Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 135 of 199
Found at i:39428181 original size:13 final size:13
Alignment explanation
Indices: 39428163--39428187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39428153 TGGTCATCAT
39428163 GGTGTGAACACAA
1 GGTGTGAACACAA
39428176 GGTGTGAACACA
1 GGTGTGAACACA
39428188 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39431447 original size:17 final size:18
Alignment explanation
Indices: 39431425--39431458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39431415 ACAACACTCC
*
39431425 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
39431442 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
39431459 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:39431566 original size:15 final size:16
Alignment explanation
Indices: 39431541--39431572 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39431531 TATCTCACAC
39431541 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39431557 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39431572 T
1 T
39431573 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:39432548 original size:17 final size:18
Alignment explanation
Indices: 39432514--39432553 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39432504 TTTAACTTGA
* *
39432514 TTTTTTTGGTCACCTTTT
1 TTTTTTTGCTCACATTTT
39432532 TTTTTTTGCTCA-ATTTT
1 TTTTTTTGCTCACATTTT
39432549 TTTTT
1 TTTTT
39432554 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTTTTTGCTCACATTTT
Found at i:39432560 original size:12 final size:12
Alignment explanation
Indices: 39432531--39432618 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 12
39432521 GGTCACCTTT
39432531 TTTTTTTTGCTCAA
1 TTTTTTTT--TCAA
*
39432545 TTTTTTTTTCAC
1 TTTTTTTTTCAA
*
39432557 TTTTTTTTTGAATA
1 TTTTTTTTT-CA-A
39432571 TTTTTTTTTCAATCAA
1 -TTTTTTTT---TCAA
39432587 TTTTTTTTTTCGAA
1 -TTTTTTTTTC-AA
39432601 TTTTTTTTT--A
1 TTTTTTTTTCAA
39432611 TTTTTTTT
1 TTTTTTTT
39432619 GTTACTCCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.14
12 12 0.19
13 12 0.19
14 10 0.16
15 8 0.13
16 10 0.16
17 1 0.02
18 1 0.02
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:39432574 original size:14 final size:14
Alignment explanation
Indices: 39432557--39432609 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
39432547 TTTTTTTCAC
39432557 TTTTTTTTTGAATA
1 TTTTTTTTTGAATA
*
39432571 TTTTTTTTTCAATCAA
1 TTTTTTTTTGAAT--A
39432587 TTTTTTTTTTCGAAT-
1 -TTTTTTTTT-GAATA
39432602 TTTTTTTT
1 TTTTTTTT
39432610 ATTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 20 0.61
16 1 0.03
17 9 0.27
18 3 0.09
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGAATA
Found at i:39432617 original size:42 final size:40
Alignment explanation
Indices: 39432528--39432618 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 40
39432518 TTTGGTCACC
*
39432528 TTTTTTTTTTTGCTCAATTTTTTTTTCACTTTTTTTTTGAA
1 TTTTTTTTTTTGCTCAATTTTTTTTTCAATTTTTTTTT-AA
*
39432569 TATTTTTTTTT-CAATCAATTTTTTTTTTCGAATTTTTTTTT-A
1 TTTTTTTTTTTGC--TCAA-TTTTTTTTTC-AATTTTTTTTTAA
39432611 TTTTTTTT
1 TTTTTTTT
39432619 GTTACTCCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 1 0.02
41 10 0.23
42 12 0.28
43 10 0.23
44 10 0.23
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (40 bp):
TTTTTTTTTTTGCTCAATTTTTTTTTCAATTTTTTTTTAA
Found at i:39436263 original size:246 final size:246
Alignment explanation
Indices: 39435829--39436325 Score: 985
Period size: 246 Copynumber: 2.0 Consensus size: 246
39435819 AAGAACAAGT
39435829 TTCATATGGATTAGTCGAAATGCTCCTCACTTTTTCTGGTTCGTTTATCTCTTTTTCTCTCGTTT
1 TTCATATGGATTAGTCGAAATGCTCCTCACTTTTTCTGGTTCGTTTATCTCTTTTTCTCTCGTTT
*
39435894 CTTTTCTAATCTCAACTTCTTTTTTTCTCTTTTCATTTCCTCTCTCATTTTCACTTTTATTTTTG
66 CTTTTCTAATCTCAACTTCTTTTTTTCTCTTTTCATTTCCTCTCTCATTTTCACTTTTATTTTCG
39435959 ACCTCACTCTCTTTTTGGATTTCTTTTTCTTTTTCAATCTCTTTTTCTTTTCTTTCGATTTCTTT
131 ACCTCACTCTCTTTTTGGATTTCTTTTTCTTTTTCAATCTCTTTTTCTTTTCTTTCGATTTCTTT
39436024 TTCTCGCTCGTACTCTTGTACAATCTCAATTTCTTTTTCGAATTCTTTCTC
196 TTCTCGCTCGTACTCTTGTACAATCTCAATTTCTTTTTCGAATTCTTTCTC
39436075 TTCATATGGATTAGTCGAAATGCTCCTCACTTTTTCTGGTTCGTTTATCTCTTTTTCTCTCGTTT
1 TTCATATGGATTAGTCGAAATGCTCCTCACTTTTTCTGGTTCGTTTATCTCTTTTTCTCTCGTTT
39436140 CTTTTCTAATCTCAACTTCTTTTTTTCTCTTTTCATTTCCTCTCTCATTTTCACTTTTATTTTCG
66 CTTTTCTAATCTCAACTTCTTTTTTTCTCTTTTCATTTCCTCTCTCATTTTCACTTTTATTTTCG
39436205 ACCTCACTCTCTTTTTGGATTTCTTTTTCTTTTTCAATCTCTTTTTCTTTTCTTTCGATTTCTTT
131 ACCTCACTCTCTTTTTGGATTTCTTTTTCTTTTTCAATCTCTTTTTCTTTTCTTTCGATTTCTTT
39436270 TTCTCGCTCGTACTCTTGTACAATCTCAATTTCTTTTTCGAATTCTTTCTC
196 TTCTCGCTCGTACTCTTGTACAATCTCAATTTCTTTTTCGAATTCTTTCTC
39436321 TTCAT
1 TTCAT
39436326 TTTCTTTTTC
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 250 1.00
ACGTcount: A:0.13, C:0.24, G:0.07, T:0.56
Consensus pattern (246 bp):
TTCATATGGATTAGTCGAAATGCTCCTCACTTTTTCTGGTTCGTTTATCTCTTTTTCTCTCGTTT
CTTTTCTAATCTCAACTTCTTTTTTTCTCTTTTCATTTCCTCTCTCATTTTCACTTTTATTTTCG
ACCTCACTCTCTTTTTGGATTTCTTTTTCTTTTTCAATCTCTTTTTCTTTTCTTTCGATTTCTTT
TTCTCGCTCGTACTCTTGTACAATCTCAATTTCTTTTTCGAATTCTTTCTC
Found at i:39438207 original size:13 final size:13
Alignment explanation
Indices: 39438189--39438213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39438179 TGGTCATCAT
39438189 GGTGTGAACACAA
1 GGTGTGAACACAA
39438202 GGTGTGAACACA
1 GGTGTGAACACA
39438214 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39439986 original size:20 final size:20
Alignment explanation
Indices: 39439963--39440009 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39439953 GGGTTAAAAT
*
39439963 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39439983 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39440003 TGAGCTG
1 TGAGCTG
39440010 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39449613 original size:30 final size:30
Alignment explanation
Indices: 39449574--39449676 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 30
39449564 CGAGTTTAAA
*
39449574 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAAGATGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
39449603 CTAAAGATGAGCTGAGGCTAAACTCCTAAG
1 CTAAAGATGAGCTAAGGTTTAGCTCGTGAG
* *
39449633 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CTAAAGATGAGCTAAGGTTTAGCTCGTGAG
*
39449663 CTAAATATGAGCTA
1 CTAAAGATGAGCTA
39449677 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
29 5 0.09
30 50 0.91
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (30 bp):
CTAAAGATGAGCTAAGGTTTAGCTCGTGAG
Found at i:39451863 original size:12 final size:12
Alignment explanation
Indices: 39451848--39451878 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39451838 TTCTTTTTGC
39451848 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39451860 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39451872 TTTTCAA
1 TTTTCAA
39451879 GTTCTCTCAA
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:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:39451955 original size:6 final size:6
Alignment explanation
Indices: 39451939--39451988 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
39451929 TTTCTTTTTA
*
39451939 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
39451988 T
1 T
39451989 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:39451971 original size:37 final size:37
Alignment explanation
Indices: 39451928--39451998 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
39451918 CTTGCCTCTC
39451928 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
39451965 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
39451999 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:39451999 original size:16 final size:16
Alignment explanation
Indices: 39451924--39451984 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
39451914 GCCTCTTGCC
*
39451924 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
39451940 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
39451956 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
39451972 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
39451985 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:39452926 original size:11 final size:10
Alignment explanation
Indices: 39452911--39452960 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
39452901 TTTTAACTCG
39452911 ATTTTTTTTC
1 ATTTTTTTTC
39452921 ACTTTTTTTTC
1 A-TTTTTTTTC
*
39452932 -CTTTTTTTC
1 ATTTTTTTTC
*
39452941 GATTTTTTTTG
1 -ATTTTTTTTC
39452952 ATTTTTTTT
1 ATTTTTTTT
39452961 GAATTTCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.24
10 10 0.29
11 16 0.47
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:39452966 original size:11 final size:10
Alignment explanation
Indices: 39452910--39452962 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
39452900 TTTTTAACTC
39452910 GATTTTTTTT
1 GATTTTTTTT
*
39452920 CACTTTTTTTT
1 GA-TTTTTTTT
** *
39452931 CCTTTTTTTC
1 GATTTTTTTT
39452941 GATTTTTTTT
1 GATTTTTTTT
39452951 GATTTTTTTT
1 GATTTTTTTT
39452961 GA
1 GA
39452963 ATTTCTTCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.09, C:0.09, G:0.08, T:0.74
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:39453062 original size:11 final size:11
Alignment explanation
Indices: 39453046--39453070 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39453036 ACTCAAAATT
39453046 TTTTTTTTTGA
1 TTTTTTTTTGA
39453057 TTTTTTTTTGA
1 TTTTTTTTTGA
39453068 TTT
1 TTT
39453071 CCTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:39454708 original size:30 final size:30
Alignment explanation
Indices: 39454674--39454770 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39454664 TAAACTAAAA
*
39454674 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
39454704 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39454734 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39454763 ATGAGCTA
1 -TGAGCTA
39454771 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:39459451 original size:11 final size:13
Alignment explanation
Indices: 39459435--39459524 Score: 60
Period size: 12 Copynumber: 6.6 Consensus size: 13
39459425 TTGGAGTAAC
39459435 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
39459446 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
39459460 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCG-A
*
39459477 AAAAAAAATTCAA
1 AAAAAAAATTCGA
*
39459490 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
*
39459502 AAAAAAAAATCGA
1 AAAAAAAATTCGA
39459515 GCAAAAAAAA
1 --AAAAAAAA
39459525 AAGGTGAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.12
12 12 0.19
13 12 0.19
14 10 0.16
15 9 0.14
16 1 0.02
17 12 0.19
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:39459453 original size:13 final size:13
Alignment explanation
Indices: 39459435--39459510 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
39459425 TTGGAGTAAC
39459435 AAAAAAAATC-AA
1 AAAAAAAATCAAA
*
39459447 AAAAAAATTCGAAA
1 AAAAAAAATC-AAA
*
39459461 AAAAAAATTGATTGAAA
1 AAAAAAA---A-TCAAA
*
39459478 AAAAAAATTCAAA
1 AAAAAAAATCAAA
* *
39459491 AAAAAAAGTGAAA
1 AAAAAAAATCAAA
39459504 AAAAAAA
1 AAAAAAA
39459511 TCGAGCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
12 9 0.18
13 22 0.43
14 9 0.18
17 10 0.20
18 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:39459462 original size:14 final size:14
Alignment explanation
Indices: 39459445--39459525 Score: 78
Period size: 13 Copynumber: 5.6 Consensus size: 14
39459435 AAAAAAAATC
39459445 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
*
39459459 AAAAAAAAATTGATTGA
1 AAAAAAAAA-T--TCGA
39459476 AAAAAAAAATTC-A
1 AAAAAAAAATTCGA
*
39459489 AAAAAAAAAGT-GA
1 AAAAAAAAATTCGA
39459502 AAAAAAAAA-TCGA
1 AAAAAAAAATTCGA
39459515 GCAAAAAAAAA
1 --AAAAAAAAA
39459526 AGGTGAGCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
12 1 0.02
13 23 0.40
14 10 0.18
15 10 0.18
16 1 0.02
17 12 0.21
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:39459491 original size:26 final size:26
Alignment explanation
Indices: 39459445--39459566 Score: 91
Period size: 33 Copynumber: 4.1 Consensus size: 26
39459435 AAAAAAAATC
39459445 AAAAAAAAATTCGAAAAAAAAAATTGATTGA
1 AAAAAAAAATTC-AAAAAAAAAA--G--TGA
39459476 AAAAAAAAATTCAAAAAAAAAAGTGA
1 AAAAAAAAATTCAAAAAAAAAAGTGA
*
39459502 AAAAAAAAATCGAGCAAAAAAAAAAGGTGAGCA
1 AAAAAAAAAT---TCAAAAAAAAAA-GT--G-A
*
39459535 AAAAAAAAAATCAAGTTAAAAAAAAGTGA
1 AAAAAAAAATTCAA---AAAAAAAAGTGA
39459564 AAA
1 AAA
39459567 GTCTTGCGAG
Statistics
Matches: 78, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
26 13 0.17
28 1 0.01
29 15 0.19
30 16 0.21
31 12 0.15
32 3 0.04
33 18 0.23
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.12
Consensus pattern (26 bp):
AAAAAAAAATTCAAAAAAAAAAGTGA
Found at i:39459520 original size:16 final size:16
Alignment explanation
Indices: 39459487--39459543 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
39459477 AAAAAAAATT
39459487 CAAAAAAAAAAGT--G
1 CAAAAAAAAAAGTGAG
39459501 -AAAAAAAAAA-TCGAG
1 CAAAAAAAAAAGT-GAG
39459516 CAAAAAAAAAAGGTGAG
1 CAAAAAAAAAA-GTGAG
39459533 CAAAAAAAAAA
1 CAAAAAAAAAA
39459544 ATCAAGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 10 0.27
15 1 0.03
16 10 0.27
17 14 0.38
18 1 0.03
ACGTcount: A:0.74, C:0.07, G:0.14, T:0.05
Consensus pattern (16 bp):
CAAAAAAAAAAGTGAG
Found at i:39459522 original size:43 final size:42
Alignment explanation
Indices: 39459435--39459526 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
39459425 TTGGAGTAAC
* *
39459435 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAAATTGATTG-AAA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAAATCGA--GCAAA
*
39459478 AAAAAAATTCAAAAAAAAAAGT-GAAAAAAAAAATCGAGCAAA
1 AAAAAAAATC-AAAAAAAAAGTCGAAAAAAAAAATCGAGCAAA
39459520 AAAAAAA
1 AAAAAAA
39459527 GGTGAGCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 10 0.23
43 23 0.52
44 10 0.23
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.12
Consensus pattern (42 bp):
AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAAATCGAGCAAA
Found at i:39465125 original size:27 final size:27
Alignment explanation
Indices: 39465087--39465138 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
39465077 TCATTGAAGC
*
39465087 ATCTTCATTGTTGTCCATGCATGTATT
1 ATCTTCAATGTTGTCCATGCATGTATT
39465114 ATCTTCAATGTTGTCCATGCATGTA
1 ATCTTCAATGTTGTCCATGCATGTA
39465139 CCTACAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (27 bp):
ATCTTCAATGTTGTCCATGCATGTATT
Found at i:39467222 original size:17 final size:18
Alignment explanation
Indices: 39467200--39467233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39467190 TTTTTCTTTT
39467200 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
39467217 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
39467234 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:39467251 original size:27 final size:28
Alignment explanation
Indices: 39467191--39467257 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
39467181 TTCAACATCT
39467191 TTTTCTTTTTCAATTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTTTCTC-ATCTCA
* *
39467220 ATTTCTTTTTCAATTTTCTTTTC-T-TCA
1 TTTTCTTTTTCAATTTT-TTCTCATCTCA
39467247 TTTTCTTTTTC
1 TTTTCTTTTTC
39467258 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTTCAATTTTTTCTCATCTCA
Found at i:39468638 original size:6 final size:6
Alignment explanation
Indices: 39468629--39468681 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
39468619 TCATTTTCGA
** * *
39468629 TTTCTT TTTCTT TTGT-AA TTTCTT TTTCTT TTTCGT TTTCTT TTTCAT
1 TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
39468677 TTTCT
1 TTTCT
39468682 CGCTCGCACT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:39468668 original size:18 final size:17
Alignment explanation
Indices: 39468622--39468680 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
39468612 GATCACATCA
*
39468622 TTTTCGATTTCTTTTTC
1 TTTTCGTTTTCTTTTTC
39468639 TTTT-GTAATTTCTTTTTC
1 TTTTCGT--TTTCTTTTTC
39468657 TTTTTCGTTTTCTTTTTC
1 -TTTTCGTTTTCTTTTTC
39468675 ATTTTC
1 -TTTTC
39468681 TCGCTCGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 25 0.69
19 4 0.11
20 2 0.06
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTCGTTTTCTTTTTC
Found at i:39471390 original size:56 final size:55
Alignment explanation
Indices: 39471274--39471391 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
39471264 TGCATGCTTT
* * * *
39471274 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
39471328 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
39471384 CATTAAAT
1 CATTAAAT
39471392 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:39472045 original size:20 final size:19
Alignment explanation
Indices: 39472022--39472069 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
39472012 AAATTGATCT
*
39472022 TGAATGAGCTTACTTGAGC
1 TGAATGAGCTAACTTGAGC
39472041 ATGAATGAGCTAACTTGAGC
1 -TGAATGAGCTAACTTGAGC
39472061 TCGAATGAG
1 T-GAATGAG
39472070 TTGAACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (19 bp):
TGAATGAGCTAACTTGAGC
Found at i:39473576 original size:17 final size:15
Alignment explanation
Indices: 39473539--39473577 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
39473529 TATCTCCCAC
39473539 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
39473555 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
39473572 TCATTT
1 TCATTT
39473578 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:39474592 original size:13 final size:13
Alignment explanation
Indices: 39474572--39474605 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
39474562 AATTGAATAC
39474572 AATTTTTTTTT--
1 AATTTTTTTTTCG
39474583 AATTTTTTTTTCG
1 AATTTTTTTTTCG
39474596 AATTTTTTTT
1 AATTTTTTTT
39474606 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:39474612 original size:11 final size:11
Alignment explanation
Indices: 39474573--39474615 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
39474563 ATTGAATACA
*
39474573 ATTTTTTTTTA
1 ATTTTTTTTTC
39474584 ATTTTTTTTTC
1 ATTTTTTTTTC
*
39474595 GAATTTTTTTTC
1 -ATTTTTTTTTC
*
39474607 CTTTTTTTT
1 ATTTTTTTT
39474616 ACAATACCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTC
Found at i:39477278 original size:56 final size:55
Alignment explanation
Indices: 39477162--39477279 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
39477152 TGCATGCTTT
* * * *
39477162 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
39477216 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
39477272 CATTAAAT
1 CATTAAAT
39477280 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:39477933 original size:20 final size:19
Alignment explanation
Indices: 39477910--39477957 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
39477900 AAATTGATCT
*
39477910 TGAATGAGCTTACTTGAGC
1 TGAATGAGCTAACTTGAGC
39477929 ATGAATGAGCTAACTTGAGC
1 -TGAATGAGCTAACTTGAGC
39477949 TCGAATGAG
1 T-GAATGAG
39477958 TTGAACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (19 bp):
TGAATGAGCTAACTTGAGC
Found at i:39480484 original size:13 final size:13
Alignment explanation
Indices: 39480464--39480497 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
39480454 AATTGAATAC
39480464 AATTTTTTTTT--
1 AATTTTTTTTTCG
39480475 AATTTTTTTTTCG
1 AATTTTTTTTTCG
39480488 AATTTTTTTT
1 AATTTTTTTT
39480498 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:39480504 original size:11 final size:11
Alignment explanation
Indices: 39480465--39480507 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
39480455 ATTGAATACA
*
39480465 ATTTTTTTTTA
1 ATTTTTTTTTC
39480476 ATTTTTTTTTC
1 ATTTTTTTTTC
*
39480487 GAATTTTTTTTC
1 -ATTTTTTTTTC
*
39480499 CTTTTTTTT
1 ATTTTTTTT
39480508 ACAATACCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTC
Found at i:39483170 original size:56 final size:55
Alignment explanation
Indices: 39483054--39483171 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
39483044 TGCATGCTTT
* * * *
39483054 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
39483108 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
39483164 CATTAAAT
1 CATTAAAT
39483172 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:39483819 original size:20 final size:20
Alignment explanation
Indices: 39483794--39483848 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39483784 ACGAGTTAAA
* *
39483794 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
39483814 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
39483834 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
39483849 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:39485171 original size:15 final size:16
Alignment explanation
Indices: 39485132--39485172 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
39485122 AACAACACTC
39485132 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
39485148 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
39485162 CTTTCTTTTTC
1 CTTTCTTTTTC
39485173 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:39486385 original size:12 final size:12
Alignment explanation
Indices: 39486368--39486414 Score: 85
Period size: 12 Copynumber: 3.8 Consensus size: 12
39486358 ATTGAATACA
39486368 AATTTTTTTTTG
1 AATTTTTTTTTG
39486380 AATTTTTTTTTG
1 AATTTTTTTTTG
39486392 AATTTTTTTTTTG
1 AA-TTTTTTTTTG
39486405 AATTTTTTTT
1 AATTTTTTTT
39486415 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 22 0.65
13 12 0.35
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:39486388 original size:13 final size:13
Alignment explanation
Indices: 39486370--39486414 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
39486360 TGAATACAAA
39486370 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
39486382 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
39486395 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
39486408 TTTTTTT
1 TTTTTTT
39486415 CCTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:39486422 original size:25 final size:25
Alignment explanation
Indices: 39486370--39486424 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
39486360 TGAATACAAA
**
39486370 TTTTTTTTTGAATTTTTTTTTGAAT
1 TTTTTTTTTGAATTTTTTTTCCAAT
39486395 TTTTTTTTTGAATTTTTTTTCC--T
1 TTTTTTTTTGAATTTTTTTTCCAAT
39486418 TTTTTTT
1 TTTTTTT
39486425 ACAATACCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 8 0.29
25 20 0.71
ACGTcount: A:0.11, C:0.04, G:0.05, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTGAATTTTTTTTCCAAT
Found at i:39487585 original size:56 final size:55
Alignment explanation
Indices: 39487469--39487586 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
39487459 TGCATGCTTT
* * * *
39487469 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
39487523 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
39487579 CATTAAAT
1 CATTAAAT
39487587 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:39488224 original size:20 final size:20
Alignment explanation
Indices: 39488193--39488264 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
39488183 AGCTAATAAC
* *
39488193 GAGCTC-AATGAGTTAAATT
1 GAGCTCGAATGAGCTAACTT
* *
39488212 GAGCTTGAATGAGCTGACTT
1 GAGCTCGAATGAGCTAACTT
*
39488232 GAGCACGAATGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
39488252 GAGCTCGAATGAG
1 GAGCTCGAATGAG
39488265 TTGAACCACA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:39490048 original size:10 final size:10
Alignment explanation
Indices: 39490033--39490070 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39490023 GCTCGTTTCC
*
39490033 AGCTCACTCG
1 AGCTCAATCG
39490043 AGCTCAAGTC-
1 AGCTCAA-TCG
39490053 AGCTCAATCG
1 AGCTCAATCG
39490063 AGCTCAAT
1 AGCTCAAT
39490071 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39490057 original size:20 final size:20
Alignment explanation
Indices: 39490032--39490069 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39490022 AGCTCGTTTC
*
39490032 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39490052 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39490070 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39490076 original size:20 final size:20
Alignment explanation
Indices: 39490033--39490093 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39490023 GCTCGTTTCC
* * *
39490033 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39490053 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39490073 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39490093 A
1 A
39490094 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39490087 original size:11 final size:10
Alignment explanation
Indices: 39490043--39490089 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39490033 AGCTCACTCG
*
39490043 AGCTCAAGTC
1 AGCTCAATTC
39490053 AGCTCAA-TC
1 AGCTCAATTC
*
39490062 GAGCTCAATTT
1 -AGCTCAATTC
39490073 AGCTACAATTC
1 AGCT-CAATTC
39490084 AGCTCA
1 AGCTCA
39490090 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39490594 original size:13 final size:13
Alignment explanation
Indices: 39490576--39490600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39490566 GTATTGATCA
39490576 TGTGTTCACACCT
1 TGTGTTCACACCT
39490589 TGTGTTCACACC
1 TGTGTTCACACC
39490601 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:39491675 original size:12 final size:12
Alignment explanation
Indices: 39491660--39491717 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
39491650 CAAAAAAATC
39491660 AAAAAAATTCGA
1 AAAAAAATTCGA
*
39491672 AAAAAAATTGATTGA
1 AAAAAAA-T--TCGA
*
39491687 AAAAAAATTCAA
1 AAAAAAATTCGA
*
39491699 AAAAAAAGT-GA
1 AAAAAAATTCGA
39491710 AAAAAAAT
1 AAAAAAAT
39491718 CGAGGAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 1 0.03
14 1 0.03
15 10 0.27
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:39491702 original size:38 final size:35
Alignment explanation
Indices: 39491651--39491730 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 35
39491641 TTGGAGTAAC
* * *
39491651 AAAAAAATC-AAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAATCAAAAAAAAGT-GAAAAAAAATCGA-GGA
39491687 AAAAAAATTCAAAAAAAAAGTGAAAAAAAATCGAGGA
1 AAAAAAA-TC-AAAAAAAAGTGAAAAAAAATCGAGGA
39491724 AAAAAAA
1 AAAAAAA
39491731 GAAGTGACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 7 0.18
37 11 0.29
38 12 0.32
39 8 0.21
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (35 bp):
AAAAAAATCAAAAAAAAGTGAAAAAAAATCGAGGA
Found at i:39491716 original size:27 final size:27
Alignment explanation
Indices: 39491660--39491716 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39491650 CAAAAAAATC
* * ***
39491660 AAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAATTCAAAAAAAAAGTGAAAAA
39491687 AAAAAAATTCAAAAAAAAAGTGAAAAA
1 AAAAAAATTCAAAAAAAAAGTGAAAAA
39491714 AAA
1 AAA
39491717 TCGAGGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.16
Consensus pattern (27 bp):
AAAAAAATTCAAAAAAAAAGTGAAAAA
Found at i:39491729 original size:29 final size:29
Alignment explanation
Indices: 39491697--39491775 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
39491687 AAAAAAATTC
39491697 AAAAAAAAAGTGAAAAAAAATCGAG-GAA
1 AAAAAAAAAGTGAAAAAAAATCGAGTGAA
* *
39491725 AAAAAAGAAGTGACAAAAAAATCGAGTTAA
1 AAAAAAAAAGTGA-AAAAAAATCGAGTGAA
* *
39491755 AAAAAATCAAGTTAAAAAAAA
1 AAAAAA-AAAGTGAAAAAAAA
39491776 AGTGAAAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.27
29 12 0.27
30 15 0.34
31 5 0.11
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAATCGAGTGAA
Found at i:39491757 original size:15 final size:15
Alignment explanation
Indices: 39491705--39491775 Score: 76
Period size: 15 Copynumber: 4.8 Consensus size: 15
39491695 TCAAAAAAAA
39491705 AGTGAAAAAAAATCG
1 AGTGAAAAAAAATCG
39491720 AG-GAAAAAAAA--G
1 AGTGAAAAAAAATCG
39491732 AAGTGACAAAAAAATCG
1 -AGTGA-AAAAAAATCG
* *
39491749 AGTTAAAAAAAATCA
1 AGTGAAAAAAAATCG
*
39491764 AGTTAAAAAAAA
1 AGTGAAAAAAAA
39491776 AGTGAAAAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
12 1 0.02
13 2 0.04
14 11 0.22
15 30 0.61
16 4 0.08
17 1 0.02
ACGTcount: A:0.66, C:0.06, G:0.15, T:0.13
Consensus pattern (15 bp):
AGTGAAAAAAAATCG
Found at i:39492733 original size:18 final size:18
Alignment explanation
Indices: 39492695--39492736 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39492685 AAATCGAAAG
* **
39492695 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
39492713 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
39492731 AAAAGA
1 AAAAGA
39492737 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:39492801 original size:33 final size:34
Alignment explanation
Indices: 39492764--39492828 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
39492754 AAAGTGAAAA
*
39492764 TGAGA-GAGGAAATGAAA-AGAGAAAAAGAGAAGT
1 TGAGATGA-GAAAAGAAACAGAGAAAAAGAGAAGT
*
39492797 TGAGATTAGAAAAGAAACGAGAGAAAAAGAGA
1 TGAGATGAGAAAAGAAAC-AGAGAAAAAGAGA
39492829 TAAACGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 1 0.04
35 13 0.48
ACGTcount: A:0.58, C:0.02, G:0.31, T:0.09
Consensus pattern (34 bp):
TGAGATGAGAAAAGAAACAGAGAAAAAGAGAAGT
Found at i:39494446 original size:10 final size:10
Alignment explanation
Indices: 39494431--39494468 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39494421 GCTCGTTTCC
*
39494431 AGCTCACTCG
1 AGCTCAATCG
39494441 AGCTCAAGTC-
1 AGCTCAA-TCG
39494451 AGCTCAATCG
1 AGCTCAATCG
39494461 AGCTCAAT
1 AGCTCAAT
39494469 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39494455 original size:20 final size:20
Alignment explanation
Indices: 39494430--39494467 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39494420 AGCTCGTTTC
*
39494430 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39494450 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39494468 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39494474 original size:20 final size:20
Alignment explanation
Indices: 39494431--39494491 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39494421 GCTCGTTTCC
* * *
39494431 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39494451 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39494471 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39494491 A
1 A
39494492 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39494485 original size:11 final size:10
Alignment explanation
Indices: 39494441--39494487 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39494431 AGCTCACTCG
*
39494441 AGCTCAAGTC
1 AGCTCAATTC
39494451 AGCTCAA-TC
1 AGCTCAATTC
*
39494460 GAGCTCAATTT
1 -AGCTCAATTC
39494471 AGCTACAATTC
1 AGCT-CAATTC
39494482 AGCTCA
1 AGCTCA
39494488 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39494992 original size:13 final size:13
Alignment explanation
Indices: 39494974--39494998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39494964 GTATTGATCA
39494974 TGTGTTCACACCT
1 TGTGTTCACACCT
39494987 TGTGTTCACACC
1 TGTGTTCACACC
39494999 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:39497757 original size:23 final size:22
Alignment explanation
Indices: 39497705--39497757 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39497695 TTCCACGTCT
*
39497705 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39497727 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39497750 TTTCTTTT
1 TTTCTTTT
39497758 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39501703 original size:10 final size:10
Alignment explanation
Indices: 39501690--39501743 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
39501680 TTTTTGAATC
39501690 TTTTTTTCGA
1 TTTTTTTCGA
**
39501700 TTTTTTTTTA
1 TTTTTTTCGA
39501710 TTTTTTTCGA
1 TTTTTTTCGA
**
39501720 TTTTCCTC--
1 TTTTTTTCGA
39501728 TTTTTTT-GA
1 TTTTTTTCGA
39501737 TTTTTTT
1 TTTTTTT
39501744 GTTCAATTAC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
8 5 0.15
9 7 0.21
10 22 0.65
ACGTcount: A:0.07, C:0.09, G:0.06, T:0.78
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:39501703 original size:20 final size:20
Alignment explanation
Indices: 39501680--39501723 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
39501670 ACTTCGAATT
*
39501680 TTTTTGAATCTTTTTTTCGA
1 TTTTTGAATATTTTTTTCGA
***
39501700 TTTTTTTTTATTTTTTTCGA
1 TTTTTGAATATTTTTTTCGA
39501720 TTTT
1 TTTT
39501724 CCTCTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.75
Consensus pattern (20 bp):
TTTTTGAATATTTTTTTCGA
Found at i:39507688 original size:12 final size:11
Alignment explanation
Indices: 39507642--39507684 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
39507632 AGTTTCGAAA
39507642 AAAAAAGAATTCG
1 AAAAAA-AATT-G
39507655 AAAAAAAATTG
1 AAAAAAAATTG
39507666 AAAAAAAATTG
1 AAAAAAAATTG
39507677 AAAAAAAA
1 AAAAAAAA
39507685 ATTGTATACG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 20 0.67
12 4 0.13
13 6 0.20
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:39510761 original size:11 final size:11
Alignment explanation
Indices: 39510745--39510784 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
39510735 AGTTTCTTCA
39510745 AAAAAAATTCG
1 AAAAAAATTCG
*
39510756 AAAAAAAATTCA
1 -AAAAAAATTCG
39510768 AAAAAAATT-G
1 AAAAAAATTCG
39510778 AAAAAAA
1 AAAAAAA
39510785 ATTGGTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 7 0.27
11 9 0.35
12 10 0.38
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:39510761 original size:12 final size:12
Alignment explanation
Indices: 39510744--39510787 Score: 74
Period size: 11 Copynumber: 3.8 Consensus size: 12
39510734 TAGTTTCTTC
39510744 AAAAAAAATTCG
1 AAAAAAAATTCG
39510756 AAAAAAAATTC-
1 AAAAAAAATTCG
39510767 AAAAAAAATT-G
1 AAAAAAAATTCG
39510778 AAAAAAAATT
1 AAAAAAAATT
39510788 GGTTTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:39510773 original size:22 final size:22
Alignment explanation
Indices: 39510741--39510787 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
39510731 TAGTAGTTTC
39510741 TTCAAAAAAAATTCGAAAAAAAA
1 TTCAAAAAAAATT-GAAAAAAAA
39510764 TTCAAAAAAAATTGAAAAAAAA
1 TTCAAAAAAAATTGAAAAAAAA
39510786 TT
1 TT
39510788 GGTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.21
Consensus pattern (22 bp):
TTCAAAAAAAATTGAAAAAAAA
Found at i:39510846 original size:14 final size:14
Alignment explanation
Indices: 39510827--39510858 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39510817 ATCAAGTTGA
39510827 AAAAAAAATTCATG
1 AAAAAAAATTCATG
*
39510841 AAAAAAAATTCGTG
1 AAAAAAAATTCATG
39510855 AAAA
1 AAAA
39510859 GAAGAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTCATG
Found at i:39512431 original size:20 final size:20
Alignment explanation
Indices: 39512385--39512431 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39512375 AGCTCGTTTC
*
39512385 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
39512405 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39512425 CAGCTCA
1 CAGCTCA
39512432 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39515114 original size:48 final size:47
Alignment explanation
Indices: 39515035--39515140 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
39515025 GAGTGTCGTG
*
39515035 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
39515083 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
39515131 GAAAAAGAAA
1 GAAAAAGAAA
39515141 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:39518334 original size:20 final size:20
Alignment explanation
Indices: 39518272--39518334 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
39518262 AGTTTTTCCC
* * *
39518272 AGCTCGATTTAGCTCAC-AT
1 AGCTCAATTTAGCTTACTTT
*
39518291 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
39518310 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
39518331 AGCT
1 AGCT
39518335 TGTTTGAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
17 1 0.03
19 12 0.35
20 16 0.47
21 4 0.12
22 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:39521123 original size:5 final size:6
Alignment explanation
Indices: 39521075--39521212 Score: 64
Period size: 6 Copynumber: 22.7 Consensus size: 6
39521065 AAAGAAATTG
* ** ** *
39521075 AAAG-A AAACAA AAAGAA AACTAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
39521122 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * * *
39521173 AAAGAA ATTGAG AATGAA AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAG
39521213 CGAAAAAAGA
Statistics
Matches: 93, Mismatches: 34, Indels: 11
0.67 0.25 0.08
Matches are distributed among these distances:
5 7 0.08
6 71 0.76
7 11 0.12
8 4 0.04
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:39521190 original size:18 final size:18
Alignment explanation
Indices: 39521096--39521212 Score: 73
Period size: 18 Copynumber: 6.7 Consensus size: 18
39521086 AAAGAAAACT
*
39521096 AAAAAGAAAAAGAAATTG
1 AAAATGAAAAAGAAATTG
*
39521114 CAAAA-GAAAAAGAAATCG
1 -AAAATGAAAAAGAAATTG
* ** * **
39521132 AAAAAGTGAGAGAAAAAG
1 AAAATGAAAAAGAAATTG
*
39521150 AAAATG---AAGAAA-AG
1 AAAATGAAAAAGAAATTG
39521164 AAAATTGAAAAAGAAATTG
1 AAAA-TGAAAAAGAAATTG
* *
39521183 AGAATGAAAAAAAAATTG
1 AAAATGAAAAAGAAATTG
*
39521201 AAAAAGAAAAAG
1 AAAATGAAAAAG
39521213 CGAAAAAAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
14 6 0.08
15 7 0.09
17 4 0.05
18 53 0.68
19 8 0.10
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (18 bp):
AAAATGAAAAAGAAATTG
Found at i:39521198 original size:30 final size:27
Alignment explanation
Indices: 39521143--39521230 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 27
39521133 AAAAGTGAGA
*
39521143 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAAAAAATT
*
39521170 GAAAAAGAAATTGAGAATGAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-GAAAAAAAAATT
* *
39521200 GAAAAAGAAAAAG-CGAAAAAAGAAATT
1 GAAAAAGAAAATGAAGAAAAAA-AAATT
39521227 GAAA
1 GAAA
39521231 GAGGCTTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.13
27 20 0.38
28 1 0.02
29 3 0.06
30 21 0.40
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAAAAAATT
Found at i:39521226 original size:57 final size:52
Alignment explanation
Indices: 39521045--39521230 Score: 169
Period size: 57 Copynumber: 3.4 Consensus size: 52
39521035 ATTGAGCGAG
* * **
39521045 AAAAGAAGAAAGAGATTGAAAAAGAAATTGAAA-GAAAACAAAAAGAAAACTA
1 AAAAGAAAAAAGAAATTGAAAAAGAAATTGAAATGAAAA-AAAAAGAAAAAGA
* ** * *
39521097 AAAAG-AAAAAGAAATTGCAAAAGAAAAAGAAATCGAAAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAAGAAATTGAAAAAGAAATTGAAAT-GAAAAA--AAAAGAAAAAGA
*
39521151 AAATGAAGAAAAGAAAATTGAAAAAGAAATTGAGAATGAAAAAAAAATTGAAAAAGA
1 AAAAGAA-AAAAG-AAATTGAAAAAGAAATTGA-AATGAAAAAAAAA--GAAAAAGA
39521208 AAAAGCGAAAAAAGAAATTGAAA
1 AAAA--GAAAAAAGAAATTGAAA
39521231 GAGGCTTGAA
Statistics
Matches: 106, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
51 22 0.21
52 6 0.06
53 5 0.05
54 12 0.11
55 3 0.03
56 5 0.05
57 42 0.40
58 8 0.08
59 3 0.03
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (52 bp):
AAAAGAAAAAAGAAATTGAAAAAGAAATTGAAATGAAAAAAAAAGAAAAAGA
Found at i:39524275 original size:13 final size:13
Alignment explanation
Indices: 39524259--39524284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39524249 AAAAAGAAGG
39524259 AAAAAAAATTGCA
1 AAAAAAAATTGCA
39524272 AAAAAAAATTGCA
1 AAAAAAAATTGCA
39524285 TACGGTCTAG
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:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGCA
Found at i:39526556 original size:17 final size:18
Alignment explanation
Indices: 39526517--39526558 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39526507 AAGAAGAAAA
39526517 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
39526534 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
39526551 TCAAAAGA
1 ACAAAAGA
39526559 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:39532047 original size:6 final size:6
Alignment explanation
Indices: 39532015--39532122 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
39532005 AAAGAAATTG
* * ** *
39532015 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
39532062 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
39532113 AAAGAA AAAG
1 AAAGAA AAAG
39532123 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:39532102 original size:14 final size:13
Alignment explanation
Indices: 39532083--39532120 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
39532073 AAAAGTGAGA
39532083 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
39532095 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
39532110 GAAAAAGAAAA
1 GAAAAAGAAAA
39532121 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:39532157 original size:12 final size:12
Alignment explanation
Indices: 39532126--39532157 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39532116 GAAAAAGCGA
*
39532126 AAAAAGAATTTG
1 AAAAAGAGTTTG
39532138 AAAAAGAGTTTG
1 AAAAAGAGTTTG
39532150 AAAAAGAG
1 AAAAAGAG
39532158 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:39543023 original size:11 final size:11
Alignment explanation
Indices: 39542998--39543052 Score: 74
Period size: 11 Copynumber: 4.7 Consensus size: 11
39542988 CGTATGCAAT
39542998 TTTTTTTTCAAAA
1 TTTTTTTTC--AA
39543011 TTTTTTTTCAA
1 TTTTTTTTCAA
*
39543022 TTTTTTTTTCGA
1 -TTTTTTTTCAA
39543034 TTTTTTTTCAA
1 TTTTTTTTCAA
39543045 TTTTTTTT
1 TTTTTTTT
39543053 TGAATCTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 20 0.51
12 10 0.26
13 9 0.23
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:39543036 original size:23 final size:24
Alignment explanation
Indices: 39542994--39543053 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
39542984 AGACCGTATG
39542994 CAATTTTTTTTTCAAAATTTTTTTT
1 CAATTTTTTTTTC-AAATTTTTTTT
*
39543019 CAATTTTTTTTTC-GATTTTTTTT
1 CAATTTTTTTTTCAAATTTTTTTT
39543042 CAATTTTTTTTT
1 CAATTTTTTTTT
39543054 GAATCTACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 21 0.62
25 13 0.38
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (24 bp):
CAATTTTTTTTTCAAATTTTTTTT
Found at i:39543053 original size:12 final size:12
Alignment explanation
Indices: 39542994--39543053 Score: 86
Period size: 12 Copynumber: 5.0 Consensus size: 12
39542984 AGACCGTATG
39542994 CAATTTTTTTTT
1 CAATTTTTTTTT
*
39543006 CAAAATTTTTTTT
1 C-AATTTTTTTTT
39543019 CAATTTTTTTTT
1 CAATTTTTTTTT
*
39543031 CGA-TTTTTTTT
1 CAATTTTTTTTT
39543042 CAATTTTTTTTT
1 CAATTTTTTTTT
39543054 GAATCTACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.24
12 21 0.50
13 11 0.26
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:39555829 original size:13 final size:13
Alignment explanation
Indices: 39555811--39555835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39555801 TGGTCATCAT
39555811 GGTGTGAACACAA
1 GGTGTGAACACAA
39555824 GGTGTGAACACA
1 GGTGTGAACACA
39555836 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39556853 original size:12 final size:12
Alignment explanation
Indices: 39556838--39556868 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39556828 ATTTTTTTTC
39556838 TTTTTTTCAATT
1 TTTTTTTCAATT
39556850 TTTTTTTCAATT
1 TTTTTTTCAATT
39556862 TTTTTTT
1 TTTTTTT
39556869 TCGAACTCTT
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:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:39560841 original size:20 final size:20
Alignment explanation
Indices: 39560818--39560874 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
39560808 GGGTTAAGAT
*
39560818 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39560838 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39560858 TGAACT-AATTCAGCTCG
1 TGAGCTGAATTGAGCTCG
39560875 CATGGATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39562549 original size:48 final size:48
Alignment explanation
Indices: 39562494--39562599 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
39562484 TTGTCTTTTC
*
39562494 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
39562542 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
39562590 TTTCTTTTTC
1 TTTCTTTTTC
39562600 CACGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39564401 original size:13 final size:13
Alignment explanation
Indices: 39564383--39564407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39564373 TGGTCATCAT
39564383 GGTGTGAACACAA
1 GGTGTGAACACAA
39564396 GGTGTGAACACA
1 GGTGTGAACACA
39564408 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39566658 original size:12 final size:13
Alignment explanation
Indices: 39566641--39566702 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 13
39566631 TTGGAGTAAC
39566641 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
39566653 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
*
39566667 AAAAAAAATTGATTGA
1 AAAAAAAATTCA---A
39566683 AAAAAAAATTCAA
1 AAAAAAAATTCAA
39566696 AAAAAAA
1 AAAAAAA
39566703 GTGAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
12 8 0.19
13 11 0.26
14 12 0.28
16 12 0.28
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:39566659 original size:13 final size:13
Alignment explanation
Indices: 39566641--39566675 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39566631 TTGGAGTAAC
39566641 AAAAAAAATCAAA
1 AAAAAAAATCAAA
* *
39566654 AAAAAAATTCGAA
1 AAAAAAAATCAAA
39566667 AAAAAAAAT
1 AAAAAAAAT
39566676 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:39566710 original size:13 final size:12
Alignment explanation
Indices: 39566641--39566714 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 12
39566631 TTGGAGTAAC
*
39566641 AAAAAAAATCAA
1 AAAAAAAATGAA
39566653 AAAAAAAATTCGAA
1 AAAAAAAA-T-GAA
39566667 AAAAAAAATTGATTGA
1 AAAAAAAA-TGA---A
*
39566683 AAAAAAAATTCAA
1 AAAAAAAA-TGAA
*
39566696 AAAAAAAGTGAA
1 AAAAAAAATGAA
39566708 AAAAAAA
1 AAAAAAA
39566715 TCGAGCAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
12 18 0.34
13 11 0.21
14 12 0.23
16 12 0.23
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:39566726 original size:24 final size:24
Alignment explanation
Indices: 39566652--39566715 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 24
39566642 AAAAAAATCA
39566652 AAAAAAAAATTCGAAAAAAAAAATTGATTG
1 AAAAAAAAATTC--AAAAAAAAA--G--TG
39566682 AAAAAAAAATTCAAAAAAAAAGTG
1 AAAAAAAAATTCAAAAAAAAAGTG
39566706 AAAAAAAAAT
1 AAAAAAAAAT
39566716 CGAGCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 12 0.35
26 1 0.03
28 9 0.26
30 12 0.35
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (24 bp):
AAAAAAAAATTCAAAAAAAAAGTG
Found at i:39566758 original size:32 final size:29
Alignment explanation
Indices: 39566694--39566768 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
39566684 AAAAAAATTC
*
39566694 AAAAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCAA
*
39566723 AAAAAAAAAGGTGACCAAAAAAAATCAAG--T
1 AAAAAAAAA-GTGA--AAAAAAAATCAAGCAA
*
39566753 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
39566769 GTCTTGCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 3 0.08
29 13 0.32
30 12 0.30
32 12 0.30
ACGTcount: A:0.71, C:0.07, G:0.13, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:39567694 original size:15 final size:16
Alignment explanation
Indices: 39567674--39567705 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39567664 AGAAAATGAA
39567674 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
39567689 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
39567705 A
1 A
39567706 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:39567820 original size:17 final size:18
Alignment explanation
Indices: 39567788--39567821 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39567778 AAAAGAGAGT
*
39567788 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
39567806 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
39567822 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:39572557 original size:13 final size:12
Alignment explanation
Indices: 39572526--39572613 Score: 59
Period size: 15 Copynumber: 6.6 Consensus size: 12
39572516 TCACCTCTTT
39572526 TTTTTTTTTGCTCGA
1 TTTTTTTTT--TC-A
39572541 TTTTTTTTTTCA
1 TTTTTTTTTTCA
*
39572553 CTTTTTTTTTTGA
1 -TTTTTTTTTTCA
**
39572566 AATTTTTTTTCAA
1 TTTTTTTTTTC-A
39572579 TCATTTTTTTTTCGAA
1 T--TTTTTTTTTC--A
*
39572595 TTTTTTTTTTGA
1 TTTTTTTTTTCA
39572607 TTTTTTT
1 TTTTTTT
39572614 GTTACTCCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
12 17 0.28
13 14 0.23
14 9 0.15
15 18 0.30
16 3 0.05
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:39572571 original size:14 final size:14
Alignment explanation
Indices: 39572540--39572606 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 14
39572530 TTTTTGCTCG
*
39572540 ATTTTTTTTTT-CA
1 ATTTTTTTTTTGAA
*
39572553 CTTTTTTTTTTGAA
1 ATTTTTTTTTTGAA
*
39572567 A--TTTTTTTTCAA
1 ATTTTTTTTTTGAA
*
39572579 TCATTTTTTTTTCG-A
1 --ATTTTTTTTTTGAA
39572594 ATTTTTTTTTTGA
1 ATTTTTTTTTTGA
39572607 TTTTTTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
12 10 0.24
13 21 0.51
14 2 0.05
15 1 0.02
16 7 0.17
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTTTGAA
Found at i:39572586 original size:15 final size:14
Alignment explanation
Indices: 39572526--39572613 Score: 73
Period size: 12 Copynumber: 6.5 Consensus size: 14
39572516 TCACCTCTTT
39572526 TTTTTTTTTGCTCG-A
1 TTTTTTTTT--TCGAA
*
39572541 TTTTTTTTTTC-AC
1 TTTTTTTTTTCGAA
39572554 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
*
39572567 -ATTTTTTTTC-AA
1 TTTTTTTTTTCGAA
39572579 TCATTTTTTTTTCGAA
1 T--TTTTTTTTTCGAA
39572595 TTTTTTTTTT-G-A
1 TTTTTTTTTTCGAA
39572607 TTTTTTT
1 TTTTTTT
39572614 GTTACTCCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
12 18 0.29
13 14 0.23
14 9 0.15
15 18 0.29
16 3 0.05
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:39573683 original size:13 final size:13
Alignment explanation
Indices: 39573665--39573689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39573655 TGGTCATCAT
39573665 GGTGTGAACACAA
1 GGTGTGAACACAA
39573678 GGTGTGAACACA
1 GGTGTGAACACA
39573690 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39576121 original size:20 final size:20
Alignment explanation
Indices: 39576098--39576154 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
39576088 GGGTTAAGAT
*
39576098 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39576118 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39576138 TGAACT-AATTCAGCTCG
1 TGAGCTGAATTGAGCTCG
39576155 CATGGATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39582605 original size:20 final size:20
Alignment explanation
Indices: 39582582--39582628 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39582572 GGGTTAAGAT
*
39582582 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39582602 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39582622 TGAGCTG
1 TGAGCTG
39582629 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39584230 original size:48 final size:48
Alignment explanation
Indices: 39584175--39584280 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
39584165 TTGTCTTTTC
*
39584175 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
** *
39584223 TTTCTTTTTTGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
39584271 TTTCTTTTTC
1 TTTCTTTTTC
39584281 CATGACACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39586893 original size:20 final size:20
Alignment explanation
Indices: 39586870--39586916 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39586860 GGGTTAAGAT
*
39586870 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39586890 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39586910 TGAGCTG
1 TGAGCTG
39586917 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39587583 original size:17 final size:15
Alignment explanation
Indices: 39587558--39587611 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
39587548 TAGCTTCTTC
39587558 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
*
39587574 TTTGTTTTTCACTAAT
1 TTT-TTTTTCACGAAT
39587590 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
39587605 TTTTTTT
1 TTTTTTT
39587612 CAACTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
15 18 0.51
16 9 0.26
17 8 0.23
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:39587668 original size:12 final size:12
Alignment explanation
Indices: 39587651--39587700 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
39587641 ATGGAAACCA
39587651 AATTTTTTTTTG
1 AATTTTTTTTTG
39587663 AA-TTTTTTTTG
1 AATTTTTTTTTG
*
39587674 AATTTTTTTTTCA
1 AATTTTTTTTT-G
39587687 AATTTTTTTTTG
1 AATTTTTTTTTG
39587699 AA
1 AA
39587701 GAAACTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 11 0.32
12 12 0.35
13 11 0.32
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:39587671 original size:13 final size:13
Alignment explanation
Indices: 39587653--39587697 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
39587643 GGAAACCAAA
39587653 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
39587665 -TTTTTTTTGAAT
1 TTTTTTTTTGAAT
**
39587677 TTTTTTTTCAAAT
1 TTTTTTTTTGAAT
39587690 TTTTTTTT
1 TTTTTTTT
39587698 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:39587695 original size:11 final size:11
Alignment explanation
Indices: 39587654--39587683 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
39587644 GAAACCAAAT
39587654 TTTTTTTTGAA
1 TTTTTTTTGAA
39587665 TTTTTTTTGAA
1 TTTTTTTTGAA
39587676 TTTTTTTT
1 TTTTTTTT
39587684 TCAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39593790 original size:21 final size:23
Alignment explanation
Indices: 39593745--39593791 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39593735 TCACCTGCAA
* *
39593745 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39593768 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39593789 TAA
1 TAA
39593792 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39599143 original size:18 final size:16
Alignment explanation
Indices: 39599120--39599174 Score: 85
Period size: 15 Copynumber: 3.4 Consensus size: 16
39599110 TAGCTTCTTC
39599120 TTTTTTTTCACGAAAATT
1 TTTTTTTTCACG--AATT
39599138 TTTTTTTTCACGAA-T
1 TTTTTTTTCACGAATT
39599153 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
39599169 TTTTTT
1 TTTTTT
39599175 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.42
16 9 0.25
18 12 0.33
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:39599235 original size:11 final size:11
Alignment explanation
Indices: 39599219--39599263 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
39599209 AACCAATTTT
39599219 TTTTTTTTGAA
1 TTTTTTTTGAA
39599230 TTTTTTTTGAA
1 TTTTTTTTGAA
39599241 TTTTTTTTTGAA
1 -TTTTTTTTGAA
39599253 TTTTTTTTGAA
1 TTTTTTTTGAA
39599264 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39599235 original size:12 final size:12
Alignment explanation
Indices: 39599218--39599260 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
39599208 AAACCAATTT
39599218 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39599230 -TTTTTTTTGAA
1 TTTTTTTTTGAA
39599241 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39599253 TTTTTTTT
1 TTTTTTTT
39599261 GAAGAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:39599248 original size:23 final size:23
Alignment explanation
Indices: 39599218--39599263 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39599208 AAACCAATTT
39599218 TTTTTTTTTGAATTTTTTTTGAA
1 TTTTTTTTTGAATTTTTTTTGAA
39599241 TTTTTTTTTGAATTTTTTTTGAA
1 TTTTTTTTTGAATTTTTTTTGAA
39599264 GAAACTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTTTTTTGAATTTTTTTTGAA
Found at i:39600295 original size:21 final size:23
Alignment explanation
Indices: 39600250--39600296 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39600240 TCACCTGCAA
* *
39600250 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39600273 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39600294 TAA
1 TAA
39600297 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39600872 original size:29 final size:27
Alignment explanation
Indices: 39600839--39600893 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
39600829 GTGATTAAAT
39600839 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
39600868 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
39600894 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:39603108 original size:20 final size:20
Alignment explanation
Indices: 39603085--39603131 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39603075 GGGTTAAAAT
*
39603085 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39603105 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39603125 TGAGCTG
1 TGAGCTG
39603132 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39607877 original size:18 final size:17
Alignment explanation
Indices: 39607843--39607876 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39607833 AAACCGTATG
39607843 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTTCTTTT
*
39607860 CAATTTTTTTTTATTTT
1 CAATTTTTTTTTCTTTT
39607877 TTTTACTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
CAATTTTTTTTTCTTTT
Done.