Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 13 of 17
Found at i:2088594 original size:24 final size:23
Alignment explanation
Indices: 2088567--2088674 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 23
2088557 GCTGCATTGC
*
2088567 TGGCATTCCTCCTCTGTTGTTTGG
1 TGGCATTCCTCC-CTGTTGTTGGG
**
2088591 TGGCATTCCTCCTCCCCAATTGTTGGG
1 TGGCA-T--TCCT-CCCTGTTGTTGGG
* *
2088618 TGGCATCCCTCCCTGATTGTTAGG
1 TGGCATTCCTCCCTG-TTGTTGGG
*
2088642 TGGCATCCCTCCCATGTTGTTGGG
1 TGGCATTCCTCCC-TGTTGTTGGG
*
2088666 AGGCATTCC
1 TGGCATTCC
2088675 AGGTGTATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.04
24 42 0.62
25 3 0.04
26 1 0.01
27 17 0.25
28 2 0.03
ACGTcount: A:0.10, C:0.30, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCATTCCTCCCTGTTGTTGGG
Found at i:2090989 original size:23 final size:22
Alignment explanation
Indices: 2090947--2090989 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2090937 GGCCGGGGTG
2090947 GAGAAGAAGGAAGAGAAAGGGC
1 GAGAAGAAGGAAGAGAAAGGGC
* *
2090969 GAGAGGAAGGGAAGAGGAAGG
1 GAGAAGAA-GGAAGAGAAAGG
2090990 AAGTTAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (22 bp):
GAGAAGAAGGAAGAGAAAGGGC
Found at i:2091395 original size:128 final size:121
Alignment explanation
Indices: 2091134--2091395 Score: 269
Period size: 128 Copynumber: 2.1 Consensus size: 121
2091124 CTTTGGGGGG
* * * * * *
2091134 TATTTTAGC-AAATTGGCATTAGTTTAATAATTAATTTTTTTAACAATAATTTTATTTTTATAAT
1 TATTATAGCAAAATTGGCATGAGTTTAATAATTAATTTTATCAAAAATAATTTTATTTTTATAAA
* * ***
2091198 AATAAAAATAAATATAATTAAAAATATTTTTAGAAAAGGTAAATTTTGTACTTTGGGGGG
66 AATAAAAATAAATATAATTAAAAATATTTTTAGAAAA-G-AAACTTTGTAATTT--GAAA
*
2091258 TATTTTAGCAAAATTGGCATGAGTTTAATAATTAATATTTATCAAAAATAATTTTTATTTTTATA
1 TATTATAGCAAAATTGGCATGAGTTTAATAATTAAT-TTTATCAAAAATAA-TTTTATTTTTATA
*
2091323 AAAATAAAAAATAAATATAATTAAAAATATTTTTTTTTAGAACAA-AACCTTTGTAATTT-AAA
64 AAAAT-AAAAATAAATATAATTAAAAATA----TTTTTAGAA-AAGAAACTTTGTAATTTGAAA
2091385 TATTAATAGCA
1 TATT-ATAGCA
2091396 TCAGTCATTA
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
124 9 0.08
125 25 0.22
126 11 0.09
127 21 0.18
128 28 0.24
130 11 0.09
132 9 0.08
133 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (121 bp):
TATTATAGCAAAATTGGCATGAGTTTAATAATTAATTTTATCAAAAATAATTTTATTTTTATAAA
AATAAAAATAAATATAATTAAAAATATTTTTAGAAAAGAAACTTTGTAATTTGAAA
Found at i:2092830 original size:18 final size:18
Alignment explanation
Indices: 2092807--2092843 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2092797 TTCAACCAGC
2092807 GAATACCTCTACCACCTT
1 GAATACCTCTACCACCTT
2092825 GAATACCTCTACCACCTT
1 GAATACCTCTACCACCTT
2092843 G
1 G
2092844 TTTACTCGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.38, G:0.08, T:0.27
Consensus pattern (18 bp):
GAATACCTCTACCACCTT
Found at i:2094074 original size:19 final size:21
Alignment explanation
Indices: 2094035--2094076 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2094025 ATTTAAATGA
*
2094035 ATAATAAATATTAAATAATTT
1 ATAATAAATATAAAATAATTT
2094056 ATAA-AAATATAAAAT-ATTT
1 ATAATAAATATAAAATAATTT
2094075 AT
1 AT
2094077 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAAATATAAAATAATTT
Found at i:2094384 original size:19 final size:18
Alignment explanation
Indices: 2094345--2094385 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2094335 TTTAAATTAA
*
2094345 ATTT-TAAAAATAAATAT
1 ATTTATAAAAATAAAAAT
2094362 -TTTATAAAAATATAAAAT
1 ATTTATAAAAATA-AAAAT
2094380 ATTTAT
1 ATTTAT
2094386 TTATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 4 0.20
19 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTATAAAAATAAAAAT
Found at i:2096095 original size:50 final size:50
Alignment explanation
Indices: 2096035--2096133 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
2096025 TATGTTGATG
*
2096035 GGCTTATTGGATTATGGAGTATGTTGATGAGCTTGGGTATTTGGGTTATA
1 GGCTTATTGGATTATGGAGTATGTTGATGAGCTTAGGTATTTGGGTTATA
* * * *
2096085 GGCTTGTTGGATTATGGATTATTTTGATGGGCTTAGGTATTTGGGTTAT
1 GGCTTATTGGATTATGGAGTATGTTGATGAGCTTAGGTATTTGGGTTAT
2096134 GGGTTTTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.18, C:0.04, G:0.33, T:0.44
Consensus pattern (50 bp):
GGCTTATTGGATTATGGAGTATGTTGATGAGCTTAGGTATTTGGGTTATA
Found at i:2097195 original size:21 final size:22
Alignment explanation
Indices: 2097135--2097195 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
2097125 TGCTTTGGAA
*
2097135 AACTTTAAAAAAATGCTTTTCTT
1 AACTTT-AAAAAATGTTTTTCTT
*
2097158 AACTTTAAAAAGAT-TTTTACTT
1 AACTTTAAAAA-ATGTTTTTCTT
2097180 -A-TTTAAAAAATGTTTT
1 AACTTTAAAAAATGTTTT
2097196 ACATAGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 1 0.03
22 11 0.32
23 8 0.24
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (22 bp):
AACTTTAAAAAATGTTTTTCTT
Found at i:2097981 original size:22 final size:23
Alignment explanation
Indices: 2097944--2097991 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2097934 GTCATATAGA
2097944 TTAAAAATAAATATTAAATATAT
1 TTAAAAATAAATATTAAATATAT
* * *
2097967 TTAAAATTAAA-ATTATATATGT
1 TTAAAAATAAATATTAAATATAT
2097989 TTA
1 TTA
2097992 TATTTATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAAAATAAATATTAAATATAT
Found at i:2098114 original size:24 final size:24
Alignment explanation
Indices: 2098067--2098114 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2098057 TATATTTTTA
*
2098067 TATTATTTTTAATACAATTATATT
1 TATTATTTTAAATACAATTATATT
*
2098091 TATTATTTATAAATATAATT-TATT
1 TATTATTT-TAAATACAATTATATT
2098115 GCAATATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTATTTTAAATACAATTATATT
Found at i:2103195 original size:28 final size:28
Alignment explanation
Indices: 2103172--2103232 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
2103162 GTAAAAGTTG
*
2103172 ATTAAAATTGATTTAATTGAAAAAATTA
1 ATTAAAATTAATTTAATTGAAAAAATTA
* *
2103200 ATTAAATTTAATTTAATT-AATTAAATTA
1 ATTAAAATTAATTTAATTGAA-AAAATTA
2103228 ATTAA
1 ATTAA
2103233 GTCTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTAAAATTAATTTAATTGAAAAAATTA
Found at i:2103206 original size:9 final size:9
Alignment explanation
Indices: 2103194--2103232 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
2103184 TTAATTGAAA
2103194 AAATTAATT
1 AAATTAATT
2103203 AAATTTAATT
1 AAA-TTAATT
*
2103213 TAATTAATT
1 AAATTAATT
2103222 AAATTAATT
1 AAATTAATT
2103231 AA
1 AA
2103233 GTCTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAATTAATT
Found at i:2103411 original size:23 final size:23
Alignment explanation
Indices: 2103380--2103441 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2103370 TAAATCTATT
*
2103380 TAAATCTAAATTAAAAG-TTCATC
1 TAAAACTAAATTAAAAGCTT-ATC
* *
2103403 TAAACCTAAATTAAAAGCTTATT
1 TAAAACTAAATTAAAAGCTTATC
*
2103426 TAAAATTAAATTAAAA
1 TAAAACTAAATTAAAA
2103442 ACCTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (23 bp):
TAAAACTAAATTAAAAGCTTATC
Found at i:2103451 original size:23 final size:23
Alignment explanation
Indices: 2103409--2103453 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2103399 CATCTAAACC
* * *
2103409 TAAATTAAAAGCTTATTTAAAAT
1 TAAATTAAAAACCTAATTAAAAT
2103432 TAAATTAAAAACCTAATTAAAA
1 TAAATTAAAAACCTAATTAAAA
2103454 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAATTAAAAACCTAATTAAAAT
Found at i:2103470 original size:28 final size:28
Alignment explanation
Indices: 2103438--2103492 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2103428 AAATTAAATT
2103438 AAAAACCTAATTAAAACAAAAAAAATAAC
1 AAAAA-CTAATTAAAACAAAAAAAATAAC
* *
2103467 AAAAACTATTTAAAATAAAAAAAATA
1 AAAAACTAATTAAAACAAAAAAAATA
2103493 TAAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (28 bp):
AAAAACTAATTAAAACAAAAAAAATAAC
Found at i:2103807 original size:2 final size:2
Alignment explanation
Indices: 2103800--2103826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2103790 TAAATAGAAG
2103800 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
2103827 CACTAACTTC
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:2104145 original size:20 final size:20
Alignment explanation
Indices: 2104122--2104166 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2104112 AGTTAAATAT
*
2104122 ATATTTTTATTAATAATTTA
1 ATATTTTTAATAATAATTTA
* * *
2104142 ATATATTTAATATTTATTTA
1 ATATTTTTAATAATAATTTA
2104162 ATATT
1 ATATT
2104167 AAATATTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTAATAATAATTTA
Found at i:2104151 original size:17 final size:17
Alignment explanation
Indices: 2104131--2104192 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
2104121 TATATTTTTA
2104131 TTAATAATTTAATATAT
1 TTAATAATTTAATATAT
*
2104148 TTAAT-ATTTATTTAATAT
1 TTAATAATTTA-AT-ATAT
* * *
2104166 TAAATATTTTAAAATAT
1 TTAATAATTTAATATAT
2104183 TTAA-AATTTA
1 TTAATAATTTA
2104193 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
16 10 0.29
17 13 0.37
18 8 0.23
19 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATTTAATATAT
Found at i:2104171 original size:18 final size:18
Alignment explanation
Indices: 2104144--2104216 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
2104134 ATAATTTAAT
*
2104144 ATATTTAATATTTATTTA
1 ATATTAAATATTTATTTA
**
2104162 ATATTAAATATTT-TAAA
1 ATATTAAATATTTATTTA
2104179 ATATTTAAA-ATTTATTTA
1 ATA-TTAAATATTTATTTA
2104197 A-A-TAAATTATTTAATTTA
1 ATATTAAA-TATTT-ATTTA
2104215 AT
1 AT
2104217 TGATTGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 4 0.09
17 14 0.32
18 26 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAATATTTATTTA
Found at i:2104171 original size:27 final size:26
Alignment explanation
Indices: 2104127--2104177 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2104117 AATATATATT
*
2104127 TTTATTAATAATTTAATATATTTAATA
1 TTTATTAATAATTAAATAT-TTTAATA
2104154 TTTATTTAAT-ATTAAATATTTTAA
1 TTTA-TTAATAATTAAATATTTTAA
2104178 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 12 0.55
28 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATTAATAATTAAATATTTTAATA
Found at i:2106264 original size:3 final size:3
Alignment explanation
Indices: 2106256--2106299 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2106246 GTTTCCCATT
2106256 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2106300 TCTGATGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2110080 original size:27 final size:27
Alignment explanation
Indices: 2110050--2110139 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
2110040 GCTGCATTCC
2110050 TGGCATTCCTCCTCCCCAATTGTTGGG
1 TGGCATTCCTCCTCCCCAATTGTTGGG
2110077 TGGCATTCCTCCTCCCCAATTGTTGGG
1 TGGCATTCCTCCTCCCCAATTGTTGGG
** *
2110104 TGGCA-T-C-CCTCCCTGATTGTTAGG
1 TGGCATTCCTCCTCCCCAATTGTTGGG
*
2110128 TGGCATCCCTCC
1 TGGCATTCCTCC
2110140 CATGTTGTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.34
25 1 0.02
26 2 0.04
27 34 0.61
ACGTcount: A:0.11, C:0.34, G:0.22, T:0.32
Consensus pattern (27 bp):
TGGCATTCCTCCTCCCCAATTGTTGGG
Found at i:2110122 original size:24 final size:24
Alignment explanation
Indices: 2110068--2110157 Score: 101
Period size: 24 Copynumber: 3.6 Consensus size: 24
2110058 CTCCTCCCCA
**
2110068 ATTGTTGGGTGGCATTCCTCCTCCCCA
1 ATTGTTGGGTGGCA-T-C-CCTCCCTG
2110095 ATTGTTGGGTGGCATCCCTCCCTG
1 ATTGTTGGGTGGCATCCCTCCCTG
*
2110119 ATTGTTAGGTGGCATCCCTCCCATG
1 ATTGTTGGGTGGCATCCCTCCC-TG
*
2110144 -TTGTTGGGAGGCAT
1 ATTGTTGGGTGGCAT
2110158 TCCAGGTGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
24 39 0.68
25 3 0.05
26 1 0.02
27 14 0.25
ACGTcount: A:0.12, C:0.27, G:0.28, T:0.33
Consensus pattern (24 bp):
ATTGTTGGGTGGCATCCCTCCCTG
Found at i:2112483 original size:23 final size:22
Alignment explanation
Indices: 2112441--2112483 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2112431 GGCCGGGGTG
2112441 GAGAAGAAGGAAGAGAAAGGGC
1 GAGAAGAAGGAAGAGAAAGGGC
* *
2112463 GAGAGGAAGGGAAGAGGAAGG
1 GAGAAGAA-GGAAGAGAAAGG
2112484 AAGTTAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (22 bp):
GAGAAGAAGGAAGAGAAAGGGC
Found at i:2112673 original size:17 final size:17
Alignment explanation
Indices: 2112646--2112697 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2112636 GCAAATTGGC
*
2112646 ATTAGTTTAATAATTAAT
1 ATTATTTTAATAA-TAAT
2112664 ATT-TTTTAATAATAAT
1 ATTATTTTAATAATAAT
* *
2112680 TTTATTTTTATAATAAT
1 ATTATTTTAATAATAAT
2112697 A
1 A
2112698 AAAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.21
17 20 0.69
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATTTTAATAATAAT
Found at i:2112678 original size:20 final size:20
Alignment explanation
Indices: 2112653--2112698 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2112643 GGCATTAGTT
2112653 TAATAATTAATATTTTT-TAA
1 TAATAATT-ATATTTTTATAA
*
2112673 TAATAATTTTATTTTTATAA
1 TAATAATTATATTTTTATAA
2112693 TAATAA
1 TAATAA
2112699 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATAATTATATTTTTATAA
Found at i:2112854 original size:126 final size:125
Alignment explanation
Indices: 2112599--2112847 Score: 373
Period size: 126 Copynumber: 2.0 Consensus size: 125
2112589 AAAAAGAAAG
* *
2112599 AGAAAAGGTAAATTTTATACCTTTGGGGGGTATTTTAGCAAATTGGCATTAGTTTAATAATTAAT
1 AGAAAAGGTAAATTTTATACCTTTGGGGGGTATTTTAGCAAACTGGCATGAGTTTAATAATT-AT
* * *
2112664 ATTTTTTAATAATAATTTTATTTTTATAATAATAAAAATAAATATAATTAAAAATATTTTT
65 ATTTATTAAAAATAATTTTATTTTTATAAAAATAAAAATAAATATAATTAAAAATATTTTT
*
2112725 AGAAAAGGTAAATTTTGTA-CTTTGGGGGGTATTTTAGCAAAACTGGCATGAGTTTAATAA-T-T
1 AGAAAAGGTAAATTTTATACCTTTGGGGGGTATTTTAGC-AAACTGGCATGAGTTTAATAATTAT
2112787 -TTTATTAAAAATAATTTTTATTTTTATAAAAATAAAAACTAAATATAATT-AAAATATTTTT
65 ATTTATTAAAAATAA-TTTTATTTTTATAAAAATAAAAA-TAAATATAATTAAAAATATTTTT
2112848 TTTAGAACAA
Statistics
Matches: 114, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
122 12 0.11
123 34 0.30
124 11 0.10
125 20 0.18
126 37 0.32
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (125 bp):
AGAAAAGGTAAATTTTATACCTTTGGGGGGTATTTTAGCAAACTGGCATGAGTTTAATAATTATA
TTTATTAAAAATAATTTTATTTTTATAAAAATAAAAATAAATATAATTAAAAATATTTTT
Found at i:2114380 original size:18 final size:18
Alignment explanation
Indices: 2114357--2114393 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2114347 TTCAACCAGC
2114357 GAATACCTCTACCACCTT
1 GAATACCTCTACCACCTT
2114375 GAATACCTCTACCACCTT
1 GAATACCTCTACCACCTT
2114393 G
1 G
2114394 TTTACTCGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.38, G:0.08, T:0.27
Consensus pattern (18 bp):
GAATACCTCTACCACCTT
Found at i:2115621 original size:19 final size:21
Alignment explanation
Indices: 2115582--2115623 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2115572 ATTTAAATGA
*
2115582 ATAATAAATATTAAATAATTT
1 ATAATAAATATAAAATAATTT
2115603 ATAA-AAATATAAAAT-ATTT
1 ATAATAAATATAAAATAATTT
2115622 AT
1 AT
2115624 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAAATATAAAATAATTT
Found at i:2115929 original size:19 final size:18
Alignment explanation
Indices: 2115890--2115930 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2115880 TTTAAATTAA
*
2115890 ATTT-TAAAAATAAATAT
1 ATTTATAAAAATAAAAAT
2115907 -TTTATAAAAATATAAAAT
1 ATTTATAAAAATA-AAAAT
2115925 ATTTAT
1 ATTTAT
2115931 TTTTACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 4 0.20
19 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTATAAAAATAAAAAT
Found at i:2118758 original size:15 final size:16
Alignment explanation
Indices: 2118738--2118778 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2118728 TTAAATTAAT
2118738 TTAAAACATACT-AAG
1 TTAAAACATACTAAAG
*
2118753 TTAAAA-ATATTAAAAG
1 TTAAAACATACT-AAAG
2118769 TTAAAACATA
1 TTAAAACATA
2118779 AATTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 9 0.41
17 3 0.14
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (16 bp):
TTAAAACATACTAAAG
Found at i:2119343 original size:21 final size:19
Alignment explanation
Indices: 2119318--2119375 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
2119308 ATATAGATTG
2119318 AAAATAAATATAAATATACTT
1 AAAATAAATAT-AATATA-TT
* *
2119339 AAAATTAATATTATATATT
1 AAAATAAATATAATATATT
*
2119358 AAAATTAAA-ATTATATAT
1 AAAA-TAAATATAATATAT
2119376 GTTTATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.45
20 8 0.24
21 10 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAAATATAATATATT
Found at i:2119361 original size:19 final size:19
Alignment explanation
Indices: 2119331--2119375 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
2119321 ATAAATATAA
*
2119331 ATATACTTAAAATTAATATT
1 ATATA-TTAAAATTAAAATT
2119351 ATATATTAAAATTAAAATT
1 ATATATTAAAATTAAAATT
2119370 ATATAT
1 ATATAT
2119376 GTTTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATTAAAATTAAAATT
Found at i:2119702 original size:38 final size:39
Alignment explanation
Indices: 2119660--2119736 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
2119650 TCATTTTAAC
* *
2119660 TAACCAAACAATTTA-ATATTA-TTACTCATTTATCTATT
1 TAACCAAACAAATTACATAATACTTA-TCATTTATCTATT
* *
2119698 TAACCAATCAAATTACATAATACTTATTATTTATCTATT
1 TAACCAAACAAATTACATAATACTTATCATTTATCTATT
2119737 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 13 0.39
39 17 0.52
40 3 0.09
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (39 bp):
TAACCAAACAAATTACATAATACTTATCATTTATCTATT
Found at i:2120915 original size:5 final size:5
Alignment explanation
Indices: 2120905--2120982 Score: 69
Period size: 5 Copynumber: 16.4 Consensus size: 5
2120895 TTAATATATT
*
2120905 TTATA TTATA TTATA TT-TA TTTATA TTAT- TTAT- TTTTA TTATA TTATA
1 TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA TTATA
* *
2120953 TTTTAA TTAT- TTTTA -TATA TTATA TT-TA TT
1 TTAT-A TTATA TTATA TTATA TTATA TTATA TT
2120983 TCTAAAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
4 19 0.31
5 36 0.59
6 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TTATA
Found at i:2120930 original size:29 final size:29
Alignment explanation
Indices: 2120898--2120983 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
2120888 ATAAATTTTA
2120898 ATATATTTTATATTATATTATATTTATTT
1 ATATATTTTATATTATATTATATTTATTT
*
2120927 ATAT-TATTTAT-TTTTATTATATTATATTT
1 ATATAT-TTTATATTATATTATATT-TATTT
2120956 -TAATTATTTT-TA-TATATTATATTTATTT
1 AT-A-TATTTTATATTATATTATATTTATTT
2120984 CTAAAATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
28 18 0.37
29 26 0.53
30 4 0.08
31 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
ATATATTTTATATTATATTATATTTATTT
Found at i:2120953 original size:38 final size:40
Alignment explanation
Indices: 2120905--2120979 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 40
2120895 TTAATATATT
*
2120905 TTATATTATATTATATTTATTTATAT-TATT-TATTTTTA
1 TTATATTATATTATAATTATTTATATATATTATATTTTTA
* *
2120943 TTATATTATATTTTAATTATTTTTATATATTATATTT
1 TTATATTATATTATAATTATTTATATATATTATATTT
2120980 ATTTCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 23 0.72
39 4 0.12
40 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (40 bp):
TTATATTATATTATAATTATTTATATATATTATATTTTTA
Found at i:2123645 original size:33 final size:32
Alignment explanation
Indices: 2123608--2123704 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
2123598 AAAGGTTTCG
*
2123608 CTTAGGTCACAACTTTAACTATCATGGTTTTGC
1 CTTA-GTCACATCTTTAACTATCATGGTTTTGC
* * * *
2123641 CTTAGTCAACTTTTTTAACTA--AAGGTTTCGC
1 CTTAGTC-ACATCTTTAACTATCATGGTTTTGC
* * *
2123672 CTTAGTCATATCATTGACTATCATGGTTTTGC
1 CTTAGTCACATCTTTAACTATCATGGTTTTGC
2123704 C
1 C
2123705 CTGGTCAGTC
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
30 8 0.16
31 15 0.31
32 12 0.24
33 14 0.29
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (32 bp):
CTTAGTCACATCTTTAACTATCATGGTTTTGC
Found at i:2124228 original size:33 final size:33
Alignment explanation
Indices: 2124170--2124234 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2124160 CACACCCAAA
*
2124170 TGTATCGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCAATACAT
**
2124203 TGTATCGATACAAATTGCTTTGTATCAATACA
1 TGTATCGATACAAATTGCTAAGTATCAATACA
2124235 CCATGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCAATACAT
Found at i:2132861 original size:52 final size:52
Alignment explanation
Indices: 2132713--2132841 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2132703 CGAAATATGA
* *
2132713 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2132765 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2132817 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2132842 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2132868 original size:13 final size:13
Alignment explanation
Indices: 2132850--2132874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2132840 CAAAGATCAG
2132850 TGTATCGATACAA
1 TGTATCGATACAA
2132863 TGTATCGATACA
1 TGTATCGATACA
2132875 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2133906 original size:49 final size:47
Alignment explanation
Indices: 2133847--2134209 Score: 232
Period size: 49 Copynumber: 7.6 Consensus size: 47
2133837 ATGCCAATAC
* *
2133847 GCTGATTCAAGGCCAACGATTTTAGACTTAAGGATGAAGGTGTCAATGT
1 GCTGATTCAAGGCCAGCGATATT-GACTTAAGGATGAAGGTG-CAATGT
* * * * * *
2133896 GCTGAATCAAGGCCAGCGACATTGATTTGAAAGATGACGAAGGCGCTAATAT
1 GCTGATTCAAGGCCAGCGATATTGACTT--AAG--GATGAAGGTGC-AATGT
*
2133948 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATT-GACTTAAGGATGAAGGTG-CAATGT
* * * *
2133997 GCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGATG-AGGTGCCAATAT
1 GCTGATTCAAGGCCAGC-GATATT-GACTTAAGGATGAAGGTG-CAATGT
* * *
2134045 GCTGATTCAAAGCTAGCGATATTGGACTT----A--AAGGTGCCAGTGT
1 GCTGATTCAAGGCCAGCGATATT-GACTTAAGGATGAAGGTG-CAATGT
* * * * * ** *
2134088 ACTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCGATATT-GACTTAAGGATGAAGGTG-CAATGT
2134137 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATT-GACTTAAGGATGAAGGTG-CAATGT
*
2134180 GCTGATTCAAGGCCAGCGACATTGGACTTA
1 GCTGATTCAAGGCCAGCGATATT-GACTTA
2134210 GAAGAAGACG
Statistics
Matches: 261, Mismatches: 36, Indels: 39
0.78 0.11 0.12
Matches are distributed among these distances:
43 75 0.29
44 1 0.00
45 1 0.00
47 1 0.00
48 39 0.15
49 100 0.38
50 4 0.02
51 3 0.01
52 33 0.13
53 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (47 bp):
GCTGATTCAAGGCCAGCGATATTGACTTAAGGATGAAGGTGCAATGT
Found at i:2133913 original size:101 final size:101
Alignment explanation
Indices: 2133747--2134205 Score: 308
Period size: 101 Copynumber: 4.7 Consensus size: 101
2133737 ATGACAATGT
* * * * ** * *
2133747 GCTGATTCATGGCCAGCGACATTTAGACTTGAAGA--AAAATGCCAATGTGCT-AAGGCAAGGGC
1 GCTGATTCAAGGCCAACGATA-TTAGACTTAAAGATGAAGGTGCCAATGTGCTGAA-TCAAGGCC
* * *
2133809 AGCGACATTGGACTTTGGAATG-TTA-AAGATGCCAATAC
64 AGCGACATTGGA-TTT-GAAAGATGACAAGACGCCAATAC
* * *
2133847 GCTGATTCAAGGCCAACGATTTTAGACTTAAGGATGAAGGTGTCAATGTGCTGAATCAAGGCCAG
1 GCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCAG
* * *
2133912 CGACATT-GATTTGAAAGATGACGAAGGCGCTAATAT
66 CGACATTGGATTTGAAAGATGAC-AAGACGCCAATAC
* * *
2133948 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA-
1 GCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCAG
** *
2134012 CTGACATTGG-TCTT-AAAGATG---AGGTGCCAATAT
66 C-GACATTGGAT-TTGAAAGATGACAAGACGCCAATAC
* * * * * * * *
2134045 GCTGATTCAAAGCTAGCGATATTGGACTT----A--AAGGTGCCAGTGTACTGATTCAAGGCTAG
1 GCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCAG
* ** *
2134104 CGACATTGG-TCTT-AAAGA-CA-AAGGTGCCAATAT
66 CGACATTGGAT-TTGAAAGATGACAAGACGCCAATAC
* * *
2134137 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAG
1 GCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCAG
2134196 CGACATTGGA
66 CGACATTGGA
2134206 CTTAGAAGAA
Statistics
Matches: 310, Mismatches: 36, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
91 42 0.14
92 76 0.25
93 1 0.00
97 37 0.12
98 4 0.01
99 16 0.05
100 20 0.06
101 109 0.35
102 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (101 bp):
GCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCAG
CGACATTGGATTTGAAAGATGACAAGACGCCAATAC
Found at i:2134094 original size:43 final size:43
Alignment explanation
Indices: 2133947--2134209 Score: 249
Period size: 43 Copynumber: 5.7 Consensus size: 43
2133937 GGCGCTAATA
*
2133947 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTT----A--AAGGTGCCAATG
* *
2133996 TGCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGATGAGGTGCCAATA
1 TGCTGATTCAAGGCCAGC-GACATTGGACTT--A-A--AGGTGCCAATG
* * * *
2134044 TGCTGATTCAAAGCTAGCGATATTGGACTTAAAGGTGCCAGTG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATG
* * * *
2134087 TACTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTT------AAAGGTGCCAATG
*
2134136 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATG
2134179 TGCTGATTCAAGGCCAGCGACATTGGACTTA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTA
2134210 GAAGAAGACG
Statistics
Matches: 182, Mismatches: 22, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
43 77 0.42
45 1 0.01
46 3 0.02
47 2 0.01
48 35 0.19
49 64 0.35
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATG
Found at i:2134166 original size:92 final size:91
Alignment explanation
Indices: 2133833--2134215 Score: 410
Period size: 92 Copynumber: 4.0 Consensus size: 91
2133823 TTGGAATGTT
* * * * * *
2133833 AAAGATGCCAATACGCTGATTCAAGGCCAACGATTTTAGACTTAAGGATGAAGGTGTCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGC
* *
2133898 TGAATCAAGGCCAGCGACATTGAT-TTGAAAGA
60 TGATTCAAGGCCAGCGACATTGGTCTT-AAAGA
* *
2133930 TGACGAAGGCGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
1 --A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAAT
2133995 GTGCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGA
56 GTGCTGATTCAAGGCCAGC-GACATTGGTCTTAAAGA
** * * * *
2134031 TGAGGTGCCAATATGCTGATTCAAAGCTAGCGATATTGGACTTAAAGGTGCCAGTGTACTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
*
2134096 AAGGCTAGCGACATTGGTCTTAAAGA
66 AAGGCCAGCGACATTGGTCTTAAAGA
2134122 CAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATT
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATT
*
2134187 CAAGGCCAGCGACATTGGACTTAGAAGA
65 CAAGGCCAGCGACATTGGTCTTA-AAGA
2134215 A
1 A
2134216 GACGCCACCA
Statistics
Matches: 249, Mismatches: 28, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
91 42 0.17
92 81 0.33
93 5 0.02
97 37 0.15
99 1 0.00
100 1 0.00
101 80 0.32
102 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (91 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGTCTTAAAGA
Found at i:2134243 original size:27 final size:28
Alignment explanation
Indices: 2134216--2134270 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
2134206 CTTAGAAGAA
*
2134216 GACGCCACCAACTTGTGTGCTTTTGAAG
1 GACGCCACCAACTTGTGGGCTTTTGAAG
** **
2134244 GTTGCCACTGACTTGTGGGCTTTTGAA
1 GACGCCACCAACTTGTGGGCTTTTGAA
2134271 AAGGGTGCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (28 bp):
GACGCCACCAACTTGTGGGCTTTTGAAG
Found at i:2134257 original size:28 final size:29
Alignment explanation
Indices: 2134226--2134295 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
2134216 GACGCCACCA
* *
2134226 ACTTGTGTGCTTTTG-AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAGGGTGCCACTG
2134254 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG-AAAGGGTGCCACTG
2134284 ACTTGTGGGCTT
1 ACTTGTGGGCTT
2134296 AAAAGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 14 0.37
30 24 0.63
ACGTcount: A:0.16, C:0.17, G:0.31, T:0.36
Consensus pattern (29 bp):
ACTTGTGGGCTTTTGAAAGGGTGCCACTG
Found at i:2134457 original size:33 final size:32
Alignment explanation
Indices: 2134390--2134471 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
2134380 TTAAAGGTGT
* *
2134390 CACGGAGTTGTGGACTTAAAAAGAAAAGGCGC
1 CACGGAGTTGTGGGCTTAAAAAGAAAAGACGC
* * *
2134422 CACGGAGTTATGGGCTTAAAAGGAAAAAGATGC
1 CACGGAGTTGTGGGCTTAAAAAG-AAAAGACGC
* *
2134455 CACAGACTTGTGGGCTT
1 CACGGAGTTGTGGGCTT
2134472 TTGGAGGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 20 0.49
33 21 0.51
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (32 bp):
CACGGAGTTGTGGGCTTAAAAAGAAAAGACGC
Found at i:2134493 original size:28 final size:29
Alignment explanation
Indices: 2134446--2134533 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
2134436 CTTAAAAGGA
*
2134446 AAAAGATGCCACAGACTTGTGGGCTTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTTG
* * * *
2134475 -GAGGTTGCCACTGATTTGTGGGC-TTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTTG
2134502 AAAAAGATGCCACTGACTTGTGGGCTTTTG
1 -AAAAGATGCCACTGACTTGTGGGCTTTTG
2134532 AA
1 AA
2134534 GGGTGAGGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
27 4 0.09
28 18 0.38
29 21 0.45
30 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTTG
Found at i:2135973 original size:16 final size:16
Alignment explanation
Indices: 2135954--2135989 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2135944 ATCCGGACCC
2135954 TTTTTG-TTGTTGTTT
1 TTTTTGTTTGTTGTTT
2135969 TTTTTGTTTGTTGTTT
1 TTTTTGTTTGTTGTTT
2135985 TTTTT
1 TTTTT
2135990 TCTTCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTTTGTTTGTTGTTT
Found at i:2145498 original size:21 final size:21
Alignment explanation
Indices: 2145472--2145546 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
2145462 TTTTTATCCA
2145472 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
2145493 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2145514 AATGTATCAATACATTTGTAG
1 AATGTATCGATACATTTGTAG
2145535 AATGTATCGATA
1 AATGTATCGATA
2145547 TAAGGTCCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2145602 original size:19 final size:19
Alignment explanation
Indices: 2145578--2145639 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
2145568 TTTTGAACTT
2145578 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
2145597 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
2145618 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
2145637 CAA
1 CAA
2145640 TGTATTGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:2145650 original size:32 final size:32
Alignment explanation
Indices: 2145606--2145678 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
2145596 ACAAACAGAA
* *
2145606 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATTGATACATAAATGTTGTATCGATAC
*
2145638 AATGTATTGATACATAAATTTTGTATCGATAC
1 AATGTATTGATACATAAATGTTGTATCGATAC
2145670 AATGTATTG
1 AATGTATTG
2145679 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
AATGTATTGATACATAAATGTTGTATCGATAC
Found at i:2145668 original size:19 final size:18
Alignment explanation
Indices: 2145608--2145670 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
2145598 AAACAGAAAA
*
2145608 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAAT-T
2145627 TGTATCGATAC---AA--
1 TGTATCGATACATAAATT
*
2145640 TGTATTGATACATAAATTT
1 TGTATCGATACATAAA-TT
2145659 TGTATCGATACA
1 TGTATCGATACA
2145671 ATGTATTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
16 3 0.09
19 22 0.63
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAATT
Found at i:2145721 original size:21 final size:21
Alignment explanation
Indices: 2145695--2145737 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2145685 AGCTACTGCC
2145695 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
2145716 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
2145737 A
1 A
2145738 TATCGATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2146613 original size:12 final size:12
Alignment explanation
Indices: 2146596--2146622 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2146586 GCTCATCTGC
2146596 TGGCCAGATATG
1 TGGCCAGATATG
2146608 TGGCCAGATATG
1 TGGCCAGATATG
2146620 TGG
1 TGG
2146623 TTAGGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (12 bp):
TGGCCAGATATG
Found at i:2149803 original size:18 final size:18
Alignment explanation
Indices: 2149780--2149815 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2149770 TGCAAGTTTC
2149780 GAGGAAGTTGTGCTAATG
1 GAGGAAGTTGTGCTAATG
*
2149798 GAGGAAGTTGTGTTAATG
1 GAGGAAGTTGTGCTAATG
2149816 TGCACACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.39, T:0.31
Consensus pattern (18 bp):
GAGGAAGTTGTGCTAATG
Found at i:2150094 original size:6 final size:6
Alignment explanation
Indices: 2150085--2150112 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2150075 AACATTTATT
2150085 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
2150113 TATCGAGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:2154617 original size:32 final size:32
Alignment explanation
Indices: 2154581--2154643 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2154571 AATTGTATTG
2154581 ATACATAAGTGTTGTATAGATACAATGTATCT
1 ATACATAAGTGTTGTATAGATACAATGTATCT
*
2154613 ATACATAAGTGTTGTATCGATACAATGTATC
1 ATACATAAGTGTTGTATAGATACAATGTATC
2154644 GCTACAAAGC
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:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
ATACATAAGTGTTGTATAGATACAATGTATCT
Found at i:2160133 original size:13 final size:13
Alignment explanation
Indices: 2160115--2160139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2160105 CATAAAGTGT
2160115 TGTATCGATACAA
1 TGTATCGATACAA
2160128 TGTATCGATACA
1 TGTATCGATACA
2160140 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2160137 original size:33 final size:33
Alignment explanation
Indices: 2160095--2160161 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2160085 TTCAACGATT
2160095 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2160128 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2160161 T
1 T
2160162 TTAAGCTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2160220 original size:13 final size:13
Alignment explanation
Indices: 2160202--2160226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2160192 ATCACTTAAA
2160202 TGTATCGATACAT
1 TGTATCGATACAT
2160215 TGTATCGATACA
1 TGTATCGATACA
2160227 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2160291 original size:52 final size:52
Alignment explanation
Indices: 2160235--2160363 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2160225 CACTAATCTT
*
2160235 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
2160287 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2160339 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2160364 TCATATTTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2165040 original size:229 final size:229
Alignment explanation
Indices: 2164606--2165065 Score: 886
Period size: 229 Copynumber: 2.0 Consensus size: 229
2164596 AAGGGTATTT
*
2164606 TGGTCATTTTAAAATATATTTAATATTCCTCCTATCATCTAGAAGGGTGTAGAAAATATTAAAAC
1 TGGTCATTTTAAAATATATTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
2164671 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
66 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
2164736 TATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
131 TATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
2164801 TTTATTTTATCATTTTAAAGTCCTTTAAGGTTAC
196 TTTATTTTATCATTTTAAAGTCCTTTAAGGTTAC
*
2164835 TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
1 TGGTCATTTTAAAATATATTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
2164900 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAAATTTTGAAAAGTTTAGGGGCTTAA
66 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATT-AATTTTGAAAAGTTTAGGGGCTTAA
2164965 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
130 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
2165030 ATTT-TTTTATCATTTTAAAGTCCTTTAAGGTTAC
195 ATTTATTTTATCATTTTAAAGTCCTTTAAGGTTAC
2165064 TG
1 TG
2165066 TGACACTTTA
Statistics
Matches: 228, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
229 134 0.59
230 94 0.41
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (229 bp):
TGGTCATTTTAAAATATATTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
TATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
TTTATTTTATCATTTTAAAGTCCTTTAAGGTTAC
Found at i:2170182 original size:52 final size:52
Alignment explanation
Indices: 2170113--2170232 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
2170103 AAAATTTATT
*
2170113 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
2170165 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGTC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
2170217 TGCATGTATCGATACA
1 TGCATGTATCGATACA
2170233 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:2170245 original size:52 final size:51
Alignment explanation
Indices: 2170104--2170252 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
2170094 CGAAATATGA
* *
2170104 AAATTTATTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
2170156 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
2170208 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2170253 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGTCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:2170259 original size:13 final size:13
Alignment explanation
Indices: 2170241--2170265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2170231 CAAAGATCAG
2170241 TGTATCGATACAA
1 TGTATCGATACAA
2170254 TGTATCGATACA
1 TGTATCGATACA
2170266 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2170347 original size:33 final size:33
Alignment explanation
Indices: 2170305--2170374 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2170295 GGCAGTAGCT
2170305 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
2170338 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
2170371 TACA
1 TACA
2170375 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:2170348 original size:13 final size:13
Alignment explanation
Indices: 2170330--2170354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2170320 CAAAAAAATA
2170330 TGTATCGATACAT
1 TGTATCGATACAT
2170343 TGTATCGATACA
1 TGTATCGATACA
2170355 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2172206 original size:20 final size:20
Alignment explanation
Indices: 2172183--2172220 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2172173 TACATGTATG
2172183 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
2172203 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
2172221 GTCTTTTTAT
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:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:2176220 original size:21 final size:21
Alignment explanation
Indices: 2176194--2176249 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2176184 TGCAATGGAT
*
2176194 AATGTATCGATATAAACAGTA
1 AATGTATCGATACAAACAGTA
2176215 AATGTATCGATACAAACAGTA
1 AATGTATCGATACAAACAGTA
2176236 AATGTATCGATACA
1 AATGTATCGATACA
2176250 TTTACTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACAAACAGTA
Found at i:2183209 original size:20 final size:19
Alignment explanation
Indices: 2183184--2183224 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2183174 CATTTCAGGC
2183184 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTA-TT
*
2183204 ATGTATCGATATATTTATT
1 ATGTATCGATACATTTATT
2183223 AT
1 AT
2183225 TTATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (19 bp):
ATGTATCGATACATTTATT
Found at i:2188428 original size:30 final size:30
Alignment explanation
Indices: 2188394--2188484 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
2188384 TAGGTTTCTA
*
2188394 GTTTTGTCTAAGCCATTTCTTTGAGTTTTG
1 GTTTTGTCTAAGCCATTTCATTGAGTTTTG
*
2188424 GTTTTGAT-TAAGCCATTT-ATAGA-TTTCTG
1 GTTTTG-TCTAAGCCATTTCATTGAGTTT-TG
** * *
2188453 GTTTCATCTAAGCCATTTCCTTGAGTCTTG
1 GTTTTGTCTAAGCCATTTCATTGAGTTTTG
2188483 GT
1 GT
2188485 CATTATTTCG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.08
29 19 0.39
30 23 0.47
31 3 0.06
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.48
Consensus pattern (30 bp):
GTTTTGTCTAAGCCATTTCATTGAGTTTTG
Found at i:2188749 original size:119 final size:118
Alignment explanation
Indices: 2188576--2188838 Score: 268
Period size: 119 Copynumber: 2.2 Consensus size: 118
2188566 GCCATTTAAA
* * ** *
2188576 TGAGTCTCGGTTTTG-CCAAGACATTGTTTAGCTTTCTAGTTTCATCCTAGCCATTTGGTTGAGT
1 TGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGCTTTCTAGTTTCATCCTAGCCATTTCATTGACT
* *
2188640 CTTGGTTTAACGCAAGTCATTATTTAAGTTTTTGGATTTGA-CAAGACCATCTCGT
66 CTTGGTTTAACGCAAGTCATTATTT-AGTTTTTGG-TTTCACCAAG-CCATCTCAT
*
2188695 TGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGGC-TTCTGGTTT-ATCAAC-A-CCATTTCATTG
1 TGAGTCTTGGTTTTGCCCAAGTCATTGTTTA-GCTTTCTAGTTTCATC--CTAGCCATTTCATTG
* * ** * * *
2188756 ACTTTTGGTTTCACTTAAGTCATTGTTTAGTTTTTGGTTTCATCCAAGCCATTTTAT
63 ACTCTTGGTTTAACGCAAGTCATTATTTAGTTTTTGGTTTCA-CCAAGCCATCTCAT
* *
2188813 TGAGTCTTGGTTTCGCCTAAGTCATT
1 TGAGTCTTGGTTTTGCCCAAGTCATT
2188839 TATAGGTTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
117 4 0.03
118 39 0.32
119 52 0.43
120 23 0.19
121 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (118 bp):
TGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGCTTTCTAGTTTCATCCTAGCCATTTCATTGACT
CTTGGTTTAACGCAAGTCATTATTTAGTTTTTGGTTTCACCAAGCCATCTCAT
Found at i:2188848 original size:59 final size:58
Alignment explanation
Indices: 2188509--2188849 Score: 244
Period size: 59 Copynumber: 5.8 Consensus size: 58
2188499 CTTCTAGACA
* * * * *
2188509 ATTTCATTGAGTTTTGGTTTTGTCCAAGACATTGTTTAGGTTTCTAGCTTT-ATCTAAGCC
1 ATTTCATTGAGTCTTGGTTTCG-CCAAGTCATTGTTTAGGTTT-TTGGTTTCATC-AAGCC
* * * * * * * * *
2188569 ATTTAAATGAGTCTCGGTTTTGCCAAGACATTGTTTAGCTTTCTAGTTTCATCCTAGCC
1 ATTTCATTGAGTCTTGGTTTCGCCAAGTCATTGTTTAGGTTTTTGGTTTCAT-CAAGCC
** * * *
2188628 ATTTGGTTGAGTCTTGGTTTAACG-CAAGTCATTATTTAAGTTTTTGGATTTGA-CAAGACC
1 ATTTCATTGAGTCTTGGTTT--CGCCAAGTCATTGTTTAGGTTTTTGG-TTTCATCAAG-CC
* * * * * *
2188688 ATCTCGTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGGCTTCTGGTTT-ATCAACACC
1 ATTTCATTGAGTCTTGGTTTCG-CCAAGTCATTGTTTAGGTTTTTGGTTTCATCAA-GCC
* * * *
2188747 ATTTCATTGACTTTTGGTTTCACTTAAGTCATTGTTTA-GTTTTTGGTTTCATCCAAGCC
1 ATTTCATTGAGTCTTGGTTTCGC-CAAGTCATTGTTTAGGTTTTTGGTTTCAT-CAAGCC
* *
2188806 ATTTTATTGAGTCTTGGTTTCGCCTAAGTCATT-TATAGGTTTTT
1 ATTTCATTGAGTCTTGGTTTCGCC-AAGTCATTGTTTAGGTTTTT
2188850 AATGTATCAT
Statistics
Matches: 219, Mismatches: 47, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
58 18 0.08
59 118 0.54
60 78 0.36
61 5 0.02
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (58 bp):
ATTTCATTGAGTCTTGGTTTCGCCAAGTCATTGTTTAGGTTTTTGGTTTCATCAAGCC
Found at i:2188913 original size:53 final size:53
Alignment explanation
Indices: 2188821--2188945 Score: 216
Period size: 53 Copynumber: 2.4 Consensus size: 53
2188811 ATTGAGTCTT
*
2188821 GGTTTCGCCTAAGTCA-TTTATAGGTTTTTAATGTATCATTTCATAGAATTTC
1 GGTTTTGCCTAAGTCATTTTATAGGTTTTTAATGTATCATTTCATAGAATTTC
* *
2188873 GGTTTTGCCTAAGTCATTTTGTAGGTTTTTAATGTATCATTTCATAGAATTTT
1 GGTTTTGCCTAAGTCATTTTATAGGTTTTTAATGTATCATTTCATAGAATTTC
2188926 GGTTTTGCCTAAGTCATTTT
1 GGTTTTGCCTAAGTCATTTT
2188946 CAGATTGTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 15 0.22
53 54 0.78
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (53 bp):
GGTTTTGCCTAAGTCATTTTATAGGTTTTTAATGTATCATTTCATAGAATTTC
Found at i:2189016 original size:59 final size:59
Alignment explanation
Indices: 2188923--2189061 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
2188913 TTCATAGAAT
* * * * *
2188923 TTTGGTTTTG-CCTAAGTCATTTTCAGATTGTTGGTTCTGT-CTAGCTTATTTTTTTGAG-
1 TTTGGTTTTGTCC-AAGTCAATGTCAGATTGTTGGTTCCGTCCAAGC-CATTTTTTTGAGC
* *
2188981 TCTTGGTTTTGTCCAAGTCAATGTCAGGTTTTTGGTTCCGTCCAAGCCATTTTTTTGAGC
1 T-TTGGTTTTGTCCAAGTCAATGTCAGATTGTTGGTTCCGTCCAAGCCATTTTTTTGAGC
**
2189041 TTTGGTTTCATCCAAGTCAAT
1 TTTGGTTTTGTCCAAGTCAAT
2189062 TTTGGGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.01
59 60 0.88
60 7 0.10
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.47
Consensus pattern (59 bp):
TTTGGTTTTGTCCAAGTCAATGTCAGATTGTTGGTTCCGTCCAAGCCATTTTTTTGAGC
Found at i:2190253 original size:14 final size:14
Alignment explanation
Indices: 2190236--2190273 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2190226 ATACATGATT
2190236 TTTAATTTTTACAA
1 TTTAATTTTTACAA
2190250 TTTAATCTTTT-CAA
1 TTTAAT-TTTTACAA
2190264 -TTAATTTTTA
1 TTTAATTTTTA
2190274 TGGTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 9 0.41
15 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTTTACAA
Found at i:2192327 original size:18 final size:18
Alignment explanation
Indices: 2192300--2192339 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2192290 AAATGCTTTG
*
2192300 TTAATATTTTTAATAAAA
1 TTAATATTTTTAAAAAAA
*
2192318 TTAATTTTTTTAAAAAAA
1 TTAATATTTTTAAAAAAA
2192336 TTAA
1 TTAA
2192340 AATATATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATATTTTTAAAAAAA
Found at i:2194041 original size:21 final size:21
Alignment explanation
Indices: 2194008--2194066 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
2193998 ATATCGATAC
* *
2194008 ATTGTATTGATACATTTTTAA
1 ATTGTATCGATACATTTGTAA
* * *
2194029 ATTGTATCAATACA-TGGTGA
1 ATTGTATCGATACATTTGTAA
2194049 ATTGTATCGATACATTTG
1 ATTGTATCGATACATTTG
2194067 GCCCAACGAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (21 bp):
ATTGTATCGATACATTTGTAA
Found at i:2196139 original size:21 final size:20
Alignment explanation
Indices: 2196115--2196169 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2196105 ATCTTATTGG
* *
2196115 AAAGAAAGTAAATGAGTTAGA
1 AAAGAAAATAAA-GAGTTACA
2196136 AAAGAAAATTAAAGAGTTACA
1 AAAGAAAA-TAAAGAGTTACA
2196157 AGAAGAAAATAAA
1 A-AAGAAAATAAA
2196170 AAATTGACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.64, C:0.02, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAGAAAATAAAGAGTTACA
Found at i:2196162 original size:22 final size:22
Alignment explanation
Indices: 2196115--2196166 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2196105 ATCTTATTGG
* *
2196115 AAAG-AAAGTAAATGAGTTAGA
1 AAAGAAAATTAAATGAGTTACA
2196136 AAAGAAAATTAAA-GAGTTACA
1 AAAGAAAATTAAATGAGTTACA
2196157 AGAAGAAAAT
1 A-AAGAAAAT
2196167 AAAAAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (22 bp):
AAAGAAAATTAAATGAGTTACA
Found at i:2200124 original size:19 final size:19
Alignment explanation
Indices: 2200074--2200128 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
2200064 GGTTTTCCAG
* *
2200074 ATTGTATCGATACAATGAAA
1 ATTGTATTGATAC-ATTAAA
*
2200094 TTTGT-TTCGATACATTAAA
1 ATTGTATT-GATACATTAAA
2200113 ATTGTATTGATACATT
1 ATTGTATTGATACATT
2200129 TCGACTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (19 bp):
ATTGTATTGATACATTAAA
Found at i:2200896 original size:33 final size:33
Alignment explanation
Indices: 2200854--2200916 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2200844 CACACCCAGA
2200854 TATATTGATACAAATTGCTAAGTATCGATATAT
1 TATATTGATACAAATTGCTAAGTATCGATATAT
**
2200887 TATATTGATACAAATTGCTTTGTATCGATA
1 TATATTGATACAAATTGCTAAGTATCGATA
2200917 CACTATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (33 bp):
TATATTGATACAAATTGCTAAGTATCGATATAT
Found at i:2202116 original size:66 final size:66
Alignment explanation
Indices: 2201785--2202457 Score: 393
Period size: 66 Copynumber: 10.2 Consensus size: 66
2201775 CCTGTCGCCT
* ** * * *
2201785 TTTTTTGACTCAGGTTTTACCTTAGTCACCTTTAGATGTTTCGTATGGTTTCATCCTAGCCAACC
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
2201850 C
66 C
* * * ** * * * ** *
2201851 -ATTTCGACTCAGGTTTCATC-AGGTCACCCTTAGTTGGTTCATATGGTTTTGTCCTAGTCAA-C
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
2201913 C
66 C
* * * * * ** ** * * * * *
2201914 TTTTTTCGAATTAAGCTTCACCTTAGTCACC-AAAGTTGGTTTATATGGATTCGTCTTAACTAAC
1 TTTTTT-GACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAAC
*
2201978 TC
65 CC
* * * * * * *
2201980 TTTTTTCGACTTAGATTTTGCCTTAGTTACAC-TTAGTT-G-TCTGTATGGCTTCGTCC-CGACC
1 TTTTTT-GACTTAGGTTTCGCCTTGGTCAC-CTTTAGTTGGTTC-GTATGGTTTCATCCTAG-CC
*
2202041 AACCT
62 AACCC
* * * **
2202046 TTTTTTTACTTAGGTTTCGCCATGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCAACC
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
2202111 C
66 C
* * * * * *
2202112 TTTTTTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTTAT-CTTGACCAAC
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAG-CCAA-
2202176 CCC
64 CCC
* * * * * *
2202179 TTTTTTGACTTAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGTATGGTTACATCCTAGCCAACT
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
*
2202244 A
66 C
* * * * * ** *
2202245 TTTTTTGACTTAGGTTCCACCTTGGTCTCTTTTAGTTGGTTTGTATGGTTTCATCCCGGCCAACT
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
2202310 C
66 C
* * * * * * *
2202311 TTTTTCGACTCAGGTTTTGCCTTGGTCACCTTAAGTTGGTTTGCATGGTTTCAT-CTCGACCAAT
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAG-CCAA-
* *
2202375 TCA
64 CCC
* * * * ** * *
2202378 TTTTCT-ACTTAGGTTTTGCCTTGGTCACCCTAAGTTTATTCGTAAGG-TTCAT-CTCAGACAA-
1 TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCT-AGCCAAC
*
2202439 TC
65 CC
2202441 TTTTTTCGACTTAGGTT
1 TTTTTT-GACTTAGGTT
2202458 CTACCCTAGT
Statistics
Matches: 470, Mismatches: 118, Indels: 39
0.75 0.19 0.06
Matches are distributed among these distances:
63 7 0.01
64 36 0.08
65 97 0.21
66 260 0.55
67 67 0.14
68 3 0.01
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (66 bp):
TTTTTTGACTTAGGTTTCGCCTTGGTCACCTTTAGTTGGTTCGTATGGTTTCATCCTAGCCAACC
C
Found at i:2202281 original size:199 final size:195
Alignment explanation
Indices: 2201785--2202408 Score: 571
Period size: 199 Copynumber: 3.2 Consensus size: 195
2201775 CCTGTCGCCT
* * *
2201785 TTTTTTGACTCAGGTTTTACCTTAGTCACCTTTAGA-TGTTTCGTATGGTTTCATCCTAGCCAAC
1 TTTTTTGACTTAGGTTTTGCCTTAGTCACCCTTA-ATTGTTT-GTATGG-TTCATCCTAGCCAAC
* * * * * * *
2201849 CCA--TTTCGACTCAGGTTTCATCAGGTCACCCTTAGTTGGTTCATATGGTTTTGTCCTAGTCAA
63 CTATTTTTTGACTTAGGTTTCACCTGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCAA
* * * ** * ** * * * * *
2201912 -CCTTTTTTCGAATTAAGCTTCACCTTAGTCACCAAAGTTGGTTTATATGGATTCGTCTTAACTA
128 CCCTTTTTT-GACTTAGGTTTTGCCTTGGTCACCTTAGTTGGTTTGTATGGTTTCATCTTGACCA
*
2201976 ACTC
192 ACCC
* * * * * * *
2201980 TTTTTTCGACTTAGATTTTGCCTTAGTTACACTTAGTTGTCTGTATGGCTTCGTCC-CGACCAAC
1 TTTTTT-GACTTAGGTTTTGCCTTAGTCACCCTTAATTGTTTGTATGG-TTCATCCTAG-CCAAC
* *
2202044 CT-TTTTTTTACTTAGGTTTCGCCATGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCA
63 CTATTTTTTGACTTAGGTTTCACC-TGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCA
* *
2202108 ACCCTTTTTTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTTATCTTGACC
127 ACCCTTTTTTGACTTAGGTTTTGCCTTGGTCA-CCTTAGTTGGTTTGTATGGTTTCATCTTGACC
2202173 AACCCC
191 AA-CCC
*
2202179 TTTTTTGACTTAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGTATGGTTACATCCTAGCCAA-C
1 TTTTTTGACTTAGGTTTTGCCTTAGTCACCCTTAATT-GTTTGTATGGTT-CATCCTAGCCAACC
* * * ** ** **
2202243 TATTTTTTGACTTAGGTTCCACCTTGGTCTCTTTTAGTTGGTTTGTATGGTTTCATCCCGGCCAA
64 TATTTTTTGACTTAGGTTTCACC-TGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCAA
* * * * *
2202308 CTCTTTTTCGACTCAGGTTTTGCCTTGGTCACCTTAAGTTGGTTTGCATGGTTTCATCTCGACCA
128 CCCTTTTTTGACTTAGGTTTTGCCTTGGTCACCTT-AGTTGGTTTGTATGGTTTCATCTTGACCA
* *
2202373 ATTCA
192 A-CCC
* *
2202378 TTTTCT-ACTTAGGTTTTGCCTTGGTCACCCT
1 TTTTTTGACTTAGGTTTTGCCTTAGTCACCCT
2202409 AAGTTTATTC
Statistics
Matches: 346, Mismatches: 69, Indels: 25
0.79 0.16 0.06
Matches are distributed among these distances:
194 1 0.00
195 24 0.07
196 40 0.12
197 54 0.16
198 90 0.26
199 136 0.39
200 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (195 bp):
TTTTTTGACTTAGGTTTTGCCTTAGTCACCCTTAATTGTTTGTATGGTTCATCCTAGCCAACCTA
TTTTTTGACTTAGGTTTCACCTGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCAACCC
TTTTTTGACTTAGGTTTTGCCTTGGTCACCTTAGTTGGTTTGTATGGTTTCATCTTGACCAACCC
Found at i:2202400 original size:132 final size:133
Alignment explanation
Indices: 2201982--2202408 Score: 355
Period size: 133 Copynumber: 3.2 Consensus size: 133
2201972 ACTAACTCTT
* * * * * * * *
2201982 TTTTC-GACTTAGATTTTGCCTTAGTTACACTTAGT-TGTCTGTATGGCTTCGTCCCGACCAA-C
1 TTTTCTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTCATCCCGACCAACC
* ** * * * * * *** *** *
2202044 CTTTTTTTTACTTAGGTTTCGCCATGGTCACCTTTAGTTGGTTCATATGGTTTTGTCCTAGCCAA
66 CCTTTTTCGACTCAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGCATGGTTACATCCGAGCCAA
**
2202109 CCC
131 CTA
* * **
2202112 TTTTTTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTTATCTTGACCAACC
1 TTTTCTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTCATCCCGACCAACC
* * * *
2202177 CCTTTTTTGACTTAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGTATGGTTACATCCTAGCCAA
66 CCTTTTTCGACTCAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGCATGGTTACATCCGAGCCAA
2202242 CTA
131 CTA
* *** * ** * *
2202245 TTTTTTGACTTAGGTTCCACCTTGGTCTCTTTTAGTTGGTTTGTATGGTTTCATCCCGGCCAA-C
1 TTTTCTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTCATCCCGACCAACC
* * * *
2202309 TCTTTTTCGACTCAGGTTTTGCCTTGGTCA-CCTTAAGTTGGTTTGCATGGTTTCATCTCGA-CC
66 CCTTTTTCGACTCAGGTTTCGCCTTAGTCACCCTTAA-TTGGTTTGCATGGTTACATC-CGAGCC
*
2202372 AATTCA
129 AACT-A
2202378 TTTTCT-ACTTAGGTTTTGCCTTGGTCACCCT
1 TTTTCTGACTTAGGTTTTGCCTTGGTCACCCT
2202409 AAGTTTATTC
Statistics
Matches: 239, Mismatches: 52, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
130 4 0.02
131 32 0.13
132 87 0.36
133 116 0.49
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (133 bp):
TTTTCTGACTTAGGTTTTGCCTTGGTCACCCTTAGTAGGTTTGTATGGTTTCATCCCGACCAACC
CCTTTTTCGACTCAGGTTTCGCCTTAGTCACCCTTAATTGGTTTGCATGGTTACATCCGAGCCAA
CTA
Found at i:2203975 original size:23 final size:23
Alignment explanation
Indices: 2203932--2203975 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2203922 AATCAAAAGT
*
2203932 AATAATAAAAAAATAACAGAATA
1 AATAATAAAAAAAAAACAGAATA
*
2203955 AATAA-AAAATAAAAAAGAGAA
1 AATAATAAAA-AAAAAACAGAA
2203976 AGATTGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (23 bp):
AATAATAAAAAAAAAACAGAATA
Found at i:2207095 original size:32 final size:32
Alignment explanation
Indices: 2207058--2207124 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
2207048 CAAGAATTCC
2207058 ATATAAGTTTAAACTCAATCAACTTTATCTCT
1 ATATAAGTTTAAACTCAATCAACTTTATCTCT
* * *
2207090 ATATAAGTTTAAACTCTATTAGCTTTATCTCT
1 ATATAAGTTTAAACTCAATCAACTTTATCTCT
2207122 ATA
1 ATA
2207125 GAATTCTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.43
Consensus pattern (32 bp):
ATATAAGTTTAAACTCAATCAACTTTATCTCT
Found at i:2207108 original size:17 final size:17
Alignment explanation
Indices: 2207058--2207108 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2207048 CAAGAATTCC
2207058 ATATAAGTTTAAACTC-
1 ATATAAGTTTAAACTCT
* *
2207074 A-ATCAACTTT-ATCTCT
1 ATAT-AAGTTTAAACTCT
2207090 ATATAAGTTTAAACTCT
1 ATATAAGTTTAAACTCT
2207107 AT
1 AT
2207109 TAGCTTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
15 6 0.22
16 12 0.44
17 9 0.33
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (17 bp):
ATATAAGTTTAAACTCT
Found at i:2207123 original size:15 final size:17
Alignment explanation
Indices: 2207080--2207124 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
2207070 ACTCAATCAA
2207080 CTTTATCTCTATATAAG
1 CTTTATCTCTATATAAG
*
2207097 -TTTAAACTCTAT-T-AG
1 CTTT-ATCTCTATATAAG
2207112 CTTTATCTCTATA
1 CTTTATCTCTATA
2207125 GAATTCTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
15 9 0.39
16 7 0.30
17 7 0.30
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (17 bp):
CTTTATCTCTATATAAG
Found at i:2207638 original size:73 final size:73
Alignment explanation
Indices: 2207519--2207666 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
2207509 CGTCTCGTAA
*
2207519 AGATATTCGAACTTAACACTAAAAATGAGATAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
1 AGATATTCGAACTTAACACTAAAAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
2207584 AAATAATG
66 AAATAATG
* * *
2207592 AGATATTGGAACTTAACACTAACAATGAGACAGGAAAAATATGTAGAAATGCCTCATGTTTCATG
1 AGATATTCGAACTTAACACTAAAAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
2207657 AAATAATG
66 AAATAATG
2207665 AG
1 AG
2207667 GGAATTAACG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.26
Consensus pattern (73 bp):
AGATATTCGAACTTAACACTAAAAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
AAATAATG
Found at i:2213057 original size:23 final size:23
Alignment explanation
Indices: 2213005--2213053 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2212995 AATCATTTAA
2213005 ATTTAAATTTAATTATAAAAATT
1 ATTTAAATTTAATTATAAAAATT
*
2213028 ATATAAATATTAA-TATAAAAA-T
1 ATTTAAAT-TTAATTATAAAAATT
2213050 ATTT
1 ATTT
2213054 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAAATTTAATTATAAAAATT
Found at i:2213334 original size:39 final size:38
Alignment explanation
Indices: 2213291--2213365 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
2213281 ATTTTTTAGT
2213291 TTTAAATGAACAAATAGCTTAAAATTTTTAAATTTAAGA
1 TTTAAATG-ACAAATAGCTTAAAATTTTTAAATTTAAGA
** * * *
2213330 TTTAAATGATTAATGGGTTGAAATTTTTAAATTTAA
1 TTTAAATGACAAATAGCTTAAAATTTTTAAATTTAA
2213366 ACTTTCAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 23 0.74
39 8 0.26
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (38 bp):
TTTAAATGACAAATAGCTTAAAATTTTTAAATTTAAGA
Found at i:2213992 original size:5 final size:5
Alignment explanation
Indices: 2213982--2214013 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2213972 AATACAAAAA
*
2213982 CATAC CATAC CATAC CATAC CTTAC CATAC CA
1 CATAC CATAC CATAC CATAC CATAC CATAC CA
2214014 AATGGTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (5 bp):
CATAC
Found at i:2216743 original size:2 final size:2
Alignment explanation
Indices: 2216738--2216780 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2216728 AAGAAAAATA
* * *
2216738 AG AG AG AG AG AG AA AG AG AG AG AC AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2216780 A
1 A
2216781 ACATATTCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2216765 original size:18 final size:18
Alignment explanation
Indices: 2216738--2216778 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2216728 AAGAAAAATA
*
2216738 AGAGAGAGAGAGAAAGAG
1 AGAGACAGAGAGAAAGAG
2216756 AGAGACAGAGAGAAAGAG
1 AGAGACAGAGAGAAAGAG
2216774 AGAGA
1 AGAGA
2216779 GAACATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.41, T:0.00
Consensus pattern (18 bp):
AGAGACAGAGAGAAAGAG
Found at i:2219795 original size:20 final size:20
Alignment explanation
Indices: 2219758--2219800 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2219748 ATCAAAATCA
* * *
2219758 AAAGTAATAATTATAAAAGT
1 AAAGGAATAAATAAAAAAGT
*
2219778 AAAGGAATAAATAAAAAATT
1 AAAGGAATAAATAAAAAAGT
2219798 AAA
1 AAA
2219801 AAAATTGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (20 bp):
AAAGGAATAAATAAAAAAGT
Found at i:2224752 original size:22 final size:21
Alignment explanation
Indices: 2224724--2224779 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
2224714 GTTACAAGCA
2224724 ATGTATCGATACAATT-TCATAC
1 ATGTATCGATACAATTATC--AC
*
2224746 ATGTATCGATAC-ATTATCCC
1 ATGTATCGATACAATTATCAC
2224766 ATGTATCGATACAA
1 ATGTATCGATACAA
2224780 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 13 0.42
21 4 0.13
22 14 0.45
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (21 bp):
ATGTATCGATACAATTATCAC
Found at i:2224870 original size:32 final size:33
Alignment explanation
Indices: 2224829--2224893 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
2224819 ATAATTATCC
* *
2224829 ATGTATCGATACAACG-AGCATGTATTGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
*
2224861 ATGTATCGATACAAAGCAGTATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
2224894 TCTGGGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAGCATGTATCGATACA
Found at i:2227373 original size:13 final size:13
Alignment explanation
Indices: 2227355--2227380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2227345 AAATAGTACC
2227355 CAATGTATCGATA
1 CAATGTATCGATA
2227368 CAATGTATCGATA
1 CAATGTATCGATA
2227381 TAAGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2230796 original size:3 final size:3
Alignment explanation
Indices: 2230783--2230812 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2230773 CTTCATCCGA
*
2230783 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2230813 TTCCTCTTCA
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:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:2231274 original size:21 final size:21
Alignment explanation
Indices: 2231241--2231281 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2231231 CTAAGTAAAA
2231241 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2231262 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2231282 CAAGATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2231346 original size:20 final size:19
Alignment explanation
Indices: 2231321--2231391 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
2231311 ACCCTGAAAA
2231321 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2231341 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
2231360 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2231381 GTATCGATACA
1 GTATCGATACA
2231392 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2231444 original size:53 final size:53
Alignment explanation
Indices: 2231361--2231497 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2231351 AGATTGCATA
2231361 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
2231415 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
2231468 GTATCGATACACAAAAAATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
2231498 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:2233884 original size:19 final size:19
Alignment explanation
Indices: 2233840--2233895 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2233830 CTGCCAGTTT
*
2233840 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
* *
2233860 CATGTAACGATACAATGAG
1 CATGTATCGATACAATGAC
2233879 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2233896 TATTGATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:2234865 original size:21 final size:21
Alignment explanation
Indices: 2234819--2234873 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2234809 AAAAACCCAG
2234819 AATGTATCGATAC-AATGGAT
1 AATGTATCGATACAAATGGAT
*
2234839 AATGTATCGATACAAATTG-T
1 AATGTATCGATACAAATGGAT
2234859 AAATGTATCGATACA
1 -AATGTATCGATACA
2234874 TTTACTTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAAATGGAT
Found at i:2234966 original size:20 final size:20
Alignment explanation
Indices: 2234941--2234979 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2234931 CATTTCAGGC
2234941 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
*
2234961 ATGTATCGATATATTTACT
1 ATGTATCGATACATTTACT
2234980 ATTTATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:2239981 original size:60 final size:58
Alignment explanation
Indices: 2239822--2240029 Score: 181
Period size: 60 Copynumber: 3.5 Consensus size: 58
2239812 AATTTCATTA
* * * *
2239822 AGTCTTGGTTTTGCCCAAGACATTGTTAAGGTTTCTAGCTTCGTCTAAGCCATTTAATTG
1 AGTCTTGGTTTAGCCCAAGACATTGTTTAGGTTTCTAGTTTC-TCT-AGCCATTTAGTTG
* * *
2239882 AGTCTCGGTTTCA-CCCAAGACATTGTTTAGCTTTCTAGTTTCATCCTAGCCATTTGGTTG
1 AGTCTTGGTTT-AGCCCAAGACATTGTTTAGGTTTCTAGTTTC-T-CTAGCCATTTAGTTG
* * *
2239942 AGTCTTGGTTTAGCCCAAGTCATTATTTAGG-TTCTTAGTTT-TGGC-AGGACCATTTCGTTG
1 AGTCTTGGTTTAGCCCAAGACATTGTTTAGGTTTC-TAGTTTCT--CTA-G-CCATTTAGTTG
* * *
2240002 AGTCTTGGTTTTGCCCAGGTCATTGTTT
1 AGTCTTGGTTTAGCCCAAGACATTGTTT
2240030 GAGATCTTGA
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.02
59 6 0.05
60 114 0.92
61 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (58 bp):
AGTCTTGGTTTAGCCCAAGACATTGTTTAGGTTTCTAGTTTCTCTAGCCATTTAGTTG
Found at i:2241472 original size:14 final size:14
Alignment explanation
Indices: 2241455--2241492 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2241445 ATACATGATT
2241455 TTTAATTTTTACAA
1 TTTAATTTTTACAA
2241469 TTTAATCTTTT-CAA
1 TTTAAT-TTTTACAA
2241483 -TTAATTTTTA
1 TTTAATTTTTA
2241493 TGGTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 9 0.41
15 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTTTACAA
Found at i:2242527 original size:21 final size:21
Alignment explanation
Indices: 2242486--2242527 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2242476 ATTATTCTTG
* *
2242486 TGATTTTTTATGTGGTTTTTA
1 TGATTTTTCATGTGGTGTTTA
2242507 TGATTTTTCATGAT-GTGTTTA
1 TGATTTTTCATG-TGGTGTTTA
2242528 GTATTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.02, G:0.19, T:0.62
Consensus pattern (21 bp):
TGATTTTTCATGTGGTGTTTA
Found at i:2244910 original size:68 final size:66
Alignment explanation
Indices: 2244774--2244976 Score: 185
Period size: 66 Copynumber: 3.0 Consensus size: 66
2244764 TAGTCACCAA
* * * * * * * * *
2244774 AGTTGGTTTATATGGATTCGT-CTGAACTAACTCTTTTTCGACTCAGATTTTGCCATGGTTACCT
1 AGTTGGTTCATATGGCTTCGTCCTG-ACCAACCCTTTTTCAACTTAGGTTTTGCCATGGTCACCC
2244838 TT
65 TT
** * * ***
2244840 AGTT-GTTTGTATGGCTTCGTCTTGACCAGCCCTTTTTTTTTTCCTTAGGTTTTGCCATGGTCAC
1 AGTTGGTTCATATGGCTTCGTCCTGACCAACCC---TTTTTCAACTTAGGTTTTGCCATGGTCAC
2244904 CCTT
63 CCTT
* * *
2244908 AGTTGGTTCATATGGTTTTGTCCTGACCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCT
1 AGTTGGTTCATATGGCTTCGTCCTGACCAACCCTTTTTCAACTTAGGTTTTGCCATGGTCACCCT
2244973 T
66 T
2244974 AGT
1 AGT
2244977 AGGTGAAAGC
Statistics
Matches: 109, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
65 19 0.17
66 38 0.35
68 30 0.28
69 22 0.20
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (66 bp):
AGTTGGTTCATATGGCTTCGTCCTGACCAACCCTTTTTCAACTTAGGTTTTGCCATGGTCACCCT
T
Found at i:2245771 original size:16 final size:13
Alignment explanation
Indices: 2245731--2245758 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2245721 CAATTTTTTG
2245731 TGTATCGATACAT
1 TGTATCGATACAT
2245744 TGTATCGATACAT
1 TGTATCGATACAT
2245757 TG
1 TG
2245759 CTGTATCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2245818 original size:21 final size:20
Alignment explanation
Indices: 2245792--2245868 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2245782 CTGCCAAGAA
*
2245792 ATGTATCGATACATATTTTTT
1 ATGTATCGATACAT-TTTTTC
****
2245813 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTC
2245833 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TTTTTC
2245854 ATGTATCGATACATT
1 ATGTATCGATACATT
2245869 GCAACATGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTC
Found at i:2245838 original size:20 final size:20
Alignment explanation
Indices: 2245813--2245885 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2245803 CATATTTTTT
2245813 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2245833 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2245854 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2245874 ATGTATCGATAC
1 ATGTATCGATAC
2245886 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2245852 original size:41 final size:41
Alignment explanation
Indices: 2245792--2245885 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2245782 CTGCCAAGAA
*
2245792 ATGTATCGATACATATTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
*
2245833 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
2245874 ATGTATCGATAC
1 ATGTATCGATAC
2245886 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
Found at i:2248347 original size:13 final size:13
Alignment explanation
Indices: 2248329--2248367 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2248319 ATAATCACCC
*
2248329 TGTATCGATACAG
1 TGTATCGATACAA
2248342 TGTATCGATACAA
1 TGTATCGATACAA
2248355 TGTATCGATACAA
1 TGTATCGATACAA
2248368 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2248378 original size:20 final size:20
Alignment explanation
Indices: 2248353--2248431 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2248343 GTATCGATAC
2248353 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2248373 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
2248398 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
2248418 CATGTATCGATACA
1 AATGTATCGATACA
2248432 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2250466 original size:15 final size:15
Alignment explanation
Indices: 2250446--2250476 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2250436 ATTTCGTTTG
*
2250446 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2250461 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2250476 G
1 G
2250477 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2252309 original size:21 final size:21
Alignment explanation
Indices: 2252280--2252324 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2252270 AAGTTTTCAT
*
2252280 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2252300 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2252322 TTT
1 TTT
2252325 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Done.