Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 5 of 8
Found at i:964172 original size:46 final size:47
Alignment explanation
Indices: 964098--964201 Score: 165
Period size: 46 Copynumber: 2.2 Consensus size: 47
964088 AGAGCCGAGG
* * *
964098 ATTCTACGTGGTTCTTCGGGACATATCTATGTGGTCCTTCGGGAC-A
1 ATTCTACGTGGTCCTTCGGGAAAAATCTATGTGGTCCTTCGGGACAA
964144 ATTCTACGTGGTCCTTCGGGAAAAATCTATGTGGTCCTTCGGGACAA
1 ATTCTACGTGGTCCTTCGGGAAAAATCTATGTGGTCCTTCGGGACAA
*
964191 ATTCTATGTGG
1 ATTCTACGTGG
964202 CACTTTGGTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 42 0.79
47 11 0.21
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (47 bp):
ATTCTACGTGGTCCTTCGGGAAAAATCTATGTGGTCCTTCGGGACAA
Found at i:965465 original size:21 final size:23
Alignment explanation
Indices: 965432--965477 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
965422 TACTTCCGAT
*
965432 GTGAAGTGGTCTTCTTA-CCTTG
1 GTGAAGTGGTCTTCTCATCCTTG
965454 GTGAAG-GGTCTTCTCATCCTTG
1 GTGAAGTGGTCTTCTCATCCTTG
965476 GT
1 GT
965478 ATGATTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.13, C:0.20, G:0.28, T:0.39
Consensus pattern (23 bp):
GTGAAGTGGTCTTCTCATCCTTG
Found at i:967069 original size:83 final size:82
Alignment explanation
Indices: 966958--967213 Score: 251
Period size: 92 Copynumber: 3.0 Consensus size: 82
966948 ATACATCGTT
* * * *
966958 ATGTATTTTCATTTATTGCATCGTTTCATGCCTTTAATGCACCGTTATGCATTTTTCATTTATGG
1 ATGTATTTTCATTTGTAGAATCCTTTCATGCCTTTAATGCACCGTTATGCA-TTTTCATTTATGG
**
967023 CATTGTTTCATGCCTTTA
65 CATCATTTCATGCCTTTA
* * * * *
967041 ATGTATTTTCATTTGCAGAATCCTTTCATACCTTTAATGCACTGTTACGTATTTTCATTTATGGC
1 ATGTATTTTCATTTGTAGAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTCATTTATGGC
* *
967106 ATCATTTCTTTCCTTTA
66 ATCATTTCATGCCTTTA
* * * *
967123 ATGCACTGTTATGAATTTTGATTTATTACATCCTTTCATGCCTTTAATGCACCGTTATACATTTT
1 ATGTA-T-TT-T-CA-TTTG---TA-GA-ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTT
*
967188 CATTTATGGCATCCTTTCATGCCTTT
56 CATTTATGGCATCATTTCATGCCTTT
967214 TATGCACCGT
Statistics
Matches: 138, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
82 31 0.22
83 43 0.31
84 2 0.01
85 1 0.01
86 1 0.01
87 4 0.03
90 1 0.01
91 1 0.01
92 54 0.39
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (82 bp):
ATGTATTTTCATTTGTAGAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTCATTTATGGC
ATCATTTCATGCCTTTA
Found at i:967096 original size:46 final size:46
Alignment explanation
Indices: 967041--967240 Score: 204
Period size: 46 Copynumber: 4.3 Consensus size: 46
967031 CATGCCTTTA
** * *
967041 ATGTATTTTCATTTGCAGAATCCTTTCATACCTTTAATGCACTGTT
1 ATGTATTTTCATTTATAGAATCCTTTCATGCCTTTAATGCACCGTT
* * * * * * *
967087 ACGTATTTTCATTTATGGCATCATTTCTTTCCTTTAATGCACTGTT
1 ATGTATTTTCATTTATAGAATCCTTTCATGCCTTTAATGCACCGTT
* * *
967133 ATGAATTTTGATTTATTA-CATCCTTTCATGCCTTTAATGCACCGTT
1 ATGTATTTTCATTTA-TAGAATCCTTTCATGCCTTTAATGCACCGTT
** * * *
967179 ATACATTTTCATTTATGGCATCCTTTCATGCCTTTTATGCACCGTT
1 ATGTATTTTCATTTATAGAATCCTTTCATGCCTTTAATGCACCGTT
*
967225 ATGTATTTTTATTTAT
1 ATGTATTTTCATTTAT
967241 TCATTCATTT
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
45 1 0.01
46 126 0.98
47 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (46 bp):
ATGTATTTTCATTTATAGAATCCTTTCATGCCTTTAATGCACCGTT
Found at i:967213 original size:92 final size:92
Alignment explanation
Indices: 967060--967241 Score: 256
Period size: 92 Copynumber: 2.0 Consensus size: 92
967050 CATTTGCAGA
* ** * *
967060 ATCCTTTCATACCTTTAATGCACTGTTACGTATTTTCATTTATGGCATCATTTCTTTCCTTTAAT
1 ATCCTTTCATACCTTTAATGCACCGTTACACATTTTCATTTATGGCATCATTTCATGCCTTTAAT
*
967125 GCACTGTTATGAATTTTGATTTATTAC
66 GCACCGTTATGAATTTTGATTTATTAC
* * * *
967152 ATCCTTTCATGCCTTTAATGCACCGTTATACATTTTCATTTATGGCATCCTTTCATGCCTTTTAT
1 ATCCTTTCATACCTTTAATGCACCGTTACACATTTTCATTTATGGCATCATTTCATGCCTTTAAT
* *
967217 GCACCGTTATGTATTTTTATTTATT
66 GCACCGTTATGAATTTTGATTTATT
967242 CATTCATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
92 78 1.00
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.49
Consensus pattern (92 bp):
ATCCTTTCATACCTTTAATGCACCGTTACACATTTTCATTTATGGCATCATTTCATGCCTTTAAT
GCACCGTTATGAATTTTGATTTATTAC
Found at i:973660 original size:46 final size:45
Alignment explanation
Indices: 973588--973716 Score: 156
Period size: 46 Copynumber: 2.9 Consensus size: 45
973578 TAGCTACATC
* *
973588 CTTTCATGCC-ATTAACGCACCGTTATGCATTTTCATTTATGGCAT
1 CTTTCATGCCTA-TAATGCACCCTTATGCATTTTCATTTATGGCAT
*
973633 CGTTTCATGCCTATAATGCACCCTTATGCATTTTCATTTATGGTAT
1 C-TTTCATGCCTATAATGCACCCTTATGCATTTTCATTTATGGCAT
* **
973679 -TCTTCATGCCTTTAATGCA-TTTTATGCATTTTCATTTA
1 CT-TTCATGCCTATAATGCACCCTTATGCATTTTCATTTA
973717 GTCATTCATT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 18 0.24
45 17 0.23
46 39 0.52
47 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (45 bp):
CTTTCATGCCTATAATGCACCCTTATGCATTTTCATTTATGGCAT
Found at i:977280 original size:3 final size:3
Alignment explanation
Indices: 977266--977331 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
977256 TTGTCTCCTG
* * *
977266 TAA TAA -AA TAA TAA TAA -AA -AA TAA TAT TAA TAAA TAG TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
977309 TAA TGA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
977332 ATTTTGACCG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 8 0.16
3 40 0.78
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:977323 original size:14 final size:14
Alignment explanation
Indices: 977266--977331 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
977256 TTGTCTCCTG
977266 TAATAA-AATAATAA
1 TAATAATAATAAT-A
977280 TAA-AA-AATAATA
1 TAATAATAATAATA
*
977292 T--TAATAAATAGTTA
1 TAATAAT-AATA-ATA
*
977306 TAATAATGATAATA
1 TAATAATAATAATA
977320 TAATAATAATAA
1 TAATAATAATAA
977332 ATTTTGACCG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 2 0.05
12 2 0.05
13 12 0.29
14 19 0.45
15 3 0.07
16 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:983238 original size:2 final size:2
Alignment explanation
Indices: 983231--983272 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
983221 AAATGGATTG
983231 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
983273 TATGCATGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:984220 original size:12 final size:12
Alignment explanation
Indices: 984169--984221 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
984159 AAATATTTTA
*
984169 TCTGATTTATGT
1 TCTGAATTATGT
*
984181 TTTGAATTATGT
1 TCTGAATTATGT
** * *
984193 TCTGTTTTCTGC
1 TCTGAATTATGT
984205 TCTGAATTATGT
1 TCTGAATTATGT
984217 TCTGA
1 TCTGA
984222 TTTCTACTAT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (12 bp):
TCTGAATTATGT
Found at i:984225 original size:24 final size:24
Alignment explanation
Indices: 984169--984226 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
984159 AAATATTTTA
* * *
984169 TCTGATTTATGTTTTGAATTATGT
1 TCTGATTTCTGCTCTGAATTATGT
*
984193 TCTGTTTTCTGCTCTGAATTATGT
1 TCTGATTTCTGCTCTGAATTATGT
984217 TCTGATTTCT
1 TCTGATTTCT
984227 ACTATGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.57
Consensus pattern (24 bp):
TCTGATTTCTGCTCTGAATTATGT
Found at i:986953 original size:2 final size:2
Alignment explanation
Indices: 986946--986975 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
986936 AGATGGATGG
986946 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
986976 GCATGTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:987907 original size:24 final size:24
Alignment explanation
Indices: 987870--987930 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
987860 TATTTTATCT
* * *
987870 GATTTATGTTCTGAATTCTGTTCG
1 GATTTCTGCTCTGAATTATGTTCG
* *
987894 GCTTTCTGCTCTGAATTATGTTCT
1 GATTTCTGCTCTGAATTATGTTCG
987918 GATTTCTGCTCTG
1 GATTTCTGCTCTG
987931 CTTTCTGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (24 bp):
GATTTCTGCTCTGAATTATGTTCG
Found at i:987907 original size:36 final size:36
Alignment explanation
Indices: 987867--987937 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
987857 GAATATTTTA
* *
987867 TCTGATTTATGTTCTGAATTCTGTTCGGCTTTCTGC
1 TCTGAATTATGTTCTGAATTCTGCTCGGCTTTCTGC
* *
987903 TCTGAATTATGTTCTGATTTCTGCTCTGCTTTCTG
1 TCTGAATTATGTTCTGAATTCTGCTCGGCTTTCTG
987938 ATATCTCCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (36 bp):
TCTGAATTATGTTCTGAATTCTGCTCGGCTTTCTGC
Found at i:987935 original size:12 final size:12
Alignment explanation
Indices: 987867--987937 Score: 52
Period size: 12 Copynumber: 5.9 Consensus size: 12
987857 GAATATTTTA
* *
987867 TCTGATTTATGT
1 TCTGATTTCTGC
* *
987879 TCTGAATTCTGT
1 TCTGATTTCTGC
* *
987891 TCGGCTTTCTGC
1 TCTGATTTCTGC
* * *
987903 TCTGAATTATGT
1 TCTGATTTCTGC
987915 TCTGATTTCTGC
1 TCTGATTTCTGC
*
987927 TCTGCTTTCTG
1 TCTGATTTCTG
987938 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGC
Found at i:990143 original size:29 final size:29
Alignment explanation
Indices: 990085--990235 Score: 123
Period size: 29 Copynumber: 5.3 Consensus size: 29
990075 CATTTTACAC
* * * *
990085 AAATAACACCCTTTTTAAAATT-ATTACCA
1 AAATAGCACCATTTTT-GAATTAATTCCCA
* * *
990114 AAATAGCACCCTTTTCGACTTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
*
990143 AAATAGCACAATTTTTGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* * ** *
990172 GAATATCA--A-TTTTGAAAAAATTACCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
990198 AAATAGCACC-TATTTTGAATTAATTCCCA
1 AAATAGCACCAT-TTTTGAATTAATTCCCA
*
990227 GAATAGCAC
1 AAATAGCAC
990236 TAAAACCGAA
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
26 20 0.21
27 1 0.01
28 3 0.03
29 73 0.75
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATAGCACCATTTTTGAATTAATTCCCA
Found at i:990193 original size:26 final size:27
Alignment explanation
Indices: 990115--990264 Score: 113
Period size: 29 Copynumber: 5.3 Consensus size: 27
990105 TTATTACCAA
* * *
990115 AATAGCACCCTTTTCGACTTAATTCCCAA
1 AATAGCA-CATTTT-GAATTAATTCCCAG
990144 AATAGCACAATTTTTGAATTAATTCCCAG
1 AATAGCAC-A-TTTTGAATTAATTCCCAG
* ** * *
990173 AATATCA-ATTTTGAAAAAATTACCAA
1 AATAGCACATTTTGAATTAATTCCCAG
990199 AATAGCACCTATTTTGAATTAATTCCCAG
1 AATAGCA-C-ATTTTGAATTAATTCCCAG
****
990228 AATAGCACTAAAACCGAATTAATTCCCAG
1 AATAGCAC--ATTTTGAATTAATTCCCAG
990257 AATAGCAC
1 AATAGCAC
990265 CGGTCAACGG
Statistics
Matches: 97, Mismatches: 18, Indels: 12
0.76 0.14 0.09
Matches are distributed among these distances:
26 20 0.21
27 1 0.01
28 2 0.02
29 70 0.72
30 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
AATAGCACATTTTGAATTAATTCCCAG
Found at i:990248 original size:84 final size:84
Alignment explanation
Indices: 990107--990260 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
990097 TTTTAAAATT
* ****
990107 ATTACCAAAATAGCACCCTTTTCGACTTAATTCCCAAAATAGCACAATTTTTGAATTAATTCCCA
1 ATTACCAAAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACAATAACCGAATTAATTCCCA
990172 GAATATCAATTTTGAAAAA
66 GAATATCAATTTTGAAAAA
* *
990191 ATTACCAAAATAGCA-CCTATTTTGAATTAATTCCCAGAATAGCACTAA-AACCGAATTAATTCC
1 ATTACCAAAATAGCACCCT-TTTCGAATTAATTCCCAAAATAGCAC-AATAACCGAATTAATTCC
990254 CAGAATA
64 CAGAATA
990261 GCACCGGTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
83 3 0.05
84 56 0.92
85 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (84 bp):
ATTACCAAAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACAATAACCGAATTAATTCCCA
GAATATCAATTTTGAAAAA
Found at i:990320 original size:26 final size:25
Alignment explanation
Indices: 990263--990322 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
990253 CCAGAATAGC
*
990263 ACCGGTCAACGGTCAACGGGTCGGG
1 ACCGGTCAACGGTAAACGGGTCGGG
* * * *
990288 TCGGGTCAACGGGTAAATGGGTCGTG
1 ACCGGTCAAC-GGTAAACGGGTCGGG
990314 ACCGGTCAA
1 ACCGGTCAA
990323 ACCTTTAAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.22, C:0.23, G:0.38, T:0.17
Consensus pattern (25 bp):
ACCGGTCAACGGTAAACGGGTCGGG
Found at i:996676 original size:29 final size:28
Alignment explanation
Indices: 996624--996774 Score: 112
Period size: 29 Copynumber: 5.4 Consensus size: 28
996614 CATTTTACAC
** *
996624 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCGAATTAATT-CCA
* *
996653 AAATAGCACCCTTTTCGACTTAATCCTCA
1 AAATAGCACCCTTTTCGAATTAATTC-CA
* *
996682 AAATAGCACCAATTTT-GAATTAATTCCC
1 AAATAGCACC-CTTTTCGAATTAATTCCA
* * * *
996710 TAATATCA--ATTTTTGAA-TAATTACCA
1 AAATAGCACCCTTTTCGAATTAATT-CCA
*
996736 AAATAGCACCCATTTCGAATTAATTCCTA
1 AAATAGCACCCTTTTCGAATTAATTCC-A
*
996765 GAATAGCACC
1 AAATAGCACC
996775 AAACCCGAAT
Statistics
Matches: 96, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
25 10 0.10
26 11 0.11
28 16 0.17
29 55 0.57
30 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (28 bp):
AAATAGCACCCTTTTCGAATTAATTCCA
Found at i:996844 original size:13 final size:13
Alignment explanation
Indices: 996811--996862 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
996801 ACCAGTCAAC
996811 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
996823 GGT---CGGGTCG
1 GGTCAACGGGTCG
*
996833 GGTCAACGGGTCA
1 GGTCAACGGGTCG
*
996846 GGTCAACAGGTCG
1 GGTCAACGGGTCG
996859 GGTC
1 GGTC
996863 GGGTCAACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
12 3 0.09
13 21 0.64
ACGTcount: A:0.15, C:0.23, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:997662 original size:20 final size:20
Alignment explanation
Indices: 997637--997678 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
997627 ATTTGTAAAA
997637 ATTCGGGTTGTTACAGAAAC
1 ATTCGGGTTGTTACAGAAAC
997657 ATTCGGGTTGTTACAGAAAC
1 ATTCGGGTTGTTACAGAAAC
997677 AT
1 AT
997679 AAGATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
ATTCGGGTTGTTACAGAAAC
Found at i:999512 original size:32 final size:32
Alignment explanation
Indices: 999469--999540 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
999459 TATGGAAAAC
999469 CCGAACCGAATCAAAAGAATGAAGACTTTAAA
1 CCGAACCGAATCAAAAGAATGAAGACTTTAAA
*
999501 CTGAACCGAATCAAAAGAATGAAGACTTTAAA
1 CCGAACCGAATCAAAAGAATGAAGACTTTAAA
999533 CCGAACCG
1 CCGAACCG
999541 TATAATGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (32 bp):
CCGAACCGAATCAAAAGAATGAAGACTTTAAA
Found at i:1002185 original size:29 final size:28
Alignment explanation
Indices: 1002149--1002287 Score: 106
Period size: 29 Copynumber: 5.0 Consensus size: 28
1002139 CATTTTACAC
* *
1002149 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCATTTTTAAATTAATT-CCA
* ** *
1002178 AAATAGCACCGTTTTCGACTTAATTCTCA
1 AAATAGCACCATTTTTAAATTAATTC-CA
* *
1002207 AAATAGCACCATTTTTGAATTAATTCCC
1 AAATAGCACCATTTTTAAATTAATTCCA
* * *
1002235 GAATATCA--ATTTTTGAA-TAATTACCA
1 AAATAGCACCATTTTTAAATTAATT-CCA
*
1002261 AAATAGCACCCA-TTTCAAATTAATTCC
1 AAATAGCA-CCATTTTTAAATTAATTCC
1002288 TGGAATAGCA
Statistics
Matches: 88, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
25 5 0.06
26 17 0.19
28 15 0.17
29 51 0.58
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (28 bp):
AAATAGCACCATTTTTAAATTAATTCCA
Found at i:1002392 original size:13 final size:13
Alignment explanation
Indices: 1002345--1002380 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1002335 CGGTCGGGTT
1002345 GGGTCGGGTCAAC
1 GGGTCGGGTCAAC
*
1002358 GGGTCAGGTCAAC
1 GGGTCGGGTCAAC
*
1002371 AGGTCGGGTC
1 GGGTCGGGTC
1002381 GGGTCAACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (13 bp):
GGGTCGGGTCAAC
Found at i:1005050 original size:32 final size:32
Alignment explanation
Indices: 1005012--1005083 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1005002 TATGGAAAAC
*
1005012 CCGAACCGAATCAAAAGAATGAAGACTTTAAA
1 CCGAACCGAATCAAAAAAATGAAGACTTTAAA
1005044 CCGAACCGAATCAAAAAAATGAAGACTTTAAA
1 CCGAACCGAATCAAAAAAATGAAGACTTTAAA
1005076 CCGAACCG
1 CCGAACCG
1005084 TATAATGCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.14
Consensus pattern (32 bp):
CCGAACCGAATCAAAAAAATGAAGACTTTAAA
Found at i:1018058 original size:7 final size:7
Alignment explanation
Indices: 1018046--1018076 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1018036 GTCAAATGAA
1018046 GTCAACG
1 GTCAACG
1018053 GTCAACG
1 GTCAACG
*
1018060 GTCAACA
1 GTCAACG
1018067 GTCAACG
1 GTCAACG
1018074 GTC
1 GTC
1018077 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1018083 original size:5 final size:5
Alignment explanation
Indices: 1018073--1018115 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1018063 AACAGTCAAC
* *
1018073 GGTCG GGTCG GGTCG GGTCG GGTC- GGTCG GGTTG GGTTG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1018116 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.00, C:0.16, G:0.58, T:0.26
Consensus pattern (5 bp):
GGTCG
Found at i:1018123 original size:24 final size:24
Alignment explanation
Indices: 1018072--1018124 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1018062 CAACAGTCAA
* **
1018072 CGGTCGGGTCGGGTCGGGTCGGGT
1 CGGTCGGGTCGGGTCGGGTCAGAC
* *
1018096 CGGTCGGGTTGGGTTGGGTCAGAC
1 CGGTCGGGTCGGGTCGGGTCAGAC
1018120 CGGTC
1 CGGTC
1018125 AAACCGGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.21, G:0.53, T:0.23
Consensus pattern (24 bp):
CGGTCGGGTCGGGTCGGGTCAGAC
Found at i:1024666 original size:5 final size:5
Alignment explanation
Indices: 1024656--1024693 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1024646 AACGGTCAAC
*
1024656 GGTCG GGTCG GGTCG GGTC- GGTCG GGTCG GGTTG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1024694 AGACCGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.18, G:0.58, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:1024679 original size:19 final size:19
Alignment explanation
Indices: 1024655--1024693 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1024645 CAACGGTCAA
1024655 CGGTCGGGTCGGGTCGGGT
1 CGGTCGGGTCGGGTCGGGT
*
1024674 CGGTCGGGTCGGGTTGGGT
1 CGGTCGGGTCGGGTCGGGT
1024693 C
1 C
1024694 AGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.56, T:0.23
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCGGGT
Found at i:1024680 original size:9 final size:9
Alignment explanation
Indices: 1024655--1024685 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1024645 CAACGGTCAA
1024655 CGGTCGGGT
1 CGGTCGGGT
1024664 CGGGTCGGGT
1 C-GGTCGGGT
1024674 CGGTCGGGT
1 CGGTCGGGT
1024683 CGG
1 CGG
1024686 GTTGGGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (9 bp):
CGGTCGGGT
Found at i:1024680 original size:14 final size:15
Alignment explanation
Indices: 1024656--1024693 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1024646 AACGGTCAAC
1024656 GGTCGGGTCGGGTCG
1 GGTCGGGTCGGGTCG
1024671 GGTC-GGTCGGGTCG
1 GGTCGGGTCGGGTCG
*
1024685 GGTTGGGTC
1 GGTCGGGTC
1024694 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.00, C:0.18, G:0.58, T:0.24
Consensus pattern (15 bp):
GGTCGGGTCGGGTCG
Found at i:1024702 original size:19 final size:19
Alignment explanation
Indices: 1024661--1024721 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
1024651 TCAACGGTCG
* * *
1024661 GGTCGGGTCGGGTCGGTCG
1 GGTCGGGTCGGGTCAGACC
*
1024680 GGTCGGGTTGGGTCAGACC
1 GGTCGGGTCGGGTCAGACC
*** *
1024699 GGTCAAATCGGTTCAGACC
1 GGTCGGGTCGGGTCAGACC
1024718 GGTC
1 GGTC
1024722 AAACCGGTTC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.11, C:0.23, G:0.44, T:0.21
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGACC
Found at i:1024722 original size:19 final size:19
Alignment explanation
Indices: 1024692--1024778 Score: 97
Period size: 19 Copynumber: 4.5 Consensus size: 19
1024682 TCGGGTTGGG
*
1024692 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
1024711 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* * *
1024730 TCAGATCGGTTAAACCGAT
1 TCAGACCGGTCAAACCGGT
1024749 TC-GAACCGGTCGAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
1024768 TCAGAACCGGT
1 TCAG-ACCGGT
1024779 TGAAAACTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.02
19 43 0.74
20 14 0.24
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1024791 original size:21 final size:20
Alignment explanation
Indices: 1024722--1024783 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
1024712 CAGACCGGTC
*
1024722 AAACCGGTTCAG-ATCGGTT-
1 AAACCGG-TCAGAACCGGTTG
* *
1024741 AAACCGATTC-GAACCGGTCG
1 AAACCG-GTCAGAACCGGTTG
1024761 AAACCGGTCAGAACCGGTTG
1 AAACCGGTCAGAACCGGTTG
1024781 AAA
1 AAA
1024784 ACTGGTCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.44
20 18 0.53
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
AAACCGGTCAGAACCGGTTG
Found at i:1026892 original size:3 final size:3
Alignment explanation
Indices: 1026884--1026920 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1026874 GACATAATAT
*
1026884 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1026921 ATATATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1029694 original size:28 final size:28
Alignment explanation
Indices: 1029682--1029815 Score: 80
Period size: 28 Copynumber: 4.6 Consensus size: 28
1029672 AATATTAAAG
1029682 AAATATATATATAATAATAATAATAATA
1 AAATATATATATAATAATAATAATAATA
* *
1029710 AAATATAGTAAAAAATAA-AATGAA-AATA
1 AAATATA-TATATAATAATAAT-AATAATA
1029738 ATTTAATATATATATATATACAT-ATAATAATA
1 A---AATATATATATA-ATA-ATAATAATAATA
* * *
1029770 ATAACAT-GA-ATAATAAAAATAAATGAATA
1 A-AATATATATATAATAATAAT-AAT-AATA
**
1029799 AAATATCCATATAATAA
1 AAATATATATATAATAA
1029816 ATAAAGGGAC
Statistics
Matches: 83, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
26 1 0.01
27 5 0.06
28 25 0.30
29 17 0.20
30 16 0.19
31 11 0.13
32 8 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATATATATATAATAATAATAATAATA
Found at i:1029784 original size:18 final size:17
Alignment explanation
Indices: 1029761--1029803 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1029751 ATATATACAT
1029761 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1029779 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1029796 ATAA-AATA
1 ATAATAATA
1029804 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1031047 original size:106 final size:106
Alignment explanation
Indices: 1030860--1031739 Score: 1400
Period size: 106 Copynumber: 8.3 Consensus size: 106
1030850 AGCTAGATAT
* * *
1030860 CCTTCATTGTGAAGTTGAAATTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
** * * * *
1030925 GGCTCCAAAATCGGGAAATTATTTGTTGACAACCAGCAGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
*
1030966 CCTTCGTTGTGACGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* **
1031031 GGCTCTGAAATTGGGAAATTGAATGTTGACAACCAGCCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
*
1031072 CCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1031137 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
* *
1031178 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * * * *
1031243 GGCCCTGAAATTGGGAAGTTATTTGCTAACAACCAGTCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
* * **
1031284 CCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAGTCCAATATCCATCATTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
1031349 GGCTCTAAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
* * *
1031390 CCTTCGTTATGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
1031455 GGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
* *
1031496 CCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAGTCAAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
1031561 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCATC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
* * *
1031602 CATTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCGTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* ** *
1031667 GGCCCTGAAATTGGGAAGTTGTTTACTGACAACCAGTCGTC
66 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
1031708 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
1031740 ATGTAGAACG
Statistics
Matches: 711, Mismatches: 63, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 711 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTC
Found at i:1033117 original size:18 final size:18
Alignment explanation
Indices: 1033090--1033125 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1033080 TGTTTAATCC
*
1033090 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1033108 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1033126 TTGATGTTGA
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:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1033342 original size:24 final size:24
Alignment explanation
Indices: 1033313--1033359 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1033303 ATATCAAAAA
1033313 AAGAGTTTTGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
1033337 AAGAGTTTTGAAAGATTTTTAAT
1 AAGAGTTTTGAAAGATGTTTAAT
1033360 ATGGTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:1033566 original size:22 final size:22
Alignment explanation
Indices: 1033540--1033592 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1033530 TGTTTGGTCA
*
1033540 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCCC
1033562 AAAGGTTTGGCATTTGATGCCC
1 AAAGGTTTGGCATTTGATGCCC
1033584 AAAGGTTTG
1 AAAGGTTTG
1033593 ATGGGGTAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCCC
Found at i:1034247 original size:20 final size:18
Alignment explanation
Indices: 1034198--1034256 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 18
1034188 TCCCTTTTTC
1034198 TTTTTGATTTTTGTTCTTT
1 TTTTTG-TTTTTGTTCTTT
1034217 TTTTT-TCTTTTGTTTTCTTT
1 TTTTTGT-TTTTG--TTCTTT
1034237 TTTTTGTTTTT-TTCCTTT
1 TTTTTGTTTTTGTT-CTTT
1034255 TT
1 TT
1034257 GTTCTGATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.09
18 11 0.31
19 5 0.14
20 15 0.43
21 1 0.03
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (18 bp):
TTTTTGTTTTTGTTCTTT
Found at i:1034249 original size:10 final size:10
Alignment explanation
Indices: 1034205--1034241 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1034195 TTCTTTTTGA
*
1034205 TTTTTGTTCT
1 TTTTTTTTCT
1034215 TTTTTTTTCT
1 TTTTTTTTCT
*
1034225 TTTGTTTTCT
1 TTTTTTTTCT
1034235 TTTTTTT
1 TTTTTTT
1034242 GTTTTTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.86
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1034255 original size:14 final size:13
Alignment explanation
Indices: 1034216--1034255 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1034206 TTTTGTTCTT
1034216 TTTTTTTCTTTTG
1 TTTTTTTCTTTTG
*
1034229 TTTTCTTTTTTTTG
1 TTTT-TTTCTTTTG
1034243 TTTTTTTCCTTTT
1 TTTTTTT-CTTTT
1034256 TGTTCTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTTTG
Found at i:1034256 original size:10 final size:9
Alignment explanation
Indices: 1034205--1034261 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
1034195 TTCTTTTTGA
*
1034205 TTTTTGTTC
1 TTTTTTTTC
1034214 TTTTTTTTTC
1 -TTTTTTTTC
1034224 TTTTGTTTTC
1 TTTT-TTTTC
*
1034234 TTTTTTTTG
1 TTTTTTTTC
*
1034243 TTTTTTTCC
1 TTTTTTTTC
*
1034252 TTTTTGTTC
1 TTTTTTTTC
1034261 T
1 T
1034262 GATTGAATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 23 0.57
10 17 0.43
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1037689 original size:27 final size:27
Alignment explanation
Indices: 1037634--1037701 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
1037624 GGTTTTTTTT
* *
1037634 TAAAAATAATAATATAATAATAATGAA
1 TAAAAATAATAAAATAATAAAAATGAA
1037661 TAAAAA-AATGAAAATAATAAAAAAT-AA
1 TAAAAATAAT-AAAATAAT-AAAAATGAA
*
1037688 TATAAATATATAAA
1 TAAAAATA-ATAAA
1037702 GTTATAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 3 0.09
27 20 0.59
28 9 0.26
29 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (27 bp):
TAAAAATAATAAAATAATAAAAATGAA
Found at i:1037975 original size:18 final size:17
Alignment explanation
Indices: 1037952--1037995 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
1037942 ATATACATAT
1037952 AATAATAATAATAACATG
1 AATAATAATAATAA-ATG
*
1037970 AATAATAAAAATAAATG
1 AATAATAATAATAAATG
1037987 AATAA-AATA
1 AATAATAATA
1037996 TCCATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (17 bp):
AATAATAATAATAAATG
Found at i:1048773 original size:12 final size:12
Alignment explanation
Indices: 1048753--1048782 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1048743 ATCAAATTAG
*
1048753 ATATATATATAT
1 ATATTTATATAT
1048765 ATATTTATATAT
1 ATATTTATATAT
1048777 ATATTT
1 ATATTT
1048783 CTGACATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:1055454 original size:18 final size:18
Alignment explanation
Indices: 1055431--1055465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1055421 CGAACCGGTC
* *
1055431 TGACCCGACCCGACCCGT
1 TGACCCAACCCAACCCGT
1055449 TGACCCAACCCAACCCG
1 TGACCCAACCCAACCCG
1055466 ACCTAGGTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.51, G:0.17, T:0.09
Consensus pattern (18 bp):
TGACCCAACCCAACCCGT
Found at i:1055518 original size:29 final size:29
Alignment explanation
Indices: 1055471--1055585 Score: 151
Period size: 29 Copynumber: 4.0 Consensus size: 29
1055461 ACCCGACCTA
* *
1055471 GGTGCTATTTTCGTAAATATTTTTAAACA-
1 GGTGTTATTTTCATAAATATTTTTAAA-AG
*
1055500 AGTGTTATTTTCATAAATATTTTTAAAAG
1 GGTGTTATTTTCATAAATATTTTTAAAAG
*
1055529 GGTGTTATTTTCATAGATATTTTTAAAAG
1 GGTGTTATTTTCATAAATATTTTTAAAAG
* * *
1055558 GGTATTAGTTTCGTAAATATTTTTAAAA
1 GGTGTTATTTTCATAAATATTTTTAAAA
1055586 AAGGGTTTGA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
28 1 0.01
29 75 0.99
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (29 bp):
GGTGTTATTTTCATAAATATTTTTAAAAG
Found at i:1056306 original size:2 final size:2
Alignment explanation
Indices: 1056299--1056330 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1056289 AACTGGTTTG
1056299 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
1056331 TCACTGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1062932 original size:36 final size:36
Alignment explanation
Indices: 1062892--1062980 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
1062882 CCGAACCATA
** * * *
1062892 TTGACCCGACCTGACCCGTTGACCCTACTCGACCCG
1 TTGACCCGACCCCACCCGTTGACCCAACCCCACCCG
*
1062928 TTGACCCAACCCCACCCGTTGACCCAACCCCACCCG
1 TTGACCCGACCCCACCCGTTGACCCAACCCCACCCG
1062964 TTGA-CCGACCCCACCCG
1 TTGACCCGACCCCACCCG
1062981 ACCCGGGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 12 0.26
36 34 0.74
ACGTcount: A:0.19, C:0.51, G:0.16, T:0.15
Consensus pattern (36 bp):
TTGACCCGACCCCACCCGTTGACCCAACCCCACCCG
Found at i:1062976 original size:17 final size:18
Alignment explanation
Indices: 1062905--1062980 Score: 109
Period size: 18 Copynumber: 4.3 Consensus size: 18
1062895 ACCCGACCTG
* * *
1062905 ACCCGTTGACCCTACTCG
1 ACCCGTTGACCCAACCCC
1062923 ACCCGTTGACCCAACCCC
1 ACCCGTTGACCCAACCCC
1062941 ACCCGTTGACCCAACCCC
1 ACCCGTTGACCCAACCCC
*
1062959 ACCCGTTGA-CCGACCCC
1 ACCCGTTGACCCAACCCC
1062976 ACCCG
1 ACCCG
1062981 ACCCGGGTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
17 12 0.22
18 42 0.78
ACGTcount: A:0.20, C:0.53, G:0.14, T:0.13
Consensus pattern (18 bp):
ACCCGTTGACCCAACCCC
Found at i:1063045 original size:28 final size:29
Alignment explanation
Indices: 1062984--1063132 Score: 128
Period size: 29 Copynumber: 5.0 Consensus size: 29
1062974 CCACCCGACC
* *
1062984 CGGGTGCTATTTTTGTAAATATTTTTAAA
1 CGGGTTCTATTTTCGTAAATATTTTTAAA
*
1063013 CGGGTTCTATTTTCGTATATATTTTTAAA
1 CGGGTTCTATTTTCGTAAATATTTTTAAA
1063042 -GGGTGT-TATTTTCGTAAATATTTTTAAGA
1 CGGGT-TCTATTTTCGTAAATATTTTTAA-A
* *
1063071 TGGTGTTGTGTTATTTTCGTAAATATTTTTAAGA
1 CGG-G-T-T-CTATTTTCGTAAATATTTTTAA-A
*
1063105 -GGGTGT-TAGTTTT-ATAAATATTTTTAAA
1 CGGGT-TCTA-TTTTCGTAAATATTTTTAAA
1063133 AAATGGTTTT
Statistics
Matches: 107, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
28 25 0.23
29 43 0.40
30 6 0.06
31 4 0.04
32 4 0.04
33 2 0.02
34 23 0.21
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (29 bp):
CGGGTTCTATTTTCGTAAATATTTTTAAA
Found at i:1063087 original size:34 final size:34
Alignment explanation
Indices: 1063044--1063111 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1063034 TTTTTAAAGG
*
1063044 GTGTTATTTTCGTAAATATTTTTAAGATGGTGTT
1 GTGTTATTTTCGTAAATATTTTTAAGAGGGTGTT
1063078 GTGTTATTTTCGTAAATATTTTTAAGAGGGTGTT
1 GTGTTATTTTCGTAAATATTTTTAAGAGGGTGTT
1063112 AGTTTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (34 bp):
GTGTTATTTTCGTAAATATTTTTAAGAGGGTGTT
Found at i:1063309 original size:20 final size:20
Alignment explanation
Indices: 1063284--1063335 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1063274 ATTCTGACAT
1063284 TTTTCGAAGTCCTAACTTCG
1 TTTTCGAAGTCCTAACTTCG
1063304 TTTTCGAAGTCCTAACTTCG
1 TTTTCGAAGTCCTAACTTCG
1063324 TTTTCGAAGTCC
1 TTTTCGAAGTCC
1063336 GTTTCGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTTCGAAGTCCTAACTTCG
Found at i:1077144 original size:81 final size:81
Alignment explanation
Indices: 1077050--1077381 Score: 423
Period size: 81 Copynumber: 4.1 Consensus size: 81
1077040 TAGCCTTTAG
* ** ** * * *
1077050 TCTTTTA-TCCAAAGGCATTTAGTCTTTCATCTAACTTACATTATTGGCACCTTTCTGCCAAATG
1 TCTTTTACT-CAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATG
* *
1077114 CAAAACTAGACTATTAA
65 CACAACTAGGCTATTAA
* *
1077131 TCTTTTACGCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1077196 ACAACTAGGCTATTAA
66 ACAACTAGGCTATTAA
* * * *
1077212 TCTTTTACTAAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1077277 ACAGCTAGGCTATTAA
66 ACAACTAGGCTATTAA
** * * *
1077293 TCTTTTACTCAAATATATTTAACCTTTCATCTTACTGGCATAATTGGCACCTTTCTGTGAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
** *
1077358 ACGTCTAGCCTATTAA
66 ACAACTAGGCTATTAA
1077374 TCTTTTAC
1 TCTTTTAC
1077382 ATTAAAGAAT
Statistics
Matches: 219, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 219 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAACTAGGCTATTAA
Found at i:1077826 original size:22 final size:22
Alignment explanation
Indices: 1077798--1077839 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1077788 CTTACCATGC
1077798 TATCGATAATTCTATACTATGG
1 TATCGATAATTCTATACTATGG
1077820 TATCGATAATTCTATACTAT
1 TATCGATAATTCTATACTAT
1077840 ATTATCGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATCGATAATTCTATACTATGG
Found at i:1077845 original size:22 final size:22
Alignment explanation
Indices: 1077798--1077846 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1077788 CTTACCATGC
*
1077798 TATCGATAATTCTATACTATGG
1 TATCGATAATTCTATACTATAG
*
1077820 TATCGATAATTCTATACTATAT
1 TATCGATAATTCTATACTATAG
1077842 TATCG
1 TATCG
1077847 CTAGCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATCGATAATTCTATACTATAG
Found at i:1082733 original size:15 final size:16
Alignment explanation
Indices: 1082703--1082735 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1082693 TAAAAGTGTT
*
1082703 TAAATTATATAAATAA
1 TAAATAATATAAATAA
1082719 TAAATAATA-AAATAA
1 TAAATAATATAAATAA
1082734 TA
1 TA
1082736 TATCGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATAATATAAATAA
Found at i:1097531 original size:31 final size:31
Alignment explanation
Indices: 1097493--1097567 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1097483 GGGGCCTATA
*
1097493 GGCCTACCCAAGAAAGTTCTCAAGGCCACAT
1 GGCCTACCCAAGAAAGATCTCAAGGCCACAT
* * *
1097524 GGCCTACCCAAGAATGATCTCAGGGCCGCAT
1 GGCCTACCCAAGAAAGATCTCAAGGCCACAT
* *
1097555 AGCCTACACAAGA
1 GGCCTACCCAAGA
1097568 GTCATATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (31 bp):
GGCCTACCCAAGAAAGATCTCAAGGCCACAT
Found at i:1102003 original size:3 final size:3
Alignment explanation
Indices: 1101997--1102083 Score: 74
Period size: 3 Copynumber: 29.0 Consensus size: 3
1101987 ATTTTTCTTT
*
1101997 TTA TTA TTA TTA TT- TTA TT- TGT- TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * *
1102040 CTA TTA -TA TTA TTA TTA TTTA TTT TTG TTAA CTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A -TTA TTA TTA TTA
1102084 CAAAACATGC
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
2 6 0.08
3 59 0.83
4 4 0.06
5 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1104754 original size:21 final size:22
Alignment explanation
Indices: 1104730--1104780 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
1104720 GTTTTCATAA
*
1104730 TATTTATTATATATTTTT-CTT
1 TATTTATTATAAATTTTTACTT
* *
1104751 TA-TTATTTTTAAATTTTTATTT
1 TATTTA-TTATAAATTTTTACTT
1104773 TATTTATT
1 TATTTATT
1104781 TTCAGGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 6 0.25
23 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTTATTATAAATTTTTACTT
Found at i:1106444 original size:21 final size:20
Alignment explanation
Indices: 1106420--1106463 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1106410 ATTTACATTG
1106420 TTGCA-TTTGCATCTTTGTATT
1 TTGCACTTTGCA--TTTGTATT
1106441 TTGCATCTTTGCATTTGTATT
1 TTGCA-CTTTGCATTTGTATT
1106462 TT
1 TT
1106464 TATGTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 15 0.71
23 6 0.29
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (20 bp):
TTGCACTTTGCATTTGTATT
Found at i:1106445 original size:15 final size:15
Alignment explanation
Indices: 1106420--1106456 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1106410 ATTTACATTG
1106420 TTGCA-TTTGCATCT
1 TTGCATTTTGCATCT
*
1106434 TTGTATTTTGCATCT
1 TTGCATTTTGCATCT
1106449 TTGCATTT
1 TTGCATTT
1106457 GTATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (15 bp):
TTGCATTTTGCATCT
Found at i:1114139 original size:54 final size:52
Alignment explanation
Indices: 1114047--1114149 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 52
1114037 ACCATAAATG
*
1114047 TGTGCAGAAGCCACAACTGAATAAATGTGTTGTCAAATGTTTTACGAACATC
1 TGTGCAGAAGCCACAACTGAATAAATGTATTGTCAAATGTTTTACGAACATC
1114099 TGTGCAGAAGCCAC-A-TGAAATGATGAATGTATTGTCAAATGTTTTACGAAC
1 TGTGCAGAAGCCACAACTG-AAT-A--AATGTATTGTCAAATGTTTTACGAAC
1114150 TAGTTATGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
50 2 0.04
51 4 0.09
52 15 0.33
54 25 0.54
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (52 bp):
TGTGCAGAAGCCACAACTGAATAAATGTATTGTCAAATGTTTTACGAACATC
Found at i:1115103 original size:113 final size:113
Alignment explanation
Indices: 1114905--1115357 Score: 450
Period size: 113 Copynumber: 3.9 Consensus size: 113
1114895 TAGCAAAGAT
* *
1114905 TTGAATCCATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
* *
1114970 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTATTCAACATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
*
1115018 TTGAATTCATCACTCGATGGATCAACATTGCCAGGTAGTGTTCGTAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
* * * *
1115083 AGAAGGGAGAATAACTTCATAATGAA-AAGAACTTGTTCAACCTTTTTC
66 AGAAGGAAGAAGAAGTTCATAAT-AAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * * *
1115131 TTTAAATCATCACTCGATGGATCATCTTTTTCTAGAG-AAAGTTCATAATGAGAAGAACTTATCT
1 TTGAATTCATCACTCGATGGATCAAC-ATTGCCAG-GTAGAGTTCGTAATGAGAAGAACTCATCT
* *
1115195 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
64 GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * * * *
1115244 ATG-ACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCA-GAAGTGGTCATAATAAGAA
1 TTGAATTC-ATCAC---------TCGAT--GGATCAACATTGCCAGGTAGAGTTCGTAATGAGAA
*
1115307 GAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATAAGAAGAATTTGTTCAA
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
1115358 TCCTGCTTTA
Statistics
Matches: 281, Mismatches: 41, Indels: 27
0.81 0.12 0.08
Matches are distributed among these distances:
112 4 0.01
113 167 0.59
114 34 0.12
115 1 0.00
121 1 0.00
122 60 0.21
123 8 0.03
124 6 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
TTGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
Found at i:1115725 original size:3 final size:3
Alignment explanation
Indices: 1115719--1115800 Score: 73
Period size: 3 Copynumber: 27.3 Consensus size: 3
1115709 TTTTTGTTTT
* *
1115719 TTA TTA TTA TTA TT- TTA TT- TGT- TTA TTA GTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
*
1115762 TTA -TA TTA TTA TTTA TTT TTA TTAA CTTA TTA TTA TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TT-A -TTA TTA TTA TTA T
1115801 AAAACAGGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
2 6 0.09
3 53 0.80
4 5 0.08
5 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1115783 original size:10 final size:11
Alignment explanation
Indices: 1115720--1115797 Score: 63
Period size: 11 Copynumber: 7.1 Consensus size: 11
1115710 TTTTGTTTTT
1115720 TATTATTATTA
1 TATTATTATTA
* *
1115731 TTTTATT-TGTT
1 TATTATTAT-TA
*
1115742 TATTAGTATTA
1 TATTATTATTA
*
1115753 TTATTACTATTA
1 -TATTATTATTA
1115765 TATTATTATT-
1 TATTATTATTA
*
1115775 TATTTTTATTA
1 TATTATTATTA
1115786 -ACTTATTATTA
1 TA-TTATTATTA
1115797 T
1 T
1115798 TATAAAACAG
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
10 11 0.21
11 30 0.58
12 11 0.21
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:1120602 original size:30 final size:30
Alignment explanation
Indices: 1120568--1120624 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1120558 CATTCAAAAG
1120568 ATGTATGATTCCATGTGATTTTATATACAT
1 ATGTATGATTCCATGTGATTTTATATACAT
1120598 ATGTATGATTCCATGTGATTTTATATA
1 ATGTATGATTCCATGTGATTTTATATA
1120625 TATGGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (30 bp):
ATGTATGATTCCATGTGATTTTATATACAT
Found at i:1123135 original size:27 final size:27
Alignment explanation
Indices: 1123103--1123173 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
1123093 TTATGTGAAG
*
1123103 ATTTATGGGACATTCAAGGAAATGTCG
1 ATTTATGGGACATTCAAGGAAATGTCA
* *
1123130 GTTTATGGGACATTCAAGGTAATGTCA
1 ATTTATGGGACATTCAAGGAAATGTCA
*
1123157 ATTTATGAGACATTCAA
1 ATTTATGGGACATTCAA
1123174 AGTCAGGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (27 bp):
ATTTATGGGACATTCAAGGAAATGTCA
Found at i:1126522 original size:15 final size:16
Alignment explanation
Indices: 1126492--1126524 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1126482 TAAAAGTGTT
*
1126492 TAAATTATAGAAATAA
1 TAAATAATAGAAATAA
1126508 TAAATAATA-AAATAA
1 TAAATAATAGAAATAA
1126523 TA
1 TA
1126525 TATCGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAATAATAGAAATAA
Found at i:1126673 original size:24 final size:24
Alignment explanation
Indices: 1126642--1126694 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1126632 GACAAAGAAA
*
1126642 AATAATGTGATTAAGCTACTTGTT
1 AATAATGTGATTAAGCTAATTGTT
1126666 AATAATGTGATTAAGCTAATTGTT
1 AATAATGTGATTAAGCTAATTGTT
*
1126690 GATAA
1 AATAA
1126695 AGACATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
AATAATGTGATTAAGCTAATTGTT
Found at i:1127687 original size:25 final size:25
Alignment explanation
Indices: 1127641--1127688 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1127631 GTATTGTTTT
* **
1127641 ATTAAATTGTTGTCTGGGATTGTGA
1 ATTAAATTGTTGACCAGGATTGTGA
*
1127666 ATTAAATTGTTGACCAGTATTGT
1 ATTAAATTGTTGACCAGGATTGT
1127689 TATTGATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (25 bp):
ATTAAATTGTTGACCAGGATTGTGA
Found at i:1130973 original size:3 final size:3
Alignment explanation
Indices: 1130965--1131012 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
1130955 ACATAGGAAC
*
1130965 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1131013 CTGTGCTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1132322 original size:11 final size:11
Alignment explanation
Indices: 1132306--1132330 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1132296 GAGTCCCATA
1132306 CTTGAATTGTG
1 CTTGAATTGTG
1132317 CTTGAATTGTG
1 CTTGAATTGTG
1132328 CTT
1 CTT
1132331 CAGAGAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (11 bp):
CTTGAATTGTG
Found at i:1135216 original size:60 final size:60
Alignment explanation
Indices: 1135139--1135252 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
1135129 ATCGAATGAT
* * ** * *
1135139 ATTTTGTAACTTTTAATAGTCGAAAGACTCAACAAAA-CAATATCCTATAGTTGAATTATC
1 ATTTTATAACTTCTAATAACCGAAAGACTCAA-AAAAGCAACATCCTATAATTGAATTATC
* *
1135199 ATTTTATAACTTCTAATAACCGAAGGACTCAAAAAAGTAACATCCTATAATTGA
1 ATTTTATAACTTCTAATAACCGAAAGACTCAAAAAAGCAACATCCTATAATTGA
1135253 GGGACCATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 4 0.09
60 41 0.91
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (60 bp):
ATTTTATAACTTCTAATAACCGAAAGACTCAAAAAAGCAACATCCTATAATTGAATTATC
Found at i:1149783 original size:17 final size:18
Alignment explanation
Indices: 1149755--1149798 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
1149745 GCACCCTATA
1149755 GGTTTAACCCCTTCAGGT
1 GGTTTAACCCCTTCAGGT
1149773 GGTTT-ACCCCTTCAGGT
1 GGTTTAACCCCTTCAGGT
*
1149790 GGTTCAACC
1 GGTTTAACC
1149799 AAAGTCCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.32
Consensus pattern (18 bp):
GGTTTAACCCCTTCAGGT
Found at i:1157528 original size:18 final size:18
Alignment explanation
Indices: 1157505--1157549 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1157495 GCACCCTATA
1157505 GGTTTAACCCCTAAAGGT
1 GGTTTAACCCCTAAAGGT
**
1157523 GGTTTAACCCCTTCAGGT
1 GGTTTAACCCCTAAAGGT
*
1157541 GGTTCAACC
1 GGTTTAACC
1157550 AAAGTCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (18 bp):
GGTTTAACCCCTAAAGGT
Found at i:1160675 original size:29 final size:29
Alignment explanation
Indices: 1160639--1160819 Score: 154
Period size: 29 Copynumber: 6.3 Consensus size: 29
1160629 CATTTTACAC
* * *
1160639 AAATAGCACCCATTTTAAAATAATTACCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
1160668 AAATAGCACCC-TTTTTAACTTAATTCCCA
1 AAATAGCACCCATTTTGAA-TTAATTCCCA
*
1160697 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
* * ** * *
1160726 GAATATCA-CTTTTTTGAA-AAATTACCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
* * *
1160753 AAATAGTACCTATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
****
1160782 AAATAGCA-CCAAAACGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
1160810 GAATAGCACC
1 AAATAGCACC
1160820 GGTCAACGGT
Statistics
Matches: 123, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
27 12 0.10
28 45 0.37
29 60 0.49
30 6 0.05
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAATTAATTCCCA
Found at i:1170331 original size:27 final size:27
Alignment explanation
Indices: 1170275--1170336 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1170265 GAAAGAACTG
* * **
1170275 AAATACCCTTGAACTCTAAAATGATTA
1 AAATACCCTTAAACTCTAAAATAACCA
*
1170302 AAATGCCCTTAAACTCTAAAATAACCA
1 AAATACCCTTAAACTCTAAAATAACCA
1170329 AAATACCC
1 AAATACCC
1170337 CAAGCTCGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (27 bp):
AAATACCCTTAAACTCTAAAATAACCA
Found at i:1171109 original size:39 final size:39
Alignment explanation
Indices: 1171063--1171156 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
1171053 ATGTTACGGC
*
1171063 TAGGGTAAGTTCTTACCGCAGACTCCTTTACTTTATGCA
1 TAGGGTAAGTTCTTACCGCAGACTCCATTACTTTATGCA
* * * *
1171102 TAGGGTAAGTCCTTATCGCAGACTCCATTGCTTTGTGCA
1 TAGGGTAAGTTCTTACCGCAGACTCCATTACTTTATGCA
1171141 TAGGGTAAGTTCTTAC
1 TAGGGTAAGTTCTTAC
1171157 GATAAGCTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (39 bp):
TAGGGTAAGTTCTTACCGCAGACTCCATTACTTTATGCA
Found at i:1171261 original size:39 final size:39
Alignment explanation
Indices: 1171165--1171263 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 39
1171155 ACGATAAGCT
1171165 CATTTG-CTTCGTGCATAGGGGAAAACCTTACCGCATGCC
1 CATTTGCCTT-GTGCATAGGGGAAAACCTTACCGCATGCC
* * ** * *
1171204 CATTTTGCATCGTGCATAGGGGAAAATTTTACCGTATGTTC
1 CA-TTTGCCTTGTGCATAGGGGAAAACCTTACCGCATG-CC
1171245 C-TTTGCCTTGTGCATAGGG
1 CATTTGCCTTGTGCATAGGG
1171264 AAATTTGTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
39 18 0.37
40 28 0.57
41 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (39 bp):
CATTTGCCTTGTGCATAGGGGAAAACCTTACCGCATGCC
Found at i:1173213 original size:39 final size:39
Alignment explanation
Indices: 1173159--1173257 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 39
1173149 AACTCTCCAT
* *
1173159 CTTCCAAGA-ACTCTTAAATTCACAATAAATCACTCTAA
1 CTTCCAAGAGAATCTTAAATTCACAATAAAACACTCTAA
*
1173197 C-TCCTAAGAGAATCTTAATTTCACAATAAAACACTCTAA
1 CTTCC-AAGAGAATCTTAAATTCACAATAAAACACTCTAA
* *
1173236 CTTCCAATAGACTCTTAAATTC
1 CTTCCAAGAGAATCTTAAATTC
1173258 CCCCTTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
37 3 0.06
38 5 0.10
39 41 0.79
40 3 0.06
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.30
Consensus pattern (39 bp):
CTTCCAAGAGAATCTTAAATTCACAATAAAACACTCTAA
Found at i:1180942 original size:24 final size:24
Alignment explanation
Indices: 1180915--1180973 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1180905 ATCTAATTTT
* *
1180915 TGTTCTTATTTCTGATATGAATTC
1 TGTTCTGATTTCTGATATGAATTA
* * *
1180939 TGTTATGATTTCTGATCTGGATTA
1 TGTTCTGATTTCTGATATGAATTA
1180963 TGTTCTGATTT
1 TGTTCTGATTT
1180974 ATACTCTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (24 bp):
TGTTCTGATTTCTGATATGAATTA
Found at i:1182312 original size:98 final size:98
Alignment explanation
Indices: 1182143--1182338 Score: 311
Period size: 98 Copynumber: 2.0 Consensus size: 98
1182133 ATTCTATAAT
** **
1182143 AAGTATACCAAAGTATCTTATCTGTTATGACTCAATCTGTGCAAAAAAAAGAATTTTGTCAGTAT
1 AAGTATACCAAAGTATCTTATCAATTATGACTCAATCTGTGCAAAAAAAAGAATAATGTCAGTAT
*
1182208 TCGTCCCAATTTTGGAAGTTACCCTGCGAGTAA
66 TCGTCCCAATTTTGGAAGTTACCCCGCGAGTAA
* ** *
1182241 AAGTATACCAAAGTATCTTATCAATTATGATTCAATCTGTGCAAAAAAGGGAATAATGTCAGTTT
1 AAGTATACCAAAGTATCTTATCAATTATGACTCAATCTGTGCAAAAAAAAGAATAATGTCAGTAT
1182306 TCGTCCCAATTTTGGAAGTTACCCCGCGAGTAA
66 TCGTCCCAATTTTGGAAGTTACCCCGCGAGTAA
1182339 TGTGGGAGAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (98 bp):
AAGTATACCAAAGTATCTTATCAATTATGACTCAATCTGTGCAAAAAAAAGAATAATGTCAGTAT
TCGTCCCAATTTTGGAAGTTACCCCGCGAGTAA
Found at i:1190743 original size:84 final size:85
Alignment explanation
Indices: 1190617--1190771 Score: 208
Period size: 84 Copynumber: 1.8 Consensus size: 85
1190607 ATCTTTGTAT
**
1190617 TTTAGTTTAAATAAGTTTTAGTATTTCAATTAGGATTTAAGATATTATTTTAA-ATAGTAT-TTT
1 TTTAGTTTAAATAAGTTTTAGTATTTCAATTAGGATAAAAGATATTATTTTAAGA-AGTATATTT
1190680 AGCTTATCTTTGTTTTAGGTA
65 AGCTTATCTTTGTTTTAGGTA
* ** * *
1190701 TTTAGTTTAAAT-AGTTTTAAGTGTTTTTATTCGGATAAAAGATATTATTTTAAGAATTATATTT
1 TTTAGTTTAAATAAGTTTT-AGTATTTCAATTAGGATAAAAGATATTATTTTAAGAAGTATATTT
1190765 AGCTTAT
65 AGCTTAT
1190772 TTTTAGGATT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
83 6 0.10
84 44 0.72
85 11 0.18
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (85 bp):
TTTAGTTTAAATAAGTTTTAGTATTTCAATTAGGATAAAAGATATTATTTTAAGAAGTATATTTA
GCTTATCTTTGTTTTAGGTA
Found at i:1192935 original size:28 final size:28
Alignment explanation
Indices: 1192856--1192944 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
1192846 AACCAAGACC
1192856 TCATTTTCAACAGCAAACGCAAAAATCA
1 TCATTTTCAACAGCAAACGCAAAAATCA
*** * * *
1192884 TCATTGGAGGAAC-TCATA-GGAAAAATCA
1 TCATT--TTCAACAGCAAACGCAAAAATCA
1192912 TCATTTTCAACAGCAAACGCAAAAATCA
1 TCATTTTCAACAGCAAACGCAAAAATCA
1192940 TCATT
1 TCATT
1192945 GCATCCCAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 33 0.73
29 3 0.07
30 3 0.07
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (28 bp):
TCATTTTCAACAGCAAACGCAAAAATCA
Found at i:1213619 original size:17 final size:15
Alignment explanation
Indices: 1213579--1213624 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
1213569 GAATCACATG
1213579 AAATATAAAAGAA-T
1 AAATATAAAAGAATT
*
1213593 AAACATAAAAGAATCT
1 AAATATAAAAGAAT-T
1213609 AAAATATAAAAGAATT
1 -AAATATAAAAGAATT
1213625 TGAGAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (15 bp):
AAATATAAAAGAATT
Found at i:1214845 original size:37 final size:38
Alignment explanation
Indices: 1214803--1214876 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
1214793 ATTTAAGAGC
1214803 CTCTTGGGAGTTAGA-ATGTTATTGTGAAATTAAGATT
1 CTCTTGGGAGTTAGATATGTTATTGTGAAATTAAGATT
* *
1214840 CTCTTGGGAGTTAGATTATTTTATTGTGAATTTAAGA
1 CTCTTGGGAGTTAGA-TATGTTATTGTGAAATTAAGA
1214877 GTTATTGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 15 0.45
39 18 0.55
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.43
Consensus pattern (38 bp):
CTCTTGGGAGTTAGATATGTTATTGTGAAATTAAGATT
Found at i:1214875 original size:39 final size:37
Alignment explanation
Indices: 1214791--1214877 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
1214781 TTAATGGGGG
1214791 GAATTTAAGAGCCTCTTGGGAGTTAGAATGTTATTGT
1 GAATTTAAGAGCCTCTTGGGAGTTAGAATGTTATTGT
* ** *
1214828 GAAATTAAGATTCTCTTGGGAGTTAGATTATTTTATTGT
1 GAATTTAAGAGCCTCTTGGGAGTTAGA--ATGTTATTGT
1214867 GAATTTAAGAG
1 GAATTTAAGAG
1214878 TTATTGGAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 24 0.57
39 18 0.43
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (37 bp):
GAATTTAAGAGCCTCTTGGGAGTTAGAATGTTATTGT
Found at i:1217354 original size:26 final size:26
Alignment explanation
Indices: 1217318--1217375 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
1217308 CACTTATCCT
1217318 AAAACGCGGTTCTCCCCCTGCTCATC
1 AAAACGCGGTTCTCCCCCTGCTCATC
1217344 AAAACGCGGTTCTCCCCCTGCTCATC
1 AAAACGCGGTTCTCCCCCTGCTCATC
1217370 AAAACG
1 AAAACG
1217376 TTGTCGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.21
Consensus pattern (26 bp):
AAAACGCGGTTCTCCCCCTGCTCATC
Found at i:1218076 original size:2 final size:2
Alignment explanation
Indices: 1218069--1218148 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1218059 ATAGCTGATG
1218069 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
1218111 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
1218149 TGTTTCTCAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1219252 original size:55 final size:54
Alignment explanation
Indices: 1218805--1219571 Score: 447
Period size: 55 Copynumber: 14.1 Consensus size: 54
1218795 ATTTGATAAG
* * * *
1218805 AATCTTCCACAAATGGGTTTGCTCCCTATTTCTTTCAGGTAGTATAGAACTCGAAT
1 AATCTTCTA-AAATGGGTTCGCTCCCTATTTCTTT-AGGGAGTATAGAACTCGAAC
** * * *
1218861 AATCTTCTAGGGACGGGTTCGCTCCCTATTTCTTTCAGGCAGTATAGAACTCGAAT
1 AATCTTCTA-AAATGGGTTCGCTCCCTATTTCTTT-AGGGAGTATAGAACTCGAAC
* * * * * * * *
1218917 AATCTT-GAACAATCGCG-TCTGCTCTCTATTCCTTCAGAGAGTATA-AGTCTTGAAC
1 AATCTTCTAA-AAT-GGGTTC-GCTCCCTATTTCTTTAGGGAGTATAGA-ACTCGAAC
** * *
1218972 AATCTTC-AATAATCATGTAT-GCTCCCTATTTCTTCAGAGAGTAT-GAGACTCGAAC
1 AATCTTCTAA-AAT-GGGT-TCGCTCCCTATTTCTTTAGGGAGTATAGA-ACTCGAAC
* * *
1219027 AATCTTC-AATAAT-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAAC
1 AATCTTCTAA-AATGGGT-TC-GCTCCCTATTTCTTTAGGGAGTATAGA-ACTCGAAC
* * *
1219082 AATCTTC-AATAAT-CGTATCTGCTCCCTATTTCTTCA--GAGTATA-AGAGTCGAAC
1 AATCTTCTAA-AATGGGT-TC-GCTCCCTATTTCTTTAGGGAGTATAGA-ACTCGAAC
* * * * *
1219135 AATCTT-TAACAAT-CGTGTCTACTCCCTATTTCTTCAGAGAGTCTA-AGACTCGAAC
1 AATCTTCTAA-AATGGGT-TC-GCTCCCTATTTCTTTAGGGAGTATAGA-ACTCGAAC
* *
1219190 AATCTTCTGAAAATGGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGAACTCGAAC
1 AATCTTCT-AAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
* * * *
1219245 AATCTTCTGCAAACGGGTTCGCTCCCTCTTTATTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCT-AAAATGGGTTCGCTCCCTATTTCTTT-AGGGAGTATAGAACTCGAAC
* * *
1219301 -ATCTTC--AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-GAAACTCAAAC
1 AATCTTCTAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAG-AACTCGAAC
* * * *
1219352 -ATCTTCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCAAAC
1 AATCTTC-TAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
*** * * * * * * *
1219406 -ATCTTCTTCTTACGGGTTTGGTCCCTCTTTCTTTAGGGAGTATAGAATTTGAGC
1 AATCTTC-TAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
* * * *
1219460 -ATCTTC--AAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAC
1 AATCTTCTAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
*** * * * * * *
1219511 -ATCTTCTTCTTACGAGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAC
1 AATCTTC-TAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
1219565 -ATCTTCT
1 AATCTTCT
1219572 TCTTAAGAGT
Statistics
Matches: 611, Mismatches: 73, Indels: 57
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.00
51 65 0.11
52 24 0.04
53 52 0.09
54 140 0.23
55 229 0.37
56 95 0.16
57 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (54 bp):
AATCTTCTAAAATGGGTTCGCTCCCTATTTCTTTAGGGAGTATAGAACTCGAAC
Found at i:1219271 original size:163 final size:161
Alignment explanation
Indices: 1218823--1219411 Score: 492
Period size: 163 Copynumber: 3.6 Consensus size: 161
1218813 ACAAATGGGT
* ** *
1218823 TTGCTCCCTATTTCTTTCAG-GTAGTAT-AGAACTCGAATAATCTTCTAGGGACGGGTTCGCTCC
1 TTGCTCCCTATTTC-TTCAGAG-AGTATAAG-ACTCGAACAATCTTCTA-AAATGGGTTCGCTCC
* * * * *
1218886 CTATTTCTTTCAGGCAGTATAGAACTCGAATAATCTTGAACAATCGCG-TCTGCTCTCTATTCCT
62 CTATTTCTTT-AGGAAGTATAGAACTCGAACAATCTTCAACAATCG-GTTCTGCTCCCTATTTCT
* * * * *
1218950 TCAGAGAGTATAAGTCTTGAACAATCTTCAATAATCATG
125 TC--AGAGTATAAGACTCGAACAATCTTTAACAATCGTG
* *
1218989 TATGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC-AATAAT-CGTGTCTGCTCC
1 T-TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCTAA-AATGGGT-TC-GCTCC
* *
1219052 CTATTTCTTCA-GAGAGTATA-AGACTCGAACAATCTTCAATAATC-GTATCTGCTCCCTATTTC
62 CTATTTCTTTAGGA-AGTATAGA-ACTCGAACAATCTTCAACAATCGGT-TCTGCTCCCTATTTC
*
1219114 TTCAGAGTATAAGAGTCGAACAATCTTTAACAATCGTG
124 TTCAGAGTATAAGACTCGAACAATCTTTAACAATCGTG
* *
1219152 TCTACTCCCTATTTCTTCAGAGAGTCTAAGACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCT
1 T-TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCT-AAAATGGGTTCGCTCCCT
* ** * * *
1219217 CTTTCTTTAGGAAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTC-GCTCCCTCTTTATTTC
64 ATTTCTTTAGGAAGTATAGAACTCGAACAATCTTCAACAATC-GGTTCTGCTCCCTATTT-CTTC
* *
1219281 AGGGAGTAT-AGAACTCGAAC-ATC-TT--CAAACGGG
127 A--GAGTATAAG-ACTCGAACAATCTTTAACAATCGTG
* * * * *
1219314 TTCGCTCCCTCTTTCTTTAGGGAGTATGAA-ACTCAAAC-ATCTTCTTCAAATGGGTTCGCTCCC
1 TT-GCTCCCTATTTCTTCAGAGAGTAT-AAGACTCGAACAATCTTC-TAAAATGGGTTCGCTCCC
* * * *
1219377 TCTTTCTTTAGGGAGTATGGAACTCAAAC-ATCTTC
63 TATTTCTTTAGGAAGTATAGAACTCGAACAATCTTC
1219412 TTCTTACGGG
Statistics
Matches: 355, Mismatches: 44, Indels: 54
0.78 0.10 0.12
Matches are distributed among these distances:
160 6 0.02
161 49 0.14
162 34 0.10
163 121 0.34
164 20 0.06
165 57 0.16
166 52 0.15
167 16 0.05
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (161 bp):
TTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCTAAAATGGGTTCGCTCCCTAT
TTCTTTAGGAAGTATAGAACTCGAACAATCTTCAACAATCGGTTCTGCTCCCTATTTCTTCAGAG
TATAAGACTCGAACAATCTTTAACAATCGTG
Found at i:1219478 original size:105 final size:105
Alignment explanation
Indices: 1219204--1219570 Score: 463
Period size: 105 Copynumber: 3.4 Consensus size: 105
1219194 TTCTGAAAAT
*
1219204 GGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATC-T-T-CAAACGGGTTCGCTC
* * **
1219269 CCTCTTTATTTCAGGGAGTATAGAACTCGAACA---TCTTCAAAC
62 CCTCTTTCTTT-AGGGAGTATGGAACTCGAACATCTTCTTCTTAC
* *
1219311 GGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-GAAACTCAAACATCTTCTTCAAATGGGTTCGCTC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAG-AACTCGAACA---TCTTCAAACGGGTTCGCTC
*
1219375 CCTCTTTCTTTAGGGAGTATGGAACTCAAACATCTTCTTCTTAC
62 CCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTAC
* * * * *
1219419 GGGTTTGGTCCCTCTTTCTTTAGGGAGTATAGAATTTGAGCATCTTCAAACGGGTTCGCTCCCTC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTC
*
1219484 TTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTAC
66 TTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTAC
* * * *
1219524 GAGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTC
1219571 TTCTTAAGAG
Statistics
Matches: 226, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
105 117 0.52
106 26 0.12
107 38 0.17
108 42 0.19
109 3 0.01
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (105 bp):
GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTC
TTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTAC
Found at i:1219482 original size:159 final size:160
Alignment explanation
Indices: 1219156--1219576 Score: 558
Period size: 159 Copynumber: 2.6 Consensus size: 160
1219146 ATCGTGTCTA
* * * * **
1219156 CTCCCTATTTCTTCAGAGAGTCT-AAGACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTT
1 CTCCCTCTTTCTTTAGGGAGTATGAA-ACTCGAAC-ATCTTCTTCAAATGGGTTCGCTCCCTCTT
* * * **
1219220 TCTTTAGGAAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTATTTCAGGG
64 TCTTTAGGGAGTATGGAACTCGAAC-ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATTTCAGGG
1219285 AGTATAGAACTCGAACATCTTCAAACGGGTTCG
128 AGTATAGAACTCGAACATCTTCAAACGGGTTCG
*
1219318 CTCCCTCTTTCTTTAGGGAGTATGAAACTCAAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTC
1 CTCCCTCTTTCTTTAGGGAGTATGAAACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTC
* * * *
1219383 TTTAGGGAGTATGGAACTCAAACATCTTCTTCTTACGGGTTTGGTCCCTCTTTCTTT-AGGGAGT
66 TTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTATTTCAGGGAGT
* * *
1219447 ATAGAATTTGAGCATCTTCAAACGGGTTCG
131 ATAGAACTCGAACATCTTCAAACGGGTTCG
* * ** * * *
1219477 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGAGTTCACTCCCTCTTTC
1 CTCCCTCTTTCTTTAGGGAGTATGAAACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTC
*
1219542 TCTAGGGAGTATGGAACTCGAACATCTTCTTCTTA
66 TTTAGGGAGTATGGAACTCGAACATCTTCTTCTTA
1219577 AGAGTTTGTA
Statistics
Matches: 229, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
159 124 0.54
160 28 0.12
161 49 0.21
162 26 0.11
163 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (160 bp):
CTCCCTCTTTCTTTAGGGAGTATGAAACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTC
TTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTATTTCAGGGAGT
ATAGAACTCGAACATCTTCAAACGGGTTCG
Found at i:1219582 original size:54 final size:54
Alignment explanation
Indices: 1219182--1219573 Score: 481
Period size: 54 Copynumber: 7.3 Consensus size: 54
1219172 AGAGTCTAAG
** * * *
1219182 ACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTTCTTTAGGAAGTATAGA
1 ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
1219237 ACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTCTTTATTTCAGGGAGTATAGA
1 ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTT-AGGGAGTATGGA
*
1219293 ACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* *
1219344 ACTCAAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* ** * * *
1219398 ACTCAAACATCTTCTTCTTACGGGTTTGGTCCCTCTTTCTTTAGGGAGTATAGA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * *
1219452 ATTTGAGCA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
** * * *
1219503 ACTCGAACATCTTCTTCTTACGAGTTCACTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
1219557 ACTCGAACATCTTCTTC
1 ACTCGAACATCTTCTTC
1219574 TTAAGAGTTT
Statistics
Matches: 296, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
51 60 0.20
52 28 0.09
54 148 0.50
55 41 0.14
56 19 0.06
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (54 bp):
ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
Found at i:1224184 original size:27 final size:27
Alignment explanation
Indices: 1224125--1224207 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
1224115 GCCCAATGGC
* * *
1224125 ATTTCGGTCATTTTAGAG-CTCAGGGT
1 ATTTTGGTCATTTTAGAGTTTAAGGGT
1224151 ATTTTGGTCATTTTAGAGTTTAAGGGT
1 ATTTTGGTCATTTTAGAGTTTAAGGGT
1224178 ATTTTGGTCATTTTAGAGTTTAA-GGT
1 ATTTTGGTCATTTTAGAGTTTAAGGGT
1224204 ATTT
1 ATTT
1224208 CAATCCTTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
26 24 0.45
27 29 0.55
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (27 bp):
ATTTTGGTCATTTTAGAGTTTAAGGGT
Found at i:1224926 original size:14 final size:14
Alignment explanation
Indices: 1224909--1224936 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1224899 TACATTTCCG
1224909 GAAAACATTTTACA
1 GAAAACATTTTACA
1224923 GAAAACATTTTACA
1 GAAAACATTTTACA
1224937 TTGTTTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GAAAACATTTTACA
Found at i:1225170 original size:25 final size:25
Alignment explanation
Indices: 1225142--1225199 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1225132 ATATTAGAAC
* *
1225142 AACATTGATAAAATGATATTATCCA
1 AACAGTGAGAAAATGATATTATCCA
1225167 AACAGTGAGAAAATGATATTATCCA
1 AACAGTGAGAAAATGATATTATCCA
1225192 AACAGTGA
1 AACAGTGA
1225200 AACAATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (25 bp):
AACAGTGAGAAAATGATATTATCCA
Found at i:1227961 original size:19 final size:19
Alignment explanation
Indices: 1227939--1227976 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1227929 CTTATTTGGC
*
1227939 ATTTGGGTTAAGTTATTTT
1 ATTTGGGTTAAGATATTTT
*
1227958 ATTTGGTTTAAGATATTTT
1 ATTTGGGTTAAGATATTTT
1227977 TATCTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (19 bp):
ATTTGGGTTAAGATATTTT
Found at i:1235664 original size:22 final size:23
Alignment explanation
Indices: 1235628--1235673 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
1235618 TTTACAAATC
1235628 TAAACCCCAAACATATTAAACGG
1 TAAACCCCAAACATATTAAACGG
*
1235651 TAAA-CCCAAGCATATTAAACGG
1 TAAACCCCAAACATATTAAACGG
1235673 T
1 T
1235674 CGTGTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.20
Consensus pattern (23 bp):
TAAACCCCAAACATATTAAACGG
Found at i:1239124 original size:19 final size:19
Alignment explanation
Indices: 1239086--1239125 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1239076 ACAATATATG
* *
1239086 TTATAACTATAATTAAAAT
1 TTATAAATATAAGTAAAAT
*
1239105 TTATAAATATAAGTATAAT
1 TTATAAATATAAGTAAAAT
1239124 TT
1 TT
1239126 CTCACAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TTATAAATATAAGTAAAAT
Found at i:1239644 original size:416 final size:413
Alignment explanation
Indices: 1238849--1239693 Score: 1107
Period size: 416 Copynumber: 2.0 Consensus size: 413
1238839 TATAAAACTT
* * * *
1238849 TTACTATATAACATTTTTGACACCAAAAAATAGGGATAAATTTTTTTATAGTATAATTTTTCATA
1 TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAATGTTCTGATAGTATAATTTTTCATA
1238914 ATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATGTGATGT
66 ATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATGTGATGT
* *
1238979 GATAATTTTTTCTAGAACAATAACTATAAATTATAATTACAAAACTTATCAATATAGCTTTTTGA
131 GATAATTTTTTCT-----AATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTG-
* *
1239044 AACAAAAAAAAAAGTGGAGAAAAATATTTATCACAATATATGTTATAACTATAATTAAAATTTAT
190 -A-AAAAAAAAAAGTGGAGAAAAATAGTTATCACAATATATGCTATAACTATAATTAAAATTTAT
* * * *
1239109 AAATATAAGTATAATTTCTCACAAAAATGTGAATACCATTATTTTTTGTGACAATGTTTTTTGTA
253 AAATACAAATATAATTTCTCACAAAAATGTGAATACAATTATTTTTTGTAACAATGTTTTTTGTA
*
1239174 ATAATTTTAAACACTTATAGTTAAAAAAATTGTTACTATATGATTTTGTTGGTGCAAAAAAATAT
318 ATAATTTTAAACACTTATAGTTAAAAAAATTGTTACCATATGATTTTGTTGGTGCAAAAAAATAT
1239239 GGAGGAAAATCTGTATGACAATATA-TTTTG
383 GGAGGAAAATCTGTATGACAATATATTTTTG
* ***
1239269 TTACTATATAGCATTTTTGACTTTAAAAAATAGGGAGAAATGGTTCTGATAGTATAATTTTTCAT
1 TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAAT-GTTCTGATAGTATAATTTTTCAT
* *
1239334 AATGATTAAAATATATATAAGTACAAAAATAATCT-ATTACAAAAAAACTTGAATTTTATTATTT
65 AATGATT-AAA-ATATATAACTACAAAAATAAT-TGATTAC-AAAAAACTTGAATTTTATTATGT
*
1239398 GATGTGATAATTTTTTCT-ATAACTATAAATTATAATTATAAAAATTATCAATATAAC-TTTTG-
126 GATGTGATAATTTTTTCTAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGA
* * * * *
1239460 AAATAAAAAAGTGGAG-AAAATAGTTATGACAATTAATATATGCTATCACTATAGTTAGAATTTA
191 AAAAAAAAAAGTGGAGAAAAATAGTTAT--C-A-CAATATATGCTATAACTATAATTAAAATTTA
* *
1239524 TAACTACAAATATAA-TTCGTCACAAAAATGTGAATATAATTATTTTTTGTAACAATGTTTTTTG
252 TAAATACAAATATAATTTC-TCACAAAAATGTGAATACAATTATTTTTTGTAACAATGTTTTTTG
* * * * *
1239588 TAATAATTATT-AACATTTATAGTT-ACAAACTTTTTCACCATATTACTTTT-TTGGTGCAAAAA
316 TAATAATT-TTAAACACTTATAGTTAAAAAAATTGTT-ACCATATGA-TTTTGTTGGTGCAAAAA
* * *
1239650 AATATGGAGGGAAATCTTTGTGACAATATATTTTTG
378 AATATGGAGGAAAATCTGTATGACAATATATTTTTG
*
1239686 TCACTATA
1 TTACTATA
1239694 ATTAAAACAT
Statistics
Matches: 375, Mismatches: 36, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
412 10 0.03
413 15 0.04
414 1 0.00
415 12 0.03
416 146 0.39
417 23 0.06
418 36 0.10
420 36 0.10
421 27 0.07
422 3 0.01
423 25 0.07
424 41 0.11
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (413 bp):
TTACTATATAACATTTTTGACACCAAAAAATAGGGAGAAATGTTCTGATAGTATAATTTTTCATA
ATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTGAATTTTATTATGTGATGT
GATAATTTTTTCTAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGAAAAAA
AAAAAGTGGAGAAAAATAGTTATCACAATATATGCTATAACTATAATTAAAATTTATAAATACAA
ATATAATTTCTCACAAAAATGTGAATACAATTATTTTTTGTAACAATGTTTTTTGTAATAATTTT
AAACACTTATAGTTAAAAAAATTGTTACCATATGATTTTGTTGGTGCAAAAAAATATGGAGGAAA
ATCTGTATGACAATATATTTTTG
Found at i:1240205 original size:15 final size:15
Alignment explanation
Indices: 1240185--1240219 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1240175 CCAAAAAGCT
1240185 ATTAATAGTGACAAA
1 ATTAATAGTGACAAA
**
1240200 ATTAATTTTGACAAA
1 ATTAATAGTGACAAA
1240215 ATTAA
1 ATTAA
1240220 ATTTATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (15 bp):
ATTAATAGTGACAAA
Found at i:1240933 original size:2 final size:2
Alignment explanation
Indices: 1240926--1240988 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1240916 TTTTTAAAAC
1240926 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
1240968 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1240989 CCCCCATCCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1241101 original size:35 final size:35
Alignment explanation
Indices: 1241050--1241124 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
1241040 CATCACGAAC
*
1241050 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
*
1241085 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
1241120 AGTAA
1 AGTAA
1241125 TCTTCCACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.28, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
Found at i:1241234 original size:24 final size:23
Alignment explanation
Indices: 1241206--1241301 Score: 102
Period size: 24 Copynumber: 4.1 Consensus size: 23
1241196 ATTCAAGTCA
1241206 AGTATCATATCAGAATCCAGATC
1 AGTATCATATCAGAATCCAGATC
* *
1241229 ATGTATCATATCATAATCCATATC
1 A-GTATCATATCAGAATCCAGATC
* * *
1241253 AATATCAGATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGATC
* * *
1241276 AGGTATCATAACAGAATTCAAATC
1 A-GTATCATATCAGAATCCAGATC
1241300 AG
1 AG
1241302 AAATCAGATA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
23 20 0.34
24 38 0.66
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGATC
Found at i:1245309 original size:26 final size:27
Alignment explanation
Indices: 1245275--1245328 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1245265 TTATAAAATT
*
1245275 ATTTATCAGTATAAAAAAGTAAAACAA
1 ATTTATCAGAATAAAAAAGTAAAACAA
* * *
1245302 ATTT-TCAGAATCAAATATTAAAACAA
1 ATTTATCAGAATAAAAAAGTAAAACAA
1245328 A
1 A
1245329 ATACAATTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (27 bp):
ATTTATCAGAATAAAAAAGTAAAACAA
Found at i:1245929 original size:24 final size:24
Alignment explanation
Indices: 1245902--1245992 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
1245892 CATAATTCAA
* *
1245902 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
1245926 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
1245950 GTCAA-TATTAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * * *
1245973 GTTAGGTATCACAACAGAAT
1 GTCAAGTATCAGATCAGAAT
1245993 TCAAATCAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1251461 original size:508 final size:507
Alignment explanation
Indices: 1250243--1251772 Score: 2893
Period size: 508 Copynumber: 3.0 Consensus size: 507
1250233 ATTAATATTT
* * *
1250243 AAATAATATTTTTTATTAATTAATTTAAATTTAAATGATTATGATAATTATACATTATGTATATA
1 AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
* *
1250308 TAATTTTCATATATGATATACATATATCATGTAAAGTTGAAGTATTCGATTTAAACTTGAAAATC
66 TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
1250373 AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
131 AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
*
1250438 A-ATTTTTCAAGTCAAATTTATAAAATTACAAGTCAAACTAAATCTACTCGAAAGAATTTCAAAT
196 ATA-TTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAAT
1250502 AAAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAA
260 AAAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAA
1250567 TTTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATA
325 TTTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATA
*
1250632 TAAAAGTGTCCAAAGTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAAGTGAATAT
390 TAAAAGTGTCCAAATTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAAGTGAATAT
1250697 CTAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTT-AA
455 CTAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTTAAA
1250749 AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
1 AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
1250814 TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
66 TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
1250879 AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
131 AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
*
1250944 ATTTTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAATA
196 ATATTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAATA
*
1251009 AAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGGAAATTTAAATTTTTTAATCAAGTCAAAT
261 AAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAAT
1251074 TTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATAT
326 TTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATAT
*
1251139 AAAAAGTGTCCAAATTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCACTCAAAGTGAATAT
391 -AAAAGTGTCCAAATTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAAGTGAATAT
1251204 CTAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTTAAA
455 CTAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTTAAA
1251257 AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
1 AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
1251322 TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
66 TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
* *
1251387 AATATGCTAGATACTAAAATATTTGAGTTATTCAAATCCTAATTTACACTCAAATTTTATTTGAA
131 AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
1251452 ATATTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAATA
196 ATATTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAATA
1251517 AAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAAT
261 AAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAAT
1251582 TTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATAT
326 TTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATAT
* *
1251647 AAAAGTGTCCAAATTATATAATGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAATTGAATATC
391 AAAAGTGTCCAAATTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAAGTGAATATC
*
1251712 TAACGTCTCTAACGTTACATTTTTAAATATCTATGTTGTAAAGGTCGTTAAA
456 TAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTTAAA
1251764 AAATACTAT
1 AAATACTAT
1251773 GATCTAACAA
Statistics
Matches: 1003, Mismatches: 18, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
506 381 0.38
507 234 0.23
508 388 0.39
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (507 bp):
AAATACTATTGTTTATTAATTAATTTAAATTTAAATGATTATTATAATTATACATTATGTATATA
TATTTTTCATATATGATATACATATATCATGTAAAGTTGAAGGATTCGATTTAAACTTGAAAATC
AATCTGCTAGATACTAAAATATTTGAGTTATTCAAATCCTATTTTACACTCAAATTTTATTTGAA
ATATTTTCAAGTCAAATTTATAAAATTACAAGTCGAACTAAATCTACTCGAAAGAATTTCAAATA
AAGTTATAAAATTACGAGTCGAATCAAATCAAGTTGAAAATTTAAATTTTTTAATCAAGTCAAAT
TTTACTCTCTCATACATAATGAGGTTCCCCTTTCTTTTACATTTGACTTTTTTATGCCTTAATAT
AAAAGTGTCCAAATTATATAACGTTAACTTTAGGTGTCTAAATTTTTTCGCTCAAAGTGAATATC
TAACGTCTCTAACGTTACATTTTTAAATACCTATGTTGTAAAGGTCGTTAAA
Found at i:1252452 original size:16 final size:16
Alignment explanation
Indices: 1252431--1252463 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1252421 TTTTATTAAA
1252431 TCTAAAAACCCTAATT
1 TCTAAAAACCCTAATT
1252447 TCTAAAAACCCTAATT
1 TCTAAAAACCCTAATT
1252463 T
1 T
1252464 AAAATCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (16 bp):
TCTAAAAACCCTAATT
Found at i:1254581 original size:45 final size:46
Alignment explanation
Indices: 1254513--1254628 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
1254503 AAGAGTGCAC
* * * * * *
1254513 CGATGCATAAAATGCATTTGATGTTTTCA-AATAGCCTGAGTACAT
1 CGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTAAATACAT
*
1254558 CGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTAAATGCAT
1 CGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTAAATACAT
* *
1254604 CGATACGTCAAATGCATTCGATGTT
1 CGATGCATCAAATGCATTCGATGTT
1254629 CAATTAATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 27 0.44
46 34 0.56
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (46 bp):
CGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTAAATACAT
Found at i:1258210 original size:20 final size:20
Alignment explanation
Indices: 1258185--1258225 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1258175 ACATTCCCTC
1258185 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
1258205 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
1258225 T
1 T
1258226 ACATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:1258872 original size:15 final size:15
Alignment explanation
Indices: 1258842--1258906 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
1258832 GAGCAAGGAT
* *
1258842 AAAAGCAAACAGAAA
1 AAAAACAAAGAGAAA
* *
1258857 AAAGACAATGAGAAAA
1 AAAAACAAAGAG-AAA
1258873 AAAAACAAAGAGAAA
1 AAAAACAAAGAGAAA
1258888 AGAAAA-AAAGA-AAA
1 A-AAAACAAAGAGAAA
1258902 AAAAA
1 AAAAA
1258907 ATAAAAGCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.10
14 4 0.10
15 17 0.40
16 17 0.40
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAACAAAGAGAAA
Found at i:1258895 original size:18 final size:16
Alignment explanation
Indices: 1258854--1258907 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1258844 AAGCAAACAG
* *
1258854 AAAAAAGACAATGAGA
1 AAAAAAAACAAAGAGA
1258870 AAAAAAAACAAAGAGA
1 AAAAAAAACAAAGAGA
*
1258886 AAAGAAAA-AAAGA-A
1 AAAAAAAACAAAGAGA
1258900 AAAAAAAA
1 AAAAAAAA
1258908 TAAAAGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
16 21 0.62
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (16 bp):
AAAAAAAACAAAGAGA
Found at i:1260674 original size:36 final size:34
Alignment explanation
Indices: 1260634--1260749 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 34
1260624 GTTGATTTCA
* *
1260634 CTTGAGATCGCTTTCTCAAAAACAACCTTTTTCTCG
1 CTTGAGA-CGATTTCTCAAAAACAA-ATTTTTCTCG
* *
1260670 CTTGAGACAATTTTTCTAAAAACAAATTTTTGTCTCG
1 CTTGAGACGATTTCTC-AAAAACAAA-TTTT-TCTCG
* * * *
1260707 CTTTAGACGTTTTCTTGAAAAACAAATTTCGTCTCG
1 CTTGAGACGATTTC-TCAAAAACAAATTT-TTCTCG
1260743 CTTGAGA
1 CTTGAGA
1260750 TATTTTTCCT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
35 6 0.09
36 33 0.52
37 24 0.38
38 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (34 bp):
CTTGAGACGATTTCTCAAAAACAAATTTTTCTCG
Done.