Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:3122807 original size:6 final size:6
Alignment explanation
Indices: 3122796--3122876 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
3122786 TCTCGTCTCG
3122796 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3122844 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
3122877 AATACGTGTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:3123020 original size:23 final size:20
Alignment explanation
Indices: 3122938--3123085 Score: 156
Period size: 20 Copynumber: 7.0 Consensus size: 20
3122928 TGCAATACTA
*
3122938 TCTTGGAATCGTATTGCGAT
1 TCTTGGAATCGCATTGCGAT
*
3122958 TCTTCGAAGATCGCATTGCGAT
1 TCTT-GGA-ATCGCATTGCGAT
3122980 TCTTGGAATCGCATTGCGAT
1 TCTTGGAATCGCATTGCGAT
3123000 TCTTGGAATCGCAGCATTGCGAT
1 TCTTGGAAT--C-GCATTGCGAT
*
3123023 TCTTTCG-ATCGCATTGCGAT
1 TC-TTGGAATCGCATTGCGAT
*
3123043 TCTTTCG-ATCGCATTGCGAT
1 TC-TTGGAATCGCATTGCGAT
*
3123063 TCTTGGAAGATCGCGTTGCGAT
1 TCTTGG-A-ATCGCATTGCGAT
3123085 T
1 T
3123086 TTCTTTTGAC
Statistics
Matches: 113, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.03
20 58 0.51
21 5 0.04
22 30 0.27
23 14 0.12
24 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
TCTTGGAATCGCATTGCGAT
Found at i:3123054 original size:43 final size:41
Alignment explanation
Indices: 3122943--3123066 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 41
3122933 TACTATCTTG
* *
3122943 GAATCGTATTGCGATTCTTCGAAGATCGCATTGCGATTC-TTG
1 GAATCGCATTGCGATTCTTCG-A-ATCGCATTGCGATTCTTTC
*
3122985 GAATCGCATTGCGATTCTTGGAATCGCAGCATTGCGATTCTTTC
1 GAATCGCATTGCGATTCTTCGAAT--C-GCATTGCGATTCTTTC
3123029 G-ATCGCATTGCGATTCTTTCG-ATCGCATTGCGATTCTT
1 GAATCGCATTGCGATTC-TTCGAATCGCATTGCGATTCTT
3123067 GGAAGATCGC
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
40 16 0.22
41 2 0.03
42 20 0.27
43 29 0.40
44 6 0.08
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (41 bp):
GAATCGCATTGCGATTCTTCGAATCGCATTGCGATTCTTTC
Found at i:3123101 original size:20 final size:20
Alignment explanation
Indices: 3123076--3123129 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3123066 TGGAAGATCG
* *
3123076 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
3123096 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
3123116 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
3123130 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:3123156 original size:19 final size:19
Alignment explanation
Indices: 3123116--3123167 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3123106 TTCTTTTCAA
*
3123116 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
*
3123136 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
3123155 CGTTGCGATTTTG
1 CGTTGCGATTTTG
3123168 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:3125276 original size:2 final size:2
Alignment explanation
Indices: 3125259--3125375 Score: 98
Period size: 2 Copynumber: 58.5 Consensus size: 2
3125249 CCTTACAACT
* *
3125259 TA TA T- TA TA T- TA TA TA TA TA TA TA TA CA TA TA CT- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
3125299 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
3125342 CTT TT TA TA TA TA CA T- TA TA GTT TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA T
3125376 TAAAAAAGAT
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
1 4 0.04
2 86 0.91
3 4 0.04
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3125558 original size:20 final size:20
Alignment explanation
Indices: 3125509--3125559 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
3125499 TATATATATA
*
3125509 TATATATATATATGATGAATG
1 TATATATA-ATAAGATGAATG
3125530 T-TATGATAATAAGAT-ACATG
1 TATAT-ATAATAAGATGA-ATG
3125550 TATATATAAT
1 TATATATAAT
3125560 GTACATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (20 bp):
TATATATAATAAGATGAATG
Found at i:3127013 original size:2 final size:2
Alignment explanation
Indices: 3127006--3127077 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
3126996 ACTGGATTTA
3127006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3127048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3127078 GACTTTAGCT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3138754 original size:2 final size:2
Alignment explanation
Indices: 3138747--3138794 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3138737 GTTATCAATA
3138747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3138789 AT AT AT
1 AT AT AT
3138795 TGCGTGTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3139224 original size:60 final size:60
Alignment explanation
Indices: 3139153--3139276 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 60
3139143 TCCTCTGTCA
* * * * *
3139153 CTTTTTTATCCTCATTCTTATTACCACCTTTGACCTCTTTTGAACTCTCTGTTTTCTCTT
1 CTTTTTCATCCTCATTCTCATTACCACCTTGGACCTCTTTTGAACACTCTGTTTTCTCTC
* * *
3139213 CTTTTTCATCCTCCTTCTCATTACCATCTTGGATCTCTTTTGAACACTCTGTTTTCTCTC
1 CTTTTTCATCCTCATTCTCATTACCACCTTGGACCTCTTTTGAACACTCTGTTTTCTCTC
3139273 CTTT
1 CTTT
3139277 ACTTTCTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.13, C:0.30, G:0.06, T:0.52
Consensus pattern (60 bp):
CTTTTTCATCCTCATTCTCATTACCACCTTGGACCTCTTTTGAACACTCTGTTTTCTCTC
Found at i:3141787 original size:26 final size:26
Alignment explanation
Indices: 3141758--3141837 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
3141748 AAGTTAGTAT
*
3141758 ATATCTCATATTTAACCTCGTAATTG
1 ATATCTCATATTTAACCTCATAATTG
3141784 ATATCTCATATTTAACCTCATAATTG
1 ATATCTCATATTTAACCTCATAATTG
3141810 ATATCTCATATTTAACCTCATAATTG
1 ATATCTCATATTTAACCTCATAATTG
3141836 AT
1 AT
3141838 GTATATCTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (26 bp):
ATATCTCATATTTAACCTCATAATTG
Found at i:3141805 original size:12 final size:12
Alignment explanation
Indices: 3141762--3141831 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
3141752 TAGTATATAT
3141762 CTCATATTTAAC
1 CTCATATTTAAC
* * *
3141774 CTCGTAATTGATAT
1 CTCAT-ATTTA-AC
3141788 CTCATATTTAAC
1 CTCATATTTAAC
* *
3141800 CTCATAATTGATAT
1 CTCAT-ATTTA-AC
3141814 CTCATATTTAAC
1 CTCATATTTAAC
3141826 CTCATA
1 CTCATA
3141832 ATTGATGTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
12 17 0.39
13 16 0.36
14 11 0.25
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.41
Consensus pattern (12 bp):
CTCATATTTAAC
Found at i:3143335 original size:11 final size:11
Alignment explanation
Indices: 3143319--3143347 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3143309 GTCAACGGTA
3143319 AACGGTCGATC
1 AACGGTCGATC
3143330 AACGGTCGATC
1 AACGGTCGATC
3143341 AACGGTC
1 AACGGTC
3143348 AACGGGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (11 bp):
AACGGTCGATC
Found at i:3152824 original size:40 final size:40
Alignment explanation
Indices: 3152728--3152910 Score: 118
Period size: 42 Copynumber: 4.4 Consensus size: 40
3152718 GTGTTTTTTG
* ** *
3152728 TAACAAATGCCGCTATATCCTCATTTATTAGTGGCGTTTGTC
1 TAACAAACGCCGCTATAGACTC--TTATTAGTGGCGTTTGAC
* *
3152770 TTACAAACGCCGCTATAGACTCTTATTAGTGGCGTTTGAG
1 TAACAAACGCCGCTATAGACTCTTATTAGTGGCGTTTGAC
* * * * * *
3152810 TAAC-AACTGTCGCTATAGACACGTACATTGGTGACATTTGAC
1 TAACAAAC-GCCGCTATAGACTC-T-TATTAGTGGCGTTTGAC
* * * * *
3152852 TAACAAACACCACTATAGACGCGTACATTAGTGGCATTT-ATC
1 TAACAAACGCCGCTATAGACTC-T-TATTAGTGGCGTTTGA-C
*
3152894 AAACAAACGCCGCTATA
1 TAACAAACGCCGCTATA
3152911 TCCTCATATA
Statistics
Matches: 113, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
39 3 0.03
40 31 0.27
41 2 0.02
42 74 0.65
43 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (40 bp):
TAACAAACGCCGCTATAGACTCTTATTAGTGGCGTTTGAC
Found at i:3153425 original size:44 final size:43
Alignment explanation
Indices: 3153372--3153516 Score: 170
Period size: 44 Copynumber: 3.3 Consensus size: 43
3153362 TAACATATAG
*
3153372 CGGCATTTGGGGTGAAAA-ACGCTACCATATATCATGACTATTAA
1 CGGCGTTT-GGGTGAAAACAC-CTACCATATATCATGACTATTAA
*
3153416 CGAG-GTTTGGGTGAAAACACC-ACCATATATCGTGACTATTAA
1 CG-GCGTTTGGGTGAAAACACCTACCATATATCATGACTATTAA
** * *
3153458 CGGCGTTTGGGTGAAAACAATTTACTATATATCATGACTATTAG
1 CGGCGTTTGGGTGAAAAC-ACCTACCATATATCATGACTATTAA
*
3153502 CGGCGTTTTGGTGAA
1 CGGCGTTTGGGTGAA
3153517 CAAACGATGC
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.01
42 36 0.41
43 11 0.12
44 39 0.44
45 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (43 bp):
CGGCGTTTGGGTGAAAACACCTACCATATATCATGACTATTAA
Found at i:3155894 original size:31 final size:31
Alignment explanation
Indices: 3155859--3155980 Score: 111
Period size: 31 Copynumber: 3.8 Consensus size: 31
3155849 TTTTGATTGG
3155859 ATTTAAAAATTAAATTATTATTTTATATAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
** * * *
3155890 ATTTAAATGTTAAATTGTTACTTTATCTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
* * * *
3155921 ATTTAAGAATTAAGTTAGT-TTTTATTTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
*
3155951 ATTTATTTAAGAATTAAATTAATATTTTAT
1 ATTTA---AA-AATTAAATTATTATTTTAT
3155981 TTAATTTTTT
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
30 14 0.20
31 39 0.56
33 1 0.01
34 10 0.14
35 6 0.09
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (31 bp):
ATTTAAAAATTAAATTATTATTTTATATAAA
Found at i:3156798 original size:2 final size:2
Alignment explanation
Indices: 3156791--3156843 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3156781 CATGGTTTTG
3156791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3156833 AT AT AT AT AT A
1 AT AT AT AT AT A
3156844 CACGCATTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3157365 original size:28 final size:28
Alignment explanation
Indices: 3157325--3157415 Score: 173
Period size: 28 Copynumber: 3.2 Consensus size: 28
3157315 GCATAGATAT
3157325 TGCATGTGCATCTGCAAAGCAATTACAA
1 TGCATGTGCATCTGCAAAGCAATTACAA
3157353 TGCATGTGCATCTGCAAAGCAATTACAA
1 TGCATGTGCATCTGCAAAGCAATTACAA
*
3157381 TGCATGTGCATCTACAAAGCAATTACAA
1 TGCATGTGCATCTGCAAAGCAATTACAA
3157409 TGCATGT
1 TGCATGT
3157416 TTTGGGGAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (28 bp):
TGCATGTGCATCTGCAAAGCAATTACAA
Found at i:3160980 original size:17 final size:17
Alignment explanation
Indices: 3160955--3160992 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3160945 GCAGTAGTTC
*
3160955 GAAAGAAAGAAAGAA-AA
1 GAAAAAAAG-AAGAAGAA
3160972 GAAAAAAAGAAGAAGAA
1 GAAAAAAAGAAGAAGAA
3160989 GAAA
1 GAAA
3160993 GAAGCTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAAAAAGAAGAAGAA
Found at i:3160996 original size:13 final size:14
Alignment explanation
Indices: 3160957--3160996 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
3160947 AGTAGTTCGA
3160957 AAGAAAGAAAGAA-
1 AAGAAAGAAAGAAG
*
3160970 AAGAAAAAAAGAAG
1 AAGAAAGAAAGAAG
3160984 AAG-AAGAAAGAAG
1 AAGAAAGAAAGAAG
3160997 CTGTTCGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAGAAG
Found at i:3168806 original size:2 final size:2
Alignment explanation
Indices: 3168801--3168834 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3168791 TTTTTTTGTA
3168801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3168835 GTTATGCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3168970 original size:31 final size:31
Alignment explanation
Indices: 3168935--3169062 Score: 139
Period size: 31 Copynumber: 4.0 Consensus size: 31
3168925 TTTTGATTGG
3168935 ATTTAAAAATTAAATTATTATTTTATATAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
** * *
3168966 ATTTAAATGTTAAATTGTTACTTTATATAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
* * *
3168997 ATTTAAGAATTAAATTAGTATTTTATTTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
* *
3169028 ATTTATTTAAGAATTAAATTAATATTTTATTTAAA
1 ATTTA---AA-AATTAAATTATTATTTTATATAAA
3169063 GTTTTTTGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
31 56 0.70
34 1 0.01
35 23 0.29
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTTAAAAATTAAATTATTATTTTATATAAA
Found at i:3171166 original size:28 final size:28
Alignment explanation
Indices: 3171121--3171183 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
3171111 AAATAGATAT
* * *
3171121 TGCATGTGTATCTGCAAAGCAATTACAA
1 TGCATGTGCACCTACAAAGCAATTACAA
3171149 TGCATGTGCACCTACAAAGCAATTACAA
1 TGCATGTGCACCTACAAAGCAATTACAA
3171177 TGCATGT
1 TGCATGT
3171184 TTTGGGGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (28 bp):
TGCATGTGCACCTACAAAGCAATTACAA
Found at i:3175542 original size:216 final size:215
Alignment explanation
Indices: 3175291--3175966 Score: 1005
Period size: 216 Copynumber: 3.2 Consensus size: 215
3175281 TTAAGAATTC
* *
3175291 AATTGAACAAATATGAAATCACAAATAAAAATTTAAATAAATTAAACAAAACACATTGATGATGG
1 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAAACACATTGATGAGGG
3175356 ATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCT
66 ATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACC-
* * * * *
3175421 ATTTAAAAAGTTATGGGCCAATTAAAAAATATAATTAAGTAAAAAGTATGGATCAATTTCACATG
130 ATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATG
3175486 CAAATAAAATTTGGAGGACTA
195 CAAATAAAATTTGGAGGACTA
* *
3175507 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACAACACACATTGATGAGGG
1 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAAACACATTGATGAGGG
*
3175572 ATAAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
66 ATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA-CC
*
3175637 ATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATG
130 ATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATG
3175702 CAAATAAAATTTGGAGGACTA
195 CAAATAAAATTTGGAGGACTA
* * *
3175723 AATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAAAC--AACACA---A-AAGGG
1 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAAACACATTGATGAGGG
* * *
3175782 ATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAC-----A--A--AAA-TGTA-C-
66 ATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCA
*
3175835 --TAAAAAGTTATGGGCCAATTAATAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGC
131 TTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGC
*
3175898 AAATAAAATGTGGAGGACTA
196 AAATAAAATTTGGAGGACTA
* *
3175918 AATTGAACAAATATGAAATTACAAACAAAAATTTTAATAAATTAAACAA
1 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAA
3175967 CTATTGTAAT
Statistics
Matches: 430, Mismatches: 27, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
195 123 0.29
198 1 0.00
200 3 0.01
201 3 0.01
203 1 0.00
205 1 0.00
210 44 0.10
211 1 0.00
214 5 0.01
216 246 0.57
217 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (215 bp):
AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAAACACATTGATGAGGG
ATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCA
TTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGC
AAATAAAATTTGGAGGACTA
Found at i:3176054 original size:15 final size:17
Alignment explanation
Indices: 3176033--3176098 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
3176023 AAAACAACTA
3176033 ATATATATATATAGT-TT
1 ATATATATATAT-GTATT
3176050 ATATA-AGTATATGTATT
1 ATATATA-TATATGTATT
*
3176067 ATATATATAAACTGTATAGT
1 ATATATATATA-TGTAT--T
*
3176087 TTATATATATAT
1 ATATATATATAT
3176099 TATGTATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.08
17 20 0.50
18 6 0.15
19 1 0.03
20 10 0.25
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (17 bp):
ATATATATATATGTATT
Found at i:3176206 original size:11 final size:11
Alignment explanation
Indices: 3176192--3176309 Score: 59
Period size: 11 Copynumber: 10.8 Consensus size: 11
3176182 CCTACATAGT
3176192 TTATATATAAA
1 TTATATATAAA
*
3176203 TTATATATGAA
1 TTATATATAAA
3176214 TTATATATAAA
1 TTATATATAAA
* * *
3176225 CTATACGATTATA
1 TTATA-TA-TAAA
3176238 TT-TATAT--A
1 TTATATATAAA
*
3176246 TTATGTAT-AA
1 TTATATATAAA
*
3176256 TTATAAAT-AA
1 TTATATATAAA
*
3176266 TATATTGTATAAA
1 T-TA-TATATAAA
**
3176279 TTATATAGTTTA
1 TTATATA-TAAA
3176291 TTA-ATATAAA
1 TTATATATAAA
*
3176301 CTATATATA
1 TTATATATA
3176310 TGGTTTAGGG
Statistics
Matches: 80, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 15 0.19
11 38 0.47
12 13 0.16
13 7 0.09
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (11 bp):
TTATATATAAA
Found at i:3176333 original size:14 final size:14
Alignment explanation
Indices: 3176314--3176351 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3176304 TATATATGGT
3176314 TTAGGGTTTAAATA
1 TTAGGGTTTAAATA
*
3176328 TTAGGGTTTAAGTA
1 TTAGGGTTTAAATA
3176342 TTAGGGTTTA
1 TTAGGGTTTA
3176352 GGGTGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTAAATA
Found at i:3176368 original size:6 final size:6
Alignment explanation
Indices: 3176357--3176391 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3176347 GTTTAGGGTG
3176357 TATATT TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
3176392 AAACTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3176424 original size:20 final size:20
Alignment explanation
Indices: 3176399--3176470 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 20
3176389 TATAAACTAC
3176399 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
* *
3176419 ATACTATTTATATACTATTTAT
1 ATACTA-TAATTTA-TATTTAT
* *
3176441 ATAAACTATAGTTTATACTTAT
1 AT--ACTATAATTTATATTTAT
3176463 ATACTATA
1 ATACTATA
3176471 TATAATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 17 0.40
23 4 0.10
24 4 0.10
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.50
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:3176441 original size:9 final size:11
Alignment explanation
Indices: 3176412--3176443 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3176402 CTATAATTTA
3176412 TATTTATATAC
1 TATTTATATAC
3176423 TATTTATATAC
1 TATTTATATAC
3176434 TATTTATATA
1 TATTTATATA
3176444 AACTATAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTATATAC
Found at i:3176463 original size:44 final size:40
Alignment explanation
Indices: 3176401--3176495 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 40
3176391 TAAACTACAT
* * *
3176401 ACTATAATTTATATTTATATACTATTTATATACTATTTATATAA
1 ACTATAGTTTATACTTATATACTA--TATATA--ATATATATAA
*
3176445 ACTATAGTTTATACTTATATACTATATATAATATATATGA
1 ACTATAGTTTATACTTATATACTATATATAATATATATAA
3176485 ACTATAGTTTA
1 ACTATAGTTTA
3176496 CATATGAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 19 0.40
42 6 0.13
44 22 0.47
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (40 bp):
ACTATAGTTTATACTTATATACTATATATAATATATATAA
Found at i:3176490 original size:18 final size:17
Alignment explanation
Indices: 3176469--3176661 Score: 81
Period size: 18 Copynumber: 10.8 Consensus size: 17
3176459 TTATATACTA
3176469 TATATAATATATATGAAC
1 TATAT-ATATATATGAAC
* *
3176487 TATAGTTTACATATGAAC
1 TATA-TATATATATGAAC
*
3176505 TATATATATA-CT-AAC
1 TATATATATATATGAAC
*
3176520 GTTGATATTTATATATGAAC
1 --T-ATATATATATATGAAC
* * *
3176540 TATAATTTACATATAAAC
1 TAT-ATATATATATGAAC
3176558 TATATAGTTTATATACT-AAC
1 TATATA---TATATA-TGAAC
* *
3176578 TATAGTTTAAATATGAAC
1 TATA-TATATATATGAAC
* * *
3176596 TATAGTTTACACATGAAC
1 TATA-TATATATATGAAC
3176614 TATATATATATA--AAC
1 TATATATATATATGAAC
* * *
3176629 AATATAGTTTACATATGACC
1 --TATA-TATATATATGAAC
3176649 TATATATATATAT
1 TATATATATATAT
3176662 ATATTATAGT
Statistics
Matches: 134, Mismatches: 23, Indels: 37
0.69 0.12 0.19
Matches are distributed among these distances:
15 6 0.04
16 1 0.01
17 26 0.19
18 80 0.60
19 2 0.01
20 17 0.13
21 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (17 bp):
TATATATATATATGAAC
Found at i:3176529 original size:91 final size:90
Alignment explanation
Indices: 3176434--3176599 Score: 221
Period size: 91 Copynumber: 1.8 Consensus size: 90
3176424 ATTTATATAC
* * *
3176434 TATTTATATA-AACTATAGTTTATACTTATATACTATATA-TAATATATA-TGAACTATAGTTTA
1 TATTTATATAGAACTATA-ATT-TACATATAAACTATATAGT-ATATATACT-AACTATAGTTTA
*
3176496 CATATGAACTATATATATACTAACGTTGA
62 AATATGAACTATATATATACTAACGTTGA
*
3176525 TATTTATATATGAACTATAATTTACATATAAACTATATAGTTTATATACTAACTATAGTTTAAAT
1 TATTTATATA-GAACTATAATTTACATATAAACTATATAGTATATATACTAACTATAGTTTAAAT
3176590 ATGAACTATA
65 ATGAACTATA
3176600 GTTTACACAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
91 55 0.83
92 4 0.06
93 7 0.11
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (90 bp):
TATTTATATAGAACTATAATTTACATATAAACTATATAGTATATATACTAACTATAGTTTAAATA
TGAACTATATATATACTAACGTTGA
Found at i:3176624 original size:91 final size:86
Alignment explanation
Indices: 3176465--3176745 Score: 239
Period size: 91 Copynumber: 3.1 Consensus size: 86
3176455 ATACTTATAT
* * *
3176465 ACTATATATAATATATATGAACTATAGTTTACATATGAACTATATATATAC-TAACGTTGATATT
1 ACTATATAT-ATATATAT-AACTATAGTTTAAATATGAACTATATTTATACATAAC--T-ATATA
*
3176529 TATATATGAACTATAATTTACATATAA
61 TATATAT-AACTATAATTTACATATGA
* *
3176556 ACTATATAGTTTATATACTAACTATAGTTTAAATATGAACTATAGTTTACACATGAACTATATAT
1 ACTATATA-TATATATA-TAACTATAGTTTAAATATGAACTATA-TTTATACAT-AACTATATAT
*
3176621 ATATA-AACAATATAGTTTACATATGA
62 ATATATAAC--TATAATTTACATATGA
* * * *
3176647 CCTATATATATATATAT-ATTATAGTTTATATTTAT-ATACTATATTATATATATATAAACTATA
1 ACTATATATATATATATAACTATAGTTTA-A-ATATGA-ACTATA-T-T-TATACAT-AACTATA
*
3176710 TATACTATAT-AGTATAATTTACATATGA
59 TATA-TATATAACTATAATTTACATATGA
3176738 ACTATATA
1 ACTATATA
3176746 AAACCAAATA
Statistics
Matches: 158, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
88 10 0.06
89 6 0.04
90 17 0.11
91 92 0.58
92 24 0.15
93 6 0.04
94 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.42
Consensus pattern (86 bp):
ACTATATATATATATATAACTATAGTTTAAATATGAACTATATTTATACATAACTATATATATAT
ATAACTATAATTTACATATGA
Found at i:3176640 original size:35 final size:33
Alignment explanation
Indices: 3176475--3176674 Score: 145
Period size: 35 Copynumber: 5.6 Consensus size: 33
3176465 ACTATATATA
*
3176475 ATATATATGAACTATAGTTTACATATGAACTAT
1 ATATATATAAACTATAGTTTACATATGAACTAT
*
3176508 ATATATACT-AACGTTGATA-TTTATATATGAACTAT
1 ATATATA-TAAAC--T-ATAGTTTACATATGAACTAT
* *
3176543 AATTTACATATAAACTATATAGTTTATATACT-AACTAT
1 -A--TATATATAAAC--TATAGTTTACATA-TGAACTAT
* * *
3176581 AGTTTAAATATGAACTATAGTTTACACATGAACTAT
1 A---TATATATAAACTATAGTTTACATATGAACTAT
*
3176617 ATATATATAAACAATATAGTTTACATATGACCTAT
1 ATATATATAAAC--TATAGTTTACATATGAACTAT
*
3176652 ATATATATATATATTATAGTTTA
1 ATATATATA-A-ACTATAGTTTA
3176675 TATTTATATA
Statistics
Matches: 138, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
33 19 0.14
34 1 0.01
35 54 0.39
36 23 0.17
37 6 0.04
38 34 0.25
39 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (33 bp):
ATATATATAAACTATAGTTTACATATGAACTAT
Found at i:3176645 original size:109 final size:106
Alignment explanation
Indices: 3176479--3176677 Score: 267
Period size: 109 Copynumber: 1.8 Consensus size: 106
3176469 TATATAATAT
* ** *
3176479 ATATGAACTATAGTTTACATATGAACTATATATATACTAACGTTGATATTTATATATGAACTATA
1 ATATGAACTATAGTTTACACATGAACTATATATATACTAACAATGATATTTACATATGAACTAT-
*
3176544 ATTTACATATAAACTATATAGTTTATATACTAACTATAGTTTAA
65 ATATACATATAAA-T-TATAGTTTATATACTAACTATAGTTTAA
*
3176588 ATATGAACTATAGTTTACACATGAACTATATATATA-TAAACAAT-ATAGTTTACATATGACCTA
1 ATATGAACTATAGTTTACACATGAACTATATATATACT-AACAATGATA-TTTACATATGAACTA
* *
3176651 TATATATATATATATTATAGTTTATAT
64 TATATACATATAAATTATAGTTTATAT
3176678 TTATATACTA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
106 12 0.15
107 1 0.01
108 14 0.17
109 53 0.66
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (106 bp):
ATATGAACTATAGTTTACACATGAACTATATATATACTAACAATGATATTTACATATGAACTATA
TATACATATAAATTATAGTTTATATACTAACTATAGTTTAA
Found at i:3176652 original size:53 final size:53
Alignment explanation
Indices: 3176479--3176652 Score: 199
Period size: 53 Copynumber: 3.2 Consensus size: 53
3176469 TATATAATAT
** *
3176479 ATATGAACTATAGTTTACATATGAACTATATATATACT-AACGTTGATA-TTTAT
1 ATATGAACTATAGTTTACATATGAACTATATATATA-TAAACAAT-ATAGTTTAA
* * * *
3176532 ATATGAACTATAATTTACATATAAACTATATAGTTTATATACTAACTATAGTTTAA
1 ATATGAACTATAGTTTACATATGAACTATATA-TATATAAAC-AA-TATAGTTTAA
* *
3176588 ATATGAACTATAGTTTACACATGAACTATATATATATAAACAATATAGTTTAC
1 ATATGAACTATAGTTTACATATGAACTATATATATATAAACAATATAGTTTAA
*
3176641 ATATGACCTATA
1 ATATGAACTATA
3176653 TATATATATA
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
53 51 0.50
54 7 0.07
55 10 0.10
56 34 0.33
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (53 bp):
ATATGAACTATAGTTTACATATGAACTATATATATATAAACAATATAGTTTAA
Found at i:3176656 original size:2 final size:2
Alignment explanation
Indices: 3176649--3177019 Score: 72
Period size: 2 Copynumber: 179.0 Consensus size: 2
3176639 ACATATGACC
* *
3176649 TA TA TA TA TA TA TA TA T- TA TA GTT TA TA TT TA TA TA CTA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * *
3176691 TA TA TA TA TA TA AA CTA TA TA TA CTA TA TA GTA TA -A TT TA CA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * *
3176733 TA TGA -A CTA TA TA -A AA CCA AA TA AA CTA TA TA CTA TA GT- TGA
1 TA T-A TA -TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA -TA T-A
* * *
3176775 TA TT TA TA TA CTA TA TA -A AA TA -A TT TA TA CTA TA T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
3176816 TA AA CTA TA TA AA CTA TA TA T- TA TA TA GT- TCA T- TA -A TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA
* * * * * *
3176856 TA TA AA CTA TA TA GTA TA TG TA AA CTA TA TA GTA CA TG TA TG TA
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * *
3176900 TA AA CTA TA TA TA -A TA TA TA TA AA CTA TG TA TA GTA CA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* ** * *
3176942 AA CTA TA TA TA TA TA TA TA TA -A CC TA TA GCA TA TG TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* ** *
3176985 AA CTA TA TA TA TA -A CC TA TA GTA TA TG TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
3177020 CAATCTATTT
Statistics
Matches: 264, Mismatches: 60, Indels: 90
0.64 0.14 0.22
Matches are distributed among these distances:
1 16 0.06
2 209 0.79
3 39 0.15
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3176712 original size:35 final size:39
Alignment explanation
Indices: 3176614--3176712 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 39
3176604 ACACATGAAC
*
3176614 TATATATATATAAACAATATAGTTTACATATGACCTATATA
1 TATATATATATAAACTATATA-TTTA-ATATGACCTATATA
* * *
3176655 TATATATATATTATAGTTTATATTT-ATAT-A-CTATAT-
1 TATATATATA-TAAACTATATATTTAATATGACCTATATA
3176691 TATATATATATAAACTATATAT
1 TATATATATATAAACTATATAT
3176713 ACTATATAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 9 0.18
36 10 0.20
37 6 0.12
38 1 0.02
39 4 0.08
41 13 0.26
42 7 0.14
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (39 bp):
TATATATATATAAACTATATATTTAATATGACCTATATA
Found at i:3176791 original size:71 final size:71
Alignment explanation
Indices: 3176708--3176840 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 71
3176698 ATATAAACTA
**
3176708 TATATACTATATAGTATAATTTACA-TATGAACTATATA-AAACCAAATAAACTATATACTATAG
1 TATATACTATATAAAATAATTTACACTAT--ACTATATATAAACCAAATAAACTATATACTATAG
3176771 TTGATATT
64 TTGATATT
* * * * *
3176779 TATATACTATATAAAATAATTTATACTATATTATATATAAACTATATAAACTATATATTATA
1 TATATACTATATAAAATAATTTACACTATACTATATATAAACCAAATAAACTATATACTATA
3176841 TAGTTCATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 7 0.13
71 43 0.81
72 3 0.06
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (71 bp):
TATATACTATATAAAATAATTTACACTATACTATATATAAACCAAATAAACTATATACTATAGTT
GATATT
Found at i:3176835 original size:20 final size:21
Alignment explanation
Indices: 3176810--3176995 Score: 140
Period size: 20 Copynumber: 8.9 Consensus size: 21
3176800 TATACTATAT
*
3176810 TATATATAAACTATATA-AAC
1 TATATATAAACTATATATAAG
*
3176830 TATATAT-TA-TATAGTTCATTAA-
1 TATATATAAACTATA--T-A-TAAG
3176852 TATATATAAAC--TATAT-AG
1 TATATATAAACTATATATAAG
*
3176870 TATATGTAAACTATATAGTACATG
1 TATATATAAACTATATA-TA-A-G
*
3176894 TATGTATAAACTATATATAA-
1 TATATATAAACTATATATAAG
*
3176914 TATATATAAACTATGTAT-AG
1 TATATATAAACTATATATAAG
*
3176934 TACATATAAACTATATATATA-
1 TATATATAAACTATATATA-AG
* * *
3176955 TATATATAACCTATAGCATATG
1 TATATATAAACTATA-TATAAG
3176977 TATATATAAACTATATATA
1 TATATATAAACTATATATA
3176996 TAACCTATAG
Statistics
Matches: 132, Mismatches: 15, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
17 1 0.01
18 15 0.11
19 3 0.02
20 45 0.34
21 18 0.14
22 28 0.21
23 6 0.05
24 16 0.12
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (21 bp):
TATATATAAACTATATATAAG
Found at i:3176855 original size:71 final size:70
Alignment explanation
Indices: 3176709--3176859 Score: 155
Period size: 71 Copynumber: 2.1 Consensus size: 70
3176699 TATAAACTAT
** *
3176709 ATATACTATATAGTATAATTTACATATGAACTATATAAAACCAAATAAACTATATACTATAGTTG
1 ATATACTATATAAAATAATTTACATAT-AACTATATAAAACCAAATAAACTATATACTATAGTAG
*
3176774 ATATTT
65 ATATTA
* * * * *
3176780 ATATACTATATAAAATAATTTATACTAT-ATTATATATAAACTATATAAACTATATATTATA-TA
1 ATATACTATATAAAATAATTTACA-TATAACTATATA-AAACCAAATAAACTATATACTATAGTA
*
3176843 GTTCATTA
64 GAT-ATTA
3176851 ATATA-TATA
1 ATATACTATA
3176860 AACTATATAG
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
70 14 0.21
71 50 0.75
72 3 0.04
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (70 bp):
ATATACTATATAAAATAATTTACATATAACTATATAAAACCAAATAAACTATATACTATAGTAGA
TATTA
Found at i:3176975 original size:35 final size:35
Alignment explanation
Indices: 3176898--3177010 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 35
3176888 TACATGTATG
*
3176898 TATAAACTATATATA-ATATATATAAACTATGTATAGTACA
1 TATAAACTATATATATATATATAT-AAC---CTATAG--CA
3176938 TATAAACTATATATATATATATATAACCTATAGCA
1 TATAAACTATATATATATATATATAACCTATAGCA
** * *
3176973 TATGTA-TATATAAACTATATATATAACCTATAGTA
1 TATAAACTATATATA-TATATATATAACCTATAGCA
3177008 TAT
1 TAT
3177011 GTATATATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
34 7 0.11
35 28 0.42
37 5 0.08
40 18 0.27
41 8 0.12
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (35 bp):
TATAAACTATATATATATATATATAACCTATAGCA
Found at i:3176993 original size:13 final size:13
Alignment explanation
Indices: 3176977--3177010 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3176967 ATAGCATATG
3176977 TATATATAAACTA
1 TATATATAAACTA
*
3176990 TATATATAACCTA
1 TATATATAAACTA
3177003 TAGTATAT
1 TA-TATAT
3177011 GTATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:3177011 original size:35 final size:35
Alignment explanation
Indices: 3176945--3177033 Score: 126
Period size: 35 Copynumber: 2.5 Consensus size: 35
3176935 ACATATAAAC
*
3176945 TATATATA-TATATATATAACCTATAGCATATGTA
1 TATATAAACTATATATATAACCTATAGCATATGTA
*
3176979 TATATAAACTATATATATAACCTATAGTATATGTA
1 TATATAAACTATATATATAACCTATAGCATATGTA
*
3177014 TATATACAATCTATTTATAT
1 TATATA-AA-CTATATATAT
3177034 GTTATATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 7 0.14
35 31 0.63
36 2 0.04
37 9 0.18
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
TATATAAACTATATATATAACCTATAGCATATGTA
Found at i:3177015 original size:20 final size:20
Alignment explanation
Indices: 3176854--3177048 Score: 83
Period size: 20 Copynumber: 9.7 Consensus size: 20
3176844 TTCATTAATA
3176854 TATATAAACTATA-TAGTA--
1 TATATAAACTATAGTA-TATG
* *
3176872 TATGTAAACTATATAGTACATG
1 TATATAAAC--TATAGTATATG
*
3176894 TATGTATAAACTATA-TATAATA
1 TA--TATAAACTATAGTAT-ATG
3176916 TATATAAACTAT-GTATA-G
1 TATATAAACTATAGTATATG
*
3176934 TACATATAAACTATA-TATATA
1 T--ATATAAACTATAGTATATG
*
3176955 TATATATAACCTATAGCATATG
1 TATATA-AA-CTATAGTATATG
* *
3176977 TATAT--A-TAAACTATA--
1 TATATAAACTATAGTATATG
*
3176992 TATATAACCTATAGTATATG
1 TATATAAACTATAGTATATG
*
3177012 TATATATACAATCTAT-TTATATG
1 --TATATA-AA-CTATAGTATATG
3177035 TTATATAAACTATA
1 -TATATAAACTATA
3177049 TATGTAACCT
Statistics
Matches: 133, Mismatches: 18, Indels: 49
0.67 0.09 0.25
Matches are distributed among these distances:
15 5 0.04
17 6 0.05
18 16 0.12
19 7 0.05
20 39 0.29
21 12 0.09
22 31 0.23
23 7 0.05
24 10 0.08
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
TATATAAACTATAGTATATG
Found at i:3177015 original size:24 final size:22
Alignment explanation
Indices: 3176990--3177048 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3176980 ATATAAACTA
*
3176990 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
3177012 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
3177035 T-TATATAAACTATA
1 TATATATAAACTATA
3177049 TATGTAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:3177082 original size:21 final size:20
Alignment explanation
Indices: 3177058--3177148 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
3177048 ATATGTAACC
3177058 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
* **
3177079 TATATTAATGTACTATATAGTT
1 TATATTTATAAAC-A-ATAGTT
* * *
3177101 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
3177122 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
3177143 TATATT
1 TATATT
3177149 AATGTACTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.16
21 30 0.55
22 11 0.20
23 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:3177098 original size:22 final size:21
Alignment explanation
Indices: 3177073--3177175 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
3177063 TTTATAAACA
3177073 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
3177095 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
3177116 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
3177137 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
*
3177159 ATAATTTATATTAATGT
1 ATAGTTTATATTAATGT
3177176 TAATTATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.10
21 23 0.34
22 33 0.49
23 4 0.06
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:3177304 original size:21 final size:21
Alignment explanation
Indices: 3177189--3177291 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 21
3177179 TTATCTTAAC
*
3177189 TATAATTTATATTAA-TATAGTA
1 TATAATTTATA--AACTATACTA
*
3177211 TATAGTTTATAAACTATACTA
1 TATAATTTATAAACTATACTA
* * *
3177232 TACTATATTAATATTAATTATATTAA
1 TA-TA-ATT--TATAAACTATACT-A
3177258 CTATAATTTATAAACTATACTA
1 -TATAATTTATAAACTATACTA
3177280 TATAATTTATAA
1 TATAATTTATAA
3177292 CATATAGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.03
21 20 0.31
22 13 0.20
23 12 0.18
25 13 0.20
26 3 0.05
27 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAATTTATAAACTATACTA
Found at i:3177334 original size:31 final size:31
Alignment explanation
Indices: 3177158--3177347 Score: 123
Period size: 31 Copynumber: 5.7 Consensus size: 31
3177148 TAATGTACTA
* * * * *
3177158 TATAATTTATATTAATGTTAATTATCTTAAC
1 TATATTTTATATTAATATTAATTTTATAAAC
*
3177189 TATAATTTATATTAATATAGTATATAGTTTATAAAC
1 TATATTTTATATTAATAT--TA-AT--TTTATAAAC
* * *
3177225 TATACTATACTATATTAATATTAATTATATTAAC
1 TATA-T-T-TTATATTAATATTAATTTTATAAAC
* *
3177259 TATAATTTATAAACTATACTATATAA-TTTAT-AAC
1 TAT-ATTT-TATA-T-TAATAT-TAATTTTATAAAC
*
3177293 ATATAGTTTATATTAATATTAATTTTATAAAC
1 -TATATTTTATATTAATATTAATTTTATAAAC
*
3177325 TATATTTTATATTAATTTTAATT
1 TATATTTTATATTAATATTAATT
3177348 ACAAATTATA
Statistics
Matches: 126, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
30 3 0.02
31 48 0.38
32 4 0.03
33 9 0.07
34 20 0.16
35 13 0.10
36 15 0.12
37 2 0.02
38 1 0.01
39 11 0.09
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (31 bp):
TATATTTTATATTAATATTAATTTTATAAAC
Found at i:3177357 original size:136 final size:137
Alignment explanation
Indices: 3177122--3177369 Score: 313
Period size: 136 Copynumber: 1.8 Consensus size: 137
3177112 ACCTATAGTA
* * * * * *
3177122 TATAATTTATAAACTATAGTTTATATTAATGTACTATATAATTTATATTAATGTTAATTATCTTA
1 TATAATTTATAAACTATACTATATATTAATGAACTATATAATTTATATTAATATTAATTATATAA
* * **
3177187 ACTATAATTTATATTAATATAGTATATAGTTTATAAACTATACTATACTATATTAATATTAATTA
66 ACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATACTATATTAATATTAATTA
3177252 TATTAAC
131 TATTAAC
* * *
3177259 TATAATTTATAAACTATACTATATAATTTAT-AAC-ATATAGTTTATATTAATATTAATTTTATA
1 TATAATTTATAAACTATACTATAT-ATTAATGAACTATATAATTTATATTAATATTAATTATATA
* * *
3177322 AACTATATTTTATATTAATTTTAAT-TACAAATTATAAACTATATTATA
65 AACTATAATTTATATTAA-TATAATATACAAATTATAAACTATACTATA
3177370 TTAATATAAG
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
136 60 0.65
137 28 0.30
138 5 0.05
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (137 bp):
TATAATTTATAAACTATACTATATATTAATGAACTATATAATTTATATTAATATTAATTATATAA
ACTATAATTTATATTAATATAATATACAAATTATAAACTATACTATACTATATTAATATTAATTA
TATTAAC
Found at i:3177387 original size:21 final size:20
Alignment explanation
Indices: 3177362--3177457 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 20
3177352 ATTATAAACT
3177362 ATATTATATTAA-TATAAGTTA
1 ATATTATATTAATTAT-A-TTA
3177383 ATATTAATATTAATTATATTA
1 ATATT-ATATTAATTATATTA
3177404 ATATTA-ATTATAATATATAATT-
1 ATATTATA-T-TAAT-TAT-ATTA
*
3177426 ATTTTAATATTAATTATA--A
1 ATATT-ATATTAATTATATTA
*
3177445 ATATTTTATTAAT
1 ATATTATATTAAT
3177458 ATAAATTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 3 0.05
21 20 0.32
22 19 0.30
23 8 0.13
24 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
ATATTATATTAATTATATTA
Found at i:3177389 original size:6 final size:6
Alignment explanation
Indices: 3177362--3177459 Score: 59
Period size: 6 Copynumber: 16.7 Consensus size: 6
3177352 ATTATAAACT
*
3177362 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
3177404 ATATTA AT-TATA ATATATA ATTATTTTA ATATTA ATTATAA ATATT-
1 ATATTA ATAT-TA ATAT-TA A-TA--TTA ATATTA A-TATTA ATATTA
*
3177450 TTATTA ATAT
1 ATATTA ATAT
3177460 AAATTTTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
4 4 0.05
5 20 0.27
6 33 0.44
7 10 0.13
8 4 0.05
9 3 0.04
10 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (6 bp):
ATATTA
Found at i:3177433 original size:28 final size:28
Alignment explanation
Indices: 3177351--3177464 Score: 107
Period size: 28 Copynumber: 4.1 Consensus size: 28
3177341 TTTAATTACA
3177351 AATTATAA-ACTAT-ATTATATTAATA-T
1 AATTATAATA-TATAATTATATTAATATT
*
3177377 AAGTTAATATTAATATTAATTATATTAATATT
1 AA-TT-ATAAT-ATA-TAATTATATTAATATT
*
3177409 AATTATAATATATAATTATTTTAATATT
1 AATTATAATATATAATTATATTAATATT
*
3177437 AATTATAA-ATAT--TT-TATTAATATA
1 AATTATAATATATAATTATATTAATATT
3177461 AATT
1 AATT
3177465 TTATACGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
24 12 0.16
25 2 0.03
26 2 0.03
27 6 0.08
28 26 0.34
29 5 0.07
30 6 0.08
31 14 0.18
32 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
AATTATAATATATAATTATATTAATATT
Found at i:3177468 original size:15 final size:15
Alignment explanation
Indices: 3177364--3177443 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
3177354 TATAAACTAT
3177364 ATTATATTAATATAA
1 ATTATATTAATATAA
* *
3177379 GTTAATATTAATATTA
1 ATT-ATATTAATATAA
*
3177395 ATTATATTAATATTA
1 ATTATATTAATATAA
*
3177410 ATTATAAT-ATAT-A
1 ATTATATTAATATAA
* *
3177423 ATTATTTTAATATTA
1 ATTATATTAATATAA
3177438 ATTATA
1 ATTATA
3177444 AATATTTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
13 7 0.13
14 8 0.15
15 27 0.49
16 13 0.24
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTATATTAATATAA
Found at i:3179850 original size:23 final size:23
Alignment explanation
Indices: 3179824--3179877 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3179814 TTTATGCAGA
*
3179824 ATGCTTGCTGAATTGATGTAATG
1 ATGCTTGCTGAATTGATATAATG
* * *
3179847 ATGCTTGTTGAATTGGTATATTG
1 ATGCTTGCTGAATTGATATAATG
3179870 ATGCTTGC
1 ATGCTTGC
3179878 CGGTTGTTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (23 bp):
ATGCTTGCTGAATTGATATAATG
Found at i:3180467 original size:13 final size:13
Alignment explanation
Indices: 3180448--3180485 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3180438 TAATTTAGTG
3180448 ATTATAAATAA-A
1 ATTATAAATAAGA
3180460 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
3180475 ATTATAAATAA
1 ATTATAAATAA
3180486 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:3180495 original size:19 final size:19
Alignment explanation
Indices: 3180464--3180510 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3180454 AATAAAATTT
3180464 ATAATAT-AAGAATT-ATAA
1 ATAATATAAAGAATTGA-AA
3180482 ATAATATAAAGAATTGAAA
1 ATAATATAAAGAATTGAAA
*
3180501 TTAATATAAA
1 ATAATATAAA
3180511 AATCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTGAAA
Found at i:3182828 original size:26 final size:26
Alignment explanation
Indices: 3182792--3182841 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3182782 CTGACGTGGT
*
3182792 AGTTTCTAGAAGGTCCAGTCAGCGAC
1 AGTTTCTAGAAGATCCAGTCAGCGAC
*
3182818 AGTTTCTAGAAGATCTAGTCAGCG
1 AGTTTCTAGAAGATCCAGTCAGCG
3182842 CACCTTCAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (26 bp):
AGTTTCTAGAAGATCCAGTCAGCGAC
Found at i:3185372 original size:29 final size:30
Alignment explanation
Indices: 3185331--3185413 Score: 105
Period size: 29 Copynumber: 2.7 Consensus size: 30
3185321 TTTTGATTGG
3185331 ATTTAAAAATTAAATTATTATTTTATATAAA
1 ATTT-AAAATTAAATTATTATTTTATATAAA
* * *
3185362 ATTT-AAATTAAATTGTTACTTTATCTAAA
1 ATTTAAAATTAAATTATTATTTTATATAAA
*
3185391 ATTTAAGAATTAAATTAATATTT
1 ATTTAA-AATTAAATTATTATTT
3185414 GATTTAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 26 0.59
30 1 0.02
31 17 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTTAAAATTAAATTATTATTTTATATAAA
Found at i:3189578 original size:28 final size:28
Alignment explanation
Indices: 3189546--3189608 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 28
3189536 ACATAGATAT
3189546 TGCATGTGCAA-CTACAAAGCAATTACAA
1 TGCATGTG-AATCTACAAAGCAATTACAA
3189574 TGCATGTGAATCTACAAAGCAATTACAA
1 TGCATGTGAATCTACAAAGCAATTACAA
3189602 TGCATGT
1 TGCATGT
3189609 TTTGGGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (28 bp):
TGCATGTGAATCTACAAAGCAATTACAA
Found at i:3191513 original size:27 final size:27
Alignment explanation
Indices: 3191475--3191529 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3191465 CAAAACTCCA
3191475 ATGATTGCTGGTTTAATCTTAGGACCT
1 ATGATTGCTGGTTTAATCTTAGGACCT
3191502 ATGATTGCTGGTTTAATCTTAGGACCT
1 ATGATTGCTGGTTTAATCTTAGGACCT
3191529 A
1 A
3191530 AGCCCCGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (27 bp):
ATGATTGCTGGTTTAATCTTAGGACCT
Found at i:3191648 original size:14 final size:14
Alignment explanation
Indices: 3191629--3191670 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
3191619 CAGCAATTCT
3191629 ATTACAATTTTATA
1 ATTACAATTTTATA
3191643 ATTACAATTTTATA
1 ATTACAATTTTATA
3191657 ATTACAATTTTATA
1 ATTACAATTTTATA
3191671 CACTTCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTACAATTTTATA
Found at i:3194963 original size:19 final size:20
Alignment explanation
Indices: 3194939--3194979 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3194929 GAGTAGGTTG
3194939 ACCGGTTGGACCGGTCT-GA
1 ACCGGTTGGACCGGTCTAGA
*
3194958 ACCGGTTGGACCTGTCTAGA
1 ACCGGTTGGACCGGTCTAGA
3194978 AC
1 AC
3194980 GAGCCAACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.22
Consensus pattern (20 bp):
ACCGGTTGGACCGGTCTAGA
Found at i:3195833 original size:18 final size:18
Alignment explanation
Indices: 3195810--3195850 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3195800 TAAATTAAAA
3195810 GATTGGAAAGAAGGAAAG
1 GATTGGAAAGAAGGAAAG
**
3195828 GATTGGACGGAAGGAAAG
1 GATTGGAAAGAAGGAAAG
3195846 GATTG
1 GATTG
3195851 AAATACCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.41, T:0.15
Consensus pattern (18 bp):
GATTGGAAAGAAGGAAAG
Found at i:3196949 original size:24 final size:24
Alignment explanation
Indices: 3196922--3197014 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
3196912 ATCTGATTTC
* * *
3196922 TGATTTGAATTCTGTTATGATACT
1 TGATCTGAATTATGTTCTGATACT
3196946 TGATCTGAATTATGTTCTGATACT
1 TGATCTGAATTATGTTCTGATACT
*
3196970 TGATCTGAATTCTGTTCTGATA-T
1 TGATCTGAATTATGTTCTGATACT
*
3196993 CTGATCTGAATTATGTTTTGAT
1 -TGATCTGAATTATGTTCTGAT
3197015 TTCTGATATG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
23 1 0.02
24 61 0.98
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATCTGAATTATGTTCTGATACT
Found at i:3196979 original size:48 final size:48
Alignment explanation
Indices: 3196922--3197014 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
3196912 ATCTGATTTC
*
3196922 TGATTTGAATTCTGTTATGATA-CTTGATCTGAATTATGTTCTGATACT
1 TGATCTGAATTCTGTTATGATATC-TGATCTGAATTATGTTCTGATACT
* *
3196970 TGATCTGAATTCTGTTCTGATATCTGATCTGAATTATGTTTTGAT
1 TGATCTGAATTCTGTTATGATATCTGATCTGAATTATGTTCTGAT
3197015 TTCTGATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (48 bp):
TGATCTGAATTCTGTTATGATATCTGATCTGAATTATGTTCTGATACT
Found at i:3196988 original size:12 final size:12
Alignment explanation
Indices: 3196913--3197019 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 12
3196903 GAATGTTTTA
*
3196913 TCTGATTTCTGAT
1 TCTGAATTCTG-T
3196926 T-TGAATTCTGT
1 TCTGAATTCTGT
* * *
3196937 TATG-ATACTTGA
1 TCTGAATTC-TGT
*
3196949 TCTGAATTATGT
1 TCTGAATTCTGT
* *
3196961 TCTG-ATACTTGA
1 TCTGAATTC-TGT
3196973 TCTGAATTCTGT
1 TCTGAATTCTGT
*
3196985 TCTG-ATATCTGA
1 TCTGAAT-TCTGT
*
3196997 TCTGAATTATGT
1 TCTGAATTCTGT
* *
3197009 TTTGATTTCTG
1 TCTGAATTCTG
3197020 ATATGTCCGT
Statistics
Matches: 69, Mismatches: 18, Indels: 15
0.68 0.18 0.15
Matches are distributed among these distances:
11 9 0.13
12 52 0.75
13 8 0.12
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (12 bp):
TCTGAATTCTGT
Found at i:3197019 original size:24 final size:24
Alignment explanation
Indices: 3196913--3197021 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
3196903 GAATGTTTTA
* *
3196913 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTATGT
* *
3196937 TATGA-TACTTGATCTGAATTATGT
1 TCTGATTTC-TGATCTGAATTATGT
* *
3196961 TCTGA-TACTTGATCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTATGT
*
3196985 TCTGATATCTGATCTGAATTATGT
1 TCTGATTTCTGATCTGAATTATGT
*
3197009 TTTGATTTCTGAT
1 TCTGATTTCTGAT
3197022 ATGTCCGTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
23 2 0.03
24 69 0.96
25 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTATGT
Found at i:3200121 original size:24 final size:24
Alignment explanation
Indices: 3200094--3200152 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
3200084 ATTTTTTATT
*
3200094 TGAATTATGTTCTGATA-CTTGATC
1 TGAATTATGTTATGATATC-TGATC
* **
3200118 TGAATTCTAATATGATATCTGATC
1 TGAATTATGTTATGATATCTGATC
3200142 TGAATTATGTT
1 TGAATTATGTT
3200153 TTTATTTCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (24 bp):
TGAATTATGTTATGATATCTGATC
Found at i:3206562 original size:31 final size:31
Alignment explanation
Indices: 3206508--3206603 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
3206498 TTGATTGGAT
*
3206508 TTTAA-AATTAAATTATTATTTTATATAAAA
1 TTTAAGAATTAAATTGTTATTTTATATAAAA
* * *
3206538 TTTAA-ATGTTAAATTGTTACTTTATCTAAAA
1 TTTAAGA-ATTAAATTGTTATTTTATATAAAA
*
3206569 TTTAAGAATTAAATTAG-TATTTTATTTAAAA
1 TTTAAGAATTAAATT-GTTATTTTATATAAAA
3206600 TTTA
1 TTTA
3206604 TTTAATAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
30 6 0.11
31 48 0.86
32 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (31 bp):
TTTAAGAATTAAATTGTTATTTTATATAAAA
Found at i:3206614 original size:35 final size:35
Alignment explanation
Indices: 3206568--3206637 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3206558 TTTATCTAAA
**
3206568 ATTTAAGAATTAAATTAGTATTTTATTTAAAATTT
1 ATTTAAGAATTAAATTAAAATTTTATTTAAAATTT
*
3206603 ATTTAATAATTAAATTAAAATTTTATTTAAAATTT
1 ATTTAAGAATTAAATTAAAATTTTATTTAAAATTT
3206638 TTTGTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
ATTTAAGAATTAAATTAAAATTTTATTTAAAATTT
Found at i:3206638 original size:12 final size:12
Alignment explanation
Indices: 3206587--3206638 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
3206577 TTAAATTAGT
3206587 ATTTTATTTAAA
1 ATTTTATTTAAA
3206599 A-TTTATTTAATA
1 ATTTTATTTAA-A
* *
3206611 A-TTAAATTAAA
1 ATTTTATTTAAA
3206622 ATTTTATTTAAA
1 ATTTTATTTAAA
3206634 ATTTT
1 ATTTT
3206639 TTGTTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTATTTAAA
Found at i:3209274 original size:3 final size:3
Alignment explanation
Indices: 3209266--3209294 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3209256 TAAACACACT
3209266 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3209295 TTTTTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3211185 original size:28 final size:28
Alignment explanation
Indices: 3211153--3211213 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
3211143 ACATAGATAT
* *
3211153 TGCATGTGCATCTGCAAAGGAATTACAA
1 TGCATGTGCATCTACAAAGCAATTACAA
3211181 TGCATGTGCATCTACAAAGCAATTACAA
1 TGCATGTGCATCTACAAAGCAATTACAA
3211209 TGCAT
1 TGCAT
3211214 ATTTTGGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (28 bp):
TGCATGTGCATCTACAAAGCAATTACAA
Found at i:3213240 original size:14 final size:14
Alignment explanation
Indices: 3213221--3213247 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3213211 CAGCAATTTT
3213221 ATTACAATTTTAAA
1 ATTACAATTTTAAA
3213235 ATTACAATTTTAA
1 ATTACAATTTTAA
3213248 TATGTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTACAATTTTAAA
Found at i:3213851 original size:41 final size:41
Alignment explanation
Indices: 3213773--3213852 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
3213763 CGTTTTATCA
* *
3213773 ACAAACGCCGCAAAAGAGTAGTCATTTAGCGGCGTTTTTAT
1 ACAAACGCCGCAAAAGAGTAGTAATGTAGCGGCGTTTTTAT
* * *
3213814 ACAAACGCCGCTATAGAGTAGTAATGGT-GCGGTGTTTTT
1 ACAAACGCCGCAAAAGAGTAGTAAT-GTAGCGGCGTTTTT
3213853 TGATAAACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 32 0.97
42 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (41 bp):
ACAAACGCCGCAAAAGAGTAGTAATGTAGCGGCGTTTTTAT
Found at i:3218679 original size:31 final size:31
Alignment explanation
Indices: 3218635--3218732 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 31
3218625 TTTTGATTGG
**
3218635 ATTTAAAAATTAAATTATTGTTTTATATAAA
1 ATTTAAAAATTAAATTATTACTTTATATAAA
** * *
3218666 ATTTAAATGTTAAATTGTTACTTTATCTAAA
1 ATTTAAAAATTAAATTATTACTTTATATAAA
* * * * *
3218697 ATTTAAGAATTAAAATAGTATTTTATTTAAA
1 ATTTAAAAATTAAATTATTACTTTATATAAA
3218728 ATTTA
1 ATTTA
3218733 TTTAAGAATT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTTAAAAATTAAATTATTACTTTATATAAA
Found at i:3219565 original size:28 final size:28
Alignment explanation
Indices: 3219532--3219594 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
3219522 ACATAGATAT
* *
3219532 TGCATGTGCATCTACATAGCAATTACAA
1 TGCATGTGCATCTACAAAGAAATTACAA
3219560 TGCATGTGCATCTACAAAGAAATTACAA
1 TGCATGTGCATCTACAAAGAAATTACAA
3219588 TGCATGT
1 TGCATGT
3219595 TTTGGGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (28 bp):
TGCATGTGCATCTACAAAGAAATTACAA
Found at i:3219998 original size:74 final size:75
Alignment explanation
Indices: 3219909--3220113 Score: 292
Period size: 74 Copynumber: 2.8 Consensus size: 75
3219899 ACATTATATT
* *
3219909 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGTATATT
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
**
3219974 ATTT-TTATA
66 ATTTAGAATA
* *
3219983 TTATCTTTGTTTTAGGCATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
3220048 ATTTAGAATA
66 ATTTAGAATA
* * *
3220058 TTAT-TAT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
3220114 AGATGCTTTA
Statistics
Matches: 120, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
72 5 0.04
73 41 0.34
74 67 0.56
75 7 0.06
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (75 bp):
TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
ATTTAGAATA
Found at i:3220051 original size:12 final size:12
Alignment explanation
Indices: 3220036--3220062 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3220026 TTTAATTAGG
3220036 ATTTAGAATATT
1 ATTTAGAATATT
3220048 ATTTAGAATATT
1 ATTTAGAATATT
3220060 ATT
1 ATT
3220063 ATTTTTAGGT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTTAGAATATT
Found at i:3220705 original size:9 final size:9
Alignment explanation
Indices: 3220691--3220723 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3220681 TTTATCTCAA
3220691 TTTATTTAT
1 TTTATTTAT
3220700 TTTATTTAT
1 TTTATTTAT
3220709 TTT-TTTAT
1 TTTATTTAT
*
3220717 TTAATTT
1 TTTATTT
3220724 TTATCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3220715 original size:17 final size:17
Alignment explanation
Indices: 3220690--3220723 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3220680 CTTTATCTCA
*
3220690 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
3220707 ATTTTTTTATTTAATTT
1 ATTTATTTATTTAATTT
3220724 TTATCTCATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:3220723 original size:13 final size:12
Alignment explanation
Indices: 3220690--3220725 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
3220680 CTTTATCTCA
3220690 ATTTATTTATTTT
1 ATTTATTT-TTTT
3220703 ATTTATTTTTTT
1 ATTTATTTTTTT
3220715 ATTTAATTTTT
1 ATTT-ATTTTT
3220726 ATCTCATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:3220807 original size:26 final size:26
Alignment explanation
Indices: 3220764--3220832 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 26
3220754 AAACCCCTTT
*
3220764 TTATTTTACTACTATTATTTATTATTTTA
1 TTATTTT-CT-CT-TTATTTATTATTATA
3220793 TTATTTTCTCTTTATTTATTATTATA
1 TTATTTTCTCTTTATTTATTATTATA
*
3220819 -TATTTTAT-TTTATT
1 TTATTTTCTCTTTATT
3220833 AAATCTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 6 0.16
25 7 0.18
26 14 0.37
27 2 0.05
28 2 0.05
29 7 0.18
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (26 bp):
TTATTTTCTCTTTATTTATTATTATA
Found at i:3220953 original size:17 final size:17
Alignment explanation
Indices: 3220933--3220968 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3220923 GACCATGCTT
3220933 CTCTATACTACATGTTC
1 CTCTATACTACATGTTC
* *
3220950 CTCTATACTGCATTTTC
1 CTCTATACTACATGTTC
3220967 CT
1 CT
3220969 TTCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (17 bp):
CTCTATACTACATGTTC
Found at i:3226604 original size:29 final size:28
Alignment explanation
Indices: 3226523--3226611 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 28
3226513 ATGAAAAAAT
* *
3226523 AGTGCAGAAAAACTGACTTGGTTCGAAC
1 AGTGCAGAAAAACTGATTTGATTCGAAC
* * * *
3226551 TGTGCAG-AAAA---ATTCGAATAGAAC
1 AGTGCAGAAAAACTGATTTGATTCGAAC
3226575 AGTGCAGAAAAAACTGATTTGATTCGAAC
1 AGTGCAG-AAAAACTGATTTGATTCGAAC
*
3226604 ATTGCAGA
1 AGTGCAGA
3226612 TAAATACATA
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
24 14 0.31
26 4 0.09
27 4 0.09
28 7 0.16
29 16 0.36
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.22
Consensus pattern (28 bp):
AGTGCAGAAAAACTGATTTGATTCGAAC
Found at i:3228429 original size:56 final size:59
Alignment explanation
Indices: 3228325--3228438 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 59
3228315 ATTTTAAACA
*
3228325 TTATATTTTATCTTTGTTTTAAATAGGTTTTAGTATTTTAATTAGGTTTTAGGATATTATTT
1 TTATATTTTATCTTTGTTTTAAATA-GTTTTAG--TTTTAAATAGGTTTTAGGATATTATTT
** *
3228387 TTATATTTTATCTTTG-TTTAGGTA-TTTTAG-TTTAAATAGGTTTTAGTATATT
1 TTATATTTTATCTTTGTTTTAAATAGTTTTAGTTTTAAATAGGTTTTAGGATATT
3228439 TTTAATTAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 20 0.42
59 6 0.12
61 6 0.12
62 16 0.33
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (59 bp):
TTATATTTTATCTTTGTTTTAAATAGTTTTAGTTTTAAATAGGTTTTAGGATATTATTT
Found at i:3228443 original size:22 final size:24
Alignment explanation
Indices: 3228417--3228470 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
3228407 GGTATTTTAG
* *
3228417 TTTAAATAGGTTTTAGTATA-T-T
1 TTTAAATAGGATTTAGAATATTAT
*
3228439 TTTAATTAGGATTTAGAATATTAT
1 TTTAAATAGGATTTAGAATATTAT
3228463 TTTAAATA
1 TTTAAATA
3228471 TTATTAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 17 0.65
23 1 0.04
24 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTAAATAGGATTTAGAATATTAT
Found at i:3228483 original size:16 final size:16
Alignment explanation
Indices: 3228457--3228501 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
3228447 GGATTTAGAA
3228457 TATTA-TTTTAAATAT
1 TATTAGTTTTAAATAT
*
3228472 TATTAGTTTTAAGGTAT
1 TATTAGTTTTAA-ATAT
3228489 T-TTAG-TTTAAATA
1 TATTAGTTTTAAATA
3228502 GTTTTAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 10 0.38
17 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TATTAGTTTTAAATAT
Found at i:3228497 original size:77 final size:75
Alignment explanation
Indices: 3228342--3228527 Score: 229
Period size: 78 Copynumber: 2.5 Consensus size: 75
3228332 TTATCTTTGT
* * * * *
3228342 TTTAAATAGGTTTTAG-TATTTTAATTAGGTTTTAGGATATTATTTTTATATTTTATCTTTGTTT
1 TTTAAATAGGTTTTAGATATTTTAATTAGGATTTAGAATATTATTTTAATATTTTA-CGTTGTTA
3228406 AGGTATTTTAG
65 AGGTATTTTAG
3228417 TTTAAATAGGTTTTAGTATATTTTTAATTAGGATTTAGAATATTATTTTAAATATTATTA-GTT-
1 TTTAAATAGGTTTTAG-ATA-TTTTAATTAGGATTTAGAATATTATTTT-AATATT-TTACGTTG
3228480 TTAAGGTATTTTAG
62 TTAAGGTATTTTAG
*
3228494 TTTAAATA-GTTTTA-AGTGTTTTAATTAGGATTTA
1 TTTAAATAGGTTTTAGA-TATTTTAATTAGGATTTA
3228528 AGATGTTTTA
Statistics
Matches: 99, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
74 17 0.17
75 17 0.17
76 6 0.06
77 23 0.23
78 28 0.28
79 5 0.05
80 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (75 bp):
TTTAAATAGGTTTTAGATATTTTAATTAGGATTTAGAATATTATTTTAATATTTTACGTTGTTAA
GGTATTTTAG
Found at i:3229228 original size:19 final size:20
Alignment explanation
Indices: 3229177--3229249 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 20
3229167 AAAAAACCCT
* *
3229177 TTTTATTTTACTACTAT-TA
1 TTTTATTTTATTATTATCTA
* *
3229196 TTTATTATTTTATTATTTTCTC
1 -TT-TTATTTTATTATTATCTA
3229218 TTTTA-TTTATTATTATCTA
1 TTTTATTTTATTATTATCTA
3229237 TTTTATTTTATTA
1 TTTTATTTTATTA
3229250 AATCTTTTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 17 0.39
20 12 0.27
21 14 0.32
22 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTATTATTATCTA
Found at i:3231585 original size:20 final size:20
Alignment explanation
Indices: 3231562--3231604 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3231552 TTTGAAACTT
3231562 AAATTCACAACACGAAAATG
1 AAATTCACAACACGAAAATG
* *
3231582 AAATTCGCAACGCGAAAATG
1 AAATTCACAACACGAAAATG
3231602 AAA
1 AAA
3231605 ATCGCAACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (20 bp):
AAATTCACAACACGAAAATG
Found at i:3231609 original size:20 final size:20
Alignment explanation
Indices: 3231569--3231617 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3231559 CTTAAATTCA
* *
3231569 CAACACGAAAATGAAATTCG
1 CAACGCGAAAATGAAAATCG
3231589 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
3231609 CAACGCGAA
1 CAACGCGAA
3231618 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:3231995 original size:22 final size:22
Alignment explanation
Indices: 3231968--3232022 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3231958 GGAGATAGAT
3231968 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
3231990 GGATTTCACCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
* *
3232012 AGATGTCGCCG
1 GGATTTCGCCG
3232023 TAGAGAGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.18
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:3235143 original size:221 final size:225
Alignment explanation
Indices: 3234760--3235208 Score: 703
Period size: 221 Copynumber: 2.0 Consensus size: 225
3234750 CACCCTAAAT
* *
3234760 CTGTTCTGGTAGAAGATGAATCTAGTGTGTCACTTTGGTCCATAAGTAGGGGCGGAACCAGAAAT
1 CTGTTCTGGTACAAGATGAATCTAGTGTGTCACTTTGGTCCATAAGTAAGGGCGGAACCAGAAAT
* *
3234825 TTATTAAGGCGGGGTTAAAATATTTTTTATTTTCATAAATACAATTTTTTAATTGAGGTGACCGA
66 TTATTAAGGCAGGGTTAAAATATTTTTTATTTTCATAAATACAATTTTTTAATTGAAGTGACCGA
*
3234890 TTAAATTTTAATTTTTTTTT--A-AATATATATATATATTTCAAAATTAATTAATACTT-AAAAA
131 GTAAATTTT-ATTTTTTTTTAAATAATATATATATATATTTCAAAATTAATTAATACTTAAAAAA
* *
3234951 TTTGACGGAGG-TCAAGGCTTCTCTTGACCC
195 ATTGACGGAGGCCCAAGGCTTCTCTTGACCC
3234981 CTGTTCTGGTACAAGATGAATCTAGTGTGTCACTTTGGTCCATAAGTAAGGGCGGAACCAGAAAT
1 CTGTTCTGGTACAAGATGAATCTAGTGTGTCACTTTGGTCCATAAGTAAGGGCGGAACCAGAAAT
*
3235046 TTATTAAGGCAGGGTTAAAATATTTTTTATTTTCATAGATACAATTTTTTAATTGAAGTGACCGA
66 TTATTAAGGCAGGGTTAAAATATTTTTTATTTTCATAAATACAATTTTTTAATTGAAGTGACCGA
*** *
3235111 GTAAATTTT-TTTTTATTTATTTTTAAATATATATATATATTTCAATATTAATTAATACTTAAAA
131 GTAAATTTTATTTTT-TTT-TAAAT-AATATATATATATATTTCAAAATTAATTAATACTTAAAA
*
3235175 AAATTGACGGAGGCCCAGGGCTTCTCTTGACCC
193 AAATTGACGGAGGCCCAAGGCTTCTCTTGACCC
3235208 C
1 C
3235209 GTGAAGTTCC
Statistics
Matches: 209, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
219 5 0.02
220 3 0.01
221 134 0.64
225 34 0.16
226 15 0.07
227 18 0.09
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (225 bp):
CTGTTCTGGTACAAGATGAATCTAGTGTGTCACTTTGGTCCATAAGTAAGGGCGGAACCAGAAAT
TTATTAAGGCAGGGTTAAAATATTTTTTATTTTCATAAATACAATTTTTTAATTGAAGTGACCGA
GTAAATTTTATTTTTTTTTAAATAATATATATATATATTTCAAAATTAATTAATACTTAAAAAAA
TTGACGGAGGCCCAAGGCTTCTCTTGACCC
Found at i:3235646 original size:25 final size:25
Alignment explanation
Indices: 3235610--3235659 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3235600 CGATCAATAG
3235610 TTCAGGTCTGGTTCGATCAGATCGA
1 TTCAGGTCTGGTTCGATCAGATCGA
*
3235635 TTCA-GTCATGGTTCGGTCAGATCGA
1 TTCAGGTC-TGGTTCGATCAGATCGA
3235660 CTCAACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (25 bp):
TTCAGGTCTGGTTCGATCAGATCGA
Found at i:3238344 original size:42 final size:42
Alignment explanation
Indices: 3238250--3238460 Score: 125
Period size: 42 Copynumber: 5.0 Consensus size: 42
3238240 TTACGTGAAT
* ** * * * * *
3238250 ACGCCACTATAGATACATACATTAGTGGCATTTTTGTAAGAA
1 ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
* * * * * *
3238292 ATGCCTCTATATCCTCATATATTAGTGGTGTTTGTCTTACAA
1 ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
* * * * * * *
3238334 ACGCCGCTATAGACACGTACATTGGTGACATTTGACTAACAA
1 ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
** * * * *
3238376 ACGCTACTATAGGCACGTAGATTAGTGGCGTTTGTCAAACAA
1 ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
* * * * * *
3238418 ATGCCGCTATATCCTCATATATTAGTGGCATTTGACAAACAA
1 ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
3238460 A
1 A
3238461 TGCCACATGA
Statistics
Matches: 124, Mismatches: 45, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
42 124 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (42 bp):
ACGCCGCTATAGCCACATATATTAGTGGCGTTTGTCTAACAA
Found at i:3238902 original size:43 final size:43
Alignment explanation
Indices: 3238855--3238988 Score: 121
Period size: 43 Copynumber: 3.1 Consensus size: 43
3238845 GTTTGTAGTA
* * *
3238855 AAAAATGCCACTAAATATCATAAC-ATATAGC-AGCGTTTGGGTG
1 AAAAACGCCACCAAATATCATAACTAT-TAACGAG-GTTTGGGTG
* * *
3238898 AAAAACGCTACCATATATCATGACTATTAACGAGGTTTGGGTG
1 AAAAACGCCACCAAATATCATAACTATTAACGAGGTTTGGGTG
* * * **
3238941 AAAAACACCACCATATATCGTGTCTATTAACG-GCGTTTGGGTG
1 AAAAACGCCACCAAATATCATAACTATTAACGAG-GTTTGGGTG
3238984 AAAAA
1 AAAAA
3238989 ATGTTACTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.01
43 73 0.94
44 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (43 bp):
AAAAACGCCACCAAATATCATAACTATTAACGAGGTTTGGGTG
Found at i:3239012 original size:44 final size:43
Alignment explanation
Indices: 3238887--3239029 Score: 173
Period size: 43 Copynumber: 3.3 Consensus size: 43
3238877 ACATATAGCA
*
3238887 GCGTTTGGGTGAAAAACGCTACCATATATCATGACTATTAACG
1 GCGTTTGGGTGAAAAAAGCTACCATATATCATGACTATTAACG
* * *
3238930 AG-GTTTGGGTGAAAAACA-CCACCATATATCGTGTCTATTAACG
1 -GCGTTTGGGTGAAAAA-AGCTACCATATATCATGACTATTAACG
* * *
3238973 GCGTTTGGGTGAAAAAATGTTACTATATATCATGACTATTAGCG
1 GCGTTTGGGTGAAAAAA-GCTACCATATATCATGACTATTAACG
*
3239017 GCGTTTTGGTGAA
1 GCGTTTGGGTGAA
3239030 CAAACGCCGC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 50 0.60
44 32 0.38
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (43 bp):
GCGTTTGGGTGAAAAAAGCTACCATATATCATGACTATTAACG
Found at i:3239427 original size:18 final size:18
Alignment explanation
Indices: 3239404--3239445 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3239394 CCTATAATAG
3239404 GATTAAAATAACAAAAGA
1 GATTAAAATAACAAAAGA
* *
3239422 GATTAAAATGACGAAAGA
1 GATTAAAATAACAAAAGA
*
3239440 AATTAA
1 GATTAA
3239446 CGTTGGAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (18 bp):
GATTAAAATAACAAAAGA
Found at i:3240319 original size:43 final size:43
Alignment explanation
Indices: 3240255--3240544 Score: 219
Period size: 43 Copynumber: 6.8 Consensus size: 43
3240245 CTAGACCCTC
** *
3240255 TCAAGATCTATAGCGTAGTTTTTGGAACAAACGCGGCAAAAGG
1 TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
* * *
3240298 TCAAGATCTATAGCGGCGTTTTTGGACCAAATGCCGCAAAAGT
1 TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
* * * * **
3240341 TCAA-ATCTATAGCAGCATTTTTAGAACTAACGCTACAAAAGG
1 TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
** * * *
3240383 TTGAGATCGATAGCGACATTTTTGGAACAAACGCCGCAAAAGG
1 TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
** * * * * ** *
3240426 TTGAGATATATAACGGTGTTTTTGAAACAAACGTAGCAAAATG
1 TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
* * * ***
3240469 TCAA-ATCTATAGAGGCGCTTTTT-GAACAAACGTCGTAAATTA
1 TCAAGATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGG
* *
3240511 T-TAGATCCATAGCGGCGCTTTTTGGATACAAACG
1 TCAAGATCTATAGCGGCG-TTTTTGGA-ACAAACG
3240545 TCGCTAATTA
Statistics
Matches: 194, Mismatches: 48, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 72 0.37
43 114 0.59
44 7 0.04
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (43 bp):
TCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG
Found at i:3240405 original size:85 final size:86
Alignment explanation
Indices: 3240255--3240424 Score: 209
Period size: 85 Copynumber: 2.0 Consensus size: 86
3240245 CTAGACCCTC
* * * * * *
3240255 TCAAGATCTATAGCGTAGTTTTTGGAACAAACGCGGCAAAAGGTCAAGATCTATAGCGGCGTTTT
1 TCAAGATCTATAGCGCAGTTTTTAGAACAAACGCGACAAAAGGTCAAGATCGATAGCGACATTTT
* *
3240320 TGGACCAAATGCCGCAAAAGT
66 TGGAACAAACGCCGCAAAAGT
* * **
3240341 TCAA-ATCTATAGCAGCA-TTTTTAGAACTAACGCTACAAAAGGTTGAGATCGATAGCGACATTT
1 TCAAGATCTATAGC-GCAGTTTTTAGAACAAACGCGACAAAAGGTCAAGATCGATAGCGACATTT
3240404 TTGGAACAAACGCCGCAAAAG
65 TTGGAACAAACGCCGCAAAAG
3240425 GTTGAGATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 65 0.92
86 6 0.08
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (86 bp):
TCAAGATCTATAGCGCAGTTTTTAGAACAAACGCGACAAAAGGTCAAGATCGATAGCGACATTTT
TGGAACAAACGCCGCAAAAGT
Found at i:3247171 original size:31 final size:31
Alignment explanation
Indices: 3247136--3247232 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
3247126 TTTTGATTGG
*
3247136 ATTTAAAAAATAAATTATTATTTTATATAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
** * * *
3247167 ATTTAAATGTTAAATTGTTACTTTATCTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
* * *
3247198 ATTTAAGAATTAAATTAGTATTTTATTTAAGA
1 ATTTAAAAATTAAATTATTATTTTATATAA-A
3247230 ATT
1 ATT
3247233 AAATTAATAT
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
31 48 0.92
32 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTTAAAAATTAAATTATTATTTTATATAAA
Found at i:3247225 original size:24 final size:24
Alignment explanation
Indices: 3247198--3247251 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3247188 TTTATCTAAA
*
3247198 ATTTAAGAATTAAATTAGTATTTT
1 ATTTAAGAATTAAATTAATATTTT
3247222 ATTTAAGAATTAAATTAATATTTT
1 ATTTAAGAATTAAATTAATATTTT
3247246 ATTTAA
1 ATTTAA
3247252 AAGATTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
ATTTAAGAATTAAATTAATATTTT
Found at i:3248882 original size:2 final size:2
Alignment explanation
Indices: 3248875--3248899 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3248865 CATGGTTTTG
3248875 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 A
3248900 CTCATTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3249411 original size:28 final size:28
Alignment explanation
Indices: 3249379--3249441 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
3249369 ACATAGATAT
3249379 TGCATGTGCATCTACAAAGCAATGACAA
1 TGCATGTGCATCTACAAAGCAATGACAA
*
3249407 TGCATGTGCATCTACAAAGCAATTACAA
1 TGCATGTGCATCTACAAAGCAATGACAA
3249435 TGCATGT
1 TGCATGT
3249442 TTTGGGGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (28 bp):
TGCATGTGCATCTACAAAGCAATGACAA
Found at i:3261158 original size:42 final size:42
Alignment explanation
Indices: 3261106--3261231 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 42
3261096 CACTATAGAT
* * * *
3261106 GCATACATTAGTGGCGTTTTTGTAACAAATGCTGCTATATCC
1 GCATATATTAGTGGCGTTTGTGTAACAAATGCCGCTATATAC
* * * * * *
3261148 TCATATATTAGCGGCGTTTGTCTTACAAACGCCGCTATAGAC
1 GCATATATTAGTGGCGTTTGTGTAACAAATGCCGCTATATAC
* *
3261190 GC-T-TATTAGTGGCGTTTGAGTAACAACTGCCGCTATATAC
1 GCATATATTAGTGGCGTTTGTGTAACAAATGCCGCTATATAC
3261230 GC
1 GC
3261232 GTACATTGGT
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 32 0.48
41 1 0.02
42 33 0.50
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
GCATATATTAGTGGCGTTTGTGTAACAAATGCCGCTATATAC
Found at i:3261806 original size:44 final size:43
Alignment explanation
Indices: 3261756--3261882 Score: 150
Period size: 42 Copynumber: 2.9 Consensus size: 43
3261746 ACATATAGAG
*
3261756 GCGTTTGGGGTGAAAAACACTACCATATATCATGACTATTAACGA
1 GCGTTT-GGGTGAAAAAAACTACCATATATCATGACTATTAAC-A
*** *
3261801 G-GTTTGGGTGAAAATGTC-ACCATATATCGTGACTATTAACA
1 GCGTTTGGGTGAAAAAAACTACCATATATCATGACTATTAACA
* *
3261842 GCGTTTGGGTGAAAAAAATTTACTATATATCATGACTATTA
1 GCGTTTGGGTGAAAAAAA-CTACCATATATCATGACTATTA
3261883 GCGGTGTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.03
42 34 0.49
43 10 0.14
44 22 0.32
45 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (43 bp):
GCGTTTGGGTGAAAAAAACTACCATATATCATGACTATTAACA
Found at i:3261897 original size:44 final size:43
Alignment explanation
Indices: 3261777--3261898 Score: 133
Period size: 42 Copynumber: 2.8 Consensus size: 43
3261767 GAAAAACACT
3261777 ACCATATATCATGACTATTAACGAGGTTTGGGTG--AAAATGTC
1 ACCATATATCATGACTATTAACG-GGTTTGGGTGAAAAAATGTC
* * *
3261819 ACCATATATCGTGACTATTAACAGCGTTTGGGTGAAAAAAAT-TT
1 ACCATATATCATGACTATTAAC-GGGTTTGGGTG-AAAAAATGTC
* * *
3261863 ACTATATATCATGACTATTAGCGGTGTTTTGGTGAA
1 ACCATATATCATGACTATTAACGG-GTTTGGGTGAA
3261899 CAAACGCCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
42 30 0.45
43 4 0.06
44 28 0.42
45 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (43 bp):
ACCATATATCATGACTATTAACGGGTTTGGGTGAAAAAATGTC
Found at i:3262294 original size:18 final size:18
Alignment explanation
Indices: 3262271--3262312 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3262261 CCTATAATAG
3262271 GATTAAAATAACAAAAGA
1 GATTAAAATAACAAAAGA
* *
3262289 GATTAAAATGACGAAAGA
1 GATTAAAATAACAAAAGA
*
3262307 AATTAA
1 GATTAA
3262313 CGTTGGAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (18 bp):
GATTAAAATAACAAAAGA
Found at i:3263240 original size:42 final size:42
Alignment explanation
Indices: 3263154--3263422 Score: 294
Period size: 42 Copynumber: 6.4 Consensus size: 42
3263144 ATAGCGCCAA
** *
3263154 TTTTGGAACAAACGCGGCAAAATTTCGAGATCTATAGCGGCGT
1 TTTTGGAACAAACGCCACAAAAGTTC-AGATCTATAGCGGCGT
* *
3263197 TTTTGGACCAAACGCCACAAAAGTTCAGATCTATAGCAGCGT
1 TTTTGGAACAAACGCCACAAAAGTTCAGATCTATAGCGGCGT
* * *
3263239 TTTTGGAACAAA--CTACAAAAGGTCGAGATCTATAGCAGCGT
1 TTTTGGAACAAACGCCACAAAAGTTC-AGATCTATAGCGGCGT
* * * * *
3263280 TTTTGGAACAAATGCCGCAAAGGTTGAGATCTATAGTGGCGT
1 TTTTGGAACAAACGCCACAAAAGTTCAGATCTATAGCGGCGT
** *
3263322 TTTTTAAACAAACGCCGCAAAA-TATCAGATCTATAGCGGCGT
1 TTTTGGAACAAACGCCACAAAAGT-TCAGATCTATAGCGGCGT
* *
3263364 TTTTGGAACAAATGCCACAAAGGATT-AGATCTATAGCGGCGCT
1 TTTTGGAACAAACGCCACAAAAG-TTCAGATCTATAGCGGCG-T
3263407 TTTTGGATACAAACGC
1 TTTTGGA-ACAAACGC
3263423 TGCTAATTAC
Statistics
Matches: 191, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
40 10 0.05
41 29 0.15
42 106 0.55
43 38 0.20
44 8 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
TTTTGGAACAAACGCCACAAAAGTTCAGATCTATAGCGGCGT
Found at i:3263369 original size:84 final size:84
Alignment explanation
Indices: 3263160--3263410 Score: 310
Period size: 83 Copynumber: 3.0 Consensus size: 84
3263150 CCAATTTTGG
* * * * *
3263160 AACAAACGCGGCAAAATTTCGAGATCTATAGCGGCGTTTTTGGACCAAACGCCACAAAAGTTCAG
1 AACAAACGCCGCAAAATATCGAGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAGGTT-AG
* **
3263225 ATCTATAGCAGCGTTTTTGG
65 ATCTATAGCGGCGTTTTTTA
** ** * *
3263245 AACAAA--CTACAAAAGGTCGAGATCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAGGTTGAG
1 AACAAACGCCGCAAAATATCGAGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAGGTT-AG
*
3263308 ATCTATAGTGGCGTTTTTTA
65 ATCTATAGCGGCGTTTTTTA
3263328 AACAAACGCCGCAAAATATC-AGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAGGATTAG
1 AACAAACGCCGCAAAATATCGAGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAGG-TTAG
*
3263392 ATCTATAGCGGCGCTTTTT
65 ATCTATAGCGGCGTTTTTT
3263411 GGATACAAAC
Statistics
Matches: 141, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
83 69 0.49
84 56 0.40
85 16 0.11
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (84 bp):
AACAAACGCCGCAAAATATCGAGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAGGTTAGA
TCTATAGCGGCGTTTTTTA
Found at i:3264089 original size:42 final size:43
Alignment explanation
Indices: 3263923--3264080 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 43
3263913 GTTTGTATGA
* * ** * *
3263923 AAAAATGCCACTAAATATCAT-AAAATATAACGGCATTTGGGTG
1 AAAAATGCTACTATATATCATGACTAT-TAACGACGTTTGGGTG
* *
3263966 AAAAAATGCTACCATATATCATGACTAATAACGACGTTTGGGTG
1 -AAAAATGCTACTATATATCATGACTATTAACGACGTTTGGGTG
* * *
3264010 AAAAACGCCACTATATATCGTGACTATTAACGACGTTTGGGTG
1 AAAAATGCTACTATATATCATGACTATTAACGACGTTTGGGTG
* *
3264053 -AAAATGTTACTATATATCATGTCTATTA
1 AAAAATGCTACTATATATCATGACTATTA
3264081 GTGGCGTTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
42 23 0.24
43 38 0.40
44 32 0.34
45 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (43 bp):
AAAAATGCTACTATATATCATGACTATTAACGACGTTTGGGTG
Found at i:3264485 original size:18 final size:18
Alignment explanation
Indices: 3264462--3264503 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3264452 CCTATAATAG
3264462 GATTAAAATAACAAAAGA
1 GATTAAAATAACAAAAGA
* *
3264480 GATTAAAATGACGAAAGA
1 GATTAAAATAACAAAAGA
*
3264498 AATTAA
1 GATTAA
3264504 CGTTGGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (18 bp):
GATTAAAATAACAAAAGA
Found at i:3266277 original size:24 final size:24
Alignment explanation
Indices: 3266250--3266300 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3266240 AACACATAGA
* *
3266250 AAAGAATATTGATTGTCTAACGTT
1 AAAGAATATTGATTGCCTAACATT
3266274 AAAGAATATTGATTGCCTAACATT
1 AAAGAATATTGATTGCCTAACATT
3266298 AAA
1 AAA
3266301 AAAACATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (24 bp):
AAAGAATATTGATTGCCTAACATT
Found at i:3266332 original size:23 final size:23
Alignment explanation
Indices: 3266302--3266352 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
3266292 AACATTAAAA
3266302 AAAC-ATGTTCGCGAATGTAATC
1 AAACGATGTTCGCGAATGTAATC
3266324 AAACGATGTTCGCGAATGTAATC
1 AAACGATGTTCGCGAATGTAATC
3266347 AAACGA
1 AAACGA
3266353 ACGCGAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (23 bp):
AAACGATGTTCGCGAATGTAATC
Found at i:3270829 original size:60 final size:61
Alignment explanation
Indices: 3270737--3270894 Score: 202
Period size: 60 Copynumber: 2.7 Consensus size: 61
3270727 ACTTTTAAAT
* **
3270737 ATTCCAATTTCATCCCAAACTATGAC-TATCATTCTATATTAGTCCTTAAAC-TTTT-GAGC
1 ATTCCAATTTCATCCCAAACTATGACATATCATTCTAAATTAGTCCCCAAACTTTTTGGA-C
* *
3270796 ATTTCAATTCCATCCCCAAACTATGACAT-TCATTCTAAATTAGTCCCCAAACTTTTTGGAC
1 ATTCCAATTTCAT-CCCAAACTATGACATATCATTCTAAATTAGTCCCCAAACTTTTTGGAC
*
3270857 ATTCCAATTTCATCCCAAACTAT-ACATAT-ATACTAAAT
1 ATTCCAATTTCATCCCAAACTATGACATATCATTCTAAAT
3270895 ACTAATCACA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
59 23 0.27
60 44 0.51
61 17 0.20
62 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (61 bp):
ATTCCAATTTCATCCCAAACTATGACATATCATTCTAAATTAGTCCCCAAACTTTTTGGAC
Found at i:3271128 original size:60 final size:61
Alignment explanation
Indices: 3271012--3271162 Score: 148
Period size: 60 Copynumber: 2.5 Consensus size: 61
3271002 GGGTAAATTT
* * * * *
3271012 GGGATTAAATTGGAATGTTAAAAAAGTTT-GGGTACTAATTTAGAAAGAGGGTCATAGTTTA
1 GGGATGAAATTGAAATGTT-CAAAAGTTTAAGGTACTAATTTAGAAAGAAGGTCATAGTTTA
* * *
3271073 GGGATGAAATTGAAATGTTCAAAAGTTTAAGG-ACTAGTTTAGAATGATAGG-CATAGTTTG
1 GGGATGAAATTGAAATGTTCAAAAGTTTAAGGTACTAATTTAGAAAGA-AGGTCATAGTTTA
* * *
3271133 GGGATGATATT-AGAATATTCAAAAGCTTAA
1 GGGATGAAATTGA-AATGTTCAAAAGTTTAA
3271163 TGACCAATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 54 0.71
61 21 0.28
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (61 bp):
GGGATGAAATTGAAATGTTCAAAAGTTTAAGGTACTAATTTAGAAAGAAGGTCATAGTTTA
Done.