Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 129 of 173
Found at i:39352283 original size:17 final size:17
Alignment explanation
Indices: 39352257--39352292 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
39352247 AATTCGGTCG
39352257 TATAAAATTATTTTTCA
1 TATAAAATTATTTTTCA
*
39352274 TATAAGATTATTTTTCA
1 TATAAAATTATTTTTCA
39352291 TA
1 TA
39352293 CCTTAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
TATAAAATTATTTTTCA
Found at i:39355101 original size:17 final size:17
Alignment explanation
Indices: 39355079--39355176 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
39355069 AATTCAAGAC
39355079 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
39355096 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
39355115 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* **
39355133 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTTTTA-A
*
39355152 TTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
39355170 TTATGTA
1 TTATGTA
39355177 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 24 0.41
18 9 0.16
19 8 0.14
20 17 0.29
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:39355158 original size:20 final size:18
Alignment explanation
Indices: 39355094--39355185 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 18
39355084 TAATGTTTTT
*
39355094 AATTATGTAGTGATTCAA
1 AATTATGTAGTGATTTAA
* **
39355112 AGACTTATGTAAT-ATTTTT
1 A-A-TTATGTAGTGATTTAA
39355131 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
39355149 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
39355168 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
39355186 TTCGGGTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
17 20 0.36
18 8 0.15
19 7 0.13
20 20 0.36
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:39355183 original size:37 final size:37
Alignment explanation
Indices: 39355074--39355185 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
39355064 GTGTTAATTC
*
39355074 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
*
39355111 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
39355148 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
39355185 A
1 A
39355186 TTCGGGTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:39355197 original size:9 final size:9
Alignment explanation
Indices: 39355183--39355274 Score: 103
Period size: 9 Copynumber: 9.6 Consensus size: 9
39355173 TGTAGTGATT
39355183 TAATTCGGG
1 TAATTCGGG
39355192 TAATTCGGG
1 TAATTCGGG
*
39355201 TAATTTGGG
1 TAATTCGGG
*
39355210 TAATTTTTGGG
1 TAA--TTCGGG
39355221 TAATTCGGG
1 TAATTCGGG
39355230 TAATTTTCGGG
1 TAA--TTCGGG
*
39355241 TAATTCGAG
1 TAATTCGGG
39355250 TAATTTTCGGG
1 TAA--TTCGGG
39355261 TAATTCGGG
1 TAATTCGGG
39355270 TAATT
1 TAATT
39355275 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
9 47 0.64
11 26 0.36
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:39355223 original size:20 final size:20
Alignment explanation
Indices: 39355183--39355276 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
39355173 TGTAGTGATT
39355183 TAATTCGGGTAA--TTCGGG
1 TAATTCGGGTAATTTTCGGG
* *
39355201 TAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAATTTTCGGG
39355221 TAATTCGGGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
*
39355241 TAATTCGAGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
39355261 TAATTCGGGTAATTTT
1 TAATTCGGGTAATTTT
39355277 TAACCAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
18 11 0.16
20 57 0.84
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (20 bp):
TAATTCGGGTAATTTTCGGG
Found at i:39358827 original size:21 final size:20
Alignment explanation
Indices: 39358811--39358888 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 20
39358801 GCTTAATACT
*
39358811 TTTTAAATATTTTTTAATAAA
1 TTTTAAA-ACTTTTTAATAAA
39358832 TTTTAAAACTTTTTAAAATAAA
1 TTTTAAAACTTTTT--AATAAA
*
39358854 TTGTTTACAAA-TTTTT-ATAAT
1 -T-TTTA-AAACTTTTTAATAAA
*
39358875 TTTTAAAAGTTTTT
1 TTTTAAAACTTTTT
39358889 TTTACATTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.06
19 9 0.18
20 7 0.14
21 11 0.22
22 6 0.12
23 1 0.02
24 9 0.18
25 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTAAAACTTTTTAATAAA
Found at i:39366753 original size:3 final size:3
Alignment explanation
Indices: 39366745--39366775 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39366735 TATTGGCACC
39366745 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
39366776 TTGATTTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:39371867 original size:16 final size:16
Alignment explanation
Indices: 39371846--39371877 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39371836 GTTTTGTTGC
*
39371846 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39371862 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39371878 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39372160 original size:51 final size:51
Alignment explanation
Indices: 39372105--39372295 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 51
39372095 CCGGTTCATA
* *
39372105 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* ***
39372156 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGTA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * * *
39372207 TAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
39372257 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
39372296 TTCACTTTCA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 40 0.34
51 70 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:39372284 original size:101 final size:102
Alignment explanation
Indices: 39372103--39372287 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
39372093 TACCGGTTCA
*
39372103 TATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 TATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
39372168 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
39372205 TATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 TATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
39372268 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
39372288 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (102 bp):
TATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:39391083 original size:21 final size:20
Alignment explanation
Indices: 39391057--39391113 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
39391047 ATAAACTTTT
39391057 TTTTTGCTATTTTTTTTGCGC
1 TTTTTGCTATTTTTTTTGC-C
* * *
39391078 TTTTTGCTTTTTTTCTTTTCT
1 TTTTTGCTATTTTT-TTTGCC
39391099 TTTTTGCTATTTTTT
1 TTTTTGCTATTTTTT
39391114 CTTCAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.04, C:0.12, G:0.09, T:0.75
Consensus pattern (20 bp):
TTTTTGCTATTTTTTTTGCC
Found at i:39391852 original size:29 final size:31
Alignment explanation
Indices: 39391820--39391879 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39391810 AGATAATTTT
39391820 AAAGAG-TTT-TTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
39391849 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
39391880 TAATTTGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.21
30 3 0.10
31 20 0.69
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:39392444 original size:20 final size:20
Alignment explanation
Indices: 39392421--39392467 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39392411 AAAAAAATAG
39392421 AAAAAAAGCAAAAAGCGCAA
1 AAAAAAAGCAAAAAGCGCAA
*
39392441 AAAAAAAGCAACAAGCGCAA
1 AAAAAAAGCAAAAAGCGCAA
39392461 AAAAAAA
1 AAAAAAA
39392468 AGTTGCCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.72, C:0.15, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAAGCAAAAAGCGCAA
Found at i:39392577 original size:40 final size:39
Alignment explanation
Indices: 39392522--39392602 Score: 153
Period size: 40 Copynumber: 2.1 Consensus size: 39
39392512 GTTATTATTT
39392522 TTATTTTTATTTTTCCCAAAATTGAATTTTTTTTTCTTCC
1 TTATTTTTATTTTTCCCAAAATTGAA-TTTTTTTTCTTCC
39392562 TTATTTTTATTTTTCCCAAAATTGAATTTTTTTTCTTCC
1 TTATTTTTATTTTTCCCAAAATTGAATTTTTTTTCTTCC
39392601 TT
1 TT
39392603 CTTCTTTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 15 0.37
40 26 0.63
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (39 bp):
TTATTTTTATTTTTCCCAAAATTGAATTTTTTTTCTTCC
Found at i:39398085 original size:29 final size:31
Alignment explanation
Indices: 39398053--39398112 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39398043 AGATAATTTT
39398053 AAAGAG-TTT-TTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
39398082 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
39398113 TAATTTGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.21
30 3 0.10
31 20 0.69
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:39399311 original size:15 final size:15
Alignment explanation
Indices: 39399291--39399321 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39399281 TGGTGTAAAT
39399291 TACTGAATTAGTACA
1 TACTGAATTAGTACA
39399306 TACTGAATTAGTACA
1 TACTGAATTAGTACA
39399321 T
1 T
39399322 CCCAGGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
TACTGAATTAGTACA
Found at i:39405232 original size:75 final size:75
Alignment explanation
Indices: 39405153--39405308 Score: 226
Period size: 75 Copynumber: 2.1 Consensus size: 75
39405143 AAGGCATATG
* *
39405153 ATAGAATACAATACAAAC-AGTTTTTGATTTTTTTCT-TAGATTGAAAATAAGTGTATATTATTG
1 ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAA--GTATATTATTG
39405216 ATATAAAATACA
64 ATATAAAATACA
* * * *
39405228 ATAGAGTACAATACAAACAATTTTTTTAATTTCTTCTGTAGATTGTAAATAAGTATATTATTGAT
1 ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAAGTATATTATTGAT
39405293 ATAAAATACA
66 ATAAAATACA
39405303 ATAGAA
1 ATAGAA
39405309 AAAATTGTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 45 0.62
76 14 0.19
77 13 0.18
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (75 bp):
ATAGAATACAATACAAACAAGTTTTTGAATTTCTTCTGTAGATTGAAAATAAGTATATTATTGAT
ATAAAATACA
Found at i:39412640 original size:50 final size:50
Alignment explanation
Indices: 39412524--39412764 Score: 216
Period size: 50 Copynumber: 4.7 Consensus size: 50
39412514 ATAATAACAA
* * ** * **
39412524 GCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATTTTTC-T-TGCACT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGT
* * * **
39412573 ACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* ** *
39412623 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* *
39412673 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGT
* * *
39412729 GCCAATGTCATGTTCCAAACATGGTCTTACATGGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
39412765 TCTCATCACC
Statistics
Matches: 156, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
49 35 0.22
50 84 0.54
51 1 0.01
53 2 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
Found at i:39441124 original size:24 final size:24
Alignment explanation
Indices: 39441096--39441159 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
39441086 TTTCTACAAG
* *
39441096 ATTTAATATTGATTAGTATAATAT
1 ATTTAACATTGATTAGCATAATAT
*
39441120 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTGATTAGCATAATAT
* *
39441144 ATTTGACATTAATTAG
1 ATTTAACATTGATTAG
39441160 AATTAGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTAACATTGATTAGCATAATAT
Found at i:39443174 original size:20 final size:20
Alignment explanation
Indices: 39443149--39443187 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39443139 CAAATAAGAA
39443149 AAATATAATAATATAAAAAG
1 AAATATAATAATATAAAAAG
* *
39443169 AAATATTATATTATAAAAA
1 AAATATAATAATATAAAAA
39443188 TCAAATTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATATAATAATATAAAAAG
Found at i:39453108 original size:25 final size:25
Alignment explanation
Indices: 39453074--39453162 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
39453064 ATAATTCGCT
*
39453074 ACAAAAGCTTTCCAAATGATACGCC
1 ACAAAGGCTTTCCAAATGATACGCC
* * * *
39453099 ATAAAGGCTTTCTAGA-GAATTCGCC
1 ACAAAGGCTTTCCAAATG-ATACGCC
* *
39453124 ACAAAAGCTTTCCAAATGATACACC
1 ACAAAGGCTTTCCAAATGATACGCC
*
39453149 ACAAAGACTTTCCA
1 ACAAAGGCTTTCCA
39453163 GAGAATTTGC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (25 bp):
ACAAAGGCTTTCCAAATGATACGCC
Found at i:39453114 original size:50 final size:50
Alignment explanation
Indices: 39453055--39453178 Score: 185
Period size: 50 Copynumber: 2.5 Consensus size: 50
39453045 CACTACAACA
* * * *
39453055 ACTTTCTAGATAATTCGCTACAAAAGCTTTCCAAATGATACGCCATAAAG
1 ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
*
39453105 GCTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
1 ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
* *
39453155 ACTTTCCAGAGAATTTGCCACAAA
1 ACTTTCTAGAGAATTCGCCACAAA
39453179 GGTTTTCTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (50 bp):
ACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACCACAAAG
Found at i:39453185 original size:25 final size:25
Alignment explanation
Indices: 39453147--39453194 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39453137 AAATGATACA
*
39453147 CCACAAAGACTTTCCAGAGAATTTG
1 CCACAAAGACTTTCCAAAGAATTTG
** *
39453172 CCACAAAGGTTTTCTAAAGAATT
1 CCACAAAGACTTTCCAAAGAATT
39453195 CTCGAGTTTG
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:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
CCACAAAGACTTTCCAAAGAATTTG
Found at i:39459093 original size:131 final size:131
Alignment explanation
Indices: 39458856--39459110 Score: 372
Period size: 131 Copynumber: 1.9 Consensus size: 131
39458846 TGAAACATCG
* * *
39458856 AAAATAAAGAACATACTCATGATCACATCAGCGGCATCTCTTTCCTCTCAGCGTCGAGCAGTATA
1 AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAGCGTCAAGCAGTATA
* *
39458921 AACCAGTGCAGGCTACCTCGCCTCAGTTTGATTAGTACCTCTGCCCGGT-ACTCTCTGTCCTCGG
66 AACCAGTGCAGGCTACCTCGCCTCAGTCTAATTAGTACCTCTGCCCGGTGA-TCTCTGTCCTCGG
39458985 TA
130 TA
* * *
39458987 AAAATAAAGAACGTACCCGTGATCACATCAGGGGCATCTCTGTCCTCTC-GACGTCAAGCAGTAT
1 AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAG-CGTCAAGCAGTAT
* *
39459051 AAACCAGTGTAGGCTACCTCGCCTCAGTCTAATTAGCT-CCTCTGCCTGGTGATCTCTGTC
65 AAACCAGTGCAGGCTACCTCGCCTCAGTCTAATTAG-TACCTCTGCCCGGTGATCTCTGTC
39459111 ATTAACCCAT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
130 1 0.01
131 108 0.97
132 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (131 bp):
AAAATAAAGAACATACCCATGATCACATCAGCGGCATCTCTGTCCTCTCAGCGTCAAGCAGTATA
AACCAGTGCAGGCTACCTCGCCTCAGTCTAATTAGTACCTCTGCCCGGTGATCTCTGTCCTCGGT
A
Found at i:39460374 original size:26 final size:25
Alignment explanation
Indices: 39460345--39460395 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
39460335 TTAGTCTCTA
39460345 ACTAACT-CAGTATAGTTTCAGAAAGT
1 ACTAACTACAGTAT--TTTCAGAAAGT
*
39460371 ACTAACTACAGTGTTTTCAGAAAGT
1 ACTAACTACAGTATTTTCAGAAAGT
39460396 TCTATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 7 0.30
27 5 0.22
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (25 bp):
ACTAACTACAGTATTTTCAGAAAGT
Found at i:39461774 original size:67 final size:67
Alignment explanation
Indices: 39461666--39461796 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
39461656 TTTTCAATTT
*
39461666 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTA
39461731 CA
66 CA
**
39461733 AGAGAGCACACTCTTGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
39461797 GCAACGACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTA
CA
Found at i:39461958 original size:57 final size:60
Alignment explanation
Indices: 39461865--39462012 Score: 178
Period size: 57 Copynumber: 2.5 Consensus size: 60
39461855 ACCCTAATTC
* * * * *
39461865 GGATTACTCGTCCGGACTAAATCCATTTTCCACATATTCTTCGAGAGGGCTATATC-A-A
1 GGATCACTCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGGATATATCGATA
*
39461923 -GATCACTCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGATATATCAGGATA
1 GGATCACTCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGAGAGGGATATATC--GATA
*
39461984 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACTCGTCCGGGCTAGATCCTTTTT
39462013 ACTGTCAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 6 0.08
57 42 0.55
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (60 bp):
GGATCACTCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGGATATATCGATA
Found at i:39464993 original size:12 final size:13
Alignment explanation
Indices: 39464976--39465005 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
39464966 GCCTAGCCTG
39464976 TGTGGCATGTCC-
1 TGTGGCATGTCCA
39464988 TGTGGCATGTCCA
1 TGTGGCATGTCCA
39465001 TGTGG
1 TGTGG
39465006 GCCCACACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGGCATGTCCA
Found at i:39474857 original size:14 final size:14
Alignment explanation
Indices: 39474838--39474871 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
39474828 GCTTGTAGGA
39474838 AACTTTGACTATCG
1 AACTTTGACTATCG
39474852 AACTTTGACTATCG
1 AACTTTGACTATCG
39474866 AACTTT
1 AACTTT
39474872 TTGTTACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (14 bp):
AACTTTGACTATCG
Found at i:39479152 original size:31 final size:31
Alignment explanation
Indices: 39479117--39479178 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39479107 GCTTAATGGT
39479117 GATTGGCGTGGCATTAAATCAAATGTTAAAC
1 GATTGGCGTGGCATTAAATCAAATGTTAAAC
39479148 GATTGGCGTGGCATTAAATCAAATGTTAAAC
1 GATTGGCGTGGCATTAAATCAAATGTTAAAC
39479179 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (31 bp):
GATTGGCGTGGCATTAAATCAAATGTTAAAC
Found at i:39484855 original size:25 final size:24
Alignment explanation
Indices: 39484807--39484856 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
39484797 CAAAGGGAAA
*
39484807 AAAAGAAAGAAAAAAGATTGCAGT
1 AAAAGAAAGAAAAAAAATTGCAGT
39484831 AAAAGAAAGGAAAAAAAAATT-CAGT
1 AAAAGAAA-G-AAAAAAAATTGCAGT
39484856 A
1 A
39484857 GCCAAAGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 6 0.26
26 9 0.39
ACGTcount: A:0.66, C:0.04, G:0.18, T:0.12
Consensus pattern (24 bp):
AAAAGAAAGAAAAAAAATTGCAGT
Found at i:39486933 original size:20 final size:19
Alignment explanation
Indices: 39486888--39486934 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
39486878 GATTCTCAGG
39486888 AAATTTTTTACAAAATTTA
1 AAATTTTTTACAAAATTTA
39486907 AAATTTTTTACAAAATTTA
1 AAATTTTTTACAAAATTTA
39486926 AAATTTTTT
1 AAATTTTTT
39486935 CTCATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTTTTACAAAATTTA
Found at i:39487518 original size:50 final size:49
Alignment explanation
Indices: 39487464--39487619 Score: 150
Period size: 50 Copynumber: 3.1 Consensus size: 49
39487454 TCGAATAGAA
39487464 TAAAGCCACAACGGTGAATCTTGCTCCCTTGACATTGCGGTTAAAAAGAT
1 TAAAGCCACAACGGTGAATCTTGCTCCC-TGACATTGCGGTTAAAAAGAT
* * * * ** **** * ** *
39487514 TAAAGCTACAACAGCGAATCTTATCTCCAAGGTGGTGCAGTGGAACAGAT
1 TAAAGCCACAACGGTGAATCTT-GCTCCCTGACATTGCGGTTAAAAAGAT
*
39487564 TAAAGCCACAACGGTGAACCTTGCCTCCCTGACATTGCGGTTAAAAAGAT
1 TAAAGCCACAACGGTGAATCTTG-CTCCCTGACATTGCGGTTAAAAAGAT
39487614 TAAAGC
1 TAAAGC
39487620 TATAGCAGCG
Statistics
Matches: 75, Mismatches: 29, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
50 71 0.95
51 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (49 bp):
TAAAGCCACAACGGTGAATCTTGCTCCCTGACATTGCGGTTAAAAAGAT
Found at i:39487568 original size:100 final size:100
Alignment explanation
Indices: 39487332--39487702 Score: 419
Period size: 100 Copynumber: 3.7 Consensus size: 100
39487322 AGAATTTAAG
* * * * * * *
39487332 ATCTTATCTCCCT-GGCGATGCAGTGGAGCATATTAAAGCCACGACGGCGTATCTTGCTTCCCCG
1 ATCTTATCT-CCTAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTG
* * * *
39487396 ACATTGCAG-TAAAAAGACTAAAGCCACAGCGGCGA
65 ACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGA
* * * * * * *
39487431 GTGTTA-CTTCCTTGGTGATGCAGTCGAATAGAATAAAGCCACAACGGTGAATCTTG-CTCCCTT
1 ATCTTATC-TCCTAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCC-T
*
39487494 GACATTGCGGTTAAAAAGATTAAAGCTACAACAGCGA
64 GACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGA
* * * *
39487531 ATCTTATCTCCAAGGTGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAACCTTGCCTCCCTGA
1 ATCTTATCTCCTAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGA
*
39487596 CATTGCGGTTAAAAAGATTAAAGCTATAGCAGCGA
66 CATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGA
* * * * *
39487631 ATCCTACCTCCTAGGCGGTGTAGTGGAACAGATTAAAGCCA-TACGGTGAATCTTGCCTCCCTGA
1 ATCTTATCTCCTAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGA
39487695 CATTGCGG
66 CATTGCGG
39487703 CTACAGCAGC
Statistics
Matches: 230, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
98 8 0.03
99 77 0.33
100 139 0.60
101 6 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (100 bp):
ATCTTATCTCCTAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGA
CATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGA
Found at i:39487679 original size:199 final size:199
Alignment explanation
Indices: 39487332--39487702 Score: 449
Period size: 199 Copynumber: 1.9 Consensus size: 199
39487322 AGAATTTAAG
** * * * * * *
39487332 ATCTTATCTCCCTGGCGATGCAGTGGAGCATATTAAAGCCACGACGGCGTATCTTGCTTCCCCGA
1 ATCTTATCTCCAAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGCGAACCTTGCCTCCCCGA
* * ** * * * *
39487397 CATTGCAGTAAAAAGACTAAAGCCACAGCGGCGAGTGTTACTTCCTTGGTGATGCAGTCGAATAG
66 CATTGCAGTAAAAAGACTAAAGCCACAGCAGCGAATCCTACCTCCTAGGCGATGCAGTCGAACAG
39487462 AATAAAGCCACAACGGTGAATCTTG-CTCCCTTGACATTGCGGTTAAAAAGATTAAAGCTACAAC
131 AATAAAGCCACAACGGTGAATCTTGCCTCCC-TGACATTGCGGTTAAAAAGATTAAAGCTACAAC
39487526 AGCGA
195 AGCGA
* * * *
39487531 ATCTTATCTCCAAGGTGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAACCTTGCCTCCCTGA
1 ATCTTATCTCCAAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGCGAACCTTGCCTCCCCGA
* * * * * * *
39487596 CATTGCGGTTAAAAAGATTAAAGCTATAGCAGCGAATCCTACCTCCTAGGCGGTGTAGTGGAACA
66 CATTGCAG-TAAAAAGACTAAAGCCACAGCAGCGAATCCTACCTCCTAGGCGATGCAGTCGAACA
* *
39487661 GATTAAAGCCA-TACGGTGAATCTTGCCTCCCTGACATTGCGG
130 GAATAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCGG
39487703 CTACAGCAGC
Statistics
Matches: 141, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
199 84 0.60
200 57 0.40
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (199 bp):
ATCTTATCTCCAAGGCGATGCAGTGGAACAGATTAAAGCCACAACGGCGAACCTTGCCTCCCCGA
CATTGCAGTAAAAAGACTAAAGCCACAGCAGCGAATCCTACCTCCTAGGCGATGCAGTCGAACAG
AATAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAACA
GCGA
Found at i:39487771 original size:86 final size:84
Alignment explanation
Indices: 39487618--39487786 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 84
39487608 AAAGATTAAA
* * * * *
39487618 GCTATAGCAGCGAATCCTACCTCCTAGGCGGTGTAGTGGAACAGATTAAAGCCATACGGTGAATC
1 GCTACAGCAGCGAATCCTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCAAACGGTGAATC
*
39487683 TTGCCTCCCTGACATTGCG
66 TTGCCTCCCCGACATTGCG
*
39487702 GCTACAGCAGCGAATCTTACACTCCCAGGCAGTGCAGT-GAAGCAGATTAAAGCCACAACGGTGA
1 GCTACAGCAGCGAATCCTAC-CTCCCAGGCAGTGCAGTGGAA-CAGATTAAAGCCA-AACGGTGA
*
39487766 ATCTTGCTTCCCCGACATTGC
63 ATCTTGCCTCCCCGACATTGC
39487787 AGTTAAAAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 21 0.28
85 27 0.36
86 26 0.35
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.22
Consensus pattern (84 bp):
GCTACAGCAGCGAATCCTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCAAACGGTGAATC
TTGCCTCCCCGACATTGCG
Found at i:39492158 original size:3 final size:3
Alignment explanation
Indices: 39492152--39492200 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
39492142 TATTCAGTAA
* *
39492152 TAT TAT TAT TAAT CTAT TAG TAT TAT TAA T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39492198 TAT
1 TAT
39492201 CACCGTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 33 0.85
4 4 0.10
5 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:39492177 original size:17 final size:17
Alignment explanation
Indices: 39492155--39492196 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
39492145 TCAGTAATAT
39492155 TATTATTAATCTATTAG
1 TATTATTAATCTATTAG
* *
39492172 TATTATTAATTTATTAT
1 TATTATTAATCTATTAG
39492189 TATTATTA
1 TATTATTA
39492197 TTATCACCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTAATCTATTAG
Found at i:39497011 original size:6 final size:6
Alignment explanation
Indices: 39497002--39497075 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
39496992 AAAAAGAAGA
* * ** **
39497002 AAAATC AAAATC AAAATC AAAGTC AAAA-- AGAAGA AAAAGA AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * *
39497048 AAAATC AAAGTC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
39497076 AAGAGAGAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
4 3 0.05
6 54 0.95
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:39497023 original size:34 final size:34
Alignment explanation
Indices: 39496979--39497063 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
39496969 AGATTCAAAA
* **
39496979 AAAATTCAAAGGCAAAAAGAAGAAAAATCAAAATC
1 AAAA-TCAAAGTCAAAAAGAAGAAAAAGAAAAATC
39497014 AAAATCAAAGTCAAAAAGAAGAAAAAGAAAAATC
1 AAAATCAAAGTCAAAAAGAAGAAAAAGAAAAATC
39497048 AAAATCAAAGTCAAAA
1 AAAATCAAAGTCAAAA
39497064 TGAAAATGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 43 0.91
35 4 0.09
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (34 bp):
AAAATCAAAGTCAAAAAGAAGAAAAAGAAAAATC
Found at i:39498690 original size:175 final size:175
Alignment explanation
Indices: 39498399--39498838 Score: 763
Period size: 175 Copynumber: 2.5 Consensus size: 175
39498389 GCCAAAAATA
*
39498399 TTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
39498464 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTAGGTCT
66 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
* *
39498529 TGTCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATC
131 TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGATC
** *
39498574 TTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
39498639 GGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
66 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
*
39498704 TATCTCTCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGATC
131 TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGATC
* * *
39498749 TTATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCAATCTCCCTGAGATTATAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
39498814 GGAGCAGATTAAAATAAAGGATCTT
66 GGAGCGGATTAAAATAAAGGATCTT
39498839 CTCCCTGAGA
Statistics
Matches: 248, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 248 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (175 bp):
TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGATC
Found at i:39498754 original size:46 final size:46
Alignment explanation
Indices: 39498526--39499023 Score: 179
Period size: 44 Copynumber: 11.3 Consensus size: 46
39498516 TCGCATTAGG
* *
39498526 TCTTGTCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
** * ** ****
39498572 TCTTATCTCCCTGAGATTACAG-CAAAGCAGATTGAAGCTGGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAA-TAGACCGAAGAAATTCAGA
* * * ** **
39498616 TCCTATCTCCCTGAGATTACAGTGGAGTGGA--TTA-AAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCA-GA
* * * * * *
39498660 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATC---G-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGACCGAAGAAATTCAGA
*
39498701 TCTTATCTCTCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
* * ** ** ** *
39498747 TCTTATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
** * ** ** **
39498791 TCCAATCTCCCTGAGATTATAGTGGAGCAGA--TTA-AAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCA-GA
* *
39498835 TC-T-TCTCCCTGAGATTACAGTGGAATAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
* * * ** ** ** *
39498879 TCATATCTCCCTGAGACTACAGCGGAGCAGATTGAAGCTAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
* * * **
39498923 TCCTATCTCCCTAAGATTACAGTGG---AG-CGGATTA-AAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGA--AGAAATTCA-GA
* *
39498967 TCTTATCT--CTGAGATTACAGTGGAATAGACCGAAGAATTTCAAA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
39499011 TCTTATCTCCCTG
1 TCTTATCTCCCTG
39499024 GCGATGCAGT
Statistics
Matches: 325, Mismatches: 92, Indels: 70
0.67 0.19 0.14
Matches are distributed among these distances:
40 2 0.01
41 33 0.10
42 45 0.14
43 2 0.01
44 126 0.39
45 18 0.06
46 99 0.30
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGA
Found at i:39498880 original size:132 final size:132
Alignment explanation
Indices: 39498706--39499023 Score: 528
Period size: 132 Copynumber: 2.4 Consensus size: 132
39498696 TCAGGTCTTA
* * *
39498706 TCTCTCTGAGATTACAGTGGAATAGACCGAAGAAATTCAGATCTTATCTCTCTGAGATTACAGCG
1 TCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGACTACAGCG
* *
39498771 GAGCAGATTGAAGCTAGTAATCCAATCTCCCTGAGATTATAGTGGAGCAGATTAAAATAAAGGAT
66 GAGCAGATTGAAGCTAGTAATCCAATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAAAGGAT
39498836 CT
131 CT
* * *
39498838 TCTCCCTGAGATTACAGTGGAATAGACCGGAGAATTTCAGATCATATCTCCCTGAGACTACAGCG
1 TCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGACTACAGCG
* *
39498903 GAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
66 GAGCAGATTGAAGCTAGTAATCCAATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAAAGGAT
39498968 CT
131 CT
* *
39498970 TATCTCTGAGATTACAGTGGAATAGACCGAAGAATTTCAAATCTTATCTCCCTG
1 TCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTG
39499024 GCGATGCAGT
Statistics
Matches: 171, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 171 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (132 bp):
TCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGACTACAGCG
GAGCAGATTGAAGCTAGTAATCCAATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAAAGGAT
CT
Found at i:39499191 original size:100 final size:99
Alignment explanation
Indices: 39499017--39499387 Score: 415
Period size: 100 Copynumber: 3.7 Consensus size: 99
39499007 CAAATCTTAT
** * * * *
39499017 CTCCCTGGCGATGCAGTGGAGTAGATTAAAGCCACGACGG-CATATCTTGCTTCCCCGACATTGC
1 CTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGA-ATCTTGCCTCCCTGACATTGC
* * * *
39499081 AGTTAAAAAGACTAAAGCCACAGCGGCGAGTGTCAC
65 GGTTAAAAAGATTAAAGCCACAGCAGCGAAT-TCAC
* * *
39499117 TTCCCTGGCGATGCAGTCGAACAGATTAAAGCCACAACGGTGAATCTTG-CTCCATTGACATTGC
1 CTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCC-CTGACATTGC
** * *
39499181 GGTTAAAAAGATTAAAGGTACAACAGCGAATCTTAC
65 GGTTAAAAAGATTAAAGCCACAGCAGCGAAT-TCAC
* * *
39499217 CTCCAAT-GCGGTGCAGTGGAACACATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGC
1 CTCC-CTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGC
* * *
39499281 GGTTAAAAAGATTAAAGCGATAGCAGCGAATCCTAC
65 GGTTAAAAAGATTAAAGCCACAGCAGCGAATTC-AC
* * * *
39499317 CTCCCAGGCGGTGCAGTGGAACATATTAAAGCCATAACGGTGAATCTTGCCTCCCTGACATTGCG
1 CTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCG
*
39499382 GCTAAA
66 GTTAAA
39499388 GCAGCGAATC
Statistics
Matches: 230, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
99 3 0.01
100 221 0.96
101 6 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (99 bp):
CTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCG
GTTAAAAAGATTAAAGCCACAGCAGCGAATTCAC
Found at i:39499193 original size:50 final size:50
Alignment explanation
Indices: 39499139--39499298 Score: 162
Period size: 50 Copynumber: 3.2 Consensus size: 50
39499129 GCAGTCGAAC
*
39499139 AGATTAAAGCCACAACGGTGAATCTTGCTCCATTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTCCAATGACATTGCGGTTAAAA
** * * * ** * ** *
39499189 AGATTAAAGGTACAACAGCGAATCTTACCTCCAATG-CGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTT-GCTCCAATGACATTGCGGTTAAAA
* *
39499239 ACATTAAAGCCACAACGGTGAATCTTGCCTCC-CTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTG-CTCCAATGACATTGCGGTTAAAA
39499289 AGATTAAAGC
1 AGATTAAAGC
39499299 GATAGCAGCG
Statistics
Matches: 81, Mismatches: 26, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
49 2 0.02
50 72 0.89
51 7 0.09
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGCTCCAATGACATTGCGGTTAAAA
Found at i:39499312 original size:50 final size:50
Alignment explanation
Indices: 39499139--39499387 Score: 151
Period size: 50 Copynumber: 5.0 Consensus size: 50
39499129 GCAGTCGAAC
* * * *
39499139 AGATTAAAGCCACAACGGTGAATCTTG-CTCCATTGACATTGCGGTTAAAA
1 AGATTAAAGCCATAACAGCGAATCTTGCCTCC-CTGACATTGCGGTTAAAA
** * * * ** * ** *
39499189 AGATTAAAGGTACAACAGCGAATCTTACCTCCAATG-CGGTGCAGTGGAAC
1 AGATTAAAGCCATAACAGCGAATCTTGCCTCC-CTGACATTGCGGTTAAAA
* * * *
39499239 ACATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCGGTTAAAA
1 AGATTAAAGCCATAACAGCGAATCTTGCCTCCCTGACATTGCGGTTAAAA
* * * * * * ** * ** *
39499289 AGATTAAAGCGATAGCAGCGAATCCTACCTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCATAACAGCGAATCTTGCCTCCCTGACATTGCGGTTAAAA
* * * *
39499339 ATATTAAAGCCATAACGGTGAATCTTGCCTCCCTGACATTGCGGCTAAA
1 AGATTAAAGCCATAACAGCGAATCTTGCCTCCCTGACATTGCGGTTAAA
39499388 GCAGCGAATC
Statistics
Matches: 141, Mismatches: 56, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
49 2 0.01
50 132 0.94
51 7 0.05
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (50 bp):
AGATTAAAGCCATAACAGCGAATCTTGCCTCCCTGACATTGCGGTTAAAA
Found at i:39499446 original size:86 final size:85
Alignment explanation
Indices: 39499302--39499465 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 85
39499292 TTAAAGCGAT
* * *
39499302 AGCAGCGAATCCTACCTCCCAGGCGGTGCAGTGGAACATATTAAAGCCATAACGGTGAATCTTGC
1 AGCAGCGAATCCTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
*
39499367 CTCCCTGACATTGCGGCTAA
66 CTCCCCGACATTGCGGCTAA
*
39499387 AGCAGCGAATCTTACACTCCCAGGCAGTGCAGT-GAAGCAGATTAAAGCCACAACGGTGAATCTT
1 AGCAGCGAATCCTAC-CTCCCAGGCAGTGCAGTGGAA-CAGATTAAAGCCACAACGGTGAATCTT
*
39499451 GCTTCCCCGACATTG
64 GCCTCCCCGACATTG
39499466 TAGTTAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
85 17 0.24
86 54 0.76
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (85 bp):
AGCAGCGAATCCTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
CTCCCCGACATTGCGGCTAA
Found at i:39500901 original size:17 final size:17
Alignment explanation
Indices: 39500879--39500920 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
39500869 TCAGTAATAT
39500879 TATTATTAATCTATTAG
1 TATTATTAATCTATTAG
* *
39500896 TATTATTAATTTATTAT
1 TATTATTAATCTATTAG
39500913 TATTATTA
1 TATTATTA
39500921 TCACCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTAATCTATTAG
Found at i:39500901 original size:20 final size:20
Alignment explanation
Indices: 39500876--39500921 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
39500866 TATTCAGTAA
39500876 TATTATT-ATTAATCTATTAG
1 TATTATTAATTAAT-TATTAG
* *
39500896 TATTATTAATTTATTATTAT
1 TATTATTAATTAATTATTAG
39500916 TATTAT
1 TATTAT
39500922 CACCGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTATTAATTAATTATTAG
Found at i:39503157 original size:47 final size:48
Alignment explanation
Indices: 39503074--39503182 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 48
39503064 TTGCACATCG
*
39503074 TCACATATCACACACCGAAGCCATAGCCCAGCTATGGTCTTACACGGAAA
1 TCACATAT--CACACCGAAGCCATAGCCCAGATATGGTCTTACACGGAAA
* * * * *
39503124 -CACATATCACACCGATGCCATATCCTAGATATGGTCTTATATGGAAA
1 TCACATATCACACCGAAGCCATAGCCCAGATATGGTCTTACACGGAAA
39503171 TCACATATCACA
1 TCACATATCACA
39503183 TCACACCGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 34 0.65
48 11 0.21
49 7 0.13
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (48 bp):
TCACATATCACACCGAAGCCATAGCCCAGATATGGTCTTACACGGAAA
Found at i:39503192 original size:53 final size:53
Alignment explanation
Indices: 39503129--39503236 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
39503119 GGAAACACAT
* * * *
39503129 ATCACACCGATGCCATATCCTAGATATGGTCTTATATGGAAATCACAT-ATCAC
1 ATCACACCGATACCATAACCTAGATATGGTCTTATACGG-AAGCACATAATCAC
* *
39503182 ATCACACCGATACCATAACCTAGCTATGGTTTTATACGGAAGCACATAATCAC
1 ATCACACCGATACCATAACCTAGATATGGTCTTATACGGAAGCACATAATCAC
39503235 AT
1 AT
39503237 TTTGACATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 7 0.15
53 41 0.85
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (53 bp):
ATCACACCGATACCATAACCTAGATATGGTCTTATACGGAAGCACATAATCAC
Found at i:39515176 original size:15 final size:15
Alignment explanation
Indices: 39515156--39515186 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39515146 TTTACAATGT
39515156 TTATCTGAAGGATGC
1 TTATCTGAAGGATGC
39515171 TTATCTGAAGGATGC
1 TTATCTGAAGGATGC
39515186 T
1 T
39515187 GTAGTGGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (15 bp):
TTATCTGAAGGATGC
Found at i:39517262 original size:63 final size:63
Alignment explanation
Indices: 39517163--39517291 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 63
39517153 TCATACGAGT
* * * *
39517163 TTCCGTTCAGCTCTATTGAGCTTCTATTTAACCTTTATGGGTTTCTGTTAAGCTCTTATGAGC
1 TTCCGTTCAGCTCTATCGAGCTTCCATTCAACCTTTATGGGTTTCTGTTAAGCTCTCATGAGC
* *
39517226 TTCCGTTCAGCTCT-TACGAGCTTCCGTTCAACCTTTATGGGTTTCTGTTTAGCTCTCATGAGC
1 TTCCGTTCAGCTCTAT-CGAGCTTCCATTCAACCTTTATGGGTTTCTGTTAAGCTCTCATGAGC
39517289 TTC
1 TTC
39517292 TGTTTAGCCT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 1 0.02
63 58 0.98
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (63 bp):
TTCCGTTCAGCTCTATCGAGCTTCCATTCAACCTTTATGGGTTTCTGTTAAGCTCTCATGAGC
Found at i:39517296 original size:21 final size:21
Alignment explanation
Indices: 39517121--39517299 Score: 105
Period size: 21 Copynumber: 8.5 Consensus size: 21
39517111 CGTGTTTACA
39517121 TTCTGTTTAGCT-TTCATGAGC
1 TTCTGTTTAGCTCTT-ATGAGC
* * * * *
39517142 TTATGTTTAACTCATACGAGT
1 TTCTGTTTAGCTCTTATGAGC
* *
39517163 TTCCGTTCAGCTC-TATTGAGC
1 TTCTGTTTAGCTCTTA-TGAGC
* * * *
39517184 TTCTATTTAAC-CTTTATGGGT
1 TTCTGTTTAGCTC-TTATGAGC
*
39517205 TTCTGTTAAGCTCTTATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
39517226 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
39517247 TTCCGTTCAAC-CTTTATGGGT
1 TTCTGTTTAGCTC-TTATGAGC
*
39517268 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
39517289 TTCTGTTTAGC
1 TTCTGTTTAGC
39517300 CTTCGGGCTT
Statistics
Matches: 116, Mismatches: 35, Indels: 14
0.70 0.21 0.08
Matches are distributed among these distances:
20 4 0.03
21 107 0.92
22 5 0.04
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:39518143 original size:42 final size:42
Alignment explanation
Indices: 39518051--39518143 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
39518041 GTGTGTCTTA
* * *
39518051 GCCGTGTGAGACACACGACCTAGTACATGGGCGTGTGGTTTG
1 GCCGTGTGTGACACACGACCTAGCACATGGGAGTGTGGTTTG
*
39518093 GCCGTGTGTGACACACGACCTAGCACATGGGAGTGTGTTTTG
1 GCCGTGTGTGACACACGACCTAGCACATGGGAGTGTGGTTTG
*
39518135 GTCGTGTGT
1 GCCGTGTGT
39518144 CCTCTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.27
Consensus pattern (42 bp):
GCCGTGTGTGACACACGACCTAGCACATGGGAGTGTGGTTTG
Found at i:39526116 original size:13 final size:13
Alignment explanation
Indices: 39526098--39526127 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39526088 AGTTTAGTGG
39526098 TACAAATTATAAT
1 TACAAATTATAAT
39526111 TACAAATTATAAT
1 TACAAATTATAAT
39526124 TACA
1 TACA
39526128 TATTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
TACAAATTATAAT
Found at i:39527347 original size:24 final size:24
Alignment explanation
Indices: 39527315--39527366 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39527305 AATCAAAGTC
* *
39527315 AAATATATTATGCACATAAATGCT
1 AAATATATTATACACATAAATACT
* *
39527339 AAATTTATTATACTCATAAATACT
1 AAATATATTATACACATAAATACT
39527363 AAAT
1 AAAT
39527367 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACACATAAATACT
Found at i:39531691 original size:24 final size:24
Alignment explanation
Indices: 39531641--39531692 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39531631 AATCAAAGTC
* **
39531641 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
39531665 AAATATATTATACTTATAAATACT
1 AAATATATTATACTAATAAATACT
39531689 AAAT
1 AAAT
39531693 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:39533279 original size:14 final size:16
Alignment explanation
Indices: 39533251--39533282 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
39533241 TTAATGTTGA
39533251 TTTTCTTCTCTCTTTT
1 TTTTCTTCTCTCTTTT
39533267 TTTTCTT-TC-CTTTT
1 TTTTCTTCTCTCTTTT
39533281 TT
1 TT
39533283 AATGTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTCTCTCTTTT
Found at i:39543283 original size:30 final size:30
Alignment explanation
Indices: 39543241--39543299 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39543231 ATAATTAATA
*
39543241 TATTATGAAAATT-TTGAAAATTTATAAAAC
1 TATTATGAAAATTATAGAAAA-TTATAAAAC
39543271 TATTATTG-AAATTATAGAAAATTATAAAA
1 TATTA-TGAAAATTATAGAAAATTATAAAA
39543300 AATAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (30 bp):
TATTATGAAAATTATAGAAAATTATAAAAC
Found at i:39543406 original size:20 final size:21
Alignment explanation
Indices: 39543381--39543429 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
39543371 TCTAGAAATG
39543381 ATAGAAAA-ATATAAAAATTT
1 ATAGAAAACATATAAAAATTT
39543401 ATAGAAAACTATATAAAAA-TT
1 ATAGAAAAC-ATATAAAAATTT
39543422 ATA-AAAAC
1 ATAGAAAAC
39543430 TTGTAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.48
21 5 0.19
22 9 0.33
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAGAAAACATATAAAAATTT
Found at i:39543417 original size:22 final size:21
Alignment explanation
Indices: 39543376--39543447 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 21
39543366 GGAATTCTAG
*
39543376 AAATGATAGAAAA--ATATAA
1 AAATTATAGAAAACTATATAA
39543395 AAATTTATAGAAAACTATATAA
1 AAA-TTATAGAAAACTATATAA
*
39543417 AAATTATA-AAAACT-TGTAA
1 AAATTATAGAAAACTATATAA
*
39543436 AACTTATA-AAAA
1 AAATTATAGAAAA
39543448 TTTTGTTAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 18 0.38
20 15 0.32
21 5 0.11
22 9 0.19
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTATAGAAAACTATATAA
Found at i:39543436 original size:19 final size:20
Alignment explanation
Indices: 39543389--39543447 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
39543379 TGATAGAAAA
39543389 ATATAAAAATTTATAGAAAACT
1 ATATAAAAA-TTATA-AAAACT
39543411 ATATAAAAATTATAAAAACT
1 ATATAAAAATTATAAAAACT
* *
39543431 -TGTAAAACTTATAAAAA
1 ATATAAAAATTATAAAAA
39543448 TTTTGTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 15 0.43
20 6 0.17
21 5 0.14
22 9 0.26
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
ATATAAAAATTATAAAAACT
Found at i:39546671 original size:19 final size:20
Alignment explanation
Indices: 39546642--39546679 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39546632 GCTAATATTT
*
39546642 TTTTATTTATAAATTTTTAG
1 TTTTATTTATAAATATTTAG
39546662 TTTT-TTTATAAATATTTA
1 TTTTATTTATAAATATTTA
39546680 ATAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATTTATAAATATTTAG
Found at i:39547996 original size:120 final size:120
Alignment explanation
Indices: 39547769--39548008 Score: 401
Period size: 120 Copynumber: 2.0 Consensus size: 120
39547759 ATATAAATAA
* *
39547769 AATTATTAATATTTTGATTTAGGGATTTTTTTAATAATTTTTTATTTGGGGTAGATGGTGAAAAG
1 AATTATTAATATTTAGATTTAGGGATTTTTTTAATAATTTTTTATTTGGGGTAGATGGTAAAAAG
*
39547834 TAAAAGTTTAGTGGGAAAATAAAAAGTTTTGAGGGTTAGCGGAGTAAAATTTTGG
66 TAAAAGTTTAGTGGGAAAATAAAAAGTTTTGAAGGTTAGCGGAGTAAAATTTTGG
* * *
39547889 AATT-TTATTATTTAGATTTAGGGATTTTTTTGATGATTTTTTTATTTGGGGTAGATGGTAAAAA
1 AATTATTAATATTTAGATTTAGGGATTTTTTTAAT-AATTTTTTATTTGGGGTAGATGGTAAAAA
*
39547953 GTAAAAGTTTAGTGGGAAAATAAAAAGTTTTGAAGGTTGGCGGAGTAAAATTTTGG
65 GTAAAAGTTTAGTGGGAAAATAAAAAGTTTTGAAGGTTAGCGGAGTAAAATTTTGG
39548009 GAGGAAAGTA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
119 27 0.24
120 85 0.76
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (120 bp):
AATTATTAATATTTAGATTTAGGGATTTTTTTAATAATTTTTTATTTGGGGTAGATGGTAAAAAG
TAAAAGTTTAGTGGGAAAATAAAAAGTTTTGAAGGTTAGCGGAGTAAAATTTTGG
Found at i:39553351 original size:25 final size:25
Alignment explanation
Indices: 39553321--39553390 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
39553311 TTTGTAAACA
* *
39553321 GGAAGCTCATGCGAGTTGAATAATG
1 GGAAGCTCATGCGAGCTGAATAACG
*
39553346 GGAAGCTCATGCGAGCTGACTAACG
1 GGAAGCTCATGCGAGCTGAATAACG
* **
39553371 GGACGCTCATAAGAGCTGAA
1 GGAAGCTCATGCGAGCTGAA
39553391 ATCGGTGACC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (25 bp):
GGAAGCTCATGCGAGCTGAATAACG
Found at i:39558358 original size:14 final size:14
Alignment explanation
Indices: 39558318--39558364 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
39558308 CCAAACCCAG
* *
39558318 CAAAGCCAAGTAAC
1 CAAAACCAAATAAC
*
39558332 CAAAAAC-AATAAC
1 CAAAACCAAATAAC
39558345 CAAAACCAAATAACC
1 CAAAACCAAATAA-C
39558360 CAAAA
1 CAAAA
39558365 TTAGTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.41
14 10 0.37
15 6 0.22
ACGTcount: A:0.62, C:0.28, G:0.04, T:0.06
Consensus pattern (14 bp):
CAAAACCAAATAAC
Found at i:39558786 original size:34 final size:34
Alignment explanation
Indices: 39558714--39558788 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
39558704 GTTCATAGAA
*
39558714 GGAAGAAGAAAAAAATAAAAGAAAAGGGAAATTG
1 GGAAGAAGAAAAAAATAAAAGAAAAGGGAAAATG
* *
39558748 GGAAGAAGAAAAAGATAATCAGGAAAA-GGAAAAT-
1 GGAAGAAGAAAAAAATAA--AAGAAAAGGGAAAATG
39558782 GGAAGAA
1 GGAAGAA
39558789 AATGAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 24 0.67
35 6 0.17
36 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.28, T:0.08
Consensus pattern (34 bp):
GGAAGAAGAAAAAAATAAAAGAAAAGGGAAAATG
Found at i:39568565 original size:20 final size:20
Alignment explanation
Indices: 39568540--39568591 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
39568530 AAGCTTATGC
39568540 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* * *
39568560 TAAGTAAATGGATTGGTAAG
1 TAAGTAAATGAAATGGAAAG
39568580 TAAGTAAATGAA
1 TAAGTAAATGAA
39568592 GTAGTTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:39577117 original size:40 final size:40
Alignment explanation
Indices: 39577073--39577166 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 40
39577063 ATTACTAATG
39577073 GCTTGACCACATTACTGGCAATTTATCTGCAATATTGGCA
1 GCTTGACCACATTACTGGCAATTTATCTGCAATATTGGCA
*** * * * * **
39577113 GCTTGTTTACACTACTGGCAGTTTATTTGCATTATTGGTG
1 GCTTGACCACATTACTGGCAATTTATCTGCAATATTGGCA
*
39577153 GCTCGACCACATTA
1 GCTTGACCACATTA
39577167 TTGACAGCTT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (40 bp):
GCTTGACCACATTACTGGCAATTTATCTGCAATATTGGCA
Found at i:39577144 original size:80 final size:80
Alignment explanation
Indices: 39577005--39577172 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 80
39576995 AAAGAAAAAG
* *
39577005 TACTGACAATTAATCTATAATACTGGCAGTGTGTTTGCACTACTGGCAGCTTATCTGCATTACTA
1 TACTGACAATTAATCTACAATACTGGCAGTGTGTTTACACTACTGGCAGCTTATCTGCATTACTA
*
39577070 ATGGCTTGACCACAT
66 ATGGCTCGACCACAT
* * * * * * *
39577085 TACTGGCAATTTATCTGCAATATTGGCAGCT-TGTTTACACTACTGGCAGTTTATTTGCATTATT
1 TACTGACAATTAATCTACAATACTGGCAG-TGTGTTTACACTACTGGCAGCTTATCTGCATTACT
**
39577149 GGTGGCTCGACCACAT
65 AATGGCTCGACCACAT
*
39577165 TATTGACA
1 TACTGACA
39577173 GCTTGTTTGT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 72 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (80 bp):
TACTGACAATTAATCTACAATACTGGCAGTGTGTTTACACTACTGGCAGCTTATCTGCATTACTA
ATGGCTCGACCACAT
Found at i:39583873 original size:18 final size:18
Alignment explanation
Indices: 39583850--39583895 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
39583840 GATCAGTATG
39583850 ATTTCATAACTTTCCATA
1 ATTTCATAACTTTCCATA
*
39583868 ATTTCATACCTTTCCATA
1 ATTTCATAACTTTCCATA
39583886 ATTTCATAAC
1 ATTTCATAAC
39583896 ATAGTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCATAACTTTCCATA
Found at i:39586823 original size:20 final size:21
Alignment explanation
Indices: 39586798--39586837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39586788 GAGAAATAAT
*
39586798 GTGTTTTTA-GGTTAAAAAAG
1 GTGTTTTGATGGTTAAAAAAG
39586818 GTGTTTTGATGGTTAAAAAA
1 GTGTTTTGATGGTTAAAAAA
39586838 TTAGGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
GTGTTTTGATGGTTAAAAAAG
Found at i:39603307 original size:3 final size:3
Alignment explanation
Indices: 39603301--39603332 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
39603291 TTTGCATCTA
*
39603301 TTG TTG TTG TTG TTT TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39603333 ATTTTTGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (3 bp):
TTG
Found at i:39611728 original size:34 final size:34
Alignment explanation
Indices: 39611690--39611758 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
39611680 TCTCAAGACA
39611690 ATCCTCTAATCTCTTCACCTCTTTCAATTTTTCT
1 ATCCTCTAATCTCTTCACCTCTTTCAATTTTTCT
39611724 ATCCTCTAATCTCTTCACCTCTTTCAATTTTTCT
1 ATCCTCTAATCTCTTCACCTCTTTCAATTTTTCT
39611758 A
1 A
39611759 CATTTGTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (34 bp):
ATCCTCTAATCTCTTCACCTCTTTCAATTTTTCT
Found at i:39614615 original size:18 final size:17
Alignment explanation
Indices: 39614557--39614608 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
39614547 TTTTTTAGAG
* *
39614557 AAATTAATTTTATGGTTTT
1 AAATTAATTTT-TGG-GTA
39614576 AAA-TAATTTTTGGGTA
1 AAATTAATTTTTGGGTA
39614592 AAATTAATATTTTGGGT
1 AAATTAAT-TTTTGGGT
39614609 CTAATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 15 0.52
19 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
AAATTAATTTTTGGGTA
Found at i:39622469 original size:21 final size:22
Alignment explanation
Indices: 39622426--39622469 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
39622416 GCATCTACTC
* * *
39622426 AGGGAAATTATAATCCACGACA
1 AGGGAAATTACAATCAACAACA
39622448 AGGG-AATTACAATCAACAACA
1 AGGGAAATTACAATCAACAACA
39622469 A
1 A
39622470 AACTACAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (22 bp):
AGGGAAATTACAATCAACAACA
Found at i:39625199 original size:23 final size:23
Alignment explanation
Indices: 39625172--39625247 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
39625162 AATGTTATTG
39625172 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
39625195 TTCAGTGTTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39625218 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39625241 ATCAGTG
1 ATCAGTG
39625248 TGGGACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39630598 original size:18 final size:18
Alignment explanation
Indices: 39630561--39630603 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39630551 TTGATGCTGT
*
39630561 AGAAAAAGTTGTTATCGA
1 AGAAGAAGTTGTTATCGA
* * *
39630579 AGCAGAAGTTGTTTTTGA
1 AGAAGAAGTTGTTATCGA
39630597 AGAAGAA
1 AGAAGAA
39630604 AAAGTTACTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.28
Consensus pattern (18 bp):
AGAAGAAGTTGTTATCGA
Found at i:39636095 original size:36 final size:35
Alignment explanation
Indices: 39636055--39636125 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
39636045 TTAGCACAGC
*
39636055 GGCATGCTTAACATGCGAATCAGAATCAGAAATAAT
1 GGCATGCTTAACATGCGAATCAAAATCAG-AATAAT
* *
39636091 GGCATGCTTAACATGCGAGTCAAAATTAGAATAAT
1 GGCATGCTTAACATGCGAATCAAAATCAGAATAAT
39636126 AGAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (35 bp):
GGCATGCTTAACATGCGAATCAAAATCAGAATAAT
Found at i:39638331 original size:11 final size:11
Alignment explanation
Indices: 39638315--39638340 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39638305 CTTCATTCAT
39638315 CATCCCTCAAG
1 CATCCCTCAAG
39638326 CATCCCTCAAG
1 CATCCCTCAAG
39638337 CATC
1 CATC
39638341 ATTCTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.46, G:0.08, T:0.19
Consensus pattern (11 bp):
CATCCCTCAAG
Found at i:39644630 original size:23 final size:23
Alignment explanation
Indices: 39644599--39644651 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
39644589 AGTGTTATTG
39644599 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39644622 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39644645 ATCAGTG
1 ATCAGTG
39644652 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39651703 original size:18 final size:17
Alignment explanation
Indices: 39651670--39651708 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39651660 TTTTATAAAT
39651670 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39651688 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39651705 TGTG
1 TGTG
39651709 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39651960 original size:23 final size:23
Alignment explanation
Indices: 39651934--39652009 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
39651924 AGTGTTATTG
39651934 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39651957 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
39651980 TTCAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39652003 ATCAGTG
1 ATCAGTG
39652010 TGACACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39657681 original size:43 final size:44
Alignment explanation
Indices: 39657634--39657819 Score: 196
Period size: 44 Copynumber: 4.2 Consensus size: 44
39657624 TTTATGTGAA
* * * *
39657634 AAACGCCACTGAAGATCATGGTCTTTAGCGACAC-TTTTGCCAC
1 AAACGCCGCTAAAGATCATGATCTTTAGCGACACTTTTTACCAC
* * * * * *
39657677 AAACGCTGCTAAAGATCATGAACTTTAGCGGCGC-TTTTACAAAA
1 AAACGCCGCTAAAGATCATGATCTTTAGCGACACTTTTTAC-CAC
* * * * *
39657721 AAACGCCGCTAAAGAACATGACCTTTACCGGCACTTTTTATCAC
1 AAACGCCGCTAAAGATCATGATCTTTAGCGACACTTTTTACCAC
* *
39657765 AAACGCCGCTAAAGGTCATGATCTTTAGCGACACTTTTTGCCAC
1 AAACGCCGCTAAAGATCATGATCTTTAGCGACACTTTTTACCAC
39657809 AAACGCCGCTA
1 AAACGCCGCTA
39657820 TAAAACAAGC
Statistics
Matches: 116, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
43 32 0.28
44 79 0.68
45 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (44 bp):
AAACGCCGCTAAAGATCATGATCTTTAGCGACACTTTTTACCAC
Found at i:39657834 original size:131 final size:129
Alignment explanation
Indices: 39657634--39657868 Score: 312
Period size: 131 Copynumber: 1.8 Consensus size: 129
39657624 TTTATGTGAA
* * * * *
39657634 AAACGCCACTGAAGATCATGGTCTTTAGCGACACTTTTGCCACAAACGCTGCTAAAGATCATGAA
1 AAACGCCACTAAAGATCATGATCTTTAGCGACACTTTTGCCACAAACGCCGCTAAAGAACAAGAA
*
39657699 CTTTAGCGGCGCTTTTACAAAAAAACGCCGCTAAAGAACATGACCTTTACCGGCACTTTTTATCA
66 CTTTAGCGGCGCTTCT-CAAAAAAACGCCGCTAAA-AACATGACCTTTACCGGCACTTTTTATCA
39657764 C
129 C
* *
39657765 AAACGCCGCTAAAGGTCATGATCTTTAGCGACACTTTTTGCCACAAACGCCGCTATAA-AACAAG
1 AAACGCCACTAAAGATCATGATCTTTAGCGACAC-TTTTGCCACAAACGCCGCTA-AAGAACAAG
* * **
39657829 -CCTTTAGCGTCGCTTCTCGCAAAAACGCCGCTAAAAACAT
64 AACTTTAGCGGCGCTTCTCAAAAAAACGCCGCTAAAAACAT
39657869 AACATTTAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
129 5 0.06
130 16 0.18
131 44 0.49
132 23 0.26
133 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (129 bp):
AAACGCCACTAAAGATCATGATCTTTAGCGACACTTTTGCCACAAACGCCGCTAAAGAACAAGAA
CTTTAGCGGCGCTTCTCAAAAAAACGCCGCTAAAAACATGACCTTTACCGGCACTTTTTATCAC
Found at i:39657903 original size:17 final size:18
Alignment explanation
Indices: 39657881--39657918 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
39657871 CATTTAAAAA
*
39657881 ATTTTATTTAAATATT-T
1 ATTTTATATAAATATTAT
39657898 ATTTTATATAAATATTAT
1 ATTTTATATAAATATTAT
39657916 ATT
1 ATT
39657919 ATGTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATATAAATATTAT
Found at i:39658914 original size:16 final size:16
Alignment explanation
Indices: 39658893--39658923 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39658883 AGTCCCAAAC
39658893 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
39658909 TATTGTAAACATCAG
1 TATTGTAAACATCAG
39658924 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:39659932 original size:20 final size:21
Alignment explanation
Indices: 39659907--39659946 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39659897 AAAATTTTAT
*
39659907 TTATTTT-TATTTGTTAAAAA
1 TTATTTTATATATGTTAAAAA
39659927 TTATTTTATATATGTTAAAA
1 TTATTTTATATATGTTAAAA
39659947 TGAGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTATATATGTTAAAAA
Found at i:39661223 original size:7 final size:8
Alignment explanation
Indices: 39661197--39661222 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39661187 ATAAATACTG
39661197 AAATCAGA
1 AAATCAGA
39661205 AAATCAGA
1 AAATCAGA
39661213 AAATCAGA
1 AAATCAGA
39661221 AA
1 AA
39661223 TGACAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATCAGA
Found at i:39662040 original size:41 final size:41
Alignment explanation
Indices: 39661978--39662115 Score: 206
Period size: 41 Copynumber: 3.4 Consensus size: 41
39661968 AAAAGAAGAT
* * * * *
39661978 CGCTTTTTTAAAAACGTCGCTAAAGACCC-GATCATTAGTGG
1 CGCTTTTTAAAAAACGCCGCT-AATACCCTGAGCATTAGCGG
*
39662019 CACTTTTTAAAAAACGCCGCTAATACCCTGAGCATTAGCGG
1 CGCTTTTTAAAAAACGCCGCTAATACCCTGAGCATTAGCGG
39662060 CGCTTTTTAAAAAACGCCGCTAATACCCTGAGCATTAGCGG
1 CGCTTTTTAAAAAACGCCGCTAATACCCTGAGCATTAGCGG
39662101 CGCTTTTTAAAAAAC
1 CGCTTTTTAAAAAAC
39662116 ACCACAAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 6 0.07
41 83 0.93
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (41 bp):
CGCTTTTTAAAAAACGCCGCTAATACCCTGAGCATTAGCGG
Found at i:39662287 original size:40 final size:40
Alignment explanation
Indices: 39662162--39662299 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 40
39662152 AGGGCTTAGG
* * *
39662162 TTTTTTGCGGTGCTTTTTGAAAAA-CGCCGCTAATGC-TCA
1 TTTTTAGCGGTG-TTTTTTAAAAAGCGCCGCTAATGCTTAA
* ** * *
39662201 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATACTCAA
1 TTTTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATGCTTAA
* ** * *
39662241 TCTTTAGCGGTGTTTTTTTTAAAGCGTCGCTAATGCTTGA
1 TTTTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATGCTTAA
**
39662281 TTTTTAGCGGCATTTTTTA
1 TTTTTAGCGGTGTTTTTTA
39662300 TCCAAACGCC
Statistics
Matches: 76, Mismatches: 21, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
38 9 0.12
39 21 0.28
40 46 0.61
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (40 bp):
TTTTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATGCTTAA
Found at i:39663840 original size:27 final size:27
Alignment explanation
Indices: 39663819--39664196 Score: 400
Period size: 27 Copynumber: 14.0 Consensus size: 27
39663809 CGATATCTGC
*
39663819 ACCGAAATACCCTCATAGGATAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* *
39663846 ACCGAAATACCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* * *
39663873 ATCGAAATACCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* ** *
39663900 ATCGAAATACCCTTATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* * * *
39663927 ACCAAAATAACCCTATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* *
39663954 ACCAAAAT-CCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* * *
39663980 ATCGAAATATCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* *
39664007 ACCAAAATACCCCCATACGATAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
*
39664034 ACCGAAATACCCCTATATGG-TAAAATG
1 ACCGAAATACCCCCATA-GGATAAAATG
* * *
39664061 ACCAAAATACCCCCAAAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* *
39664088 ATCGAAATACCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* * * *
39664115 ATCGAAATATCTCCATAGGATAGAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* ** *
39664142 ACCAAAATACCCTTATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
* *
39664169 ACCGAAATACCCCAATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGATAAAATG
39664196 A
1 A
39664197 TTGTTTTACC
Statistics
Matches: 303, Mismatches: 45, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
26 24 0.08
27 278 0.92
28 1 0.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
ACCGAAATACCCCCATAGGATAAAATG
Found at i:39664088 original size:81 final size:81
Alignment explanation
Indices: 39663823--39664196 Score: 473
Period size: 81 Copynumber: 4.6 Consensus size: 81
39663813 ATCTGCACCG
* * *
39663823 AAATACCCTCATAGGATAAAATGACCGAAATACCCCCATAGGGTAGAATGATCGAAATACCCCCA
1 AAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCA
* * *
39663888 TAGGGTAGAATGATCG
66 TAGGGTAAAATGACCA
* * * * *
39663904 AAATACCCTTATAGGGTAAAATGACCAAAATAACCCTATAGGGTAAAATGACCAAAAT-CCCCCA
1 AAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCA
* *
39663968 TAGGGTAAAATGATCG
66 TAGGGTAAAATGACCA
* * * *
39663984 AAATATCCC-CATAGGGTAAAATGACCAAAATACCCCCATACGATAAAATGACCGAAATACCCCT
1 AAATA-CCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
*
39664048 ATATGGTAAAATGACCA
65 ATAGGGTAAAATGACCA
* * * * * *
39664065 AAATACCCCCAAAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATATCTCCA
1 AAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCA
* *
39664130 TAGGATAGAATGACCA
66 TAGGGTAAAATGACCA
* *
39664146 AAATACCCTTATAGGGTAAAATGACCGAAATACCCCAATAGGGTAAAATGA
1 AAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGA
39664197 TTGTTTTACC
Statistics
Matches: 254, Mismatches: 36, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
80 72 0.28
81 182 0.72
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (81 bp):
AAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCA
TAGGGTAAAATGACCA
Found at i:39664207 original size:54 final size:54
Alignment explanation
Indices: 39663821--39664197 Score: 468
Period size: 54 Copynumber: 7.0 Consensus size: 54
39663811 ATATCTGCAC
* * *
39663821 CGAAATACCCTCATAGGATAAAATGACCGAAATACCCCCATAGGGTAGAATGAT
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* * ** *
39663875 CGAAATACCCCCATAGGGTAGAATGATCGAAATACCCTTATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* * * *
39663929 CAAAATAACCCTATAGGGTAAAATGACCAAAAT-CCCCCATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* * * * *
39663982 CGAAATATCCCCATAGGGTAAAATGACCAAAATACCCCCATACGATAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* * * *
39664036 CGAAATACCCCTATATGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* * * * * *
39664090 CGAAATACCCCCATAGGGTAAAATGATCGAAATATCTCCATAGGATAGAATGAC
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
* ** *
39664144 CAAAATACCCTTATAGGGTAAAATGACCGAAATACCCCAATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
39664198 TGTTTTACCC
Statistics
Matches: 272, Mismatches: 50, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 47 0.17
54 225 0.83
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (54 bp):
CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAT
Found at i:39665954 original size:11 final size:11
Alignment explanation
Indices: 39665938--39665963 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39665928 CTTCATTCAT
39665938 CATCCCTCAAG
1 CATCCCTCAAG
39665949 CATCCCTCAAG
1 CATCCCTCAAG
39665960 CATC
1 CATC
39665964 ATTCTCGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.46, G:0.08, T:0.19
Consensus pattern (11 bp):
CATCCCTCAAG
Found at i:39671335 original size:36 final size:36
Alignment explanation
Indices: 39671288--39671357 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
39671278 ACAATTGGCT
39671288 AATTCAGGTCTCAAAAACGAGTAAAATAAGGCAACC
1 AATTCAGGTCTCAAAAACGAGTAAAATAAGGCAACC
* * *
39671324 AATTCGGGTCTCAAAAATGAGTAAAATGAGGCAA
1 AATTCAGGTCTCAAAAACGAGTAAAATAAGGCAA
39671358 TTTTCACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (36 bp):
AATTCAGGTCTCAAAAACGAGTAAAATAAGGCAACC
Found at i:39680020 original size:17 final size:17
Alignment explanation
Indices: 39679986--39680023 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
39679976 TTTTAGACTC
*
39679986 AATTATCAATTAAATAA
1 AATTATCAAATAAATAA
*
39680003 AATT-TCAAATAAATTA
1 AATTATCAAATAAATAA
39680019 AATTA
1 AATTA
39680024 ATCTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTATCAAATAAATAA
Found at i:39682234 original size:22 final size:23
Alignment explanation
Indices: 39682192--39682234 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39682182 TATTTTCACG
*
39682192 TTTATATATTTGATAAAAGAACT
1 TTTATATATTTGAAAAAAGAACT
*
39682215 TTTATAT-TTTTAAAAAAGAA
1 TTTATATATTTGAAAAAAGAA
39682235 AGCCACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
TTTATATATTTGAAAAAAGAACT
Found at i:39682520 original size:57 final size:57
Alignment explanation
Indices: 39682430--39682542 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
39682420 AAAACAAACT
**
39682430 CTCAAAAATAATTAATTACTTAAATGGCCTATTTTTTGATAAAATATGAAATTAACA
1 CTCAAAAATAATTAATTACTTAAATAACCTATTTTTTGATAAAATATGAAATTAACA
**
39682487 CTCAAAAATAATTAATTACTTAAATAATTTATTTTTTGATAAAATATGAAATTAAC
1 CTCAAAAATAATTAATTACTTAAATAACCTATTTTTTGATAAAATATGAAATTAAC
39682543 CTAACATCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (57 bp):
CTCAAAAATAATTAATTACTTAAATAACCTATTTTTTGATAAAATATGAAATTAACA
Found at i:39682997 original size:31 final size:32
Alignment explanation
Indices: 39682959--39683036 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 32
39682949 TCTAATGTAT
*
39682959 ATTTTAAATGTTTT-ATAA-TATTATTTTTTAA
1 ATTTTAAATATTTTGA-AATTATTATTTTTTAA
39682990 ATTTTAAATATATTTGAAATTATTATTTTTTAA
1 ATTTTAAATAT-TTTGAAATTATTATTTTTTAA
*
39683023 AATTTAAATATTTT
1 ATTTTAAATATTTT
39683037 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 10 0.24
32 8 0.19
33 24 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
ATTTTAAATATTTTGAAATTATTATTTTTTAA
Found at i:39683039 original size:19 final size:19
Alignment explanation
Indices: 39683015--39683052 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39683005 GAAATTATTA
39683015 TTTTTTAAAATTTAAATAT
1 TTTTTTAAAATTTAAATAT
39683034 TTTTTTAAAATTTAAATAT
1 TTTTTTAAAATTTAAATAT
39683053 AATTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTAAAATTTAAATAT
Found at i:39683058 original size:20 final size:19
Alignment explanation
Indices: 39682983--39683059 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
39682973 ATAATATTAT
*
39682983 TTTTTAAATTTTAAATATA
1 TTTTTAAAATTTAAATATA
* *
39683002 --TTTGAAA-TT-ATTAT-
1 TTTTTAAAATTTAAATATA
*
39683016 TTTTTAAAATTTAAATATT
1 TTTTTAAAATTTAAATATA
39683035 TTTTTAAAATTTAAATATAA
1 TTTTTAAAATTTAAATAT-A
39683055 TTTTT
1 TTTTT
39683060 TGATATTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
15 4 0.09
16 8 0.17
17 7 0.15
18 4 0.09
19 18 0.39
20 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTTAAATATA
Found at i:39683158 original size:22 final size:21
Alignment explanation
Indices: 39683122--39683222 Score: 87
Period size: 23 Copynumber: 4.5 Consensus size: 21
39683112 ATTTATTATT
*
39683122 TATTTTATAATATTTTAAATGTA
1 TATTTTA-AAAATTTTAAAT-TA
39683145 TATTTTAAAAATTTTAAAAATTA
1 TATTTTAAAAATTTT--AAATTA
*
39683168 TTTTTTAAAAATTTTAAAAATTA
1 TATTTTAAAAATTTT--AAATTA
*
39683191 T-TTTTTAAAATTTTGAATATTA
1 TATTTTAAAAATTTT-AA-ATTA
*
39683213 TTTTTTAAAA
1 TATTTTAAAA
39683223 TTATTATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.03
22 24 0.35
23 39 0.57
24 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTAAAAATTTTAAATTA
Found at i:39683173 original size:23 final size:23
Alignment explanation
Indices: 39683138--39683222 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
39683128 ATAATATTTT
*
39683138 AAATGTATATTTTAAAAATTTTAA
1 AAAT-TATTTTTTAAAAATTTTAA
39683162 AAATTATTTTTTAAAAATTTTAA
1 AAATTATTTTTTAAAAATTTTAA
*
39683185 AAATTATTTTTT-AAAATTTTGA
1 AAATTATTTTTTAAAAATTTTAA
*
39683207 ATATTATTTTTTAAAA
1 AAATTATTTTTTAAAA
39683223 TTATTATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
22 20 0.35
23 33 0.58
24 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATTATTTTTTAAAAATTTTAA
Found at i:39683223 original size:22 final size:22
Alignment explanation
Indices: 39683121--39683224 Score: 122
Period size: 22 Copynumber: 4.7 Consensus size: 22
39683111 AATTTATTAT
* *
39683121 TTATTTTATAATATTTT--AAA
1 TTATTTTTTAAAATTTTAAAAA
*
39683141 TGTATATTTTAAAAATTTTAAAAA
1 T-TAT-TTTTTAAAATTTTAAAAA
39683165 TTATTTTTTAAAAATTTTAAAAA
1 TTATTTTTT-AAAATTTTAAAAA
* *
39683188 TTATTTTTTAAAATTTTGAATA
1 TTATTTTTTAAAATTTTAAAAA
39683210 TTATTTTTTAAAATT
1 TTATTTTTTAAAATT
39683225 ATTATTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 40 0.55
23 25 0.34
24 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTTTTTAAAATTTTAAAAA
Found at i:39683229 original size:16 final size:16
Alignment explanation
Indices: 39683208--39683243 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39683198 AAATTTTGAA
39683208 TATTATTTTTTAAAAT
1 TATTATTTTTTAAAAT
39683224 TATTATTTTTTAAAAT
1 TATTATTTTTTAAAAT
39683240 TATT
1 TATT
39683244 TTAAAGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTTTTTAAAAT
Found at i:39683318 original size:11 final size:10
Alignment explanation
Indices: 39683302--39683347 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 10
39683292 TAATACTTTA
39683302 TTTATTTGTCT
1 TTTATTTGT-T
39683313 TTTATTTGTT
1 TTTATTTGTT
39683323 TATTATTTGTT
1 T-TTATTTGTT
39683334 TATTAATTTGTT
1 T-TT-ATTTGTT
39683346 TT
1 TT
39683348 ACAATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 23 0.70
12 8 0.24
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (10 bp):
TTTATTTGTT
Found at i:39683626 original size:18 final size:19
Alignment explanation
Indices: 39683603--39683646 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
39683593 AATGAAAAAA
39683603 TAAAAAAT-ATTTATTTAT
1 TAAAAAATGATTTATTTAT
*
39683621 TAAAAAATGATTTATTTGT
1 TAAAAAATGATTTATTTAT
39683640 TAAAAAA
1 TAAAAAA
39683647 CTACGACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAAAAATGATTTATTTAT
Found at i:39691402 original size:145 final size:145
Alignment explanation
Indices: 39691136--39691405 Score: 441
Period size: 145 Copynumber: 1.9 Consensus size: 145
39691126 AACCAACATC
39691136 ACCTTCTACAATTTCACCATAAAAAAGAATATACACAAAAAAAACCTTATTATTCATATTCAACA
1 ACCTTCTACAATTTCACCATAAAAAAGAATATACACAAAAAAAACCTTATTATTCATATTCAACA
* *
39691201 GAAATTTTGAACTCTCCTACTAAACACAACAACTTCATCATTCTATATATGGTAGAGAACTAAGA
66 GAAATTTTGAACTCTCCTACTAAACACAACAACTTCACCATTCTATATATGCTAGAGAACTAAGA
39691266 GGTGGAGCCATTCTT
131 GGTGGAGCCATTCTT
* ** * * *
39691281 ACCTTCTACAATTTCACCATAAAAAAGAATATACACCAAAAGCACCTTGTTATTTATCTTCAACA
1 ACCTTCTACAATTTCACCATAAAAAAGAATATACACAAAAAAAACCTTATTATTCATATTCAACA
* * *
39691346 GAATTTTTGAACTCTCTTACTAAACACAACAACTTCCCCATTCTATATATGCTAGAGAAC
66 GAAATTTTGAACTCTCCTACTAAACACAACAACTTCACCATTCTATATATGCTAGAGAAC
39691406 AATGGCTCCA
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
145 114 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.30
Consensus pattern (145 bp):
ACCTTCTACAATTTCACCATAAAAAAGAATATACACAAAAAAAACCTTATTATTCATATTCAACA
GAAATTTTGAACTCTCCTACTAAACACAACAACTTCACCATTCTATATATGCTAGAGAACTAAGA
GGTGGAGCCATTCTT
Found at i:39691626 original size:21 final size:22
Alignment explanation
Indices: 39691585--39691663 Score: 85
Period size: 21 Copynumber: 3.7 Consensus size: 22
39691575 TAAAAATAAT
39691585 AATTTT-AAA-AAATATTT-AA
1 AATTTTAAAACAAATATTTAAA
39691604 AATTTTAAAA-AAATATTTAAA
1 AATTTTAAAACAAATATTTAAA
* * *
39691625 AATTTTAAAATATACATTTAAA
1 AATTTTAAAACAAATATTTAAA
*
39691647 ATATTATAAAACAAATA
1 A-ATTTTAAAACAAATA
39691664 ATAAATTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.12
20 11 0.22
21 12 0.24
22 10 0.20
23 11 0.22
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTTAAAACAAATATTTAAA
Found at i:39691778 original size:17 final size:18
Alignment explanation
Indices: 39691744--39691783 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
39691734 TAAAATTTTA
*
39691744 AAAATAATATTTAAATTT
1 AAAATAATATATAAATTT
*
39691762 AAAA-AATATATATATTT
1 AAAATAATATATAAATTT
39691779 AAAAT
1 AAAAT
39691784 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATAATATATAAATTT
Found at i:39691811 original size:24 final size:21
Alignment explanation
Indices: 39691710--39691814 Score: 104
Period size: 21 Copynumber: 4.7 Consensus size: 21
39691700 TTTTAAATGT
* *
39691710 TTTATAATATTAAAAAATTATA
1 TTTAAAAT-TTAAAAAATAATA
*
39691732 TTTAAAATTTTAAAAATAATA
1 TTTAAAATTTAAAAAATAATA
39691753 TTT-AAATTTAAAAAATATATATA
1 TTTAAAATTT-AAAAA-ATA-ATA
39691776 TTTAAAATTTTAAAAAATAATA
1 TTTAAAA-TTTAAAAAATAATA
39691798 TTATAGAACATTTAAAA
1 TT-TA-AA-ATTTAAAA
39691815 TATACATTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
20 6 0.08
21 18 0.25
22 15 0.21
23 11 0.15
24 17 0.24
25 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
TTTAAAATTTAAAAAATAATA
Found at i:39691863 original size:13 final size:13
Alignment explanation
Indices: 39691831--39691868 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
39691821 TTAAAATATT
*
39691831 ATAAAACCAAT-A
1 ATAAAACAAATAA
39691843 AT-AAACAAATAA
1 ATAAAACAAATAA
39691855 ATAAAACAAATAA
1 ATAAAACAAATAA
39691868 A
1 A
39691869 GGACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 7 0.30
12 5 0.22
13 11 0.48
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAACAAATAA
Found at i:39701943 original size:8 final size:8
Alignment explanation
Indices: 39701924--39701958 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
39701914 ACTCGACATG
39701924 TTTATATTT
1 TTTAT-TTT
39701933 TTTATTTT
1 TTTATTTT
39701941 TTTATTTT
1 TTTATTTT
39701949 TTTATTTT
1 TTTATTTT
39701957 TT
1 TT
39701959 GCCAAGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.81
9 5 0.19
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTATTTT
Found at i:39702388 original size:16 final size:16
Alignment explanation
Indices: 39702367--39702397 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39702357 ATATTTTATC
39702367 TATTTTTTAGATTTTT
1 TATTTTTTAGATTTTT
*
39702383 TATTTTTTTGATTTT
1 TATTTTTTAGATTTT
39702398 CTTACAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
TATTTTTTAGATTTTT
Found at i:39703978 original size:39 final size:37
Alignment explanation
Indices: 39703935--39704025 Score: 87
Period size: 42 Copynumber: 2.4 Consensus size: 37
39703925 AAAAATCAAG
* *
39703935 ATTAATATTATTATATTGATAATAAAAT-TTATTTTTATT
1 ATTAATATTATTATATTAAT-ATAAAATATTA-TATT-TT
*
39703974 ATTAAAAATATTAATATATTAATATAAAATATTATATTTT
1 ATT---AATATTATTATATTAATATAAAATATTATATTTT
39704014 -TTAATATTATTA
1 ATTAATATTATTA
39704026 AACATACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
36 9 0.20
39 5 0.11
40 2 0.05
41 10 0.23
42 18 0.41
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (37 bp):
ATTAATATTATTATATTAATATAAAATATTATATTTT
Found at i:39704003 original size:21 final size:21
Alignment explanation
Indices: 39703938--39704008 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
39703928 AATCAAGATT
*
39703938 AATATTATTATATTGATAATAA
1 AATATTATTATATTAAT-ATAA
* *
39703960 AAT-TTATTTTTATTATTA-AA
1 AATATTA-TTATATTAATATAA
*
39703980 AATATTAATATATTAATATAA
1 AATATTATTATATTAATATAA
39704001 AATATTAT
1 AATATTAT
39704009 ATTTTTTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 13 0.33
21 16 0.41
22 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
AATATTATTATATTAATATAA
Found at i:39704017 original size:22 final size:22
Alignment explanation
Indices: 39703956--39704020 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
39703946 TATATTGATA
*
39703956 ATAAAAT-TTAT-TTTTATTATT
1 ATAAAATATTATATTTT-TTAAT
* *
39703977 A-AAAATATTA-ATATATTAAT
1 ATAAAATATTATATTTTTTAAT
39703997 ATAAAATATTATATTTTTTAAT
1 ATAAAATATTATATTTTTTAAT
39704019 AT
1 AT
39704021 TATTAAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 10 0.29
21 15 0.43
22 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATATTATATTTTTTAAT
Done.