Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold323
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: 1512004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:892631 original size:21 final size:21
Alignment explanation
Indices: 892605--892680 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
892595 ACATGTTGCA
892605 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
892626 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
892646 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
892667 ATGTATCGATACAT
1 ATGTATCGATACAT
892681 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:892638 original size:41 final size:41
Alignment explanation
Indices: 892587--892680 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
892577 ACAATTCAAA
*
892587 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
892628 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
892669 GTATCGATACAT
1 GTATCGATACAT
892681 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:892737 original size:13 final size:13
Alignment explanation
Indices: 892719--892744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
892709 TACAGCAAGT
892719 ATGTATCGATACA
1 ATGTATCGATACA
892732 ATGTATCGATACA
1 ATGTATCGATACA
892745 CAAAAAATTG
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:896826 original size:15 final size:15
Alignment explanation
Indices: 896806--896836 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
896796 TAAAAATGTC
*
896806 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
896821 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
896836 C
1 C
896837 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:898929 original size:20 final size:21
Alignment explanation
Indices: 898850--898928 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
898840 AATGTCCAAA
*
898850 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
898870 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
898895 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
898915 TTGTATCGATACAT
1 ATGTATCGATACAT
898929 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:898933 original size:13 final size:13
Alignment explanation
Indices: 898915--898953 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
898905 ACATTTTTCT
898915 TTGTATCGATACA
1 TTGTATCGATACA
898928 TTGTATCGATACA
1 TTGTATCGATACA
*
898941 CTGTATCGATACA
1 TTGTATCGATACA
898954 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:900751 original size:17 final size:17
Alignment explanation
Indices: 900729--900795 Score: 83
Period size: 17 Copynumber: 4.3 Consensus size: 17
900719 GGAGAGAAAA
900729 GTGAAATAAATTTTGAT
1 GTGAAATAAATTTTGAT
900746 GTGAAATAAATTTTGA-
1 GTGAAATAAATTTTGAT
900762 -T----TAAATTTTGAT
1 GTGAAATAAATTTTGAT
900774 GTGAAATAAATTTTGAT
1 GTGAAATAAATTTTGAT
*
900791 ATGAA
1 GTGAA
900796 TTACTTGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
11 10 0.23
13 1 0.02
15 1 0.02
17 31 0.72
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (17 bp):
GTGAAATAAATTTTGAT
Found at i:900775 original size:28 final size:28
Alignment explanation
Indices: 900735--900790 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
900725 AAAAGTGAAA
900735 TAAATTTTGATGTGAAATAAATTTTGAT
1 TAAATTTTGATGTGAAATAAATTTTGAT
900763 TAAATTTTGATGTGAAATAAATTTTGAT
1 TAAATTTTGATGTGAAATAAATTTTGAT
900791 ATGAATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (28 bp):
TAAATTTTGATGTGAAATAAATTTTGAT
Found at i:901464 original size:20 final size:20
Alignment explanation
Indices: 901441--901513 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
901431 ACAATTCAAA
901441 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
901461 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
901482 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
901502 GTATCGATACAT
1 GTATCGATACAT
901514 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:901485 original size:21 final size:21
Alignment explanation
Indices: 901459--901534 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
901449 ACATGTTGCA
901459 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
901480 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
901500 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
901521 ATGTATCGATACAT
1 ATGTATCGATACAT
901535 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:901492 original size:41 final size:41
Alignment explanation
Indices: 901441--901534 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
901431 ACAATTCAAA
*
901441 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
901482 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
901523 GTATCGATACAT
1 GTATCGATACAT
901535 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:901591 original size:13 final size:13
Alignment explanation
Indices: 901573--901598 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
901563 TACAGCAAGT
901573 ATGTATCGATACA
1 ATGTATCGATACA
901586 ATGTATCGATACA
1 ATGTATCGATACA
901599 CAAAAAATTG
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:904575 original size:22 final size:22
Alignment explanation
Indices: 904550--904595 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
904540 AATTTTTTAT
904550 AAATAATTTGACAAAGGGGGAG
1 AAATAATTTGACAAAGGGGGAG
** **
904572 AAATGCTTTGATTAAGGGGGAG
1 AAATAATTTGACAAAGGGGGAG
904594 AA
1 AA
904596 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (22 bp):
AAATAATTTGACAAAGGGGGAG
Found at i:905205 original size:13 final size:13
Alignment explanation
Indices: 905187--905213 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
905177 ACATTATGCT
905187 TTGTATCGATACA
1 TTGTATCGATACA
905200 TTGTATCGATACA
1 TTGTATCGATACA
905213 T
1 T
905214 GCTCATTATA
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:905247 original size:20 final size:19
Alignment explanation
Indices: 905197--905253 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
905187 TTGTATCGAT
905197 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* * *
905216 TCATTATATCGATACATGG
1 ACATTGTATCGATACATGC
905235 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
905254 AGATTAGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:905321 original size:13 final size:13
Alignment explanation
Indices: 905303--905351 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
905293 CATGGGACAA
905303 TGTATCGATACAT
1 TGTATCGATACAT
905316 TGTATCGATACA-
1 TGTATCGATACAT
905328 TG-AT-GA-A-AT
1 TGTATCGATACAT
905337 TGTATCGATACAT
1 TGTATCGATACAT
905350 TG
1 TG
905352 CTTGTAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:905324 original size:33 final size:34
Alignment explanation
Indices: 905282--905351 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
905272 CTATCACTAT
905282 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
905315 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
905349 TTG
1 TTG
905352 CTTGTAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:910544 original size:20 final size:20
Alignment explanation
Indices: 910519--910595 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
910509 GTAAAAAGAC
910519 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
910539 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
910559 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
910579 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
910596 CTAGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:912606 original size:15 final size:16
Alignment explanation
Indices: 912581--912622 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
912571 CTTTTTCTAG
*
912581 TTCAACTATTTTC-TT
1 TTCAACAATTTTCATT
*
912596 TTCAAGAA-TTTCATT
1 TTCAACAATTTTCATT
912611 TTCAACAATTTT
1 TTCAACAATTTT
912623 TTATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (16 bp):
TTCAACAATTTTCATT
Found at i:913077 original size:15 final size:15
Alignment explanation
Indices: 913053--913084 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
913043 GTCAACTTTT
913053 TCATCATTATCATCA
1 TCATCATTATCATCA
*
913068 TCATCTTTATCATCA
1 TCATCATTATCATCA
913083 TC
1 TC
913085 TTTTGATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:914702 original size:13 final size:13
Alignment explanation
Indices: 914684--914713 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
914674 ATAATCCTTC
914684 ATGTATCGATATA
1 ATGTATCGATATA
914697 ATGTATCGATATA
1 ATGTATCGATATA
914710 ATGT
1 ATGT
914714 GAGTTTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:915423 original size:105 final size:106
Alignment explanation
Indices: 915057--915496 Score: 478
Period size: 106 Copynumber: 4.2 Consensus size: 106
915047 GATCCTAGCA
* * * *
915057 CTAAATATTTTCATAATCTTTGACTTTAGGAAAACTCCAACCCCATTACTCTGAGGATATAC-TC
1 CTAAATATTTTCATAATCTTCGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAGATACTTC
* * * * * * * *
915121 TAACGCTATTCTT--CAAAAAACTTAATTTTACTCTTTGTTC
66 -AACCCCACTCTTAAAAAAAAACTCAAATTTACTATTTATTC
* * *
915161 CTAAACATTTTCATAATCTTTGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAAATACTTC
1 CTAAATATTTTCATAATCTTCGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAGATACTTC
** * * *
915226 AATTCCACTCTTCAAAAAAAACTCAAATTTGCTTTTTATTC
66 AACCCCACTCTTAAAAAAAAACTCAAATTTACTATTTATTC
* * * *
915267 CTACATATTTTCATAATCTTCGACTTTGGGGAAACTCCAACCCTACTACTCT-AGGGGAATACTT
1 CTAAATATTTTCATAATCTTCGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAG-ATACTT
915331 CAACCCCACTCTTAAAAAAAAACTCAAATTTACTATTTATT-
65 CAACCCCACTCTTAAAAAAAAACTCAAATTTACTATTTATTC
* * * * *
915372 CGAAATATTATCATAATCTTCAACTTTGGGAAAACTCCAACCCCACGACTCTGAGGAGATACTCC
1 CTAAATATTTTCATAATCTTCGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAGATACTTC
* * * * * *
915437 AATCCCATTGTCCATAAAAAAAACTCAAATTTTCTATTTCCTT-
66 AACCCCACTCT-TA-AAAAAAAACTCAAATTTACTATTT-ATTC
915480 CTAAATATTTTCATAAT
1 CTAAATATTTTCATAAT
915497 TTTATCTTTA
Statistics
Matches: 285, Mismatches: 43, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
104 66 0.23
105 64 0.22
106 115 0.40
107 23 0.08
108 17 0.06
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (106 bp):
CTAAATATTTTCATAATCTTCGACTTTGGGAAAACTCCAACCCCACTACTCTGAGGAGATACTTC
AACCCCACTCTTAAAAAAAAACTCAAATTTACTATTTATTC
Found at i:916741 original size:23 final size:23
Alignment explanation
Indices: 916708--916761 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
916698 ACTTAATTGG
* **
916708 AAATTTTCAAAAATATGGGGGAC
1 AAATTTCCAAAAATATGGGAAAC
*
916731 AAATTTCCAAAAATATTGGAAAC
1 AAATTTCCAAAAATATGGGAAAC
916754 AAATTTCC
1 AAATTTCC
916762 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (23 bp):
AAATTTCCAAAAATATGGGAAAC
Found at i:916742 original size:22 final size:22
Alignment explanation
Indices: 916712--916767 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
916702 AATTGGAAAT
* **
916712 TTTCAAAAATATGGGGGACAAA
1 TTTCCAAAATATGGGAAACAAA
*
916734 TTTCCAAAAATATTGGAAACAAA
1 TTTCC-AAAATATGGGAAACAAA
*
916757 TTTCCTAAATA
1 TTTCCAAAATA
916768 AAATTCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
TTTCCAAAATATGGGAAACAAA
Found at i:917229 original size:13 final size:13
Alignment explanation
Indices: 917211--917254 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
917201 CGATACATGG
*
917211 TACATTGTATTGA
1 TACATTGTATCGA
917224 TACATTGTATCGA
1 TACATTGTATCGA
917237 TACATTGTATCGA
1 TACATTGTATCGA
917250 TACAT
1 TACAT
917255 AGTGTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:926020 original size:32 final size:33
Alignment explanation
Indices: 925962--926024 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
925952 TATCCAGATG
*
925962 TATCGATACATTATTCTTTGTATCGATACATTA
1 TATCGATACATTATTCATTGTATCGATACATTA
*
925995 TATCGATACA-TGTTCATTGTATCGATACAT
1 TATCGATACATTATTCATTGTATCGATACAT
926025 ACTCAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (33 bp):
TATCGATACATTATTCATTGTATCGATACATTA
Found at i:926038 original size:52 final size:53
Alignment explanation
Indices: 925942--926044 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 53
925932 CCCTAGAAAG
* * *
925942 TATCGATACATATCCAGATGTATCGATACATTATTCTTTGTATCGATACATTA
1 TATCGATACATATCCAGATGTATCGATACATTACTCATTATATCGATACATTA
* * *
925995 TATCGATACATGTTCA-TTGTATCGATACA-TACTCAATTATATCGATACAT
1 TATCGATACATATCCAGATGTATCGATACATTACTC-ATTATATCGATACAT
926045 GAAACTGGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
51 4 0.09
52 25 0.58
53 14 0.33
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (53 bp):
TATCGATACATATCCAGATGTATCGATACATTACTCATTATATCGATACATTA
Found at i:926039 original size:20 final size:19
Alignment explanation
Indices: 925990--926044 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
925980 TGTATCGATA
**
925990 CATTATATCGATACATGTT
1 CATTATATCGATACATACT
*
926009 CATTGTATCGATACATACT
1 CATTATATCGATACATACT
926028 CAATTATATCGATACAT
1 C-ATTATATCGATACAT
926045 GAAACTGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (19 bp):
CATTATATCGATACATACT
Found at i:926109 original size:13 final size:13
Alignment explanation
Indices: 926088--926125 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
926078 ATCGATACAT
926088 GATACATTGTATC
1 GATACATTGTATC
*
926101 GATATATTGTATC
1 GATACATTGTATC
*
926114 GATACATAGTAT
1 GATACATTGTAT
926126 TAAGGATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:927227 original size:6 final size:6
Alignment explanation
Indices: 927216--927245 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
927206 GAGAGCTTGG
*
927216 TTTTTA TTTTTA TATTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
927246 AGGTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:935954 original size:140 final size:139
Alignment explanation
Indices: 935714--935965 Score: 326
Period size: 140 Copynumber: 1.8 Consensus size: 139
935704 TATATATATA
* *
935714 TATATATATTATGTATTTAATTGCAATATTGGAACTCGATTTTGTTAGTACAATTGTGCCCATGA
1 TATATATATTATGTATTTAATTGCAATATTGGAACTCGATTTCGTTAGTACAATTATGCCCATGA
* *
935779 TTAACACCATATTAGAGTTTAAGGCATGGTAGTTGTTCACGAACCATCGAATCTTGATTTATTTA
66 TTAACACCATATTAGAGTTTAAGCCATGATAGTTGTTCACGAACCATCGAATCTTGATTTATTTA
935844 TTATTTATT
131 TTATTTATT
* * ** ****
935853 TATATGTATTCATGTATTTAATTGCAATATTGGAACTCTATTTCGTTAAG-ACTGTTATGTTTGT
1 TATATATATT-ATGTATTTAATTGCAATATTGGAACTCGATTTCGTT-AGTACAATTATGCCCAT
* * * * *
935917 GGTTGACACCATATTGGAGTTTAAGCCATGATGGTTGTTCATGAACCAT
64 GATTAACACCATATTAGAGTTTAAGCCATGATAGTTGTTCACGAACCAT
935966 ACAATTCTCT
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
139 9 0.10
140 83 0.88
141 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (139 bp):
TATATATATTATGTATTTAATTGCAATATTGGAACTCGATTTCGTTAGTACAATTATGCCCATGA
TTAACACCATATTAGAGTTTAAGCCATGATAGTTGTTCACGAACCATCGAATCTTGATTTATTTA
TTATTTATT
Found at i:942377 original size:2 final size:2
Alignment explanation
Indices: 942370--942410 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
942360 AAGATTTCCT
942370 TC 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 TC T
942411 GACAGACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:944334 original size:3 final size:3
Alignment explanation
Indices: 944326--944373 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
944316 TATTCATATC
944326 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
944374 TCTTCATCGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:945535 original size:16 final size:15
Alignment explanation
Indices: 945510--945553 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
945500 CCTATTTGAG
*
945510 TTCGAATTTTTTCAGA
1 TTCGAGTTTTTTC-GA
945526 TTCGAGTTTTTTTCGA
1 TTCGAG-TTTTTTCGA
945542 TTCAGAGTTTTT
1 TTC-GAGTTTTT
945554 CGAGTTTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (15 bp):
TTCGAGTTTTTTCGA
Found at i:945538 original size:17 final size:17
Alignment explanation
Indices: 945516--945553 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
945506 TGAGTTCGAA
945516 TTTTTTCAGATTC-GAGT
1 TTTTTTC-GATTCAGAGT
945533 TTTTTTCGATTCAGAGT
1 TTTTTTCGATTCAGAGT
945550 TTTT
1 TTTT
945554 CGAGTTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (17 bp):
TTTTTTCGATTCAGAGT
Found at i:946784 original size:24 final size:21
Alignment explanation
Indices: 946742--946786 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
946732 ATAAATTAAG
*
946742 TTTTTAATATTTAGTTAAATT
1 TTTTTAATATTTAGATAAATT
946763 TTTTTAATAATATTAGAATAAATT
1 TTTTTAAT-AT-TTAG-ATAAATT
946787 GATGATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 4 0.20
24 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTAATATTTAGATAAATT
Found at i:946932 original size:16 final size:16
Alignment explanation
Indices: 946913--946952 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
946903 TTTTTTCAGG
*
946913 TTCGGGTTTGGATTCT
1 TTCGGGTTCGGATTCT
*
946929 TTC-GGTTCGGGTTCT
1 TTCGGGTTCGGATTCT
946944 TTCGGGTTC
1 TTCGGGTTC
946953 AGACTATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.03, C:0.17, G:0.33, T:0.47
Consensus pattern (16 bp):
TTCGGGTTCGGATTCT
Found at i:946937 original size:21 final size:22
Alignment explanation
Indices: 946901--946941 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
946891 CTTGAGTTCA
*
946901 GATTTTTTCAGGTTCGGGTTTG
1 GATTCTTTCAGGTTCGGGTTTG
946923 GATTCTTTC-GGTTCGGGTT
1 GATTCTTTCAGGTTCGGGTT
946942 CTTTCGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.07, C:0.12, G:0.32, T:0.49
Consensus pattern (22 bp):
GATTCTTTCAGGTTCGGGTTTG
Found at i:946979 original size:32 final size:31
Alignment explanation
Indices: 946928--946998 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
946918 GTTTGGATTC
*
946928 TTTCG-GTTCGGGTTCTTTCGGGTTCAGACTA
1 TTTCGAGTTCGGGTTCTTTCGGATTCAGA-TA
946959 TTTCGAGTTCGGG-TCATTTCGGATTCAGATA
1 TTTCGAGTTCGGGTTC-TTTCGGATTCAGATA
*
946990 TTTTGAGTT
1 TTTCGAGTT
946999 TGAATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 17 0.47
32 19 0.53
ACGTcount: A:0.14, C:0.15, G:0.27, T:0.44
Consensus pattern (31 bp):
TTTCGAGTTCGGGTTCTTTCGGATTCAGATA
Found at i:947119 original size:21 final size:20
Alignment explanation
Indices: 947089--947127 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
947079 ACGCCTATAA
947089 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
947109 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
947128 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:947286 original size:14 final size:14
Alignment explanation
Indices: 947269--947298 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
947259 TATTATTATT
947269 TATTTAAATATATA
1 TATTTAAATATATA
*
947283 TATTTAGATATATA
1 TATTTAAATATATA
947297 TA
1 TA
947299 AATGTAATTA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATTTAAATATATA
Found at i:949037 original size:25 final size:22
Alignment explanation
Indices: 948977--949038 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 22
948967 CTCGAGTTTC
948977 AAGTTA-ATTATTTTAATTTTT
1 AAGTTATATTATTTTAATTTTT
948998 AAGTTATATTATATTTTAAATTTTT
1 AAGTTATA-T-TATTTT-AATTTTT
*
949023 AAAATTTATATTATTT
1 --AAGTTATATTATTT
949039 GAAGTATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 1 0.03
24 6 0.18
25 12 0.35
26 1 0.03
27 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
AAGTTATATTATTTTAATTTTT
Found at i:949075 original size:16 final size:15
Alignment explanation
Indices: 949054--949143 Score: 90
Period size: 16 Copynumber: 5.7 Consensus size: 15
949044 ATAGAACATA
949054 TTAAATTTAAATATTT
1 TTAAATTTAAAT-TTT
**
949070 TTAAATTTTTATTATT
1 TTAAATTTAAATT-TT
949086 TTAAATTTAAATTATT
1 TTAAATTTAAATT-TT
**
949102 TTTTATTTAAATTTTT
1 TTAAATTTAAA-TTTT
*
949118 TTAATTTTAAATTATT
1 TTAAATTTAAATT-TT
949134 TTAAATTTAA
1 TTAAATTTAA
949144 TTTACTTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
15 3 0.05
16 56 0.92
17 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATTTAAATTTT
Found at i:949090 original size:32 final size:32
Alignment explanation
Indices: 949054--949143 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
949044 ATAGAACATA
**
949054 TTAAATTTAAATATTTTTAAATTTTTATTATT
1 TTAAATTTAAATATTTTTAAATTTAAATTATT
* *
949086 TTAAATTTAAATTATTTTT-TATTTAAATTTTT
1 TTAAATTTAAA-TATTTTTAAATTTAAATTATT
*
949118 TTAATTTTAAAT-TATTTTAAATTTAA
1 TTAAATTTAAATAT-TTTTAAATTTAA
949144 TTTACTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 5 0.10
32 36 0.73
33 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TTAAATTTAAATATTTTTAAATTTAAATTATT
Found at i:949094 original size:22 final size:22
Alignment explanation
Indices: 949069--949115 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
949059 TTTAAATATT
949069 TTTAAATT-TTTATTATTTTAAA
1 TTTAAATTATTTATTA-TTTAAA
*
949091 TTTAAATTATTTTTTATTTAAA
1 TTTAAATTATTTATTATTTAAA
949113 TTT
1 TTT
949116 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTAAATTATTTATTATTTAAA
Found at i:949124 original size:22 final size:23
Alignment explanation
Indices: 949058--949141 Score: 64
Period size: 26 Copynumber: 3.4 Consensus size: 23
949048 AACATATTAA
*
949058 ATTTAAATATTTTTAAATTTTTATT
1 ATTTAAAT-TTTTTTAA-TTTTATT
**
949083 ATTTTAAATTTAAATT-ATTTT-TT
1 A-TTTAAATTT-TTTTAATTTTATT
949106 ATTTAAATTTTTTTAATTTTAAATT
1 ATTTAAATTTTTTTAATTTT--ATT
949131 ATTTTAAATTT
1 A-TTTAAATTT
949142 AATTTACTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
23 3 0.06
24 4 0.09
25 7 0.15
26 17 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTAAATTTTTTTAATTTTATT
Found at i:951353 original size:2 final size:2
Alignment explanation
Indices: 951346--951403 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
951336 TTCATTCTTT
* * * *
951346 TA TA TA TA TA TA TA TA TA TA CA T- TA TA GA TA GA T- TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
951386 T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
951404 TAAATTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:951582 original size:16 final size:15
Alignment explanation
Indices: 951558--951591 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
951548 TAAGTCAATC
*
951558 TTAAGTTTGATTCATT
1 TTAAATTTGATTC-TT
951574 TTAAATTTGATTCTT
1 TTAAATTTGATTCTT
951589 TTA
1 TTA
951592 TTTAAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (15 bp):
TTAAATTTGATTCTT
Found at i:951692 original size:22 final size:22
Alignment explanation
Indices: 951664--951706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
951654 AAATTAGATC
951664 ATTTTAAATTAAAATTTTTTAA
1 ATTTTAAATTAAAATTTTTTAA
* * *
951686 ATTTTAATTTTAACTTTTTTA
1 ATTTTAAATTAAAATTTTTTA
951707 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTAAATTAAAATTTTTTAA
Found at i:952214 original size:20 final size:20
Alignment explanation
Indices: 952166--952230 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
952156 TAAATTTAAA
* *
952166 ATTTTATATATTTAT-ATAA
1 ATTTTATATATTAATAATAT
*
952185 ATTTTGATATATTAATAATTT
1 ATTTT-ATATATTAATAATAT
952206 ATTTTATATAATTAATAATAT
1 ATTTTATAT-ATTAATAATAT
952227 ATTT
1 ATTT
952231 GTACATTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.13
20 13 0.33
21 21 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTATATATTAATAATAT
Found at i:953933 original size:18 final size:18
Alignment explanation
Indices: 953895--953939 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
953885 GGTAAAAATG
*
953895 AAAGTCAAC-TCAAAGTG
1 AAAGTCAACTTCAAAGTC
*
953912 AAAGTCAACTTTAAAGTC
1 AAAGTCAACTTCAAAGTC
*
953930 AAAGGCAACT
1 AAAGTCAACT
953940 AAAAAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (18 bp):
AAAGTCAACTTCAAAGTC
Found at i:959403 original size:32 final size:30
Alignment explanation
Indices: 959147--959721 Score: 598
Period size: 28 Copynumber: 19.4 Consensus size: 30
959137 TCGACTCGTA
*
959147 GGCTTTGAAA-GGGTGCCATTGACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* *
959175 GGCTTT-AAAAGGGTGCCACTAACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* *
959203 GGCTTTGAAA-GGATGCCACTAACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* * *
959231 GGCTTTGAAAAGAGTGCCACTAACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* *
959260 GGCTTTGAAAAGAGTGCCACTGACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
959289 GGCTTTGAAA-GGGTGCCACTGACT-TGTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* * *
959317 GGCTTTGAAAAGAGTGCCACTGACT-TGTA
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
959346 GGCTTTGAAA-GGGTGCCACTGACTTGTGTG
1 GGCTTTGAAATGGGTGCCACTGAC-TGTGTG
**
959376 GGCTTTGAAATGGGTTGCCACCAACTTGTGTG
1 GGCTTTGAAATGGG-TGCCACTGAC-TGTGTG
*
959408 GGCTTTGAAATGGGCTGCCACCGACTTGTGTG
1 GGCTTTGAAATGGG-TGCCACTGAC-TGTGTG
* * *
959440 GGCTTTGAAATGAGTTTCCACCGACTTGTGTG
1 GGCTTTGAAATG-GGTGCCACTGAC-TGTGTG
959472 GGCTTTGAAAT-GGTGCCACTGACTG-GTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* *
959500 GGCTTTGAAATGAGTTTCCACTGACTTGTGTG
1 GGCTTTGAAATG-GGTGCCACTGAC-TGTGTG
959532 GGCTTTGAAAT-GGTGCCACTGACTG-GTG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
* *
959560 GGCTTTGAAA-AGGTGCCACTGACT-TATG
1 GGCTTTGAAATGGGTGCCACTGACTGTGTG
*
959588 GGCTTTGAAA-GGGTGCCACTAACTTGTGTG
1 GGCTTTGAAATGGGTGCCACTGAC-TGTGTG
**
959618 GGCTTTGAAATGGGTTGCCACAAACT-TGTG
1 GGCTTTGAAATGGG-TGCCACTGACTGTGTG
* *
959648 GGCTTTG-AAGGGGTGCCACTGACTTGTGTA
1 GGCTTTGAAATGGGTGCCACTGAC-TGTGTG
* **
959678 GGCTTTGAAATGGTTTGCCACCAACTTGTGTG
1 GGCTTTGAAATGG-GTGCCACTGAC-TGTGTG
959710 GGCTTTGAAATG
1 GGCTTTGAAATG
959722 CTTTGCCACC
Statistics
Matches: 486, Mismatches: 38, Indels: 42
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.01
28 165 0.34
29 95 0.20
30 76 0.16
31 13 0.03
32 133 0.27
33 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (30 bp):
GGCTTTGAAATGGGTGCCACTGACTGTGTG
Found at i:959526 original size:60 final size:58
Alignment explanation
Indices: 959147--959719 Score: 606
Period size: 60 Copynumber: 9.7 Consensus size: 58
959137 TCGACTCGTA
* * * * *
959147 GGCTTTGAAA-G-GGTGCCATTGACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTG
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTGGTG
* * * * *
959203 GGCTTTGAAA-G-GATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTG
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTGGTG
* *
959260 GGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTGGTG
* *
959317 GGCTTTGAAAAGAG-TGCCACTGACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGTG
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC-TG-GTG
* ** *
959376 GGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGCTGCCACCGACTTGTGTG
1 GGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACTGAC-TG-GTG
* * *
959440 GGCTTTGAAATGAGTTTCCACCGACTTGTGTGGGCTTTGAAATGGTGCCACTGACTGGTG
1 GGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTGGTG
* *
959500 GGCTTTGAAATGAGTTTCCACTGACTTGTGTGGGCTTTGAAATGGTGCCACTGACTGGTG
1 GGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTGGTG
* * *
959560 GGCTTTGAAA--AGGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGTG
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC-TG-GTG
* ** * *
959618 GGCTTTGAAATGGGTTGCCACAAACTTGTGGGCTTTGAAGGGGTGCCACTGACTTGTGTA
1 GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC-TG-GTG
**
959678 GGCTTTGAAATG-GTTTGCCACCAACTTGTGTGGGCTTTGAAA
1 GGCTTTGAAATGAG-TTGCCACTGAC-T-TGTGGGCTTTGAAA
959720 TGCTTTGCCA
Statistics
Matches: 463, Mismatches: 37, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
56 55 0.12
57 103 0.22
58 47 0.10
59 17 0.04
60 142 0.31
61 4 0.01
62 35 0.08
63 5 0.01
64 55 0.12
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (58 bp):
GGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTGGTG
Found at i:969283 original size:23 final size:23
Alignment explanation
Indices: 969257--969301 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
969247 AAATAATGGG
*
969257 AATGAATAGCAAAAAAAAAAAAA
1 AATGAACAGCAAAAAAAAAAAAA
* *
969280 AATGAACATCAATAAAAAAAAA
1 AATGAACAGCAAAAAAAAAAAA
969302 GTGGCCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.11
Consensus pattern (23 bp):
AATGAACAGCAAAAAAAAAAAAA
Found at i:973867 original size:13 final size:13
Alignment explanation
Indices: 973849--973874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
973839 TACACACAAG
973849 ATGTATCGATACA
1 ATGTATCGATACA
973862 ATGTATCGATACA
1 ATGTATCGATACA
973875 TTCCAAAATG
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:973891 original size:33 final size:32
Alignment explanation
Indices: 973831--973894 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
973821 CTTAATTGTT
*
973831 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
973863 TGTATCGATACATTC-CAAAATGTATCGATACA
1 TGTATCGATACA--CACAAAATGTATCGATACA
973895 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 16 0.55
34 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:974755 original size:51 final size:51
Alignment explanation
Indices: 974698--974840 Score: 225
Period size: 51 Copynumber: 2.8 Consensus size: 51
974688 TTTTAACTAG
*
974698 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* * * *
974749 ATGTATCGATACATTGAAGAATGTATCGATACATCCGGGTAAAAGGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
974800 ATGTATCGATACATT-AAAGAATGTATCGATACATCTGGGTA
1 ATGTATCGATACATTGAAA-AATGTATCGATACATCTGGGTA
974841 CCTTTCCATA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 2 0.02
51 82 0.98
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:981008 original size:310 final size:308
Alignment explanation
Indices: 980228--981020 Score: 861
Period size: 310 Copynumber: 2.6 Consensus size: 308
980218 ATCTCGGTAA
* *
980228 CCCTAAAAGACTT-AAAAAGATTATAGATGAGATGAAACTATCCTAAATACCCACATTCAGCATA
1 CCCTAAAAGACTTAAAAAAGAGTATAGATGAGATGAACCTATCCTAAATACCCAC-TTCAGCATA
* * *
980292 AAAACGGACTCGGTGACAACCTAGGAGTTGGTTCTAA-AAAATTACAAAGATACCTCTAGGGGAT
65 AAAGCGGACTCGGTGATAACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATA-CTCTAGGGGAT
* * * *
980356 ACTTTCGATGTAGAAGTA-CCTGATACCCTTAAAGGACTTAAAAAAGATTTTAAAAGGGATGAGC
129 ACCTTCGATATAGAAGTACCCGGA-ACCC-TAAAGGACTTAAAAAAGATTTTAAAAGGGATGAAC
* * * *
980420 CTATCCTAAATATCCACCTTCAACATAAAGGCAGATCTAGTGAGGACCCAAGAGTTAGTTCTAGA
192 CTATCCTAAATATCCACCTTCAACATAAAAGCAGACCTAGTGAGGACCCAAGACTCAGTTCTAGA
* * *
980485 AAATTACAAAAATGCCTTTAGGGGATACCTTTGATGTAAAAGTACTCAATAC
257 AAATTACAAAAATACCCTTAGGGGATACCTTTGATGTAAAAGTACCCAATAC
** * * * *
980537 CCCTAAAAGACTTAAAATGGAGTTTAAATGGGAT-AATCCTATCCTAAATATCCACCTTCAGCAT
1 CCCTAAAAGACTTAAAAAAGAGTATAGATGAGATGAA-CCTATCCTAAATACCCA-CTTCAGCAT
* * * * * *
980601 AAAAGTGGAC-CTAGTGATGACCTAGGAGTTGGTT-TTAGAAAATTACAAAAATACTCATAAGAG
64 AAAAGCGGACTC-GGTGATAACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATACTC-TAGGGG
* * * *
980664 ATACCTTCGACATAAAAGTACTC-GATACCCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGA
127 ATACCTTCGATATAGAAGTACCCGGA-A-CCCTAAAGGACTTAAAAAAGATTTTAAAAGGGATGA
* * * * ** * *
980728 ATCTATCCTAAATATCCACCTTCGACATAAAAGCGGACCT-GATGATGACTTAGGACTCGGTTCT
190 ACCTATCCTAAATATCCACCTTCAACATAAAAGCAGACCTAG-TGAGGACCCAAGACTCAGTTCT
* *** * * * *
980792 AATAAAATTATGGAAATACCCTTAGGGGATATCTTTGACT-TAGAAGTGCCCGATAC
254 -AGAAAATTACAAAAATACCCTTAGGGGATACCTTTGA-TGTAAAAGTACCCAATAC
*
980848 CCCTAAAA-ACTTAAAAAAGA-TATAGATGAGATGAACCTATCCTAAATACCCATCTTCAACATA
1 CCCTAAAAGACTTAAAAAAGAGTATAGATGAGATGAACCTATCCTAAATACCCA-CTTCAGCATA
* * *
980911 AAAGCAGACTCGGTGATAACCTAGGACTCGGTTCTAAGAAAATTACAAAAATATCTCTAGGGGAT
65 AAAGCGGACTCGGTGATAACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATA-CTCTAGGGGAT
* * * *
980976 ACCCTCGATTTAGAAGTACCCGGCAACCCTAAAGGGCTAAAAAAA
129 ACCTTCGATATAGAAGTACCCGG-AACCCTAAAGGACTTAAAAAA
981021 TGAAAGAAAT
Statistics
Matches: 395, Mismatches: 72, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
309 81 0.21
310 252 0.64
311 60 0.15
312 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (308 bp):
CCCTAAAAGACTTAAAAAAGAGTATAGATGAGATGAACCTATCCTAAATACCCACTTCAGCATAA
AAGCGGACTCGGTGATAACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATACTCTAGGGGATAC
CTTCGATATAGAAGTACCCGGAACCCTAAAGGACTTAAAAAAGATTTTAAAAGGGATGAACCTAT
CCTAAATATCCACCTTCAACATAAAAGCAGACCTAGTGAGGACCCAAGACTCAGTTCTAGAAAAT
TACAAAAATACCCTTAGGGGATACCTTTGATGTAAAAGTACCCAATAC
Found at i:981017 original size:154 final size:156
Alignment explanation
Indices: 980225--981020 Score: 720
Period size: 155 Copynumber: 5.1 Consensus size: 156
980215 AGTATCTCGG
* * * * * * * *
980225 TAACCCTAAAAGACTT-AAAAAGATTATAGATGAGATGAAACTATCCTAAATACCCACATTCAGC
1 TAACCCTAAAGGACTTAAAAAAGATTTTAAATGGGATGAACCTATCCTAAATATCCACCTTCAAC
* ** *
980289 ATAAAAACGGACTC-GGTGACAACCTAGGAGTTGGTTCTAA-AAAATTACAAAGATACCTCTAGG
66 ATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATA-CTCTAGG
* *
980352 GGATACTTTCGATGTAGAAGTACCTGA
130 GGATACCTTCGATGTAGAAGTACCCGA
* *
980379 T-ACCCTTAAAGGACTTAAAAAAGATTTTAAAAGGGATGAGCCTATCCTAAATATCCACCTTCAA
1 TAACCC-TAAAGGACTTAAAAAAGATTTTAAATGGGATGAACCTATCCTAAATATCCACCTTCAA
* * * * * * * * *
980443 CATAAAGGCAGA-TCTAGTGAGGACCCAAGAGTTAGTTCT-AGAAAATTACAAAAATGCCTTTAG
65 CATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAAT-ACTCTAG
* * * *
980506 GGGATACCTTTGATGTAAAAGTACTCAA
129 GGGATACCTTCGATGTAGAAGTACCCGA
* * ** * *
980534 TACCCCTAAAAGACTTAAAATGGAGTTTAAATGGGAT-AATCCTATCCTAAATATCCACCTTCAG
1 TAACCCTAAAGGACTTAAAAAAGATTTTAAATGGGATGAA-CCTATCCTAAATATCCACCTTCAA
* * * *
980598 CATAAAAGTGGAC-CTAGTGATGACCTAGGAGTTGGTT-TTAGAAAATTACAAAAATACTCATAA
65 CATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATACTC-TAG
* ** * *
980661 GAGATACCTTCGACATAAAAGTACTCGA
129 GGGATACCTTCGATGTAGAAGTACCCGA
* * * * *
980689 TACCCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAATCTATCCTAAATATCCACCTTCGAC
1 TAACCCTAAAGGACTTAAAAAAGATTTTAAATGGGATGAACCTATCCTAAATATCCACCTTCAAC
* * * * * *** *
980754 ATAAAAGCGGAC-CTGATGATGACTTAGGACTCGGTTCTAATAAAATTATGGAAATACCCTTAGG
66 ATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATACTC-TAGG
* * *
980818 GGATATCTTTGACT-TAGAAGTGCCCGA
130 GGATACCTTCGA-TGTAGAAGTACCCGA
* * * * * * *
980845 TACCCCTAAA-AACTTAAAAAAGA-TATAGATGAGATGAACCTATCCTAAATACCCATCTTCAAC
1 TAACCCTAAAGGACTTAAAAAAGATTTTAAATGGGATGAACCTATCCTAAATATCCACCTTCAAC
* * * *
980908 ATAAAAGCAGACTC-GGTGATAACCTAGGACTCGGTTCTAAGAAAATTACAAAAATATCTCTAGG
66 ATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATA-CTCTAGG
* * *
980972 GGATACCCTCGATTTAGAAGTACCCGG
130 GGATACCTTCGATGTAGAAGTACCCGA
* * *
980999 CAACCCTAAAGGGCTAAAAAAA
1 TAACCCTAAAGGACTTAAAAAA
981021 TGAAAGAAAT
Statistics
Matches: 517, Mismatches: 108, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
153 5 0.01
154 127 0.25
155 332 0.64
156 53 0.10
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (156 bp):
TAACCCTAAAGGACTTAAAAAAGATTTTAAATGGGATGAACCTATCCTAAATATCCACCTTCAAC
ATAAAAGCGGACTCTGGTGATGACCTAGGAGTTGGTTCTAAGAAAATTACAAAAATACTCTAGGG
GATACCTTCGATGTAGAAGTACCCGA
Found at i:983228 original size:13 final size:13
Alignment explanation
Indices: 983210--983235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
983200 CATGGGACAA
983210 TGTATCGATACAT
1 TGTATCGATACAT
983223 TGTATCGATACAT
1 TGTATCGATACAT
983236 AAGGAAATTG
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:983253 original size:34 final size:33
Alignment explanation
Indices: 983189--983258 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
983179 TTATCACTTT
*
983189 TTGTATCGATACATGGGACAATGTATCGATACA
1 TTGTATCGATACATAGGACAATGTATCGATACA
983222 TTGTATCGATACATAAGGA-AATTGTATCGATACA
1 TTGTATCGATACAT-AGGACAA-TGTATCGATACA
983256 TTG
1 TTG
983259 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.47
34 18 0.53
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATAGGACAATGTATCGATACA
Found at i:983712 original size:13 final size:13
Alignment explanation
Indices: 983694--983719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
983684 TACAGCAAGT
983694 ATGTATCGATACA
1 ATGTATCGATACA
983707 ATGTATCGATACA
1 ATGTATCGATACA
983720 CAAAAAATTG
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:985971 original size:21 final size:21
Alignment explanation
Indices: 985938--985982 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
985928 TTGCAAGTTG
*
985938 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
985960 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
985980 AAA
1 AAA
985983 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:989911 original size:13 final size:13
Alignment explanation
Indices: 989893--989931 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
989883 TCATTTTTCT
989893 TTGTATCGATACA
1 TTGTATCGATACA
989906 TTGTATCGATACA
1 TTGTATCGATACA
989919 TTGTATCGATACA
1 TTGTATCGATACA
989932 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:992503 original size:13 final size:13
Alignment explanation
Indices: 992485--992510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
992475 TACAGCAAGT
992485 ATGTATCGATACA
1 ATGTATCGATACA
992498 ATGTATCGATACA
1 ATGTATCGATACA
992511 CAAAAAATTG
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:994801 original size:3 final size:3
Alignment explanation
Indices: 994793--994822 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
994783 TGAAGAGAAA
*
994793 GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
994823 TCGGATGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1001251 original size:56 final size:57
Alignment explanation
Indices: 1001191--1001301 Score: 197
Period size: 56 Copynumber: 1.9 Consensus size: 57
1001181 AATAAATAAT
1001191 TTTTTTATTATTTGACAAAGAGGGAGAGACAAA-GGGAGAATTTTAGAAATGCTAAA
1 TTTTTTATTATTTGACAAAGAGGGAGAGACAAAGGGGAGAATTTTAGAAATGCTAAA
*
1001247 TTTTTTATTATTTGACAAAGGGGGAGAGACAAAGGGGGAGAATTTTAGAAATGCT
1 TTTTTTATTATTTGACAAAGAGGGAGAGACAAA-GGGGAGAATTTTAGAAATGCT
1001302 TTAATTAAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
56 32 0.62
58 20 0.38
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (57 bp):
TTTTTTATTATTTGACAAAGAGGGAGAGACAAAGGGGAGAATTTTAGAAATGCTAAA
Found at i:1001279 original size:14 final size:14
Alignment explanation
Indices: 1001260--1001287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1001250 TTTATTATTT
1001260 GACAAAGGGGGAGA
1 GACAAAGGGGGAGA
1001274 GACAAAGGGGGAGA
1 GACAAAGGGGGAGA
1001288 ATTTTAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.50, T:0.00
Consensus pattern (14 bp):
GACAAAGGGGGAGA
Found at i:1001963 original size:20 final size:19
Alignment explanation
Indices: 1001915--1002010 Score: 129
Period size: 19 Copynumber: 4.9 Consensus size: 19
1001905 TTGTATCAAT
1001915 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* * *
1001934 TCACTGTATCGATACATGG
1 ACATTGTATCGATACATGC
1001953 ACAATTGTATCGATACATGC
1 AC-ATTGTATCGATACATGC
* *
1001973 TCACTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1001992 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1002011 AGATTGGCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 34 0.52
20 31 0.48
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1001971 original size:39 final size:39
Alignment explanation
Indices: 1001917--1002010 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
1001907 GTATCAATAC
*
1001917 ATTGTATCGATACATGCTCACTGTATCGATACATGGACA
1 ATTGTATCGATACATGCTCACTGTATCGATACATGCACA
1001956 ATTGTATCGATACATGCTCACTGTATCGATACATGCACA
1 ATTGTATCGATACATGCTCACTGTATCGATACATGCACA
1001995 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1002011 AGATTGGCAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (39 bp):
ATTGTATCGATACATGCTCACTGTATCGATACATGCACA
Found at i:1002078 original size:13 final size:13
Alignment explanation
Indices: 1002060--1002108 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1002050 CATGGGACAA
1002060 TGTATCGATACAT
1 TGTATCGATACAT
1002073 TGTATCGATACA-
1 TGTATCGATACAT
*
1002085 TG-A-GGA-A-AT
1 TGTATCGATACAT
1002094 TGTATCGATACAT
1 TGTATCGATACAT
1002107 TG
1 TG
1002109 CTTGTAACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 3 0.10
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1002103 original size:34 final size:33
Alignment explanation
Indices: 1002039--1002108 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 33
1002029 CTATCACTAT
1002039 TTGTATCGATACATGGGACAATGTATCGATACA
1 TTGTATCGATACATGGGACAATGTATCGATACA
1002072 TTGTATCGATACATGAGGA-AATTGTATCGATACA
1 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1002106 TTG
1 TTG
1002109 CTTGTAACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 17 0.49
34 18 0.51
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGGGACAATGTATCGATACA
Found at i:1003999 original size:9 final size:9
Alignment explanation
Indices: 1003934--1003999 Score: 53
Period size: 9 Copynumber: 7.4 Consensus size: 9
1003924 ACAAAAAATT
*
1003934 AAAAATCAA
1 AAAAATAAA
*
1003943 AGAAATAAA
1 AAAAATAAA
**
1003952 AAAAATTCA
1 AAAAATAAA
1003961 AAAAAT-AA
1 AAAAATAAA
* *
1003969 AATAATAAT
1 AAAAATAAA
* *
1003978 AATAATAAT
1 AAAAATAAA
1003987 AAAAATAAA
1 AAAAATAAA
1003996 AAAA
1 AAAA
1004000 TGATGATGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
8 6 0.13
9 40 0.87
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1004154 original size:63 final size:63
Alignment explanation
Indices: 1003993--1004181 Score: 272
Period size: 63 Copynumber: 3.0 Consensus size: 63
1003983 TAATAAAAAT
* *
1003993 AAAAAAATGATGATGATGGCCGGATTAGTGGAGGTTCCATTAATTAAGCCACCTACACCATT-
1 AAAAAAATGATGATGATGGCCGAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
* * * * * *
1004055 CAAAAACTAATGATGATGGCCGAATTAGTGGAGGTTCCGCTAATGAAGCCACCTACACCGTTA
1 AAAAAAATGATGATGATGGCCGAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
* * *
1004118 AAAAAAATGATGATGATGACCAAATTAGTGGAGGTTCCACTAATTTAGCCACCTACACCATTA
1 AAAAAAATGATGATGATGGCCGAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
1004181 A
1 A
1004182 GGTGGGAAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 54 0.50
63 55 0.50
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (63 bp):
AAAAAAATGATGATGATGGCCGAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
Found at i:1006425 original size:97 final size:97
Alignment explanation
Indices: 1006293--1006641 Score: 468
Period size: 97 Copynumber: 3.6 Consensus size: 97
1006283 AATTTTATTT
* * * *
1006293 ATCA-GGATACTCCAACCCTATTCCTCCGAAGGGATACTCCAACCCTGCTTTTAATCACATCAAA
1 ATCAGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAATCACATCAAA
* *
1006357 GTTTAAATCTTATTCTCACTTAAATTGTCGTT
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * ** * *
1006389 ATCAGGGATAGTCTAACCCCATTCCTTTGAGGGGATACTCCAACCCCACTTTTAAACACATCAAA
1 ATCAGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAATCACATCAAA
1006454 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
** * *
1006486 ATTGGGGACACTCCAACCCTATTCCTCCGAGGGGATACTCTAACCCCGCTTTTAAAT-ACATCAA
1 ATCAGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT-AATCACATCAA
*
1006550 TGTTTAAATCTTATTCTCACTTAAATTGTCATC
65 AGTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * *
1006583 ATCAGGGACACTCCAACCCCATTCCTCCGAGGAGATACTCTAATCCCGTTTTTCAATCA
1 ATCAGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT-AATCA
1006642 AAAATTAAAT
Statistics
Matches: 220, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
96 4 0.02
97 213 0.97
98 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (97 bp):
ATCAGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAATCACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:1007620 original size:22 final size:22
Alignment explanation
Indices: 1007592--1007638 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1007582 AATGTTTTGA
* * *
1007592 TCGGTCATTGGTTTCATCCGTT
1 TCGGTCACTAGTTTCATCAGTT
*
1007614 TCGGTCACTAGTTTTATCAGTT
1 TCGGTCACTAGTTTCATCAGTT
1007636 TCG
1 TCG
1007639 ATCAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (22 bp):
TCGGTCACTAGTTTCATCAGTT
Found at i:1010486 original size:31 final size:31
Alignment explanation
Indices: 1010445--1010510 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
1010435 TAGAGAGGAA
*
1010445 GCCTCTATACCCTCA-TCGATATAACCCCAAT
1 GCCTCCATACCCTCACT-GATATAACCCCAAT
1010476 GCCTCCATACCCTCACTGATATAACCCCAAT
1 GCCTCCATACCCTCACTGATATAACCCCAAT
1010507 GCCT
1 GCCT
1010511 ATTGTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.41, G:0.08, T:0.24
Consensus pattern (31 bp):
GCCTCCATACCCTCACTGATATAACCCCAAT
Found at i:1011788 original size:13 final size:13
Alignment explanation
Indices: 1011770--1011802 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1011760 CCTAGTCACT
1011770 AAAAAAAAGAA-C
1 AAAAAAAAGAAGC
1011782 AAAAAAAAGAAGC
1 AAAAAAAAGAAGC
1011795 AAAAAAAA
1 AAAAAAAA
1011803 AAAAAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGC
Found at i:1012930 original size:62 final size:61
Alignment explanation
Indices: 1012847--1012964 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 61
1012837 TTCATTCCTT
* *
1012847 TAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCC-CATACGAGTTGGTGGCACTCTGC
1 TAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCACA-A-AAGTTGGTGGCACTCTGC
1012910 TAGTCCTCAAAGAGCA-GATGCCTTTTTCTTTTAAAGCCACAAAAGTTGGTGGCAC
1 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCACAAAAGTTGGTGGCAC
1012965 CCTTTTAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
60 12 0.23
61 11 0.21
62 14 0.27
63 15 0.29
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (61 bp):
TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCACAAAAGTTGGTGGCACTCTGC
Found at i:1013029 original size:32 final size:31
Alignment explanation
Indices: 1012937--1013039 Score: 102
Period size: 32 Copynumber: 3.4 Consensus size: 31
1012927 ATGCCTTTTT
* * * *
1012937 CTTTTAAAG-CCACAAAAGTTGGTGGC-ACC
1 CTTTCAAAGCCCACACAAGCTGATGGCAACC
* * * * *
1012966 CTTTTAAAGCCCACATAAGTTGGTGGGAACC
1 CTTTCAAAGCCCACACAAGCTGATGGCAACC
1012997 CTTTCAAACGCCCACACAAGCTGATGGCAACC
1 CTTTCAAA-GCCCACACAAGCTGATGGCAACC
1013029 CTTTCAAAGCC
1 CTTTCAAAGCC
1013040 TACAAGTCAG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
29 9 0.14
30 15 0.23
31 13 0.20
32 27 0.42
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (31 bp):
CTTTCAAAGCCCACACAAGCTGATGGCAACC
Found at i:1013066 original size:28 final size:28
Alignment explanation
Indices: 1013028--1013596 Score: 448
Period size: 28 Copynumber: 20.0 Consensus size: 28
1013018 TGATGGCAAC
*
1013028 CCTTTCAAAGCCTACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
1013056 CCTTTTAAAGCCCAC--GTTAGTGGCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
1013082 CCTTTCAAAGCCTACGAGTCGGTGGCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*** *
1013110 CCTTTCAAAGCCCATGGGTGAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
** *
1013138 CCTTTCAAAGCCCATGAGTGAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
1013166 CCTTTCAAAGCCCACAAGTCGGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
** * *
1013194 CCTTTCAAAAGCCCATGAGTC-GGGGCAC
1 CCTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
1013222 CCTTTCATAGCCCACGAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
1013250 CATTTCAAAAGCCCACAAGTTAGTGGCA-
1 CCTTTC-AAAGCCCACAAGTCAGTGGCAT
* * * * *
1013278 CCTTTTTAAAAGCCCACGAGTCAATGGTAC
1 CC--TTTCAAAGCCCACAAGTCAGTGGCAT
*
1013308 CCTTTCAAAGCCAACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
1013336 CCTTTCAAAAGCCCAACGAGTCGGTGGCAC
1 CCTTTC-AAAGCCC-ACAAGTCAGTGGCAT
* *
1013366 CCTTTCAAAG-CTATAAGTCAGTGGCA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* **
1013392 CCTTTTCAAAGCCCACACAAATTGGTGGCACAT
1 CC-TTTCAAAG-CC-CACAAGTCAGTGG--CAT
* * **
1013425 CTTTTCAAAGCCCACACAAATTGGTGGTACAT
1 CCTTTCAAAG-CC-CACAAGTCAGTGG--CAT
* *
1013457 CTTTTCAAAGCCCACAAGTCAGTGTCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
1013485 CCTTTTAAAGCGCACAAGTTAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
1013513 CCTTTCAAAAGCCCATAAGTTAGTGGCAC
1 CCTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
1013542 CCTTTCAAAGCCCACGAGTCGGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
1013570 CCTTTCAAAGCTCATAAGTCGGTGGCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
1013597 CATTTTTAAA
Statistics
Matches: 444, Mismatches: 79, Indels: 36
0.79 0.14 0.06
Matches are distributed among these distances:
26 24 0.05
27 31 0.07
28 221 0.50
29 84 0.19
30 40 0.09
31 2 0.00
32 41 0.09
33 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:1013326 original size:57 final size:56
Alignment explanation
Indices: 1013021--1013574 Score: 341
Period size: 57 Copynumber: 9.7 Consensus size: 56
1013011 CACAAGCTGA
* *
1013021 TGGCAACCCTTTCAAAGCCTACAAGTCAGTGGCATCCTTTT-AAAGCCCAC--GTTAG
1 TGGC-ACCCTTTCAAAGCCAACAAGTCAGTGGCA-CCTTTTAAAAGCCCACGAGTCAG
* * * * * * * *
1013076 TGGCAACCTTTCAAAGCCTACGAGTCGGTGGCAACC-TTTCAAAGCCCATGGGTGAG
1 TGGCACCCTTTCAAAGCCAACAAGTCAGTGGC-ACCTTTTAAAAGCCCACGAGTCAG
* * ** * * * *
1013132 TGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCC-TTTCAAAGCCCACAAGTCGG
1 TGGCACCCTTTCAAAGCCAACAAGTCAGTGGCA-CCTTTTAAAAGCCCACGAGTCAG
* * ** * * * *
1013188 TGGCATCCTTTCAAAAGCCCATGAGTC-GGGGCACCCTTTCATAGCCCACGAGTCAG
1 TGGCACCCTTTC-AAAGCCAACAAGTCAGTGGCACCTTTTAAAAGCCCACGAGTCAG
* * * * *
1013244 TGGCATCATTTCAAAAGCCCACAAGTTAGTGGCACCTTTTTAAAAGCCCACGAGTCAA
1 TGGCACCCTTTC-AAAGCCAACAAGTCAGTGGCACC-TTTTAAAAGCCCACGAGTCAG
* * *
1013302 TGGTACCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAAGCCCAACGAGTCGG
1 TGGCACCCTTTCAAAGCCAACAAGTCAGTGGCA-CCTTTTAAAAGCCC-ACGAGTCAG
* * * * * **
1013360 TGGCACCCTTTCAAAG-CTATAAGTCAGTGGCACCTTTTCAAAGCCCACACAAATTGG
1 TGGCACCCTTTCAAAGCCAACAAGTCAGTGGCACCTTTTAAAAG-CC-CACGAGTCAG
* * ** * * *
1013417 TGGCACATCTTTTCAAAGCCCACACAAATTGGTGGTACATCTTTTCAAAGCCCACAAGTCAG
1 TGGCAC--CCTTTCAAAG-CCA-ACAAGTCAGTGG--CACCTTTTAAAAGCCCACGAGTCAG
* * * * * ** *
1013479 TGTCATCCTTTTAAAGCGC-ACAAGTTAGTGGCACCCTTTCAAAAGCCCATAAGTTAG
1 TGGCACCCTTTCAAAGC-CAACAAGTCAGTGGCA-CCTTTTAAAAGCCCACGAGTCAG
* * *
1013536 TGGCACCCTTTCAAAGCCCACGAGTCGGTGGCATCCTTT
1 TGGCACCCTTTCAAAGCCAACAAGTCAGTGGCA-CCTTT
1013575 CAAAGCTCAT
Statistics
Matches: 403, Mismatches: 73, Indels: 44
0.77 0.14 0.08
Matches are distributed among these distances:
53 3 0.01
54 35 0.09
55 8 0.02
56 117 0.29
57 126 0.31
58 61 0.15
59 10 0.02
60 9 0.02
61 1 0.00
62 19 0.05
63 2 0.00
64 12 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (56 bp):
TGGCACCCTTTCAAAGCCAACAAGTCAGTGGCACCTTTTAAAAGCCCACGAGTCAG
Found at i:1013575 original size:57 final size:56
Alignment explanation
Indices: 1012958--1013597 Score: 448
Period size: 56 Copynumber: 11.1 Consensus size: 56
1012948 ACAAAAGTTG
* ** * * *
1012958 GTGGCACCCTTTTAAAGCCCACATAAGTTGGTGGGAACCCTTTCAAACGCCCACACAAG-CT
1 GTGGCACCCTTTCAAAGCCCAC--AAGTCAGT-GGCATCCTTTCAAA-G-CC-CACAAGTCA
* * *
1013019 GATGGCAACCCTTTCAAAGCCTACAAGTCAGTGGCATCCTTTTAAAGCCCAC--GTTA
1 G-TGGC-ACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * * *** *
1013075 GTGGCAACCTTTCAAAGCCTACGAGTCGGTGGCAACCTTTCAAAGCCCATGGGTGA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* ** * *
1013131 GTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGCCCACAAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* ** * * * *
1013187 GTGGCATCCTTTCAAAAGCCCATGAGTC-GGGGCACCCTTTCATAGCCCACGAGTCA
1 GTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
1013243 GTGGCATCATTTCAAAAGCCCACAAGTTAGTGGCA-CCTTTTTAAAAGCCCACGAGTCA
1 GTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCATCC--TTTCAAAGCCCACAAGTCA
* * * * *
1013301 ATGGTACCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAAGCCCAACGAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCC-ACAAGTCA
* * * **
1013359 GTGGCACCCTTTCAAAG-CTATAAGTCAGTGGCA-CCTTTTCAAAGCCCACACAAATTG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAG-CC-CACAAGTCA
* * ** *
1013416 GTGGCACATCTTTTCAAAGCCCACACAAATTGGTGGTACATCTTTTCAAAGCCCACAAGTCA
1 GTGGCAC--CCTTTCAAAG-CC-CACAAGTCAGTGG--CATCCTTTCAAAGCCCACAAGTCA
* * * * * * * *
1013478 GTGTCATCCTTTTAAAGCGCACAAGTTAGTGGCACCCTTTCAAAAGCCCATAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCA
* * * * *
1013535 GTGGCACCCTTTCAAAGCCCACGAGTCGGTGGCATCCTTTCAAAGCTCATAAGTCG
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
1013591 GTGGCAC
1 GTGGCAC
1013598 ATTTTTAAAT
Statistics
Matches: 468, Mismatches: 87, Indels: 53
0.77 0.14 0.09
Matches are distributed among these distances:
54 39 0.08
55 5 0.01
56 146 0.31
57 125 0.27
58 64 0.14
59 11 0.02
60 19 0.04
61 8 0.02
62 23 0.05
63 17 0.04
64 10 0.02
65 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (56 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:1013739 original size:31 final size:31
Alignment explanation
Indices: 1013392--1014155 Score: 327
Period size: 32 Copynumber: 24.7 Consensus size: 31
1013382 GTCAGTGGCA
*
1013392 CCTTTTCAAAGCCCACACAAATTGGTGGC-AC
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCAAC
* * *
1013423 ATCTTTTCAAAGCCCACACAAATTGGTGG-TAC
1 -CCTTTT-AAAGCCCACACAAGTTGGTGGCAAC
* ** * *
1013455 ATCTTTTCAAAG-CC-CACAAGTCAGTGTC-AT
1 -CCTTTT-AAAGCCCACACAAGTTGGTGGCAAC
* *
1013485 CCTTTTAAAG--CGCACAAGTTAGTGGC-AC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * *
1013513 CCTTTCAAAAG-CC-CATAAGTTAGTGGC-AC
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCAAC
* * * *
1013542 CCTTTCAAAG-CC-CACGAGTCGGTGGC-AT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * * *
1013570 CCTTTCAAAG--CTCATAAGTCGGTGGC-AC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
** * *
1013598 ATTTTTAAATCCTACACAAGCTGCTGGTGGCAA-
1 CCTTTTAAAGCCCACACAAG-T--TGGTGGCAAC
* *
1013631 CCTTTCTCAAAGCCCACACAAATTGATGGCAA-
1 CCTTT-T-AAAGCCCACACAAGTTGGTGGCAAC
* *
1013663 CCTTTCTCAAAGCCCACATAAATTGGTGGCAAC
1 CCTTT-T-AAAGCCCACACAAGTTGGTGGCAAC
* * * *
1013696 CTTTCTTAAAGCCTACATAAGTTGGTGGTAAC
1 CCTT-TTAAAGCCCACACAAGTTGGTGGCAAC
*
1013728 CCTTTTAAAGCCCACACAAGTCT-ATGGC-AC
1 CCTTTTAAAGCCCACACAAGT-TGGTGGCAAC
** * * *
1013758 TTTTTTAAAGTCTACACAAGCTGGTGGCAAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * * *
1013789 CCCTTTAAAGCCCATACAAGTCGGTGGTAA-
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * * *
1013819 TCTTTTAAAGCCCACATAATTTGGTGGTAA-
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* *
1013849 CCTTTTGAAGCCCACACAAGTCGGTGGCAAAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGC-AAC
* * * * * *
1013881 CTTTTCTAAAGTCCATATAAATCGGTGGC-AC
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCAAC
* * * ** *
1013912 CCTTTTAAAGTCCATATAAGTCAGTGGTAAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * * **
1013943 CTTTTTGAAGCTCACACAAGTCAGTGGCAAAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGC-AAC
** * * * * * ***
1013975 TTTTTCTAAAGTCTATAGAAGTTGATAAAAAC
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCAAC
*
1014007 CCTTTTCAAAGCCCACACAAGTTAGTGGCAAC
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCAAC
** * * *
1014039 CCTCTCAAAAGCCCACAAAAGTTGGCGGCATC
1 CCT-TTTAAAGCCCACACAAGTTGGTGGCAAC
* *
1014071 TCCTTCTAAAGCCTACACAAGTTGGTGGCAA-
1 -CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
* * * *
1014102 CCTTGTCAAAGCCCACACAAGCTGGTGGTAAT
1 CCTT-TTAAAGCCCACACAAGTTGGTGGCAAC
*
1014134 CTTTTTCAAAGCCCACACAAGT
1 CCTTTT-AAAGCCCACACAAGT
1014156 CAGGGTCAAC
Statistics
Matches: 568, Mismatches: 133, Indels: 62
0.74 0.17 0.08
Matches are distributed among these distances:
27 2 0.00
28 68 0.12
29 30 0.05
30 108 0.19
31 98 0.17
32 201 0.35
33 46 0.08
34 4 0.01
35 11 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (31 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCAAC
Found at i:1013885 original size:61 final size:61
Alignment explanation
Indices: 1012937--1014155 Score: 364
Period size: 56 Copynumber: 20.3 Consensus size: 61
1012927 ATGCCTTTTT
* * * *
1012937 CTTTTAAAG-CCACAAAAGTTGGTGGC-ACCCTTTTAAAGCCCACATAAGTTGGTGGGAACC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAA-C
* * * * * * *
1012997 CTTTCAAACGCCCACACAAGCTGATGGCAACCCTTTCAAAG-CC-TACAAGTCAGTGGCATC
1 CTTTTAAA-GCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * *
1013057 CTTTTAAAG-CC-CAC--GTTAGTGGCAA-CCTTTCAAAG-CC-TACGAGTCGGTGGCAAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* ** * * * ** *
1013111 CTTTCAAAG-CC-CA-TGGGTGAGTGGC-ATCCTTTCAAAG-CC-CATGAGT-GAGTGGCATC
1 CTTTTAAAGCCCACACAAGTTG-GTGGCAACCCTTTTAAAGCCCACACAAGTCG-GTGGCAAC
* * * * ** *
1013167 CTTTCAAAG-CC-CACAAGTCGGTGGC-ATCCTTTCAAAAG-CC-CATGAGTCGG-GGCACC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTT-TAAAGCCCACACAAGTCGGTGGCAAC
* * * ** * * * **
1013223 CTTTCATAG-CC-CACGAGTCAGTGGC-ATCATTTCAAAAG-CC-CACAAGTTAGTGGC-AC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTT-TAAAGCCCACACAAGTCGGTGGCAAC
* *** * * * *
1013279 CTTTTTAAAAG-CC-CACGAGTCAATGG-TACCCTTTCAAAG-CCA-ACAAGTCAGTGGCATC
1 C-TTTT-AAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * * * * *
1013337 CTTTCAAAAGCCCA-ACGAGTCGGTGGC-ACCCTTTCAAAG--C-TATAAGTCAGTGGC-AC
1 CTTT-TAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * * * *
1013393 CTTTTCAAAGCCCACACAAATTGGTGGC-ACATCTTTTCAAAGCCCACACAAATTGGTGGTACAT
1 CTTTT-AAAGCCCACACAAGTTGGTGGCAAC-CCTTTT-AAAGCCCACACAAGTCGGTGGCA-AC
** * * * ** *
1013457 CTTTTCAAAG-CC-CACAAGTCAGTGTC-ATCCTTTTAAAG--CGCACAAGTTAGTGGCACC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * * * *
1013514 CTTTCAAAAG-CC-CATAAGTTAGTGGC-ACCCTTTCAAAG-CC-CACGAGTCGGTGGCATC
1 CTTT-TAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * * ** * *
1013571 CTTTCAAAG--CTCATAAGTCGGTGGC-ACATTTTTAAATCCTACACAAGCTGCTGGTGGCAAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAG-T-C-GGTGGCAAC
* * * * *
1013632 CTTTCTCAAAGCCCACACAAATTGATGGCAA-CCTTTCTCAAAGCCCACATAAATTGGTGGCAAC
1 CTTT-T-AAAGCCCACACAAGTTGGTGGCAACCCTTT-T-AAAGCCCACACAAGTCGGTGGCAAC
* * * **
1013696 CTTTCTTAAAGCCTACATAAGTTGGTGGTAACCCTTTTAAAGCCCACACAAGTCTATGGC-AC
1 C-TT-TTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * * * * * *
1013758 TTTTTTAAAGTCTACACAAGCTGGTGGCAACCCCTTTAAAGCCCATACAAGTCGGTGGTAAT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * * *
1013820 CTTTTAAAGCCCACATAATTTGGTGGTAA-CCTTTTGAAGCCCACACAAGTCGGTGGCAAAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGC-AAC
* * * * * * * * * *
1013881 CTTTTCTAAAGTCCATATAAATCGGTGGC-ACCCTTTTAAAGTCCATATAAGTCAGTGGTAAC
1 C-TTT-TAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
* * ** ** * * * * * * ***
1013943 CTTTTTGAAGCTCACACAAGTCAGTGGCAAACTTTTTCTAAAGTCTATAGAAGTTGATAAAAACC
1 C-TTTTAAAGCCCACACAAGTTGGTGGC-AACCCTTT-TAAAGCCCACACAAGTCGGTGGCAA-C
* ** * * * *
1014008 CTTTTCAAAGCCCACACAAGTTAGTGGCAACCCTCTCAAAAGCCCACAAAAGTTGGCGGCATCTC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCAACCCT-TTTAAAGCCCACACAAGTCGGTGGCA--AC
* * * *
1014073 CTTCTAAAGCCTACACAAGTTGGTGGCAA-CCTTGTCAAAGCCCACACAAG-CTGGTGGTAATC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTT-TTAAAGCCCACACAAGTC-GGTGGCAA-C
*
1014135 TTTTTCAAAGCCCACACAAGT
1 CTTTT-AAAGCCCACACAAGT
1014156 CAGGGTCAAC
Statistics
Matches: 891, Mismatches: 201, Indels: 131
0.73 0.16 0.11
Matches are distributed among these distances:
54 38 0.04
55 13 0.01
56 140 0.16
57 124 0.14
58 74 0.08
59 6 0.01
60 44 0.05
61 116 0.13
62 57 0.06
63 114 0.13
64 102 0.11
65 49 0.05
66 4 0.00
67 10 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (61 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1013933 original size:63 final size:61
Alignment explanation
Indices: 1013356--1013958 Score: 234
Period size: 61 Copynumber: 9.9 Consensus size: 61
1013346 GCCCAACGAG
* * * * * *
1013356 TCGGTGGCACCCTTTCAAAG--C-TATAAGTCAGTGG-CACCTTTTCAAAGCCCACACAAA
1 TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
* * * * * * * *
1013413 TTGGTGGCACATCTTTTCAAAGCCCACACAAATTGGTGGTACATCTTTTCAAAGCCCAC--AAG
1 TCGGTGGCAC-CCTTTT-AAAGCCCATACAAGTCGGTGGTA-ACCTTTTTAAAGCCCACATAAA
* * * * ** * * ** *
1013475 TCAGTGTCATCCTTTTAAAGCGC--ACAAGTTAGTGGCACCCTTTCAAAAG-CC-CATAAG
1 TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
** * * * * * * *
1013532 TTAGTGGCACCCTTTCAAAGCCC--ACGAGTCGGTGGCATCC-TTTCAAAG--CTCATAAG
1 TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
** * * * * * *
1013588 TCGGTGGCACATTTTTAAATCCTACACAAGCTGCTGGTGGCAACCTTTCTCAAAGCCCACACAAA
1 TCGGTGGCACCCTTTTAAAGCCCATACAAG-T-C-GGTGGTAACCTTT-TTAAAGCCCACATAAA
* * * * * * * * * *
1013653 TTGATGGCAACCTTTCTCAAAGCCCACATAAATTGGTGGCAACCTTTCTTAAAGCCTACATAAG
1 TCGGTGGCACCCTTT-T-AAAGCCCATACAAGTCGGTGGTAACCTTT-TTAAAGCCCACATAAA
* * * ** * * * * *
1013717 TTGGTGGTAACCCTTTTAAAGCCCACACAAGTCTATGG-CACTTTTTTAAAGTCTACA-CAA
1 TCGGTGG-CACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
* * * *
1013777 GCTGGTGGCAACCCCTTTAAAGCCCATACAAGTCGGTGGTAATC-TTTTAAAGCCCACATAAT
1 TC-GGTGGC-ACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
* * * * * * * *
1013839 TTGGTGGTAACCTTTTGAAGCCCACACAAGTCGGTGGCAAACCTTTTCTAAAGTCCATATAAA
1 TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGG-TAACCTTTT-TAAAGCCCACATAAA
* * * * *
1013902 TCGGTGGCACCCTTTTAAAGTCCATATAAGTCAGTGGTAACCTTTTTGAAGCTCACA
1 TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACA
1013959 CAAGTCAGTG
Statistics
Matches: 404, Mismatches: 113, Indels: 54
0.71 0.20 0.09
Matches are distributed among these distances:
55 2 0.00
56 30 0.07
57 51 0.13
58 19 0.05
59 5 0.01
60 33 0.08
61 83 0.21
62 36 0.09
63 63 0.16
64 49 0.12
65 21 0.05
66 2 0.00
67 10 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (61 bp):
TCGGTGGCACCCTTTTAAAGCCCATACAAGTCGGTGGTAACCTTTTTAAAGCCCACATAAA
Found at i:1014166 original size:63 final size:61
Alignment explanation
Indices: 1014009--1014166 Score: 147
Period size: 63 Copynumber: 2.5 Consensus size: 61
1013999 ATAAAAACCC
* *
1014009 TTTTCAAAGCCCACACAAGTTAGTGGCAACCCTCTCAAAAGCCCACAAAAGTTGGCGGCATCT
1 TTTTCAAAGCCCACACAAG-TAG-GGCAACCCTCTCAAAAGCCCACAAAAGCTGGCGGAATCT
** * * * * * *
1014072 CCTTCTAAAGCCTACACAAGTTGGTGGCAACCTTGTC-AAAGCCCACACAAGCTGGTGGTAATCT
1 TTTTC-AAAGCCCACACAAG-TAG-GGCAACCCTCTCAAAAGCCCACAAAAGCTGGCGG-AATCT
1014136 TTTTCAAAGCCCACACAAGTCAGGGTCAACC
1 TTTTCAAAGCCCACACAAGT-AGGG-CAACC
1014167 ATTCTAAAGC
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
62 3 0.04
63 40 0.52
64 34 0.44
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTAGGGCAACCCTCTCAAAAGCCCACAAAAGCTGGCGGAATCT
Found at i:1014259 original size:60 final size:60
Alignment explanation
Indices: 1014187--1014376 Score: 151
Period size: 60 Copynumber: 3.2 Consensus size: 60
1014177 CCGCATAGCT
1014187 TTTCTAAGCCCAATGTCATTGGCCTTGAATCAACACATTGGCACTCATTAAATCTTCTTTC
1 TTTC-AAGCCCAATGTCATTGGCCTTGAATCAACACATTGGCACTCATTAAATCTTCTTTC
* * * * * * * *
1014248 TTTTAAGCCCAA--T-A-TCG-CTTGAATCAGCATATTGGCAC-CTTTATCAGTTTTCTCATC
1 TTTCAAGCCCAATGTCATTGGCCTTGAATCAACACATTGGCACTCATTA--AATCTTCT-TTC
** * * ** *
1014305 -TTCAAGCCTGATGTCGTTGGCTTTGAATCAACACATTGGCACTTGTCAAATCTTCTTTC
1 TTTCAAGCCCAATGTCATTGGCCTTGAATCAACACATTGGCACTCATTAAATCTTCTTTC
*
1014364 TTTCAATCCCAAT
1 TTTCAAGCCCAAT
1014377 ATCGCTAGCC
Statistics
Matches: 94, Mismatches: 25, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
54 4 0.04
55 19 0.20
56 16 0.17
57 3 0.03
58 2 0.02
59 2 0.02
60 25 0.27
61 21 0.22
62 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTCAAGCCCAATGTCATTGGCCTTGAATCAACACATTGGCACTCATTAAATCTTCTTTC
Found at i:1014334 original size:116 final size:120
Alignment explanation
Indices: 1014199--1014433 Score: 334
Period size: 116 Copynumber: 2.0 Consensus size: 120
1014189 TCTAAGCCCA
* *
1014199 ATGTCATTGGCCTTGAATCAACACATTGGCACTCATTAAATCTTCTTTCTTTTAAGCCCAATAT-
1 ATGTCATTGGCCTTGAATCAACACATTGGCACTCATCAAATCTTCTTTCTTTCAAGCCCAATATC
1014263 C-G-CTTGAATCAGCATATTGGCACCTTTATCAGTTTTCTCATC-TTCAAGCCTG
66 CAGCCTTGAATCAGCATATTGGCACCTTTATCAGTTTTCTCATCTTTCAAGCCTG
* * ** *
1014315 ATGTCGTTGGCTTTGAATCAACACATTGGCACTTGTCAAATCTTCTTTCTTTCAATCCCAATATC
1 ATGTCATTGGCCTTGAATCAACACATTGGCACTCATCAAATCTTCTTTCTTTCAAGCCCAATATC
** *
1014380 GCTAGCCTTGAATTGGCATATTGGCACCTTTATCATTTTTCTCATCTTTCAAGC
66 -C-AGCCTTGAATCAGCATATTGGCACCTTTATCAGTTTTCTCATCTTTCAAGC
1014434 TCGATATCAC
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
116 57 0.55
118 1 0.01
120 1 0.01
121 37 0.36
122 7 0.07
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (120 bp):
ATGTCATTGGCCTTGAATCAACACATTGGCACTCATCAAATCTTCTTTCTTTCAAGCCCAATATC
CAGCCTTGAATCAGCATATTGGCACCTTTATCAGTTTTCTCATCTTTCAAGCCTG
Found at i:1015395 original size:3 final size:3
Alignment explanation
Indices: 1015387--1015434 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1015377 AAAATCAAAA
1015387 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1015435 CAAAAAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1015541 original size:62 final size:62
Alignment explanation
Indices: 1015436--1015560 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
1015426 AATAATAATC
* *
1015436 AAAAAATGATGATGATGGCTAAATTAGTGGAGGTTCCATTAATTAAGCCACCTACACCATTA
1 AAAAAATGATGATGATGGCCAAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
* * *
1015498 AAAAAATGATGATGATGGCCGAATTAGTGGAGGTTTCACTAATTAAGCCACTTACACCATTA
1 AAAAAATGATGATGATGGCCAAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
1015560 A
1 A
1015561 GGTGGGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (62 bp):
AAAAAATGATGATGATGGCCAAATTAGTGGAGGTTCCACTAATTAAGCCACCTACACCATTA
Found at i:1015974 original size:17 final size:18
Alignment explanation
Indices: 1015952--1015989 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1015942 TAGGGAAAAT
1015952 AAAAAA-GAAGCAAATAA
1 AAAAAAGGAAGCAAATAA
*
1015969 AAAAAAGGGAGCAAATAA
1 AAAAAAGGAAGCAAATAA
1015987 AAA
1 AAA
1015990 GGCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAAAAGGAAGCAAATAA
Found at i:1018137 original size:96 final size:97
Alignment explanation
Indices: 1017867--1018182 Score: 422
Period size: 97 Copynumber: 3.3 Consensus size: 97
1017857 TATCGGGGGT
* * * * *
1017867 ACTCCAACCATATTCCTTCGAGGGGATA-ATCCAACCCTGCTTTTAAACATATCAATGTTTAAAT
1 ACTCCAACCCTATTCCTCCGAGGGGATATA-CCAACCCCGCTTTTAAACACATCAAAGTTTAAAT
*
1017931 CTTATTCTCACTTAAATTGTCATCATCGGGGAC
65 CTTATTCTCACTTAAATTGTCATCATCGGAGAC
* * * *
1017964 ACTCCAACCCTATTCCTCTGAGGAGACACT-CCAACCTCGCTTTTAAACACATCAAAGTTTAAAT
1 ACTCCAACCCTATTCCTCCGAGGGGATA-TACCAACCCCGCTTTTAAACACATCAAAGTTTAAAT
*
1018028 CTTATTCTCACTTAAATTGTCATCATCGTAGAC
65 CTTATTCTCACTTAAATTGTCATCATCGGAGAC
* * *
1018061 ACTTCAACCC-ATTCCTCCGAGGGGATATACCAACCCCGCTTTTAAACACATTAAAATTTAAATC
1 ACTCCAACCCTATTCCTCCGAGGGGATATACCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
* * *
1018125 CTATTCTCACTTAAATTGTCATCATCGGGGAT
66 TTATTCTCACTTAAATTGTCATCATCGGAGAC
* *
1018157 ACTCCAACCCTATTCTTCCAAGGGGA
1 ACTCCAACCCTATTCCTCCGAGGGGA
1018183 AACTCTAACC
Statistics
Matches: 190, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 83 0.44
97 106 0.56
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (97 bp):
ACTCCAACCCTATTCCTCCGAGGGGATATACCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
TTATTCTCACTTAAATTGTCATCATCGGAGAC
Found at i:1020592 original size:398 final size:400
Alignment explanation
Indices: 1019850--1020638 Score: 1237
Period size: 398 Copynumber: 2.0 Consensus size: 400
1019840 GGCTTTGATT
* ** * *
1019850 CCCTCTCTTGACCCGATGATTGTGTCACCTTTTGGTTATGAATCATTTTCACTTACTGCTTCCTT
1 CCCTCTCTTGACCCAATGATCATGTCACCTTTTGGCTACGAATCATTTTCACTTACTGCTTCCTT
* *
1019915 GACTGTACATTAGCCTTGCATCCTAAGCCTCTTTTGTCAACTTGAGTGGTGATTTGTAAGGCTCA
66 GACTGCACATTAGCCTTGCATCCTAAGCCTCTTTTATCAACTTGAGTGGTGATTTGTAAGGCTCA
1019980 GGCCATCCCTTGAAGATTCTTGTTGAGTCCTTTTCCAGCACAGCAACCTTTACCAACGGTCATTT
131 GGCCATCCCTTGAAGATTCTTGTTGAGTCCTTTTCCAGCACAGCAACCTTTACCAACGGTCATTT
* * * *
1020045 TTAAACCCAAGTGGGTGTTTTTCAGCAGGCAAGGTTCAATTATTGGCAATCATTCTCCTGCAAAT
196 TTAAACCCAAGTGAGTGTTTTTCAACAGGCAAGGTTCAATTATTAGCAATCATTCTCCTACAAAT
** * * *
1020110 GTCATGTTAATGAACTCGAAGGATTGAAAAGACAACATTTGTGCATTTTCATTGGGCTCTATATA
261 GTCACATTAACGAACTCAAAGGATTGAAAAGACAACATTTGTGCATTTTCATTAGGCTCTATATA
* *
1020175 GGTATCATCACTGAAAGCAATGGCAATCATTTCTTCTTTTGCCTCGATGGTGACTACCTTGTCAT
326 GGTATCATCACTGAAAGCAATGGAAATCATTTCTTATTTTGCCTCGATGGTGACTACCTTGTCAT
1020240 CTACCTTGTC
391 CTACCTTGTC
* *
1020250 CCCT-TCTTGACCCAATGATCATGTCATCTTTTGGCTACGAATCATTTTCACTTATTGCTTCCTT
1 CCCTCTCTTGACCCAATGATCATGTCACCTTTTGGCTACGAATCATTTTCACTTACTGCTTCCTT
*
1020314 G-CTTGCACATTAGCCTTGCAT-CTAAGCCTCTTTTATCAACTTGAGTGGTGATTTGTAAGGCTT
66 GAC-TGCACATTAGCCTTGCATCCTAAGCCTCTTTTATCAACTTGAGTGGTGATTTGTAAGGCTC
* * **
1020377 AGGCCATCCCTTGAAGATTCTTGTCT-AGTCCTTTTCCAGCATAGCACCCTTTACCAGTGGTCAT
130 AGGCCATCCCTTGAAGATTCTTGT-TGAGTCCTTTTCCAGCACAGCAACCTTTACCAACGGTCAT
* *
1020441 TTTTAAACCCAAGTGAGTGTTTTTCAATAGGCAAGGTTCAATTATTAGCAATCCTTCTCCTACAA
194 TTTTAAACCCAAGTGAGTGTTTTTCAACAGGCAAGGTTCAATTATTAGCAATCATTCTCCTACAA
1020506 ATGTCACATTAACGAACTCAAAGGATTGAAAAGACAAC-TTTGGTGCATTTTCATTAGGCTCTAT
259 ATGTCACATTAACGAACTCAAAGGATTGAAAAGACAACATTT-GTGCATTTTCATTAGGCTCTAT
* * * *
1020570 GTAGGTATCATCATTGAAAGCAATGGAAATCATTTCTTATTTTGCCTCGGTGGTGACTTCCTTGT
323 ATAGGTATCATCACTGAAAGCAATGGAAATCATTTCTTATTTTGCCTCGATGGTGACTACCTTGT
1020635 CATC
388 CATC
1020639 CTTGTCATCT
Statistics
Matches: 355, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
397 3 0.01
398 276 0.78
399 72 0.20
400 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (400 bp):
CCCTCTCTTGACCCAATGATCATGTCACCTTTTGGCTACGAATCATTTTCACTTACTGCTTCCTT
GACTGCACATTAGCCTTGCATCCTAAGCCTCTTTTATCAACTTGAGTGGTGATTTGTAAGGCTCA
GGCCATCCCTTGAAGATTCTTGTTGAGTCCTTTTCCAGCACAGCAACCTTTACCAACGGTCATTT
TTAAACCCAAGTGAGTGTTTTTCAACAGGCAAGGTTCAATTATTAGCAATCATTCTCCTACAAAT
GTCACATTAACGAACTCAAAGGATTGAAAAGACAACATTTGTGCATTTTCATTAGGCTCTATATA
GGTATCATCACTGAAAGCAATGGAAATCATTTCTTATTTTGCCTCGATGGTGACTACCTTGTCAT
CTACCTTGTC
Found at i:1021198 original size:48 final size:48
Alignment explanation
Indices: 1021110--1021201 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
1021100 TTGGTGGCAC
*
1021110 ATATACCTTGTTTAACACCTTCAGCAATATATTTCAGTGAACCTTTAA
1 ATATACCTTGTTTAACACCTTCAGCAATACATTTCAGTGAACCTTTAA
* * **
1021158 ATATGCCTTGTTTAACACCTTCAGCAATGCATTTTGGTGAACCT
1 ATATACCTTGTTTAACACCTTCAGCAATACATTTCAGTGAACCT
1021202 CTGAATTAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (48 bp):
ATATACCTTGTTTAACACCTTCAGCAATACATTTCAGTGAACCTTTAA
Found at i:1026907 original size:111 final size:111
Alignment explanation
Indices: 1026713--1026939 Score: 445
Period size: 111 Copynumber: 2.0 Consensus size: 111
1026703 TTTTTTACTC
1026713 TGACTTTACCACATTTATTGAAATGACATTTATTGCATGATGAGATGATTCTGACATCCACATCA
1 TGACTTTACCACATTTATTGAAATGACATTTATTGCATGATGAGATGATTCTGACATCCACATCA
*
1026778 TAAAAAAAATTAGTAAACAAGATAAAAGGGTATCATAACCAAATAA
66 TAAAAAAAAATAGTAAACAAGATAAAAGGGTATCATAACCAAATAA
1026824 TGACTTTACCACATTTATTGAAATGACATTTATTGCATGATGAGATGATTCTGACATCCACATCA
1 TGACTTTACCACATTTATTGAAATGACATTTATTGCATGATGAGATGATTCTGACATCCACATCA
1026889 TAAAAAAAAATAGTAAACAAGATAAAAGGGTATCATAACCAAATAA
66 TAAAAAAAAATAGTAAACAAGATAAAAGGGTATCATAACCAAATAA
1026935 TGACT
1 TGACT
1026940 AAAACTGACG
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 115 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (111 bp):
TGACTTTACCACATTTATTGAAATGACATTTATTGCATGATGAGATGATTCTGACATCCACATCA
TAAAAAAAAATAGTAAACAAGATAAAAGGGTATCATAACCAAATAA
Found at i:1028901 original size:13 final size:13
Alignment explanation
Indices: 1028883--1028909 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1028873 ACAATTGTGC
1028883 ATGTATTGATACA
1 ATGTATTGATACA
1028896 ATGTATTGATACA
1 ATGTATTGATACA
1028909 A
1 A
1028910 AGCATAATGT
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:1029873 original size:33 final size:33
Alignment explanation
Indices: 1029821--1029888 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1029811 AAGTCCACTA
*
1029821 AAGTGCTCATCCATATGCTGCGAGAGTGAAGTG
1 AAGTGCTCATCCATATGCTGCGAAAGTGAAGTG
*
1029854 AAGTGCTCA-CTCATGTGCTGCGAAAGTGAAGTG
1 AAGTGCTCATC-CATATGCTGCGAAAGTGAAGTG
1029887 AA
1 AA
1029889 TCAACTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (33 bp):
AAGTGCTCATCCATATGCTGCGAAAGTGAAGTG
Found at i:1035591 original size:6 final size:6
Alignment explanation
Indices: 1035580--1035614 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1035570 TTGTTTTATT
* *
1035580 TATATG TATATG TATATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
1035615 ATTGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:1041651 original size:14 final size:16
Alignment explanation
Indices: 1041620--1041666 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1041610 AAATACACTC
1041620 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
1041636 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
1041650 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
1041666 A
1 A
1041667 TAAAAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:1041940 original size:1 final size:1
Alignment explanation
Indices: 1041934--1041972 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
1041924 ACCTAATCCT
* * *
1041934 AAAAAAAGAAAAAAAACAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1041973 CCTTTTCACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.05, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1041973 original size:11 final size:12
Alignment explanation
Indices: 1041942--1041972 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1041932 CTAAAAAAAG
1041942 AAAAAAAACAAA
1 AAAAAAAACAAA
1041954 AAAAAAAACAAA
1 AAAAAAAACAAA
1041966 AAAAAAA
1 AAAAAAA
1041973 CCTTTTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:1043048 original size:28 final size:28
Alignment explanation
Indices: 1043007--1044036 Score: 953
Period size: 28 Copynumber: 36.3 Consensus size: 28
1042997 AGTGGCATTT
* **
1043007 CTTTTCAAAGTCCACAACTCCATGGCATA
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
*
1043036 TTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
1043064 CTTTTTAAGTCCACAACTCCATGGTATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043092 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
1043120 TTTTTAAAGTCCACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
1043148 CTTTTTAAGTCCACAACTCCGTGGTATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
1043176 CTTCTAAAGTCCATAACTTCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
1043204 CTTTTAAAGTCCACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
1043232 CTTTTTAAGTCCACAACTCCATGGTATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043260 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* ** *
1043288 TTTTTAAAGTCCACAACTCTATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
1043316 C-TTTAAAGTCCATAACTCCGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043342 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043370 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043398 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
1043426 CTTTT-AAGTCCATAATTTCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
1043453 CTTTAAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
1043481 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
** *
1043509 CTTTTAAAGTCCACAACTCTATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * **
1043537 CTTTT-AAGTCTACCACTCTATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
1043564 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
1043592 CTTTTAAAGTCCATAACTCCGTGGTACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
1043620 C-TTTAAAGTCCACAACTCCGTGGGACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
1043647 CTTTTGAAGTCCACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
1043675 CTTTT-AAGTTCACAACGT-CGTGGCATC
1 CTTTTAAAGTCCACAAC-TCCGTGGCACC
* * * **
1043702 CTTTTAAGGCCCACAAGTGAGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
1043729 CTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CTTT-TAAAG-TC-CACAACTCCGTGGCACC
* * * *
1043760 CTATTTCAAAGCCCACACAAGTCGGTGGAAACC
1 CT-TTT-AAAG-TC-CACAACTCCGTGG-CACC
* * * *
1043793 CATTTGAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTTAAAG-TC-CACAACTCCGTGGC-ACC
* * * *
1043825 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTTAAAG-TC-CACAACTCCGTGGC-ACC
* * * *
1043857 CATTTCAAAGCCCACAAGTCGGTGGCAACC
1 C-TTTTAAAGTCCACAACTCCGTGGC-ACC
* ** * * *
1043887 CATTTCAAAACCCACAAATCAGTGGCATC
1 C-TTTTAAAGTCCACAACTCCGTGGCACC
* * * **
1043916 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
1043944 CTTTCAAAG-CCAACAAGTCAGTGGCACC
1 CTTTTAAAGTCC-ACAACTCCGTGGCACC
* * * *
1043972 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
1044000 CTTTCAAAGTCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
1044028 CTTTCAAAG
1 CTTTTAAAG
1044037 CCCATGAGTT
Statistics
Matches: 884, Mismatches: 98, Indels: 39
0.87 0.10 0.04
Matches are distributed among these distances:
26 2 0.00
27 146 0.17
28 571 0.65
29 11 0.01
30 54 0.06
31 6 0.01
32 88 0.10
33 5 0.01
34 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:1043776 original size:32 final size:31
Alignment explanation
Indices: 1043713--1044111 Score: 328
Period size: 28 Copynumber: 13.5 Consensus size: 31
1043703 TTTTAAGGCC
*
1043713 CACAAGTGAGTGGC-ACC-TTTCTAAAGCCCA
1 CACAAGTCAGTGGCAACCATTTC-AAAGCCCA
*
1043743 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACC-ATTTCAAAGCCCA
* * *
1043775 CACAAGTCGGTGGAAACCCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAA-CCATTTCAAAGCCCA
*
1043807 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAA-CCATTTCAAAGCCCA
*
1043839 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAA-CCATTTCAAAGCCCA
* *
1043869 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCAGTGGCAA-CCATTTCAAAGCCCA
*
1043901 CA-AA-TCAGTGGCATCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
* *
1043927 CACAAGTTAGTGGC-ACCCTTTCAAAG-CCA
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
*
1043956 -ACAAGTCAGTGGC-ACCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
* *
1043983 CACAAGTCAGTGGC-ACCCTTTCAAAG-TC-
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
*
1044011 CACAAGTCAGTGGCATCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
** * *
1044039 CATGAGTTAGTGGCATCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCATTTCAAAGCCCA
* * * *
1044067 TACAAGTCAATGG-TATC-TCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCAT-TTCAAAGCCCA
*
1044097 CACAAGTTAGTGGCA
1 CACAAGTCAGTGGCA
1044112 TTTTTTTTTG
Statistics
Matches: 322, Mismatches: 31, Indels: 31
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.01
27 8 0.02
28 139 0.43
29 6 0.02
30 57 0.18
31 9 0.03
32 95 0.30
33 6 0.02
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (31 bp):
CACAAGTCAGTGGCAACCATTTCAAAGCCCA
Found at i:1043807 original size:64 final size:64
Alignment explanation
Indices: 1043730--1044014 Score: 318
Period size: 64 Copynumber: 4.7 Consensus size: 64
1043720 GAGTGGCACC
*
1043730 TTTCTAAAGCCCACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
* *
1043795 TTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
* * * *
1043859 TTTCAAAG-CC-CACAAGTCGGTGGCAACCCATTTCAAAACCCACA-AA-TCAGTGG-CATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
** * *
1043917 TTTCAAAG-CC-CACAAGTTAGTGGC-ACCC-TTTCAAAG-CCA-ACAAGTCAGTGG-CACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
* *
1043973 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGTCCACA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA
1044015 AGTCAGTGGC
Statistics
Matches: 203, Mismatches: 13, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
54 1 0.00
55 5 0.02
56 53 0.26
57 7 0.03
58 23 0.11
59 3 0.01
60 6 0.03
61 2 0.01
62 33 0.16
63 2 0.01
64 65 0.32
65 3 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.19
Consensus pattern (64 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGAAACCCA
Found at i:1044281 original size:48 final size:48
Alignment explanation
Indices: 1044222--1044353 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
1044212 GGCACCTTTA
*
1044222 TTAGCTCAATGTCTTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCTTTGGCCTTGAATAAGCACATTGTCCACTTTTCCC
* * *
1044270 TTAGCTAAATGT-TGCTAGCCTTGAATAAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCT-TTGGCCTTGAATAAGCACATTGTCCACTTTTCCC
* * * **
1044318 TTAGCTCGATGTCATTGACCTTGAATTGGCACATTG
1 TTAGCTCAATGTCTTTGGCCTTGAATAAGCACATTG
1044354 GCACCCCTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.01
48 69 0.99
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (48 bp):
TTAGCTCAATGTCTTTGGCCTTGAATAAGCACATTGTCCACTTTTCCC
Found at i:1045829 original size:6 final size:6
Alignment explanation
Indices: 1045818--1045852 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1045808 TTGTTTTATT
* *
1045818 TATATG TATATG TATATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
1045853 TGAAAATCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:1055658 original size:13 final size:14
Alignment explanation
Indices: 1055640--1055668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1055630 AAAAAAATTA
1055640 TTTATTA-TTTTAT
1 TTTATTATTTTTAT
1055653 TTTATTATTTTTAT
1 TTTATTATTTTTAT
1055667 TT
1 TT
1055669 CCAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTATTTTTAT
Found at i:1056528 original size:11 final size:10
Alignment explanation
Indices: 1056488--1056524 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1056478 AAATCCTAAC
*
1056488 TATTTTTTCC
1 TATTTTTTCT
1056498 TA-TTTTTCT
1 TATTTTTTCT
1056507 TATTTTTTCT
1 TATTTTTTCT
1056517 TATTTTTT
1 TATTTTTT
1056525 TCTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (10 bp):
TATTTTTTCT
Found at i:1056539 original size:17 final size:18
Alignment explanation
Indices: 1056514--1056547 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1056504 TCTTATTTTT
1056514 TCTTATTTTTT-TCTTTC
1 TCTTATTTTTTCTCTTTC
*
1056531 TCTTTTTTTTTCTCTTT
1 TCTTATTTTTTCTCTTT
1056548 TTTTGCTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTATTTTTTCTCTTTC
Found at i:1056550 original size:12 final size:12
Alignment explanation
Indices: 1056520--1056551 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
1056510 TTTTTCTTAT
1056520 TTTTTTCTTTCTC
1 TTTTTT-TTTCTC
1056533 TTTTTTTTTCTC
1 TTTTTTTTTCTC
1056545 TTTTTTT
1 TTTTTTT
1056552 GCTAAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:1057577 original size:89 final size:88
Alignment explanation
Indices: 1057465--1057858 Score: 363
Period size: 87 Copynumber: 4.4 Consensus size: 88
1057455 CCTCGCCTTA
* * * * * *
1057465 GAAATCAGGCTTTGTGATGCATTAATATCATCTAATGGTTGAATGAAGGAGATATGATTGGGAAT
1 GAAATTAGGCTTTGTGATGCATCAATA-CATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
1057530 GTATGGGCCGCAC-CTTGCTCTAAG
65 GTATGGGCCGCACTCTTGC-CTAAG
* * * *
1057554 GAAATTAGGCTTTGTGATGCATTATTACCATCTAGTGGTTGAATGAAGGGGATATGATT-GGGA-
1 GAAATTAGGCTTTGTGATGCATCAATA-CATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
* * * * *
1057617 CTATGCGACTCCCTCTTGCCTCAAG
65 GTATGGGCCGCACTCTTGCCT-AAG
* *
1057642 GAAATTAGGCTTTGTCATGCATCAATACATCTAGTGGTTGAATGAAGGGGATATAATAAGGAATG
1 GAAATTAGGCTTTGTGATGCATCAATACATCTAGTGGTTGAATGAAGGGGATATAATTAGGAATG
* *
1057707 TGT-GGCTC-C-CTCTTGCCTTGAG
66 TATGGGC-CGCACTCTTGCC-TAAG
* *
1057729 AAAATTAGGCTTTGTGATGCATCAATACTATCTAGTGGTTGAATGAAAGGGATATAATTTAGGAA
1 GAAATTAGGCTTTGTGATGCATCAATAC-ATCTAGTGGTTGAATGAAGGGGATATAA-TTAGGAA
* * * *
1057794 TGTGTAGGCTGCACGC-TGCCCTAAG
64 TGTATGGGCCGCACTCTTG-CCTAAG
* * ** *
1057819 GAAATCAGG-TTCTATGATGTGTTAATACTATCTAGTGGTT
1 GAAATTAGGCTT-TGTGATGCATCAATAC-ATCTAGTGGTT
1057859 AGGAAAGTGG
Statistics
Matches: 257, Mismatches: 35, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
87 75 0.29
88 68 0.26
89 70 0.27
90 40 0.16
91 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (88 bp):
GAAATTAGGCTTTGTGATGCATCAATACATCTAGTGGTTGAATGAAGGGGATATAATTAGGAATG
TATGGGCCGCACTCTTGCCTAAG
Found at i:1057716 original size:87 final size:89
Alignment explanation
Indices: 1057465--1057803 Score: 384
Period size: 87 Copynumber: 3.8 Consensus size: 89
1057455 CCTCGCCTTA
* * * * * * *
1057465 GAAATCAGGCTTTGTGATGCATTAATATCATCTAATGGTTGAATGAAGGAGATATGATTGGGAAT
1 GAAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
* *
1057530 GTATGGGC-CGCAC-CTTG-CTCTAAG
66 GTGTAGGCTC-C-CTCTTGCCTC-AAG
* * * * *
1057554 GAAATTAGGCTTTGTGATGCATTATTACCATCTAGTGGTTGAATGAAGGGGATATGATTGGGACT
1 GAAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
* * *
1057619 ATG-CGACTCCCTCTTGCCTCAAG
66 GTGTAGGCTCCCTCTTGCCTCAAG
* *
1057642 GAAATTAGGCTTTGTCATGCATCAATA-CATCTAGTGGTTGAATGAAGGGGATATAATAAGGAAT
1 GAAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
**
1057706 GTGT-GGCTCCCTCTTGCCTTGAG
66 GTGTAGGCTCCCTCTTGCCTCAAG
* * *
1057729 AAAATTAGGCTTTGTGATGCATCAATACTATCTAGTGGTTGAATGAAAGGGATATAATTTAGGAA
1 GAAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGATATAA-TTAGGAA
1057794 TGTGTAGGCT
65 TGTGTAGGCT
1057804 GCACGCTGCC
Statistics
Matches: 217, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
87 77 0.35
88 61 0.28
89 75 0.35
90 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (89 bp):
GAAATTAGGCTTTGTGATGCATCAATACCATCTAGTGGTTGAATGAAGGGGATATAATTAGGAAT
GTGTAGGCTCCCTCTTGCCTCAAG
Found at i:1059458 original size:12 final size:11
Alignment explanation
Indices: 1059401--1059449 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1059391 CATTTTGCTC
1059401 TTTTTTTGTTT
1 TTTTTTTGTTT
* ***
1059412 CTTTTCCCTTT
1 TTTTTTTGTTT
1059423 TTTTTTTGTTT
1 TTTTTTTGTTT
1059434 TTGTTTTTGTTT
1 TT-TTTTTGTTT
1059446 TTTT
1 TTTT
1059450 GTATTTTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:1059463 original size:20 final size:20
Alignment explanation
Indices: 1059423--1059463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1059413 TTTTCCCTTT
*
1059423 TTTTTTTGTTTTTGTTTTTG
1 TTTTTTTGTTTTTGTTATTG
1059443 TTTTTTTGTATTTT-TTATTG
1 TTTTTTTGT-TTTTGTTATTG
1059463 T
1 T
1059464 GTAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.83
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTATTG
Found at i:1061016 original size:17 final size:17
Alignment explanation
Indices: 1060976--1061017 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1060966 TGAATTTTCC
*
1060976 TTTTCTCTTTGTTTCTT
1 TTTTCTTTTTGTTTCTT
*
1060993 TTTTCTTTTTTTTTCTT
1 TTTTCTTTTTGTTTCTT
1061010 TTTTCTTT
1 TTTTCTTT
1061018 AAATCCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTTGTTTCTT
Found at i:1061636 original size:7 final size:7
Alignment explanation
Indices: 1061624--1061658 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1061614 TCATCAAAAT
1061624 ATTCAAA
1 ATTCAAA
1061631 ATTCAAA
1 ATTCAAA
1061638 ATTC-AA
1 ATTCAAA
1061644 ATTC-AA
1 ATTCAAA
1061650 ATTCAAA
1 ATTCAAA
1061657 AT
1 AT
1061659 ATACATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (7 bp):
ATTCAAA
Found at i:1061926 original size:28 final size:28
Alignment explanation
Indices: 1061856--1062375 Score: 429
Period size: 28 Copynumber: 18.5 Consensus size: 28
1061846 AGGAAAGTTA
*
1061856 TGGGCTTTGAAAAGGATGCTACTGACTTG
1 TGGGCTTTGAAAAGG-TGCCACTGACTTG
* *
1061885 TGGGCTCTCG-AAAGGTGCCATTGACTTG
1 TGGGCT-TTGAAAAGGTGCCACTGACTTG
* *
1061913 TGAGCTTTGAAAAGGTGCCACTGACTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
*
1061941 TGGGCTTTTGAAAAGATGCCACTGACTTG
1 TGGGC-TTTGAAAAGGTGCCACTGACTTG
* *
1061970 TGGGCTTTGAAAAGGTGCCACTAATTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * * *
1061998 TGGACTTGGAAAAGGTGCCACTGATTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * *
1062026 TGGACTTTG-AAAGGATACCACTGACTTA
1 TGGGCTTTGAAAAGG-TGCCACTGACTTG
* *
1062054 TGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
*
1062082 TGGGCTTTCGAAAAGGTGCCACT-AATT-
1 TGGGCTTT-GAAAAGGTGCCACTGACTTG
*
1062109 TGGGAACTTTG-AAAGCATGCCACTGACTTG
1 TGGG--CTTTGAAAAG-GTGCCACTGACTTG
* *
1062139 TGGGCTTTGGAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1062167 TGGGCTTTGGAAGGGTGCCACTTGACTTG
1 TGGGCTTTGAAAAGGTGCCAC-TGACTTG
* *
1062196 TGGGCTTTGGAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1062224 TGGGC-TTG-AAAGTATGCCA-TGAAGTTG
1 TGGGCTTTGAAAAG-GTGCCACTG-ACTTG
* * * * *
1062251 TGGAC-TTAAAAAGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * *
1062278 TGGACTTT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGG-TGCCACTGACTTG
* * *
1062306 TGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGG-TGCCACTGACTTG
* * *
1062333 TGGAC-TTCAAAAGGATGCCACTGGAGTTG
1 TGGGCTTTGAAAAGG-TGCCACT-GACTTG
*
1062362 TGGACTTT-AAAAGG
1 TGGGCTTTGAAAAGG
1062376 ATACCGTACA
Statistics
Matches: 430, Mismatches: 39, Indels: 44
0.84 0.08 0.09
Matches are distributed among these distances:
26 5 0.01
27 83 0.19
28 225 0.52
29 109 0.25
30 8 0.02
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (28 bp):
TGGGCTTTGAAAAGGTGCCACTGACTTG
Found at i:1061999 original size:85 final size:84
Alignment explanation
Indices: 1061853--1062234 Score: 441
Period size: 85 Copynumber: 4.5 Consensus size: 84
1061843 TCTAGGAAAG
* * * * *
1061853 TTATGGGCTTTGAAAAGGATGCTACTGACTTGTGGGCTCTCG-AAAGGTGCCATTGACTTGTGAG
1 TTATGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCT-TTGAAAAGGTGCCACTAACTTGTGGG
1061917 CTTTGAAAAGGTGCCACTGAC
64 CTTTGAAAAGGTGCCACTGAC
* *
1061938 TTATGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAATTTGTGGAC
1 TTATGGGC-TTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGC
* *
1062003 TTGGAAAAGGTGCCACTGAT
65 TTTGAAAAGGTGCCACTGAC
* * * * *
1062023 TTATGGACTTTGAAAGGATACCACTGACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
1 TTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCT
*
1062088 TTCGAAAAGGTGCCACT-AA
66 TT-GAAAAGGTGCCACTGAC
* * *
1062107 TT-TGGGAACTTTG-AAAGCATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGG
1 TTATGGG--CTTTGAAAAG-ATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGG
* *
1062170 GCTTTGGAAGGGTGCCACTTGAC
63 GCTTTGAAAAGGTGCCAC-TGAC
* * * *
1062193 TTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGC-TTGAAA
1 TTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAA
1062235 GTATGCCATG
Statistics
Matches: 257, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
83 3 0.01
84 76 0.30
85 160 0.62
86 14 0.05
87 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (84 bp):
TTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCT
TTGAAAAGGTGCCACTGAC
Found at i:1062251 original size:27 final size:27
Alignment explanation
Indices: 1062221--1062566 Score: 395
Period size: 27 Copynumber: 12.4 Consensus size: 27
1062211 TGCCACTGAC
* * * *
1062221 TTGTGGGCTTGAAAGTATGCCATGAAG
1 TTGTGGACTTAAAAGGATGCCATGGAG
* *
1062248 TTGTGGACTTAAAAAGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCATGGAG
*
1062275 TTGTGGACTTTAAAAGGATGCCACGGAG
1 TTGTGGAC-TTAAAAGGATGCCATGGAG
*
1062303 TTGTGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCATGGAG
1062330 TTGTGGACTTCAAAAGGATGCCACTGGAG
1 TTGTGGACTT-AAAAGGATGCCA-TGGAG
* * **
1062359 TTGTGGACTTTAAAAGGATACCGTACAG
1 TTGTGGAC-TTAAAAGGATGCCATGGAG
1062387 TTGTGGACTTAAAAGGATGCCATGGAG
1 TTGTGGACTTAAAAGGATGCCATGGAG
*
1062414 TGGTGGACTTAAAAGGATGCCATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCAT-----GGAG
* *
1062446 TGGTGGACTTTAAAGGGATGCCATGGAG
1 TTGTGGAC-TTAAAAGGATGCCATGGAG
* *
1062474 TTGTGGACTTTAAAGGGATGCCACGGAG
1 TTGTGGAC-TTAAAAGGATGCCATGGAG
* * *
1062502 TTATGGACTTTAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCATGGAG
*
1062529 TTGTGAACTTTAAAAGGATGCCATGGAG
1 TTGTGGAC-TTAAAAGGATGCCATGGAG
1062557 TTGTGGACTT
1 TTGTGGACTT
1062567 TGAAAAGAAA
Statistics
Matches: 280, Mismatches: 28, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
27 120 0.43
28 110 0.39
29 22 0.08
30 2 0.01
32 12 0.04
33 14 0.05
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (27 bp):
TTGTGGACTTAAAAGGATGCCATGGAG
Done.