Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold49
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: 1668912
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 42860 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:675 original size:2 final size:2
Alignment explanation
Indices: 668--712 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
658 CAAGAAGCCA
*
668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
710 AT A
1 AT A
713 GTCACAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:970 original size:7 final size:7
Alignment explanation
Indices: 960--995 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
950 TTAAAAATCA
960 AAAATTT
1 AAAATTT
967 AAAATTT
1 AAAATTT
974 AAAATATT
1 AAAAT-TT
*
982 AAAATAT
1 AAAATTT
989 AAAATTT
1 AAAATTT
996 TCATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:977 original size:15 final size:15
Alignment explanation
Indices: 949--1032 Score: 55
Period size: 15 Copynumber: 5.4 Consensus size: 15
939 TTTATTTGAT
* *
949 TTTAAAAATCAAAAA
1 TTTAAAATTTAAAAA
964 TTTAAAATTT-AAAA
1 TTTAAAATTTAAAAA
* *
978 TATTAAAATATAAAAT
1 T-TTAAAATTTAAAAA
* *
994 TTTCATATAATTTTATAA
1 TTT-A-A-AATTTAAAAA
1012 TTT-AAATTTAAAAAA
1 TTTAAAATTT-AAAAA
1027 TTTAAA
1 TTTAAA
1033 TCATAACTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
14 10 0.19
15 25 0.48
16 7 0.13
17 1 0.02
18 9 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAATTTAAAAA
Found at i:977 original size:22 final size:22
Alignment explanation
Indices: 949--995 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
939 TTTATTTGAT
*
949 TTTAAAA-ATCAAAAATTTAAAA
1 TTTAAAATAT-AAAAATATAAAA
*
971 TTTAAAATATTAAAATATAAAA
1 TTTAAAATATAAAAATATAAAA
993 TTT
1 TTT
996 TCATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATATAAAAATATAAAA
Found at i:1100 original size:16 final size:16
Alignment explanation
Indices: 1040--1102 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
1030 AAATCATAAC
1040 TTAATAATAATATAAAAT
1 TTAA-AATAAT-TAAAAT
* **
1058 ATTAAAATAATCATATTT
1 -TTAAAATAATTA-AAAT
*
1076 TTAACATAATTAAAAT
1 TTAAAATAATTAAAAT
1092 TTAAAATAATT
1 TTAAAATAATT
1103 TTAACTTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 12 0.34
17 11 0.31
18 8 0.23
19 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAATAATTAAAAT
Found at i:1813 original size:21 final size:23
Alignment explanation
Indices: 1786--1830 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1776 ATAATTTTTT
* *
1786 AATTTTATTTATGA-ATTTAAAA
1 AATTTAATTTATGATATATAAAA
1808 AATTTAATTTATGATATATAAAA
1 AATTTAATTTATGATATATAAAA
1831 TACAATCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTTAATTTATGATATATAAAA
Found at i:4979 original size:25 final size:25
Alignment explanation
Indices: 4945--4993 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4935 GAAGGGTGTC
4945 AATTTATTGCAAACGGATTCTGATT
1 AATTTATTGCAAACGGATTCTGATT
* *
4970 AATTTATTGCCAATGGATTCTGAT
1 AATTTATTGCAAACGGATTCTGAT
4994 GCAACTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (25 bp):
AATTTATTGCAAACGGATTCTGATT
Found at i:5611 original size:15 final size:14
Alignment explanation
Indices: 5585--5655 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 14
5575 AACTTAAATG
5585 ATTCAA-AA-TTAA
1 ATTCAATAATTTAA
*
5597 ATTGATATAATTTAAA
1 ATTCA-ATAATTT-AA
* *
5613 ACTCAATAATTTAG
1 ATTCAATAATTTAA
5627 ATTCGAGATAATTTAA
1 ATTC-A-ATAATTTAA
5643 ATTCAAATAATTT
1 ATTC-AATAATTT
5656 GAGCATTATC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
12 4 0.09
13 1 0.02
14 6 0.13
15 17 0.37
16 18 0.39
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (14 bp):
ATTCAATAATTTAA
Found at i:5639 original size:16 final size:15
Alignment explanation
Indices: 5593--5655 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
5583 TGATTCAAAA
* *
5593 TTAAATTGATATAAT
1 TTAAATTCAAATAAT
*
5608 TTAAAACTC-AATAAT
1 TT-AAATTCAAATAAT
* *
5623 TTAGATTCGAGATAAT
1 TTAAATTC-AAATAAT
5639 TTAAATTCAAATAAT
1 TTAAATTCAAATAAT
5654 TT
1 TT
5656 GAGCATTATC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
14 4 0.11
15 17 0.46
16 16 0.43
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
TTAAATTCAAATAAT
Found at i:5957 original size:101 final size:101
Alignment explanation
Indices: 5782--5980 Score: 389
Period size: 101 Copynumber: 2.0 Consensus size: 101
5772 TGCAATAGGA
5782 ATTCAGCAAATTTTACAACTTCATTTACTAACTATCTATTAATTATTCATAATTACTATGAATTT
1 ATTCAGCAAATTTTACAACTTCATTTACTAACTATCTATTAATTATTCATAATTACTATGAATTT
5847 TTAACATTAATTATAGACTAAAATTTAATAAAATTC
66 TTAACATTAATTATAGACTAAAATTTAATAAAATTC
5883 ATTCAGCAAATTTTACAACTTCATTTACTAACTATCTATTAATTATTCATAATTACTATGAATTT
1 ATTCAGCAAATTTTACAACTTCATTTACTAACTATCTATTAATTATTCATAATTACTATGAATTT
*
5948 TTAATATTAATTATAGACTAAAATTTAATAAAA
66 TTAACATTAATTATAGACTAAAATTTAATAAAA
5981 CTCAAATATA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (101 bp):
ATTCAGCAAATTTTACAACTTCATTTACTAACTATCTATTAATTATTCATAATTACTATGAATTT
TTAACATTAATTATAGACTAAAATTTAATAAAATTC
Found at i:6983 original size:28 final size:26
Alignment explanation
Indices: 6936--6987 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
6926 ATTATTAAAC
6936 ATACATATTTATATTTTAATAATATA
1 ATACATATTTATATTTTAATAATATA
*
6962 ATACAATATTTTTCATTTTAATAATA
1 ATAC-ATATTTAT-ATTTTAATAATA
6988 AATTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 7 0.30
28 12 0.52
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (26 bp):
ATACATATTTATATTTTAATAATATA
Found at i:7030 original size:16 final size:16
Alignment explanation
Indices: 7011--7041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7001 ACTAATTATT
7011 TTAATAAAAATTTTAG
1 TTAATAAAAATTTTAG
*
7027 TTAATAAAAGTTTTA
1 TTAATAAAAATTTTA
7042 ATAATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTAATAAAAATTTTAG
Found at i:7207 original size:29 final size:28
Alignment explanation
Indices: 7154--7209 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
7144 TTATACTATA
*
7154 AATATTTAATAATAAAAGTTTTTAATATT
1 AATATTTAATAATAAAAG-TATTAATATT
7183 AATATTCTAATAATAAACA-TATTAATA
1 AATATT-TAATAATAAA-AGTATTAATA
7210 GAAATAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 13 0.54
30 10 0.42
31 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (28 bp):
AATATTTAATAATAAAAGTATTAATATT
Found at i:7215 original size:29 final size:28
Alignment explanation
Indices: 7153--7215 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
7143 ATTATACTAT
* *
7153 AAATATTTAATAATAAAAGTTTTTAATAT
1 AAATATTTAATAATAAAAG-TATTAATAG
*
7182 TAATATTCTAATAATAAACA-TATTAATAG
1 AAATATT-TAATAATAAA-AGTATTAATAG
7211 AAATA
1 AAATA
7216 ACATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 17 0.61
30 10 0.36
31 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (28 bp):
AAATATTTAATAATAAAAGTATTAATAG
Found at i:7509 original size:15 final size:15
Alignment explanation
Indices: 7489--7526 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7479 TCATATATTT
7489 TAAATA-TTTATATAA
1 TAAATATTTTA-ATAA
*
7504 TTAATATTTTAATAA
1 TAAATATTTTAATAA
7519 TAAATATT
1 TAAATATT
7527 ATAGTTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATTTTAATAA
Found at i:9065 original size:15 final size:14
Alignment explanation
Indices: 9027--9065 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
9017 AAATTAATTT
9027 TTTAAATATACTCA
1 TTTAAATATACTCA
*
9041 ATTAAATATACTTCA
1 TTTAAATATAC-TCA
*
9056 TTTAATTATA
1 TTTAAATATA
9066 GGAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAAATATACTCA
Found at i:9210 original size:2 final size:2
Alignment explanation
Indices: 9203--9234 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9193 AGATAATTTG
9203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9235 GTATGTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9799 original size:11 final size:12
Alignment explanation
Indices: 9770--9818 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
9760 ATTAAACATG
*
9770 AATATAAAATAA
1 AATATAATATAA
*
9782 AAAATAAT-TAA
1 AATATAATATAA
9793 AATATAATATAA
1 AATATAATATAA
*
9805 CATA-AATATAA
1 AATATAATATAA
9816 AAT
1 AAT
9819 TATATTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 19 0.61
12 12 0.39
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATATAATATAA
Found at i:11833 original size:20 final size:22
Alignment explanation
Indices: 11789--11836 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
11779 GACTAATATA
*
11789 TAAAAATATAAATAATTTTTTT
1 TAAAAATATAAATAATTTATTT
11811 TAAAAA-ATAAATAA-TTATTT
1 TAAAAATATAAATAATTTATTT
11831 TAAAAA
1 TAAAAA
11837 GTGAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 8 0.32
22 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATATAAATAATTTATTT
Found at i:11947 original size:19 final size:19
Alignment explanation
Indices: 11909--11970 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
11899 TATAATTTAA
*
11909 TTTTAAATGAA-TAGTTTT
1 TTTTAAATGAAGTAATTTT
11927 TTTTAAATGAAGTAATTTT
1 TTTTAAATGAAGTAATTTT
** *
11946 TTAAAAAATG-AGTCATTTT
1 TT-TTAAATGAAGTAATTTT
11965 TTTTAA
1 TTTTAA
11971 GAAGTGGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 13 0.36
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
TTTTAAATGAAGTAATTTT
Found at i:11984 original size:21 final size:21
Alignment explanation
Indices: 11942--11986 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11932 AATGAAGTAA
*
11942 TTTTTTAAAAAATGAGTCATT
1 TTTTTTAAAAAATGAGTAATT
* * *
11963 TTTTTTAAGAAGTGGGTAATT
1 TTTTTTAAAAAATGAGTAATT
11984 TTT
1 TTT
11987 ATAGTTTTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (21 bp):
TTTTTTAAAAAATGAGTAATT
Found at i:12475 original size:31 final size:32
Alignment explanation
Indices: 12408--12476 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
12398 ATTATATATT
** *** *
12408 TAAAAATTTTATTAAAATATATATTTAGTTAT
1 TAAAAATTAAATTAAAATATATATTTAAAAAA
12440 TAAAAATTAAATTAAAA-ATATATTTAAAAAA
1 TAAAAATTAAATTAAAATATATATTTAAAAAA
12471 TAAAAA
1 TAAAAA
12477 ATATATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
TAAAAATTAAATTAAAATATATATTTAAAAAA
Found at i:12491 original size:20 final size:20
Alignment explanation
Indices: 12447--12492 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
12437 TATTAAAAAT
*
12447 TAAATTAAAAATATATTTAAA
1 TAAA-TAAAAATATATATAAA
12468 -AAATAAAAA-ATATATAATA
1 TAAATAAAAATATATATAA-A
12487 TAAATA
1 TAAATA
12493 TGCTTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATAAAAATATATATAAA
Found at i:12639 original size:2 final size:2
Alignment explanation
Indices: 12632--12665 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12622 TAGGTCAACC
12632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12666 TGAATCATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12926 original size:16 final size:16
Alignment explanation
Indices: 12905--12949 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
12895 TCTATTTTTT
12905 AATTTATATTTTTAAA
1 AATTTATATTTTTAAA
*
12921 AATTTA-ATTTTTAAT
1 AATTTATATTTTTAAA
12936 AATTTAATATTTTT
1 AATTT-ATATTTTT
12950 TATTAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 13 0.50
16 7 0.27
17 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTATATTTTTAAA
Found at i:13300 original size:13 final size:15
Alignment explanation
Indices: 13265--13311 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
13255 TGAACACCTC
*
13265 TAATTTAAATCAATA
1 TAATTTAAATTAATA
13280 TAATTTAAATTAAT-
1 TAATTTAAATTAATA
13294 T-ATTTAAATTTAATA
1 TAATTTAAA-TTAATA
13309 TAA
1 TAA
13312 CTATTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
14 6 0.21
15 14 0.50
16 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTAAATTAATA
Found at i:13751 original size:2 final size:2
Alignment explanation
Indices: 13738--13770 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13728 GAGATTAAAG
*
13738 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13771 AACAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:14006 original size:21 final size:21
Alignment explanation
Indices: 13980--14041 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
13970 TACCTACATA
*
13980 TATCGATAAATGCCTTCCATG
1 TATCGATAAATACCTTCCATG
* *
14001 TATCGATACATACTTTCCATG
1 TATCGATAAATACCTTCCATG
* *
14022 TATCGATACATACTTTCCAT
1 TATCGATAAATACCTTCCAT
14042 CGATCAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (21 bp):
TATCGATAAATACCTTCCATG
Found at i:14192 original size:20 final size:20
Alignment explanation
Indices: 14164--14236 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
14154 GGAAAAATTG
* *
14164 TATCAATACATTCACTTATA
1 TATCGATACATTCACTAATA
**
14184 TATCGATACATGTGGC-AATA
1 TATCGATACAT-TCACTAATA
* *
14204 TATCGATACA-TCACTCATTG
1 TATCGATACATTCACT-AATA
14224 TATCGATACATTC
1 TATCGATACATTC
14237 TAGGTTTTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
20 35 0.85
21 4 0.10
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
TATCGATACATTCACTAATA
Found at i:16538 original size:79 final size:79
Alignment explanation
Indices: 16163--16548 Score: 332
Period size: 79 Copynumber: 4.9 Consensus size: 79
16153 TGGGGATAAC
* * * * ** * *
16163 AACGGGGCTGGAGTATCTCCGATTATGGAAAATTGATGTTTTAAAAATAAAATTGGGGCTGAAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
* *
16228 ATTCCCC-CTGGAAT
66 A-TCCCCTCAGAAAT
** * * * * *
16242 AACAAGGTTAGAGTATCCCTGATTAT-AGAAAATTGGTGTTTT-GAAAATAAAATCGGGTTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATTGATGTTTTAG-AAATAAAACCGGGGTTGGA
*
16305 GTATCCTCTC-GAAAAT
64 GTATCCCCTCAG-AAAT
* * * ** *
16321 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
*
16386 ATCCCCATGA-AAAT
66 ATCCCC-TCAGAAAT
* * * * ** * * * *
16400 AATGGGGTTGGTGTATCCCCGATTGTGAGAAATCAATATGTTAGAAATAAAGCCAGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
16465 ATCCCCTCAGAAAT
66 ATCCCCTCAGAAAT
* * * * *
16479 AACGGGATTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAACCGGGGTTAGAAT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
16544 ATCCC
66 ATCCC
16549 TGAGATGAAA
Statistics
Matches: 244, Mismatches: 54, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
78 7 0.03
79 234 0.96
80 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
ATCCCCTCAGAAAT
Found at i:16559 original size:50 final size:50
Alignment explanation
Indices: 16492--16612 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 50
16482 GGGATTGGAG
* ** *
16492 TATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAACCGGGGTTAGAA
1 TATCCCCGA-GATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAA
* * * *
16543 TATCCCTGAGATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAG
1 TATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAA
16593 TATCCCCGAGATGAAAAATC
1 TATCCCCGAGATGAAAAATC
16613 TAGAAATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 53 0.87
51 8 0.13
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (50 bp):
TATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAA
Found at i:18328 original size:20 final size:20
Alignment explanation
Indices: 18300--18355 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
18290 ATGTATTGAT
*
18300 ACAATGTATCGATACACTGA
1 ACAATGTATCGATACAATGA
* *
18320 ACCATGTATCGATGCAATGA
1 ACAATGTATCGATACAATGA
18340 ACAATGTATCGATACA
1 ACAATGTATCGATACA
18356 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:19157 original size:82 final size:83
Alignment explanation
Indices: 18980--19158 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 83
18970 GGAAGTGGGA
* ** * * *
18980 ATCCTGCTCTTTGAGGATTAAGGAAAAAGAGAATGAAATGGGTCCTGCTTCTTGAGGACAAAGGA
1 ATCCTGCTCTTTGAAGACAAAAGAAAAAGAGAATGAAATAGGTCATGCTTCTTGAGGACAAAGGA
19045 AAAAAGGAAATAAAATGC
66 AAAAAGGAAATAAAATGC
* * * * * *
19063 ATCATGCCCTTTGAAGACAAAAGAAAAAG-GAATTAAATATGTCATGCTTTTTGAGGATAAAGGA
1 ATCCTGCTCTTTGAAGACAAAAGAAAAAGAGAATGAAATAGGTCATGCTTCTTGAGGACAAAGGA
* *
19127 AAATA-GAGAATAAAGTGC
66 AAAAAGGA-AATAAAATGC
*
19145 GTCCTGCTCTTTGA
1 ATCCTGCTCTTTGA
19159 GAACTAGAAG
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 2 0.03
82 53 0.68
83 23 0.29
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (83 bp):
ATCCTGCTCTTTGAAGACAAAAGAAAAAGAGAATGAAATAGGTCATGCTTCTTGAGGACAAAGGA
AAAAAGGAAATAAAATGC
Found at i:19159 original size:42 final size:41
Alignment explanation
Indices: 18981--19244 Score: 177
Period size: 42 Copynumber: 6.4 Consensus size: 41
18971 GAAGTGGGAA
* *
18981 TCCTGCTCTTTGAGGATTAAGGAAAAAGAGAATGAAA-TGGG
1 TCCTGCTCTTTGAGGATAAAGGAAAAAGAGAAT-AAAGTGCG
* * *
19022 TCCTGCT-TCTTGAGGACAAAGGAAAAA-AGGAAATAAAATGCA
1 TCCTGCTCT-TTGAGGATAAAGGAAAAAGA-G-AATAAAGTGCG
* * * * * **
19064 TCATGCCCTTTGAAGACAAAAGAAAAAG-GAATTAAA-TATG
1 TCCTGCTCTTTGAGGATAAAGGAAAAAGAGAA-TAAAGTGCG
* *
19104 TCATGCTTTTTGAGGATAAAGGAAAATAGAGAATAAAGTGCG
1 TCCTGCTCTTTGAGGATAAAGGAAAA-AGAGAATAAAGTGCG
* * * **
19146 TCCTGCTCTTTGAGAACTAGAAGGGAAAAGAAGGAAATGAAGTAAG
1 TCCTGCTCTTTGAGGA-TA-AAGGAAAAAG-A-G-AATAAAGTGCG
*
19192 TCCTGCTCCTTGAGGATAAAGGAGAAAA-AG-A-AAAG-GCG
1 TCCTGCTCTTTGAGGATAAAGGA-AAAAGAGAATAAAGTGCG
19230 TCCTGCTCTTTGAGG
1 TCCTGCTCTTTGAGG
19245 GCTAAAAAGT
Statistics
Matches: 175, Mismatches: 32, Indels: 35
0.72 0.13 0.14
Matches are distributed among these distances:
38 15 0.09
39 3 0.02
40 27 0.15
41 38 0.22
42 45 0.26
43 6 0.03
44 12 0.07
45 7 0.04
46 22 0.13
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGATAAAGGAAAAAGAGAATAAAGTGCG
Found at i:19221 original size:46 final size:44
Alignment explanation
Indices: 19113--19223 Score: 104
Period size: 46 Copynumber: 2.5 Consensus size: 44
19103 GTCATGCTTT
* ** *
19113 TTGAGGATAAAGGA-AAATAG-AGAATAAAGTGCGTCCTGCTCT
1 TTGAGGATAAAGGAGAAAAAGAAGAATAAAGTAAGTCCTGCTCC
* *
19155 TTGAGAACTAGAAGG-G-AAAAGAAGGAAATGAAGTAAGTCCTGCTCC
1 TTGAGGA-TA-AAGGAGAAAAAGAA-G-AATAAAGTAAGTCCTGCTCC
19201 TTGAGGATAAAGGAGAAAAAGAA
1 TTGAGGATAAAGGAGAAAAAGAA
19224 AAGGCGTCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
42 6 0.11
43 6 0.11
44 9 0.17
45 4 0.07
46 29 0.54
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (44 bp):
TTGAGGATAAAGGAGAAAAAGAAGAATAAAGTAAGTCCTGCTCC
Found at i:19312 original size:61 final size:61
Alignment explanation
Indices: 19216--19928 Score: 855
Period size: 61 Copynumber: 11.7 Consensus size: 61
19206 GATAAAGGAG
* * * *
19216 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGGCTAAAAAGTGCCACCAACTCGTGTGGACTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
19277 GAAAA-GAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTT
1 -AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
19338 AAAAGGAAAAAGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
19400 AAAAGGAAAAGGCGTCCTGCTCTTTAAGGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *** * *
19460 GAAAGGCGAAA-GCATCCTGCTTTTTGAGGACGGGAAGGTGCCACCAACTTGTGTGGACTTT
1 AAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * *
19521 AAAAGAAAAAGGTATCCTACTCTTTGAGGACTAGAAAAGTGACACCAACCTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* *
19583 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
19644 AAAAAGAAAAGACGTCCTGCTCTTTGAGGACT-AGAAGTTGCCACCAACTTGTGTGGGCTTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTTGTGTGGGC-TTT
* * * * * *
19706 AAAAGGAAAATGCGTCCTGCTCTTTAAGGACT-GAAGGTGCCACCAACTTATGTGGGTTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * ** *
19766 GAAAGGCGAAA-GCATCCCGCTCTTTGAGGACT-GGAAGATGCCACCAACTTGTGTGGACTTT
1 AAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTTGTGTGGGCTTT
* * *
19827 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGACTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
*
19889 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTTAAAAGTG
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTG
19929 AAAAGAGAAA
Statistics
Matches: 560, Mismatches: 78, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
60 89 0.16
61 271 0.48
62 197 0.35
63 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:19810 original size:306 final size:304
Alignment explanation
Indices: 19217--19926 Score: 1106
Period size: 306 Copynumber: 2.3 Consensus size: 304
19207 ATAAAGGAGA
* *
19217 AAAAGAAAAGGCGTCCTGCTCTTTGAGGGCTA-AAAAGTGCCACCAA-CTCGTGTGGACTTTGAA
1 AAAAGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCT-GTGTGGACTTT-AA
* *
19280 AA-GAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAGG
64 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAG
*
19344 AAAAAGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
129 AAAAAGCGTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
19409 AGGCGTCCTGCTCTTTAAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCGAAAGCA
193 AGGCGTCCTGCTCTTTAAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGAAAGCA
* * *
19474 TCCTGCTTTTTGAGGACGGGAAGGTGCCACCAACTTGTGTGGACTTT
258 TCCCGCTCTTTGAGGACGGGAAGATGCCACCAACTTGTGTGGACTTT
* * * *
19521 AAAAGAAAAAGGTATCCTACTCTTTGAGGACTAGAAAAGTGACACCAACCTGTGTGGGCTTTAAA
1 AAAAG-AAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGACTTTAAA
* *
19586 AGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-
65 AGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGA
19650 AAAAGACGTCCTGCTCTTTGAGGACTAG-AAGTTGCCACCAACTTGTGTGGGCTTTTAAAAGGAA
130 AAAAG-CGTCCTGCTCTTTGAGGACTAGAAAG-TGCCACCAACTTGTGTGGGC-TTTAAAAGGAA
* * *
19714 AATGCGTCCTGCTCTTTAAGGACTGAAGGTGCCACCAACTTATGTGGGTTTTGAAAGGCGAAAGC
192 AAGGCGTCCTGCTCTTTAAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGAAAGC
*
19779 ATCCCGCTCTTTGAGGACTGGAAGATGCCACCAACTTGTGTGGACTTT
257 ATCCCGCTCTTTGAGGACGGGAAGATGCCACCAACTTGTGTGGACTTT
* *
19827 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGACTTTAAA
1 AAAA-GAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGACTTTAAA
19892 AGGAAAAGGCGTCCTGCTCTTTGAGGACTTAAAAG
65 AGGAAAAGGCGTCCTGCTCTTTGAGGAC-TAAAAG
19927 TGAAAAGAGA
Statistics
Matches: 370, Mismatches: 27, Indels: 15
0.90 0.07 0.04
Matches are distributed among these distances:
304 8 0.02
305 52 0.14
306 302 0.82
307 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (304 bp):
AAAAGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGACTTTAAAA
GGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAA
AAAGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
CGTCCTGCTCTTTAAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGAAAGCATCC
CGCTCTTTGAGGACGGGAAGATGCCACCAACTTGTGTGGACTTT
Found at i:20927 original size:1 final size:1
Alignment explanation
Indices: 20923--20982 Score: 66
Period size: 1 Copynumber: 60.0 Consensus size: 1
20913 TGTTTTGTTG
* * * * * *
20923 TTTTTTTTTTGTTTTTTTTTTGTTTTTTCTTTTTGTTTTTTGTTTTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20983 ATTTAAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:20929 original size:11 final size:10
Alignment explanation
Indices: 20911--20982 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
20901 ATTTTTTTCC
*
20911 TTTGTTTTGT
1 TTTGTTTTTT
*
20921 TGT-TTTTTT
1 TTTGTTTTTT
20930 TTTGTTTTTTT
1 TTTG-TTTTTT
20941 TTTGTTTTTT
1 TTTGTTTTTT
*
20951 CTTT-TTGTTT
1 -TTTGTTTTTT
20961 TTTGTTTTTT
1 TTTGTTTTTT
20971 TTT-TTATTTT
1 TTTGTT-TTTT
20981 TT
1 TT
20983 ATTTAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
9 12 0.23
10 27 0.52
11 13 0.25
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:20932 original size:24 final size:21
Alignment explanation
Indices: 20902--20975 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
20892 TTCTTTTCTA
**
20902 TTTTTTTCCTTTGTTTTGTTGT
1 TTTTTTTTTTTTGTTTT-TTGT
*
20924 TTTTTTTTTGTTTTTTTTTTG-
1 TTTTTTTTT-TTTGTTTTTTGT
*
20945 TTTTTTCTTTTTGTTTTTTGT
1 TTTTTTTTTTTTGTTTTTTGT
20966 TTTTTTTTTT
1 TTTTTTTTTT
20976 ATTTTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.23
21 17 0.39
22 10 0.23
23 7 0.16
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.86
Consensus pattern (21 bp):
TTTTTTTTTTTTGTTTTTTGT
Found at i:20949 original size:43 final size:41
Alignment explanation
Indices: 20903--20982 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 41
20893 TCTTTTCTAT
*
20903 TTTTTTC-CTTTGTTTTGTTGTTTTTTTTTTGTTTTTTTTTTG
1 TTTTTTCTCTTTGTTTT-TTGTTTTTTTTTT-TATTTTTTTTG
*
20945 TTTTTTCTTTTTGTTTTTTGTTTTTTTTTTTATTTTTT
1 TTTTTTCTCTTTGTTTTTTGTTTTTTTTTTTATTTTTT
20983 ATTTAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 7 0.20
42 20 0.57
43 8 0.23
ACGTcount: A:0.01, C:0.04, G:0.09, T:0.86
Consensus pattern (41 bp):
TTTTTTCTCTTTGTTTTTTGTTTTTTTTTTTATTTTTTTTG
Found at i:29069 original size:22 final size:23
Alignment explanation
Indices: 29041--29096 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
29031 TGGACATGTT
29041 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
29063 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
29086 AAAAATGCATG
1 AAAAATGCATG
29097 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:30054 original size:20 final size:20
Alignment explanation
Indices: 30007--30081 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
29997 AAAAAGACAT
*
30007 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
30026 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
30047 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
30067 AATGTATCGATACAT
1 AATGTATCGATACAT
30082 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:30075 original size:40 final size:39
Alignment explanation
Indices: 30004--30081 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
29994 GGTAAAAAGA
* *
30004 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
30043 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
30082 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:30613 original size:32 final size:32
Alignment explanation
Indices: 30572--31174 Score: 1044
Period size: 32 Copynumber: 18.8 Consensus size: 32
30562 GATTTGAAAA
* ** * **
30572 GGGTTGCCACTGACTTGCATAGGCTTTTAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
30604 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30636 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
30668 GGGTTGCCACCGACTTGTGTGGGTTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30700 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
30732 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
30764 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30796 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30828 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
30860 GGGTTGCCACCGATTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
30892 AGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30924 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30956 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
30988 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
31020 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
31052 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
31084 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* * *
31116 AGGTTGCCACCAACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
31148 GGGTTGCCACCGACTTGTGTGGGCTTT
1 GGGTTGCCACCGACTTGTGTGGGCTTT
31175 AAAAGGATGC
Statistics
Matches: 548, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 548 1.00
ACGTcount: A:0.14, C:0.19, G:0.35, T:0.32
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
Found at i:31212 original size:27 final size:27
Alignment explanation
Indices: 31173--31807 Score: 1011
Period size: 27 Copynumber: 23.2 Consensus size: 27
31163 TGTGTGGGCT
*
31173 TTAAAAGGATGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31200 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31227 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31254 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31281 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31308 TTAAAAGAGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31335 TTAAAAAGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
**
31362 TTAAAAGGGTGCCACAAAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31389 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
* *
31416 TTAAAAAAGATGCCACGGAGTTGTGGAC
1 TT-AAAAGGGTGCCACGGAGTTGTGGAC
31444 TTAAAAGGGATGCCACGGAGTTGTGGAC
1 TTAAAAGGG-TGCCACGGAGTTGTGGAC
31472 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31499 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
31526 TTAAAGAGGGTGCCACGGAGTTGTGGAC
1 TTAAA-AGGGTGCCACGGAGTTGTGGAC
* * *
31554 TTTAAAAGAGCGCTACGGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC
31582 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
* *
31609 TTTGAAA-GGTGCCACAGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31636 TTAAAAGGGTGCCACGGAGCTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31663 TTTAAAAGAGTGCCACGGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC
**
31691 TTTGAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31718 TTAAAAGGGTGCCACAGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31745 TTTAAAAGGGTGCCACAGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC
*
31773 TTTAAAAGGATGCCACGGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC
31801 TTCAAAA
1 TT-AAAA
31808 AGAAATGCCA
Statistics
Matches: 565, Mismatches: 34, Indels: 17
0.92 0.06 0.03
Matches are distributed among these distances:
26 5 0.01
27 375 0.66
28 180 0.32
29 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
TTAAAAGGGTGCCACGGAGTTGTGGAC
Found at i:31498 original size:110 final size:110
Alignment explanation
Indices: 31173--31807 Score: 1005
Period size: 110 Copynumber: 5.8 Consensus size: 110
31163 TGTGTGGGCT
*
31173 TTAAAAGGATGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
31236 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
31281 TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAAGG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
**
31344 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGAC
66 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
31389 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
31453 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
31499 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
* *
31564 CGCTACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
31609 TTTGAAA-GGTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGAGCTGTGGACTTTAAAAGA
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
**
31672 GTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGAC
65 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
31718 TTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGA
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
31783 TGCCACGGAGTTGTGGACTTCAAAA
66 TGCCACGGAGTTGTGGACTT-AAAA
31808 AGAAATGCCA
Statistics
Matches: 488, Mismatches: 32, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
108 137 0.28
109 126 0.26
110 210 0.43
111 15 0.03
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (110 bp):
TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
Found at i:39349 original size:22 final size:23
Alignment explanation
Indices: 39321--39376 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
39311 TGGACATGTT
39321 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
39343 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
39366 AAAAATGCATG
1 AAAAATGCATG
39377 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:40334 original size:20 final size:20
Alignment explanation
Indices: 40287--40361 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
40277 AAAAAGACAT
*
40287 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
40306 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
40327 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
40347 AATGTATCGATACAT
1 AATGTATCGATACAT
40362 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:40355 original size:40 final size:39
Alignment explanation
Indices: 40284--40361 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
40274 GGTAAAAAGA
* *
40284 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
40323 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
40362 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:46990 original size:25 final size:26
Alignment explanation
Indices: 46944--47000 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
46934 TGTTAGTAAA
*
46944 ACAAAAAAAATAACAGACAAATCTAT
1 ACAAAAAAAATAACAGACAAATATAT
*
46970 ACAAAACAAAT-ACACGA-AAATATAT
1 ACAAAAAAAATAACA-GACAAATATAT
46995 A-AAAAA
1 ACAAAAA
47001 GGGAGACGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.15
25 11 0.41
26 12 0.44
ACGTcount: A:0.68, C:0.14, G:0.04, T:0.14
Consensus pattern (26 bp):
ACAAAAAAAATAACAGACAAATATAT
Found at i:47372 original size:79 final size:79
Alignment explanation
Indices: 47241--47618 Score: 381
Period size: 79 Copynumber: 4.8 Consensus size: 79
47231 ACAATGGGGC
* ** * * * * *
47241 TGGAGTATCCCCAATTATGAAAAATCGGTGTTCTGGAAACAAAATCGGGGTTGGAGTATCCTATC
1 TGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCATC
**
47306 GGGAATAACAGGGT
66 GAAAATAACAGGGT
* * *
47320 TGGAGTATCCCTGATTAT-AGAAAATCAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCTC-
1 TGGAGTATCCCCGATTATGA-AAAATCAATGTTTTGAAAATAAAACCGGGGTTGGAGTATCC-CA
* *
47383 TCGAAAATAACATGAT
64 TCGAAAATAACAGGGT
* * * ** * *
47399 TGGAGTATCCCCGA-TAGTGAAAAATAAATGCTTTAAAAATAAGGCCGGAGTTGGAATATCCCCA
1 TGGAGTATCCCCGATTA-TGAAAAATCAATGTTTTGAAAATAAAACCGGGGTTGGAGTAT-CCCA
*
47463 -CGAAAATAACGGGGT
64 TCGAAAATAACAGGGT
* * * *
47478 TGGAGTATCCCCGATTGTGAGAAATCAATATTTT-AGAAATAAAGCCGGGGTTGGAGTATCCCAT
1 TGGAGTATCCCCGATTATGAAAAATCAATGTTTTGA-AAATAAAACCGGGGTTGGAGTATCCCAT
*
47542 CAAAAATAAC-GGGAT
65 CGAAAATAACAGGG-T
* * *
47557 TGGAGTATCCTCGATTATGAAAAATTAATGTTTTGAAAATAAAACCGGGGTTAGAGTATCCC
1 TGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
47619 CAAGATGAAA
Statistics
Matches: 248, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
78 11 0.04
79 232 0.94
80 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCATC
GAAAATAACAGGGT
Found at i:47617 original size:51 final size:50
Alignment explanation
Indices: 47559--47682 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
47549 AACGGGATTG
* * *
47559 GAGTATCCTCGATTATGAAAAATTAATGTTTT-GAAAATAAAACCGGGGTTA
1 GAGTATCCTCGA-GATGAAAAATCAATATTTTAG-AAATAAAACCGGGGTTA
* * * * *
47610 GAGTATCCCCAAGATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTTG
1 GAGTATCCTCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
47660 GAGTATCCTCGAGATGAAAAATC
1 GAGTATCCTCGAGATGAAAAATC
47683 TAGAAATTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 51 0.82
51 11 0.18
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (50 bp):
GAGTATCCTCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
Found at i:53125 original size:51 final size:51
Alignment explanation
Indices: 53019--53132 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
53009 TTTAAAATTG
* * *
53019 TATCGATACATTTCTATCAAAACCTAGAATGTATCAATGCAATGAGAAATG
1 TATCGATACATTTCTATCAAAACCTAGAATGTATCAATACAATGACAAATC
* ** **
53070 TATCGATACATTTCTATCAAAACCTAGAATGTATCGATACAATTTCTTATC
1 TATCGATACATTTCTATCAAAACCTAGAATGTATCAATACAATGACAAATC
53121 TATCGATACATT
1 TATCGATACATT
53133 GAAAAATATA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (51 bp):
TATCGATACATTTCTATCAAAACCTAGAATGTATCAATACAATGACAAATC
Found at i:58583 original size:21 final size:21
Alignment explanation
Indices: 58559--58611 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
58549 CATGGTCCTA
*
58559 TATCGATACATTTCAGGCATG
1 TATCGATACATTTCACGCATG
**
58580 TATCGATACA-TTCACTTATG
1 TATCGATACATTTCACGCATG
58600 TATCGATACATT
1 TATCGATACATT
58612 ACCTTATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (21 bp):
TATCGATACATTTCACGCATG
Found at i:58624 original size:21 final size:20
Alignment explanation
Indices: 58577--58630 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
58567 CATTTCAGGC
58577 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
58597 ATGTATCGATACATT-ACCTT
1 ATGTATCGATACATTCA-CTT
58617 ATTGTATCGATACA
1 A-TGTATCGATACA
58631 AATTGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:59936 original size:32 final size:30
Alignment explanation
Indices: 59900--59958 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
59890 GAAAACAAAT
59900 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
59932 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
59959 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:60257 original size:13 final size:13
Alignment explanation
Indices: 60239--60264 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60229 CAATTTTTTG
60239 TGTATCGATACAT
1 TGTATCGATACAT
60252 TGTATCGATACAT
1 TGTATCGATACAT
60265 ACTTGGTGTA
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:60279 original size:32 final size:33
Alignment explanation
Indices: 60219--60282 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
60209 TACAAGCCAA
** *
60219 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
60252 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
60283 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:62816 original size:13 final size:13
Alignment explanation
Indices: 62798--62835 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
62788 ATAATCCCCC
62798 TGTATCGATACAG
1 TGTATCGATACAG
*
62811 TGTATCGATACAT
1 TGTATCGATACAG
62824 TGTATCGATACA
1 TGTATCGATACA
62836 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:68691 original size:32 final size:30
Alignment explanation
Indices: 68655--68713 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
68645 GAAAACAAAT
68655 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
68687 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
68714 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:69012 original size:13 final size:13
Alignment explanation
Indices: 68994--69019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68984 CAATTTTTTG
68994 TGTATCGATACAT
1 TGTATCGATACAT
69007 TGTATCGATACAT
1 TGTATCGATACAT
69020 ACATGGTGTA
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:69023 original size:17 final size:18
Alignment explanation
Indices: 69001--69037 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
68991 TTGTGTATCG
69001 ATACAT-TGTATCGATAC
1 ATACATGTGTATCGATAC
69018 ATACATGGTGTATCGATAC
1 ATACAT-GTGTATCGATAC
69037 A
1 A
69038 AGTTTGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (18 bp):
ATACATGTGTATCGATAC
Found at i:70529 original size:78 final size:76
Alignment explanation
Indices: 70424--70644 Score: 271
Period size: 78 Copynumber: 2.9 Consensus size: 76
70414 TTCATCTTTG
* * * *
70424 GAGATACTCTAACCTCGTTTCTACTTCCAAAATGTCAAATTTTTCATCTCTGGATACTCCAACCC
1 GAGAAACTCCAACCTCGTTTTTACTTCCAAAACGTCAAATTTTTCATCTCTGGATACTCCAACCC
70489 TACCATCTCCGAA
66 -ACCATCTCCG-A
* * * *
70502 GAGAAACTCCAACCCCGTTTTTACTTCCAAAACGCCAATTTTTTCATCTCTGGATACTCTAACCC
1 GAGAAACTCCAACCTCGTTTTTACTTCCAAAACGTCAAATTTTTCATCTCTGGATACTCCAACCC
*
70567 ACTATCTCCGA
66 ACCATCTCCGA
* * * ** *
70578 GGGAAACTCCAACCTTGTTTTTACTTCCAAAACATTGAATTTTGCATCTCTAGGGATACTCCAAC
1 GAGAAACTCCAACCTCGTTTTTACTTCCAAAACGTCAAATTTTTCATCTCT--GGATACTCCAAC
70643 CC
64 CC
70645 CACCTCCAAG
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
76 43 0.35
77 9 0.07
78 70 0.57
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.31
Consensus pattern (76 bp):
GAGAAACTCCAACCTCGTTTTTACTTCCAAAACGTCAAATTTTTCATCTCTGGATACTCCAACCC
ACCATCTCCGA
Found at i:72177 original size:30 final size:30
Alignment explanation
Indices: 72141--72198 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
72131 TAAAGTCACA
*
72141 AATTTTAATAAA-TGAAGTATTTTTTAATTT
1 AATTTTAATAAATTAAAGT-TTTTTTAATTT
72171 AATTTTAATAAATTAAAGTTTTTTTAAT
1 AATTTTAATAAATTAAAGTTTTTTTAAT
72199 CATTTAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
AATTTTAATAAATTAAAGTTTTTTTAATTT
Found at i:72195 original size:19 final size:19
Alignment explanation
Indices: 72173--72209 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
72163 TTTAATTTAA
72173 TTTTAATAAATTAAAGTTT
1 TTTTAATAAATTAAAGTTT
* *
72192 TTTTAATCATTTAAAGTT
1 TTTTAATAAATTAAAGTT
72210 GGTGATGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAATAAATTAAAGTTT
Found at i:72302 original size:12 final size:12
Alignment explanation
Indices: 72261--72304 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
72251 GTTGTAATGT
*
72261 AAATATAATACA
1 AAATATAATATA
72273 AAATAATAAT-TA
1 AAAT-ATAATATA
72285 AAATATAATATA
1 AAATATAATATA
72297 AAATATAA
1 AAATATAA
72305 CACGAAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 5 0.17
12 19 0.66
13 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAATATA
Found at i:77073 original size:6 final size:7
Alignment explanation
Indices: 77058--77083 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
77048 ACAACTTTAG
77058 AAAATAA
1 AAAATAA
77065 AAAATAA
1 AAAATAA
77072 AAAATAA
1 AAAATAA
77079 AAAAT
1 AAAAT
77084 TGCATCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:81197 original size:21 final size:22
Alignment explanation
Indices: 81156--81203 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
81146 TAATAATATA
81156 AATTTAAATATAATTATATTTT
1 AATTTAAATATAATTATATTTT
81178 AATTTAAA-AT-ATTAATATTTT
1 AATTTAAATATAATT-ATATTTT
*
81199 TATTT
1 AATTT
81204 TTATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 13 0.54
22 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAAATATAATTATATTTT
Found at i:81213 original size:65 final size:68
Alignment explanation
Indices: 81144--81273 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 68
81134 TAAAAATATT
* * * *
81144 AATAATAATATAAATTTAAATATAATTATA-TTTTAATTTAAAA-TATTAATA-TTTTTATTTTT
1 AATAATAATATAAACTTAAACATAATTATACTTTTAATTTAAAAGAACTAATACTTTTTATTTTT
81206 ATA
66 ATA
*
81209 AATAATAATATAAACTTAAACATAATTATATCTTTTTATTTAAAAGAACTAATACTTTTTATTTT
1 AATAATAATATAAACTTAAACATAATTATA-CTTTTAATTTAAAAGAACTAATACTTTTTATTTT
81274 CATATTTGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 28 0.50
67 12 0.21
68 6 0.11
69 10 0.18
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (68 bp):
AATAATAATATAAACTTAAACATAATTATACTTTTAATTTAAAAGAACTAATACTTTTTATTTTT
ATA
Found at i:81655 original size:39 final size:40
Alignment explanation
Indices: 81612--81690 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
81602 ATTTTGAAAA
* * *
81612 AAAATTTAAAA-GATATGATTAAAATATAGATTTTTTATT
1 AAAATTCAAAAGGATATAATTAAAACATAGATTTTTTATT
* **
81651 AAAATTCAAAAGGATGTAATTAATGCATAGATTTTTTATT
1 AAAATTCAAAAGGATATAATTAAAACATAGATTTTTTATT
81691 GCGATCCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 10 0.30
40 23 0.70
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.42
Consensus pattern (40 bp):
AAAATTCAAAAGGATATAATTAAAACATAGATTTTTTATT
Found at i:82037 original size:13 final size:13
Alignment explanation
Indices: 82019--82043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82009 CATAAAGTGT
82019 TGTATCGATACAA
1 TGTATCGATACAA
82032 TGTATCGATACA
1 TGTATCGATACA
82044 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:86034 original size:19 final size:20
Alignment explanation
Indices: 86008--86062 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
85998 GTATCGATAC
*
86008 ATTGTATCAATACATGG--A
1 ATTGTATCGATACATGGACA
86026 ATATGTATCGATACATGGACA
1 AT-TGTATCGATACATGGACA
86047 ATTGTATCGATACATG
1 ATTGTATCGATACATG
86063 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 14 0.42
21 3 0.09
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:86116 original size:20 final size:20
Alignment explanation
Indices: 86091--86144 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
86081 CTACCACTGC
*
86091 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
86111 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
86131 TTGTATCGATACAT
1 TTGTATCGATACAT
86145 TGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:94969 original size:13 final size:13
Alignment explanation
Indices: 94951--95016 Score: 90
Period size: 13 Copynumber: 5.5 Consensus size: 13
94941 CGATACATGG
94951 TACATTGTATCGA
1 TACATTGTATCGA
94964 TACATTGTATCGA
1 TACATTGTATCGA
94977 TACATTGTATCGA
1 TACATTGTATCGA
94990 TACA-TG-AT-G-
1 TACATTGTATCGA
94999 -A-ATTGTATCGA
1 TACATTGTATCGA
95010 TACATTG
1 TACATTG
95017 CTTGTAACGG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
7 1 0.02
8 3 0.06
9 2 0.04
10 2 0.04
11 2 0.04
12 3 0.06
13 34 0.72
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:94987 original size:26 final size:23
Alignment explanation
Indices: 94935--95016 Score: 95
Period size: 20 Copynumber: 3.7 Consensus size: 23
94925 CTACCACCGT
94935 TTGTATCGATACA-TG--GTACA
1 TTGTATCGATACATTGATGTACA
94955 TTGTATCGATACATTGTATCGATACA
1 TTGTATCGATACATTG-AT-G-TACA
94981 TTGTATCGATACA-TGATG-A-A
1 TTGTATCGATACATTGATGTACA
95001 TTGTATCGATACATTG
1 TTGTATCGATACATTG
95017 CTTGTAACGG
Statistics
Matches: 55, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
20 27 0.49
21 5 0.09
23 1 0.02
24 2 0.04
25 3 0.05
26 17 0.31
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (23 bp):
TTGTATCGATACATTGATGTACA
Found at i:100248 original size:21 final size:20
Alignment explanation
Indices: 100206--100256 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
100196 TAACAAAAAT
*
100206 AAATAAATTTAATTATAACAA
1 AAATAAATTTAATGATAAC-A
**
100227 AAATAAATTTAATGATTGCA
1 AAATAAATTTAATGATAACA
100247 AAAT-AATTTA
1 AAATAAATTTA
100257 TATTTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 5 0.19
21 16 0.59
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATAAATTTAATGATAACA
Found at i:102690 original size:25 final size:25
Alignment explanation
Indices: 102640--102690 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
102630 GAAACTATTT
* *
102640 ATTTAATAAAAATATTTATATTTAA
1 ATTTAATAAAAATATTTAAATATAA
*
102665 ATTTAATTATAAATA-TTAAATATAA
1 ATTTAA-TAAAAATATTTAAATATAA
102690 A
1 A
102691 AATAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAATAAAAATATTTAAATATAA
Found at i:105151 original size:16 final size:16
Alignment explanation
Indices: 105126--105159 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
105116 TATTATTCAT
*
105126 TTTTAGTTAATTACAA
1 TTTTACTTAATTACAA
*
105142 TTTTACTTAATTTCAA
1 TTTTACTTAATTACAA
105158 TT
1 TT
105160 GACTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTACTTAATTACAA
Found at i:108548 original size:16 final size:16
Alignment explanation
Indices: 108465--108569 Score: 86
Period size: 16 Copynumber: 6.6 Consensus size: 16
108455 TAAACTCAAT
108465 TGACCCGAACCTAAAA
1 TGACCCGAACCTAAAA
* * *
108481 CGATCCGAACCTGAAA
1 TGACCCGAACCTAAAA
** * ***
108497 CAACCCAAACCCGCAA
1 TGACCCGAACCTAAAA
* *
108513 TGATCCGAATCC-AAAG
1 TGACCCGAA-CCTAAAA
108529 TGACCCGAACCTAAAA
1 TGACCCGAACCTAAAA
*
108545 TGACCCGAACCCAAAA
1 TGACCCGAACCTAAAA
108561 TGACCCGAA
1 TGACCCGAA
108570 ATAAAAAATA
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
15 2 0.03
16 65 0.94
17 2 0.03
ACGTcount: A:0.41, C:0.34, G:0.14, T:0.10
Consensus pattern (16 bp):
TGACCCGAACCTAAAA
Found at i:108576 original size:16 final size:16
Alignment explanation
Indices: 108529--108576 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
108519 GAATCCAAAG
* *
108529 TGACCCGAACCTAAAA
1 TGACCCGAAACAAAAA
* *
108545 TGACCCGAACCCAAAA
1 TGACCCGAAACAAAAA
*
108561 TGACCCGAAATAAAAA
1 TGACCCGAAACAAAAA
108577 ATAACCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.29, G:0.12, T:0.10
Consensus pattern (16 bp):
TGACCCGAAACAAAAA
Found at i:110449 original size:2 final size:2
Alignment explanation
Indices: 110442--110478 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
110432 CTGAATGTGT
110442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110479 GTTTCTGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112319 original size:23 final size:24
Alignment explanation
Indices: 112286--112330 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
112276 ATTATAATGC
* *
112286 ATAAAAGTAAAT-TATAAAAAAAT
1 ATAAAACTAAATAAATAAAAAAAT
112309 ATAAAACTAAATAAATAAAAAA
1 ATAAAACTAAATAAATAAAAAA
112331 TTTATTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
ATAAAACTAAATAAATAAAAAAAT
Found at i:115363 original size:12 final size:12
Alignment explanation
Indices: 115346--115371 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
115336 CCTAAGAGAG
115346 AGATGGATCACA
1 AGATGGATCACA
115358 AGATGGATCACA
1 AGATGGATCACA
115370 AG
1 AG
115372 GAAACTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (12 bp):
AGATGGATCACA
Found at i:115684 original size:378 final size:378
Alignment explanation
Indices: 114989--115739 Score: 1475
Period size: 378 Copynumber: 2.0 Consensus size: 378
114979 AGTTGAAAAG
114989 ACAAGGAAACTATTAAAGTAATACCACTTGATGATTATGGCTATGTGGTTGGCTTAAATTTTCTT
1 ACAAGGAAACTATTAAAGTAATACCACTTGATGATTATGGCTATGTGGTTGGCTTAAATTTTCTT
115054 GATCGAATTAATGTTTTCCTTGTACCATTTTCCAATTGTATATGCATCTTGGATGCCCGCTATCA
66 GATCGAATTAATGTTTTCCTTGTACCATTTTCCAATTGTATATGCATCTTGGATGCCCGCTATCA
115119 ATGCATTAAGCCGTTAAATTGAGAAATAGGTGTTAAAGCCAAAGTGTTGTTTACAATCCAATTTA
131 ATGCATTAAGCCGTTAAATTGAGAAATAGGTGTTAAAGCCAAAGTGTTGTTTACAATCCAATTTA
115184 ACAAGGGTGTACGTAGAGATGAAGTCACTTACTTGGTAACTTTGAAAATTGATGAGCTTTAAAAA
196 ACAAGGGTGTACGTAGAGATGAAGTCACTTACTTGGTAACTTTGAAAATTGATGAGCTTTAAAAA
115249 CCTATAAAAGAGACCCCTTTGGAGGTGCTAGAGGTATTATAGTCCTTCAATGATGTGATACATGC
261 CCTATAAAAGAGACCCCTTTGGAGGTGCTAGAGGTATTATAGTCCTTCAATGATGTGATACATGC
115314 AAAATTACCAAAGAAGTTACCACCTAAGAGAGAGATGGATCACAAGATGGATC
326 AAAATTACCAAAGAAGTTACCACCTAAGAGAGAGATGGATCACAAGATGGATC
115367 ACAAGGAAACTATTAAAGTAATACCACTTGATGATTATGGCTATGTGGTTGGCTTAAATTTTCTT
1 ACAAGGAAACTATTAAAGTAATACCACTTGATGATTATGGCTATGTGGTTGGCTTAAATTTTCTT
* *
115432 GATCGAATTAATGTTTTCTTTGTACCATTTTCCAATTGTATATGCATCTTGGATGCTCGCTATCA
66 GATCGAATTAATGTTTTCCTTGTACCATTTTCCAATTGTATATGCATCTTGGATGCCCGCTATCA
*
115497 ATGCATTAAGCCGTTAAATTGAGAAATAGGTGTTAAAGCCAAAGTGTTGTTTGCAATCCAATTTA
131 ATGCATTAAGCCGTTAAATTGAGAAATAGGTGTTAAAGCCAAAGTGTTGTTTACAATCCAATTTA
115562 ACAAGGGTGTACGTAGAGATGAAGTCACTTACTTGGTAACTTTGAAAATTGATGAGCTTTAAAAA
196 ACAAGGGTGTACGTAGAGATGAAGTCACTTACTTGGTAACTTTGAAAATTGATGAGCTTTAAAAA
115627 CCTATAAAAGAGACCCCTTTGGAGGTGCTAGAGGTATTATAGTCCTTCAATGATGTGATACATGC
261 CCTATAAAAGAGACCCCTTTGGAGGTGCTAGAGGTATTATAGTCCTTCAATGATGTGATACATGC
115692 AAAATTACCAAAGAAGTTACCACCTAAGAGAGAGATGGATCACAAGAT
326 AAAATTACCAAAGAAGTTACCACCTAAGAGAGAGATGGATCACAAGAT
115740 TGAACTGGTG
Statistics
Matches: 370, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
378 370 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (378 bp):
ACAAGGAAACTATTAAAGTAATACCACTTGATGATTATGGCTATGTGGTTGGCTTAAATTTTCTT
GATCGAATTAATGTTTTCCTTGTACCATTTTCCAATTGTATATGCATCTTGGATGCCCGCTATCA
ATGCATTAAGCCGTTAAATTGAGAAATAGGTGTTAAAGCCAAAGTGTTGTTTACAATCCAATTTA
ACAAGGGTGTACGTAGAGATGAAGTCACTTACTTGGTAACTTTGAAAATTGATGAGCTTTAAAAA
CCTATAAAAGAGACCCCTTTGGAGGTGCTAGAGGTATTATAGTCCTTCAATGATGTGATACATGC
AAAATTACCAAAGAAGTTACCACCTAAGAGAGAGATGGATCACAAGATGGATC
Found at i:117441 original size:138 final size:138
Alignment explanation
Indices: 117193--117468 Score: 552
Period size: 138 Copynumber: 2.0 Consensus size: 138
117183 CTTTATAAAA
117193 TTGAAAGAAGATGGGAGGATGCTTGTGGTTTGTCTCTATATAAATGATTTAATTTACACTGGCAA
1 TTGAAAGAAGATGGGAGGATGCTTGTGGTTTGTCTCTATATAAATGATTTAATTTACACTGGCAA
117258 TAACAAGGCCATGTTTGATAAGTTTGAAAAGCCTATGATGATTGAGTTTGACATGACTGATCTTA
66 TAACAAGGCCATGTTTGATAAGTTTGAAAAGCCTATGATGATTGAGTTTGACATGACTGATCTTA
117323 GATTGATG
131 GATTGATG
117331 TTGAAAGAAGATGGGAGGATGCTTGTGGTTTGTCTCTATATAAATGATTTAATTTACACTGGCAA
1 TTGAAAGAAGATGGGAGGATGCTTGTGGTTTGTCTCTATATAAATGATTTAATTTACACTGGCAA
117396 TAACAAGGCCATGTTTGATAAGTTTGAAAAGCCTATGATGATTGAGTTTGACATGACTGATCTTA
66 TAACAAGGCCATGTTTGATAAGTTTGAAAAGCCTATGATGATTGAGTTTGACATGACTGATCTTA
117461 GATTGATG
131 GATTGATG
117469 CATTATTTTC
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (138 bp):
TTGAAAGAAGATGGGAGGATGCTTGTGGTTTGTCTCTATATAAATGATTTAATTTACACTGGCAA
TAACAAGGCCATGTTTGATAAGTTTGAAAAGCCTATGATGATTGAGTTTGACATGACTGATCTTA
GATTGATG
Found at i:118421 original size:24 final size:24
Alignment explanation
Indices: 118394--118444 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
118384 TGTTAGAAAT
*
118394 TTTAAGTTT-TATTTATAGTTTTTA
1 TTTAAGTTTATATTTA-AATTTTTA
*
118418 TTTATGTTTAATATTTAAATTTTTA
1 TTTAAGTTT-ATATTTAAATTTTTA
118443 TT
1 TT
118445 AAATAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 9 0.39
26 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTAAGTTTATATTTAAATTTTTA
Found at i:119299 original size:21 final size:23
Alignment explanation
Indices: 119273--119314 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
119263 ATAAATATAA
*
119273 TATAAAA-ATA-ATTATTTTATT
1 TATAAAATATATAATATTTTATT
119294 TATAAAATATATAATATTTTA
1 TATAAAATATATAATATTTTA
119315 AATATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATAAAATATATAATATTTTATT
Found at i:119363 original size:29 final size:27
Alignment explanation
Indices: 119298--119364 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
119288 TTTATTTATA
* *
119298 AAATATAT-AATATTTTAAATATTATT
1 AAATATATAAAAATTTTAAATATAATT
* *
119324 ATTATAAATAAAAATTTATAAATATAATAT
1 A-AATATATAAAAATTT-TAAATATAAT-T
119354 AAATATATAAA
1 AAATATATAAA
119365 TTATTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
28 6 0.19
29 17 0.55
30 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATATATAAAAATTTTAAATATAATT
Found at i:119365 original size:27 final size:29
Alignment explanation
Indices: 119289--119373 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 29
119279 AATAATTATT
119289 TTAT-TTATAAAATATATAATATTTTAAATA
1 TTATATTAT-AAATATATAA-ATTTTAAATA
119319 TTATTATTATAAATA-A-AAATTTATAAATA
1 TTA-TATTATAAATATATAAATTT-TAAATA
119348 -TA-A-TATAAATATATAAATTATTAAAT
1 TTATATTATAAATATATAAATT-TTAAAT
119374 TTAAAATCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 10 0.20
28 7 0.14
29 8 0.16
30 4 0.08
31 6 0.12
32 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATATTATAAATATATAAATTTTAAATA
Found at i:119443 original size:8 final size:8
Alignment explanation
Indices: 119430--119545 Score: 55
Period size: 8 Copynumber: 14.4 Consensus size: 8
119420 ATATTCAAAT
119430 TATATTTA
1 TATATTTA
*
119438 TATATTTT
1 TATATTTA
119446 TATATATTA
1 TATAT-TTA
119455 TA-A-TTA
1 TATATTTA
*
119461 T-GATTTA
1 TATATTTA
*
119468 AATA-TTA
1 TATATTTA
119475 TATATTTA
1 TATATTTA
119483 TATAAATTTTAA
1 TAT--A-TTT-A
* *
119495 AATATTAA
1 TATATTTA
119503 T-TATTTA
1 TATATTTA
*
119510 TAT-TATA
1 TATATTTA
*
119517 TAAATTTTAA
1 TATA-TTT-A
119527 TATATTTA
1 TATATTTA
*
119535 TTTATTTA
1 TATATTTA
119543 TAT
1 TAT
119546 TATATTTATA
Statistics
Matches: 80, Mismatches: 15, Indels: 26
0.66 0.12 0.21
Matches are distributed among these distances:
6 5 0.06
7 20 0.25
8 32 0.40
9 11 0.14
10 6 0.08
11 3 0.04
12 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:119497 original size:27 final size:27
Alignment explanation
Indices: 119467--119545 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 27
119457 ATTATGATTT
119467 AAATATTATATATTTATATAAATTTTA
1 AAATATTATATATTTATATAAATTTTA
119494 AAATATTAATTATTTATATTATATAAATTTTA
1 AAATATT-A-TA--TAT-TTATATAAATTTTA
* *
119526 ATATATTTATTTATTTATAT
1 AAATA-TTATATATTTATAT
119546 TATATTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
29 5 0.11
31 4 0.09
32 19 0.43
33 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATTATATATTTATATAAATTTTA
Found at i:119521 original size:32 final size:33
Alignment explanation
Indices: 119463--119550 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 33
119453 TATAATTATG
*
119463 ATTTAAATATTATATATTTATATAAATTTTAAAAT
1 ATTTAATTATT-TATA-TTATATAAATTTTAAAAT
*
119498 A-TTAATTATTTATATTATATAAATTTTAATAT
1 ATTTAATTATTTATATTATATAAATTTTAAAAT
*
119530 ATTTATTTATTTATATTATAT
1 ATTTAATTATTTATATTATAT
119551 TTATATTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 18 0.37
33 22 0.45
34 8 0.16
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATTTAATTATTTATATTATATAAATTTTAAAAT
Found at i:119555 original size:25 final size:26
Alignment explanation
Indices: 119527--119579 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
119517 TAAATTTTAA
*
119527 TATATTTATTTAT-TTATATTATA-TT
1 TATA-TTATTTATATTATATAATACTT
*
119552 TATATTATTTTTATTATATAATACTT
1 TATATTATTTATATTATATAATACTT
119578 TA
1 TA
119580 CTTGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATATTATTTATATTATATAATACTT
Found at i:119556 original size:27 final size:28
Alignment explanation
Indices: 119419--119570 Score: 82
Period size: 29 Copynumber: 5.2 Consensus size: 28
119409 AGAATCGGTA
*
119419 TATATTCAAATTATATTTATATATTT-TT
1 TATATT-ATATTATATTTATATATTTATT
* *
119447 ATATATTATAATTATGATTTAAATA-TTATA
1 -TATATTAT-ATTAT-ATTTATATATTTATT
* *
119477 TAT-TTATA-TAAATTTTAAAATATTAATTATT
1 TATATTATATTATA-TTT---ATA-TATTTATT
*
119508 TATATTATA-TAAATTTTAATATATTTATT
1 TATATTATATTATA-TTT-ATATATTTATT
*
119537 TAT-TTATATTATATTTATATTATTTTTAT
1 TATATTATATTATATTTATA-TATTTAT-T
119566 TATAT
1 TATAT
119571 AATACTTTAC
Statistics
Matches: 100, Mismatches: 9, Indels: 27
0.74 0.07 0.20
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 4 0.04
28 19 0.19
29 35 0.35
30 16 0.16
31 7 0.07
32 13 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TATATTATATTATATTTATATATTTATT
Found at i:119560 original size:9 final size:9
Alignment explanation
Indices: 119502--119568 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
119492 TAAAATATTA
119502 ATTATTTAT
1 ATTATTTAT
* *
119511 ATTATATAA
1 ATTATTTAT
*
119520 ATT-TTAAT
1 ATTATTTAT
119528 A-TATTTAT
1 ATTATTTAT
119536 -TTATTTAT
1 ATTATTTAT
119544 ATTATATTTAT
1 A-T-TATTTAT
*
119555 ATTATTTTT
1 ATTATTTAT
119564 ATTAT
1 ATTAT
119569 ATAATACTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.02
8 14 0.30
9 21 0.46
10 2 0.04
11 8 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTATTTAT
Found at i:120030 original size:10 final size:10
Alignment explanation
Indices: 120017--120115 Score: 57
Period size: 9 Copynumber: 11.1 Consensus size: 10
120007 CATTATATAA
120017 ATATATAAAT
1 ATATATAAAT
120027 ATAT-TAAA-
1 ATATATAAAT
120035 AT-TA-AAAT
1 ATATATAAAT
120043 A-ATATAAAT
1 ATATATAAAT
120052 -TAT-T-AAT
1 ATATATAAAT
120059 ATATATTAAA-
1 ATATA-TAAAT
120069 AT-TA-AAAT
1 ATATATAAAT
120077 A-ATATAAAT
1 ATATATAAAT
120086 -TAT-T-AAT
1 ATATATAAAT
120093 ATATATTAAAAT
1 ATATA-T-AAAT
*
120105 TTATATAAAT
1 ATATATAAAT
120115 A
1 A
120116 ATTAACATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 36
0.64 0.02 0.34
Matches are distributed among these distances:
7 13 0.19
8 16 0.23
9 18 0.26
10 12 0.17
11 3 0.04
12 7 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATAAAT
Found at i:120060 original size:13 final size:12
Alignment explanation
Indices: 120011--120100 Score: 59
Period size: 13 Copynumber: 7.8 Consensus size: 12
120001 TTGTATCATT
120011 ATATAAATATATA
1 ATATAAAT-TATA
* *
120024 A-ATATATTAAA
1 ATATAAATTATA
120035 AT-TAAA--ATA
1 ATATAAATTATA
120044 ATATAAATTATTA
1 ATATAAATTA-TA
* *
120057 ATATATATTAAA
1 ATATAAATTATA
120069 AT-TAAA--ATA
1 ATATAAATTATA
120078 ATATAAATTATTA
1 ATATAAATTA-TA
*
120091 ATATATATTA
1 ATATAAATTA
120101 AAATTTATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 10 0.17
12 10 0.17
13 23 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAAATTATA
Found at i:120066 original size:34 final size:34
Alignment explanation
Indices: 120011--120105 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 34
120001 TTGTATCATT
120011 ATATAAA-TATATAA-ATATATTAAAATTAAAATA
1 ATATAAATTAT-TAATATATATTAAAATTAAAATA
120044 ATATAAATTATTAATATATATTAAAATTAAAATA
1 ATATAAATTATTAATATATATTAAAATTAAAATA
120078 ATATAAATTATTAATATATATTAAAATT
1 ATATAAATTATTAATATATATTAAAATT
120106 TATATAAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
33 10 0.17
34 50 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
ATATAAATTATTAATATATATTAAAATTAAAATA
Found at i:120110 original size:16 final size:16
Alignment explanation
Indices: 120025--120111 Score: 79
Period size: 16 Copynumber: 5.2 Consensus size: 16
120015 AAATATATAA
*
120025 ATATATTAAAATTAAA
1 ATATATTAAAATTAAT
120041 ATA-ATATAAATTATTAAT
1 ATATAT-TAAA--ATTAAT
*
120059 ATATATTAAAATTAAA
1 ATATATTAAAATTAAT
120075 ATA-ATATAAATTATTAAT
1 ATATAT-TAAA--ATTAAT
*
120093 ATATATTAAAATTTAT
1 ATATATTAAAATTAAT
120109 ATA
1 ATA
120112 AATAATTAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.07
16 27 0.46
18 24 0.41
19 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATTAAAATTAAT
Found at i:120159 original size:44 final size:43
Alignment explanation
Indices: 120015--120163 Score: 112
Period size: 44 Copynumber: 3.4 Consensus size: 43
120005 ATCATTATAT
* * * *
120015 AAATATATAAATATATTAAAATTAAAATAATATAA-AT-TATTA
1 AAATATATAAAAATATTAACATTTAAATTAT-TAATATATATTA
* * *
120057 ATATATAT-TAAA-ATTAAAATAATATAAATTATTAATATATATTA
1 AAATATATAAAAATATTAACAT--T-TAAATTATTAATATATATTA
* *
120101 AAATTTATATAAATAATTAACATTTAAATTA-TAATTATAATATTA
1 AAATATATAAAAAT-ATTAACATTTAAATTATTAA-TAT-ATATTA
120146 AAA-ATATAAAAATATTAA
1 AAATATATAAAAATATTAA
120164 ACAATGCCAG
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
40 8 0.09
41 2 0.02
42 11 0.13
43 16 0.18
44 29 0.33
45 14 0.16
47 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (43 bp):
AAATATATAAAAATATTAACATTTAAATTATTAATATATATTA
Found at i:120485 original size:14 final size:14
Alignment explanation
Indices: 120445--120495 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
120435 ACACATTTTT
*
120445 TTTATCAATTTAATA
1 TTTAT-AATTAAATA
* * *
120460 TTTAAAAATAAAAA
1 TTTATAATTAAATA
120474 TTTATAATTAAATA
1 TTTATAATTAAATA
120488 TTTA-AATT
1 TTTATAATT
120496 TCAAATTCGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTATAATTAAATA
Found at i:123668 original size:2 final size:2
Alignment explanation
Indices: 123663--123699 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
123653 AAAAAATAAA
*
123663 AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
123700 GAGCATAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:127469 original size:12 final size:12
Alignment explanation
Indices: 127452--127499 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
127442 CATGTTTGAC
127452 ATAAAATATGAA
1 ATAAAATATGAA
127464 ATAAAATATGAA
1 ATAAAATATGAA
* **
127476 AT-GAATATGTT
1 ATAAAATATGAA
127487 ATAAATATATGAA
1 ATAAA-ATATGAA
127500 TATATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 8 0.29
12 15 0.54
13 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (12 bp):
ATAAAATATGAA
Found at i:127882 original size:21 final size:22
Alignment explanation
Indices: 127856--127896 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
127846 CTCTCCAATG
127856 GCAG-TTTCTTTAAAAAAAACT
1 GCAGTTTTCTTTAAAAAAAACT
*
127877 GCAGTTTTTTTTAAAAAAAA
1 GCAGTTTTCTTTAAAAAAAA
127897 GAGGTCACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (22 bp):
GCAGTTTTCTTTAAAAAAAACT
Found at i:129792 original size:48 final size:51
Alignment explanation
Indices: 129734--129833 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 51
129724 CCAATCAAAA
* * * *
129734 TATCTTTAATTAAATTAAATTAATTAAGAAAT-AATAATAAA-ATAA-TTT
1 TATCTCTAATTAAATTAAAATAATTAAAAAATAAATAAGAAAGATAAGTTT
*
129782 TATCTCTAATTAAATTAAAATATTTAAAAAATAAATAAGAAAGATAAGTTT
1 TATCTCTAATTAAATTAAAATAATTAAAAAATAAATAAGAAAGATAAGTTT
129833 T
1 T
129834 TTTTAAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
48 28 0.64
49 8 0.18
50 4 0.09
51 4 0.09
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (51 bp):
TATCTCTAATTAAATTAAAATAATTAAAAAATAAATAAGAAAGATAAGTTT
Found at i:133046 original size:31 final size:31
Alignment explanation
Indices: 132985--133046 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
132975 AGCTGTTATT
* **
132985 ATATTGCTCCTAAACAAGAGCTTACGTTGCC
1 ATATTACTCCTAAACAAGAGCTTAAATTGCC
*
133016 ATATTACTCTTAAACATA-AGCTTAAATTGCC
1 ATATTACTCCTAAACA-AGAGCTTAAATTGCC
133047 CATTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (31 bp):
ATATTACTCCTAAACAAGAGCTTAAATTGCC
Found at i:133526 original size:31 final size:31
Alignment explanation
Indices: 133488--133557 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
133478 AAGCACGAGG
* *
133488 TTAAACTATTGTATTACTTCTAAACAAGAGC
1 TTAAACTATTCTAATACTTCTAAACAAGAGC
* * * *
133519 TTAAACTATTCTAATGCTTTTAATCACGAGC
1 TTAAACTATTCTAATACTTCTAAACAAGAGC
133550 TTAAACTA
1 TTAAACTA
133558 CACATTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (31 bp):
TTAAACTATTCTAATACTTCTAAACAAGAGC
Found at i:134026 original size:45 final size:45
Alignment explanation
Indices: 133962--134050 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
133952 TTTGTACTAG
*
133962 TACTAATTGTATTGATTGGTATATATTGATTTCTAAGCATAACAA
1 TACTAATTGTATTGATTGGTATATATCGATTTCTAAGCATAACAA
*
134007 TACTAATTGTATTGGTTGGTATATATCGATTTCTAAGCATAACA
1 TACTAATTGTATTGATTGGTATATATCGATTTCTAAGCATAACA
134051 GCACCGATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (45 bp):
TACTAATTGTATTGATTGGTATATATCGATTTCTAAGCATAACAA
Found at i:137993 original size:32 final size:32
Alignment explanation
Indices: 137943--138027 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
137933 GATTTCATCT
* * *
137943 TATTTGATTTGCTAAATGAATGATCTTATTTG
1 TATTGGATTTGCTTAATGAATGACCTTATTTG
* *
137975 TATTGGATTTGCTTAATGACTGACCTTGTTTG
1 TATTGGATTTGCTTAATGAATGACCTTATTTG
138007 TATTAGG-TTTGCTTAAT-AATG
1 TATT-GGATTTGCTTAATGAATG
138028 TTTTGTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 3 0.07
32 41 0.89
33 2 0.04
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (32 bp):
TATTGGATTTGCTTAATGAATGACCTTATTTG
Found at i:138834 original size:21 final size:20
Alignment explanation
Indices: 138793--138836 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
138783 AATAAATTCT
*
138793 AAAAATTCTAAAGAAAAATA
1 AAAAATTCTAAAAAAAAATA
138813 AAAAATT-TAAAAACAAACATA
1 AAAAATTCTAAAAA-AAA-ATA
138834 AAA
1 AAA
138837 TAAAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAAATTCTAAAAAAAAATA
Found at i:140737 original size:14 final size:14
Alignment explanation
Indices: 140718--140745 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
140708 CCACATATCT
140718 GCAATTCCCAATGC
1 GCAATTCCCAATGC
140732 GCAATTCCCAATGC
1 GCAATTCCCAATGC
140746 TTTCCCTATT
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:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
GCAATTCCCAATGC
Found at i:141026 original size:3 final size:3
Alignment explanation
Indices: 141020--141048 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
141010 CATAATAATA
141020 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
141049 AATGTTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:142681 original size:12 final size:13
Alignment explanation
Indices: 142657--142689 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
142647 TATTTATATT
142657 ATTTTTATGTTAA
1 ATTTTTATGTTAA
142670 ATTTTTAT-TTAA
1 ATTTTTATGTTAA
*
142682 AATTTTAT
1 ATTTTTAT
142690 ATATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
ATTTTTATGTTAA
Found at i:142719 original size:18 final size:19
Alignment explanation
Indices: 142681--142718 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
142671 TTTTTATTTA
142681 AAATTTTATATATTAATAT
1 AAATTTTATATATTAATAT
142700 AAATTTTAATATATTAATA
1 AAATTTT-ATATATTAATA
142719 ATTCATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTTATATATTAATAT
Found at i:142733 original size:22 final size:21
Alignment explanation
Indices: 142679--142736 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
142669 AATTTTTATT
*
142679 TAAA-ATTTTATATATTAATA
1 TAAATATTTAATATATTAATA
142699 TAAAT-TTTAATATATTAATAA
1 TAAATATTTAATATATTAAT-A
** *
142720 TTCATATTTCATATATT
1 TAAATATTTAATATATT
142737 CTTATACTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 17 0.55
21 4 0.13
22 10 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATATTTAATATATTAATA
Found at i:143589 original size:2 final size:2
Alignment explanation
Indices: 143582--143606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143572 GAAAAATACA
143582 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
143607 AGCGGGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:143779 original size:13 final size:13
Alignment explanation
Indices: 143759--143793 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
143749 AATTTTAATA
143759 TATTTTTAAAATT
1 TATTTTTAAAATT
* *
143772 TGTTTTTAAGATT
1 TATTTTTAAAATT
143785 TATTTTTAA
1 TATTTTTAA
143794 TTTATTTAAT
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:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TATTTTTAAAATT
Found at i:143798 original size:11 final size:11
Alignment explanation
Indices: 143746--143812 Score: 50
Period size: 13 Copynumber: 6.0 Consensus size: 11
143736 TATGAATAAG
*
143746 TTTAATTTTAA
1 TTTATTTTTAA
*
143757 TATATTTTTAAAA
1 TTTATTTTT--AA
*
143770 TTTGTTTTTAAGA
1 TTTATTTTT-A-A
143783 TTTATTTTTAA
1 TTTATTTTTAA
143794 TTTA--TTTAA
1 TTTATTTTTAA
143803 TTT-TTTTTAA
1 TTTATTTTTAA
143813 ATATACCCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
9 8 0.17
10 5 0.11
11 12 0.26
12 3 0.07
13 18 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
TTTATTTTTAA
Found at i:144086 original size:20 final size:20
Alignment explanation
Indices: 144061--144109 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
144051 AATTTTCATA
*
144061 TATTAAA-ATTTTTAAATATT
1 TATTAAATAATTTTAAA-ATT
144081 TATTAAATAATTTTAAAATT
1 TATTAAATAATTTTAAAATT
144101 T-TT-AATAAT
1 TATTAAATAAT
144110 AAATCATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.22
19 2 0.07
20 11 0.41
21 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAAATAATTTTAAAATT
Done.