Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 31
Found at i:995251 original size:14 final size:14
Alignment explanation
Indices: 995232--995267 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
995222 ATTGTTTAAT
995232 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
995246 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
995260 TGATTTGT
1 TGATTTGT
995268 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:995389 original size:19 final size:19
Alignment explanation
Indices: 995365--995418 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
995355 ATCGCAACGA
*
995365 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
995384 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
995403 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
995419 TTTTCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:995462 original size:20 final size:20
Alignment explanation
Indices: 995437--995494 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
995427 TCGCATTGCG
995437 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
995457 ATTTTCACGTTACGATAGCC
1 ATTTTCGCGTTGCGATAGCC
995477 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
995495 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:996574 original size:24 final size:24
Alignment explanation
Indices: 996547--996600 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
996537 GTATTTGAAA
* *
996547 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
996571 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
996595 TTTGAT
1 TTTGAT
996601 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:999113 original size:19 final size:19
Alignment explanation
Indices: 999091--999221 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
999081 GGAAATTACT
999091 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
999110 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
999124 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
999143 ATTGCAATGC----T-AAT
1 ATCGCAATGCGAAATGAAA
*
999157 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
999176 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
999190 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
999209 ATCGCAACGCGAA
1 ATCGCAATGCGAA
999222 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 29 0.35
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 41 0.49
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:999133 original size:33 final size:33
Alignment explanation
Indices: 999091--999217 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
999081 GGAAATTACT
999091 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
999124 ATCGCAATGCGAAATGAAAATTGCAATGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
999156 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
999190 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
999218 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:999198 original size:66 final size:66
Alignment explanation
Indices: 999092--999224 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
999082 GAAATTACTA
* * *
999092 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
999157 T
66 T
*
999158 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
999223 T
66 T
999224 T
1 T
999225 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:999239 original size:19 final size:20
Alignment explanation
Indices: 999217--999259 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
999207 AAATCGCAAC
999217 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
999236 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
999256 GCGA
1 GCGA
999260 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:999419 original size:14 final size:14
Alignment explanation
Indices: 999400--999436 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
999390 CATCAATTAA
999400 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
999414 ACAAATCACCTTTT
1 ACAAATCAACTTTT
999428 ACAAATCAA
1 ACAAATCAA
999437 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1000859 original size:21 final size:21
Alignment explanation
Indices: 1000793--1000859 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1000783 GTGAATCGGG
*
1000793 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1000813 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1000835 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1000856 CTCT
1 CTCT
1000860 CGAGGAATGA
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:1000878 original size:42 final size:41
Alignment explanation
Indices: 1000793--1000915 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1000783 GTGAATCGGG
* * * *
1000793 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1000835 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1000877 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1000916 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1003037 original size:19 final size:19
Alignment explanation
Indices: 1002920--1003084 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
1002910 TCTTTTGGTT
*
1002920 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1002939 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1002959 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1002977 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1002993 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1003011 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1003026 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1003045 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
1003064 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1003083 GA
1 GA
1003085 TTTTTGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 61 0.51
20 27 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1003062 original size:38 final size:36
Alignment explanation
Indices: 1002920--1003084 Score: 144
Period size: 33 Copynumber: 4.6 Consensus size: 36
1002910 TCTTTTGGTT
*
1002920 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCG--AA-GAGAATCGCAACGC
**
1002959 GGAAATGACTATCGCAA--CG-AGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
** * *
1002993 GAAATGACTATCGCGAC-C--AGACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
* *
1003026 GAAATGAAAATCGCAACGCGAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGCG-AA-GAGAATCGCAACGC
*
1003064 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
1003085 TTTTTGTTTC
Statistics
Matches: 108, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
33 43 0.40
34 16 0.15
35 1 0.01
37 2 0.02
38 32 0.30
40 14 0.13
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
Found at i:1003116 original size:19 final size:19
Alignment explanation
Indices: 1003080--1003124 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1003070 AAAATCGCAA
*
1003080 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1003099 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
1003118 TGCGATT
1 TGCGATT
1003125 CTCTCATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1003134 original size:14 final size:14
Alignment explanation
Indices: 1003117--1003151 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1003107 TTATTTCGCG
1003117 TTGCGATTCTCTCA
1 TTGCGATTCTCTCA
*
1003131 TTGCGATTCTCTCG
1 TTGCGATTCTCTCA
1003145 TTGCGAT
1 TTGCGAT
1003152 AGTTATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCA
Found at i:1003717 original size:20 final size:20
Alignment explanation
Indices: 1003692--1003744 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1003682 GCGCTATGTA
1003692 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1003712 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1003732 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1003745 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1003779 original size:20 final size:20
Alignment explanation
Indices: 1003756--1003801 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1003746 TTTGTATTAT
1003756 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
1003776 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
1003796 GCATTG
1 GCATTG
1003802 TGATTTTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Found at i:1003800 original size:40 final size:40
Alignment explanation
Indices: 1003693--1003801 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 40
1003683 CGCTATGTAA
* * * *
1003693 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGT
* * * *
1003733 ATCTCGTTGCGATTTTGT-ATTAT-GCATTGCGATAGTAAGT
1 ATCGCGTTGCGA--TAGTCAGTATCGCATTGCGAAAGTAAGT
*
1003773 ATCGCATTGCGATAGTCAGTATCGCATTG
1 ATCGCGTTGCGATAGTCAGTATCGCATTG
1003802 TGATTTTCCC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
38 3 0.06
39 4 0.08
40 41 0.77
41 3 0.06
42 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (40 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGT
Found at i:1004754 original size:30 final size:29
Alignment explanation
Indices: 1004718--1004789 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
1004708 AGAGTGTGCT
1004718 TATAATAACAAATATTAAAAAAATTGGACC
1 TATAATAACAAATATTAAAAAAATTGGA-C
* * *
1004748 TCTAATAA-AAAGTATTGAAAAATTTGGAC
1 TATAATAACAAA-TATTAAAAAAATTGGAC
1004777 TAT-ATAACAAATA
1 TATAATAACAAATA
1004790 AATATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.17
29 9 0.25
30 21 0.58
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (29 bp):
TATAATAACAAATATTAAAAAAATTGGAC
Found at i:1004893 original size:31 final size:29
Alignment explanation
Indices: 1004824--1004897 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 29
1004814 TAAAAGTATG
1004824 CCCTTAATAATAAATATTGAAAAAATTAGA
1 CCCTTAATAA-AAATATTGAAAAAATTAGA
*
1004854 CCCCTAATAAAAAGTATTGAAAAAATTAG-
1 CCCTTAATAAAAA-TATTGAAAAAATTAGA
1004883 CCTCTTTAATAAAAA
1 CC-C-TTAATAAAAA
1004898 AATGTTAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 5 0.13
30 25 0.64
31 9 0.23
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (29 bp):
CCCTTAATAAAAATATTGAAAAAATTAGA
Found at i:1005986 original size:2 final size:2
Alignment explanation
Indices: 1005981--1006008 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1005971 TTAGCAAGTA
1005981 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
1006009 GGTAAAAGAT
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:1010408 original size:36 final size:36
Alignment explanation
Indices: 1010345--1010486 Score: 232
Period size: 36 Copynumber: 4.0 Consensus size: 36
1010335 AAAGATGAAC
*
1010345 ACTTGAATCGAAAGTG-CGATGCCTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
*
1010380 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCATTCG
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
*
1010416 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTTG
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
* *
1010452 ACTTGAATCGAAAGTGCAGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
1010487 TTCTTATGCA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
35 16 0.16
36 83 0.84
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:1011808 original size:36 final size:35
Alignment explanation
Indices: 1011745--1011880 Score: 182
Period size: 36 Copynumber: 3.8 Consensus size: 35
1011735 AAAGATGGAC
* * * *
1011745 ACTTGAAGCAAAAGTGCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCATTCG
*
1011780 ACTTGAATCTAAAGTGACGATGCTTCCTTCCATTCG
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCATTCG
*
1011816 ACTTGAATCGAAGGTGTCGATGCTTCCTTCCATTCG
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCATTCG
*
1011852 ACTTAAATCGAAAGTGCAGATGCTTCCTT
1 ACTTGAATCGAAAGTGC-GATGCTTCCTT
1011881 TCGGTCTTCT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.17
36 75 0.83
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCATTCG
Found at i:1013788 original size:36 final size:35
Alignment explanation
Indices: 1013713--1013854 Score: 178
Period size: 36 Copynumber: 4.0 Consensus size: 35
1013703 AAAGATGAAT
*
1013713 ACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
* * * *
1013748 ACTTGAATCTAAAGTGTCGATGCTTCATTCCATTCA
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTTCG
*
1013784 ACTTGAATC-AAAGGTGTCGATGCTTCCTTCCGTTTG
1 ACTTGAATCGAAA-GTG-CGATGCTTCCTTCCGTTCG
*
1013820 ACTTGAATCGAAAGTGCAGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGC-GATGCTTCCTTCCGTTC
1013855 TTCTTATTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
35 19 0.21
36 70 0.76
37 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
Found at i:1013834 original size:72 final size:71
Alignment explanation
Indices: 1013713--1013845 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 71
1013703 AAAGATGAAT
*
1013713 ACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCTAAAGTGTC-GATGCTTCATT
1 ACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTG-CAGATGCTTCATT
1013777 CCATTCA
65 CCATTCA
* *
1013784 ACTTGAATC-AAAGGTGTCGATGCTTCCTTCCGTTTGACTTGAATCGAAAGTGCAGATGCTTC
1 ACTTGAATCGAAA-GTG-CGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGCAGATGCTTC
1013846 CTTTCGTTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
70 3 0.05
71 13 0.23
72 40 0.71
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (71 bp):
ACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGCAGATGCTTCATTC
CATTCA
Found at i:1019999 original size:18 final size:18
Alignment explanation
Indices: 1019976--1020027 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
1019966 TATGTGATAT
* *
1019976 GTGGTCATTCGAGACATA
1 GTGGTCCTTCGGGACATA
*
1019994 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
1020012 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
1020028 AGTTTCTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1025487 original size:32 final size:32
Alignment explanation
Indices: 1025446--1025512 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
1025436 TAATTTAGGG
*
1025446 ATTAGTTTCTTTTCAATTGGTAAGATTGGAAT
1 ATTAGTTTCTTTTCAATTGGAAAGATTGGAAT
*
1025478 ATTAGTTTCTTTTCAATTGGAAATATTGGAAT
1 ATTAGTTTCTTTTCAATTGGAAAGATTGGAAT
1025510 ATT
1 ATT
1025513 TTATATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (32 bp):
ATTAGTTTCTTTTCAATTGGAAAGATTGGAAT
Found at i:1030393 original size:90 final size:90
Alignment explanation
Indices: 1030219--1030393 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 90
1030209 CATATTATAT
* * *
1030219 TACTATTATATATAATAAAGATTGAGTTATCCCTCTAAATCAATTGGTTAATCACCCCGGCTTTA
1 TACTATTATATACAATAAAGATTGAGCTATCCCTCTAAAGCAATTGGTTAATCACCCCGGCTTTA
**
1030284 TGGATAATATTCAGCTAGCCTATTA
66 TGGATAATATTCAAATAGCCTATTA
* * * ** *
1030309 TACTATTATATGCAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAATTGCCCTGGCTTTA
1 TACTATTATATACAATAAAGATTGAGCTATCCCTCTAAAGCAATTGGTTAATCACCCCGGCTTTA
1030374 TGGATAAGT-TTCAAATAGCC
66 TGGATAA-TATTCAAATAGCC
1030394 AAAAAAAGGG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 72 0.99
91 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (90 bp):
TACTATTATATACAATAAAGATTGAGCTATCCCTCTAAAGCAATTGGTTAATCACCCCGGCTTTA
TGGATAATATTCAAATAGCCTATTA
Found at i:1033013 original size:42 final size:42
Alignment explanation
Indices: 1032954--1033035 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
1032944 TCTTGATTTG
* *
1032954 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCACGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGCT
*
1032996 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG
1033036 ATAATACCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGCT
Found at i:1033161 original size:271 final size:271
Alignment explanation
Indices: 1032679--1033895 Score: 1918
Period size: 271 Copynumber: 4.5 Consensus size: 271
1032669 TATTTCCCAA
* * * * * * *
1032679 ATTTGTAAGTACTTTGGGCCATCAGTAAGTCTTTCGAGAATGATGTTTAAATCCTTCGGGTCATT
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
* * * * *
1032744 TGTAAG-CTTTCGAGTAAGAAGATAAGACCTTCGGGCCATCCATATGACCTTCGGGCTTG-ATGT
66 TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGC-AGAATGT
1032807 TTTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTT
130 TTTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTT
*
1032872 GTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCATTGACAACTAAGAAACTAAGCTTGATTTTC
195 GTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTC
1032937 AAGGGTTTCTTG
260 AAGGGTTTCTTG
*
1032949 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCACGATGCTTAAATCCTTCGGGTCATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
* * *
1033014 TGTAAGCCTTTCGAGCAAGATGATAATACCTTCGGGCCATCCATAAGACCTTCGGGCAGAATATT
66 TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGCAGAATGTT
*
1033079 TTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGTGTTG
131 TTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTTG
* *
1033144 TTAAAGGAAGCTAAGCCTAATTTTAAGGGATTCCTTGACAACTAAGAAACTAATCTTGATTTTCA
196 TTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
*
1033209 AGGGTTT-TTT
261 AGGGTTTCTTG
* *
1033219 ATTTGTAAATCCTTCAGGTCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
* * * *
1033284 TGTAAGCCTTTCGAGCTAGATTATAAGACATTTGGGCCATCCATAAGACCTTCGGGCAGGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGCAGAATGTT
* * *
1033349 TTGAAATGAGATTTTAAAAACTAAGCCTAATTTTAAAGGGTTTCTTAATTATCTTAAAAGAGTTG
131 TTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTTG
* * *
1033414 TTAAAGGAAGTTGAGCCTAATTTTAAAGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
196 TTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
1033479 AGGGTTTCTTG
261 AGGGTTTCTTG
* * *
1033490 ATTTGTAAATCCTTCGAGTCATCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
* * * * *
1033555 TATAAGCCTTTCGAGCAAGAAGATAAGACCTTTGTGCCATCCATAAGACCTTCGGGCTGGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGCAGAATGTT
*
1033620 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTTG
131 TTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTTG
* *
1033685 TTAAAAGAAGCTAAGCATAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
196 TTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
*
1033750 AGTGTTTCTTG
261 AGGGTTTCTTG
* *
1033761 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCAGGTCATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
* * * * * * *
1033826 TGTAAGCCATTCGAGTAAGATGATAAGTCCTTTGGGCTATTCATAAGACCTTCAGGTAGAATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGCAGAATGTT
1033891 TTCAA
131 TTCAA
1033896 CATTTCCATT
Statistics
Matches: 868, Mismatches: 76, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
270 314 0.36
271 554 0.64
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (271 bp):
ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
TGTAAGCCTTTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACCTTCGGGCAGAATGTT
TTCAAATGAGATTTTAAAAACTAAGCCTAATTTTAAGGGGTTTCTTAATTATCTCAAAAGAGTTG
TTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTTCA
AGGGTTTCTTG
Found at i:1034505 original size:16 final size:16
Alignment explanation
Indices: 1034484--1034527 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1034474 AGACAAATAG
*
1034484 CAGACCTGACCCGATC
1 CAGACCCGACCCGATC
* *
1034500 CAGACCCGATCCGGTC
1 CAGACCCGACCCGATC
*
1034516 CAGACTCGACCC
1 CAGACCCGACCC
1034528 AACAGACCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.45, G:0.20, T:0.11
Consensus pattern (16 bp):
CAGACCCGACCCGATC
Found at i:1037184 original size:17 final size:17
Alignment explanation
Indices: 1037162--1037212 Score: 102
Period size: 17 Copynumber: 3.0 Consensus size: 17
1037152 TCCCCAATGG
1037162 TAAATCAAAACAACATT
1 TAAATCAAAACAACATT
1037179 TAAATCAAAACAACATT
1 TAAATCAAAACAACATT
1037196 TAAATCAAAACAACATT
1 TAAATCAAAACAACATT
1037213 CAAGCCAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCAAAACAACATT
Found at i:1037451 original size:20 final size:18
Alignment explanation
Indices: 1037416--1037458 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
1037406 TTAGCATTAT
*
1037416 GAAAAGAAAATAATGAAA
1 GAAAAGAAAAAAATGAAA
1037434 GAAAAGTAAAAAAGATGAAA
1 GAAAAG-AAAAAA-ATGAAA
1037454 GAAAA
1 GAAAA
1037459 ATAGAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (18 bp):
GAAAAGAAAAAAATGAAA
Found at i:1037611 original size:19 final size:19
Alignment explanation
Indices: 1037551--1037615 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
1037541 AAGTTCTAAG
1037551 TAAAT-AAAATAACTAATTCA
1 TAAATAAAAATAA-TAA-TCA
* * * *
1037571 T-AATCAAACTAAAAATCC
1 TAAATAAAAATAATAATCA
1037589 TAAATAAAAATAATAATCA
1 TAAATAAAAATAATAATCA
1037608 TAAA-AAAA
1 TAAATAAAA
1037616 TAAAATTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 7 0.19
19 22 0.61
20 7 0.19
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAATAAAAATAATAATCA
Found at i:1037628 original size:22 final size:23
Alignment explanation
Indices: 1037590--1037633 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1037580 TAAAAATCCT
1037590 AAATAAAAATAATAATCATAAAA
1 AAATAAAAATAATAATCATAAAA
* *
1037613 AAATAAAATTAA-AATCCTAAA
1 AAATAAAAATAATAATCATAAA
1037634 TCTAAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAAAATAATAATCATAAAA
Found at i:1037962 original size:58 final size:58
Alignment explanation
Indices: 1037897--1038038 Score: 194
Period size: 58 Copynumber: 2.4 Consensus size: 58
1037887 ATCTCGATTT
* *
1037897 ATTTTGGGGGCCCTATTTTTTGGGGCTTCTTAATGGCAACAACTGATAAATATACTCG
1 ATTTTGGGGCCCCTATTTTTTGGGACTTCTTAATGGCAACAACTGATAAATATACTCG
* * * * *
1037955 ATTTTGGGGTCTCTATTTTTTGGGACTTCTTAATGGCAATAATTGATAGATATACTCG
1 ATTTTGGGGCCCCTATTTTTTGGGACTTCTTAATGGCAACAACTGATAAATATACTCG
***
1038013 ATTTTGAAACCCCTATTTTTTGGGAC
1 ATTTTGGGGCCCCTATTTTTTGGGAC
1038039 CCTGCGCGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (58 bp):
ATTTTGGGGCCCCTATTTTTTGGGACTTCTTAATGGCAACAACTGATAAATATACTCG
Found at i:1050804 original size:25 final size:26
Alignment explanation
Indices: 1050755--1050805 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1050745 GTTTACAAAT
* **
1050755 CTAATTCAAATGACAAATTCTAAAAA
1 CTAATTCAAATGAAAAATTAGAAAAA
1050781 CTAATT-AAATGAAAAATTAGAAAAA
1 CTAATTCAAATGAAAAATTAGAAAAA
1050806 ACGACCCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (26 bp):
CTAATTCAAATGAAAAATTAGAAAAA
Found at i:1052308 original size:3 final size:3
Alignment explanation
Indices: 1052302--1052342 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1052292 ATAATATTCT
1052302 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1052343 TTAGGTCGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1053351 original size:20 final size:20
Alignment explanation
Indices: 1053328--1053393 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1053318 GCCCGAATGT
1053328 CTTATGGATGGCTCGAAGGA
1 CTTATGGATGGCTCGAAGGA
* * *
1053348 CTTAAGCGTCAT-TCTCGAAAGA
1 CTTATG-G--ATGGCTCGAAGGA
1053370 CTTACT-GATGGCTCGAAGGA
1 CTTA-TGGATGGCTCGAAGGA
1053390 CTTA
1 CTTA
1053394 AGCATCATGC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 2 0.06
20 17 0.49
21 2 0.06
22 12 0.34
23 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (20 bp):
CTTATGGATGGCTCGAAGGA
Found at i:1053364 original size:22 final size:21
Alignment explanation
Indices: 1053338--1053415 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
1053328 CTTATGGATG
*
1053338 GCTCGAAGGACTTAAGCGTCAT
1 GCTCGAAAGACTTAAGC-TCAT
* *
1053360 TCTCGAAAGACTT-A-CTGAT
1 GCTCGAAAGACTTAAGCTCAT
*
1053379 GGCTCGAAGGACTTAAGCATCAT
1 -GCTCGAAAGACTTAAGC-TCAT
*
1053402 GCTCAAAAGACTTA
1 GCTCGAAAGACTTA
1053416 CTGATGGCCC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
20 12 0.27
21 2 0.05
22 24 0.55
23 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
GCTCGAAAGACTTAAGCTCAT
Found at i:1053393 original size:42 final size:42
Alignment explanation
Indices: 1053334--1053435 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
1053324 ATGTCTTATG
* * *
1053334 GATGGCTCGAAGGACTTAAGCGTCATTCTCGAAAGACTTACT
1 GATGGCTCGAAGGACTTAAGCATCATGCTCAAAAGACTTACT
1053376 GATGGCTCGAAGGACTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCTCGAAGGACTTAAGCATCATGCTCAAAAGACTTACT
* *
1053418 GATGGCCCAAAGGACTTA
1 GATGGCTCGAAGGACTTA
1053436 CTAAGTAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (42 bp):
GATGGCTCGAAGGACTTAAGCATCATGCTCAAAAGACTTACT
Found at i:1053433 original size:20 final size:20
Alignment explanation
Indices: 1053368--1053437 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1053358 ATTCTCGAAA
*
1053368 GACTTACTGATGGCTCGAAG
1 GACTTACTGATGGCTCAAAG
* *
1053388 GACTTAAGCATCAT-GCTCAAAA
1 GACTT-A-C-TGATGGCTCAAAG
*
1053410 GACTTACTGATGGCCCAAAG
1 GACTTACTGATGGCTCAAAG
1053430 GACTTACT
1 GACTTACT
1053438 AAGTAAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.08
20 20 0.50
21 2 0.05
22 12 0.30
23 3 0.08
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTTACTGATGGCTCAAAG
Found at i:1053715 original size:237 final size:239
Alignment explanation
Indices: 1053260--1053716 Score: 579
Period size: 237 Copynumber: 1.9 Consensus size: 239
1053250 AAATGATAAA
1053260 AAATGAGAAACTTTAGAAATTGATTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCCGAA
1 AAATGAGAAACTTTAGAAATTGATTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCCGAA
* * * * * *
1053325 TGTCTTATGGATGGCTCGAAGGACTTAAGCGTCATTCTCGAAAGACTTACTGATGGCTCGAAGGA
66 GGTCTTATGGATGGCTCGAAAGACTTAAGCATCATTCTCGAAAGACTTACTGATGACCCGAACGA
* * *
1053390 CTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGA
131 CTTAAGCATCATGCTCAAAAGACTTACAGATGGCCCAAAGGACTTACTAAGTAAGAAACCTTGAA
**** *
1053455 AATCATTTTCTTATTTTTTAAAAACCAATTTTTAGAAAAGATTT
196 AATCATAAGATTATTTCTTAAAAACCAATTTTTAGAAAAGATTT
* * *
1053499 AAATGAGAAACTTT-G-AATTCGCTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTGCTCGA
1 AAATGAGAAACTTTAGAAATT-GATTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCCGA
* *
1053562 AGGTCTTATGGATGGC-CTGAAAGACTT-ATCATC-TTGCTTGAAAGACTTA-TAGATGACCCGA
65 AGGTCTTATGGATGGCTC-GAAAGACTTAAGCATCATT-CTCGAAAGACTTACT-GATGACCCGA
* * * * * *
1053623 ACGATTTAAGCATCATGCTCGAAAGACTTACAGATTGCTCGAAGGACTTACTAATTAAGAAACCC
127 ACGACTTAAGCATCATGCTCAAAAGACTTACAGATGGCCCAAAGGACTTACTAAGTAAGAAA-CC
1053688 TTGAAAAT-A-AAGATTAGTTTCTTAAAAAC
191 TTGAAAATCATAAGATTA-TTTCTTAAAAAC
1053717 TTTCATTTAT
Statistics
Matches: 187, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
236 6 0.03
237 95 0.51
238 72 0.39
239 14 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (239 bp):
AAATGAGAAACTTTAGAAATTGATTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCCGAA
GGTCTTATGGATGGCTCGAAAGACTTAAGCATCATTCTCGAAAGACTTACTGATGACCCGAACGA
CTTAAGCATCATGCTCAAAAGACTTACAGATGGCCCAAAGGACTTACTAAGTAAGAAACCTTGAA
AATCATAAGATTATTTCTTAAAAACCAATTTTTAGAAAAGATTT
Found at i:1053988 original size:61 final size:58
Alignment explanation
Indices: 1053832--1053989 Score: 196
Period size: 55 Copynumber: 2.7 Consensus size: 58
1053822 TCAAAAGTTC
** *
1053832 ATCATGTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTT-GCAAACTCATTTAAAA
1 ATCATGTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAAAATCATTTAAAA
* * * *
1053889 A-C-TATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAAAATTATTTTGAAAAA
1 ATCATGTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAAAATCA-TTT--AAAA
*
1053948 ATCATGTCAAGAAACCTCTAAAAATCAGACTTAGTTTCTTTA
1 ATCATGTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTA
1053990 TAGATATCAT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
55 34 0.40
56 6 0.07
57 4 0.05
59 5 0.06
60 1 0.01
61 34 0.40
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (58 bp):
ATCATGTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAAAATCATTTAAAA
Found at i:1061801 original size:33 final size:33
Alignment explanation
Indices: 1061764--1061831 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1061754 ACTGAACCCC
*
1061764 TTATTTAGCAAATTTGGTTTAATTTTTCATTGT
1 TTATTTAGCAAATTTGATTTAATTTTTCATTGT
* *
1061797 TTATTTGGTAAATTTGATTTAATTTTTCATTGT
1 TTATTTAGCAAATTTGATTTAATTTTTCATTGT
1061830 TT
1 TT
1061832 GGCTAGCTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (33 bp):
TTATTTAGCAAATTTGATTTAATTTTTCATTGT
Found at i:1061863 original size:2 final size:2
Alignment explanation
Indices: 1061856--1061918 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
1061846 AGCTTTATTG
1061856 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1061898 TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1061919 ATTTCCTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1068752 original size:20 final size:20
Alignment explanation
Indices: 1068712--1068753 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1068702 ATTCTACCAC
* *
1068712 ATGCAACTATATGCTTTTAA
1 ATGCAACTATATGATTCTAA
*
1068732 ATGCATCTATATGATTCTAA
1 ATGCAACTATATGATTCTAA
1068752 AT
1 AT
1068754 TAGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
ATGCAACTATATGATTCTAA
Found at i:1071418 original size:32 final size:31
Alignment explanation
Indices: 1071376--1071458 Score: 95
Period size: 26 Copynumber: 2.8 Consensus size: 31
1071366 CGAGAAAATG
1071376 ACAAAAGTAAAAGTAAAAAATTAAACCCT--
1 ACAAAAGTAAAAGTAAAAAATTAAACCCTAA
*
1071405 ---AAAGCAAAAGTAAAAAATTAAACCCTAA
1 ACAAAAGTAAAAGTAAAAAATTAAACCCTAA
* *
1071433 ACAAAAGTAAAAAATTAAAAATTAAA
1 ACAAAAGT-AAAAGTAAAAAATTAAA
1071459 AAAGTTTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 25 0.57
31 4 0.09
32 15 0.34
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (31 bp):
ACAAAAGTAAAAGTAAAAAATTAAACCCTAA
Found at i:1071458 original size:25 final size:26
Alignment explanation
Indices: 1071379--1071451 Score: 130
Period size: 26 Copynumber: 2.8 Consensus size: 26
1071369 GAAAATGACA
*
1071379 AAAGTAAAAGTAAAAAATTAAACCCT
1 AAAGCAAAAGTAAAAAATTAAACCCT
1071405 AAAGCAAAAGTAAAAAATTAAACCCT
1 AAAGCAAAAGTAAAAAATTAAACCCT
1071431 AAA-CAAAAGTAAAAAATTAAA
1 AAAGCAAAAGTAAAAAATTAAA
1071452 AATTAAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 18 0.39
26 28 0.61
ACGTcount: A:0.66, C:0.11, G:0.07, T:0.16
Consensus pattern (26 bp):
AAAGCAAAAGTAAAAAATTAAACCCT
Found at i:1075282 original size:3 final size:3
Alignment explanation
Indices: 1075274--1075342 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
1075264 TTTATCTCAT
* *
1075274 TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1075320 TTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1075343 AATGATAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 6 0.10
3 53 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1075351 original size:40 final size:37
Alignment explanation
Indices: 1075275--1075353 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
1075265 TTATCTCATT
*
1075275 TATTATTATTATTATATTATTATATTATTATTATAAA
1 TATTATTATTATTATATTATTATATTATTATGATAAA
*
1075312 TATTATTATTATTATTTTATTATTATTATTAAATGATAAA
1 TATTATTATTATTATATTATTA-TATTATT--ATGATAAA
1075352 TA
1 TA
1075354 ATTACAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 21 0.57
38 7 0.19
40 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (37 bp):
TATTATTATTATTATATTATTATATTATTATGATAAA
Found at i:1076418 original size:13 final size:14
Alignment explanation
Indices: 1076390--1076419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1076380 TTTTTATGCA
1076390 TTTTAATTCGGTTT
1 TTTTAATTCGGTTT
*
1076404 TTTTAATTCTGTTT
1 TTTTAATTCGGTTT
1076418 TT
1 TT
1076420 ATTTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (14 bp):
TTTTAATTCGGTTT
Found at i:1077419 original size:2 final size:2
Alignment explanation
Indices: 1077412--1077456 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1077402 TAAAAACTTA
* *
1077412 AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT AT AG AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1077451 AT AT AT
1 AT AT AT
1077457 TTTCTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1082819 original size:17 final size:17
Alignment explanation
Indices: 1082797--1082838 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1082787 ATAAAGTGCT
1082797 AAATTAAAATGAATTTA
1 AAATTAAAATGAATTTA
1082814 AAATTAAAATGAATTTA
1 AAATTAAAATGAATTTA
1082831 AAATTAAA
1 AAATTAAA
1082839 TGATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATTAAAATGAATTTA
Found at i:1083283 original size:110 final size:109
Alignment explanation
Indices: 1083025--1083298 Score: 266
Period size: 110 Copynumber: 2.5 Consensus size: 109
1083015 TCATTACATA
* * * * *
1083025 TGACCAAAATGTAAAAACATGCTTAAATAAGAGGGACTAAACATAAAATATACCAATAAATATAT
1 TGACCAAAATGTAAAAACATGC-TAACTTAGGGGGACTAAACATCAAATATCCCAATAAATATAT
* *
1083090 AACATGCATATAAAAAGGGTAAATAAAAAAGTCGGTCTTCACAGG
65 AACATGCATAAAAAAAGGGTAAATAAAAAAGTCGGTCCTCACAGG
* * * * * *
1083135 TAACCAAAATGTAAAAACACGCTAAAC-TATGGGAGACTAAACGTCAAATATCCCAA-AAATTTG
1 TGACCAAAATGTAAAAACATGCT-AACTTA-GGGGGACTAAACATCAAATATCCCAATAAATATA
* * * ** * ** *
1083198 TAGCATGCATGAAAAAAATGGTAAATACAAATTTTGGTCCTCGTATG
64 TAACATGCAT-AAAAAAAGGGTAAATAAAAAAGTCGGTCCTCACAGG
*
1083245 TGACCAAAATGTAAAAGCATGACTAACTTAGGGGGACTAAA-ATGCAAATATCCC
1 TGACCAAAATGTAAAAACATG-CTAACTTAGGGGGACTAAACAT-CAAATATCCC
1083299 CTAAATTTCC
Statistics
Matches: 131, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
109 17 0.13
110 110 0.84
111 4 0.03
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (109 bp):
TGACCAAAATGTAAAAACATGCTAACTTAGGGGGACTAAACATCAAATATCCCAATAAATATATA
ACATGCATAAAAAAAGGGTAAATAAAAAAGTCGGTCCTCACAGG
Found at i:1084256 original size:3 final size:3
Alignment explanation
Indices: 1084250--1084277 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1084240 ATAATTTTTT
1084250 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1084278 GATGATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1093424 original size:9 final size:8
Alignment explanation
Indices: 1093404--1093491 Score: 56
Period size: 8 Copynumber: 10.6 Consensus size: 8
1093394 ATTTGGGCCT
*
1093404 ATAATATA
1 ATAAAATA
1093412 ATAAAATTA
1 ATAAAA-TA
1093421 ATAATAATA
1 ATAA-AATA
1093430 ATAAAA-A
1 ATAAAATA
1093437 ATAAAAATA
1 AT-AAAATA
*
1093446 A-AAATATT
1 ATAAA-ATA
*
1093454 ATAATATA
1 ATAAAATA
1093462 ATAATAATA
1 ATAA-AATA
* *
1093471 TTAAAACA
1 ATAAAATA
1093479 A-AATAATA
1 ATAA-AATA
1093487 ATAAA
1 ATAAA
1093492 TAAAACAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
7 8 0.13
8 28 0.45
9 24 0.39
10 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (8 bp):
ATAAAATA
Found at i:1093425 original size:3 final size:3
Alignment explanation
Indices: 1093404--1093490 Score: 64
Period size: 3 Copynumber: 31.3 Consensus size: 3
1093394 ATTTGGGCCT
*
1093404 ATA AT- ATA ATA A-A ATTA ATA ATA ATA ATA A-A A-A ATA AAA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1093446 AAA AT- ATT ATA AT- ATA ATA ATA ATA TTA A-A ACA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1093490 A
1 A
1093491 ATAAAACAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
2 16 0.23
3 51 0.74
4 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1093501 original size:19 final size:19
Alignment explanation
Indices: 1093404--1093501 Score: 65
Period size: 19 Copynumber: 4.9 Consensus size: 19
1093394 ATTTGGGCCT
**
1093404 ATAATATAATAAAATTAATA
1 ATAATA-AATAAAACAAATA
* *
1093424 ATAAT-AATAAAAAATAAAA
1 ATAATAAATAAAACA-AATA
** *
1093443 ATAA-AAATATTATAATATA
1 ATAATAAATAAAACAA-ATA
1093462 ATAATAATATTAAAACAAAATA
1 ATAATAA-A-TAAAAC-AAATA
1093484 ATAATAAATAAAACAAAT
1 ATAATAAATAAAACAAAT
1093502 GAAATATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
18 8 0.13
19 23 0.38
20 13 0.21
21 2 0.03
22 13 0.21
23 2 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATAAATAAAACAAATA
Found at i:1094071 original size:45 final size:48
Alignment explanation
Indices: 1094020--1094110 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
1094010 TAAATTGTCT
*
1094020 CTATTA-TTAGAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATC
1 CTATTATTTA-AAATTATAATAATGAAAAATATATATTAATTTATAATC
*
1094065 CTATTATTTTAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTA-TTTAAAATTATAATAATGAAAAATATATATTAATTTATA
1094111 TATATTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 6 0.15
46 6 0.15
47 5 0.13
48 12 0.31
49 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (48 bp):
CTATTATTTAAAATTATAATAATGAAAAATATATATTAATTTATAATC
Found at i:1094233 original size:20 final size:19
Alignment explanation
Indices: 1094194--1094245 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1094184 TTTCTTTGAT
1094194 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1094213 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1094233 ATTTATAAAATAA
1 A-TTAAAAAATAA
1094246 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1094308 original size:120 final size:117
Alignment explanation
Indices: 1094103--1094327 Score: 281
Period size: 120 Copynumber: 1.9 Consensus size: 117
1094093 AATATATATT
* * * *
1094103 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
* * *
1094168 GCCTTAAGACAACTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 ACCTTAAGACAACTCCTTTC-TTAATATTAAAAAATAAATAAATAATTAAAAC
*
1094221 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** ** *
1094286 GTTATTTTAAGACTGC-CCTTTCTTAATATTGAAAAATAAATA
63 GGTACCTTAAGACAACTCCTTTCTTAATATTAAAAAATAAATA
1094328 TTAAAATAGG
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
118 10 0.11
119 24 0.27
120 40 0.44
121 16 0.18
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (117 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
ACCTTAAGACAACTCCTTTCTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:1094430 original size:3 final size:3
Alignment explanation
Indices: 1094422--1094451 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1094412 ATTATGATTA
*
1094422 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1094452 TAAAAGTAAA
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:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1095908 original size:3 final size:3
Alignment explanation
Indices: 1095888--1095971 Score: 65
Period size: 3 Copynumber: 30.0 Consensus size: 3
1095878 TTTGGGCTTG
* *
1095888 TAA T-A TAA TAA -AA TTAA TAA TAA TAA -AA AAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1095931 T-A TTA TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1095972 ATAAAACAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
2 14 0.21
3 51 0.76
4 2 0.03
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1095917 original size:17 final size:18
Alignment explanation
Indices: 1095888--1095977 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 18
1095878 TTTGGGCTTG
*
1095888 TAAT-ATAATAAAATTAA
1 TAATAATAATAAAAATAA
1095905 TAATAATAA-AAAAATAA
1 TAATAATAATAAAAATAA
*
1095922 AAATAATAATATTATAATATAA
1 TAATAATAATA--A-AA-ATAA
* *
1095944 TAATAATATTAAAACAAAA
1 TAATAATAATAAAA-ATAA
1095963 TAATAATAAATAAAA
1 TAATAAT-AATAAAA
1095978 CAAATGAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.32
18 5 0.08
19 12 0.20
20 8 0.14
21 2 0.03
22 13 0.22
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAATAATAAAAATAA
Found at i:1095982 original size:19 final size:19
Alignment explanation
Indices: 1095888--1095982 Score: 79
Period size: 19 Copynumber: 4.9 Consensus size: 19
1095878 TTTGGGCTTG
*
1095888 TAATATAATAAAATTAATAA
1 TAATA-AATAAAATAAATAA
1095908 TAATAAA-AAAATAAA-AA
1 TAATAAATAAAATAAATAA
*
1095925 TAATAATATTATAATATAATAA
1 TAATAA-A-TAAAATA-AATAA
* *
1095947 TAAT-ATTAAAACAAAATAA
1 TAATAAATAAAA-TAAATAA
*
1095966 TAATAAATAAAACAAAT
1 TAATAAATAAAATAAAT
1095983 GAAATAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
17 8 0.13
18 8 0.13
19 19 0.31
20 17 0.28
21 3 0.05
22 6 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATAAATAAAATAAATAA
Found at i:1096662 original size:20 final size:20
Alignment explanation
Indices: 1096639--1096704 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1096629 GTTGAACAAG
1096639 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* * * **
1096659 TTCTTC-CTTTTTCAGA-TGAG
1 TTCTTCTCATTATGA-ACT-TC
1096679 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
1096699 TTCTTC
1 TTCTTC
1096705 CTTCTTCAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 6 0.19
20 20 0.62
21 6 0.19
ACGTcount: A:0.17, C:0.24, G:0.08, T:0.52
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:1096681 original size:40 final size:40
Alignment explanation
Indices: 1096637--1096736 Score: 182
Period size: 40 Copynumber: 2.5 Consensus size: 40
1096627 AAGTTGAACA
* *
1096637 AGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATG
1096677 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATG
1096717 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1096737 CGACCTGGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATG
Found at i:1096768 original size:153 final size:150
Alignment explanation
Indices: 1096527--1096849 Score: 529
Period size: 153 Copynumber: 2.1 Consensus size: 150
1096517 AGGTTGAACA
* **
1096527 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTACTCATTATGAACCTTCTGG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTACTCATTATGAACCACCTGG
1096592 CAACGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
66 CAACGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
*
1096657 TCTTCTTCCTTTTTCAGATG
131 TCTTCTTCCTTCTTCAGATG
* *
1096677 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAAATAAGTTCTACTCATTATGAAC-C-ACC
* * *
1096742 TGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGA
63 TGGCAACGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGA
1096807 ACTTCTTCTTCCTTCTTCAGATG
128 ACTTCTTCTTCCTTCTTCAGATG
*
1096830 AGTTCTTCTAATTATGAACT
1 AGTTCTTCTCATTATGAACT
1096850 CGACCTGGTA
Statistics
Matches: 160, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
150 29 0.18
151 26 0.16
152 1 0.01
153 104 0.65
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (150 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTACTCATTATGAACCACCTGG
CAACGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATG
Found at i:1096808 original size:113 final size:113
Alignment explanation
Indices: 1096677--1096885 Score: 391
Period size: 113 Copynumber: 1.8 Consensus size: 113
1096667 TTTTCAGATG
*
1096677 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTAATTATGAACTCGACC
*
1096742 TGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
66 TGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
*
1096790 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTAATTATGAACTCGACC
1096855 TGGTAATGCTGATCCATCGAATGATGAATTC
66 TGGTAATGCTGATCCATCGAATGATGAATTC
1096886 GAACTTTGCT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 93 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTAATTATGAACTCGACC
TGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
Found at i:1097312 original size:22 final size:22
Alignment explanation
Indices: 1097287--1097341 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1097277 GATAAAGCTT
*
1097287 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1097309 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1097331 TCATCTTTGAA
1 TCATCTTTGAA
1097342 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1097856 original size:55 final size:54
Alignment explanation
Indices: 1097708--1097864 Score: 242
Period size: 54 Copynumber: 2.9 Consensus size: 54
1097698 AGAATAGCAG
***
1097708 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
1097762 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
1097816 GTTCGTAAAGCGTTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1 GTTCGTAAAAC-ATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1097865 CAAAATTTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 60 0.64
55 34 0.36
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1100118 original size:114 final size:113
Alignment explanation
Indices: 1099918--1100257 Score: 518
Period size: 114 Copynumber: 3.0 Consensus size: 113
1099908 GATCATGCAG
* * * * * *
1099918 TTCATCTTCCTAATCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAAT-CAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1099983 ACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
1100032 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATC-AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1100097 ACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTATACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
1100146 TTTATCTTTCAAATACAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAAT-CAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1100211 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
1100258 CATGGCACTT
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.00
114 203 0.99
115 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (113 bp):
TTCATCTTTCAAATCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1102429 original size:16 final size:16
Alignment explanation
Indices: 1102408--1102457 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1102398 ATTTCTCCCC
1102408 TTTTTCTTTTTCCTTT
1 TTTTTCTTTTTCCTTT
* *
1102424 TTTTTCTTTATGC-TT
1 TTTTTCTTTTTCCTTT
*
1102439 TTTTGCATTTTTCCTTT
1 TTTTTC-TTTTTCCTTT
1102456 TT
1 TT
1102458 CATCTCATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 7 0.26
16 16 0.59
17 4 0.15
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTTCCTTT
Found at i:1106165 original size:14 final size:14
Alignment explanation
Indices: 1106127--1106180 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1106117 CATAAAAATA
* *
1106127 CAAATGCAAAGATG
1 CAAATGTAAATATG
*
1106141 CCAAATATAAATATG
1 -CAAATGTAAATATG
*
1106156 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
1106170 TAAATGTAAAT
1 CAAATGTAAAT
1106181 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1107226 original size:13 final size:13
Alignment explanation
Indices: 1107208--1107232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1107198 AACATACATG
1107208 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1107221 AAAAAAAAAGAA
1 AAAAAAAAAGAA
1107233 TAGTTAGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:1107896 original size:25 final size:23
Alignment explanation
Indices: 1107856--1107915 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
1107846 ATAAAAAATA
*
1107856 TAATAAATATTATGAAAATAATAAG
1 TAATAAAAATTATG-AAATAA-AAG
*
1107881 TAATAAAAATTTTGAAATAAAAG
1 TAATAAAAATTATGAAATAAAAG
1107904 -AATTAAAAATTA
1 TAA-TAAAAATTA
1107916 AATAAATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 2 0.06
23 11 0.35
24 6 0.19
25 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TAATAAAAATTATGAAATAAAAG
Found at i:1108526 original size:20 final size:19
Alignment explanation
Indices: 1108487--1108538 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1108477 TTCCTTTGAT
1108487 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1108506 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1108526 ATTTATAAAATAA
1 A-TTAAAAAATAA
1108539 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1110127 original size:9 final size:8
Alignment explanation
Indices: 1110107--1110194 Score: 56
Period size: 8 Copynumber: 10.6 Consensus size: 8
1110097 ATTTGGGCCT
*
1110107 ATAATATA
1 ATAAAATA
1110115 ATAAAATTA
1 ATAAAA-TA
1110124 ATAATAATA
1 ATAA-AATA
1110133 ATAAAA-A
1 ATAAAATA
1110140 ATAAAAATA
1 AT-AAAATA
*
1110149 A-AAATATT
1 ATAAA-ATA
*
1110157 ATAATATA
1 ATAAAATA
1110165 ATAATAATA
1 ATAA-AATA
* *
1110174 TTAAAACA
1 ATAAAATA
1110182 A-AATAATA
1 ATAA-AATA
1110190 ATAAA
1 ATAAA
1110195 TAAAACAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
7 8 0.13
8 28 0.45
9 24 0.39
10 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (8 bp):
ATAAAATA
Found at i:1110128 original size:3 final size:3
Alignment explanation
Indices: 1110107--1110193 Score: 64
Period size: 3 Copynumber: 31.3 Consensus size: 3
1110097 ATTTGGGCCT
*
1110107 ATA AT- ATA ATA A-A ATTA ATA ATA ATA ATA A-A A-A ATA AAA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1110149 AAA AT- ATT ATA AT- ATA ATA ATA ATA TTA A-A ACA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1110193 A
1 A
1110194 ATAAAACAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
2 16 0.23
3 51 0.74
4 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1110148 original size:19 final size:19
Alignment explanation
Indices: 1110107--1110215 Score: 57
Period size: 19 Copynumber: 5.7 Consensus size: 19
1110097 ATTTGGGCCT
*
1110107 ATAAT-ATAATAAAATTAATA
1 ATAATAATAA-AAAA-TAAAA
1110127 ATAATAATAAAAAATAAAA
1 ATAATAATAAAAAATAAAA
* * * *
1110146 ATAAAAATATTATAAT-ATA
1 ATAATAATA-AAAAATAAAA
* *
1110165 ATAATAATATTAAAA-CAAA
1 ATAATAATA-AAAAATAAAA
*
1110184 ATAATAATAAATAAA-ACAA
1 ATAATAATAAA-AAATAAAA
*
1110203 ATGA-AATAAAAAA
1 ATAATAATAAAAAA
1110216 CTAGTGTCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
17 3 0.04
18 7 0.10
19 46 0.63
20 13 0.18
21 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.27
Consensus pattern (19 bp):
ATAATAATAAAAAATAAAA
Found at i:1111341 original size:2 final size:2
Alignment explanation
Indices: 1111334--1111373 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1111324 CCCTAGACTA
*
1111334 AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1111374 ATGTTAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1113712 original size:20 final size:20
Alignment explanation
Indices: 1113687--1113750 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
1113677 AATTCTCGTT
1113687 GCGATTTTCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
*
1113707 GTGATTTTCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
1113727 GCGATTTTCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
1113747 GCGA
1 GCGA
1113751 ATATGTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (20 bp):
GCGATTTTCAAATTCGCAAC
Found at i:1113765 original size:20 final size:20
Alignment explanation
Indices: 1113740--1113818 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
1113730 ATTTTCAAAT
1113740 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
1113760 TTGCAACGCGAA-ACTGTAAA
1 TCGCAACGCGAATA-TGTAAA
*
1113780 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
*
1113800 TCGCAACGCGAATTTGTAA
1 TCGCAACGCGAATATGTAA
1113819 TTCACAACAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 52 0.98
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1113766 original size:40 final size:39
Alignment explanation
Indices: 1113687--1113810 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 39
1113677 AATTCTCGTT
* *
1113687 GCGATTTTCAAATTCGCAACGTG-ATTTTCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAACGCGAATTGT-AAATT-GCAAC
1113727 GCGATTTTCAAATTCGCAACGCGAATATGTAAATTGCAAC
1 GCGATTTTCAAATTCGCAACGCGAAT-TGTAAATTGCAAC
* * *
1113767 GCGAAACTGT-AAA-TCGCAACGCGAATCTGTAAATCGCAAC
1 GCG--ATTTTCAAATTCGCAACGCGAAT-TGTAAATTGCAAC
1113807 GCGA
1 GCGA
1113811 ATTTGTAATT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.01
40 58 0.78
41 10 0.14
42 5 0.07
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (39 bp):
GCGATTTTCAAATTCGCAACGCGAATTGTAAATTGCAAC
Found at i:1113818 original size:40 final size:41
Alignment explanation
Indices: 1113720--1113826 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 41
1113710 ATTTTCAAAT
1113720 TCGCAACGCG-ATTT-TCAAATTCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGT-AAATTCGCAACGCGAATATGTAAA
* ** *
1113760 TTGCAACGCGAAACTGTAAA-TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAATTCGCAACGCGAATATGTAAA
*
1113800 TCGCAACGCGAATTTGT-AATTCACAAC
1 TCGCAACGCGAATTTGTAAATTCGCAAC
1113827 ACATAAGTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.04
40 48 0.86
41 5 0.09
42 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGAATTTGTAAATTCGCAACGCGAATATGTAAA
Found at i:1113826 original size:20 final size:20
Alignment explanation
Indices: 1113717--1113826 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
1113707 GTGATTTTCA
* * **
1113717 AATTCGCAACGCGATTTTCA
1 AATTCGCAACGCGAATCTGT
*
1113737 AATTCGCAACGCGAATATGT
1 AATTCGCAACGCGAATCTGT
*
1113757 AAATT-GCAACGCGAAACTGT
1 -AATTCGCAACGCGAATCTGT
*
1113777 AAATCGCAACGCGAATCTGT
1 AATTCGCAACGCGAATCTGT
* *
1113797 AAATCGCAACGCGAATTTGT
1 AATTCGCAACGCGAATCTGT
*
1113817 AATTCACAAC
1 AATTCGCAAC
1113827 ACATAAGTCA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 70 0.91
21 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
AATTCGCAACGCGAATCTGT
Found at i:1113844 original size:60 final size:61
Alignment explanation
Indices: 1113714--1113865 Score: 140
Period size: 60 Copynumber: 2.5 Consensus size: 61
1113704 AACGTGATTT
* * *
1113714 TCAAATTCGCAACGCGATTTTCAAATTCGCAACGCGAATATGTAAATTGCAACGCGAAACTG
1 TCAAATTCGCAACGCGATTGTCAAATTCGCAACGCGAATATGTAAATTACAACACGAAAC-G
*
1113776 T-AAA-TCGCAACGCGAATCTGT-AAA-TCGCAACGCGAATTTGT-AATTCACAACAC-ATAA-G
1 TCAAATTCGCAACGCG-AT-TGTCAAATTCGCAACGCGAATATGTAAATT-ACAACACGA-AACG
* *
1113834 TCAAATTCGCAACAC-ATAAGTCAAATTCGCAA
1 TCAAATTCGCAACGCGAT-TGTCAAATTCGCAA
1113866 AGCACATTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
58 6 0.08
59 11 0.15
60 47 0.63
61 8 0.11
62 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (61 bp):
TCAAATTCGCAACGCGATTGTCAAATTCGCAACGCGAATATGTAAATTACAACACGAAACG
Found at i:1113862 original size:20 final size:20
Alignment explanation
Indices: 1113817--1113865 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1113807 GCGAATTTGT
*
1113817 AATTCACAACACATAAGTCA
1 AATTCGCAACACATAAGTCA
1113837 AATTCGCAACACATAAGTCA
1 AATTCGCAACACATAAGTCA
1113857 AATTCGCAA
1 AATTCGCAA
1113866 AGCACATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACATAAGTCA
Found at i:1114427 original size:17 final size:19
Alignment explanation
Indices: 1114399--1114447 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1114389 TATTTTGAAA
1114399 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1114417 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1114436 CACCGATGCACT
1 CATCGATGCACT
1114448 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1114427 original size:64 final size:64
Alignment explanation
Indices: 1114218--1114427 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
1114208 TTTTTCAGAG
* * **
1114218 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATT-AAACATCGAATGCA
1 TGATGCATCGATGCACC-ATCCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
1114281 TT
63 TT
* * * ** * *
1114283 TCATGCATCGATGCA-CATACCATGCACCGTTGCACTAAGGATGTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCAT-CCATGCATCGATGCACTCTGGATATTTTG-AAACATCGAATGCAT
1114347 T
64 T
*
1114348 TGATGCATCGATGCACCAGT-CATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCA-TCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
1114412 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1114428 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
63 4 0.03
64 48 0.40
65 65 0.54
66 2 0.02
67 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:1114443 original size:64 final size:64
Alignment explanation
Indices: 1114267--1114451 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 64
1114257 GAATTAAATT
* * *
1114267 AAACATCGAATGCATTTCATGCATCGATGCACATAC-CATGCACCGTTGCACTAAGGATGTTATG
1 AAACATCGAATGCATTTGATGCATCGATGCAC-T-CTCATGCACCGATGCACTAAGGATATTATG
1114331 A
64 A
* ** *
1114332 AAACATCGAATGCATTTGATGCATCGATGCAC-CAGTCATGCATCGATGCACTCTGGATATTTTG
1 AAACATCGAATGCATTTGATGCATCGATGCACTC--TCATGCACCGATGCACTAAGGATATTATG
1114396 -
64 A
* *
1114396 AAACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACTAAGG
1 AAACATCGAATGCATTTGATGCATCGATGCACTCTCA-TGCACCGATGCACTAAGG
1114452 GTCCAACGGT
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 46 0.45
65 54 0.52
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (64 bp):
AAACATCGAATGCATTTGATGCATCGATGCACTCTCATGCACCGATGCACTAAGGATATTATGA
Found at i:1114446 original size:129 final size:130
Alignment explanation
Indices: 1114218--1114451 Score: 316
Period size: 129 Copynumber: 1.8 Consensus size: 130
1114208 TTTTTCAGAG
*
1114218 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTAAACATCGAATGCATT
1 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTAAACATCGAATGCACT
*
1114283 TCATGCATCGATGCACATACCATGCACCGTTGCACTAAGGATGTTATGAAAACATCGAATGCATT
66 TCATGCATCGATGCACATACCATGCACCGATGCACTAAGGATGTTATGAAAACATCGAATGCATT
* * * **
1114348 TGATGCATCGATGCACCAGT-CATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATT-AAACATCGAATGCA
* *
1114410 CTTGATGCATCGATGCAC-T-CTTAGTGCACCGATGCACTAAGG
64 CTTCATGCATCGATGCACATAC-CA-TGCACCGATGCACTAAGG
1114452 GTCCAACGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
127 1 0.01
128 6 0.07
129 65 0.71
130 19 0.21
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (130 bp):
TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTAAACATCGAATGCACT
TCATGCATCGATGCACATACCATGCACCGATGCACTAAGGATGTTATGAAAACATCGAATGCATT
Found at i:1123076 original size:65 final size:63
Alignment explanation
Indices: 1123007--1123190 Score: 226
Period size: 65 Copynumber: 2.9 Consensus size: 63
1122997 AATTAAATTG
* *
1123007 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTAAGGATGTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACAT-CCATGCACCGATGCACTAAGGATATTATG-A
* * ** * *
1123072 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATCCATGCACCGATGCACTAAGGATATTATGA
* *
1123136 AACATCGAATGCACTTGATGCATCGATGCAC-TCTTAGTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCACATC-CA-TGCACCGATGCACTAAGG
1123191 GTCCAACGGT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 45 0.44
65 52 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATCCATGCACCGATGCACTAAGGATATTATGA
Found at i:1123166 original size:17 final size:19
Alignment explanation
Indices: 1123138--1123186 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1123128 TATTTTGAAA
1123138 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1123156 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1123175 CACCGATGCACT
1 CATCGATGCACT
1123187 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1123596 original size:13 final size:14
Alignment explanation
Indices: 1123567--1123593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1123557 TGCAAATATA
1123567 TTTTTCTTGTGAGG
1 TTTTTCTTGTGAGG
1123581 TTTTTCTTGTGAG
1 TTTTTCTTGTGAG
1123594 TTTGCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.26, T:0.59
Consensus pattern (14 bp):
TTTTTCTTGTGAGG
Found at i:1124392 original size:20 final size:20
Alignment explanation
Indices: 1124367--1124426 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
1124357 TTTAGTTTTG
1124367 CGTTGCGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCA
*
1124387 CGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCA
1124407 CGTTGCGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCA
1124427 GAAACTACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:1126622 original size:21 final size:21
Alignment explanation
Indices: 1126598--1126662 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1126588 CCTATCTTTT
1126598 AAGAGGCCCCTCCCACCGTTC
1 AAGAGGCCCCTCCCACCGTTC
* *
1126619 AAGAGGCCCCTCTCATCGTTC
1 AAGAGGCCCCTCCCACCGTTC
1126640 AAGAGG--CC-CCCACCGTTC
1 AAGAGGCCCCTCCCACCGTTC
1126658 AAGAG
1 AAGAG
1126663 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
21 25 0.62
ACGTcount: A:0.23, C:0.40, G:0.22, T:0.15
Consensus pattern (21 bp):
AAGAGGCCCCTCCCACCGTTC
Found at i:1126652 original size:39 final size:41
Alignment explanation
Indices: 1126574--1126662 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
1126564 CCTGTCATCA
* *
1126574 TTCAAGAGGCCTCCCCTATCTTTTAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCTCCCCTATCGTTCAAGAGG-CCCTCCCACCG
*
1126616 TTCAAGAGGCC-CCTCTCATCGTTCAAGAGG-CC-CCCACCG
1 TTCAAGAGGCCTCCCCT-ATCGTTCAAGAGGCCCTCCCACCG
1126655 TTCAAGAG
1 TTCAAGAG
1126663 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 15 0.35
40 2 0.05
41 4 0.09
42 22 0.51
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (41 bp):
TTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCCTCCCACCG
Found at i:1126658 original size:18 final size:19
Alignment explanation
Indices: 1126574--1126662 Score: 81
Period size: 21 Copynumber: 4.4 Consensus size: 19
1126564 CCTGTCATCA
* *
1126574 TTCAAGAGGCCTCCCCTATCT
1 TTCAAGAGGCC-CCCC-ACCG
*
1126595 TTTAAGAGGCCCCTCCCACCG
1 TTCAAGAGG-CCC-CCCACCG
*
1126616 TTCAAGAGGCCCCTCTCATCG
1 TTCAAGAGGCCCC-C-CACCG
1126637 TTCAAGAGG-CCCCCACCG
1 TTCAAGAGGCCCCCCACCG
1126655 TTCAAGAG
1 TTCAAGAG
1126663 CCCGATTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
18 12 0.21
19 2 0.03
20 7 0.12
21 32 0.55
22 5 0.09
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (19 bp):
TTCAAGAGGCCCCCCACCG
Found at i:1128140 original size:20 final size:20
Alignment explanation
Indices: 1128115--1128171 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1128105 TACACTTTCA
1128115 CAACGTGAAAGTCAAATTCG
1 CAACGTGAAAGTCAAATTCG
1128135 CAACGTGAAAGTCAAATTCG
1 CAACGTGAAAGTCAAATTCG
1128155 CAAC-TCGAAAGTCAAAT
1 CAACGT-GAAAGTCAAAT
1128172 GCGCGTTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (20 bp):
CAACGTGAAAGTCAAATTCG
Found at i:1128214 original size:15 final size:14
Alignment explanation
Indices: 1128173--1128215 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1128163 AAGTCAAATG
1128173 CGCGTTGTGATTTT
1 CGCGTTGTGATTTT
*
1128187 CGCGTTGCGATTTT
1 CGCGTTGTGATTTT
*
1128201 TGCGTTGTGAATTTT
1 CGCGTTGTG-ATTTT
1128216 ACTTTCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (14 bp):
CGCGTTGTGATTTT
Found at i:1128281 original size:29 final size:29
Alignment explanation
Indices: 1128228--1128302 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1128218 TTTCACATTT
* *
1128228 CGAATTTGATTTTTCACAACAATCGCAACG
1 CGAATTTGA-CTTTCGCAACAATCGCAACG
*
1128258 CGAATTTGACTTTCGCAATAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
* *
1128287 TGAATTTAACTTTCGC
1 CGAATTTGACTTTCGC
1128303 GTTGCGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 31 0.77
30 9 0.22
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:1130797 original size:24 final size:24
Alignment explanation
Indices: 1130739--1130798 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1130729 CTGAAACATC
1130739 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
** *
1130763 ATCAAGGTTCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
1130787 ATCAAATTTCGA
1 ATCAAAATTCGA
1130799 ATACTAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:1131769 original size:20 final size:21
Alignment explanation
Indices: 1131744--1131854 Score: 72
Period size: 20 Copynumber: 5.4 Consensus size: 21
1131734 AAATAAAACT
1131744 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAAATTCAAAATTCG
1131764 TGTTGC-AAATTCAAAAATT-G
1 TGTTGCGAAATTC-AAAATTCG
* ** * *
1131784 AGTTGCGATTTTCCAAATTAG
1 TGTTGCGAAATTCAAAATTCG
*
1131805 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATTCA-AAATTCG
* **
1131825 AGTTGCG-AATTTGAAATTCAG
1 TGTTGCGAAATTCAAAATTC-G
1131846 TGTTGCGAA
1 TGTTGCGAA
1131855 TTTGGAAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
19 8 0.11
20 34 0.49
21 27 0.39
22 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (21 bp):
TGTTGCGAAATTCAAAATTCG
Found at i:1131851 original size:41 final size:41
Alignment explanation
Indices: 1131745--1131896 Score: 150
Period size: 41 Copynumber: 3.8 Consensus size: 41
1131735 AATAAAACTT
* * * *
1131745 GTTGCGAAATTAAAATTC-GTGTTGCAAATTCAAAAATTGA
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTCAGAAATTGA
* * * *
1131785 GTTGCGATTTTCCAAATT-AGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAATTT-GAAATTCAGTGTTGCGAATTCAGAAATTGA
**
1131826 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATTGCA
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTCAGAAATTG-A
* *
1131868 -TTGCGAATTTG-ACTTCTGTGTTGCGAATT
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATT
1131897 TGACTTCTGT
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 30 0.32
41 62 0.67
42 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCAGTGTTGCGAATTCAGAAATTGA
Found at i:1131891 original size:20 final size:20
Alignment explanation
Indices: 1131826--1131913 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
1131816 CAGAAATCGA
*
1131826 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-AATTCTGT
* *
1131847 GTTGCGAATTTGGAAAT-TGC
1 GTTGCGAATTT-GAATTCTGT
* *
1131867 ATTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAATTCTGT
*
1131887 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAATTCTGT
1131907 GTTGCGA
1 GTTGCGA
1131914 TTTACAGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.05
20 39 0.68
21 14 0.25
22 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGAATTCTGT
Found at i:1131930 original size:20 final size:20
Alignment explanation
Indices: 1131907--1131986 Score: 151
Period size: 20 Copynumber: 4.0 Consensus size: 20
1131897 TGACTTCTGT
1131907 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
1131927 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCGC
1131947 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
1131967 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
1131987 ATTGTGAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:1132006 original size:40 final size:40
Alignment explanation
Indices: 1131908--1132011 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
1131898 GACTTCTGTG
* *
1131908 TTGCGATTTACAGATTCGCGTTGCGATTTACAGATTCACG
1 TTGCGAATTACAGATTCGCGTTGCGATTTACAGATTCACA
* *
1131948 TTGCGATTTACAGATTCGCGTTGCGATTTACAGATTCGCA
1 TTGCGAATTACAGATTCGCGTTGCGATTTACAGATTCACA
* *
1131988 TTGTGAAATTAGAG-TTCGCGTTGC
1 TTGCG-AATTACAGATTCGCGTTGC
1132012 AAATTCGAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 52 0.90
41 6 0.10
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (40 bp):
TTGCGAATTACAGATTCGCGTTGCGATTTACAGATTCACA
Found at i:1132010 original size:60 final size:59
Alignment explanation
Indices: 1131907--1132032 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 59
1131897 TGACTTCTGT
* * * *
1131907 GTTGCGATTTACAGATTCGCGTTGCGATTTACAGATTCACGTTGCGATTTAC-AGATTCGC
1 GTTGCGATTTACAGATTCGCATTGCGAATTACAGATTCACGTTGCAAATT-CGAGA-TCGC
* * *
1131967 GTTGCGATTTACAGATTCGCATTGTGAAATTAGAG-TTCGCGTTGCAAATTCGAGATCGC
1 GTTGCGATTTACAGATTCGCATTGCG-AATTACAGATTCACGTTGCAAATTCGAGATCGC
1132026 GTTGCGA
1 GTTGCGA
1132033 ATTTGTTAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 12 0.21
60 39 0.68
61 6 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (59 bp):
GTTGCGATTTACAGATTCGCATTGCGAATTACAGATTCACGTTGCAAATTCGAGATCGC
Found at i:1132025 original size:19 final size:19
Alignment explanation
Indices: 1131993--1132035 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1131983 TCGCATTGTG
*
1131993 AAATTAGAGTTCGCGTTGC
1 AAATTAGAGATCGCGTTGC
*
1132012 AAATTCGAGATCGCGTTGC
1 AAATTAGAGATCGCGTTGC
*
1132031 GAATT
1 AAATT
1132036 TGTTAGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (19 bp):
AAATTAGAGATCGCGTTGC
Found at i:1132169 original size:24 final size:24
Alignment explanation
Indices: 1132140--1132199 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
1132130 TGAATTGACA
1132140 TGTATTAATTTTTTATAAATATTT
1 TGTATTAATTTTTTATAAATATTT
1132164 TGTATTAATTTTTTATAAATATTT
1 TGTATTAATTTTTTATAAATATTT
1132188 TGTATTAATTTT
1 TGTATTAATTTT
1132200 CATTTACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TGTATTAATTTTTTATAAATATTT
Found at i:1132177 original size:13 final size:13
Alignment explanation
Indices: 1132140--1132199 Score: 56
Period size: 12 Copynumber: 4.9 Consensus size: 13
1132130 TGAATTGACA
1132140 TGTATTAA-TTTT
1 TGTATTAATTTTT
* *
1132152 T-TATAAATATTT
1 TGTATTAATTTTT
1132164 TGTATTAA-TTTT
1 TGTATTAATTTTT
* *
1132176 T-TATAAATATTT
1 TGTATTAATTTTT
1132188 TGTATTAATTTT
1 TGTATTAATTTT
1132200 CATTTACTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 10 0.28
12 13 0.36
13 13 0.36
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (13 bp):
TGTATTAATTTTT
Found at i:1137391 original size:25 final size:23
Alignment explanation
Indices: 1137367--1137426 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 23
1137357 TTTAAATAAT
1137367 TTTTATATTTTTAAAAATTTGTAA
1 TTTTATATTTTTAAAAATTT-TAA
*
1137391 TTTTATATGTTTTAAATATTTT-A
1 TTTTATAT-TTTTAAAAATTTTAA
1137414 TTTTATATTTTTA
1 TTTTATATTTTTA
1137427 TATAAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.15
23 9 0.26
24 9 0.26
25 11 0.32
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (23 bp):
TTTTATATTTTTAAAAATTTTAA
Found at i:1138649 original size:16 final size:17
Alignment explanation
Indices: 1138630--1138669 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1138620 ATTAATCGAT
*
1138630 AATCA-AAGTTGGAAAA
1 AATCATAAGTTAGAAAA
1138646 AATCATTAAGTTAGAAAA
1 AATCA-TAAGTTAGAAAA
1138664 AATCAT
1 AATCAT
1138670 TAACCGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 1 0.05
18 15 0.71
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (17 bp):
AATCATAAGTTAGAAAA
Found at i:1138662 original size:18 final size:18
Alignment explanation
Indices: 1138635--1138672 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1138625 TCGATAATCA
*
1138635 AAGTTGGAAAAAATCATT
1 AAGTTAGAAAAAATCATT
1138653 AAGTTAGAAAAAATCATT
1 AAGTTAGAAAAAATCATT
1138671 AA
1 AA
1138673 CCGGTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (18 bp):
AAGTTAGAAAAAATCATT
Found at i:1139487 original size:162 final size:161
Alignment explanation
Indices: 1139043--1139542 Score: 707
Period size: 163 Copynumber: 3.1 Consensus size: 161
1139033 CCATTCAAAT
* * * * * *
1139043 ATGTATCGATACATAACAATATATCAGGTAAAAATATGACATAACCGGTAAGGCGCTGCCGAATA
1 ATGTATCGATACATAACAATATATCA-GT-AAAATATGACAAAACCGGTAAAGCACTACTGGATA
* * * *
1139108 TGTTGAATGTATCGATACCATTAAAATAAGTATCGATACTTTTGAAATTTAAAAGGAAAGCAATA
64 TGTTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGCAATA
1139173 ATAGCGCCTATAAAGTATCGATACTTTATAAAC
129 ATAGCGCCTATAAAGTATCGATACTTTATAAAC
* * *
1139206 ATGTATCGATACATAACATTATATCAGATTAAAATATGACAAAACCAGTAAAG-AGCTACTAGAT
1 ATGTATCGATACATAACAATATATCAG--TAAAATATGACAAAACCGGTAAAGCA-CTACTGGAT
* * *
1139270 ATGTTGAAGGTATTGATACCATTCAAATAAGTATCGATACATTTAGAATTTAAAAGAAAAGCAAT
63 ATGTTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGCAAT
* * *
1139335 AATAGCGCCTATAAAGTATTGATACATTATAAAA
128 AATAGCGCCTATAAAGTATCGATACTTTATAAAC
* *
1139369 ATGTATCGATACATAACAATATAACATGTAAAATATGACAAAACTGGTAAAGCACTACTGGATAT
1 ATGTATCGATACATAACAATATATCA-GTAAAATATGACAAAACCGGTAAAGCACTACTGGATAT
*
1139434 GTTGAAGGTATCGATACCATTCAAATAAGTA-CGGATACTTTTGGAATTTAAAAGAAAAGCAGTA
65 GTTGAAGGTATCGATACCATTCAAATAAGTATC-GATACTTTTGGAATTTAAAAGAAAAGCAATA
* *
1139498 ATAGCGCCTATAAAATATCAATACTTTATAAAC
129 ATAGCGCCTATAAAGTATCGATACTTTATAAAC
1139531 ATGTATCGATAC
1 ATGTATCGATAC
1139543 TTTATAAACA
Statistics
Matches: 298, Mismatches: 33, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
161 1 0.00
162 131 0.44
163 164 0.55
164 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (161 bp):
ATGTATCGATACATAACAATATATCAGTAAAATATGACAAAACCGGTAAAGCACTACTGGATATG
TTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGCAATAAT
AGCGCCTATAAAGTATCGATACTTTATAAAC
Found at i:1139542 original size:21 final size:21
Alignment explanation
Indices: 1139513--1139562 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1139503 GCCTATAAAA
*
1139513 TATCAATACTTTATAAACATG
1 TATCGATACTTTATAAACATG
1139534 TATCGATACTTTATAAACATG
1 TATCGATACTTTATAAACATG
1139555 TATCGATA
1 TATCGATA
1139563 TATAACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
TATCGATACTTTATAAACATG
Found at i:1141408 original size:15 final size:15
Alignment explanation
Indices: 1141388--1141429 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1141378 GAGACCTTAT
1141388 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
*
1141403 CCGCCCCGTATCCGC
1 CCGCCCCGCATCCGC
*
1141418 CCGCCCCACATC
1 CCGCCCCGCATC
1141430 TACCCGCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.64, G:0.17, T:0.10
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:1143268 original size:20 final size:20
Alignment explanation
Indices: 1143241--1143285 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1143231 ATCATAAACT
1143241 TTTATATAT-GTATCAATAC
1 TTTATATATCGTATCAATAC
*
1143260 TTTATTATATCGGTCTCAATAC
1 TTTA-TATATC-GTATCAATAC
1143282 TTTA
1 TTTA
1143286 ATTCCACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
22 13 0.59
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTATATATCGTATCAATAC
Done.