Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_pilon, 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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2835087 original size:9 final size:8
Alignment explanation
Indices: 2835034--2835092 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 8
2835024 ATTAAATTTT
2835034 AAATATAA
1 AAATATAA
2835042 AAATATAAA
1 AAATAT-AA
2835051 AAATACTAA
1 AAATA-TAA
*
2835060 AAA-AT-T
1 AAATATAA
2835066 AAATATAAA
1 AAATAT-AA
2835075 AAATACTAA
1 AAATA-TAA
2835084 AAATA-AA
1 AAATATAA
2835091 AA
1 AA
2835093 TTGAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
6 3 0.07
7 7 0.16
8 7 0.16
9 24 0.56
10 2 0.05
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATATAA
Found at i:2835093 original size:24 final size:24
Alignment explanation
Indices: 2835010--2835093 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
2835000 TAATATTTTT
* **
2835010 AAATAAAAATATATATTAAATTTTAA
1 AAATAAAAATATA-A-AAAATACTAA
*
2835036 ATATAAAAATATAAAAAATACTAA
1 AAATAAAAATATAAAAAATACTAA
*
2835060 AAA-ATTAAATATAAAAAATACTAA
1 AAATA-AAAATATAAAAAATACTAA
2835084 AAATAAAAAT
1 AAATAAAAAT
2835094 TGAATTATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 1 0.02
24 34 0.69
25 2 0.04
26 12 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAAAATATAAAAAATACTAA
Found at i:2836653 original size:22 final size:20
Alignment explanation
Indices: 2836603--2836659 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
2836593 AACAAAAGGT
* *
2836603 TGGTATCGATACTCTTTCTT
1 TGGTATCGATACTTTTTCTG
*
2836623 TAGTATCGATACTTTTGGTCTG
1 TGGTATCGATACTTTT--TCTG
2836645 TGGTATCGATACTTT
1 TGGTATCGATACTTT
2836660 CCTGAGTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (20 bp):
TGGTATCGATACTTTTTCTG
Found at i:2837375 original size:20 final size:20
Alignment explanation
Indices: 2837350--2837463 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 20
2837340 TTTTCCCAAT
*
2837350 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTA
* * *
2837370 TCGCAATGAGATACTTACTA
1 TCGCAACGCGATACTGACTA
* * * **
2837390 TCGCAATGCGATAATATAAAA
1 TCGCAACGCGATACT-GACTA
* * *
2837411 TCGCAACGAGATACTAACTT
1 TCGCAACGCGATACTGACTA
* *
2837431 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTA
2837451 TCGCAACGCGATA
1 TCGCAACGCGATA
2837464 ATACATAATC
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 61 0.80
21 15 0.20
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTA
Found at i:2837424 original size:61 final size:61
Alignment explanation
Indices: 2837350--2837477 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 61
2837340 TTTTCCCAAT
* * * * * * *
2837350 TCGCAATGCGATACTGACTATCGCAATGAGATACTTACTATCGCAATGCGATAATATAAAA
1 TCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAAA
* * * * *
2837411 TCGCAACGAGATACTAACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAA
1 TCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAAA
2837472 TCGCAA
1 TCGCAA
2837478 TGCTATTTTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (61 bp):
TCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAAA
Found at i:2838011 original size:20 final size:20
Alignment explanation
Indices: 2837957--2838015 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2837947 GCGATTCTCT
* **
2837957 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2837977 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2837997 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2838016 ACAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2839356 original size:18 final size:18
Alignment explanation
Indices: 2839335--2839379 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2839325 TCCACTTCGG
*
2839335 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2839353 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2839371 GAGCCATCA
1 GAGCCATCA
2839380 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2839791 original size:12 final size:13
Alignment explanation
Indices: 2839776--2839804 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2839766 TTTGTTAGTA
2839776 TTTGTTTTTGT-T
1 TTTGTTTTTGTCT
2839788 TTTGTTTTTGTCT
1 TTTGTTTTTGTCT
2839801 TTTG
1 TTTG
2839805 GTTGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.79
Consensus pattern (13 bp):
TTTGTTTTTGTCT
Found at i:2839886 original size:20 final size:20
Alignment explanation
Indices: 2839861--2839906 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2839851 TAGTTTACTT
2839861 TCGCAACATGAAAATGACTA
1 TCGCAACATGAAAATGACTA
* * *
2839881 TCGCAACGTGGAAATGGCTA
1 TCGCAACATGAAAATGACTA
2839901 TCGCAA
1 TCGCAA
2839907 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAACATGAAAATGACTA
Found at i:2839922 original size:19 final size:19
Alignment explanation
Indices: 2839900--2839958 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2839890 GGAAATGGCT
2839900 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
2839919 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATAAAA
*
2839933 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
2839952 ATCGCAA
1 ATCGCAA
2839959 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:2839935 original size:14 final size:14
Alignment explanation
Indices: 2839916--2839974 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2839906 ATGCGAAATA
2839916 AAAATCGCAATGAC
1 AAAATCGCAATGAC
*
2839930 AAAATCGCAATGCGAAATG
1 AAAATCGCAAT--G--A-C
*
2839949 AAAATCGCAACGAC
1 AAAATCGCAATGAC
2839963 AAAATCGCAATG
1 AAAATCGCAATG
2839975 TGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAATGAC
Found at i:2839942 original size:33 final size:33
Alignment explanation
Indices: 2839900--2839992 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2839890 GGAAATGGCT
*
2839900 ATCGCAATGCGAAATAAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
2839933 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
* *
2839966 ATCGCAATGTGAAATGAAAGTCGCAAT
1 ATCGCAATGCGAAATGAAAATCGCAAT
2839993 CCGATTTGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:2840067 original size:20 final size:20
Alignment explanation
Indices: 2840022--2840108 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
2840012 GCGATTTTGT
*
2840022 CGTTGCGAT-TTCA-TTTCG
1 CGTTGCGATAATCATTTTCG
* ** *
2840040 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAATCATTTTCG
2840060 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTTCG
2840080 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTTCG
2840100 CGTTGCGAT
1 CGTTGCGAT
2840109 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
18 8 0.14
19 2 0.03
20 49 0.83
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAATCATTTTCG
Found at i:2840118 original size:20 final size:20
Alignment explanation
Indices: 2840058--2840127 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
2840048 TAGCCATTTC
* *
2840058 CGCGTTGCGATAATCATTTT
1 CGCGTTGCGATAATAAGTTT
* *
2840078 CGCGTTGCGATAATCATTTT
1 CGCGTTGCGATAATAAGTTT
**
2840098 CGCGTTGCGATTTTAAGTTT
1 CGCGTTGCGATAATAAGTTT
*
2840118 CGTGTTGCGA
1 CGCGTTGCGA
2840128 AAGTAAACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATAATAAGTTT
Found at i:2840119 original size:40 final size:39
Alignment explanation
Indices: 2840022--2840127 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
2840012 GCGATTTTGT
* *
2840022 CGTTGCGA-TTTCATTTCGCATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATAACCATTTCCG
** * *
2840060 CGTTGCGATAATCATTTTCGCGTTGCGATAATCATTTTCG
1 CGTTGCGATTTTCA-TTTCGCGTTGCGATAACCATTTCCG
* *
2840100 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTTCA-TTTCGCGTTGCGA
2840128 AAGTAAACTA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 8 0.15
39 3 0.05
40 44 0.80
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.40
Consensus pattern (39 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATAACCATTTCCG
Found at i:2840569 original size:41 final size:42
Alignment explanation
Indices: 2840475--2840560 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
2840465 CTAACCTGTT
* *
2840475 ATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATC
1 ATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATC
* * *
2840517 CTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTGTC
1 ATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATC
2840558 ATC
1 ATC
2840561 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 22 0.58
42 16 0.42
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
ATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATC
Found at i:2842003 original size:14 final size:14
Alignment explanation
Indices: 2841969--2842007 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2841959 TTGATTGTTT
2841969 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2841983 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2841997 TGTTGATTTGT
1 AATTGATTTGT
2842008 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2842153 original size:14 final size:14
Alignment explanation
Indices: 2842134--2842187 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2842124 GAAACTGACT
2842134 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2842148 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
2842167 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2842181 ATCGCAA
1 ATCGCAA
2842188 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:2842236 original size:20 final size:20
Alignment explanation
Indices: 2842211--2842286 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
2842201 TCGCATTACG
*
2842211 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
2842231 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
2842252 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
2842271 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
2842287 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.10
20 35 0.83
21 3 0.07
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:2842247 original size:34 final size:34
Alignment explanation
Indices: 2842199--2842302 Score: 91
Period size: 40 Copynumber: 2.9 Consensus size: 34
2842189 GCGATTTTCA
* *
2842199 TTTCGCATTACGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
2842233 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* * **
2842273 TTTCACGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
2842303 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
34 20 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 26 0.46
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:2842525 original size:20 final size:20
Alignment explanation
Indices: 2842500--2842549 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2842490 TTGAAGATGA
2842500 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
2842520 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
2842540 TTGCGATTTT
1 TTGCGATTTT
2842550 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:2842606 original size:21 final size:20
Alignment explanation
Indices: 2842580--2842627 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2842570 TCAGTATCGT
*
2842580 ATTGCGATTTTCCAAATTCGC
1 ATTGCGA-TTTACAAATTCGC
**
2842601 ATTGCGATTTACTTATTCGC
1 ATTGCGATTTACAAATTCGC
2842621 ATTGCGA
1 ATTGCGA
2842628 ATTAGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTGCGATTTACAAATTCGC
Found at i:2842843 original size:12 final size:12
Alignment explanation
Indices: 2842824--2842857 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2842814 CTCTCCGGCG
2842824 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2842836 ATATCCGTTCCT
1 ACATCCGTTCCT
2842848 ACATCC-TTCC
1 ACATCCGTTCC
2842858 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2843433 original size:24 final size:24
Alignment explanation
Indices: 2843406--2843452 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2843396 AGTCAGTATT
*
2843406 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACC
* *
2843430 CGAACTTTTATATTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
2843453 TCGGATTTTG
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:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:2843656 original size:12 final size:12
Alignment explanation
Indices: 2843639--2843663 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2843629 ATATAATCCT
2843639 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2843651 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2843663 G
1 G
2843664 TCCCCGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2845977 original size:19 final size:18
Alignment explanation
Indices: 2845955--2846041 Score: 64
Period size: 19 Copynumber: 5.1 Consensus size: 18
2845945 GGAAATTACT
2845955 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
2845974 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
2845988 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
**
2846007 ATCGCAA-CG--A-GGGA
1 ATCGCAATCGAAATGAAA
2846021 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
2846040 AT
1 AT
2846042 TTAATTTCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
14 19 0.37
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 21 0.40
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:2846001 original size:33 final size:33
Alignment explanation
Indices: 2845955--2846041 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
2845945 GGAAATTACT
2845955 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2845988 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2846021 ATCGCAATGCGAAATGAAAAT
1 ATCGCAATGCGAAATGAAAAT
2846042 TTAATTTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2846070 original size:14 final size:14
Alignment explanation
Indices: 2846051--2846107 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2846041 TTTAATTTCA
2846051 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2846065 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2846084 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2846098 CGTTGCGATT
1 CGTTGCGATT
2846108 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2846088 original size:33 final size:33
Alignment explanation
Indices: 2846045--2846125 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2846035 TGAAAATTTA
*
2846045 ATTTCACGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
2846078 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
*
2846111 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
2846126 AGTACTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
Found at i:2846089 original size:19 final size:19
Alignment explanation
Indices: 2846065--2846125 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2846055 GCGATTCTCT
2846065 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2846084 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
2846098 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2846117 CATTGCGAT
1 CGTTGCGAT
2846126 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2846253 original size:14 final size:14
Alignment explanation
Indices: 2846234--2846268 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2846224 TCAATTAAAT
2846234 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
2846248 AAATCACCTTTTAC
1 AAATCAACTTTTAC
2846262 AAATCAA
1 AAATCAA
2846269 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:2847690 original size:21 final size:21
Alignment explanation
Indices: 2847624--2847690 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2847614 GTGAATCGGG
*
2847624 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2847644 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2847666 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2847687 CTCT
1 CTCT
2847691 CGAGGAATAA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2848140 original size:90 final size:90
Alignment explanation
Indices: 2847965--2848148 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
2847955 ATTTCAAACT
* *
2847965 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2848030 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
2848058 TTCAACCAAAAGACAAAAAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCAG
1 TTCAACCAAAAGAC-AAAAAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAG
* *
2848122 TATTGGCAGTAACCGAATAAATTTAC
65 AATTGGCAGCAACCGAATAAATTTAC
2848148 T
1 T
2848149 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
90 41 0.48
93 14 0.16
94 31 0.36
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2849880 original size:20 final size:19
Alignment explanation
Indices: 2849835--2850008 Score: 101
Period size: 19 Copynumber: 9.8 Consensus size: 19
2849825 TCTTTTGGTT
2849835 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2849854 GATAATGAGAATCGCAATGCG-
1 GA-AATGAAAATCGCAA--CGA
** *
2849875 GAAATGACTATCACAACGA
1 GAAATGAAAATCGCAACGA
* *
2849894 G--A-G--AATCGTAACGC
1 GAAATGAAAATCGCAACGA
** *
2849908 GAAATGACTATCACAACGA
1 GAAATGAAAATCGCAACGA
*
2849927 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
2849941 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
2849960 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2849979 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
2849993 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2850009 TGCGATTTTG
Statistics
Matches: 119, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
14 28 0.24
16 6 0.05
17 6 0.05
18 2 0.02
19 49 0.41
20 24 0.20
21 2 0.02
22 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2849954 original size:19 final size:19
Alignment explanation
Indices: 2849930--2850013 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
2849920 ACAACGAGAG
2849930 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2849949 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2849968 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2849982 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2850001 AATCGCAATGCGA
1 AATCGCAACGCGA
2850014 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2849958 original size:33 final size:33
Alignment explanation
Indices: 2849860--2849947 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
2849850 ACGAGATAAT
*
2849860 GAGAATCGCAATGCGGAAATGACTATCACAACGA
1 GAGAATCGCAACGC-GAAATGACTATCACAACGA
*
2849894 GAGAATCGTAACGCGAAATGACTATCACAACGA
1 GAGAATCGCAACGCGAAATGACTATCACAACGA
2849927 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
2849948 AAATCGCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 39 0.76
34 12 0.24
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCACAACGA
Found at i:2849960 original size:52 final size:52
Alignment explanation
Indices: 2849897--2850013 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
2849887 ACAACGAGAG
* **
2849897 AATCGTAACGCGAAATGACTATCACAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
*
2849949 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
*
2850001 AATCGCAATGCGA
1 AATCGCAACGCGA
2850014 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAA
Found at i:2850042 original size:19 final size:19
Alignment explanation
Indices: 2850009--2850075 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2849999 AAAATCGCAA
**
2850009 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2850028 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2850047 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2850067 TGCGATTTT
1 TGCGATTTT
2850076 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2850646 original size:20 final size:19
Alignment explanation
Indices: 2850594--2850647 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
2850584 GCTATGTAAA
*
2850594 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGAT-TTAAGAT
*
2850614 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTAAG-AT
2850634 TCGCATTGCGATTT
1 TCGCATTGCGATTT
2850648 TCCTAATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTAAGAT
Found at i:2850662 original size:21 final size:20
Alignment explanation
Indices: 2850612--2850665 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2850602 CGATAGTAAG
*
2850612 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
2850632 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
2850652 AATTCGTATTGCGA
1 -ATTCGCATTGCGA
2850666 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:2850688 original size:21 final size:21
Alignment explanation
Indices: 2850662--2850717 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2850652 AATTCGTATT
*
2850662 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
2850683 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
2850703 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
2850718 TGCATTCCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:2850802 original size:20 final size:21
Alignment explanation
Indices: 2850737--2850809 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
2850727 ATAGTCAGTA
2850737 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
2850758 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
2850779 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
2850799 TCGCATTGCGA
1 TCGCATTGCGA
2850810 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2850824 original size:41 final size:42
Alignment explanation
Indices: 2850736--2850824 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
2850726 GATAGTCAGT
* * *
2850736 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
* ** **
2850778 TTCGCATTGCGA-TTTACTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
2850819 ATCGCA
1 ATCGCA
2850825 ACGCGAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (42 bp):
ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
Found at i:2850851 original size:21 final size:22
Alignment explanation
Indices: 2850799--2850851 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2850789 ATTTACTTAT
2850799 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2850820 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2850841 TCGCATTGCGA
1 TCGCATTGCGA
2850852 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2853891 original size:21 final size:21
Alignment explanation
Indices: 2853840--2853892 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2853830 ATTATGACTA
2853840 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
2853861 TCACGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2853882 TCGCAATGCGA
1 TCGCAATGCGA
2853893 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2853907 original size:20 final size:21
Alignment explanation
Indices: 2853882--2853933 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2853872 TTTTCCCAAT
*
2853882 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2853902 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2853923 TCGCAATGCGA
1 TCGCAATGCGA
2853934 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2853953 original size:20 final size:20
Alignment explanation
Indices: 2853925--2853998 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
2853915 TTGGAAAATC
*
2853925 GCAATGCGATACTGACTATT
1 GCAACGCGATACTGACTATT
* * *
2853945 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATT
2853966 GCAACGCGATACTGACT-TT
1 GCAACGCGATACTGACTATT
*
2853985 CGCAACTCGATACT
1 -GCAACGCGATACT
2853999 TAATTTCGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 23 0.55
21 14 0.33
22 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATT
Found at i:2853964 original size:41 final size:41
Alignment explanation
Indices: 2853919--2854056 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
2853909 GCGAATTTGG
2853919 AAAATCGCAATGCGATACTGACTATT-GCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACT-TTCGCAACGCGATAATAC
* * * *
2853960 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
** * *
2854000 AATTTCGCAACT-CAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAA-TGCGATACTGACTTTCGCAACGCGATAATAC
*
2854041 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
2854057 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
40 34 0.44
41 43 0.56
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:2854005 original size:20 final size:20
Alignment explanation
Indices: 2853964--2854030 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2853954 TAATACAAAA
*
2853964 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGACTT
* *
2853984 TCGCAACTCGATACTTAATT
1 TCGCAACTCGATACTGACTT
*
2854004 TCGCAACTCAATACTGACTT
1 TCGCAACTCGATACTGACTT
2854024 TCGCAAC
1 TCGCAAC
2854031 GAGATAATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (20 bp):
TCGCAACTCGATACTGACTT
Found at i:2854251 original size:22 final size:22
Alignment explanation
Indices: 2854223--2854266 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2854213 CACTCTCTCA
*
2854223 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2854245 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2854267 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2854559 original size:20 final size:20
Alignment explanation
Indices: 2854510--2854567 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2854500 TTTATTCTCT
* **
2854510 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2854530 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2854550 TGTTGCGATTTTCATTTT
1 CGTTGCGATTGTCATTTT
2854568 TAGAAACTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2854759 original size:25 final size:24
Alignment explanation
Indices: 2854705--2854759 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2854695 TGTTTATTAT
* *
2854705 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2854729 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2854755 TGTTT
1 TGTTT
2854760 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2855909 original size:18 final size:18
Alignment explanation
Indices: 2855888--2855935 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2855878 TCCACTTTGG
2855888 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2855906 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2855924 GAGCCATCACCT
1 GAGCCATCACCT
2855936 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2856524 original size:19 final size:20
Alignment explanation
Indices: 2856470--2856535 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2856460 TAGTTTACTT
* *
2856470 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2856490 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2856510 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2856529 TCGCAAC
1 TCGCAAC
2856536 AACAAAATCG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.34
20 25 0.66
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2856563 original size:19 final size:19
Alignment explanation
Indices: 2856509--2856591 Score: 122
Period size: 19 Copynumber: 4.6 Consensus size: 19
2856499 GGAAATGGCT
2856509 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2856528 ATCGCAA--C--AA-CAAA
1 ATCGCAATGCGAAATGAAA
2856542 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2856561 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2856580 ATCGCAATGCGA
1 ATCGCAATGCGA
2856592 TTTGTGTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 1 0.02
17 1 0.02
18 2 0.04
19 41 0.72
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2856622 original size:14 final size:14
Alignment explanation
Indices: 2856603--2856661 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2856593 TTGTGTTTCG
2856603 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2856617 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2856634 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2856650 CGTTGCGATTTT
1 CGTTGCGATTTT
2856662 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2856635 original size:33 final size:33
Alignment explanation
Indices: 2856598--2856677 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
2856588 GCGATTTGTG
*
2856598 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2856631 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2856664 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2856678 AGTCATTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2856689 original size:20 final size:20
Alignment explanation
Indices: 2856650--2856736 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
2856640 GCGATTTTGT
**
2856650 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
*
2856669 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2856689 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
2856709 CGTTGCGAAAGTAAGTTTCG
1 CGTTGCGATAGTCATTTTCG
*
2856729 TGTTGCGA
1 CGTTGCGA
2856737 AAGTAAACTA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 11 0.19
20 48 0.81
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2857136 original size:21 final size:20
Alignment explanation
Indices: 2857084--2857144 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
2857074 GACTCACCTG
2857084 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
2857104 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
2857125 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
2857145 CTACCTTTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:2858616 original size:14 final size:14
Alignment explanation
Indices: 2858582--2858620 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2858572 TTGATTGTTT
2858582 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2858596 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2858610 TGTTGATTTGT
1 AATTGATTTGT
2858621 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2858840 original size:12 final size:12
Alignment explanation
Indices: 2858821--2858854 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2858811 CTCTCTGGCG
2858821 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2858833 ATATCCGTTCCT
1 ACATCCGTTCCT
2858845 ACATCC-TTCC
1 ACATCCGTTCC
2858855 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2859434 original size:24 final size:24
Alignment explanation
Indices: 2859407--2859462 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2859397 CAGTATTCGA
*
2859407 AATTTGATCTTGGTCAATACCCGG
1 AATTTGATATTGGTCAATACCCGG
*
2859431 AATTTGATATTGGTCAATACTCGG
1 AATTTGATATTGGTCAATACCCGG
*
2859455 ATTTTGAT
1 AATTTGAT
2859463 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTTGATATTGGTCAATACCCGG
Found at i:2860946 original size:42 final size:42
Alignment explanation
Indices: 2860900--2860979 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2860890 CGATGACAGT
* * *
2860900 GGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGAGGACTCTCGAGGAATGATAGG
* * *
2860942 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGAGGACTCTCGAGGAATGA
2860980 CAGGTGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGAGGACTCTCGAGGAATGATAGG
Found at i:2861376 original size:91 final size:90
Alignment explanation
Indices: 2861201--2861385 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
2861191 ATTTCAAACT
*
2861201 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2861266 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
2861294 TTCAACTAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
2861358 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
2861385 T
1 T
2861386 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2863158 original size:33 final size:33
Alignment explanation
Indices: 2863099--2863192 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2863089 AGATAATAAA
2863099 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
*
2863133 AATCGCAACGCGAAATGACTGTCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
2863166 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
2863193 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:2863190 original size:19 final size:19
Alignment explanation
Indices: 2863071--2863197 Score: 67
Period size: 20 Copynumber: 7.1 Consensus size: 19
2863061 TCTTTTGGTT
* *
2863071 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
*
2863090 GATAATAAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2863110 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2863128 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
***
2863144 GAAATGACTGTCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2863161 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2863177 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2863196 GA
1 GA
2863198 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
14 17 0.21
15 2 0.03
16 4 0.05
17 3 0.04
18 3 0.04
19 24 0.30
20 25 0.31
21 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2863226 original size:19 final size:19
Alignment explanation
Indices: 2863193--2863263 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
2863183 AAAATCGCAA
**
2863193 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
2863212 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2863231 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTCATTT-CGCGT
2863251 TGCGATTTTCATT
1 TGCGATTTTCATT
2863264 CTCGAAACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2863868 original size:20 final size:20
Alignment explanation
Indices: 2863772--2863889 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
2863762 ATGGCGCTAT
2863772 GTAAATCGCATTGCG-ATA-
1 GTAAATCGCATTGCGAATAC
* *
2863790 GTAAGATTCGTATTGCGATTTAC
1 GTAA-A-TCGCATTGCGA-ATAC
* *
2863813 GT-ATTCGCATTGCGAATTAT
1 GTAAATCGCATTGCGAA-TAC
* **
2863833 GAAAATCGCAACGCGAATAC
1 GTAAATCGCATTGCGAATAC
*
2863853 GTAAATCGCATTGCGAATTAG
1 GTAAATCGCATTGCGAA-TAC
* *
2863874 GAAAATTGCATTGCGA
1 GTAAATCGCATTGCGA
2863890 TAGTCAGTAT
Statistics
Matches: 75, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
18 4 0.05
19 1 0.01
20 38 0.51
21 27 0.36
22 3 0.04
23 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
GTAAATCGCATTGCGAATAC
Found at i:2863884 original size:21 final size:21
Alignment explanation
Indices: 2863817--2863971 Score: 104
Period size: 21 Copynumber: 7.5 Consensus size: 21
2863807 ATTTACGTAT
*
2863817 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTACGAAAA
** *
2863838 TCGCAACGCGAA-TACGTAAA
1 TCGCATTGCGAATTACGAAAA
*
2863858 TCGCATTGCGAATTAGGAAAA
1 TCGCATTGCGAATTACGAAAA
* * **
2863879 TTGCATTGCGATAGT-C-AGTA
1 TCGCATTGCGA-ATTACGAAAA
* ** *
2863899 TCGCATTGCGATTTAC-TTAT
1 TCGCATTGCGAATTACGAAAA
**
2863919 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTACGAAAA
**
2863940 TCGCAACGCGAAATTA-GAAAA
1 TCGCATTGCG-AATTACGAAAA
2863961 TCGCATTGCGA
1 TCGCATTGCGA
2863972 TTGTCATAAT
Statistics
Matches: 98, Mismatches: 31, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.44
21 48 0.49
22 6 0.06
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGAATTACGAAAA
Found at i:2863991 original size:102 final size:102
Alignment explanation
Indices: 2863774--2863971 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 102
2863764 GGCGCTATGT
* *
2863774 AAATCGCATTGCGATAGTAAGATTCGTATTGCGATTTACGTATTCGCATTGCGAATTATGAAAAT
1 AAATCGCATTGCGATAGTAAGATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAAT
* *
2863839 CGCAACGCGAATACGTAAATCGCATTGCGAATTAGGA
66 CGCAACGCGAATACGAAAATCGCATTGCGAATTAGCA
* * * *
2863876 AAATTGCATTGCGATAGTCAG-TATCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAA
1 AAATCGCATTGCGATAGTAAGAT-TCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAA
2863940 TCGCAACGCGAAATTA-GAAAATCGCATTGCGA
65 TCGCAACGCG-AA-TACGAAAATCGCATTGCGA
2863972 TTGTCATAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
101 1 0.01
102 66 0.77
103 17 0.20
104 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (102 bp):
AAATCGCATTGCGATAGTAAGATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAAT
CGCAACGCGAATACGAAAATCGCATTGCGAATTAGCA
Found at i:2865227 original size:20 final size:20
Alignment explanation
Indices: 2865182--2865239 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2865172 TTAAAGATTA
* *
2865182 TAAATTTAAATAAGTTAT-TT
1 TAAATTT-AATAAATTATAAT
*
2865202 TCAATTTAATAAATTATAAT
1 TAAATTTAATAAATTATAAT
* *
2865222 TAAATTAAATATATTATA
1 TAAATTTAATAAATTATA
2865240 TCAGCATACA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATTTAATAAATTATAAT
Found at i:2865414 original size:2 final size:2
Alignment explanation
Indices: 2865407--2865432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2865397 ATTTATTCAA
2865407 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
2865433 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2867284 original size:8 final size:8
Alignment explanation
Indices: 2867273--2867315 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2867263 TGTTATCATT
2867273 TTATTTAA
1 TTATTTAA
2867281 TTATTTAAA
1 TTATTT-AA
2867290 TTATTTAA
1 TTATTTAA
*
2867298 -TATTTTAT
1 TTA-TTTAA
2867306 TTATTTAA
1 TTATTTAA
2867314 TT
1 TT
2867316 TTTTTACAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 18 0.60
9 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATTTAA
Found at i:2869690 original size:26 final size:25
Alignment explanation
Indices: 2869651--2869700 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
2869641 GATTATTTTG
2869651 TTTATTACCATTTAATATCAGTTAA
1 TTTATTACCATTTAATATCAGTTAA
*
2869676 TTTATTTATCATTTAATATCAGTTA
1 TTTA-TTACCATTTAATATCAGTTA
2869701 TTGTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTATTACCATTTAATATCAGTTAA
Found at i:2871923 original size:76 final size:77
Alignment explanation
Indices: 2871764--2871973 Score: 273
Period size: 76 Copynumber: 2.8 Consensus size: 77
2871754 CAAAGCCAAA
* * * * **
2871764 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAATCGA-TCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2871828 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
2871841 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
2871906 TTT-TCTCCGAG
66 TTTGGCCCCGAG
* * * *
2871917 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
2871974 TGTACAACGG
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 19 0.16
76 58 0.49
77 41 0.35
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:2877812 original size:21 final size:21
Alignment explanation
Indices: 2877786--2877825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2877776 CCCCCTTTGA
*
2877786 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2877807 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2877826 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2880550 original size:76 final size:77
Alignment explanation
Indices: 2880391--2880600 Score: 282
Period size: 76 Copynumber: 2.8 Consensus size: 77
2880381 CAAAGCCAAA
* * * **
2880391 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGA-TCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2880455 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
2880468 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
2880533 TTT-TCTCCGAG
66 TTTGGCCCCGAG
* * * *
2880544 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
2880601 TGTACAACGG
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
75 19 0.16
76 59 0.50
77 41 0.34
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:2882816 original size:22 final size:22
Alignment explanation
Indices: 2882791--2882837 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2882781 ACAATAATTT
*
2882791 TTTTACACATAAACGTAAATCA
1 TTTTACACATAAACGTAAATAA
*
2882813 TTTTACATATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
2882835 TTT
1 TTT
2882838 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:2890468 original size:12 final size:12
Alignment explanation
Indices: 2890453--2890498 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2890443 CGGGTTTTTT
*
2890453 ACCGGATAAAAA
1 ACCGGTTAAAAA
2890465 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
2890480 ACCGGTTAAAAA
1 ACCGGTTAAAAA
2890492 ACCGGTT
1 ACCGGTT
2890499 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:2890480 original size:15 final size:13
Alignment explanation
Indices: 2890459--2890499 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
2890449 TTTTACCGGA
2890459 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2890472 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
2890486 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2890499 T
1 T
2890500 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:2892817 original size:21 final size:21
Alignment explanation
Indices: 2892793--2892832 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2892783 TTTATTTTAT
2892793 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2892814 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2892833 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2892884 original size:33 final size:33
Alignment explanation
Indices: 2892827--2892924 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2892817 TTTGTTTCAA
2892827 TTATCGAACTT-GAAG-TTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2892858 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2892891 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2892924 T
1 T
2892925 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 11 0.18
32 4 0.06
33 47 0.76
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2892953 original size:13 final size:13
Alignment explanation
Indices: 2892910--2892964 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2892900 TTGGAAGTAT
2892910 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2892923 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2892937 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2892950 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2892963 TT
1 TT
2892965 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2893186 original size:21 final size:21
Alignment explanation
Indices: 2893160--2893216 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2893150 TGGAGCGTGG
*
2893160 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
2893181 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
2893202 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
2893217 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:2893406 original size:15 final size:15
Alignment explanation
Indices: 2893381--2893419 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2893371 ATCTGGAATA
*
2893381 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2893396 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
2893411 TTAAAACCG
1 TTAAAACCG
2893420 AAACCGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2898010 original size:2 final size:2
Alignment explanation
Indices: 2898005--2898032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2897995 TTAACATTAA
2898005 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
2898033 TATTCTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2898068 original size:28 final size:29
Alignment explanation
Indices: 2898025--2898160 Score: 134
Period size: 28 Copynumber: 4.6 Consensus size: 29
2898015 ATATATATAT
*
2898025 ATATATATTATTCTTATATTAACTTAAAA
1 ATATATTTTATTCTTATATTAACTTAAAA
*
2898054 ATAT-TTTTATTCTTATTTTAACTTAAAA
1 ATATATTTTATTCTTATATTAACTTAAAA
* *
2898082 ATATATTTAAAATTTTTATATTAACTTAGAAA
1 ATATATTT--TATTCTTATATTAACTTA-AAA
** *
2898114 ATA-A-TTTATTCTTAGCTTATCTTAAATA
1 ATATATTTTATTCTTATATTAACTTAAA-A
*
2898142 TTTATATTTTATTCTTATA
1 -ATATATTTTATTCTTATA
2898161 ATATTTTAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.02
28 40 0.47
29 9 0.10
30 3 0.03
31 26 0.30
32 6 0.07
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATATTTTATTCTTATATTAACTTAAAA
Found at i:2898086 original size:59 final size:59
Alignment explanation
Indices: 2898023--2898160 Score: 161
Period size: 59 Copynumber: 2.3 Consensus size: 59
2898013 ATATATATAT
* **
2898023 ATATATATATTATTCTTATATTAACTTA-AAAATATTTTTATTCTTATTTTAACTTAAAA
1 ATATATATATTATTCTTATATTAACTTAGAAAATA-ATTTATTCTTAGCTTAACTTAAAA
* ** * * *
2898082 ATATATTTAAAATTTTTATATTAACTTAGAAAATAATTTATTCTTAGCTTATCTTAAAT
1 ATATATATATTATTCTTATATTAACTTAGAAAATAATTTATTCTTAGCTTAACTTAAAA
* *
2898141 ATTTATATTTTATTCTTATA
1 ATATATATATTATTCTTATA
2898161 ATATTTTAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
59 57 0.90
60 6 0.10
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (59 bp):
ATATATATATTATTCTTATATTAACTTAGAAAATAATTTATTCTTAGCTTAACTTAAAA
Found at i:2898217 original size:29 final size:29
Alignment explanation
Indices: 2898161--2898237 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
2898151 TATTCTTATA
* * * * *
2898161 ATATTTTAAAATTAAGATAAGAATAAAAC
1 ATATTTTTAAATTAAAACAAAAACAAAAC
*
2898190 ATATTTTTAAATTAAAACAAAAACAAAAT
1 ATATTTTTAAATTAAAACAAAAACAAAAC
*
2898219 ATACATTTTTAAACTAAAA
1 AT--ATTTTTAAATTAAAA
2898238 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 25 0.64
31 14 0.36
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (29 bp):
ATATTTTTAAATTAAAACAAAAACAAAAC
Found at i:2898283 original size:31 final size:32
Alignment explanation
Indices: 2898177--2898285 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 32
2898167 TAAAATTAAG
* * *
2898177 ATAAGAATAAAACATA-TTTTTAAATTAAAAC
1 ATAAGAATAAAATATACATTTTAAATTAAAAT
* *
2898208 A-AA-AACAAAATATACATTTTTAAACTAAAATT
1 ATAAGAATAAAATATACA-TTTTAAATTAAAA-T
* * *
2898240 AAAAAAATAAAATATACATTTTAAGTTAAAA-
1 ATAAGAATAAAATATACATTTTAAATTAAAAT
2898271 ATAAGAATAAAATAT
1 ATAAGAATAAAATAT
2898286 TTAAAAATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
29 9 0.14
30 2 0.03
31 26 0.41
32 1 0.02
33 13 0.21
34 12 0.19
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (32 bp):
ATAAGAATAAAATATACATTTTAAATTAAAAT
Found at i:2904844 original size:16 final size:16
Alignment explanation
Indices: 2904823--2904865 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2904813 AATTTTTTTA
2904823 TTATAAAAAATAGAAG
1 TTATAAAAAATAGAAG
2904839 TTATAAAAAATAGAAG
1 TTATAAAAAATAGAAG
* *
2904855 GTAGAAAAAAT
1 TTATAAAAAAT
2904866 TGATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (16 bp):
TTATAAAAAATAGAAG
Found at i:2913662 original size:24 final size:24
Alignment explanation
Indices: 2913635--2913727 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
2913625 ATAATCCAGG
2913635 TCAAAATCCAGGTCAAGTATTCGA
1 TCAAAATCCAGGTCAAGTATTCGA
*
2913659 TCAAAATCCATGTCAAGTA-TCTGA
1 TCAAAATCCAGGTCAAGTATTC-GA
* * *
2913683 TCAGAATCCAAGTCAAGTATCCGA
1 TCAAAATCCAGGTCAAGTATTCGA
* *
2913707 TCAGAATCCAGGTCAGGTATT
1 TCAAAATCCAGGTCAAGTATT
2913728 ATAATAGAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
23 2 0.03
24 57 0.95
25 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
TCAAAATCCAGGTCAAGTATTCGA
Found at i:2916253 original size:18 final size:18
Alignment explanation
Indices: 2916204--2916258 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
2916194 AAAACTGGTC
* * *
2916204 AACGGGTCAGGTCAGGTC
1 AACGGGTCGGGTCGGGTT
* *
2916222 AACAGGTTGGGTCGGGTT
1 AACGGGTCGGGTCGGGTT
2916240 AACGGGTCGGGTCGGGTT
1 AACGGGTCGGGTCGGGTT
2916258 A
1 A
2916259 TGACCGATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.44, T:0.22
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTT
Found at i:2918394 original size:12 final size:12
Alignment explanation
Indices: 2918377--2918437 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
2918367 AAACATAATC
2918377 CAGGTCAAGTAT
1 CAGGTCAAGTAT
*
2918389 CAGGTCAA-AAT
1 CAGGTCAAGTAT
2918400 CCAGGTCAAGTAT
1 -CAGGTCAAGTAT
* * *
2918413 CCGATC-AGAAT
1 CAGGTCAAGTAT
2918424 CCAGGTCAAGTAT
1 -CAGGTCAAGTAT
2918437 C
1 C
2918438 CGATCAGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 6 0.16
12 25 0.68
13 6 0.16
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (12 bp):
CAGGTCAAGTAT
Found at i:2918485 original size:24 final size:24
Alignment explanation
Indices: 2918373--2918485 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
2918363 ATCAAAACAT
* *
2918373 AATCCAGGTCAAGTA-TCAGGTCAA
1 AATCCAGGTCAAGTATTC-GATCAG
*
2918397 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
2918421 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
2918445 AATCCAGGTTAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
2918469 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
2918486 ATAATAGAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
24 80 0.99
25 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCGATCAG
Found at i:2920998 original size:18 final size:18
Alignment explanation
Indices: 2920975--2921009 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2920965 ACGATCAACT
*
2920975 GGTCGGGTTAACGGGTCA
1 GGTCGGGTCAACGGGTCA
2920993 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
2921010 GGGTTATGAC
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:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCA
Found at i:2922554 original size:13 final size:12
Alignment explanation
Indices: 2922535--2922565 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
2922525 CGCCGGTCAA
2922535 CGGTCAACGGGT
1 CGGTCAACGGGT
2922547 CAGGTCAACGGGT
1 C-GGTCAACGGGT
2922560 CGGTCA
1 CGGTCA
2922566 GGTCGGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.19, C:0.26, G:0.39, T:0.16
Consensus pattern (12 bp):
CGGTCAACGGGT
Found at i:2930877 original size:21 final size:22
Alignment explanation
Indices: 2930842--2930903 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
2930832 AGAATTTTGG
*
2930842 TAAAAGGATATTTAAA-TAATAA
1 TAAAAGGAGATTTAAAGTAA-AA
2930864 TAAAA-GAGATTTAAAGTAAAA
1 TAAAAGGAGATTTAAAGTAAAA
**
2930885 TAAAGAAAAGATTTAAAGT
1 TAAA-AGGAGATTTAAAGT
2930904 TGAAAATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 15 0.43
22 9 0.26
23 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (22 bp):
TAAAAGGAGATTTAAAGTAAAA
Found at i:2934719 original size:12 final size:12
Alignment explanation
Indices: 2934702--2934727 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2934692 GTATAAGTGT
2934702 TATACAAGATAA
1 TATACAAGATAA
2934714 TATACAAGATAA
1 TATACAAGATAA
2934726 TA
1 TA
2934728 AAGTTTGAGG
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:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
TATACAAGATAA
Found at i:2936147 original size:17 final size:17
Alignment explanation
Indices: 2936125--2936177 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
2936115 ATGTTGCGGA
*
2936125 AGACAACTGTCGGATAG
1 AGACAACTATCGGATAG
2936142 AGACAACTATCGGATAG
1 AGACAACTATCGGATAG
2936159 AGACAACTATCGGATAG
1 AGACAACTATCGGATAG
2936176 AG
1 AG
2936178 TAAAATCGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (17 bp):
AGACAACTATCGGATAG
Found at i:2939083 original size:43 final size:39
Alignment explanation
Indices: 2938990--2939069 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
2938980 AATAATTATT
*
2938990 ATTGTATTGTTTAGAGGGCTATGAGAAAGAAAATTAAGC
1 ATTGCATTGTTTAGAGGGCTATGAGAAAGAAAATTAAGC
*
2939029 ATTGCATTGTTTAGAGGGCTATGAGATAGAAAATTAAGC
1 ATTGCATTGTTTAGAGGGCTATGAGAAAGAAAATTAAGC
2939068 AT
1 AT
2939070 CTTAGGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (39 bp):
ATTGCATTGTTTAGAGGGCTATGAGAAAGAAAATTAAGC
Found at i:2939999 original size:24 final size:24
Alignment explanation
Indices: 2939956--2940029 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
2939946 CGAACAACTC
* *
2939956 TAAATTATTTAAAAAAATTAAATTT
1 TAAATTA-TTAATAATATTAAATTT
*
2939981 TAAATTATTAATAATATTAATTTT
1 TAAATTATTAATAATATTAAATTT
2940005 TAAATTATTAATAATATTAATATTT
1 TAAATTATTAATAATATTAA-ATTT
2940030 ATATACTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 34 0.77
25 10 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATTATTAATAATATTAAATTT
Found at i:2942199 original size:150 final size:150
Alignment explanation
Indices: 2941924--2942517 Score: 716
Period size: 150 Copynumber: 4.0 Consensus size: 150
2941914 ATTCATTCGT
* * ** * * * * **
2941924 GGATTGCATTCCCATCTCCAATGGCTTCAACAAATCTGAAACTACTCCACCCTCCACTACATCAG
1 GGATTGCATTCCCATCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTGG
* * *
2941989 TTCTGCATCTT-GAGCCTTCTCCATCAGCTATGACAT-TTTTTC-CACATTTTGCTTTGCCAGGA
66 TTTTGTAT-TTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACACA--TTGCTTTACCAGGA
* * *
2942051 TAATGGGAACCGATTGCACTC-G
128 TAATGAGAACCAATTCCACTCTG
* * * * * * * * * *
2942073 AGGATTGAATTCCCATCTTCTGAGGCGCCATCAAACCTAAAACTACTCCACCCA-GCTCTACAAT
1 -GGATTGCATTCCCATCTGCAGTGGCGACAACAAATCTGAAACTACCCCA-CCATGCTCTACATT
* * ** *
2942137 GG-TTCGATATTTAGAGCCTTCTCCATCACCTAAAACATCTTTTTCACATATTGCTTTACCAGGA
64 GGTTTTG-TATTTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACACATTGCTTTACCAGGA
*
2942201 TAATGAGAACCAATTCCACACTG
128 TAATGAGAACCAATTCCACTCTG
2942224 GGATTGCATT-CCAGTCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTG
1 GGATTGCATTCCCA-TCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTG
* *
2942288 GTTTTGTATTTAGAGCCTTGTCCATCAGCTATGACATCTTTTTCACACATTGCTTTATCAGGATA
65 GTTTTGTATTTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACACATTGCTTTACCAGGATA
* *
2942353 ATGAGATCCAAGTCCACTCTG
130 ATGAGAACCAATTCCACTCTG
*
2942374 GGATTGCATTCCCGTCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTGG
1 GGATTGCATTCCCATCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTGG
* * *
2942439 TTTTGTATCTAGAGCCTTGTCCATCAGCTATGACATCTTTTTCACACATTGCTTTATCAGGATAA
66 TTTTGTATTTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACACATTGCTTTACCAGGATAA
2942504 TGAGAACCAATTCC
131 TGAGAACCAATTCC
2942518 GGTCATGTAG
Statistics
Matches: 382, Mismatches: 52, Indels: 20
0.84 0.11 0.04
Matches are distributed among these distances:
149 10 0.03
150 355 0.93
151 14 0.04
152 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (150 bp):
GGATTGCATTCCCATCTGCAGTGGCGACAACAAATCTGAAACTACCCCACCATGCTCTACATTGG
TTTTGTATTTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACACATTGCTTTACCAGGATAA
TGAGAACCAATTCCACTCTG
Found at i:2943717 original size:36 final size:37
Alignment explanation
Indices: 2943675--2943766 Score: 132
Period size: 36 Copynumber: 2.5 Consensus size: 37
2943665 ACTCACAATT
* *
2943675 AATAAACTATCAATATTGCTCATAATCCTG-CTAATA
1 AATAAACTATCAATATTGCTCATAATCCTGTATAACA
*
2943711 AATAAACTATCAATATTGCTCATAATTCTGTTATAACA
1 AATAAACTATCAATATTGCTCATAATCCTG-TATAACA
*
2943749 AATAAACTATCAAGATTG
1 AATAAACTATCAATATTG
2943767 GAACAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 29 0.58
38 21 0.42
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (37 bp):
AATAAACTATCAATATTGCTCATAATCCTGTATAACA
Found at i:2951523 original size:16 final size:16
Alignment explanation
Indices: 2951504--2951551 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
2951494 TTTGGGTTAA
2951504 TTTCGGTTCGGATTGC
1 TTTCGGTTCGGATTGC
2951520 TTTCGGTTCGGATTGC
1 TTTCGGTTCGGATTGC
* *
2951536 TTTTGGTTCGGGTTGC
1 TTTCGGTTCGGATTGC
2951552 GTTTGGTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.04, C:0.17, G:0.33, T:0.46
Consensus pattern (16 bp):
TTTCGGTTCGGATTGC
Found at i:2951556 original size:16 final size:15
Alignment explanation
Indices: 2951508--2951559 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
2951498 GGTTAATTTC
2951508 GGTTCGGATTGCTTT
1 GGTTCGGATTGCTTT
2951523 CGGTTCGGATTGCTTTT
1 -GGTTCGGATTGC-TTT
*
2951540 GGTTCGGGTTGCGTTT
1 GGTTCGGATTGC-TTT
2951556 GGTT
1 GGTT
2951560 AGGGTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 30 0.91
17 3 0.09
ACGTcount: A:0.04, C:0.13, G:0.37, T:0.46
Consensus pattern (15 bp):
GGTTCGGATTGCTTT
Found at i:2951564 original size:16 final size:16
Alignment explanation
Indices: 2951532--2951565 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2951522 TCGGTTCGGA
* *
2951532 TTGCTTTTGGTTCGGG
1 TTGCGTTTGGTTAGGG
2951548 TTGCGTTTGGTTAGGG
1 TTGCGTTTGGTTAGGG
2951564 TT
1 TT
2951566 AATTTAGGCT
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:0.03, C:0.09, G:0.38, T:0.50
Consensus pattern (16 bp):
TTGCGTTTGGTTAGGG
Found at i:2951691 original size:14 final size:14
Alignment explanation
Indices: 2951672--2951705 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2951662 TGGTATTGGG
2951672 TCGGGTAAATCA-GT
1 TCGGGT-AATCATGT
2951686 TCGGGTAATCATGT
1 TCGGGTAATCATGT
2951700 TCGGGT
1 TCGGGT
2951706 CAAGTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (14 bp):
TCGGGTAATCATGT
Found at i:2957117 original size:19 final size:19
Alignment explanation
Indices: 2957085--2957130 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2957075 TTGCAAAGAA
2957085 TCGATCCC-GTGAAAAGGG
1 TCGATCCCTGTGAAAAGGG
2957103 TCGATCCCTGTGAAAAGGG
1 TCGATCCCTGTGAAAAGGG
2957122 TCGATCCCT
1 TCGATCCCT
2957131 TTCAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (19 bp):
TCGATCCCTGTGAAAAGGG
Found at i:2964404 original size:26 final size:26
Alignment explanation
Indices: 2964374--2964442 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
2964364 TGAAAAAGCC
2964374 TGAGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGATGCATCAAATGCAT
2964400 TGAGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGATGCATCAAATGCAT
2964426 TGAGTGCATCGATGCAT
1 TGAGTGCATCGATGCAT
2964443 GGTATGTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
TGAGTGCATCGATGCATCAAATGCAT
Found at i:2964414 original size:17 final size:17
Alignment explanation
Indices: 2964375--2964461 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 17
2964365 GAAAAAGCCT
2964375 GAGTGCATCGATGCATC
1 GAGTGCATCGATGCATC
* * *
2964392 AAATGCATTGAGTGCATC
1 GAGTGCATCGA-TGCATC
* *
2964410 GA-TGCATCAAATGCATT
1 GAGTGCATC-GATGCATC
*
2964427 GAGTGCATCGATGCATG
1 GAGTGCATCGATGCATC
2964444 GTATGTGCATCGATGCAT
1 G-A-GTGCATCGATGCAT
2964462 AAAATGCAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 27 0.48
18 15 0.27
19 14 0.25
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (17 bp):
GAGTGCATCGATGCATC
Found at i:2964433 original size:9 final size:9
Alignment explanation
Indices: 2964375--2964461 Score: 65
Period size: 9 Copynumber: 9.9 Consensus size: 9
2964365 GAAAAAGCCT
2964375 GAGTGCATC
1 GAGTGCATC
2964384 GA-TGCATC
1 GAGTGCATC
* * *
2964392 AAATGCATT
1 GAGTGCATC
2964401 GAGTGCATC
1 GAGTGCATC
2964410 GA-TGCATC
1 GAGTGCATC
* * *
2964418 AAATGCATT
1 GAGTGCATC
2964427 GAGTGCATC
1 GAGTGCATC
*
2964436 GA-TGCATG
1 GAGTGCATC
2964444 GTATGTGCATC
1 G-A-GTGCATC
2964455 GA-TGCAT
1 GAGTGCAT
2964462 AAAATGCAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
8 25 0.41
9 29 0.48
10 1 0.02
11 6 0.10
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (9 bp):
GAGTGCATC
Found at i:2964835 original size:13 final size:13
Alignment explanation
Indices: 2964817--2964848 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2964807 TAAGATTTTC
2964817 TTTGAAAACCAAG
1 TTTGAAAACCAAG
2964830 TTTGAAAACCAAG
1 TTTGAAAACCAAG
2964843 TTTGAA
1 TTTGAA
2964849 GTTACTCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (13 bp):
TTTGAAAACCAAG
Found at i:2967014 original size:12 final size:12
Alignment explanation
Indices: 2966997--2967026 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2966987 ATTTAGAGTA
2966997 AGAGAAGAATTT
1 AGAGAAGAATTT
2967009 AGAGAAGAATTT
1 AGAGAAGAATTT
2967021 AGAGAA
1 AGAGAA
2967027 TAAGAGAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (12 bp):
AGAGAAGAATTT
Found at i:2967205 original size:16 final size:16
Alignment explanation
Indices: 2967184--2967221 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
2967174 ATGATGAATC
2967184 GATGCACATTCAAAGG
1 GATGCACATTCAAAGG
2967200 GATGCACATTCAAAGG
1 GATGCACATTCAAAGG
2967216 GATGCA
1 GATGCA
2967222 TCGATGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (16 bp):
GATGCACATTCAAAGG
Found at i:2974994 original size:33 final size:33
Alignment explanation
Indices: 2974952--2975022 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2974942 AGTGTTTGGA
*
2974952 GTGTTTAGTTAAGTGTAACTTGCTAAACTAAAT
1 GTGTTTAGTTAAGTGTAACTTGCTAAACTAAAC
*
2974985 GTGTTTAGTTAAGTGTAACTTGGTAAACTAAAC
1 GTGTTTAGTTAAGTGTAACTTGCTAAACTAAAC
2975018 GTGTT
1 GTGTT
2975023 AGACTCTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (33 bp):
GTGTTTAGTTAAGTGTAACTTGCTAAACTAAAC
Found at i:2975384 original size:21 final size:21
Alignment explanation
Indices: 2975347--2975401 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
2975337 TCTGTTTTGC
* **
2975347 AAAGAATTGAT-CCCTGTTCA
1 AAAGGATTGATCCCCTGTGAA
2975367 AAAGGATTGATCCCCTGTGAA
1 AAAGGATTGATCCCCTGTGAA
*
2975388 AAAGGATCGATCCC
1 AAAGGATTGATCCC
2975402 TTCATTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AAAGGATTGATCCCCTGTGAA
Found at i:2978686 original size:23 final size:22
Alignment explanation
Indices: 2978649--2978693 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2978639 AATTATAAAT
* *
2978649 GAAGATGTTGGTGGTCTTGATG
1 GAAGATGTTGATGGTATTGATG
2978671 GAAGATGGTTGATGGTATTGATG
1 GAAGAT-GTTGATGGTATTGATG
2978694 TTGTATGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (22 bp):
GAAGATGTTGATGGTATTGATG
Found at i:2979911 original size:20 final size:20
Alignment explanation
Indices: 2979886--2979925 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2979876 AAGTTTCTCT
2979886 CCTTGAAAGGCTGGAGATGC
1 CCTTGAAAGGCTGGAGATGC
2979906 CCTTGAAAGGCTGGAGATGC
1 CCTTGAAAGGCTGGAGATGC
2979926 AAAGTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (20 bp):
CCTTGAAAGGCTGGAGATGC
Found at i:2981377 original size:15 final size:15
Alignment explanation
Indices: 2981357--2981438 Score: 69
Period size: 15 Copynumber: 5.5 Consensus size: 15
2981347 TGAATAACAC
*
2981357 AAAGAATATAGAAAT
1 AAAGAAAATAGAAAT
2981372 AAAGAAAATAGAAAT
1 AAAGAAAATAGAAAT
* * *
2981387 AAAGCAAAAAATAAAA
1 AAAG-AAAATAGAAAT
* *
2981403 AAAGTAAATA-AGAT
1 AAAGAAAATAGAAAT
* *
2981417 AAATAAAGTA-AAAT
1 AAAGAAAATAGAAAT
2981431 AAAGAAAA
1 AAAGAAAA
2981439 AAATAAAATA
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
14 18 0.35
15 22 0.42
16 12 0.23
ACGTcount: A:0.73, C:0.01, G:0.11, T:0.15
Consensus pattern (15 bp):
AAAGAAAATAGAAAT
Done.