAG
1484825 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
1484846 CGTTTCG
1 CGTTTCG
1484853 GGCAAAGCGT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTTAG
Found at i:1484809 original size:42 final size:42
Alignment explanation
Indices: 1484762--1484873 Score: 152
Period size: 42 Copynumber: 2.7 Consensus size: 42
1484752 GTGCGAGAAA
**
1484762 CGTTTCGTGTAAACCGTTTAGCGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTGAAGCGTTTCGTGTAAACCGTTTAG
* *
1484804 CGTTTCGTGTGAATCGTGAAGCGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTGAAGCGTTTCGTGTAAACCGTTTAG
* * * *
1484846 CGTTTCGGGCAAAGCGTGCAGCGTTTCG
1 CGTTTCGTGTAAACCGTGAAGCGTTTCG
1484874 GGCAAAGCGT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.34
Consensus pattern (42 bp):
CGTTTCGTGTAAACCGTGAAGCGTTTCGTGTAAACCGTTTAG
Found at i:1484897 original size:23 final size:21
Alignment explanation
Indices: 1484818--1484907 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
1484808 TCGTGTGAAT
* * *
1484818 CGTGAAGCGTTTCGTGTAAAC
1 CGTGAAGCGTTTCGGGCAAAG
**
1484839 CGTTTAGCGTTTCGGGCAAAG
1 CGTGAAGCGTTTCGGGCAAAG
*
1484860 CGTGCAGCGTTTCGGGCAAAG
1 CGTGAAGCGTTTCGGGCAAAG
*
1484881 CGTGTAAATCGTTTCGGGCAAAG
1 CGTG--AAGCGTTTCGGGCAAAG
1484904 CGTG
1 CGTG
1484908 CGAGAACCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 39 0.67
23 19 0.33
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (21 bp):
CGTGAAGCGTTTCGGGCAAAG
Found at i:1487384 original size:21 final size:21
Alignment explanation
Indices: 1487360--1487466 Score: 133
Period size: 21 Copynumber: 5.1 Consensus size: 21
1487350 GTGCGAGAAT
1487360 CGTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
1487381 CGTTTCGTGTAAATCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
* * * *
1487402 CGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTCAG
*
1487423 CGTTTCGTGTAAATCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
1487444 CGTTTCGTGTGAACCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
1487465 CG
1 CG
1487467 AGCGTGTAGC
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.34
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTCAG
Found at i:1487478 original size:11 final size:11
Alignment explanation
Indices: 1487462--1487506 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
1487452 GTGAACCGTT
1487462 TAGCGAGCGTG
1 TAGCGAGCGTG
1487473 TAGCGAGCGTG
1 TAGCGAGCGTG
1487484 TAGCGAGCGTG
1 TAGCGAGCGTG
*
1487495 CAGCGAGCGTG
1 TAGCGAGCGTG
1487506 T
1 T
1487507 GGTGTAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (11 bp):
TAGCGAGCGTG
Found at i:1507924 original size:21 final size:21
Alignment explanation
Indices: 1507900--1507950 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
1507890 GTGTTAAATA
1507900 GTTCGTGTAACGTG-GGTGATC
1 GTTCGTGTAACGTGCGG-GATC
1507921 GTTCGTGTAACGTGCGGGATC
1 GTTCGTGTAACGTGCGGGATC
*
1507942 GTGCGTGTA
1 GTTCGTGTA
1507951 TCAGGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.14, C:0.16, G:0.39, T:0.31
Consensus pattern (21 bp):
GTTCGTGTAACGTGCGGGATC
Found at i:1508974 original size:11 final size:11
Alignment explanation
Indices: 1508954--1509009 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
1508944 TAAGTTAGTG
*
1508954 ATCGTCCGTGT
1 ATCGTGCGTGT
1508965 ATCGTGCGTG-
1 ATCGTGCGTGT
*
1508975 ATCGTTCGTGT
1 ATCGTGCGTGT
1508986 ATCGTGCGTG-
1 ATCGTGCGTGT
*
1508996 ATCGTTCGTGT
1 ATCGTGCGTGT
1509007 ATC
1 ATC
1509010 AGAATCGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (11 bp):
ATCGTGCGTGT
Found at i:1508977 original size:21 final size:21
Alignment explanation
Indices: 1508951--1509009 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1508941 CAGTAAGTTA
*
1508951 GTGATCGTCCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
1508972 GTGATCGTTCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
1508993 GTGATCGTTCGTGTATC
1 GTGATCGTTCGTGTATC
1509010 AGAATCGTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.10, C:0.20, G:0.32, T:0.37
Consensus pattern (21 bp):
GTGATCGTTCGTGTATCGTGC
Found at i:1508984 original size:10 final size:10
Alignment explanation
Indices: 1508951--1509005 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1508941 CAGTAAGTTA
*
1508951 GTGATCGTCC
1 GTGATCGTGC
1508961 GTGTATCGTGC
1 GTG-ATCGTGC
*
1508972 GTGATCGTTC
1 GTGATCGTGC
1508982 GTGTATCGTGC
1 GTG-ATCGTGC
*
1508993 GTGATCGTTC
1 GTGATCGTGC
1509003 GTG
1 GTG
1509006 TATCAGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.09, C:0.20, G:0.35, T:0.36
Consensus pattern (10 bp):
GTGATCGTGC
Found at i:1513920 original size:21 final size:21
Alignment explanation
Indices: 1513894--1513952 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
1513884 CAGTAAGTTA
1513894 GTGATCGTCCGTGTATCGTGC
1 GTGATCGTCCGTGTATCGTGC
1513915 GTGATCG-CTCGTGTATCGTGC
1 GTGATCGTC-CGTGTATCGTGC
* *
1513936 GTGATCGTTCTTGTATC
1 GTGATCGTCCGTGTATC
1513953 AAAATTGTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.10, C:0.22, G:0.31, T:0.37
Consensus pattern (21 bp):
GTGATCGTCCGTGTATCGTGC
Found at i:1513927 original size:10 final size:10
Alignment explanation
Indices: 1513894--1513943 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
1513884 CAGTAAGTTA
*
1513894 GTGATCGTCC
1 GTGATCGTGC
1513904 GTGTATCGTGC
1 GTG-ATCGTGC
1513915 GTGATCGCT-C
1 GTGATCG-TGC
1513925 GTGTATCGTGC
1 GTG-ATCGTGC
1513936 GTGATCGT
1 GTGATCGT
1513944 TCTTGTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.10, C:0.22, G:0.34, T:0.34
Consensus pattern (10 bp):
GTGATCGTGC
Found at i:1517876 original size:17 final size:18
Alignment explanation
Indices: 1517841--1517889 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
1517831 AAGGGGAACA
1517841 TATTTTCAAAAATATCTT
1 TATTTTCAAAAATATCTT
1517859 TATTTT-AAGAAA-ATCTT
1 TATTTTCAA-AAATATCTT
*
1517876 TATTTTCAATAATA
1 TATTTTCAAAAATA
1517890 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (18 bp):
TATTTTCAAAAATATCTT
Found at i:1521570 original size:17 final size:16
Alignment explanation
Indices: 1521528--1521570 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
1521518 TAAATTGAAT
1521528 AAATAAAATAAAATTTA
1 AAAT-AAATAAAATTTA
*
1521545 AGAAAAAATAAAATTATA
1 A-AATAAATAAAATT-TA
1521563 AAATAAAT
1 AAATAAAT
1521571 TTAATAGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAAATAAAATTTA
Found at i:1534451 original size:14 final size:14
Alignment explanation
Indices: 1534416--1534445 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1534406 TCCAAGCCGA
1534416 TCAATATTAATGGG
1 TCAATATTAATGGG
*
1534430 TCAATATTGATGGG
1 TCAATATTAATGGG
1534444 TC
1 TC
1534446 GGTATTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (14 bp):
TCAATATTAATGGG
Found at i:1535344 original size:17 final size:18
Alignment explanation
Indices: 1535322--1535365 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1535312 TATTTACGCA
1535322 AACATTTGAAA-GACCTG
1 AACATTTGAAATGACCTG
*
1535339 AACATTTTAAATGACCTG
1 AACATTTGAAATGACCTG
*
1535357 AAAATTTGA
1 AACATTTGA
1535366 GTTAACCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (18 bp):
AACATTTGAAATGACCTG
Found at i:1539311 original size:63 final size:63
Alignment explanation
Indices: 1539233--1539360 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
1539223 TATAGAGATA
*
1539233 AGTCATACAACACAATGACAAGTCAATGGTCTTGAAAAGTAATGACATGGAAGACAGAAATGC
1 AGTCATACAACACAATGACAACTCAATGGTCTTGAAAAGTAATGACATGGAAGACAGAAATGC
1539296 AGTCATACAACACAATGACAACTCAATGGTCTTGAAAAGTAATGACATGGAAGACAGAAATGC
1 AGTCATACAACACAATGACAACTCAATGGTCTTGAAAAGTAATGACATGGAAGACAGAAATGC
1539359 AG
1 AG
1539361 ATACCGGTGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (63 bp):
AGTCATACAACACAATGACAACTCAATGGTCTTGAAAAGTAATGACATGGAAGACAGAAATGC
Found at i:1539539 original size:13 final size:14
Alignment explanation
Indices: 1539515--1539543 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1539505 ACACCATGCA
1539515 AATGATTATTAATG
1 AATGATTATTAATG
1539529 AATGA-TATTAATG
1 AATGATTATTAATG
1539542 AA
1 AA
1539544 GGAGTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (14 bp):
AATGATTATTAATG
Found at i:1544946 original size:19 final size:19
Alignment explanation
Indices: 1544922--1544960 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1544912 GGATGCTCAC
*
1544922 CCCACATTTACAATTGTGA
1 CCCACATTTACAAATGTGA
1544941 CCCACATTTACAAATGTGA
1 CCCACATTTACAAATGTGA
1544960 C
1 C
1544961 ATCATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (19 bp):
CCCACATTTACAAATGTGA
Found at i:1545413 original size:2 final size:2
Alignment explanation
Indices: 1545406--1545450 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1545396 TCACATTCAA
1545406 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1545448 CT C
1 CT C
1545451 CAGCAGCGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1549985 original size:32 final size:33
Alignment explanation
Indices: 1549948--1550009 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1549938 TGATTTTTTA
*
1549948 AAATGTAATTAATTAC-TCTCAATTACTTTGAT
1 AAATGTAATTAATTACATCTCAAATACTTTGAT
*
1549980 AAATGTAATTAATTACATTTCAAATACTTT
1 AAATGTAATTAATTACATCTCAAATACTTT
1550010 AGTTTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (33 bp):
AAATGTAATTAATTACATCTCAAATACTTTGAT
Found at i:1550585 original size:11 final size:11
Alignment explanation
Indices: 1550569--1550598 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1550559 TGGAAAAAAA
1550569 GTAATTGAGAT
1 GTAATTGAGAT
1550580 GTAATTGAGAT
1 GTAATTGAGAT
1550591 GTAATTGA
1 GTAATTGA
1550599 AAATACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (11 bp):
GTAATTGAGAT
Found at i:1556074 original size:15 final size:15
Alignment explanation
Indices: 1556054--1556119 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
1556044 TAGTATTATT
1556054 TGATATTGTAATATA
1 TGATATTGTAATATA
*
1556069 TGATATTGTATTATA
1 TGATATTGTAATATA
* *
1556084 TG-TCACT-TAATCTCA
1 TGAT-ATTGTAATAT-A
1556099 TGATATTGT-ATCATA
1 TGATATTGTAAT-ATA
1556114 TGATAT
1 TGATAT
1556120 GATACAATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 5 0.12
15 32 0.80
16 3 0.08
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (15 bp):
TGATATTGTAATATA
Found at i:1556301 original size:20 final size:20
Alignment explanation
Indices: 1556253--1556305 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1556243 GTACTATGCG
1556253 ATATGATATTGTATCAAATA
1 ATATGATATTGTATCAAATA
*
1556273 ATACT-ATATTGTATCATA-A
1 ATA-TGATATTGTATCAAATA
1556292 ATCATGATATTGTA
1 AT-ATGATATTGTA
1556306 CTATGTGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (20 bp):
ATATGATATTGTATCAAATA
Found at i:1558230 original size:2 final size:2
Alignment explanation
Indices: 1558223--1558250 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1558213 AAATCAGATT
1558223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1558251 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1559335 original size:2 final size:2
Alignment explanation
Indices: 1559328--1559353 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1559318 NNNNNNNNNN
1559328 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1559354 GTGACATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1560968 original size:21 final size:21
Alignment explanation
Indices: 1560944--1561134 Score: 147
Period size: 21 Copynumber: 9.1 Consensus size: 21
1560934 AAAAAATAAA
1560944 TTCGCGAATAAACGCGAAACT
1 TTCGCGAATAAACGCGAAACT
* *
1560965 TTCGCG-ATCAAACGC-ATTATT
1 TTCGCGAAT-AAACGCGA-AACT
* * *
1560986 TTCGCAAATTAACGCGTAACT
1 TTCGCGAATAAACGCGAAACT
**
1561007 TTCGCGAATAAACGCGTTACT
1 TTCGCGAATAAACGCGAAACT
* *
1561028 TTTGCTAATAAACGCGAAACT
1 TTCGCGAATAAACGCGAAACT
* * **
1561049 GTCGCGAAAAAACGCGTTACT
1 TTCGCGAATAAACGCGAAACT
* *
1561070 TTTGCG-ATATAACGCAAAACT
1 TTCGCGAATA-AACGCGAAACT
* *
1561091 TTCGCGAATAAACGCTAAACA
1 TTCGCGAATAAACGCGAAACT
* *
1561112 TTCAG-GAACAAACGCAAAACT
1 TTC-GCGAATAAACGCGAAACT
1561133 TT
1 TT
1561135 GATATAAATA
Statistics
Matches: 131, Mismatches: 32, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 5 0.04
21 120 0.92
22 6 0.05
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCGCGAATAAACGCGAAACT
Found at i:1561091 original size:84 final size:84
Alignment explanation
Indices: 1560950--1561105 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
1560940 TAAATTCGCG
* ** **
1560950 AATAAACGCGAAACTTTCGCGATCAAACGCATTATTTTCGCAAATTAACGCGTAACTTTCGCGAA
1 AATAAACGCGAAACTGTCGCGAAAAAACGCATTATTTTCGCAAATTAACGCAAAACTTTCGCGAA
1561015 TAAACGCGTTACTTTTGCT
66 TAAACGCGTTACTTTTGCT
* *
1561034 AATAAACGCGAAACTGTCGCGAAAAAACGCGTTACTTTT-GC-GATATAACGCAAAACTTTCGCG
1 AATAAACGCGAAACTGTCGCGAAAAAACGCATTA-TTTTCGCAAAT-TAACGCAAAACTTTCGCG
1561097 AATAAACGC
64 AATAAACGC
1561106 TAAACATTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
83 2 0.03
84 57 0.90
85 4 0.06
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (84 bp):
AATAAACGCGAAACTGTCGCGAAAAAACGCATTATTTTCGCAAATTAACGCAAAACTTTCGCGAA
TAAACGCGTTACTTTTGCT
Found at i:1562047 original size:42 final size:42
Alignment explanation
Indices: 1562000--1562153 Score: 127
Period size: 42 Copynumber: 3.7 Consensus size: 42
1561990 CTTAATTCTT
* * **
1562000 GAAAGTAAAGCGTTATATCGCGAGAGGTTTGT-GTTTATTCGC
1 GAAAGTAACGCGTTATATCGCGA-AAGTTACTCGTTTATTCGC
*
1562042 GAAAGTAACGCATT-TAATCGCGAAAGTTACTCGTTTATTCGC
1 GAAAGTAACGCGTTAT-ATCGCGAAAGTTACTCGTTTATTCGC
* * ** *
1562084 GAATGTTACGCGTTATATCGCGACTGTTACGCG-TTATATCGC
1 GAAAGTAACGCGTTATATCGCGAAAGTTACTCGTTTAT-TCGC
* * *
1562126 AAAAGTTACGCGTT-TATTTGCGAAAGTT
1 GAAAGTAACGCGTTATA-TCGCGAAAGTT
1562154 TCGCGGTAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
41 12 0.13
42 78 0.86
43 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
GAAAGTAACGCGTTATATCGCGAAAGTTACTCGTTTATTCGC
Found at i:1562158 original size:21 final size:21
Alignment explanation
Indices: 1562032--1562158 Score: 132
Period size: 21 Copynumber: 6.0 Consensus size: 21
1562022 AGAGGTTTGT
*
1562032 GTTTATTCGCGAAAGTAACGC
1 GTTTATTCGCGAAAGTTACGC
* * *
1562053 ATTTAATCGCGAAAGTTACTC
1 GTTTATTCGCGAAAGTTACGC
*
1562074 GTTTATTCGCGAATGTTACGC
1 GTTTATTCGCGAAAGTTACGC
**
1562095 G-TTATATCGCGACTGTTACGC
1 GTTTAT-TCGCGAAAGTTACGC
*
1562116 G-TTATATCGCAAAAGTTACGC
1 GTTTAT-TCGCGAAAGTTACGC
* *
1562137 GTTTATTTGCGAAAGTTTCGC
1 GTTTATTCGCGAAAGTTACGC
1562158 G
1 G
1562159 GTAATTTGCT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.04
21 81 0.91
22 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
GTTTATTCGCGAAAGTTACGC
Found at i:1562165 original size:21 final size:21
Alignment explanation
Indices: 1562127--1562167 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1562117 TTATATCGCA
* *
1562127 AAAGTTACGCGTTTATTTGCG
1 AAAGTTACGCGGTAATTTGCG
*
1562148 AAAGTTTCGCGGTAATTTGC
1 AAAGTTACGCGGTAATTTGC
1562168 TAAAATAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (21 bp):
AAAGTTACGCGGTAATTTGCG
Done.