Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 8 of 136
Found at i:2196772 original size:20 final size:19
Alignment explanation
Indices: 2196730--2196774 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2196720 TCTATTTTCT
* * *
2196730 TTTTATATTTTTCATTTCT
1 TTTTATACTTTTCATTCCG
2196749 TTTTATACTTTTCATGTCCG
1 TTTTATACTTTTCAT-TCCG
2196769 TTTTAT
1 TTTTAT
2196775 GGTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATACTTTTCATTCCG
Found at i:2197140 original size:9 final size:9
Alignment explanation
Indices: 2197123--2197181 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
2197113 AATTATTTAT
*
2197123 TTTTTAAAA
1 TTTTAAAAA
2197132 TTTTAAAAA
1 TTTTAAAAA
2197141 TTTTAAAAAA
1 TTTT-AAAAA
2197151 TTTTTAAAAA
1 -TTTTAAAAA
*
2197161 TTTTTAAAA
1 TTTTAAAAA
2197170 TTATCTAAAAA
1 TT-T-TAAAAA
2197181 T
1 T
2197182 GTTTTTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 22 0.51
10 11 0.26
11 10 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:2197149 original size:10 final size:10
Alignment explanation
Indices: 2197128--2197169 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
2197118 TTTATTTTTT
2197128 AAAATTTT-A
1 AAAATTTTAA
2197137 AAAATTTTAA
1 AAAATTTTAA
2197147 AAAATTTTTAA
1 AAAA-TTTTAA
*
2197158 AAATTTTTAA
1 AAAATTTTAA
2197168 AA
1 AA
2197170 TTATCTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:2200545 original size:56 final size:50
Alignment explanation
Indices: 2200428--2200527 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2200418 GTTCGTGTAA
2200428 CATAGTTTTTCAGATCATATCAATATCCGACACTAAAACCTGAGTTTGAG
1 CATAGTTTTTCAGATCATATCAATATCCGACACTAAAACCTGAGTTTGAG
2200478 CATAGTTTTTCAGATCATATCAATATCCGACACTAAAACCTGAGTTTGAG
1 CATAGTTTTTCAGATCATATCAATATCCGACACTAAAACCTGAGTTTGAG
2200528 TATCATTGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (50 bp):
CATAGTTTTTCAGATCATATCAATATCCGACACTAAAACCTGAGTTTGAG
Found at i:2203316 original size:2 final size:2
Alignment explanation
Indices: 2203309--2203335 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2203299 CAAAAATCCA
2203309 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2203336 CCTTAAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2204608 original size:22 final size:20
Alignment explanation
Indices: 2204571--2204611 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2204561 TACAAAAAAT
*
2204571 AAATTATAAAACATTATTAA
1 AAATTATAAAAAATTATTAA
2204591 AAATTATAGAAAAAATTATTA
1 AAATTAT--AAAAAATTATTA
2204612 TTTTGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAATTATAAAAAATTATTAA
Found at i:2205175 original size:18 final size:19
Alignment explanation
Indices: 2205152--2205195 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2205142 TTATACAATA
2205152 TATTAAAGTTTTA-ATTTT
1 TATTAAAGTTTTATATTTT
*
2205170 TATT-AATTTTTATATTTT
1 TATTAAAGTTTTATATTTT
2205188 TAATTAAA
1 T-ATTAAA
2205196 TAATAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 3 0.14
20 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTAAAGTTTTATATTTT
Found at i:2205822 original size:19 final size:19
Alignment explanation
Indices: 2205798--2205840 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2205788 CTTAAACCAA
2205798 TTATA-TCACAAAGATATTT
1 TTATATTCA-AAAGATATTT
* *
2205817 TTATATTCAAATGTTATTT
1 TTATATTCAAAAGATATTT
2205836 TTATA
1 TTATA
2205841 AGTCAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATATTCAAAAGATATTT
Found at i:2207833 original size:37 final size:40
Alignment explanation
Indices: 2207792--2207870 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 40
2207782 TATATATTTA
*
2207792 TAATT-AAATTTAAA-TAAAAA-TATTT-TTGATATATAAT
1 TAATTCAAA-TTAAATTAAAAAGTATTTATTGAAATATAAT
*
2207829 TAATTCAAATTAAATTTAAAAAGTATTTATTTAAATATAAT
1 TAATTCAAATTAAA-TTAAAAAGTATTTATTGAAATATAAT
2207870 T
1 T
2207871 TAATATAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
37 10 0.29
38 3 0.09
39 6 0.17
40 5 0.14
41 11 0.31
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (40 bp):
TAATTCAAATTAAATTAAAAAGTATTTATTGAAATATAAT
Found at i:2214820 original size:32 final size:32
Alignment explanation
Indices: 2214784--2214848 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2214774 CCATTTGAAT
* **
2214784 TGAGCTCTTACTCTAATATCCATGACAAACTA
1 TGAGCTCTTACTATAATATCCACAACAAACTA
2214816 TGAGCTCTTACTATAATATCCACAACAAACTA
1 TGAGCTCTTACTATAATATCCACAACAAACTA
2214848 T
1 T
2214849 CTCCCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (32 bp):
TGAGCTCTTACTATAATATCCACAACAAACTA
Found at i:2221229 original size:20 final size:20
Alignment explanation
Indices: 2221204--2221242 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2221194 TACTTTCTTC
2221204 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
2221224 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
2221243 AATACTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:2221558 original size:50 final size:52
Alignment explanation
Indices: 2221491--2221636 Score: 187
Period size: 50 Copynumber: 2.9 Consensus size: 52
2221481 TTTCCTGTAC
* * *
2221491 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAG-TC-CTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGACCTCTCATATCGG
* * * *
2221541 TGCCTATGCCATGTCCCAAACATGGTCTT--ATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGACCTCTCATATCGG
2221591 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GG-GACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGACCTCTCATA
2221637 ACCTTAATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
48 6 0.07
49 1 0.01
50 71 0.87
51 2 0.02
52 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGACCTCTCATATCGG
Found at i:2224843 original size:23 final size:22
Alignment explanation
Indices: 2224800--2224843 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
2224790 ATTTCTAAGG
2224800 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
2224823 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
2224844 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:2224954 original size:45 final size:45
Alignment explanation
Indices: 2224890--2224976 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
2224880 CAGATACTCG
* * **
2224890 GTGGATTCAGCACATAGCAACCACCTTATTAATTGATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
2224935 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
2224977 TTGGTTCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:2225061 original size:51 final size:51
Alignment explanation
Indices: 2224983--2225116 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 51
2224973 ATGTTTGGTT
* * **
2224983 CACATAGTAGTCTGCACGTAGTACTACACATGTGA-CTATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGATC-AAAACCATCCGATA
* * * *
2225034 CA-AGTAGTAGCCTACACATAGTACTACACACGTGATCAAAACTATCCGGTA
1 CACA-TAGTAGCCTGCACATAGTACTACACATGTGATCAAAACCATCCGATA
2225085 CACATAGTAGCCTGCACATAGTACTACACATG
1 CACATAGTAGCCTGCACATAGTACTACACATG
2225117 CGACCTATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 67 0.96
52 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGATCAAAACCATCCGATA
Found at i:2225107 original size:102 final size:101
Alignment explanation
Indices: 2224983--2225169 Score: 252
Period size: 101 Copynumber: 1.8 Consensus size: 101
2224973 ATGTTTGGTT
* * *
2224983 CACATAGTAGTCTGCACGTAGTACTACACATGTGA-CTATTACCA-TCCGATACAAGTAGTAGCC
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTA-T--CATTCCGATACAAGTAGTAGCC
2225046 TACACATAGTACTACACACGTGATCAAAACTATCCGGTA
63 TACACATAGTACTACACACGTGATCAAAACTATCCGGTA
* * * *
2225085 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTTCGGTACACGTAGTAGCCTGC
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACAAGTAGTAGCCTAC
**
2225150 ACATAGTGTTACACACGTGA
66 ACATAGTACTACACACGTGA
2225170 CCATCACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 2 0.03
101 36 0.49
102 33 0.45
103 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACAAGTAGTAGCCTAC
ACATAGTACTACACACGTGATCAAAACTATCCGGTA
Found at i:2230555 original size:22 final size:24
Alignment explanation
Indices: 2230523--2230569 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2230513 AGGTAATCCC
*
2230523 TAAAAAGAACAATGGG-CCCACTT
1 TAAAAAGAACAAAGGGCCCCACTT
2230546 TAAAAA-AACAAAGGGCCCCACTT
1 TAAAAAGAACAAAGGGCCCCACTT
2230569 T
1 T
2230570 TACCTTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (24 bp):
TAAAAAGAACAAAGGGCCCCACTT
Found at i:2231056 original size:40 final size:40
Alignment explanation
Indices: 2231001--2231077 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2230991 TGCTTTAACA
* *
2231001 CACTCAAATCCATATCCTCTTACATTAGGAACAATGTTCG
1 CACTCAAACCCATATCCTCTTACAGTAGGAACAATGTTCG
* *
2231041 CACTCGAACCCATATCCTTTTACAGTAGGAACAATGT
1 CACTCAAACCCATATCCTCTTACAGTAGGAACAATGT
2231078 CCATACTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (40 bp):
CACTCAAACCCATATCCTCTTACAGTAGGAACAATGTTCG
Found at i:2232186 original size:21 final size:21
Alignment explanation
Indices: 2232162--2232201 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2232152 TTTTTATTTA
2232162 AAATGAAAATTTTAATTCATT
1 AAATGAAAATTTTAATTCATT
** *
2232183 AAATTTAAATTTTTATTCA
1 AAATGAAAATTTTAATTCA
2232202 ATATTAAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATGAAAATTTTAATTCATT
Found at i:2246584 original size:75 final size:76
Alignment explanation
Indices: 2246466--2246608 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 76
2246456 GGCCAATACC
* * *
2246466 AGAGGTCTTATCCCCTTAGATGAATTGGCTTAGGTGAAAGGTCTTGTCTCCT-TTAACACCAAAG
1 AGAGGTCTTATCACCTTAGATGAATTAGCTAAGGTGAAAGGTCTTGTC-CCTCTTAACACCAAAG
2246530 AAGACCAATGTG
65 AAGACCAATGTG
* ** *
2246542 AGAGGTCTTAT-ACCTTTGATGAATTAGCTAAGGTGAGGGGTCTTGTCCCTCTTAACGCCAAAGA
1 AGAGGTCTTATCACCTTAGATGAATTAGCTAAGGTGAAAGGTCTTGTCCCTCTTAACACCAAAGA
2246606 AGA
66 AGA
2246609 TCAAGTATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 3 0.05
75 45 0.76
76 11 0.19
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (76 bp):
AGAGGTCTTATCACCTTAGATGAATTAGCTAAGGTGAAAGGTCTTGTCCCTCTTAACACCAAAGA
AGACCAATGTG
Found at i:2249685 original size:21 final size:22
Alignment explanation
Indices: 2249661--2249704 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2249651 GTTGAAAAAA
*
2249661 TTATTTAATTCAAA-AATTAAT
1 TTATCTAATTCAAATAATTAAT
*
2249682 TTATCTAATTGAAATAATTAAT
1 TTATCTAATTCAAATAATTAAT
2249704 T
1 T
2249705 AATTGATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATCTAATTCAAATAATTAAT
Found at i:2250097 original size:20 final size:22
Alignment explanation
Indices: 2250060--2250107 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
2250050 AAGTAGTGAG
*
2250060 AATT-TATTTTCTATGAA-TA-
1 AATTCTATTTTCTAGGAATTAC
*
2250079 AATTCTATTTTCTGGGAATTAC
1 AATTCTATTTTCTAGGAATTAC
2250101 AATTCTA
1 AATTCTA
2250108 CCGTTTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 2 0.08
22 7 0.29
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (22 bp):
AATTCTATTTTCTAGGAATTAC
Found at i:2253991 original size:110 final size:111
Alignment explanation
Indices: 2253843--2254064 Score: 324
Period size: 111 Copynumber: 2.0 Consensus size: 111
2253833 AAAATTTCAA
* *
2253843 ATTTTTTTTGGTGGTGGCCTGGCAATAGCCGGCGCCACCTTTATGT-AAAAAAATTTGA-ATTTT
1 ATTTTTTTTAGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAAATTT-ACA-TTT
* * * *
2253906 TTCG-TGTCATTGGTCGACACCAGTATATGAAAAAATTCAAAAAATTT
64 TGCGCAGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAATTT
*
2253953 ATTTTTTTTAGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAATTTACATTTTG
1 ATTTTTTTTAGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAAATTTACATTTTG
* *
2254018 GGCAGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAATTTT
66 CGCAGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAATTT
2254064 A
1 A
2254065 AAGTTTTTCG
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
110 49 0.49
111 51 0.51
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (111 bp):
ATTTTTTTTAGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAAATTTACATTTTG
CGCAGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAATTT
Found at i:2258048 original size:34 final size:34
Alignment explanation
Indices: 2258005--2258071 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
2257995 ACTTATAAAC
2258005 TATCCATCGCCTAACTACTCCAAGCACATATATA
1 TATCCATCGCCTAACTACTCCAAGCACATATATA
2258039 TATCCATCGCCTAACTACTCCAAGCACATATAT
1 TATCCATCGCCTAACTACTCCAAGCACATATAT
2258072 CAAACATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.33, G:0.06, T:0.27
Consensus pattern (34 bp):
TATCCATCGCCTAACTACTCCAAGCACATATATA
Found at i:2258767 original size:24 final size:25
Alignment explanation
Indices: 2258734--2258799 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
2258724 TACATTTTCC
*
2258734 GTCAACTCATCCTTTGCA-TATACT
1 GTCAATTCATCCTTTGCATTATACT
* * *
2258758 GTCAATTCATCCATTGCATTTTTCT
1 GTCAATTCATCCTTTGCATTATACT
*
2258783 ATCAATTCATCCTTTGC
1 GTCAATTCATCCTTTGC
2258800 CATAGAACGG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (25 bp):
GTCAATTCATCCTTTGCATTATACT
Found at i:2259941 original size:18 final size:18
Alignment explanation
Indices: 2259918--2259952 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2259908 TTACGGCTTA
2259918 GTTTATAAAATCGAGGTG
1 GTTTATAAAATCGAGGTG
*
2259936 GTTTATAAAATTGAGGT
1 GTTTATAAAATCGAGGT
2259953 CTCGATACCT
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:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (18 bp):
GTTTATAAAATCGAGGTG
Found at i:2263272 original size:30 final size:30
Alignment explanation
Indices: 2263236--2263385 Score: 201
Period size: 30 Copynumber: 5.0 Consensus size: 30
2263226 GGTCGGGTAA
*
2263236 TCTATTATAATGTCAGCTTGTATAAGCAAT
1 TCTATTATAATGTCAGCTTGTGTAAGCAAT
* * * *
2263266 TCTATTATAATGTTAGCTTCTGTGAGCAAA
1 TCTATTATAATGTCAGCTTGTGTAAGCAAT
* *
2263296 TCTATTATCATGTCAGCTTGTGTAAGCAAA
1 TCTATTATAATGTCAGCTTGTGTAAGCAAT
* *
2263326 TCTATTATAATATCAGCTTGTATAAGCAAT
1 TCTATTATAATGTCAGCTTGTGTAAGCAAT
* *
2263356 TCTATCATAATGTCAGCTTGTGTGAGCAAT
1 TCTATTATAATGTCAGCTTGTGTAAGCAAT
2263386 ATATTCACCT
Statistics
Matches: 103, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 103 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (30 bp):
TCTATTATAATGTCAGCTTGTGTAAGCAAT
Found at i:2270020 original size:239 final size:240
Alignment explanation
Indices: 2269601--2270074 Score: 923
Period size: 239 Copynumber: 2.0 Consensus size: 240
2269591 TTATTTCTTA
*
2269601 TATATAAATAAAAATAAAGCATGCCACCACATGAAGAGTTCTCGACTAAAGGATTGGAGGGTGCA
1 TATATAAATAAAAATAAAGCATGCCACCACATGAAGAGTTCCCGACTAAAGGATTGGAGGGTGCA
2269666 CCAAGTAATGATATAGGTTGGCACTTTGGAACTCCAGTGCCAAATGCGAAAGGAAATATCGTATG
66 CCAAGTAATGATATAGGTTGGCACTTTGGAACTCCAGTGCCAAATGCGAAAGGAAATATCGTATG
2269731 TAAACTTTGTGGTAAATTTGTGAAAGGAGGAATAACACGATTTAAAGAGCACATTACTCATAAAA
131 TAAACTTTGTGGTAAATTTGTGAAAGGAGGAATAACACGATTTAAAGAGCACATTACTCATAAAA
2269796 CCGGCAATGTTGCACCATGCCCTAATGTT-CTGGTATGTGGATAT
196 CCGGCAATGTTGCACCATGCCCTAATGTTACTGGTATGTGGATAT
*
2269840 TATATAAATAAAAATAAAGCATGCCACCACGTGAAGAGTTCCCGACTAAAGGATTGGAGGGTGCA
1 TATATAAATAAAAATAAAGCATGCCACCACATGAAGAGTTCCCGACTAAAGGATTGGAGGGTGCA
2269905 CCAAGTAATGATATAGGTTGGCACTTTGGAACTCCAGTGCCAAATGCGAAAGGAAATATCGTATG
66 CCAAGTAATGATATAGGTTGGCACTTTGGAACTCCAGTGCCAAATGCGAAAGGAAATATCGTATG
2269970 TAAACTTTGTGGTAAATTTGTGAAAGGAGGAATAACACGATTTAAAGAGCACATTACTCATAAAA
131 TAAACTTTGTGGTAAATTTGTGAAAGGAGGAATAACACGATTTAAAGAGCACATTACTCATAAAA
2270035 CCGGCAATGTTGCACCATGCCCTAATGTTACTGGTATGTG
196 CCGGCAATGTTGCACCATGCCCTAATGTTACTGGTATGTG
2270075 ATAATTTATT
Statistics
Matches: 232, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
239 222 0.96
240 10 0.04
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (240 bp):
TATATAAATAAAAATAAAGCATGCCACCACATGAAGAGTTCCCGACTAAAGGATTGGAGGGTGCA
CCAAGTAATGATATAGGTTGGCACTTTGGAACTCCAGTGCCAAATGCGAAAGGAAATATCGTATG
TAAACTTTGTGGTAAATTTGTGAAAGGAGGAATAACACGATTTAAAGAGCACATTACTCATAAAA
CCGGCAATGTTGCACCATGCCCTAATGTTACTGGTATGTGGATAT
Found at i:2274374 original size:12 final size:12
Alignment explanation
Indices: 2274334--2274375 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2274324 CATAAAAGAG
*
2274334 CATATCTTATAT
1 CATATCATATAT
2274346 CATATC-T-TAT
1 CATATCATATAT
*
2274356 CATATCATATTT
1 CATATCATATAT
2274368 CATATCAT
1 CATATCAT
2274376 GTCGTAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 16 0.59
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (12 bp):
CATATCATATAT
Found at i:2275469 original size:12 final size:12
Alignment explanation
Indices: 2275448--2275481 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2275438 TAACTGAGAG
*
2275448 AAAACTCATCTA
1 AAAACACATCTA
2275460 AAAACACATCTA
1 AAAACACATCTA
2275472 AAAACACATC
1 AAAACACATC
2275482 CTTAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAACACATCTA
Found at i:2278621 original size:5 final size:6
Alignment explanation
Indices: 2278594--2278619 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2278584 GGATTTGGTG
2278594 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
2278620 TATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2280194 original size:84 final size:84
Alignment explanation
Indices: 2280050--2280210 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
2280040 GATTTGGTTA
* ***
2280050 TTAATTAAGGAAAAAAGACCAAATCGTAAAAGATGTAAAACGTAATCGCTATTGGTTTTTATTAA
1 TTAATTAAGGAAAAAAGACCAAATCATAAAAGATGTAAAACGTAATCGCTATTAAATTTTATTAA
2280115 ATAAATGGCTTATTTATAG
66 ATAAATGGCTTATTTATAG
* ** * * *
2280134 TTAATTAAGGAAAAATGAGTAAATTATAAAATATGTAAAACTTAATCGCTATTAAATTTTATTAA
1 TTAATTAAGGAAAAAAGACCAAATCATAAAAGATGTAAAACGTAATCGCTATTAAATTTTATTAA
*
2280199 CTAAATGGCTTA
66 ATAAATGGCTTA
2280211 ATTAGTGGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (84 bp):
TTAATTAAGGAAAAAAGACCAAATCATAAAAGATGTAAAACGTAATCGCTATTAAATTTTATTAA
ATAAATGGCTTATTTATAG
Found at i:2281403 original size:12 final size:13
Alignment explanation
Indices: 2281360--2281401 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
2281350 GTTTCTTGTT
*
2281360 TTTTATTTATTTAA
1 TTTTCTTTATTT-A
2281374 TTTTCTTTATTTA
1 TTTTCTTTATTTA
2281387 TTTTC-TTA-TTA
1 TTTTCTTTATTTA
2281398 TTTT
1 TTTT
2281402 TCGTATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 6 0.22
14 11 0.41
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTATTTA
Found at i:2285131 original size:49 final size:49
Alignment explanation
Indices: 2285078--2285223 Score: 141
Period size: 51 Copynumber: 2.9 Consensus size: 49
2285068 CAAAGTCTCG
* * *
2285078 AGACATAGAACTTTGAAGGTAAAATTTGAAGATGAGGAGGTAAGTCCCA
1 AGACATAGAACTTTGAAGCTAAAGTTTGAAGCTGAGGAGGTAAGTCCCA
* * ** * * *
2285127 AGACATAAAACTTCGAAGCTAAAGTCTTGGGGCT-TGGAGGTTAATGTCTCG
1 AGACATAGAACTTTGAAGCTAAAGT-TTGAAGCTGAGGAGG-TAA-GTCCCA
* * *
2285178 AGACATAGAACTTTGAAGTTAAAGTTTGAAGCTGATGAGGCAAGTC
1 AGACATAGAACTTTGAAGCTAAAGTTTGAAGCTGAGGAGGTAAGTC
2285224 TTGAGGCATG
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
49 29 0.39
50 16 0.21
51 30 0.40
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (49 bp):
AGACATAGAACTTTGAAGCTAAAGTTTGAAGCTGAGGAGGTAAGTCCCA
Found at i:2286766 original size:20 final size:20
Alignment explanation
Indices: 2286741--2286780 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2286731 ATCTATGATG
2286741 CCTTTGTGGCATATTATGTA
1 CCTTTGTGGCATATTATGTA
* *
2286761 CCTTTGTGGCGTATTCTGTA
1 CCTTTGTGGCATATTATGTA
2286781 AGTGTCTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
CCTTTGTGGCATATTATGTA
Found at i:2288887 original size:57 final size:57
Alignment explanation
Indices: 2288726--2288904 Score: 236
Period size: 56 Copynumber: 3.1 Consensus size: 57
2288716 ATAGAAATTG
* *
2288726 TGAAAATGGAGAAATGAGAAAT-ATTTGGAAATGATTATGGTTTTCTCCAAAATGGAAA
1 TGAAAATGGAGAAATG-G-AATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAA
* * * *
2288784 TGGAATTGGGGAAAT-GAATCATTTGAAAATGATTATGGTTTTCTCCAAAATTAAAA
1 TGAAAATGGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAA
* * *
2288840 TGAAAATAGAGAAATGGAATCATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAA
*
2288897 AGAAAATG
1 TGAAAATG
2288905 ACCTGAAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
55 3 0.03
56 45 0.43
57 44 0.42
58 12 0.12
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.30
Consensus pattern (57 bp):
TGAAAATGGAGAAATGGAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAA
Found at i:2293827 original size:6 final size:6
Alignment explanation
Indices: 2293818--2293846 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2293808 TCTATCAAAA
2293818 ATAATC ATAATC ATAATC ATAATC ATAAT
1 ATAATC ATAATC ATAATC ATAATC ATAAT
2293847 AATTTCTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAATC
Found at i:2294347 original size:60 final size:60
Alignment explanation
Indices: 2294270--2294388 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
2294260 ATATAAGAAC
* * * *
2294270 CAAACCTTTCAAGATGGTCATATAAGAGCCTA-ACTTTTATAAAAGTGCTCAAATGAAGGT
1 CAAACCTTTCAAAATGGTCAGAGAAGAGCCTAGACTTTT-TAAAAGTGCTCAAATAAAGGT
* *
2294330 CAAACCTTTCAAAATGGTCAGAGAAGGGCCTAGCCTTTTTAAAAGTGCTCAAATAAAGG
1 CAAACCTTTCAAAATGGTCAGAGAAGAGCCTAGACTTTTTAAAAGTGCTCAAATAAAGG
2294389 CCTCTCAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 47 0.90
61 5 0.10
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAACCTTTCAAAATGGTCAGAGAAGAGCCTAGACTTTTTAAAAGTGCTCAAATAAAGGT
Found at i:2294391 original size:31 final size:31
Alignment explanation
Indices: 2294297--2294391 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 31
2294287 TCATATAAGA
*
2294297 GCCTAA-CTTTTATAAAAGTGCTCAAATGAAG
1 GCCTAACCTTTT-TAAAAGTGCTCAAATAAAG
* * * * * * *
2294328 GTCAAACC-TTTCAAAA-TGGTCAGAGAAGG
1 GCCTAACCTTTTTAAAAGTGCTCAAATAAAG
*
2294357 GCCTAGCCTTTTTAAAAGTGCTCAAATAAAG
1 GCCTAACCTTTTTAAAAGTGCTCAAATAAAG
2294388 GCCT
1 GCCT
2294392 CTCAAATGTC
Statistics
Matches: 45, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
29 13 0.29
30 11 0.24
31 20 0.44
32 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (31 bp):
GCCTAACCTTTTTAAAAGTGCTCAAATAAAG
Found at i:2300449 original size:22 final size:22
Alignment explanation
Indices: 2300424--2300474 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2300414 TTTTAACAAT
*
2300424 AGAAATGTATAAAATTTTTAAC
1 AGAAATGGATAAAATTTTTAAC
* *
2300446 AGAAATGGATGAAATTTTTAAT
1 AGAAATGGATAAAATTTTTAAC
2300468 AGAAATG
1 AGAAATG
2300475 ATCAGTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
AGAAATGGATAAAATTTTTAAC
Found at i:2310050 original size:102 final size:102
Alignment explanation
Indices: 2309871--2310070 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
2309861 TCAAGCCGCG
* * *
2309871 TGAGCCCAAAAATGTCCTACTTCAAGGTCAAATTTCACCCAATTGCATAGGTATCTAAACCAATA
1 TGAGCCAAAAAATGTCCTACTTCAAGCTCAAATTTCACCCAATTGCATAGGTACCTAAACCAATA
*
2309936 CAAAACATGTGATCACAAGGCTTCAAACACATATGTA
66 CAAAACACGTGATCACAAGGCTTCAAACACATATGTA
* *
2309973 TGAGCCAAAAAATGTCCTACTTCAAGCTTAAATTTCACCTAATTGCATAGGTACCTAAACCAATA
1 TGAGCCAAAAAATGTCCTACTTCAAGCTCAAATTTCACCCAATTGCATAGGTACCTAAACCAATA
2310038 CAAAACACGTGATCACAAGGCTTCAAACACATA
66 CAAAACACGTGATCACAAGGCTTCAAACACATA
2310071 CAAAAACATT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (102 bp):
TGAGCCAAAAAATGTCCTACTTCAAGCTCAAATTTCACCCAATTGCATAGGTACCTAAACCAATA
CAAAACACGTGATCACAAGGCTTCAAACACATATGTA
Found at i:2313625 original size:35 final size:35
Alignment explanation
Indices: 2313579--2313736 Score: 244
Period size: 35 Copynumber: 4.5 Consensus size: 35
2313569 CGAGTACACT
2313579 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
1 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
2313614 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
1 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
* *
2313649 CAGTACCATCCAACACACTAGTTGCTCATAAGAGT
1 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
* * ** * *
2313684 TAGTACCATCTAGTACACCAATTGTTCATAAGAGC
1 CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
2313719 CAGTACCATCCAACACAC
1 CAGTACCATCCAACACAC
2313737 TAGATAACAT
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 109 1.00
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.20
Consensus pattern (35 bp):
CAGTACCATCCAACACACCAGTTGCTCATAAGAGC
Found at i:2322207 original size:17 final size:17
Alignment explanation
Indices: 2322185--2322218 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2322175 ATTTGGGTCA
2322185 TGTGGG-TTACACGGGCG
1 TGTGGGCTTACA-GGGCG
2322202 TGTGGGCTTACAGGGCG
1 TGTGGGCTTACAGGGCG
2322219 AACATCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.24
Consensus pattern (17 bp):
TGTGGGCTTACAGGGCG
Found at i:2322787 original size:11 final size:11
Alignment explanation
Indices: 2322771--2322807 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
2322761 TAATTTTTAA
2322771 TTTTAAAATAC
1 TTTTAAAATAC
2322782 TTTTAAAATAC
1 TTTTAAAATAC
*
2322793 TTTTAAAATAA
1 TTTTAAAATAC
2322804 TTTT
1 TTTT
2322808 TTTTGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2327642 original size:18 final size:18
Alignment explanation
Indices: 2327598--2327642 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2327588 GCAATAAGAA
2327598 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
2327616 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
2327634 AATGTTTTG
1 AACGTTTTG
2327643 GAAACGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:2343483 original size:16 final size:16
Alignment explanation
Indices: 2343462--2343493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2343452 ACGATAATCT
2343462 TTCAACCCAATTAAGC
1 TTCAACCCAATTAAGC
2343478 TTCAACCCAATTAAGC
1 TTCAACCCAATTAAGC
2343494 AATCTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
TTCAACCCAATTAAGC
Found at i:2351749 original size:77 final size:79
Alignment explanation
Indices: 2351622--2351777 Score: 298
Period size: 77 Copynumber: 2.0 Consensus size: 79
2351612 TTTAGTGATC
2351622 TCAAATTACTGTTCTGACACTATCGAAAATTGGGCTGTTACATGACAAATCATAAATAACGTC-A
1 TCAAATTACTGTTCTGACACTATCGAAAATTGGGCTGTTACATGACAAATCATAAATAACGTCAA
2351686 A-ATTAAGTCTTAA
66 ATATTAAGTCTTAA
2351699 TCAAATTACTGTTCTGACACTATCGAAAATTGGGCTGTTACATGACAAATCATAAATAACGTCAA
1 TCAAATTACTGTTCTGACACTATCGAAAATTGGGCTGTTACATGACAAATCATAAATAACGTCAA
2351764 ATATTAAGTCTTAA
66 ATATTAAGTCTTAA
2351778 CTAATCGATT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
77 63 0.82
78 2 0.03
79 12 0.16
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (79 bp):
TCAAATTACTGTTCTGACACTATCGAAAATTGGGCTGTTACATGACAAATCATAAATAACGTCAA
ATATTAAGTCTTAA
Found at i:2353188 original size:31 final size:34
Alignment explanation
Indices: 2353138--2353207 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 34
2353128 GAATCAAATC
2353138 AAATTAAAAATTCACGTATG-TT-T-TTAAATTA
1 AAATTAAAAATTCACGTATGATTGTATTAAATTA
* ** *
2353169 TAATTAAAGTTTCATGTATGATTGTATTAAATTA
1 AAATTAAAAATTCACGTATGATTGTATTAAATTA
2353203 AAATT
1 AAATT
2353208 TTTATATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 16 0.52
32 2 0.06
33 1 0.03
34 12 0.39
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (34 bp):
AAATTAAAAATTCACGTATGATTGTATTAAATTA
Found at i:2354238 original size:27 final size:27
Alignment explanation
Indices: 2354205--2354281 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
2354195 AAAATTCACG
2354205 TATGTAT-TTAAATTATAATTAAAGTT
1 TATGTATATTAAATTATAATTAAAGTT
**
2354231 TCATGTATGATTGTATTA-AATTAAAGTT
1 T-ATGTAT-ATTAAATTATAATTAAAGTT
2354259 T-T-TATATTAAATTATACATTAAA
1 TATGTATATTAAATTATA-ATTAAA
2354282 TAAAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 7 0.17
25 4 0.10
26 8 0.19
27 6 0.14
28 11 0.26
29 6 0.14
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (27 bp):
TATGTATATTAAATTATAATTAAAGTT
Found at i:2354239 original size:31 final size:28
Alignment explanation
Indices: 2354189--2354259 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 28
2354179 GAATCAAATC
**
2354189 AAATTAAAAATTCACGTATGTATT-TAAATT
1 AAATTAAAGTTTCACGTATG-ATTGT--ATT
*
2354219 ATAATTAAAGTTTCATGTATGATTGTATT
1 A-AATTAAAGTTTCACGTATGATTGTATT
2354248 AAATTAAAGTTT
1 AAATTAAAGTTT
2354260 TTATATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 11 0.31
29 4 0.11
30 4 0.11
31 17 0.47
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (28 bp):
AAATTAAAGTTTCACGTATGATTGTATT
Found at i:2355214 original size:44 final size:44
Alignment explanation
Indices: 2355164--2355321 Score: 136
Period size: 45 Copynumber: 3.5 Consensus size: 44
2355154 AAACTGCTAG
**
2355164 TGGCTATGGACGCACAACAAAATCCCGCAGTTAGAATCTACCTC
1 TGGCTATGGATACACAACAAAATCCCGCAGTTAGAATCTACCTC
* * * * *
2355208 TGGCTATGGATGCACAACAAAAATCTCGCAGATAAAATCAACCTC
1 TGGCTATGGATACACAAC-AAAATCCCGCAGTTAGAATCTACCTC
* * * * * ** * *
2355253 TAGCTGTGAAAACACAACAATTATCCCAAAATTAGAATCTACCTT
1 TGGCTATGGATACACAACAA-AATCCCGCAGTTAGAATCTACCTC
* *
2355298 TGGCTGTGGATACACAAAAAAATC
1 TGGCTATGGATACACAACAAAATC
2355322 TTGCAAATAA
Statistics
Matches: 88, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
44 22 0.25
45 66 0.75
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (44 bp):
TGGCTATGGATACACAACAAAATCCCGCAGTTAGAATCTACCTC
Found at i:2355499 original size:38 final size:38
Alignment explanation
Indices: 2355456--2355580 Score: 151
Period size: 38 Copynumber: 3.3 Consensus size: 38
2355446 TCAACACTAG
* **
2355456 CAGTAGACATGTACAACATGTGTTCAATTCATTATTAA
1 CAGTAGACATGTATAACATGTACTCAATTCATTATTAA
* * * *
2355494 TAGTAGACATGTTTAACATATACTCAATTCATCATTAA
1 CAGTAGACATGTATAACATGTACTCAATTCATTATTAA
* * *
2355532 CAGTAGACATGTGTAACACGTACTCAATTTATTATTAA
1 CAGTAGACATGTATAACATGTACTCAATTCATTATTAA
*
2355570 CAATAGACATG
1 CAGTAGACATG
2355581 CAAATTATGT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (38 bp):
CAGTAGACATGTATAACATGTACTCAATTCATTATTAA
Found at i:2358729 original size:38 final size:38
Alignment explanation
Indices: 2358695--2358805 Score: 159
Period size: 38 Copynumber: 2.9 Consensus size: 38
2358685 AAACATGTAC
*
2358695 AACATGTGCTCAATTCGTTATTAACAGTAGACATGTTT
1 AACATGTGCTCAATTCATTATTAACAGTAGACATGTTT
* *
2358733 AACATGTGCTCAATTTATCATTAACAGTAGACATGTTT
1 AACATGTGCTCAATTCATTATTAACAGTAGACATGTTT
* * * *
2358771 AATATGTACTCAATTCATTATTGACAGTAGGCATG
1 AACATGTGCTCAATTCATTATTAACAGTAGACATG
2358806 CAAATCATGT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (38 bp):
AACATGTGCTCAATTCATTATTAACAGTAGACATGTTT
Found at i:2359278 original size:18 final size:19
Alignment explanation
Indices: 2359249--2359284 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2359239 AAACAAATAA
*
2359249 GAAAATTTTGGGAGAACAT
1 GAAAATTTTGGGAAAACAT
2359268 GAAAA-TTTGGGAAAACA
1 GAAAATTTTGGGAAAACA
2359285 GGGGTCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (19 bp):
GAAAATTTTGGGAAAACAT
Found at i:2361771 original size:38 final size:37
Alignment explanation
Indices: 2361721--2361850 Score: 92
Period size: 39 Copynumber: 3.5 Consensus size: 37
2361711 CGAAAATTTT
*
2361721 GCCCAG-TGCTAGTTGGATAAACTGACAATAAATAGTGA
1 GCCCAGCT-CTAGTTGGATAAACTGACAAT-AATAATGA
* *
2361759 GCCCAGCTCTAGTT--ATATA-T-ACCAATAATATTTGCA
1 GCCCAGCTCTAGTTGGATAAACTGA-CAATAATA-ATG-A
* * *
2361795 -CCCAGCGCTAGTCGGATAAACCGACAAATTAATAATGA
1 GCCCAGCTCTAGTTGGATAAACTGAC-AA-TAATAATGA
*
2361833 GCCCAACTCTAGTTGGAT
1 GCCCAGCTCTAGTTGGAT
2361851 TAACCAACGG
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
34 5 0.07
35 18 0.25
36 5 0.07
37 4 0.06
38 14 0.20
39 20 0.28
40 5 0.07
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (37 bp):
GCCCAGCTCTAGTTGGATAAACTGACAATAATAATGA
Found at i:2366316 original size:32 final size:32
Alignment explanation
Indices: 2366280--2366342 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2366270 GCTTAACATT
*
2366280 TCACCAAAATATACACACATAGATAAGAACAA
1 TCACCAAAATATACACACATAAATAAGAACAA
2366312 TCACCAAAATATACACACATAAATAAGAACA
1 TCACCAAAATATACACACATAAATAAGAACA
2366343 TTAACCTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (32 bp):
TCACCAAAATATACACACATAAATAAGAACAA
Found at i:2368335 original size:29 final size:31
Alignment explanation
Indices: 2368258--2368335 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
2368248 GGGTTTAAAG
**
2368258 TATCAGGTACTATGTACCGGTGGTTACATTA
1 TATCAGGTACTATGTACCGGTGACTACATTA
* * *
2368289 TATTAGGTGCTATGTACCGGTGACTATA-T-
1 TATCAGGTACTATGTACCGGTGACTACATTA
*
2368318 TATCAGGTACTTTGTACC
1 TATCAGGTACTATGTACC
2368336 AGTATTCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 15 0.38
30 1 0.03
31 23 0.59
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (31 bp):
TATCAGGTACTATGTACCGGTGACTACATTA
Found at i:2370103 original size:68 final size:69
Alignment explanation
Indices: 2369973--2370107 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 69
2369963 TGATTAAACT
* * *
2369973 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATACATATCAAGATAAATATTAGATTAAATATAATATT
2370038 AAGA
66 AAGA
* *
2370042 TAATCACTTTAATATTAACTTAATAAAATA-ATATTAAGATAAATATTA-ATTTAAATATAATAT
1 TAATCACTTTAATATTAAATTAATAAAATACATATCAAGATAAATATTAGA-TTAAATATAATAT
2370105 TAA
65 TAA
2370108 ATCTATTGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
67 1 0.02
68 31 0.52
69 28 0.47
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAATAAAATACATATCAAGATAAATATTAGATTAAATATAATATT
AAGA
Found at i:2372799 original size:36 final size:37
Alignment explanation
Indices: 2372751--2372829 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 37
2372741 ACATAATGAG
*
2372751 CACATGATTAAATTTAATATTACATACAACTTCTATA
1 CACATGAATAAATTTAATATTACATACAACTTCTATA
2372788 C-CATGAATAAATTTAATATTACATACAACTTCTATA
1 CACATGAATAAATTTAATATTACATACAACTTCTATA
2372824 CACATG
1 CACATG
2372830 TACAATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 35 0.88
37 5 0.12
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (37 bp):
CACATGAATAAATTTAATATTACATACAACTTCTATA
Found at i:2373866 original size:41 final size:41
Alignment explanation
Indices: 2373788--2373901 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
2373778 TTATATAAAA
* * * * * *
2373788 CACCGGCATAAAGCTTGCTAGGCACAAAGCTCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCAATACATTT
* *
2373829 CACTGGCACAGAGTCTGCTAGGCATAAAGCCCAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCAATACATTT
*
2373870 CACCGGCACAGAGCCTTCTAGGCATAAAGCCC
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCC
2373902 GAACTTACAA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCACAGAGCCTGCTAGGCATAAAGCCCAATACATTT
Found at i:2374072 original size:61 final size:61
Alignment explanation
Indices: 2373973--2374227 Score: 467
Period size: 61 Copynumber: 4.2 Consensus size: 61
2373963 ACAATTCACC
* * * *
2373973 ATAT-TACATTCGGCCATAGCTTATGTAACTTCAAATAATTTATTTCAATGTATAACAAAT
1 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
2374033 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
1 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
2374094 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
1 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
2374155 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
1 ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
2374216 ATATATACATTC
1 ATATATACATTC
2374228 GATAGTTTAA
Statistics
Matches: 190, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
60 4 0.02
61 186 0.98
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (61 bp):
ATATATACATTCAGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGTATAACAAAT
Found at i:2374255 original size:44 final size:46
Alignment explanation
Indices: 2374198--2374310 Score: 142
Period size: 47 Copynumber: 2.5 Consensus size: 46
2374188 AAATAATTTA
* *
2374198 TTTCAATGTATAACAAATATATATACATTC-G-ATAGTTTAATTCAT
1 TTTC-ATGCATAACAAATATATATACATTCAGCATAGATTAATTCAT
* *
2374243 TTCTC-TGCATAACAATTACATATACATTCAGCTATAGATTAATTCAT
1 TT-TCATGCATAACAAATATATATACATTCAGC-ATAGATTAATTCAT
2374290 TTTCATGCATAACAAATATAT
1 TTTCATGCATAACAAATATAT
2374311 TAATATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
44 21 0.37
45 3 0.05
46 4 0.07
47 29 0.51
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (46 bp):
TTTCATGCATAACAAATATATATACATTCAGCATAGATTAATTCAT
Found at i:2379082 original size:29 final size:30
Alignment explanation
Indices: 2379040--2379102 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
2379030 TTTTAGGGGT
2379040 TGTTCATATAAGGGCCAAACCTGT-CAAAG
1 TGTTCATATAAGGGCCAAACCTGTACAAAG
* * *
2379069 TGTTCATATAAGGGCCTAACTTTTACAAAG
1 TGTTCATATAAGGGCCAAACCTGTACAAAG
2379099 TGTT
1 TGTT
2379103 TAAATAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (30 bp):
TGTTCATATAAGGGCCAAACCTGTACAAAG
Found at i:2379110 original size:30 final size:29
Alignment explanation
Indices: 2379040--2379110 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2379030 TTTTAGGGGT
*
2379040 TGTTCATATAAGGGCCAAACCTGTCAAAG
1 TGTTCAAATAAGGGCCAAACCTGTCAAAG
* * * *
2379069 TGTTCATATAAGGGCCTAACTTTTACAAAG
1 TGTTCAAATAAGGGCCAAACCTGT-CAAAG
*
2379099 TGTTTAAATAAG
1 TGTTCAAATAAG
2379111 AATTTTTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (29 bp):
TGTTCAAATAAGGGCCAAACCTGTCAAAG
Found at i:2382623 original size:22 final size:21
Alignment explanation
Indices: 2382591--2382646 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2382581 TAAAATTAAA
2382591 AAAATTTAAAAAATATTT-TT
1 AAAATTTAAAAAATATTTATT
2382611 AAAATTATAAAAAATATTTATT
1 AAAATT-TAAAAAATATTTATT
* *
2382633 AAACTTTTAAAAAT
1 AAAATTTAAAAAAT
2382647 TAATCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 6 0.19
21 19 0.59
22 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATTTAAAAAATATTTATT
Found at i:2385815 original size:130 final size:125
Alignment explanation
Indices: 2385508--2385936 Score: 418
Period size: 130 Copynumber: 3.4 Consensus size: 125
2385498 TTCTTTATGG
* * ** * * * * **
2385508 AACAGAAAGCAAAGGCTAAATGGCTCGAAGATTCAATGTTTGCTCTTGCTAGTGATTGACCACCA
1 AACAAAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCA
** * *
2385573 ATCAGCTGGAGCACTTTC-TAGG-CAGGGACAACAAG-ATGGCCTTTTTTCCTTTTCTTTTCCTG
66 ATCAGCAAGAGCAATTTCTTAGGAAAGGGAC--CAAGCA-GGCC--TTTT-CTTTTCTTTT-CTG
*
2385635 AG
124 AA
**** * * * *
2385637 AATTCTAAGCAAAGGTTAAACAGCTCAAAGATTCAGTCTTTACCCTTGCTGGTGATCGAATATCA
1 AACAAAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCA
*
2385702 ATCAGCAAGAGCAATTTCTTA-G-ATGGGTACCAAGCAGGCCATTTTTCTTCTTTCTTTTTCTGA
66 ATCAGCAAGAGCAATTTCTTAGGAAAGGG-ACCAAGCAGGCC--TTTTC-T-TTTC-TTTTCTGA
*
2385765 T
125 A
*
2385766 AACACAAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATTGAATACC
1 AACA-AAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACC
* *
2385831 AATCAGCAATAGCATTTTCTTAGGTAAAGGGACCAAGCAGGCCTTTTCTTTTCTTTTCTGAA
65 AATCAGCAAGAGCAATTTCTTAGG-AAAGGGACCAAGCAGGCCTTTTCTTTTCTTTTCTGAA
* *
2385893 AATAAAAATCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACT
1 AACAAAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACT
2385937 ATTGTTAGTG
Statistics
Matches: 251, Mismatches: 39, Indels: 23
0.80 0.12 0.07
Matches are distributed among these distances:
126 39 0.16
127 12 0.05
128 18 0.07
129 79 0.31
130 86 0.34
131 1 0.00
132 12 0.05
133 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (125 bp):
AACAAAAAGCAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCA
ATCAGCAAGAGCAATTTCTTAGGAAAGGGACCAAGCAGGCCTTTTCTTTTCTTTTCTGAA
Found at i:2388083 original size:3 final size:3
Alignment explanation
Indices: 2388075--2388112 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2388065 AGTAGGTATT
2388075 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2388113 CAGACCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2389455 original size:2 final size:2
Alignment explanation
Indices: 2389440--2389505 Score: 53
Period size: 2 Copynumber: 32.5 Consensus size: 2
2389430 TTTATCTATG
* * * * * *
2389440 TA TA TA TG TCA TA TA TA TA CA TA TA AA TC TC TA TA TA TA TA TG
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2389483 TA -A TA TA TA TA TA TCA TA TA TA T
1 TA TA TA TA TA TA TA T-A TA TA TA T
2389506 GGTCTACTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
1 1 0.02
2 47 0.92
3 3 0.06
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2391047 original size:84 final size:84
Alignment explanation
Indices: 2390938--2391105 Score: 255
Period size: 84 Copynumber: 2.0 Consensus size: 84
2390928 GCAACCCTGA
* *
2390938 TTTTTTTATGCCACCCATAGAATTCTTGAGCTTGTGTTGAAAGAGAAACCCAATCTTCGAGGAGT
1 TTTTTTTATGCCACCCATAGAATTCTTGAGCTTGTGTTGAAAGAGAAACCCAATCTTCGAGAAAT
* **
2391003 TAAGTAATGTTTAAGATTT
66 TAAGAAACCTTTAAGATTT
* * * *
2391022 TTTTTTTATGCCACTCGTATAATTCTTGAGCTTGTGTTGAAAGAGAAACCCAATCTTGGAGAAAT
1 TTTTTTTATGCCACCCATAGAATTCTTGAGCTTGTGTTGAAAGAGAAACCCAATCTTCGAGAAAT
2391087 TAAGAAACCTTTAAGATTT
66 TAAGAAACCTTTAAGATTT
2391106 CTAAGGTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (84 bp):
TTTTTTTATGCCACCCATAGAATTCTTGAGCTTGTGTTGAAAGAGAAACCCAATCTTCGAGAAAT
TAAGAAACCTTTAAGATTT
Found at i:2391363 original size:83 final size:82
Alignment explanation
Indices: 2391209--2391371 Score: 195
Period size: 83 Copynumber: 2.0 Consensus size: 82
2391199 TTTTTCTTAA
* * ** *
2391209 TATTTGTGATTGTTTGGATGTTATGGTGTTTTAGATATATTGTTTGACATTGCTATGTAATTGTG
1 TATTTGTGATTGTTTGGATGTTATGATGTTTTAGATACATTACTTGACATTGCTATGTAATTATG
2391274 AATTGTTTGGATGTGTT
66 AATTGTTTGGATGTGTT
* * * *
2391291 TATTTGTGATT-TTTGGCAGTGTTGTGATGTTTTGGATACATTACTTGA-AGTTGCTATTTGATT
1 TATTTGTGATTGTTTGG-A-TGTTATGATGTTTTAGATACATTACTTGACA-TTGCTATGTAATT
*
2391354 ATGAGTTGTTTGGATGTG
63 ATGAATTGTTTGGATGTG
2391372 GTTGTGCTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 5 0.07
82 13 0.19
83 50 0.74
ACGTcount: A:0.19, C:0.04, G:0.26, T:0.51
Consensus pattern (82 bp):
TATTTGTGATTGTTTGGATGTTATGATGTTTTAGATACATTACTTGACATTGCTATGTAATTATG
AATTGTTTGGATGTGTT
Found at i:2397043 original size:17 final size:17
Alignment explanation
Indices: 2397023--2397056 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2397013 GACCAAAATA
2397023 GAAACAATCTAAAATGT
1 GAAACAATCTAAAATGT
**
2397040 GAAATGATCTAAAATGT
1 GAAACAATCTAAAATGT
2397057 TAGTGATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (17 bp):
GAAACAATCTAAAATGT
Found at i:2398525 original size:8 final size:8
Alignment explanation
Indices: 2398512--2398539 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2398502 TTTACCATTT
2398512 ATAAAATA
1 ATAAAATA
2398520 ATAAAATA
1 ATAAAATA
2398528 ATAAAATA
1 ATAAAATA
2398536 ATAA
1 ATAA
2398540 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAAATA
Found at i:2399450 original size:30 final size:31
Alignment explanation
Indices: 2399414--2399482 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2399404 GGTTTCATTT
*
2399414 CAGTCACTCAACTTTA-GAAAAA-TGACAAAA
1 CAGTCACT-AACGTTATGAAAAAGTGACAAAA
* * *
2399444 CAGTCACTATCGTTATTAAAAAGTGACAAAT
1 CAGTCACTAACGTTATGAAAAAGTGACAAAA
2399475 CAGTCACT
1 CAGTCACT
2399483 TATTAACAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 15 0.45
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (31 bp):
CAGTCACTAACGTTATGAAAAAGTGACAAAA
Found at i:2399665 original size:22 final size:22
Alignment explanation
Indices: 2399617--2399669 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2399607 TAAGGGTAAA
* *
2399617 AAGAAGAATAAAAGAAATGGAG
1 AAGAAGAAGAAAAGAAATAGAG
2399639 AAGAAGAAGAAAAGAAGA-AGAG
1 AAGAAGAAGAAAAGAA-ATAGAG
*
2399661 GAGAAGAAG
1 AAGAAGAAG
2399670 GGAAAATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (22 bp):
AAGAAGAAGAAAAGAAATAGAG
Found at i:2403467 original size:20 final size:20
Alignment explanation
Indices: 2403442--2403481 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2403432 TCAAGCTCCT
*
2403442 CGGCTAAAATCAAGGTCATA
1 CGGCTAAAATCAAGGCCATA
2403462 CGGCTAAAATCAAGGCCATA
1 CGGCTAAAATCAAGGCCATA
2403482 TACATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
CGGCTAAAATCAAGGCCATA
Found at i:2406913 original size:108 final size:108
Alignment explanation
Indices: 2406724--2406970 Score: 485
Period size: 108 Copynumber: 2.3 Consensus size: 108
2406714 CAAAAATGAG
2406724 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATAGAAATAAGTAAGACTATAGCTGAAAGAC
1 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATAGAAATAAGTAAGACTATAGCTGAAAGAC
2406789 ACTATGACATCGTATAAAAGTGTACCAAAACGGTAAATAGGAT
66 ACTATGACATCGTATAAAAGTGTACCAAAACGGTAAATAGGAT
2406832 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATAGAAATAAGTAAGACTATAGCTGAAAGAC
1 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATAGAAATAAGTAAGACTATAGCTGAAAGAC
2406897 ACTATGACATCGTATAAAAGTGTACCAAAACGGTAAATAGGAT
66 ACTATGACATCGTATAAAAGTGTACCAAAACGGTAAATAGGAT
*
2406940 TAAGACCATAGCTGAAAGATGTTATGACATC
1 TAAGACCATAGCTGAAAGATGTTATGGCATC
2406971 CTTTGGTTGT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 138 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (108 bp):
TAAGACCATAGCTGAAAGATGTTATGGCATCATGATAGAAATAAGTAAGACTATAGCTGAAAGAC
ACTATGACATCGTATAAAAGTGTACCAAAACGGTAAATAGGAT
Found at i:2407099 original size:27 final size:27
Alignment explanation
Indices: 2406988--2407106 Score: 91
Period size: 27 Copynumber: 4.4 Consensus size: 27
2406978 TGTCTACCGA
* *
2406988 GACACTAAACACGGGATAGTCCACCAG
1 GACATTAAACACGGGATAGTCCATCAG
* * ** *
2407015 GGCATTAAACATGGGATAG-CTTGTTAG
1 GACATTAAACACGGGATAGTC-CATCAG
* *
2407042 GACGA-TAAACACGGGATAGTCTAT-TG
1 GAC-ATTAAACACGGGATAGTCCATCAG
*
2407068 AGACATTAAACACGGGATTGTCCATCAG
1 -GACATTAAACACGGGATAGTCCATCAG
*
2407096 GACAGTAAACA
1 GACATTAAACA
2407107 TGGGTATCCC
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
26 3 0.04
27 65 0.92
28 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (27 bp):
GACATTAAACACGGGATAGTCCATCAG
Found at i:2411337 original size:839 final size:836
Alignment explanation
Indices: 2409605--2411607 Score: 2524
Period size: 839 Copynumber: 2.4 Consensus size: 836
2409595 TAGAGGAAGT
* * * * * *
2409605 TGTTGGATTTGATGCCCTAAGTGTAG-GTTATTCGTT-TGTACACTTGT-ATGTTTTGGAACAGA
1 TGTTGGATCTGGTACCCTAAGTGTAGTGTT-TTCTTTATGTACACTTGTAATTTTTTCGAACAGA
* * * * *
2409667 TTGGTTTAGTAAAATTATTCATGAATTACATTAATACCATTTCTATATTGTCCTTAATTGTTTTT
65 TTGG-TTAATAAAATTATTCATGAATTACATTAATACCCTTTGTATATTGTCTTTAATGGTTTTT
* * * *
2409732 GCATG-AAAATCAAAATGGAAGCAAATATT-AGCTCATTGGTTATCTAATGTTT-AGCTAATATT
129 GCATGCAAAA-CAAAATAGAAGCAAATATTGA-CTCACTGGTTATCTAATGTTTAAACTAATACT
* *
2409794 AAGCGATATTATGTGG-CTTG-TTCGTAATACGGAAAGACAACTTATATTATTAGATGAACCTAA
192 AAGCGATATTATGTGGTC-AGATT-GTAATACGAAAAGACAACTTATATTATTAGATGAACCTAA
* * * * * *
2409857 ACATGTCCCTAGTCTAATTGAGAATGAGCAAATCGATTGAAAGACTAATATGCCATCCATCAAGT
255 ACATGTCCTTAGTCTAATAGA-AATGAGCAAATCGATTGAAAGAATAATATGACGTCTATCAAGT
* * * * **** **
2409922 CCAGTTGGGGAGATGCTTTGTCTTGAGTATCGGAGTGGATGACTCTTAGAAGATAGAGACATAGA
319 CCAATTGAGGAGATGCTTTGTCTTAAGCATCGGACCAAATGACTCCCAGAAGATAGAGACATAGA
* * * *
2409987 TATGACTGATTGGATTGACAGTAAATCGGACAAGACCCAAGTAGAAAAGATCTTAAATTTATTTA
384 TATGACTAACTGGATTGACAGTAAATCGGACAAGACCCAAGTAGAAAAGATCCTAAATTCATTTA
* * * * *
2410052 TGGGTTTATTTACTTGTGACGTTCATAGTGCGACCTACCATAATCCTGAATGGATGATGGACTAT
449 TAGATTTATTCACTTGTGACGTTCATAATGCGACATACCATAATCCTGAATGGATGATGGACTAT
* *
2410117 GTATGCGTGACTTGTATACTTTGATGTAAGTAAAAACCTGAGTTTAAATAGATAAGGAACCAAAA
514 GTATGCGTGACTTGTATACTTTGATGTAAGTAAAAACATGAGTTCAAATAGATAAGGAACCAAAA
** ** * * *
2410182 GCTAGTCCGTTGGGTATATGACTTATGCAGCATGTAGCATCATTCACAGTAGTTGAATCCATAGC
579 GCTAGTCAATTGGGTATACAACTTATGCAGCATGTAGCATCATTAACAATAGTGGAATCCATAGC
* * * *
2410247 CTAAGACATGGGTAAATGATATCTCTCATTGGCATTACATGATAGATGAAAATTAAACGTGACAA
644 CCAAGACATGGGTAAATAATATCTCTCATTGACATTACATGATAGATGAAAAGTAAACGTGACAA
* *
2410312 CAAGTCATTTGTCTTTGTGATGAATGACTTAATTACTATTTGGTAGTAATTGACTTTTCATGAAA
709 CAAGTCATTTGTCTTTGTGATGAATAACTTAATTACTATTTGATAGTAATTGACTTTTCATGAAA
*
2410377 GAAGATGTAATGGTTACCATGAGATAAAATAGGATCATATTGAGAGAACAAATCTATCCCAAG
774 GAAGATGTAATGATTACCATGAGATAAAATAGGATCATATTGAGAGAACAAATCTATCCCAAG
* * *
2410440 TGTTGGATTTGGTACCCTAAGTGTAGTATTTT-TGTCTATGTACACTTGTAATTTTTTTCGAATA
1 TGTTGGATCTGGTACCCTAAGTGTAGTGTTTTCT-T-TATGTACACTTGTAA-TTTTTTCGAACA
*
2410504 GATTGGTTAATAAAATTATTCATGAATTACATTAATGCCCTTTGTATATTGTCTTTATATGGTTT
63 GATTGGTTAATAAAATTATTCATGAATTACATTAATACCCTTTGTATATTGTCTTTA-ATGGTTT
2410569 TTGCATGCAAAACAAAATAGAAGCAAATATTGACTCACTGGTT-TCTAATGTTTAAACTAATACT
127 TTGCATGCAAAACAAAATAGAAGCAAATATTGACTCACTGGTTATCTAATGTTTAAACTAATACT
* * * *
2410633 AAGCGATATTATGTGGTCAGATTGTAATACGAAAAGACAATTTATATTATTAAATAAACCTAATC
192 AAGCGATATTATGTGGTCAGATTGTAATACGAAAAGACAACTTATATTATTAGATGAACCTAAAC
* * * * **
2410698 ATGTCCTTAGTTTAATCAGAAATAAGCAAATTGATTGAAAGATTAATATGTTGTCTATCAAGTCC
257 ATGTCCTTAGTCTAAT-AGAAATGAGCAAATCGATTGAAAGAATAATATGACGTCTATCAAGTCC
* * * *
2410763 AATTGAGGAGATGCTTTTTCTTAAGCATTGGACCAAATGATTCCCAGAAGATAGAGACATAGATG
321 AATTGAGGAGATGCTTTGTCTTAAGCATCGGACCAAATGACTCCCAGAAGATAGAGACATAGATA
* * * * *
2410828 TGACTAACTGGATTGATAGTACATC-GACCAAGACCCAAGTAGAATAGATCCTGAATTCGTTTAT
386 TGACTAACTGGATTGACAGTAAATCGGA-CAAGACCCAAGTAGAAAAGATCCTAAATTCATTTAT
*
2410892 AGATTTATTCACTTGTGACGTTCATAATGCGACATA-CATTAATCTTGAATGGATGATGGACTAT
450 AGATTTATTCACTTGTGACGTTCATAATGCGACATACCA-TAATCCTGAATGGATGATGGACTAT
* **
2410956 GTATGTGTGACTTGTATACTTTGATGTAAGTAAAAACATGAGTTCAAATAGATAAGGAACTGAAA
514 GTATGCGTGACTTGTATACTTTGATGTAAGTAAAAACATGAGTTCAAATAGATAAGGAACCAAAA
* * * * * *
2411021 GCTAGTGAATTGGGTATACAACTTCTGTAGTATGTAGCGTCATTAACAATAGTGGAATTCATAGC
579 GCTAGTCAATTGGGTATACAACTTATGCAGCATGTAGCATCATTAACAATAGTGGAATCCATAGC
* *
2411086 CCAAGACATGGGTAAATAATATC-CTCCTGTTGACATTACATGATAGATGAAAAGTAAACGTGGC
644 CCAAGACATGGGTAAATAATATCTCT-C-ATTGACATTACATGATAGATGAAAAGTAAACGTGAC
* * **
2411150 CAC-AGATCGTTTGTCTTTGTGATGGGTAACTTAATTACTATTTGATAGTAATTGACTTTTCATG
707 AACAAG-TCATTTGTCTTTGTGATGAATAACTTAATTACTATTTGATAGTAATTGACTTTTCATG
* * * * ** * *
2411214 AAGGTAGATGTAATGATTATCATGAGATAAAATAGGATCATATTGGGAGAACGGATTTATCCTAA
771 AAAGAAGATGTAATGATTACCATGAGATAAAATAGGATCATATTGAGAGAACAAATCTATCCCAA
*
2411279 T
836 G
* * *
2411280 TGTTGTATCTGGTGCTCTAAGTGTAGTGTTTTCATTTATGTACACTTGTAATTTTTTCGAACAGA
1 TGTTGGATCTGGTACCCTAAGTGTAGTGTTTTC-TTTATGTACACTTGTAATTTTTTCGAACAGA
* * * * ** * *
2411345 CTGGGTAATAAAATTATTCATGAATTTCATTAATTCCCTTTGTATATTGTTCTCAAATGATTATT
65 TTGGTTAATAAAATTATTCATGAATTACATTAATACCCTTTGTATATTG-TCTTTAATGGTTTTT
* * *
2411410 GCATGCAAAGA-AAAATAGAAGCAAAGATTGGCTCACTGGTTGTCTAATGTTTAAACTAATACTA
129 GCATGCAAA-ACAAAATAGAAGCAAATATTGACTCACTGGTTATCTAATGTTTAAACTAATACTA
* * * * * * * * *
2411474 AGCAATATTACGTGGTCAAATTGTAATGCAAAAATATAACTTATATTAATAGACGAACCTAAACA
193 AGCGATATTATGTGGTCAGATTGTAATACGAAAAGACAACTTATATTATTAGATGAACCTAAACA
* * *
2411539 TGTCCTTAGTCTAATTGGAAATGAGCAAATCAATTGAAAGAATAATATGACGTTTATCAAGTCCA
258 TGTCCTTAGTCTAA-TAGAAATGAGCAAATCGATTGAAAGAATAATATGACGTCTATCAAGTCCA
2411604 ATTG
322 ATTG
2411608 GAAAGATGCT
Statistics
Matches: 1004, Mismatches: 140, Indels: 43
0.85 0.12 0.04
Matches are distributed among these distances:
835 27 0.03
836 3 0.00
837 11 0.01
838 63 0.06
839 565 0.56
840 332 0.33
841 2 0.00
842 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (836 bp):
TGTTGGATCTGGTACCCTAAGTGTAGTGTTTTCTTTATGTACACTTGTAATTTTTTCGAACAGAT
TGGTTAATAAAATTATTCATGAATTACATTAATACCCTTTGTATATTGTCTTTAATGGTTTTTGC
ATGCAAAACAAAATAGAAGCAAATATTGACTCACTGGTTATCTAATGTTTAAACTAATACTAAGC
GATATTATGTGGTCAGATTGTAATACGAAAAGACAACTTATATTATTAGATGAACCTAAACATGT
CCTTAGTCTAATAGAAATGAGCAAATCGATTGAAAGAATAATATGACGTCTATCAAGTCCAATTG
AGGAGATGCTTTGTCTTAAGCATCGGACCAAATGACTCCCAGAAGATAGAGACATAGATATGACT
AACTGGATTGACAGTAAATCGGACAAGACCCAAGTAGAAAAGATCCTAAATTCATTTATAGATTT
ATTCACTTGTGACGTTCATAATGCGACATACCATAATCCTGAATGGATGATGGACTATGTATGCG
TGACTTGTATACTTTGATGTAAGTAAAAACATGAGTTCAAATAGATAAGGAACCAAAAGCTAGTC
AATTGGGTATACAACTTATGCAGCATGTAGCATCATTAACAATAGTGGAATCCATAGCCCAAGAC
ATGGGTAAATAATATCTCTCATTGACATTACATGATAGATGAAAAGTAAACGTGACAACAAGTCA
TTTGTCTTTGTGATGAATAACTTAATTACTATTTGATAGTAATTGACTTTTCATGAAAGAAGATG
TAATGATTACCATGAGATAAAATAGGATCATATTGAGAGAACAAATCTATCCCAAG
Found at i:2418157 original size:27 final size:27
Alignment explanation
Indices: 2418119--2418174 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2418109 GACCTTACAC
* * *
2418119 TACGTACCACATGACAGATTGTCATAT
1 TACGTACCACATAACAAATTGCCATAT
2418146 TACGTACCACATAACAAATTGCCATAT
1 TACGTACCACATAACAAATTGCCATAT
2418173 TA
1 TA
2418175 TATTTCATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.29
Consensus pattern (27 bp):
TACGTACCACATAACAAATTGCCATAT
Found at i:2430370 original size:18 final size:19
Alignment explanation
Indices: 2430335--2430370 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2430325 CACTAAACCT
*
2430335 TCATTTTGTCATCTTTATA
1 TCATTTTCTCATCTTTATA
2430354 TCATTTTCTCA-CTTTAT
1 TCATTTTCTCATCTTTAT
2430371 TGAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.58
Consensus pattern (19 bp):
TCATTTTCTCATCTTTATA
Found at i:2431695 original size:45 final size:45
Alignment explanation
Indices: 2431638--2431730 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
2431628 TATCAACTCA
2431638 ATTTAACCAATTCATATAACAACTTAGTCATTTCCAACTACCATT
1 ATTTAACCAATTCATATAACAACTTAGTCATTTCCAACTACCATT
*
2431683 ATTTAACCAATTCATATAACAATTTAGTCATTTCCAACTACCATT
1 ATTTAACCAATTCATATAACAACTTAGTCATTTCCAACTACCATT
2431728 ATT
1 ATT
2431731 GCAATTTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (45 bp):
ATTTAACCAATTCATATAACAACTTAGTCATTTCCAACTACCATT
Found at i:2431707 original size:21 final size:21
Alignment explanation
Indices: 2431636--2431708 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
2431626 ATTATCAACT
2431636 CAATTTAACCAATTCATATAA
1 CAATTTAACCAATTCATATAA
* ** * *
2431657 CAACTTAGTCATTTCCA-ACTAC
1 CAATTTAACCAATT-CATA-TAA
2431679 CATTATTTAACCAATTCATATAA
1 CA--ATTTAACCAATTCATATAA
2431702 CAATTTA
1 CAATTTA
2431709 GTCATTTCCA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 16 0.43
22 6 0.16
23 6 0.16
24 9 0.24
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (21 bp):
CAATTTAACCAATTCATATAA
Found at i:2432173 original size:3 final size:3
Alignment explanation
Indices: 2432137--2432212 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
2432127 TAAATAAATG
* * * * * *
2432137 ATA ATG ATA ATG ATA ATA ATG ATG ATT ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2432185 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2432213 GATGAAAACC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2439924 original size:22 final size:22
Alignment explanation
Indices: 2439899--2439944 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2439889 CATTATTTTC
*
2439899 TAGTTCTTTTACATAGGAATCA
1 TAGTTCTTTTACATAGGAAGCA
2439921 TAGTTCTTTTACATAGGAAGCA
1 TAGTTCTTTTACATAGGAAGCA
2439943 TA
1 TA
2439945 TTCACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (22 bp):
TAGTTCTTTTACATAGGAAGCA
Found at i:2439994 original size:39 final size:39
Alignment explanation
Indices: 2439951--2440128 Score: 259
Period size: 39 Copynumber: 4.6 Consensus size: 39
2439941 CATATTCACT
* * *
2439951 TTTAAGCATATATCACATTACACATATAATTACATAAAA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
2439990 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
2440029 TTTAAGCTTATATCACAATA-ATCATATAATCACATAACA
1 TTTAAGCATATATCACAATACA-CATATAATCACATAACA
* **
2440068 TTTAAGCATATATCATAATACTTATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
2440107 TTTAAGCGTATATCACAATACA
1 TTTAAGCATATATCACAATACA
2440129 TATAAAACAT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 124 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:2441985 original size:42 final size:41
Alignment explanation
Indices: 2441876--2442064 Score: 128
Period size: 42 Copynumber: 4.5 Consensus size: 41
2441866 TGGCATGTAT
* * * *
2441876 AGTGCATCATCGGATAAACCGAAGCAAATATACTGATCA-GTA
1 AGTGCATCATCGGGTAAACCAAAG-AAATATA-TTAGCACGTA
* * ** * *
2441918 AGTGCATCATTGGATGTATCGAAGAATATATATTAGCACGTA
1 AGTGCATCATCGGGTAAACCAAAGAA-ATATATTAGCACGTA
* * * * **
2441960 AGTGCGTCATCGGGTAAACCAAAGAAATTATACTGGCCCAAA
1 AGTGCATCATCGGGTAAACCAAAGAAA-TATATTAGCACGTA
* * * **
2442002 TAGCGCAACATCGGATGTACCAAAGAAAATATATTAGCACGTA
1 -AGTGCATCATCGGGTAAACCAAAG-AAATATATTAGCACGTA
2442045 AGTGCATCATCGGGTAAACC
1 AGTGCATCATCGGGTAAACC
2442065 GAAGCTATTG
Statistics
Matches: 108, Mismatches: 34, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
41 7 0.06
42 71 0.66
43 27 0.25
44 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (41 bp):
AGTGCATCATCGGGTAAACCAAAGAAATATATTAGCACGTA
Found at i:2443366 original size:74 final size:74
Alignment explanation
Indices: 2443282--2443425 Score: 225
Period size: 74 Copynumber: 1.9 Consensus size: 74
2443272 TAAAATTCAA
* * * * **
2443282 TTCACCAATAATGTAACTTCGTAAATATTTAATAAATATATTTATGAACATTATTTATGAAAATG
1 TTCACCAATAATGTAACTCCGTAAAAATTTAATAAATATATTTACGAACACTATTTACAAAAATG
2443347 GGGTTCCAG
66 GGGTTCCAG
*
2443356 TTCACCAATAATGTAACTCCGTAAAAATTTAATAAATATATTTACGAATACTATTTACAAAAATG
1 TTCACCAATAATGTAACTCCGTAAAAATTTAATAAATATATTTACGAACACTATTTACAAAAATG
2443421 GGGTT
66 GGGTT
2443426 TCGAAACCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (74 bp):
TTCACCAATAATGTAACTCCGTAAAAATTTAATAAATATATTTACGAACACTATTTACAAAAATG
GGGTTCCAG
Found at i:2446239 original size:42 final size:42
Alignment explanation
Indices: 2446162--2446274 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
2446152 AGCTTCCATT
* * *
2446162 AACTCATATGAGTTTCCA-TTTAACCCTAATGGGTTT-TCGTTC
1 AACTCTTATGAGCTT-CAGTTTAACCCTTATGGGTTTCT-GTTC
* * *
2446204 AGCTCTTTTGAGCTTTAGTTTAACCCTTATGGGTTTCTGTTC
1 AACTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTC
* *
2446246 AACTCTTATGAGCTTCCGTTCAACCCTTA
1 AACTCTTATGAGCTTCAGTTTAACCCTTA
2446275 CGAGTTTAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
41 1 0.02
42 56 0.97
43 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (42 bp):
AACTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTC
Found at i:2446255 original size:21 final size:21
Alignment explanation
Indices: 2446225--2446274 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2446215 GCTTTAGTTT
* * *
2446225 AACCCTTATGGGTTTCTGTTC
1 AACCCTTATGAGCTTCCGTTC
*
2446246 AACTCTTATGAGCTTCCGTTC
1 AACCCTTATGAGCTTCCGTTC
2446267 AACCCTTA
1 AACCCTTA
2446275 CGAGTTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (21 bp):
AACCCTTATGAGCTTCCGTTC
Found at i:2457351 original size:4 final size:4
Alignment explanation
Indices: 2457342--2457667 Score: 652
Period size: 4 Copynumber: 81.5 Consensus size: 4
2457332 ATATATCAAA
2457342 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457390 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457438 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457486 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457534 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457582 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2457630 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2457668 ATTTATTGGA
Statistics
Matches: 322, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 322 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2461017 original size:27 final size:27
Alignment explanation
Indices: 2460987--2461041 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2460977 TTTTGAAATT
*
2460987 ATTATGTCTTGAA-TTTGTTAGATATTG
1 ATTATGT-TTGAAGCTTGTTAGATATTG
*
2461014 ATTATGTTTTAAGCTTGTTAGATATTG
1 ATTATGTTTGAAGCTTGTTAGATATTG
2461041 A
1 A
2461042 ATTTATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (27 bp):
ATTATGTTTGAAGCTTGTTAGATATTG
Found at i:2461053 original size:32 final size:32
Alignment explanation
Indices: 2461014--2461106 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
2461004 TTAGATATTG
*
2461014 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
2461046 ATTATGTTTTAAGCTTGTTGGATATTAAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
2461078 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
2461107 ATGATTGACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:2462365 original size:20 final size:20
Alignment explanation
Indices: 2462340--2462377 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2462330 ACAATTTAAA
2462340 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
2462360 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
2462378 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:2462489 original size:14 final size:14
Alignment explanation
Indices: 2462470--2462507 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2462460 CCAAAAAAGT
2462470 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
2462484 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
2462498 AAAACATTTT
1 AAATCATTTT
2462508 ACTAGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:2473232 original size:24 final size:25
Alignment explanation
Indices: 2473195--2473254 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2473185 TTGTGCCTAG
* * *
2473195 CAGGCTTTGTGTCGGTG-TGTTTAT
1 CAGGCCTTGAGTCGGTGTTGTCTAT
*
2473219 CTGGCCTTGAGTCGGTGTTGTCTAT
1 CAGGCCTTGAGTCGGTGTTGTCTAT
2473244 CAGGCCTTGAG
1 CAGGCCTTGAG
2473255 CCAATGATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.10, C:0.18, G:0.33, T:0.38
Consensus pattern (25 bp):
CAGGCCTTGAGTCGGTGTTGTCTAT
Found at i:2473249 original size:25 final size:24
Alignment explanation
Indices: 2473186--2473254 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
2473176 TATCAGGCTT
* * * *
2473186 TGTGCCTAGCAGGCTTTGTGTCGG
1 TGTGTCTATCAGGCCTTGAGTCGG
* *
2473210 TGTGTTTATCTGGCCTTGAGTCGG
1 TGTGTCTATCAGGCCTTGAGTCGG
2473234 TGTTGTCTATCAGGCCTTGAG
1 TG-TGTCTATCAGGCCTTGAG
2473255 CCAATGATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.10, C:0.19, G:0.33, T:0.38
Consensus pattern (24 bp):
TGTGTCTATCAGGCCTTGAGTCGG
Found at i:2474289 original size:21 final size:21
Alignment explanation
Indices: 2474244--2474291 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2474234 CACGATTAAG
2474244 CACACGAGCGTGTAGGGTAGA
1 CACACGAGCGTGTAGGGTAGA
* *
2474265 CACATGAGCGTGT-GGGATAGC
1 CACACGAGCGTGTAGGG-TAGA
2474286 CACACG
1 CACACG
2474292 GCCGTGTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.15
Consensus pattern (21 bp):
CACACGAGCGTGTAGGGTAGA
Found at i:2475358 original size:31 final size:31
Alignment explanation
Indices: 2475320--2475378 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2475310 ATCTACAAGA
* *
2475320 TAAATATTAAATTAATAAAATACTATTAAAT
1 TAAATATTAAACTAATAAAATAATATTAAAT
*
2475351 TAAATATTAAACTATTAAAATAATATTA
1 TAAATATTAAACTAATAAAATAATATTA
2475379 TTTTCGGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAATATTAAACTAATAAAATAATATTAAAT
Found at i:2475377 original size:19 final size:19
Alignment explanation
Indices: 2475320--2475378 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
2475310 ATCTACAAGA
2475320 TAAA-TATTAAATTAATA-
1 TAAACTATTAAATTAATAT
*
2475337 AAATACTATTAAATTAAATAT
1 TAA-ACTATTAAATT-AATAT
*
2475358 TAAACTATTAAAATAATAT
1 TAAACTATTAAATTAATAT
2475377 TA
1 TA
2475379 TTTTCGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 1 0.03
19 16 0.46
20 14 0.40
21 2 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAACTATTAAATTAATAT
Found at i:2478111 original size:22 final size:22
Alignment explanation
Indices: 2478071--2478113 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2478061 ATCATCCTCC
*
2478071 ACCGTGGTCGCCACTATCCACT
1 ACCGTGGTCGCCACCATCCACT
**
2478093 ACCGTGGTCGCTGCCATCCAC
1 ACCGTGGTCGCCACCATCCAC
2478114 CGCCGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.42, G:0.21, T:0.21
Consensus pattern (22 bp):
ACCGTGGTCGCCACCATCCACT
Found at i:2483733 original size:24 final size:24
Alignment explanation
Indices: 2483672--2483723 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2483662 TTACTCATAC
*
2483672 TGAAAAT-ACAACTAA--CAACCA
1 TGAAAATGAAAACTAAGGCAACCA
2483693 TGAAAATGAAAACTAAGGCAACCA
1 TGAAAATGAAAACTAAGGCAACCA
2483717 TGAAAAT
1 TGAAAAT
2483724 AAAGCTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.26
22 7 0.26
24 13 0.48
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (24 bp):
TGAAAATGAAAACTAAGGCAACCA
Found at i:2484702 original size:11 final size:12
Alignment explanation
Indices: 2484672--2484712 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2484662 CCACAATAAC
*
2484672 AAAATGAAGAAG
1 AAAAAGAAGAAG
2484684 AAATAAGAAGAA-
1 AAA-AAGAAGAAG
2484696 AAAAAGAAGAAG
1 AAAAAGAAGAAG
2484708 AAAAA
1 AAAAA
2484713 TGGCAACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 8 0.31
12 11 0.42
13 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:2484846 original size:19 final size:19
Alignment explanation
Indices: 2484830--2484866 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2484820 GTAAGAAATA
2484830 ATAATAAAAT-AAAGAAAAC
1 ATAA-AAAATAAAAGAAAAC
2484849 ATAAAAAATAAAAGAAAA
1 ATAAAAAATAAAAGAAAA
2484867 GAACTGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (19 bp):
ATAAAAAATAAAAGAAAAC
Found at i:2487095 original size:5 final size:5
Alignment explanation
Indices: 2487085--2487158 Score: 148
Period size: 5 Copynumber: 14.8 Consensus size: 5
2487075 AAACTAAGGA
2487085 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
2487135 ATAGT ATAGT ATAGT ATAGT ATAG
1 ATAGT ATAGT ATAGT ATAGT ATAG
2487159 CGAGTATAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 69 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (5 bp):
ATAGT
Found at i:2492926 original size:15 final size:15
Alignment explanation
Indices: 2492906--2492972 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
2492896 ATAACAAGCT
*
2492906 CACATATAGGGTTCG
1 CACATATAAGGTTCG
* *
2492921 CACATACAAGGTTTG
1 CACATATAAGGTTCG
* *
2492936 CACATATAGGGTTTG
1 CACATATAAGGTTCG
*
2492951 CACATATAAGGTTCA
1 CACATATAAGGTTCG
2492966 CACATAT
1 CACATAT
2492973 TAAATCACAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
CACATATAAGGTTCG
Found at i:2492942 original size:30 final size:30
Alignment explanation
Indices: 2492906--2492972 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
2492896 ATAACAAGCT
**
2492906 CACATATAGGGTTCGCACATACAAGGTTTG
1 CACATATAGGGTTCGCACATACAAGGTTCA
* *
2492936 CACATATAGGGTTTGCACATATAAGGTTCA
1 CACATATAGGGTTCGCACATACAAGGTTCA
2492966 CACATAT
1 CACATAT
2492973 TAAATCACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (30 bp):
CACATATAGGGTTCGCACATACAAGGTTCA
Found at i:2494583 original size:34 final size:33
Alignment explanation
Indices: 2494539--2494985 Score: 475
Period size: 34 Copynumber: 13.3 Consensus size: 33
2494529 TGGCAAATCA
* *
2494539 GGTTCGCATACTATGTCATACTAAATAACGTGG
1 GGTTCGCATACTATGTCATACTATATAACATGG
2494572 GTGTTCGCATACTATGTCATACTATATAACATAGG
1 G-GTTCGCATACTATGTCATACTATATAACAT-GG
* * *
2494607 GGTTCACATACTTTGTCATACTATATAACATGAA
1 GGTTCGCATACTATGTCATACTATATAACATG-G
* *
2494641 GGTTCGTATACTATGTCATTCTATATAACATGGG
1 GGTTCGCATACTATGTCATACTATATAACAT-GG
* * ** *
2494675 GGTTCACATACTATGTCATGCTATATAATGTAAG
1 GGTTCGCATACTATGTCATACTATATAACAT-GG
**
2494709 GGTTCGCATACTATGTCATACTATATAATGTGAG
1 GGTTCGCATACTATGTCATACTATATAACATG-G
2494743 GGTTCGCATACTATGTCATACTATATAACATGGG
1 GGTTCGCATACTATGTCATACTATATAACAT-GG
* * * ** *
2494777 GGTTTGCATAGTATGCCATTTTATATAACATAG
1 GGTTCGCATACTATGTCATACTATATAACATGG
* * * **
2494810 GGTTTGCATGCTATGTCATACTATATGATGTGGG
1 GGTTCGCATACTATGTCATACTATATAACAT-GG
* *
2494844 GGTTTGTATACTATGTCATACTATATAACATGAG
1 GGTTCGCATACTATGTCATACTATATAACATG-G
* *
2494878 GGTTTGTATAC--TGTCATACTATATAACATTGG
1 GGTTCGCATACTATGTCATACTATATAACA-TGG
* *
2494910 GGTTTGCATACCATGTCATACTATATAACATGAG
1 GGTTCGCATACTATGTCATACTATATAACATG-G
* * *
2494944 AGTTCGCATATTAAGTCATACTATATAACATGG
1 GGTTCGCATACTATGTCATACTATATAACATGG
2494977 GGTTCGCAT
1 GGTTCGCAT
2494986 GTTTCTTCCT
Statistics
Matches: 353, Mismatches: 49, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
32 28 0.08
33 40 0.11
34 280 0.79
35 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
GGTTCGCATACTATGTCATACTATATAACATGG
Found at i:2499356 original size:43 final size:44
Alignment explanation
Indices: 2499289--2499410 Score: 144
Period size: 43 Copynumber: 2.8 Consensus size: 44
2499279 TTTTGATATG
* *
2499289 TGTTTTCGTGTAATACCACT-TCTGGGACGTTGGCATCGATTTA
1 TGTTTTCGTGTAAGACCACTGTCTGGGACGTTGGCATCGATCTA
* *
2499332 TGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCGTCGATCTG
1 TGTTTTCGTGTAAGACCACTGTCTGGGAC-GTTGGCATCGATCTA
* * *
2499375 TGATTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 TGTTTTCGTGTAAGACCACTGTCTGGGACGTTGGCAT
2499411 TGTACAAGCT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
42 3 0.04
43 62 0.93
44 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.34
Consensus pattern (44 bp):
TGTTTTCGTGTAAGACCACTGTCTGGGACGTTGGCATCGATCTA
Found at i:2502447 original size:23 final size:22
Alignment explanation
Indices: 2502414--2502476 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
2502404 GGCCCGGCCC
*
2502414 ATTTTTAATTAAAATTAAAATTA
1 ATTTTT-ATTAAAATTAAAACTA
2502437 TATTTTTATTAAAATTAAAACTA
1 -ATTTTTATTAAAATTAAAACTA
*
2502460 ATTGTTATTAAAATTAA
1 ATTTTTATTAAAATTAA
2502477 TTGTTATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.43
23 15 0.41
24 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTTATTAAAATTAAAACTA
Found at i:2502471 original size:16 final size:16
Alignment explanation
Indices: 2502450--2502483 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2502440 TTTTATTAAA
2502450 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
*
2502466 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
2502482 AT
1 AT
2502484 CTTAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:2502609 original size:7 final size:7
Alignment explanation
Indices: 2502597--2502632 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
2502587 AACATTTTGT
2502597 AACTTAA
1 AACTTAA
2502604 AACTTAA
1 AACTTAA
2502611 AACTTAA
1 AACTTAA
2502618 AA--TAA
1 AACTTAA
2502623 AAC-TAA
1 AACTTAA
2502629 AACT
1 AACT
2502633 AGTATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 6 0.22
7 16 0.59
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (7 bp):
AACTTAA
Found at i:2505855 original size:24 final size:27
Alignment explanation
Indices: 2505819--2505867 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
2505809 AAATTAAAAA
2505819 ATTTAATATGTAAATATTTA-AAATGG
1 ATTTAATATGTAAATATTTACAAATGG
*
2505845 ATTTAA-A-GTAACTATTTACAAAT
1 ATTTAATATGTAAATATTTACAAAT
2505868 ATAAACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTTAATATGTAAATATTTACAAATGG
Found at i:2511426 original size:35 final size:35
Alignment explanation
Indices: 2511385--2511455 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
2511375 TCTAGGATCA
*
2511385 CATATCTTTAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTACCAAG
* *
2511420 CATATCTTTGAAGATCACTTTCCATATTTACCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTACCAAG
2511455 C
1 C
2511456 TCCGAAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (35 bp):
CATATCTTTAAAGATCACCTTCCATATTTACCAAG
Found at i:2516501 original size:22 final size:24
Alignment explanation
Indices: 2516471--2516514 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2516461 CTATCTAGAT
2516471 ATCAAATC-TCT-AAGATTACAAA
1 ATCAAATCTTCTAAAGATTACAAA
*
2516493 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
2516515 TTTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAAA
Found at i:2516574 original size:35 final size:35
Alignment explanation
Indices: 2516532--2516602 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
2516522 TCTAGGGTCA
*
2516532 CATATCTTTAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTACCAAG
* * *
2516567 CATATCTTTGAAGATCACTTTTCATATTTACCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTACCAAG
2516602 C
1 C
2516603 TCCGGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (35 bp):
CATATCTTTAAAGATCACCTTCCATATTTACCAAG
Found at i:2528697 original size:20 final size:20
Alignment explanation
Indices: 2528672--2528711 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2528662 ATAATACACA
* *
2528672 AGTGATATCATATATTGAAT
1 AGTGATACCAAATATTGAAT
2528692 AGTGATACCAAATATTGAAT
1 AGTGATACCAAATATTGAAT
2528712 GGGTTCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (20 bp):
AGTGATACCAAATATTGAAT
Found at i:2533313 original size:26 final size:26
Alignment explanation
Indices: 2533284--2533342 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
2533274 TTTCATCCCT
2533284 ATTTTACCCCCAACAAAATTTTGACG
1 ATTTTACCCCCAACAAAATTTTGACG
****
2533310 ATTTTACCCCTGTTAAAATTTTGACG
1 ATTTTACCCCCAACAAAATTTTGACG
2533336 ATTTTAC
1 ATTTTAC
2533343 TCCTGGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCAACAAAATTTTGACG
Found at i:2533347 original size:26 final size:26
Alignment explanation
Indices: 2533298--2533385 Score: 122
Period size: 26 Copynumber: 3.4 Consensus size: 26
2533288 TACCCCCAAC
*
2533298 AAAATTTTGACGATTTTACCCCTGTT
1 AAAATTTTGACGATTTTACCCCTGGT
*
2533324 AAAATTTTGACGATTTTACTCCTGGT
1 AAAATTTTGACGATTTTACCCCTGGT
* * *
2533350 AAAATTTTGATGATTTTGCCCTTGGT
1 AAAATTTTGACGATTTTACCCCTGGT
*
2533376 AAAGTTTTGA
1 AAAATTTTGA
2533386 GAAAACATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCCTGGT
Found at i:2539657 original size:23 final size:21
Alignment explanation
Indices: 2539631--2539673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2539621 AATAAAAATT
2539631 ACAAAATAATAAAAATAATTTTC
1 ACAAAAT--TAAAAATAATTTTC
*
2539654 ACAAAATTTAAAATAATTTT
1 ACAAAATTAAAAATAATTTT
2539674 TAAAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAAAATTAAAAATAATTTTC
Found at i:2539680 original size:19 final size:19
Alignment explanation
Indices: 2539642--2539720 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 19
2539632 CAAAATAATA
*
2539642 AAAATAATTTTCACAAAATTT
1 AAAATAATTTT--TAAAATTT
*
2539663 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTT
*
2539682 AAAAT-ATTTATAAAAATTTT
1 AAAATAATTT-TTAAAA-TTT
2539702 AAAATTTACATTTTTAAAA
1 AAAA--TA-ATTTTTAAAA
2539721 AATTATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.09
19 16 0.34
20 6 0.13
21 11 0.23
22 1 0.02
23 5 0.11
24 4 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTT
Done.