Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 16 of 77
Found at i:2776887 original size:3 final size:3
Alignment explanation
Indices: 2776879--2777018 Score: 75
Period size: 3 Copynumber: 47.0 Consensus size: 3
2776869 TTGCCCATTA
* * * * * * * *
2776879 AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT GAT GAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * ** * * * * * *
2776927 GAT GAT GAT AAT GGT AAT GAT GAT AAT AAT AAT AAT GAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2776975 GAT GAT AAT AAT AAT AAT GAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2777019 GAACTGATCT
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
2 2 0.02
3 122 0.98
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2776893 original size:9 final size:9
Alignment explanation
Indices: 2776879--2777020 Score: 106
Period size: 9 Copynumber: 15.9 Consensus size: 9
2776869 TTGCCCATTA
*
2776879 AATAATAAT
1 AATAATGAT
*
2776888 AATAATAAT
1 AATAATGAT
2776897 AATAATGAT
1 AATAATGAT
* *
2776906 GATGATGAT
1 AATAATGAT
* *
2776915 GATGATGAT
1 AATAATGAT
* *
2776924 GATGATGAT
1 AATAATGAT
* *
2776933 GATAATGGT
1 AATAATGAT
*
2776942 AATGATGAT
1 AATAATGAT
*
2776951 AATAATAAT
1 AATAATGAT
*
2776960 AATGATGAT
1 AATAATGAT
* *
2776969 GATGATGAT
1 AATAATGAT
* *
2776978 GATAATAAT
1 AATAATGAT
2776987 AATAATGAT
1 AATAATGAT
*
2776996 AATAATAAT
1 AATAATGAT
*
2777005 -ATAATAAT
1 AATAATGAT
2777013 AATAATGA
1 AATAATGA
2777021 ACTGATCTAC
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
8 8 0.07
9 105 0.93
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (9 bp):
AATAATGAT
Found at i:2777018 original size:6 final size:6
Alignment explanation
Indices: 2776880--2777015 Score: 94
Period size: 6 Copynumber: 22.8 Consensus size: 6
2776870 TGCCCATTAA
* * * * * * *
2776880 ATAATA ATAATA ATAATA ATAATG ATGATG ATGATG ATGATG ATGATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
* * * * * * *
2776928 ATGATG ATAATG GTAATG ATGATA ATAATA ATAATG ATGATG ATGATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
* * * * *
2776976 ATGATA ATAATA ATAATG ATAATA ATAAT- ATAATA ATAAT
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAAT
2777016 AATGAACTGA
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
5 5 0.04
6 110 0.96
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:2777144 original size:3 final size:3
Alignment explanation
Indices: 2777136--2777202 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2777126 CTTCGAACAC
2777136 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2777184 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
2777203 TCTTCATCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2777891 original size:26 final size:23
Alignment explanation
Indices: 2777855--2777901 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
2777845 TATATGAAAA
2777855 AAAATAAAAGAAGAAAGAATTACG
1 AAAATAAAAGAAGAAA-AATTACG
*
2777879 AAAATAGATAAGAAGTAAAATTA
1 AAAATA-A-AAGAAGAAAAATTA
2777902 GTTTGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 6 0.30
26 8 0.40
ACGTcount: A:0.66, C:0.02, G:0.15, T:0.17
Consensus pattern (23 bp):
AAAATAAAAGAAGAAAAATTACG
Found at i:2778738 original size:21 final size:20
Alignment explanation
Indices: 2778705--2778747 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2778695 CAACTAATTA
*
2778705 AAAGGCCACATCAAGAAAGTT
1 AAAGGCCAAATC-AGAAAGTT
* *
2778726 AAAGGCTAAATCAGCAAGTT
1 AAAGGCCAAATCAGAAAGTT
2778746 AA
1 AA
2778748 TAGAAACCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAGGCCAAATCAGAAAGTT
Found at i:2778922 original size:3 final size:3
Alignment explanation
Indices: 2778908--2778937 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2778898 CACCATTTTG
*
2778908 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2778938 ATTTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2781220 original size:10 final size:9
Alignment explanation
Indices: 2781205--2781246 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2781195 AACAAAAATG
2781205 AAAACAAAAC
1 AAAA-AAAAC
*
2781215 AAAACAAAC
1 AAAAAAAAC
2781224 AAAAAAAA-
1 AAAAAAAAC
*
2781232 AATAAAAAC
1 AAAAAAAAC
2781241 AAAAAA
1 AAAAAA
2781247 TCTCAAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 7 0.26
9 16 0.59
10 4 0.15
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:2781239 original size:26 final size:26
Alignment explanation
Indices: 2781192--2781244 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2781182 AATAAAAATC
* *
2781192 ACAAACAAAAATGAAAACAAAACAAA
1 ACAAACAAAAATAAAAAAAAAACAAA
2781218 ACAAACAAAAA-AAAAATAAAAACAAA
1 ACAAACAAAAATAAAAA-AAAAACAAA
2781244 A
1 A
2781245 AATCTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.81, C:0.13, G:0.02, T:0.04
Consensus pattern (26 bp):
ACAAACAAAAATAAAAAAAAAACAAA
Found at i:2783953 original size:25 final size:25
Alignment explanation
Indices: 2783925--2783972 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2783915 GTAAACACCA
2783925 TTTTATTTATTTA-CTATTTTTTTTC
1 TTTTATTTATTTAGCT-TTTTTTTTC
* *
2783950 TTTTTTTTTTTTAGCTTTTTTTT
1 TTTTATTTATTTAGCTTTTTTTT
2783973 GCCAGTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTATTTATTTAGCTTTTTTTTTC
Found at i:2783961 original size:15 final size:15
Alignment explanation
Indices: 2783941--2783972 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2783931 TTATTTACTA
2783941 TTTTTTTT--CTTTT
1 TTTTTTTTAGCTTTT
2783954 TTTTTTTTAGCTTTT
1 TTTTTTTTAGCTTTT
2783969 TTTT
1 TTTT
2783973 GCCAGTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
15 9 0.53
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTTTTTTAGCTTTT
Found at i:2785021 original size:15 final size:15
Alignment explanation
Indices: 2785003--2785047 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2784993 AATAAACCTT
*
2785003 TTAAAATAATAATAA
1 TTAAAATAATAAAAA
2785018 TTAAAATAATAAAAAA
1 TTAAAATAAT-AAAAA
*
2785034 TAAAAATAATAAAA
1 TTAAAATAATAAAA
2785048 GATGTAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TTAAAATAATAAAAA
Found at i:2785041 original size:16 final size:16
Alignment explanation
Indices: 2785005--2785047 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2784995 TAAACCTTTT
* *
2785005 AAAATAAT-AATAATT
1 AAAATAATAAAAAATA
2785020 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
2785036 AAAATAATAAAA
1 AAAATAATAAAA
2785048 GATGTAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:2787508 original size:16 final size:16
Alignment explanation
Indices: 2787487--2787517 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2787477 AATGTTTTAA
2787487 TTTGTTATAATAAATT
1 TTTGTTATAATAAATT
2787503 TTTGTTATAATAAAT
1 TTTGTTATAATAAAT
2787518 ACTTAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTGTTATAATAAATT
Found at i:2787612 original size:9 final size:8
Alignment explanation
Indices: 2787590--2787634 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
2787580 AATAAACCTT
2787590 ATAAAATA
1 ATAAAATA
2787598 AT--AATA
1 ATAAAATA
2787604 ATTAAAATA
1 A-TAAAATA
2787613 AT-AAATA
1 ATAAAATA
2787620 ATAAAAATA
1 AT-AAAATA
2787629 ATAAAA
1 ATAAAA
2787635 GATGTAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.16
7 8 0.25
8 7 0.22
9 12 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATAAAATA
Found at i:2787621 original size:16 final size:16
Alignment explanation
Indices: 2787591--2787633 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2787581 ATAAACCTTA
2787591 TAAAATAAT-AATAAT
1 TAAAATAATAAATAAT
2787606 TAAAATAATAAATAAT
1 TAAAATAATAAATAAT
*
2787622 AAAAATAATAAA
1 TAAAATAATAAA
2787634 AGATGTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAATAATAAATAAT
Found at i:2795467 original size:25 final size:25
Alignment explanation
Indices: 2795439--2795489 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
2795429 TTGCATTCAC
2795439 TTTCATTC-AT-TTGAATCATTTCTCT
1 TTTCATTCTATCTT-AATCATTT-TCT
2795464 TTTCATTCTATCTTAATCATTTTCT
1 TTTCATTCTATCTTAATCATTTTCT
2795489 T
1 T
2795490 GCCATTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 12 0.50
26 10 0.42
27 2 0.08
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTCATTCTATCTTAATCATTTTCT
Found at i:2799954 original size:15 final size:16
Alignment explanation
Indices: 2799923--2799956 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2799913 TTAAATTTGT
*
2799923 TGAGCTTCTTTTTAGA
1 TGAGCTTCTTTTAAGA
2799939 TGAGCTT-TTTTAAGA
1 TGAGCTTCTTTTAAGA
2799954 TGA
1 TGA
2799957 AATCTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (16 bp):
TGAGCTTCTTTTAAGA
Found at i:2800026 original size:49 final size:49
Alignment explanation
Indices: 2799813--2800036 Score: 250
Period size: 49 Copynumber: 4.6 Consensus size: 49
2799803 AATATGAATT
* * * * *
2799813 TTTAAAGTTGTTGAACCTTTACCTAGAGGAGCCTTTTCTAAGATAAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAGGAG-CTTTTCTAAGATGAAATC
** * * *
2799863 TTTAAAATTGTTGAGTTTATATTTAAAGGAGCTTTTCTAAGATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAGGAGCTTTTCTAAGATGAAATC
* * ** * *
2799912 TTTAAATTTGTTGAGCTTCTTTTTAGATGAGCTTTTTTAAGATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAGGAGCTTTTCTAAGATGAAATC
* * * *
2799961 TTTAAAGTTATGGAGCCTCTACTTAGAGGAGCTTTTCTAAAATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAGGAGCTTTTCTAAGATGAAATC
*
2800010 TTTAAAATTGTTGAGCCTCTGCTTAGA
1 TTTAAAATTGTTGAGCCTCTACTTAGA
2800037 AAAACTTTTT
Statistics
Matches: 145, Mismatches: 29, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
49 122 0.84
50 23 0.16
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (49 bp):
TTTAAAATTGTTGAGCCTCTACTTAGAGGAGCTTTTCTAAGATGAAATC
Found at i:2800036 original size:98 final size:98
Alignment explanation
Indices: 2799889--2800090 Score: 255
Period size: 98 Copynumber: 2.1 Consensus size: 98
2799879 TTATATTTAA
* * * ** ** * *
2799889 AGGAGCTTTTCTAAGATGAAATCTTTAAATTTGTTGAGCTTCTTTTTAGATGAGCTTTTTTAAGA
1 AGGAGCTTTTCTAAAATGAAATCTTTAAAATTGTTGAGCCTCTGCTTAGAAAAACTTTTTCAAGA
2799954 TG-AAATCTTTAAAGTT-ATGGAGCCTCTACTTAG
66 -GAAAATCTTTAAAGTTGATGGA-CCTCTACTTAG
2799987 AGGAGCTTTTCTAAAATGAAATCTTTAAAATTGTTGAGCCTCTGCTTAGAAAAACTTTTTCAAGA
1 AGGAGCTTTTCTAAAATGAAATCTTTAAAATTGTTGAGCCTCTGCTTAGAAAAACTTTTTCAAGA
* * * *
2800052 GAAAATTTTTAAAGTTGTTGGACTTCTGCTTAG
66 GAAAATCTTTAAAGTTGATGGACCTCTACTTAG
2800085 AGGAGC
1 AGGAGC
2800091 AATCATTATC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 1 0.01
98 84 0.94
99 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (98 bp):
AGGAGCTTTTCTAAAATGAAATCTTTAAAATTGTTGAGCCTCTGCTTAGAAAAACTTTTTCAAGA
GAAAATCTTTAAAGTTGATGGACCTCTACTTAG
Found at i:2800045 original size:49 final size:49
Alignment explanation
Indices: 2799813--2800071 Score: 227
Period size: 49 Copynumber: 5.3 Consensus size: 49
2799803 AATATGAATT
* * * * * *
2799813 TTTAAAGTTGTTGAACCTTTACCTAGAGGAGCCTTTTCTAAGATAAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAAGAG-CTTTTCTAAGATGAAATC
** * *
2799863 TTTAAAATTGTTGAGTTTATATTTA-AAGGAGCTTTTCTAAGATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAA-GAGCTTTTCTAAGATGAAATC
* * ** * *
2799912 TTTAAATTTGTTGAGCTTCTTTTTAGATGAGCTTTTTTAAGATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTTCTAAGATGAAATC
* * * * *
2799961 TTTAAAGTTATGGAGCCTCTACTTAGAGGAGCTTTTCTAAAATGAAATC
1 TTTAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTTCTAAGATGAAATC
* * * *
2800010 TTTAAAATTGTTGAGCCTCTGCTTAGAAAAACTTTT-TCAAGA-GAAAATT
1 TTTAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTTCT-AAGATG-AAATC
*
2800059 TTTAAAGTTGTTG
1 TTTAAAATTGTTG
2800072 GACTTCTGCT
Statistics
Matches: 171, Mismatches: 34, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
48 2 0.01
49 147 0.86
50 22 0.13
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (49 bp):
TTTAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTTCTAAGATGAAATC
Found at i:2800085 original size:147 final size:148
Alignment explanation
Indices: 2799813--2800090 Score: 314
Period size: 147 Copynumber: 1.9 Consensus size: 148
2799803 AATATGAATT
* * * *
2799813 TTTAAAGTTGTTGAACCTTTACCTAGAGGAGCCTTTTCTAAGATAAAATCTTTAAAATTGTTGAG
1 TTTAAAGTTATGGAACCTCTACCTAGAGGAGCCTTTTCTAAAATAAAATCTTTAAAATTGTTGAG
** * * * * ** *
2799878 TTTATATTTAAAGGAGCTTTTCTAAGATGAAATCTTTAAATTTGTTGAGCTTCTTTTTAGATGAG
66 CCTATACTTAAAGAAACTTTTCTAAGATGAAATCTTTAAAGTTGTTGAGCTTCTGCTTAGAGGAG
2799943 CTTTTTTAAGATGAAATC
131 CTTTTTTAAGATGAAATC
* * *
2799961 TTTAAAGTTATGGAGCCTCTACTTAGAGGAG-CTTTTCTAAAATGAAATCTTTAAAATTGTTGAG
1 TTTAAAGTTATGGAACCTCTACCTAGAGGAGCCTTTTCTAAAATAAAATCTTTAAAATTGTTGAG
* * *
2800025 CCTCTGCTTAGAA-AAACTTTT-TCAAGA-GAAAATTTTTAAAGTTGTTG-GACTTCTGCTTAGA
66 CCTATACTTA-AAGAAACTTTTCT-AAGATG-AAATCTTTAAAGTTGTTGAG-CTTCTGCTTAGA
2800086 GGAGC
127 GGAGC
2800091 AATCATTATC
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
146 3 0.03
147 76 0.71
148 28 0.26
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (148 bp):
TTTAAAGTTATGGAACCTCTACCTAGAGGAGCCTTTTCTAAAATAAAATCTTTAAAATTGTTGAG
CCTATACTTAAAGAAACTTTTCTAAGATGAAATCTTTAAAGTTGTTGAGCTTCTGCTTAGAGGAG
CTTTTTTAAGATGAAATC
Found at i:2800175 original size:43 final size:44
Alignment explanation
Indices: 2800127--2800230 Score: 151
Period size: 43 Copynumber: 2.4 Consensus size: 44
2800117 TCAGGCAGGA
*
2800127 TATTTATATTTTCAAAATTCGTTGAGCCTCTACTTAGAGGAG-C
1 TATTTATATTTTCAAAAGTCGTTGAGCCTCTACTTAGAGGAGCC
2800170 TATTTATATTTTTC-AAAGTCGTTGAGCCTCTACTTAGAGGAGCCC
1 TATTTATA-TTTTCAAAAGTCGTTGAGCCTCTACTTAGAGGAG-CC
*
2800215 T-TTTAAATTTTCAAAA
1 TATTTATATTTTCAAAA
2800231 AAAAAATTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
43 40 0.73
44 13 0.24
45 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (44 bp):
TATTTATATTTTCAAAAGTCGTTGAGCCTCTACTTAGAGGAGCC
Found at i:2800292 original size:43 final size:45
Alignment explanation
Indices: 2800207--2800293 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 45
2800197 CTCTACTTAG
2800207 AGGAGCCCTTTTAAATTTTCAAAAAAAAAATTTGAGCCTTTGCTGAA
1 AGGAGCCCTTTTAAATTTT--AAAAAAAAATTTGAGCCTTTGCTGAA
* *
2800254 AGGAGCTCTTTTAAATTTT-TAAAAAAA-TTGAGCCTTTGCT
1 AGGAGCCCTTTTAAATTTTAAAAAAAAATTTGAGCCTTTGCT
2800294 TATAGAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 13 0.34
44 7 0.18
47 18 0.47
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (45 bp):
AGGAGCCCTTTTAAATTTTAAAAAAAAATTTGAGCCTTTGCTGAA
Found at i:2800312 original size:42 final size:45
Alignment explanation
Indices: 2800230--2800324 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 45
2800220 AATTTTCAAA
* * *
2800230 AAAAAAATTTGAGCCTTTGCTGAAAGGAGCTCTTTTAAA-TTTTT
1 AAAAAAATTTGAGCCTTTGCTGAAAGAAACTCTTCTAAATTTTTT
* *
2800274 AAAAAAA-TTGAGCCTTTGCTTATAGAAACT-TTCTAAATTTTTT
1 AAAAAAATTTGAGCCTTTGCTGAAAGAAACTCTTCTAAATTTTTT
2800317 AATAAAAA
1 AA-AAAAA
2800325 AAAGAGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 6 0.14
43 26 0.59
44 12 0.27
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (45 bp):
AAAAAAATTTGAGCCTTTGCTGAAAGAAACTCTTCTAAATTTTTT
Found at i:2801361 original size:32 final size:30
Alignment explanation
Indices: 2801325--2801390 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 30
2801315 GTTCAAGTAA
*
2801325 ATTTTT-TTGAATTTAAAATTTTTTTATATATT
1 ATTTTTATT-AATTT-AAATTTTATTAT-TATT
2801357 ATTTTTATTAATTTAAATTTTATTATTATT
1 ATTTTTATTAATTTAAATTTTATTATTATT
2801387 ATTT
1 ATTT
2801391 ATTCATGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 8 0.25
31 11 0.34
32 11 0.34
33 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (30 bp):
ATTTTTATTAATTTAAATTTTATTATTATT
Found at i:2801371 original size:21 final size:20
Alignment explanation
Indices: 2801347--2801392 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2801337 TTAAAATTTT
*
2801347 TTTATATATTATTTTTATTAA
1 TTTATATATTATTATTATT-A
* *
2801368 TTTAAATTTTATTATTATTA
1 TTTATATATTATTATTATTA
2801388 TTTAT
1 TTTAT
2801393 TCATGTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATATTATTATTATTA
Found at i:2801377 original size:15 final size:15
Alignment explanation
Indices: 2801322--2801381 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 15
2801312 CTGGTTCAAG
*
2801322 TAAATTTTTTTGAATT
1 TAAATTTTATT-AATT
*
2801338 TAAAATTTTTTTATATAT
1 T-AAATTTTATTA-AT-T
*
2801356 T-ATTTTTATTAATT
1 TAAATTTTATTAATT
2801370 TAAATTTTATTA
1 TAAATTTTATTA
2801382 TTATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 11 0.30
16 10 0.27
17 12 0.32
18 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TAAATTTTATTAATT
Found at i:2801391 original size:28 final size:29
Alignment explanation
Indices: 2801346--2801402 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
2801336 TTTAAAATTT
2801346 TTTTATATATTATTTTTATTAAT-TTAAA
1 TTTTATATATTATTTTTATTAATGTTAAA
*
2801374 TTTTAT-TATTATTATTTATTCATGTTAAA
1 TTTTATATATTATT-TTTATTAATGTTAAA
2801403 ATGTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.27
28 14 0.54
29 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATATATTATTTTTATTAATGTTAAA
Found at i:2804301 original size:25 final size:27
Alignment explanation
Indices: 2804274--2804404 Score: 72
Period size: 29 Copynumber: 4.7 Consensus size: 27
2804264 TAAATTTTCA
2804274 AATT-TTTTTTAAAGAAAAATTAAAAAATC
1 AATTATTTTTTAAA-AAAAATT-AAAAA-C
*
2804303 AATT-TTCTTTTAAAATAAAAATTTCAAAA-
1 AATTATT-TTTT-AAA-AAAAA-TTAAAAAC
* * *
2804332 AATTATTTTTTTAAAAAAGTT-AAAAG
1 AATTATTTTTTAAAAAAAATTAAAAAC
* **
2804358 AATTAATTTTTTAAAAACAATTTTCAAAC
1 AATT-ATTTTTTAAAAA-AAATTAAAAAC
* *
2804387 AAATATTTTTTTAAAAAA
1 AATTATTTTTTAAAAAAA
2804405 TTGAAAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.05
26 6 0.07
27 17 0.20
28 17 0.20
29 20 0.24
30 6 0.07
31 12 0.14
32 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
AATTATTTTTTAAAAAAAATTAAAAAC
Found at i:2804305 original size:56 final size:55
Alignment explanation
Indices: 2804223--2804367 Score: 143
Period size: 56 Copynumber: 2.5 Consensus size: 55
2804213 TGAAAATATG
* * * *
2804223 TTTTTAAGAAAATTTAAAAGTATCAATTTT-TTTTGAAGATATAAATTTTCAAATTT
1 TTTTTAAGAAAAATTAAAAGAATCAATTTTCTTTT-AAAATA-AAAATTTCAAATTT
2804279 TTTTTAAAGAAAAATTAAAA-AATCAATTTTCTTTTAAAATAAAAATTTCAAAAAATTATT
1 TTTTT-AAGAAAAATTAAAAGAATCAATTTTCTTTTAAAATAAAAATTTC---AAA-T-TT
* *
2804339 TTTTTAA-AAAAGTTAAAAGAATTAATTTT
1 TTTTTAAGAAAAATTAAAAGAATCAATTTT
2804368 TTAAAAACAA
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
55 7 0.09
56 19 0.25
57 17 0.23
58 13 0.17
59 12 0.16
60 7 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (55 bp):
TTTTTAAGAAAAATTAAAAGAATCAATTTTCTTTTAAAATAAAAATTTCAAATTT
Found at i:2804325 original size:31 final size:31
Alignment explanation
Indices: 2804274--2804343 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2804264 TAAATTTTCA
2804274 AATTTTTTTTAAAGAAAAA-TT-AAAAAATC
1 AATTTTTTTTAAAGAAAAATTTCAAAAAATC
*
2804303 AATTTTCTTTTAAAATAAAAATTTCAAAAAAT-
1 AATTTT-TTTT-AAAGAAAAATTTCAAAAAATC
*
2804335 TATTTTTTT
1 AATTTTTTT
2804344 AAAAAAGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.17
30 4 0.11
31 11 0.31
32 7 0.20
33 7 0.20
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (31 bp):
AATTTTTTTTAAAGAAAAATTTCAAAAAATC
Found at i:2804374 original size:27 final size:26
Alignment explanation
Indices: 2804319--2804374 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2804309 CTTTTAAAAT
* *
2804319 AAAAATTTCAAAAAATTATTTTTTTA
1 AAAAAGTTCAAAAAATTAATTTTTTA
2804345 AAAAAGTT-AAAAGAATTAATTTTTTA
1 AAAAAGTTCAAAA-AATTAATTTTTTA
2804371 AAAA
1 AAAA
2804375 CAATTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAAAGTTCAAAAAATTAATTTTTTA
Found at i:2804514 original size:22 final size:22
Alignment explanation
Indices: 2804452--2804518 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
2804442 AAAGATGGAC
* ** *
2804452 TTAAAAAAAAGTATTAATTTTT
1 TTAAAAAAAATTAAAAATATTT
2804474 TTAAAATAAAATTTCAAAAATATTT
1 TTAAAA-AAAA-TT-AAAAATATTT
2804499 TTAAAAAAAATTAAAAATAT
1 TTAAAAAAAATTAAAAATAT
2804519 CAATTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 14 0.37
23 6 0.16
24 5 0.13
25 13 0.34
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
TTAAAAAAAATTAAAAATATTT
Found at i:2810129 original size:22 final size:22
Alignment explanation
Indices: 2810104--2810150 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
2810094 TTCATTTGTT
2810104 GGGGATCGATCCATG-ATTTAAA
1 GGGGATCGATCC-TGCATTTAAA
2810126 GGGGATCGATCCTGCATTTAAA
1 GGGGATCGATCCTGCATTTAAA
2810148 GGG
1 GGG
2810151 CATTGGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGGATCGATCCTGCATTTAAA
Found at i:2814055 original size:15 final size:15
Alignment explanation
Indices: 2814037--2814095 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
2814027 ATAAGTATGT
2814037 AAATAAAAAGTAAAC-
1 AAATAAAAA-TAAACA
2814052 AAATCAATAAAT-AACA
1 AAAT-AA-AAATAAACA
*
2814068 AAATAAAAATAAATA
1 AAATAAAAATAAACA
*
2814083 AAACAAAAATAAA
1 AAATAAAAATAAA
2814096 AATTTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 4 0.11
15 24 0.63
16 7 0.18
17 3 0.08
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (15 bp):
AAATAAAAATAAACA
Found at i:2826809 original size:16 final size:17
Alignment explanation
Indices: 2826788--2826820 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2826778 TCTAATCGAA
2826788 TTTTTA-TATTTAAATT
1 TTTTTATTATTTAAATT
*
2826804 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
2826821 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTATTTAAATT
Found at i:2827468 original size:16 final size:17
Alignment explanation
Indices: 2827438--2827471 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2827428 CAAATTGAAT
2827438 TAAATTTTATAAAAAAA
1 TAAATTTTATAAAAAAA
2827455 TAAATTTT-TAAAAAAA
1 TAAATTTTATAAAAAAA
2827471 T
1 T
2827472 TTTTTATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTTATAAAAAAA
Found at i:2828941 original size:31 final size:30
Alignment explanation
Indices: 2828902--2828959 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
2828892 ATATATCATA
2828902 TTATTTTTTATT-AAATTATTAAATTATAAT
1 TTATTTTTTATTAAAATT-TTAAATTATAAT
2828932 TTATGTTTTTATTAAAATTTTAAATTAT
1 TTAT-TTTTTATTAAAATTTTAAATTAT
2828960 TTTTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 4 0.15
31 17 0.65
32 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTATTTTTTATTAAAATTTTAAATTATAAT
Found at i:2828959 original size:24 final size:23
Alignment explanation
Indices: 2828917--2828967 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
2828907 TTTTATTAAA
*
2828917 TTATTAAATTATAATTTATGTTT
1 TTATTAAATTATAAATTATGTTT
* *
2828940 TTATTAAAATTTTAAATTATTTTT
1 TTATT-AAATTATAAATTATGTTT
2828964 TTAT
1 TTAT
2828968 ATGTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTATTAAATTATAAATTATGTTT
Found at i:2828974 original size:22 final size:22
Alignment explanation
Indices: 2828949--2828991 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2828939 TTTATTAAAA
* *
2828949 TTTTAAATTATTTTTTTATATG
1 TTTTAAATTATATTATTATATG
*
2828971 TTTTATATTATATTATTATAT
1 TTTTAAATTATATTATTATAT
2828992 ATACGTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAAATTATATTATTATATG
Found at i:2833832 original size:25 final size:25
Alignment explanation
Indices: 2833804--2833894 Score: 91
Period size: 25 Copynumber: 3.6 Consensus size: 25
2833794 AAATTTATTT
2833804 ATTAGTTTATTATA-TAATAATAAAA
1 ATTA-TTTATTATATTAATAATAAAA
*
2833829 ATTATTTATT-TATTATATAACAAAA
1 ATTATTTATTATATTA-ATAATAAAA
*
2833854 TTTATTT-TTATATTAAATTAAT-AAA
1 ATTATTTATTATATT-AA-TAATAAAA
2833879 ATTATTTTATTATATT
1 ATTA-TTTATTATATT
2833895 TAAACAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.04
24 10 0.18
25 29 0.53
26 7 0.13
27 7 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
ATTATTTATTATATTAATAATAAAA
Found at i:2833904 original size:25 final size:24
Alignment explanation
Indices: 2833825--2833905 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 24
2833815 ATATAATAAT
2833825 AAAAATTATTTATT-TATTATATAAC
1 AAAAATTATTTATTATATT-TA-AAC
* *
2833850 AAAATTTATTT-TTATA-TTAAATTA
1 AAAAATTATTTATTATATTTAAA--C
2833874 ATAAAATTATTTTATTATATTTAAAC
1 A-AAAATTA-TTTATTATATTTAAAC
2833900 AAAAAT
1 AAAAAT
2833906 CAAAATGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
22 2 0.04
23 2 0.04
24 4 0.09
25 23 0.51
26 4 0.09
27 5 0.11
28 5 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAAATTATTTATTATATTTAAAC
Found at i:2836735 original size:34 final size:36
Alignment explanation
Indices: 2836664--2836745 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 36
2836654 AAAATATTTA
**
2836664 AAAAATATTAATATTCAAGAATAATTATATTTTAAT
1 AAAAATATTAATATTCAAGAATAATTATATTAAAAT
*
2836700 AATAATATTTAATATT-AA-AAT-ATTATATTAAAAT
1 AAAAATA-TTAATATTCAAGAATAATTATATTAAAAT
2836734 AAAAATACTTAA
1 AAAAATA-TTAA
2836746 AATAAAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 21 0.52
35 3 0.08
36 8 0.20
37 8 0.20
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (36 bp):
AAAAATATTAATATTCAAGAATAATTATATTAAAAT
Found at i:2837087 original size:39 final size:39
Alignment explanation
Indices: 2837035--2837145 Score: 100
Period size: 42 Copynumber: 2.7 Consensus size: 39
2837025 AAAATATTCA
2837035 TATTAAGAA-AATAATATTATTATATTATTTAACATTAAT
1 TATTAA-AATAATAATATTATTATATTATTTAACATTAAT
* * * ** *
2837074 TATTAAAATAATAAAAATATTATGAGATATGTTATTATTTAT
1 TATTAAAATAATAATATTATTAT-A-TTAT-TTAACATTAAT
2837116 TATTAAAATAATAATATAATATTAT-TTATT
1 TATTAAAATAATAATAT--TATTATATTATT
2837146 ATTGAAATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
38 2 0.04
39 18 0.32
40 2 0.04
41 6 0.11
42 23 0.40
44 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.47
Consensus pattern (39 bp):
TATTAAAATAATAATATTATTATATTATTTAACATTAAT
Found at i:2837164 original size:32 final size:29
Alignment explanation
Indices: 2837106--2837164 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 29
2837096 TGAGATATGT
*
2837106 TATTATTTATTATTAAAATAATAATATAA
1 TATTATTTATTATTAAAATAAAAATATAA
2837135 TATTATTTATTATTGAAATACTAAAAATAT
1 TATTATTTATTATT-AAA-A-TAAAAATAT
2837165 TTATGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 3 0.12
31 1 0.04
32 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TATTATTTATTATTAAAATAAAAATATAA
Found at i:2846704 original size:15 final size:14
Alignment explanation
Indices: 2846675--2846713 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2846665 GAAGAATAAA
2846675 AAATTAAAAAATTT
1 AAATTAAAAAATTT
*
2846689 AAATTAAATTAATTT
1 AAATTAAA-AAATTT
2846704 AAATTTAAAA
1 AAA-TTAAAA
2846714 TAGAAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 8 0.38
15 8 0.38
16 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTAAAAAATTT
Found at i:2847253 original size:3 final size:3
Alignment explanation
Indices: 2847240--2847296 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
2847230 TTCCGTAACA
2847240 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2847286 AAT AAT AAT AA
1 AAT AAT AAT AA
2847297 GATTAAACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2859739 original size:22 final size:22
Alignment explanation
Indices: 2859712--2859755 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2859702 TATAATTTTT
*
2859712 ATTATAAT-TAAATAATTATAAA
1 ATTATAATAAAAAT-ATTATAAA
2859734 ATTATAATAAAAATATTATAAA
1 ATTATAATAAAAATATTATAAA
2859756 TTCTACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATAATAAAAATATTATAAA
Found at i:2860954 original size:16 final size:15
Alignment explanation
Indices: 2860907--2860953 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2860897 TTACTAATTA
2860907 AAATTTATTATATAAT
1 AAATTTATTATAT-AT
* *
2860923 AAATTAATAAATATAT
1 AAATTTAT-TATATAT
2860939 AAATTTATTAT-TAT
1 AAATTTATTATATAT
2860953 A
1 A
2860954 TTATGAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.15
15 2 0.08
16 16 0.62
17 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTATTATATAT
Found at i:2861668 original size:3 final size:3
Alignment explanation
Indices: 2861660--2861696 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2861650 AGCAATAAGA
2861660 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2861697 GAGATAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2867290 original size:102 final size:102
Alignment explanation
Indices: 2867111--2867319 Score: 391
Period size: 102 Copynumber: 2.0 Consensus size: 102
2867101 GTCCATTTCA
*
2867111 AATTTAAGGACAACCAATTTTCACCATAGTGGAATATTTCTTATCATTTCTAGCTAATAATATGT
1 AATTTAAGGACAACCAATTTTCACCATAGTGGAATATTCCTTATCATTTCTAGCTAATAATATGT
*
2867176 TCTCCATGTAGAGTGATAAGATCACAAGCTCGTCTAT
66 TCTCCATATAGAGTGATAAGATCACAAGCTCGTCTAT
2867213 AATTTAAGGACAACCAATTTTCACCATAGTGGAATATTCCTTATCATTTCTAGCTAATAATATGT
1 AATTTAAGGACAACCAATTTTCACCATAGTGGAATATTCCTTATCATTTCTAGCTAATAATATGT
*
2867278 TCTCCATATAGAGTGATAAGATCACAAGTTCGTCTAT
66 TCTCCATATAGAGTGATAAGATCACAAGCTCGTCTAT
2867315 AATTT
1 AATTT
2867320 TTTTAAAATA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (102 bp):
AATTTAAGGACAACCAATTTTCACCATAGTGGAATATTCCTTATCATTTCTAGCTAATAATATGT
TCTCCATATAGAGTGATAAGATCACAAGCTCGTCTAT
Found at i:2869339 original size:135 final size:135
Alignment explanation
Indices: 2869097--2869362 Score: 419
Period size: 135 Copynumber: 2.0 Consensus size: 135
2869087 AGACCATTTA
*
2869097 CTTTGCCACTTTGCTCACTTTTTAATCTTTTAGCAGCTTTCTCTTAGTTTTTACTATATGGCGTA
1 CTTTGCCACTTTGCTCACTTTTTAATCTTTTAGCAGCTTTCTCCTAGTTTTTACTATATGGCGTA
* * * *
2869162 CATTTGAAGCCCATAGCTTCCTTTAATCATGTGTATGTCATATAAATATTA-CAACTAGACTTAT
66 CACTTGAAGCCCATAACTTCCTTTAAACATGTGTATGTCATATAAATATTAGC-ACTAGACTCAT
2869226 ATTTCT
130 ATTTCT
* *
2869232 CTTTGCCACTTTGCTCACTTTTTGATCTTTTATG-AGCTTTCTCCTAGTTTTTACTATATGGCTT
1 CTTTGCCACTTTGCTCACTTTTTAATCTTTTA-GCAGCTTTCTCCTAGTTTTTACTATATGGCGT
**
2869296 ATGCTTGAAGCCCATAACTTCCTTTAAACATGTGTATGTCATATAAATATTAGCACTAGACTCAT
65 ACACTTGAAGCCCATAACTTCCTTTAAACATGTGTATGTCATATAAATATTAGCACTAGACTCAT
2869361 AT
130 AT
2869363 GTTTTTTATA
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
135 118 0.98
136 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (135 bp):
CTTTGCCACTTTGCTCACTTTTTAATCTTTTAGCAGCTTTCTCCTAGTTTTTACTATATGGCGTA
CACTTGAAGCCCATAACTTCCTTTAAACATGTGTATGTCATATAAATATTAGCACTAGACTCATA
TTTCT
Found at i:2882805 original size:2 final size:2
Alignment explanation
Indices: 2882798--2882823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2882788 TCTCATAACT
2882798 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2882824 CAAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2883039 original size:2 final size:2
Alignment explanation
Indices: 2883032--2883058 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2883022 CTAACCCAAC
2883032 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 A
2883059 CACACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2883159 original size:17 final size:18
Alignment explanation
Indices: 2883128--2883162 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2883118 AACATTCATA
*
2883128 AAAATATTATTTTTTAAT
1 AAAATATTATATTTTAAT
2883146 AAAA-ATTATATTTTAAT
1 AAAATATTATATTTTAAT
2883163 TATTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATATTATATTTTAAT
Found at i:2883978 original size:21 final size:23
Alignment explanation
Indices: 2883929--2883978 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
2883919 TCATAAAAAA
2883929 ATTTTTA-GTATAAATTATACAT
1 ATTTTTATGTATAAATTATACAT
**
2883951 -TAGTTATGTATAAA-TATA-AT
1 ATTTTTATGTATAAATTATACAT
2883971 ATTTTTAT
1 ATTTTTAT
2883979 TAAATTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
20 2 0.09
21 13 0.59
22 7 0.32
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTTTTATGTATAAATTATACAT
Found at i:2887346 original size:16 final size:16
Alignment explanation
Indices: 2887323--2887356 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2887313 AATTAAAAAC
2887323 AAAAAAAAAGAAA-GA
1 AAAAAAAAAGAAATGA
2887338 AAAAGAAAAAGAAATGA
1 AAAA-AAAAAGAAATGA
2887355 AA
1 AA
2887357 GCCAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAATGA
Found at i:2890228 original size:24 final size:25
Alignment explanation
Indices: 2890182--2890229 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2890172 TTTTACATCA
*
2890182 TATAATCAACTTAATAATCAATTAT
1 TATAATCAACTGAATAATCAATTAT
*
2890207 TATAATC-ACTGAATAATTAATTA
1 TATAATCAACTGAATAATCAATTA
2890230 ATAAAGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (25 bp):
TATAATCAACTGAATAATCAATTAT
Found at i:2900841 original size:15 final size:15
Alignment explanation
Indices: 2900814--2900850 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
2900804 TATATCACTT
2900814 TGAAATT-TGGCTTG
1 TGAAATTGTGGCTTG
2900828 TGAAATTGTGGCTTG
1 TGAAATTGTGGCTTG
2900843 TGAAATTG
1 TGAAATTG
2900851 GTATATTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (15 bp):
TGAAATTGTGGCTTG
Found at i:2901030 original size:37 final size:35
Alignment explanation
Indices: 2900979--2901078 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 35
2900969 GGAAGAGGCA
*
2900979 ATGGTATGAAAATTTTCTATTTGACTGATGATCTTG
1 ATGGTATAAAAATTTT-TATTTGACTGATGATCTTG
*
2901015 ATGGTATAAAAAATTTTTATTTGATTGATGATCTTG
1 ATGGTAT-AAAAATTTTTATTTGACTGATGATCTTG
*
2901051 ATGGTATTAAAAATTTTTACTTGA-TGAT
1 ATGGTA-TAAAAATTTTTATTTGACTGAT
2901079 ATTGACATTG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
35 4 0.07
36 46 0.78
37 9 0.15
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (35 bp):
ATGGTATAAAAATTTTTATTTGACTGATGATCTTG
Found at i:2904944 original size:16 final size:16
Alignment explanation
Indices: 2904919--2904953 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
2904909 TTTAGAAAAT
2904919 TCTTTCTCTCT-TT-C
1 TCTTTCTCTCTCTTCC
2904933 TCTTTCTCTCTCTTCC
1 TCTTTCTCTCTCTTCC
2904949 TCTTT
1 TCTTT
2904954 GAGTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 2 0.11
16 6 0.32
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (16 bp):
TCTTTCTCTCTCTTCC
Found at i:2906703 original size:31 final size:30
Alignment explanation
Indices: 2906668--2906765 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 30
2906658 TCTCTTTGAG
2906668 TTTTCCTCTTGCTCTTGTATTAAGTGTGATC
1 TTTTCCTCTT-CTCTTGTATTAAGTGTGATC
*
2906699 TTTTCCTCATTCTCTTGTATTAAGTATGATC
1 TTTTCCTC-TTCTCTTGTATTAAGTGTGATC
* * *
2906730 TTTTCCTTCTTTTCTTATACTAAGTGTGATC
1 TTTTCC-TCTTCTCTTGTATTAAGTGTGATC
2906761 ATTTT
1 -TTTT
2906766 TTCCTTCTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
31 51 0.86
32 8 0.14
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.54
Consensus pattern (30 bp):
TTTTCCTCTTCTCTTGTATTAAGTGTGATC
Found at i:2915107 original size:57 final size:58
Alignment explanation
Indices: 2915037--2915162 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 58
2915027 ATTGAAATCG
**
2915037 TTTAA-AAAGAAAATTTGATATTTCA-AAATTTCCTCAAATCTTAGAAATTATTTTCGT
1 TTTAAGAAA-AAAATTTGATATTTCATAAATTTCCTCAAAAATTAGAAATTATTTTCGT
* *** *
2915094 TTTAAGAAAAAAATTTGATATTTTATCTTTTTCCTCAAAAATTTGAAATTATTTTCGT
1 TTTAAGAAAAAAATTTGATATTTCATAAATTTCCTCAAAAATTAGAAATTATTTTCGT
* *
2915152 TTGAGGAAAAA
1 TTTAAGAAAAA
2915163 TTAATATGTC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 20 0.34
58 38 0.66
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (58 bp):
TTTAAGAAAAAAATTTGATATTTCATAAATTTCCTCAAAAATTAGAAATTATTTTCGT
Found at i:2915340 original size:54 final size:54
Alignment explanation
Indices: 2915045--2915560 Score: 454
Period size: 54 Copynumber: 9.4 Consensus size: 54
2915035 CGTTTAAAAA
* ** * *
2915045 GAAAATTTGATATTTCAA-AATTTCCTCAAATCTTAGAAATTATTTTCGTTTTAAG
1 GAAAAATTGATATTTCAACTTTTTCCTCAAAT-TTTGAAATTATTTTTG-TTTAAG
* * * * * *
2915100 AAAAAAATTTGATATTTTATCTTTTTCCTCAAAAATTTGAAATTATTTTCGTTTGAG
1 -GAAAAA-TTGATATTTCAACTTTTTCCTC-AAATTTTGAAATTATTTTTGTTTAAG
* * * * * *
2915157 GAAAAATTAATATGTCAACTTTTTTCTCTAAATTTTTTTAAAATTATTTTTATTTTATG
1 GAAAAATTGATATTTCAACTTTTTCCTC-AAA---TTTTGAAATTATTTTT-GTTTAAG
* * * * *
2915216 AAAAAAATTAATATTTTAACTTTTTCCTC-ATTTTATG-AA--ATTTTT-TATAAG
1 -GAAAAATTGATATTTCAACTTTTTCCTCAAATTT-TGAAATTATTTTTGTTTAAG
* *
2915267 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTGAT
1 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTAAG
* *
2915321 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTATTTAAT
1 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTAAG
* * **
2915375 GAAAAATTGATATTTTAACTCCTTT-CTCATTTTTTTGAAATTATTTTTGTTTAAG
1 GAAAAATTGATATTTCAACT-TTTTCCTCA-AATTTTGAAATTATTTTTGTTTAAG
* * * *
2915430 GAAAATTTGATATTTCAACTTTTTCTTCAAATTTTAAAATTAATTTTGTTTAAG
1 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTAAG
* * * ** * * *
2915484 GAAAAATTGATATTTTAA-TTTTTTCTTATTTTTTAAAATTATTTTTATTTAAA
1 GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTAAG
* *
2915537 GAAAAAATGATATTTCAATTTTTT
1 GAAAAATTGATATTTCAACTTTTT
2915561 TCTATTTTTA
Statistics
Matches: 377, Mismatches: 65, Indels: 38
0.79 0.14 0.08
Matches are distributed among these distances:
50 27 0.07
51 10 0.03
53 55 0.15
54 123 0.33
55 70 0.19
56 10 0.03
57 15 0.04
58 36 0.10
59 7 0.02
60 24 0.06
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (54 bp):
GAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTGTTTAAG
Found at i:2915440 original size:109 final size:108
Alignment explanation
Indices: 2915080--2915560 Score: 470
Period size: 109 Copynumber: 4.4 Consensus size: 108
2915070 TCAAATCTTA
* * * * *
2915080 GAAATTATTTTCGTTTTAAGAAAAAAATTTGATATTTTATCTTTTTCCTCAAAAATTTGAAATTA
1 GAAATTATTTTTG-TTTAAG-GAAAAA-TTGATATTTCAACTTTTTCCTC-AAATTTTGAAATTA
** * * *
2915145 TTTTCGTTTGAGGAAAAATTAATATGTCAACTTTTTTCTCTAAATTTTTTT
62 TTTTTATTTAAGGAAAAATTGATATTTCAACTTTTTTCTC---A-TTTTTT
* * * * * * *
2915196 AAAATTATTTTTATTTTATGAAAAAAATTAATATTTTAACTTTTTCCTC-ATTTTATGAAA-T-T
1 GAAATTATTTTT-GTTTAAG-GAAAAATTGATATTTCAACTTTTTCCTCAAATTT-TGAAATTAT
* **
2915258 TTTTA--TAAGGAAAAATTGATATTTCAACTTTTTCCTCAAATTTT
63 TTTTATTTAAGGAAAAATTGATATTTCAACTTTTTTCTCATTTTTT
* *
2915302 GAAATTATTTTTGTTTGATGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
1 GAAATTATTTTTGTTTAAGGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
* * **
2915367 TATTTAATGAAAAATTGATATTTTAACTCCTTTCTCATTTTTTT
66 TATTTAAGGAAAAATTGATATTTCAACTTTTTTCTCA-TTTTTT
* * * *
2915411 GAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAACTTTTTCTTCAAATTTTAAAATTAATTT
1 GAAATTATTTTTGTTTAAGGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
* * *
2915476 TGTTTAAGGAAAAATTGATATTTTAA-TTTTTTCTTATTTTTT
66 TATTTAAGGAAAAATTGATATTTCAACTTTTTTCTCATTTTTT
* * * * *
2915518 AAAATTATTTTTATTTAAAGAAAAAATGATATTTCAATTTTTT
1 GAAATTATTTTTGTTTAAGGAAAAATTGATATTTCAACTTTTT
2915561 TCTATTTTTA
Statistics
Matches: 308, Mismatches: 49, Indels: 25
0.81 0.13 0.07
Matches are distributed among these distances:
104 30 0.10
105 8 0.03
106 21 0.07
107 44 0.14
108 35 0.11
109 87 0.28
110 28 0.09
112 4 0.01
113 4 0.01
114 5 0.02
115 20 0.06
116 22 0.07
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (108 bp):
GAAATTATTTTTGTTTAAGGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
TATTTAAGGAAAAATTGATATTTCAACTTTTTTCTCATTTTTT
Found at i:2915451 original size:163 final size:162
Alignment explanation
Indices: 2915080--2915551 Score: 551
Period size: 163 Copynumber: 2.9 Consensus size: 162
2915070 TCAAATCTTA
* * * * *
2915080 GAAATTATTTTCGTTTTAAGAAAAAAATTTGATATTTTATCTTTTTCCTCAAAAATTTGAAATTA
1 GAAATTATTTTTG-TTTAAG--GAAAATTTGATATTTCAACTTTTTCCTC-AAATTTTGAAATTA
* * *
2915145 TTTTCGTTTGAGGAAAAATTAATATGTCAACTTTTTTCTCTAAATTTTTTTAAAATTATTTTTAT
62 TTTTTGTTTGAGGAAAAATTGATATTTCAACTTTTTTCTC-AAA---TTTTAAAATTATTTTTAT
* * *
2915210 TTTATGAAAAAAATTAATATTTTAACTTTTTCCTCATTTTAT
123 TTAATG--AAAAATTGATATTTTAACTCTTTCCTCATTTTAT
* *
2915252 G-AA--ATTTTT-TATAAGGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
1 GAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
* * *
2915313 TGTTTGATGAAAAATTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTTTATTTAATGAA
66 TGTTTGAGGAAAAATTGATATTTCAACTTTTTTCTCAAATTTTAAAATTATTTTTATTTAATGAA
*
2915378 AAATTGATATTTTAACTCCTTT-CTCATTTTTTT
131 AAATTGATATTTTAACT-CTTTCCTCA-TTTTAT
* * *
2915411 GAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAACTTTTTCTTCAAATTTTAAAATTAATTT
1 GAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
* * * ** *
2915476 TGTTTAAGGAAAAATTGATATTTTAA-TTTTTTCTTATTTTTTAAAATTATTTTTATTTAAAGAA
66 TGTTTGAGGAAAAATTGATATTTCAACTTTTTTCTCAAATTTTAAAATTATTTTTATTTAATGAA
*
2915540 AAAATGATATTT
131 AAATTGATATTT
2915552 CAATTTTTTT
Statistics
Matches: 262, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
158 22 0.08
159 9 0.03
160 24 0.09
162 49 0.19
163 73 0.28
164 48 0.18
165 24 0.09
167 5 0.02
169 5 0.02
171 2 0.01
172 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (162 bp):
GAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAACTTTTTCCTCAAATTTTGAAATTATTTT
TGTTTGAGGAAAAATTGATATTTCAACTTTTTTCTCAAATTTTAAAATTATTTTTATTTAATGAA
AAATTGATATTTTAACTCTTTCCTCATTTTAT
Found at i:2921684 original size:41 final size:41
Alignment explanation
Indices: 2921638--2921728 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
2921628 CCATTTGTGT
** *
2921638 GTGTTTCTTTATAATTTTTTATTAAGTATTCAATGACAAAA
1 GTGTTTCTTTATAATTACTTATTAAGCATTCAATGACAAAA
* *
2921679 GTGTTTTTTTATAATTACTTATTAAGCATTCCATGACAAAA
1 GTGTTTCTTTATAATTACTTATTAAGCATTCAATGACAAAA
* *
2921720 ATGTCTCTT
1 GTGTTTCTT
2921729 GATGCATGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (41 bp):
GTGTTTCTTTATAATTACTTATTAAGCATTCAATGACAAAA
Found at i:2922213 original size:21 final size:21
Alignment explanation
Indices: 2922165--2922213 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2922155 AGAAATTCAT
*
2922165 TTTC-AAAATCCTTTAAGAGG
1 TTTCGAAAATCCTTTAAAAGG
*
2922185 TTTCGAAAATCCTTTACAAATG
1 TTTCGAAAATCCTTTA-AAAGG
2922207 TTT-GAAA
1 TTTCGAAA
2922214 GCTATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 15 0.60
22 6 0.24
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
TTTCGAAAATCCTTTAAAAGG
Found at i:2930804 original size:59 final size:62
Alignment explanation
Indices: 2930661--2930822 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 62
2930651 GCTTTTATAC
* * * * *
2930661 AAGAAAAATTGATACTTTTAACTTTTCCTAAAAAAT--ATTTTTCTTGATAATTTTTATTTTTT
1 AAGAAAAATTGATAC-TTCAACTTTTTCT-CAAAATGCTTTTTTCTTGATAATTTTTATATTTT
*
2930723 AAGAAAAATTGGTACTTCCAACTTTTTCTCAAAATGCTTTTTTC-TGA-AA-TTTTA-ATTTT
1 AAGAAAAATTGATACTT-CAACTTTTTCTCAAAATGCTTTTTTCTTGATAATTTTTATATTTT
2930782 AAGAAAAATTGATACTATCAACTTTTTCTCAAAATGCTTTT
1 AAGAAAAATTGATACT-TCAACTTTTTCTCAAAATGCTTTT
2930823 GAAAATTTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
59 42 0.47
60 6 0.07
61 9 0.10
62 26 0.29
63 6 0.07
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (62 bp):
AAGAAAAATTGATACTTCAACTTTTTCTCAAAATGCTTTTTTCTTGATAATTTTTATATTTT
Found at i:2930949 original size:30 final size:32
Alignment explanation
Indices: 2930883--2930949 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
2930873 ACTTTTCCTC
* * *
2930883 AAAATATTTTTTCTTAAATTTTTTTTTCAAGG
1 AAAATATTTTTTCTAAAATTTATTTTTCAAGA
2930915 AAAATA-TTTTT-TAAAATTTGATTTTT-AAGA
1 AAAATATTTTTTCTAAAATTT-ATTTTTCAAGA
2930945 AAAAT
1 AAAAT
2930950 TGATACTGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 15 0.48
31 10 0.32
32 6 0.19
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (32 bp):
AAAATATTTTTTCTAAAATTTATTTTTCAAGA
Found at i:2931062 original size:61 final size:62
Alignment explanation
Indices: 2930935--2931107 Score: 179
Period size: 62 Copynumber: 2.7 Consensus size: 62
2930925 TTAAAATTTG
* * * * * ** *
2930935 ATTTTTAAGAAAAATTGATACTGTCAACTTTTCCTTAAAAATAATTTTTAAAAAAATTTTATTTT
1 ATTTTCAAGAAAAATTCATACTTTCAACTTTTTCTCAAAAAT-ATTTTT----TTATTTAATTTT
2931000 TT
61 TT
* *
2931002 ATTTTTC-AGAAAAAATTGATACTTTCAA-TTTTTTTCAAAAATATTTTTTTATTTAATTTTTT
1 A-TTTTCAAG-AAAAATTCATACTTTCAACTTTTTCTCAAAAATATTTTTTTATTTAATTTTTT
2931064 ATTTTCAAGAAAAATTCATACTTTCAACTTTTTCTCAAAAATAT
1 ATTTTCAAGAAAAATTCATACTTTCAACTTTTTCTCAAAAATAT
2931108 ATATTTTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
61 22 0.24
62 29 0.32
66 6 0.07
67 14 0.15
68 21 0.23
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (62 bp):
ATTTTCAAGAAAAATTCATACTTTCAACTTTTTCTCAAAAATATTTTTTTATTTAATTTTTT
Found at i:2931121 original size:61 final size:60
Alignment explanation
Indices: 2930995--2931135 Score: 164
Period size: 62 Copynumber: 2.3 Consensus size: 60
2930985 AAAAAATTTT
* * * *
2930995 ATTTTTTATTTTTC-AGAAAAAATTGATACTTTCAATTTTTTTCAAAAATATTTTTTTATTTA
1 ATTTTTTA-TTTTCAAG-AAAAATTCATACTTTCAATTTTTCTCAAAAATATTATTTTA-TAA
2931057 ATTTTTTATTTTCAAGAAAAATTCATACTTTCAACTTTTTCTCAAAAATATATATTTTA-AA
1 ATTTTTTATTTTCAAGAAAAATTCATACTTTCAA-TTTTTCTCAAAAATAT-TATTTTATAA
*
2931118 A--TTTTATTTTTAAGAAAA
1 ATTTTTTATTTTCAAGAAAA
2931136 TTATTGAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
59 16 0.23
61 24 0.34
62 25 0.35
63 6 0.08
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (60 bp):
ATTTTTTATTTTCAAGAAAAATTCATACTTTCAATTTTTCTCAAAAATATTATTTTATAA
Found at i:2932564 original size:13 final size:13
Alignment explanation
Indices: 2932546--2932585 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2932536 AAGTTGTTAG
2932546 AGAGAAAAGAAAA
1 AGAGAAAAGAAAA
*
2932559 AGAGAAGAGAAAA
1 AGAGAAAAGAAAA
*
2932572 GGAGAAAAAGAAAA
1 AGAG-AAAAGAAAA
2932586 GGGTGCATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AGAGAAAAGAAAA
Found at i:2937430 original size:34 final size:34
Alignment explanation
Indices: 2937392--2937461 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
2937382 AATAAACTTT
** * *
2937392 AATGAACTTTATATTTTTCATGTGTCTTAGCACA
1 AATGAACTCCATAATTTTCAAGTGTCTTAGCACA
2937426 AATGAACTCCATAATTTTCAAGTGTCTTAGCACA
1 AATGAACTCCATAATTTTCAAGTGTCTTAGCACA
2937460 AA
1 AA
2937462 GGTCATATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (34 bp):
AATGAACTCCATAATTTTCAAGTGTCTTAGCACA
Found at i:2938622 original size:22 final size:22
Alignment explanation
Indices: 2938598--2938639 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2938588 CCGAATTTTT
*
2938598 TTTTG-TATATTTTTTTATTTA
1 TTTTGTTATATTTGTTTATTTA
*
2938619 TTTTGTTTTATTTGTTTATTT
1 TTTTGTTATATTTGTTTATTT
2938640 TTGAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTGTTATATTTGTTTATTTA
Found at i:2941711 original size:18 final size:18
Alignment explanation
Indices: 2941690--2941730 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
2941680 TTAATTTTTT
2941690 TATAAAATT-T-AAAATA
1 TATAAAATTATAAAAATA
2941706 TATATAAATTAATAAAAATA
1 TATA-AAATT-ATAAAAATA
2941726 TATAA
1 TATAA
2941731 TTTGGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
19 2 0.10
20 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAATTATAAAAATA
Found at i:2941806 original size:13 final size:13
Alignment explanation
Indices: 2941787--2941820 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2941777 ATTTGATTTG
2941787 AATTTAATATATA
1 AATTTAATATATA
* *
2941800 TATTTAATATTTA
1 AATTTAATATATA
2941813 AATTTAAT
1 AATTTAAT
2941821 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTAATATATA
Found at i:2944311 original size:18 final size:18
Alignment explanation
Indices: 2944288--2944322 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2944278 GTGATATATA
*
2944288 TATATATGTGTGTGTGTT
1 TATATATATGTGTGTGTT
2944306 TATATATATGTGTGTGT
1 TATATATATGTGTGTGT
2944323 ATGTGTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
TATATATATGTGTGTGTT
Found at i:2944314 original size:24 final size:24
Alignment explanation
Indices: 2944282--2944328 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2944272 ATTAAAGTGA
*
2944282 TATATATATATATGTGTGTGTGTT
1 TATATATATATATGTGTATGTGTT
* *
2944306 TATATATATGTGTGTGTATGTGT
1 TATATATATATATGTGTATGTGT
2944329 GTGCATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (24 bp):
TATATATATATATGTGTATGTGTT
Found at i:2945512 original size:2 final size:2
Alignment explanation
Indices: 2945505--2945538 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2945495 TTCAATATTG
* *
2945505 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2945539 GTTGCTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2945726 original size:18 final size:19
Alignment explanation
Indices: 2945692--2945729 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2945682 ATAAGAAGGA
2945692 AATATGACAATTTAAATGC
1 AATATGACAATTTAAATGC
2945711 AATATGACAA-TTAAATGC
1 AATATGACAATTTAAATGC
2945729 A
1 A
2945730 TCTAACTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AATATGACAATTTAAATGC
Found at i:2951903 original size:22 final size:22
Alignment explanation
Indices: 2951877--2951918 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2951867 TGTATATTTA
* *
2951877 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
2951899 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
2951919 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:2963868 original size:54 final size:54
Alignment explanation
Indices: 2963542--2964034 Score: 407
Period size: 54 Copynumber: 9.1 Consensus size: 54
2963532 TATTTCAAAA
* * * *
2963542 TTTCCTCAAATCTTAGAAATTATTTTTGTTTTAAGAAAAAAAATTGATATTTTATCTT
1 TTTCCTCAAAT-TTTGAAATTATTTTT-ATTTAAG--GAAAAATTGATATTTTAACTT
* ** * * *
2963600 TTTCCTCAAAAATTTGAAATTATTTTCGTTTGAGGAAAAATTGATATGTCAACTT
1 TTTCCTC-AAATTTTGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACTT
* * * * *
2963655 TTTTCTCTAAATTTTTTAAAATTATTTTTATTTTATGAAAAAAATTAATATTTTAACTT
1 TTTCCTC-AAA--TTTTGAAATTATTTTTA-TTTAAG-GAAAAATTGATATTTTAACTT
* * *
2963714 TTTCCT-TATTTTATGAAA-T-TTTTTA--TAAGGAAAAATTGATATTTTAACTCC
1 TTTCCTCAAATTT-TGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACT-T
*** *
2963765 TTT-CT-TGTTTCTTGAAATTATTTTTTGTTTAAGGAAAAATTGATATTTTAACTT
1 TTTCCTCAAATT-TTGAAATTA-TTTTTATTTAAGGAAAAATTGATATTTTAACTT
* *
2963819 TTTCCTCAAATTTTGAAATTATTTTTATTTAATGAAAAATTGATATTTTAACTCC
1 TTTCCTCAAATTTTGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACT-T
** * *
2963874 TTT-CTCATTTTTTGAAATTATTTTTGTTTAAGG-AAAATTCGATATTTCAACTT
1 TTTCCTCAAATTTTGAAATTATTTTTATTTAAGGAAAAATT-GATATTTTAACTT
* * * *
2963927 TTTCTTCAAATTTTAAAATTAATTTTGTTTAAGGAAAAATTGATATTTTAA-TT
1 TTTCCTCAAATTTTGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACTT
* ** * * * *
2963980 TTT-CTTATTTTTTAAAATTATTTTTATTTAAAGAAAAA-TGATATTTCAATTT
1 TTTCCTCAAATTTTGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACTT
2964032 TTT
1 TTT
2964035 TTCTATTTTT
Statistics
Matches: 357, Mismatches: 58, Indels: 46
0.77 0.13 0.10
Matches are distributed among these distances:
50 29 0.08
51 18 0.05
52 33 0.09
53 19 0.05
54 110 0.31
55 74 0.21
56 6 0.02
57 19 0.05
58 24 0.07
59 25 0.07
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (54 bp):
TTTCCTCAAATTTTGAAATTATTTTTATTTAAGGAAAAATTGATATTTTAACTT
Found at i:2974382 original size:41 final size:41
Alignment explanation
Indices: 2974337--2974417 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
2974327 TGTGTGTTTC
*
2974337 TTTATAATTTA-TTATTAAGTATTCAATGAC-AAAAGTGTCTT
1 TTTATAA-TTACTTATTAAGCATTCAATGACGAAAA-TGTCTT
*
2974378 TTTATAATTACTTATTAAGCATTCCATGACGAAAATGTCT
1 TTTATAATTACTTATTAAGCATTCAATGACGAAAATGTCT
2974418 CTTGATGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 3 0.08
41 29 0.81
42 4 0.11
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (41 bp):
TTTATAATTACTTATTAAGCATTCAATGACGAAAATGTCTT
Found at i:2977230 original size:139 final size:138
Alignment explanation
Indices: 2976974--2977249 Score: 385
Period size: 139 Copynumber: 2.0 Consensus size: 138
2976964 TTCTAGTGCC
* * * *
2976974 CACTCCCTTATATACTTCTTACCTCCAACACTGATGTAACACAACCAATTTTCCTCACTTCCTAT
1 CACTCCCTTATATACTTCTTACCTCCAACACTAATGCAACACAACCAATTATCCTCACTCCCTAT
** * **
2977039 CTCTAACATCGATGATAGCATTGTATGATTTTCCTTATGCATCTTAACATCAATGAGAGCACTGC
66 CTCTAACATCGATGATAAAATTGCATGA-TTTCCCCATGCATCTTAACATCAATGAGAGCACTGC
2977104 TCGATTCTT
130 TCGATTCTT
* * * *
2977113 CACTCCTTTATATACTT-TCTACCTCTAGCACTAATGGCAACACAACCCAATTATCCTCGCTCCC
1 CACTCCCTTATATACTTCT-TACCTCCAACACTAAT-GCAACACAA-CCAATTATCCTCACTCCC
2977177 TATCTCTAACATCGATGATAAAATTGCATGA-TTCCCCATGCATCTTAACATCAATGAGAGCACT
63 TATCTCTAACATCGATGATAAAATTGCATGATTTCCCCATGCATCTTAACATCAATGAGAGCACT
2977241 GCTCGATTC
128 GCTCGATTC
2977250 CCTGTACTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
138 1 0.01
139 69 0.57
140 8 0.07
141 43 0.36
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (138 bp):
CACTCCCTTATATACTTCTTACCTCCAACACTAATGCAACACAACCAATTATCCTCACTCCCTAT
CTCTAACATCGATGATAAAATTGCATGATTTCCCCATGCATCTTAACATCAATGAGAGCACTGCT
CGATTCTT
Found at i:2983724 original size:121 final size:120
Alignment explanation
Indices: 2983491--2983741 Score: 296
Period size: 120 Copynumber: 2.1 Consensus size: 120
2983481 TGCTTTTATA
2983491 CAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAAATATTTTTCTTGATAATTTTTATTTTTTAA
1 CAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAAATATTTTTCTTGATAATTTTTATTTTTTAA
* ** * *
2983556 GGAAAATTGGTACTTCCAACTTTTCTTCAAAATATTTTTTTTAAAATTTGATTTT
66 GAAAAATTCATACTTCCAACCTTTCCTCAAAATATTTTTTTTAAAATTTGATTTT
* * * * * *
2983611 CAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTT-TTTATTTTATTTTT-TATTTT
1 CAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAAATATTTTTCTTGA--TAATTTTTAT-TTTT
* *
2983674 TAAGAAAAATTCAT-CTTTCAACCTTTCCTCAAAAATATATTTTTTT-AAATTTTATTTT
63 TAAGAAAAATTCATACTTCCAACCTTTCCTC-AAAATAT-TTTTTTTAAAATTTGATTTT
*
2983732 TAA-AAAAATT
1 CAAGAAAAATT
2983742 ATAGAAAAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
119 3 0.03
120 60 0.54
121 42 0.38
122 7 0.06
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.49
Consensus pattern (120 bp):
CAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAAATATTTTTCTTGATAATTTTTATTTTTTAA
GAAAAATTCATACTTCCAACCTTTCCTCAAAATATTTTTTTTAAAATTTGATTTT
Found at i:2985021 original size:18 final size:17
Alignment explanation
Indices: 2984996--2985036 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
2984986 GAAAGTTGTT
2984996 AGAAAGAAAAGAAGAAG
1 AGAAAGAAAAGAAGAAG
*
2985013 AGAAGAGAAAAGGAGAAG
1 AGAA-AGAAAAGAAGAAG
2985031 AAGAAA
1 -AGAAA
2985037 AGGGTGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAGAAGAAG
Found at i:2988900 original size:18 final size:18
Alignment explanation
Indices: 2988877--2988915 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2988867 TGTCAGAAGC
2988877 TATTATCATA-TATATATA
1 TATTATCATATTATAT-TA
*
2988895 TATTATGATATTATATTA
1 TATTATCATATTATATTA
2988913 TAT
1 TAT
2988916 GTTTTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTATCATATTATATTA
Found at i:2991124 original size:28 final size:27
Alignment explanation
Indices: 2991070--2991124 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2991060 GTCAAGCCGA
** *
2991070 TTTTTTTTTGTATATTTTTTTATTATT
1 TTTTTTTTTGTATATTTTTGAAATATT
*
2991097 TTTTTTATTTGTTTATTTTTGAAATATT
1 TTTTTT-TTTGTATATTTTTGAAATATT
2991125 ATACATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (27 bp):
TTTTTTTTTGTATATTTTTGAAATATT
Found at i:2994182 original size:18 final size:18
Alignment explanation
Indices: 2994161--2994201 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
2994151 TTAATTTTTT
2994161 TATAAAATT-T-AAAATA
1 TATAAAATTATAAAAATA
2994177 TATATAAATTAATAAAAATA
1 TATA-AAATT-ATAAAAATA
2994197 TATAA
1 TATAA
2994202 TTTGGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
19 2 0.10
20 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAATTATAAAAATA
Found at i:2994278 original size:13 final size:13
Alignment explanation
Indices: 2994259--2994292 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2994249 ATTTGATTTG
2994259 AATTTAATATATA
1 AATTTAATATATA
* *
2994272 TATTTAATATTTA
1 AATTTAATATATA
2994285 AATTTAAT
1 AATTTAAT
2994293 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTAATATATA
Found at i:2994665 original size:2 final size:2
Alignment explanation
Indices: 2994658--2994699 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2994648 TTCACATCTA
* * *
2994658 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2994700 TAGTGGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2994680 original size:14 final size:14
Alignment explanation
Indices: 2994658--2994699 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2994648 TTCACATCTA
*
2994658 ATATATATATATAT
1 ATATGTATATATAT
2994672 ATATGTATATATAT
1 ATATGTATATATAT
*
2994686 ATATGTATGTATAT
1 ATATGTATATATAT
2994700 TAGTGGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:2996249 original size:15 final size:15
Alignment explanation
Indices: 2996194--2996249 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 15
2996184 TAAAACTTTT
2996194 ATTAATGTTGATTTA
1 ATTAATGTTGATTTA
2996209 ATTATATTGCATTGGATTTTA
1 ATTA-A-TG--TT-GA-TTTA
2996230 A-TAATGTTGATTTA
1 ATTAATGTTGATTTA
2996244 ATTAAT
1 ATTAAT
2996250 TATTTCCGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 5 0.15
15 10 0.29
16 3 0.09
17 2 0.06
18 2 0.06
19 3 0.09
20 4 0.12
21 5 0.15
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTAATGTTGATTTA
Found at i:2996785 original size:18 final size:18
Alignment explanation
Indices: 2996762--2996796 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2996752 TATATATATA
*
2996762 TATATATGTGTGTGTGTT
1 TATATATATGTGTGTGTT
2996780 TATATATATGTGTGTGT
1 TATATATATGTGTGTGT
2996797 ATGTGTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
TATATATATGTGTGTGTT
Found at i:2996788 original size:24 final size:24
Alignment explanation
Indices: 2996756--2996802 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2996746 AAGTGATATA
*
2996756 TATATATATATATGTGTGTGTGTT
1 TATATATATATATGTGTATGTGTT
* *
2996780 TATATATATGTGTGTGTATGTGT
1 TATATATATATATGTGTATGTGT
2996803 GTGCATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (24 bp):
TATATATATATATGTGTATGTGTT
Found at i:2996801 original size:26 final size:26
Alignment explanation
Indices: 2996754--2996804 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2996744 TAAAGTGATA
*
2996754 TATATATATATATATGTGTGTGTGTT
1 TATATATATATATATGTATGTGTGTT
* * *
2996780 TATATATATGTGTGTGTATGTGTGT
1 TATATATATATATATGTATGTGTGT
2996805 GCATGTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (26 bp):
TATATATATATATATGTATGTGTGTT
Found at i:2998037 original size:2 final size:2
Alignment explanation
Indices: 2998030--2998067 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2998020 TTCAATATTG
* *
2998030 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2998068 GTTGCTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2998245 original size:21 final size:21
Alignment explanation
Indices: 2998221--2998262 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2998211 ATAAGAAGGA
2998221 AATATGACAATTTAAATGCAT
1 AATATGACAATTTAAATGCAT
2998242 AATATGACAATTTAAATGCAT
1 AATATGACAATTTAAATGCAT
2998263 CTAACTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (21 bp):
AATATGACAATTTAAATGCAT
Found at i:3004436 original size:22 final size:22
Alignment explanation
Indices: 3004410--3004451 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3004400 TGTATATTTA
* *
3004410 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
3004432 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
3004452 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:3008408 original size:22 final size:22
Alignment explanation
Indices: 3008368--3008409 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3008358 TGTATATTTA
*
3008368 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
3008390 TATTTGTATC-CTTAAAATTA
1 TATTTGTATCTC-TAAAATTA
3008410 GGATAGACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:3011776 original size:22 final size:22
Alignment explanation
Indices: 3011751--3011794 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3011741 TATATATTTA
*
3011751 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3011773 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3011795 GATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3013340 original size:30 final size:29
Alignment explanation
Indices: 3013304--3013366 Score: 103
Period size: 27 Copynumber: 2.2 Consensus size: 29
3013294 TGACCAAGTT
3013304 AATGATACTACTATCAAATATAATTGCAAA
1 AATGATA-TACTATCAAATATAATTGCAAA
3013334 AATG--ATACTATCAAATATAATTGCAAA
1 AATGATATACTATCAAATATAATTGCAAA
3013361 AATGAT
1 AATGAT
3013367 CCAAGTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 26 0.84
28 1 0.03
30 4 0.13
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (29 bp):
AATGATATACTATCAAATATAATTGCAAA
Found at i:3013348 original size:27 final size:27
Alignment explanation
Indices: 3013312--3013366 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3013302 TTAATGATAC
3013312 TACTATCAAATATAATTGCAAAAATGA
1 TACTATCAAATATAATTGCAAAAATGA
3013339 TACTATCAAATATAATTGCAAAAATGA
1 TACTATCAAATATAATTGCAAAAATGA
3013366 T
1 T
3013367 CCAAGTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (27 bp):
TACTATCAAATATAATTGCAAAAATGA
Found at i:3017023 original size:19 final size:19
Alignment explanation
Indices: 3017001--3017040 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3016991 TGCATTTTAC
3017001 CAGAATACTTAAATTTGGA
1 CAGAATACTTAAATTTGGA
3017020 CAGAATACTTAAATTTGGA
1 CAGAATACTTAAATTTGGA
3017039 CA
1 CA
3017041 AAAGTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (19 bp):
CAGAATACTTAAATTTGGA
Found at i:3023581 original size:22 final size:21
Alignment explanation
Indices: 3023523--3023582 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 21
3023513 TATTCATTTA
*
3023523 ATTTTAATTATT-AATTAATTAT
1 ATTTT-ATTATTAAATT-ATCAT
3023545 -TTTTATTA-TACAATTATCAT
1 ATTTTATTATTA-AATTATCAT
3023565 ATTTTATTTATTAAATTA
1 ATTTTA-TTATTAAATTA
3023583 AATTAGCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
19 1 0.03
20 8 0.25
21 13 0.41
22 8 0.25
23 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTATTATTAAATTATCAT
Found at i:3024013 original size:19 final size:18
Alignment explanation
Indices: 3023981--3024020 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3023971 TTAAATTCTC
*
3023981 ATATTAATTTAATTTAATA
1 ATATTAATTCAA-TTAATA
*
3024000 ATATTGATTCAATTAATA
1 ATATTAATTCAATTAATA
3024018 ATA
1 ATA
3024021 ATATTACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTAATTCAATTAATA
Found at i:3024209 original size:31 final size:31
Alignment explanation
Indices: 3024160--3024252 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
3024150 GTAAATGATT
* * * *
3024160 TTTATATTCATATAAAATTTAAAATATAATC
1 TTTATATTCACACAAAATTTGAAATTTAATC
*
3024191 TTTATATTCACACGAAATTTGAAATTTAATC
1 TTTATATTCACACAAAATTTGAAATTTAATC
** *
3024222 CCTATACTCACACAAAATTTGAAATTTAATC
1 TTTATATTCACACAAAATTTGAAATTTAATC
3024253 CCTTTAATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTATATTCACACAAAATTTGAAATTTAATC
Found at i:3025263 original size:17 final size:20
Alignment explanation
Indices: 3025220--3025265 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3025210 ATAAATGATA
3025220 ATAATATATTAATATGATATT
1 ATAATA-ATTAATATGATATT
3025241 ATTAATAATTAAT-T-ATA-T
1 A-TAATAATTAATATGATATT
3025259 ATAATAA
1 ATAATAA
3025266 AAACTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 3 0.12
20 1 0.04
21 7 0.29
22 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATGATATT
Found at i:3025274 original size:52 final size:52
Alignment explanation
Indices: 3025171--3025280 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 52
3025161 CATTACTTTG
* * *
3025171 ATATATTAATTTAAATTATTAATATTATAATTAATAGATATAAATGATAATA
1 ATATATTAATTGAAATTATTAATAATATAATTAATAGATATAAATAATAATA
* *
3025223 ATATATTAATATGATATTATTAATAAT-TAATT-AT--ATAT-AATAAAAACTA
1 ATATATTAAT-TGAAATTATTAATAATATAATTAATAGATATAAATAATAA-TA
3025272 ATATATTAA
1 ATATATTAA
3025281 AAGAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
48 6 0.12
49 15 0.29
51 2 0.04
52 15 0.29
53 13 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (52 bp):
ATATATTAATTGAAATTATTAATAATATAATTAATAGATATAAATAATAATA
Found at i:3031035 original size:22 final size:22
Alignment explanation
Indices: 3031010--3031053 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3031000 TATATATTTA
*
3031010 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3031032 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3031054 GATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3043229 original size:19 final size:18
Alignment explanation
Indices: 3043197--3043236 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3043187 TTAAATTTTT
*
3043197 ATATTAATTTAATTTAATA
1 ATATTAATTCAA-TTAATA
*
3043216 ATATTGATTCAATTAATA
1 ATATTAATTCAATTAATA
3043234 ATA
1 ATA
3043237 GTATTACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTAATTCAATTAATA
Found at i:3043410 original size:31 final size:31
Alignment explanation
Indices: 3043370--3043466 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 31
3043360 AATCATGTAA
*
3043370 ATAAT-TTTATATTCATACAAAATTTAAAAT
1 ATAATCTTTATATTCACACAAAATTTAAAAT
*
3043400 ATAATCTTTATATTCACACGAAATTTAAAAT
1 ATAATCTTTATATTCACACAAAATTTAAAAT
* * * *
3043431 TTAGTCCTTATATTCACACAAAATTTGAAAT
1 ATAATCTTTATATTCACACAAAATTTAAAAT
*
3043462 TTAAT
1 ATAAT
3043467 TCCTTTAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 5 0.09
31 53 0.91
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (31 bp):
ATAATCTTTATATTCACACAAAATTTAAAAT
Found at i:3045960 original size:30 final size:30
Alignment explanation
Indices: 3045924--3045987 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3045914 CTAGGGCTAA
* *
3045924 AATTGGATGAAAATAGATATTTAATTGTTT
1 AATTGGATGAAAATAGATATTTAAATGTTC
3045954 AATTGGATGAAAATAGATATTTAAATGTTC
1 AATTGGATGAAAATAGATATTTAAATGTTC
3045984 AATT
1 AATT
3045988 AATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTGGATGAAAATAGATATTTAAATGTTC
Found at i:3047029 original size:17 final size:19
Alignment explanation
Indices: 3047007--3047041 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3046997 CATAAAATAT
3047007 AATATT-TTTTT-AAAACA
1 AATATTGTTTTTCAAAACA
3047024 AATATTGTTTTTCAAAAC
1 AATATTGTTTTTCAAAAC
3047042 TCATTTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (19 bp):
AATATTGTTTTTCAAAACA
Found at i:3048666 original size:19 final size:20
Alignment explanation
Indices: 3048623--3048669 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3048613 ATGACCAATC
*
3048623 CAACTTAGCATCAAACAAAT
1 CAACTTGGCATCAAACAAAT
*
3048643 AAACTTGGCATCAAA-AAAT
1 CAACTTGGCATCAAACAAAT
3048662 CAACTTGG
1 CAACTTGG
3048670 AAATGCATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (20 bp):
CAACTTGGCATCAAACAAAT
Found at i:3048935 original size:25 final size:23
Alignment explanation
Indices: 3048881--3048936 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
3048871 TTCCTCTCTT
*
3048881 CCCCTTTTGGTAGCTTCCTTCCT
1 CCCCTTTTGGTAGCTTCCTTCCG
*
3048904 CTTCCTTTTGGTAGCTTCCCTTCCAG
1 C-CCCTTTTGGTAGCTT-CCTTCC-G
3048930 CCCCTTT
1 CCCCTTT
3048937 CTTTTGGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 14 0.52
25 11 0.41
26 1 0.04
ACGTcount: A:0.05, C:0.39, G:0.12, T:0.43
Consensus pattern (23 bp):
CCCCTTTTGGTAGCTTCCTTCCG
Found at i:3049816 original size:150 final size:144
Alignment explanation
Indices: 3049415--3049808 Score: 506
Period size: 144 Copynumber: 2.7 Consensus size: 144
3049405 TTAAAACACC
*
3049415 AAAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
1 AAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
* * * ** *
3049480 GTCAAATTACAAAAATACCTTTATAAGGGTATTTTGGTAATTTCATATTTTTCAAGGTACTACTA
66 GTCAAATTACAAAAATAACTTTAT-AGGGTATTTTGGTAATTTCACACTTCCCAAGATACTACTA
*
3049545 TGATTTCAAATGCAC
130 TGATTTCAAATGCAA
* * * * ****
3049560 CAAAAATCATGAAATATTATGAAATTAATATCTAAAAAG-TTCATGAAGATCCAAGCTTGGGAAG
1 AAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
*
3049624 GTCAAATTACAAAAA-AACATTTATAGTGGTATTTTGGTAATTTCACACTTCCCACGATA-TGAC
66 GTCAAATTACAAAAATAAC-TTTATAG-GGTATTTTGGTAATTTCACACTTCCCAAGATACT-AC
3049687 TATGATTTCAAATGCAAAAAAA
128 TATGATTTCAAATGC-----AA
*
3049709 AAAAAATCATGAAATATTATGAAATTAAGATATGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
1 AAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
*
3049774 GTCAAATTACAAAAATATCTGTTATAGGGTATTTT
66 GTCAAATTACAAAAATAACT-TTATAGGGTATTTT
3049809 TATAATTTTT
Statistics
Matches: 211, Mismatches: 27, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
143 5 0.02
144 83 0.39
145 35 0.17
149 36 0.17
150 44 0.21
151 8 0.04
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (144 bp):
AAAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAGCTCAAAAAG
GTCAAATTACAAAAATAACTTTATAGGGTATTTTGGTAATTTCACACTTCCCAAGATACTACTAT
GATTTCAAATGCAA
Found at i:3050431 original size:22 final size:22
Alignment explanation
Indices: 3050404--3050462 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
3050394 CTTTTGCCCA
*
3050404 AAGGTCTTAAAAATTATACTTG
1 AAGGTCTTAAAAATTATACTCG
* * *
3050426 AAGGTCTTAGAGATTATGCTCG
1 AAGGTCTTAAAAATTATACTCG
*
3050448 AAGGTCTTACAAATT
1 AAGGTCTTAAAAATT
3050463 TTAAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (22 bp):
AAGGTCTTAAAAATTATACTCG
Done.