Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 9 of 228
Found at i:3198514 original size:16 final size:17
Alignment explanation
Indices: 3198480--3198511 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3198470 TTAGAAATTT
3198480 TATTTAATGAAATAAAA
1 TATTTAATGAAATAAAA
3198497 TATTTAA-G-AATAAAA
1 TATTTAATGAAATAAAA
3198512 ATACGTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
TATTTAATGAAATAAAA
Found at i:3201584 original size:52 final size:51
Alignment explanation
Indices: 3201513--3201728 Score: 235
Period size: 46 Copynumber: 4.1 Consensus size: 51
3201503 ATCAAGTGAC
* **
3201513 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
3201565 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
3201611 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-------AAGTG
* *
3201669 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
3201722 ATAAGTG
1 A-AAGTG
3201729 GCTACACTTA
Statistics
Matches: 141, Mismatches: 9, Indels: 27
0.80 0.05 0.15
Matches are distributed among these distances:
46 44 0.31
52 42 0.30
53 11 0.08
59 44 0.31
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:3201619 original size:98 final size:101
Alignment explanation
Indices: 3201499--3201729 Score: 360
Period size: 98 Copynumber: 2.3 Consensus size: 101
3201489 TTTGAGTACT
*
3201499 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTA
3201563 G-G-AAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
3201597 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
3201662 AAAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
65 ---AGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
3201702 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
3201730 CTACACTTAT
Statistics
Matches: 120, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
98 61 0.51
103 1 0.01
104 1 0.01
105 57 0.47
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (101 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTA
GTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:3201661 original size:7 final size:7
Alignment explanation
Indices: 3201650--3201683 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3201640 TTATCTGATC
*
3201650 AAGTGAC
1 AAGTGAA
3201657 AAGTGAA
1 AAGTGAA
3201664 AAGTGAA
1 AAGTGAA
*
3201671 AAGTGAT
1 AAGTGAA
3201678 AAGTGA
1 AAGTGA
3201684 TAGCTTCGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (7 bp):
AAGTGAA
Found at i:3201680 original size:59 final size:61
Alignment explanation
Indices: 3201604--3201728 Score: 209
Period size: 59 Copynumber: 2.1 Consensus size: 61
3201594 TTATCTGATC
*
3201604 AAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTGAA
1 AAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGAA
* *
3201664 AAGTGA-AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGAT
1 AAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGAA
3201724 AAGTG
1 AAGTG
3201729 GCTACACTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 44 0.72
60 17 0.28
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.26
Consensus pattern (61 bp):
AAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGAA
Found at i:3201738 original size:37 final size:37
Alignment explanation
Indices: 3201691--3201837 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
3201681 TGATAGCTTC
* *
3201691 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
3201728 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
3201765 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
3201802 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
3201837 G
1 G
3201838 ATCATACGTA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:3203408 original size:65 final size:65
Alignment explanation
Indices: 3203327--3203456 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
3203317 TCGACTAAAC
3203327 CCAAATAATACAAAACCAAAAGTAGAAAGACACGTAAAGCCTCGGCAAGGGACCAACAACACCCT
1 CCAAATAATACAAAACCAAAAGTAGAAAGACACGTAAAGCCTCGGCAAGGGACCAACAACACCCT
* *
3203392 CCAAATAATACAAAACCAAAAGTAGAAAGAGATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
1 CCAAATAATACAAAACCAAAAGTAGAAAGACACGTAAAGCCTCGGCAAGGGACCAACAACACCCT
3203457 TTATAAGGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (65 bp):
CCAAATAATACAAAACCAAAAGTAGAAAGACACGTAAAGCCTCGGCAAGGGACCAACAACACCCT
Found at i:3208848 original size:11 final size:11
Alignment explanation
Indices: 3208832--3208856 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3208822 ACAGCAATGG
3208832 CCAATGTTCAT
1 CCAATGTTCAT
3208843 CCAATGTTCAT
1 CCAATGTTCAT
3208854 CCA
1 CCA
3208857 TCAGAGGATG
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (11 bp):
CCAATGTTCAT
Found at i:3210089 original size:10 final size:10
Alignment explanation
Indices: 3210074--3210103 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3210064 AAATTTATAA
3210074 TTTATATTTT
1 TTTATATTTT
3210084 TTTATATTTT
1 TTTATATTTT
*
3210094 TTTAGATTTT
1 TTTATATTTT
3210104 ATACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTATATTTT
Found at i:3224063 original size:29 final size:30
Alignment explanation
Indices: 3224026--3224085 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3224016 TATTTTCTTC
* * * *
3224026 TTCT-TTTTTTTTACTGTTTTGTTATTATT
1 TTCTGTTTTTTTCACTATTTTATTATCATT
3224055 TTCTGTTTTTTTCACTATTTTATTATCATT
1 TTCTGTTTTTTTCACTATTTTATTATCATT
3224085 T
1 T
3224086 CACTATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (30 bp):
TTCTGTTTTTTTCACTATTTTATTATCATT
Found at i:3224085 original size:11 final size:11
Alignment explanation
Indices: 3224070--3224168 Score: 56
Period size: 11 Copynumber: 8.6 Consensus size: 11
3224060 TTTTTTTCAC
3224070 TATTTTATTAT
1 TATTTTATTAT
* * *
3224081 CATTTCACTAT
1 TATTTTATTAT
*
3224092 TATATTATTAT
1 TATTTTATTAT
* *
3224103 TATTTTGTTGT
1 TATTTTATTAT
*
3224114 TATTGT-TTAT
1 TATTTTATTAT
* *
3224124 ATATTGTATAACTCT
1 -TATT-T-T-ATTAT
*
3224139 TGTTTTATTAT
1 TATTTTATTAT
3224150 TAATTTTATTAT
1 T-ATTTTATTAT
3224162 TATTTTA
1 TATTTTA
3224169 GAGATATTTG
Statistics
Matches: 63, Mismatches: 19, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
10 3 0.05
11 42 0.67
12 11 0.17
13 2 0.03
14 3 0.05
15 2 0.03
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:3229021 original size:15 final size:16
Alignment explanation
Indices: 3229001--3229034 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3228991 ATCATTCAAA
3229001 AAATTACAAAAAT-AT
1 AAATTACAAAAATAAT
*
3229016 AAATTACTAAAATAAT
1 AAATTACAAAAATAAT
3229032 AAA
1 AAA
3229035 ATTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTACAAAAATAAT
Found at i:3229633 original size:4 final size:4
Alignment explanation
Indices: 3229624--3229654 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3229614 GGTGGCAGTG
3229624 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3229655 GAAGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3230080 original size:21 final size:21
Alignment explanation
Indices: 3230056--3230096 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3230046 AAAAAAAATT
3230056 AAAAGTCTTAA-AATATATATG
1 AAAAGTC-TAATAATATATATG
*
3230077 AAAATTCTAATAATATATAT
1 AAAAGTCTAATAATATATAT
3230097 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAGTCTAATAATATATATG
Found at i:3238225 original size:43 final size:43
Alignment explanation
Indices: 3238166--3238260 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
3238156 AATGATGATA
* *
3238166 TAAAATT-ATACAAATATAAATTATTTTCTTTTATATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
*
3238208 TAAAATTAAAACAAATATAAATTATTTTATTTTGTATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
3238251 TAAAATTAAA
1 TAAAATTAAA
3238261 GGAAACAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 7 0.14
43 42 0.86
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (43 bp):
TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
Found at i:3241688 original size:27 final size:27
Alignment explanation
Indices: 3241650--3241714 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
3241640 ATTGATAAGG
*
3241650 ACGTAAAATTTTAGTGGGTTACACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
3241677 ACGTAAAATTTTAGTGGGTTAAACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
*
3241704 ACATAAGAATT
1 ACGTAA-AATT
3241715 GATAAGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (27 bp):
ACGTAAAATTTTAGTGGGTTAAACTAC
Found at i:3251291 original size:20 final size:20
Alignment explanation
Indices: 3251254--3251291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3251244 CTTAATTATT
3251254 AAAATGTAAAAAATTATAGA
1 AAAATGTAAAAAATTATAGA
3251274 AAAAT-TAAAAAATATATA
1 AAAATGTAAAAAAT-TATA
3251292 AAGTTTCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAATGTAAAAAATTATAGA
Found at i:3255153 original size:42 final size:41
Alignment explanation
Indices: 3255107--3255232 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 41
3255097 GATTGAACGT
* * *
3255107 CAGTATTCGGTTTGCCCCTCGAGAGCCTGGGTGATTGAAATG
1 CAGTA-TCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
* *
3255149 CAGTATCTGGTTTGTCCTTGGAGAGCCTGGGCGACTGAAATG
1 CAGTATC-GGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
* * *
3255191 CAGTATCGGATTTGTCCTTGGAGAGCCTAGGTGGTTCAAATG
1 CAGTATCGG-TTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
3255233 TACCATCGGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
41 4 0.06
42 68 0.94
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (41 bp):
CAGTATCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
Found at i:3255241 original size:42 final size:42
Alignment explanation
Indices: 3255159--3255247 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
3255149 CAGTATCTGG
* * **
3255159 TTTGTCCTTGGAGAGCCTGGGCGACTGAAATGCAGTATCGGA
1 TTTGTCCTTGGAGAGCCTAGGCGACTCAAATGCACCATCGGA
* ** *
3255201 TTTGTCCTTGGAGAGCCTAGGTGGTTCAAATGTACCATCGGA
1 TTTGTCCTTGGAGAGCCTAGGCGACTCAAATGCACCATCGGA
3255243 TTTGT
1 TTTGT
3255248 TCATGGGGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (42 bp):
TTTGTCCTTGGAGAGCCTAGGCGACTCAAATGCACCATCGGA
Found at i:3258838 original size:21 final size:21
Alignment explanation
Indices: 3258812--3258851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3258802 CATATATTGA
3258812 TAGATAAAAAATAAAGTAGAT
1 TAGATAAAAAATAAAGTAGAT
**
3258833 TAGATATCAAATAAAGTAG
1 TAGATAAAAAATAAAGTAG
3258852 GCAGACCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (21 bp):
TAGATAAAAAATAAAGTAGAT
Found at i:3260576 original size:23 final size:22
Alignment explanation
Indices: 3260549--3260591 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3260539 AAATTTTTCA
3260549 AAAATTAAATAAATACAAAAATT
1 AAAATTAAATAAATA-AAAAATT
*
3260572 AAAATTAAATAATTAAAAAA
1 AAAATTAAATAAATAAAAAA
3260592 GTGCATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATTAAATAAATAAAAAATT
Found at i:3263228 original size:22 final size:24
Alignment explanation
Indices: 3263184--3263228 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
3263174 GCTTCATGTT
*
3263184 ATTTTTTATAAACTTTATATATAG
1 ATTTTTTATAAACTATATATATAG
*
3263208 ATTTTTTA-AAA-TATATTTATA
1 ATTTTTTATAAACTATATATATA
3263229 AGTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTTTATAAACTATATATATAG
Found at i:3267191 original size:33 final size:33
Alignment explanation
Indices: 3267154--3267232 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
3267144 GCCTATAGAT
*
3267154 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
1 AAAAGGAATATATTTATAGCAGTAGTACAAGCC
*
3267187 AAAAGGAATATATTTATAGCAGTAGTAGAAGCC
1 AAAAGGAATATATTTATAGCAGTAGTACAAGCC
*
3267220 AAAACGAATATAT
1 AAAAGGAATATAT
3267233 CATATCTAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (33 bp):
AAAAGGAATATATTTATAGCAGTAGTACAAGCC
Found at i:3272948 original size:109 final size:110
Alignment explanation
Indices: 3272767--3273061 Score: 438
Period size: 110 Copynumber: 2.7 Consensus size: 110
3272757 ATATTTGGCT
* * * * *
3272767 ATTTGGTTAAATGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTCAAATTTCCAAACG
1 ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
*
3272829 CAAAACATTGCCTTATTTTGAAA-TTTTTAAAAGGATATTTAA-CC
66 CAAAACATTGCCTTATTTTAAAATTTTTTAAAAGGATA-TTAAGCC
3272873 ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
*
3272938 CCAAACATTGCCTTATTTTAAAATTTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTTAAAAGGATATTAAGCC
* *
3272983 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAAC
1 ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTT-CCAAAC
* *
3273048 GCTAAATATTGCCT
65 GCAAAACATTGCCT
3273062 CAATTAGAAA
Statistics
Matches: 172, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
106 14 0.08
108 25 0.15
109 43 0.25
110 72 0.42
111 18 0.10
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (110 bp):
ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTTAAAAGGATATTAAGCC
Found at i:3273948 original size:3 final size:3
Alignment explanation
Indices: 3273942--3274007 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
3273932 AAATATGATG
* * *
3273942 ATA ATA AAA ATA ATA TTAA ATA ATA ATA ATA ATA ATA AT- AGA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
3273987 ATGA ACA A-A ATA ATA AAA ATA
1 AT-A ATA ATA ATA ATA ATA ATA
3274008 CTACAAAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 3 0.06
3 43 0.86
4 4 0.08
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:3273998 original size:23 final size:21
Alignment explanation
Indices: 3273948--3274015 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 21
3273938 GATGATAATA
* *
3273948 AAAATAATATTAAATAATAAT
1 AAAATAATAATAAATAATAAC
3273969 AATAATAATAATAGAATAATGAAC
1 AA-AATAATAATA-AATAAT-AAC
*
3273993 AAAATAATAA-AAATACT-AC
1 AAAATAATAATAAATAATAAC
3274012 AAAA
1 AAAA
3274016 GGGCTTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.15
21 7 0.17
22 10 0.24
23 14 0.34
24 4 0.10
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAATAATAATAAATAATAAC
Found at i:3275816 original size:44 final size:44
Alignment explanation
Indices: 3275582--3276136 Score: 280
Period size: 44 Copynumber: 12.8 Consensus size: 44
3275572 GTATTTTTCG
* ** * * **
3275582 TCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTGGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* *** *
3275625 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCC-TGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCCTTTATTTTAA
* ** **
3275668 TCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCT-TTATT-TT-AA
* * * ***
3275714 TCTACTCCACTGTAACCTCAGGGAGATAAGA-CC-TGA-TGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* ** *
3275755 TCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* * ** * * **
3275799 TCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTGGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* * * *
3275842 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTCTAGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCCTTTA-TTTTAA
* ** **
3275886 TCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCT-TTATT-TT-AA
* * * ***
3275932 TCTACTCCACTGTAACCTCAGGGAGATAAGA-CC-TGA-TGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* ** * *
3275973 TCTACTCTGCTGTAACTTCAGAGAGATGAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* ** * * **
3276017 TCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
* *** *
3276060 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCCT-TTATTTTAA
*
3276104 TCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC
3276137 TGAAATATTC
Statistics
Matches: 392, Mismatches: 93, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
41 55 0.14
42 11 0.03
43 128 0.33
44 133 0.34
45 3 0.01
46 62 0.16
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAA
Found at i:3275959 original size:218 final size:218
Alignment explanation
Indices: 3275585--3276142 Score: 1073
Period size: 218 Copynumber: 2.6 Consensus size: 218
3275575 TTTTTCGTCT
3275585 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
3275650 ATAAGATC-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGG
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGG
3275714 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
131 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
3275779 GATAAGATCCTTTATTTTAATCC
196 GATAAGATCCTTTATTTTAATCC
3275802 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
*
3275867 ATAAGATCTCTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGG
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGG
3275932 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
131 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
* *
3275997 GATGAGATCCTTTATTTTAATCT
196 GATAAGATCCTTTATTTTAATCC
*
3276020 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
3276085 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
66 ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
3276143 ATTCACTGAT
Statistics
Matches: 335, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
217 73 0.22
218 262 0.78
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (218 bp):
GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAG
ATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGG
TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
GATAAGATCCTTTATTTTAATCC
Found at i:3275975 original size:131 final size:129
Alignment explanation
Indices: 3275582--3276137 Score: 344
Period size: 131 Copynumber: 4.3 Consensus size: 129
3275572 GTATTTTTCG
* * * * ** * *
3275582 TCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTGGATCTGCTCCGCTGTAATCTCAG
1 TCTGCTCCGCTGTAAC-TCAGGGAGATAAGAT-CTCTACTTCAATCTGCTCCACTGTAACCTCAG
** * * * *
3275646 GGAGATAAGATCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA--TCTGAAATTC
64 GGAGATAAGATAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTG-GA---
* *
3275709 TTCGG
125 TGCGA
* * * * * ** *
3275714 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTGA-TGCGATCTACTCTGCTGTAACTTCAG
1 TCTGCTCCGCTGTAA-CTCAGGGAGATAAGATCTCT-ACTTCAATCTGCTCCACTGTAACCTCAG
* ** * * ** ** * * ** **
3275776 AGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTG
64 GGAGATAAGATAATGT-CTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTG-GATG
3275840 -GA
127 CGA
3275842 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTGCTCCACTGTAACCTCAG
1 TCTGCTCCGCTGTAA-CTCAGGGAGATAAGATCTCTA-CTTCAATCTGCTCCACTGTAACCTCAG
*
3275907 GGAGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GA
64 GGAGATAAGA--T--AATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTGGA
3275968 TGCGA
125 TGCGA
* * * * * * * *
3275973 TCTACTCTGCTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCTGCTCCACTGTAACTTCAG
1 TCTGCTCCGCTGTAAC-TCAGGGAGATAAGAT-CTCTACTTCAATCTGCTCCACTGTAACCTCAG
* * * * * * * *
3276038 GGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
64 GGAGATAAGATAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTGGATGCG
3276103 A
129 A
*
3276104 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
1 TCTGCTCCGCTGTAA-CTCAGGGAGATAAGATCT
3276138 GAAATATTCA
Statistics
Matches: 332, Mismatches: 70, Indels: 46
0.74 0.16 0.10
Matches are distributed among these distances:
127 2 0.01
128 63 0.19
129 6 0.02
130 42 0.13
131 151 0.45
132 35 0.11
133 31 0.09
134 1 0.00
135 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (129 bp):
TCTGCTCCGCTGTAACTCAGGGAGATAAGATCTCTACTTCAATCTGCTCCACTGTAACCTCAGGG
AGATAAGATAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTCTGGATGCGA
Found at i:3275986 original size:87 final size:84
Alignment explanation
Indices: 3275582--3276139 Score: 288
Period size: 87 Copynumber: 6.4 Consensus size: 84
3275572 GTATTTTTCG
* * * * * *
3275582 TCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTG-GATCTGCTCCGCTGTAATCTCAG
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-ACTG--ATGCGATCTACTCCGCTGTAACCTCAG
**
3275646 GGAGATAAGATCCT-GGCTTCAA
63 GGAGATAAGAT-CTATTCTTCAA
* * * *
3275668 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTC
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGAACTG--A---TGCGATCTACTCCGCTGTAACCTC
* * *
3275733 AGGGAGATAAGACCTGA---TGCGA
61 AGGGAGATAAGATCT-ATTCTTCAA
* ** * * * * *** ** * *
3275755 TCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAG
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-AC-TGA-TGCGATCTACTCCGCTGTAACCTCAG
* **
3275820 GGAGATAGGA--TAGTGTCTTGGA
63 GGAGATAAGATCTA-T-TCTTCAA
* * * * * * * *
3275842 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTGCTCCACTGTAACCTCAG
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA--ACT-GATGCGATCTACTCCGCTGTAACCTCAG
**
3275907 GGAGATAAGATCTGAAATTCTTCGG
63 GGAGATAAGATCT---ATTCTTCAA
* * * * *
3275932 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGAACTGATGCGATCTACTCCGCTGTAACCTCAGGGA
*
3275997 GATGAGATCCTTTATT-TT-AA
66 GATAAGAT-C--TATTCTTCAA
* * * * * * *
3276017 TCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGG
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-ACTG-ATGCGATCTACTCCGCTGTAACCTCAGG
* *
3276082 GAGATAAGATCTCTGGCTTCAA
64 GAGATAAGATCTAT-TCTTCAA
*
3276104 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGAACTGA
3276140 AATATTCACT
Statistics
Matches: 362, Mismatches: 82, Indels: 57
0.72 0.16 0.11
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 2 0.01
85 59 0.16
86 38 0.10
87 186 0.51
88 8 0.02
89 31 0.09
90 34 0.09
91 1 0.00
92 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (84 bp):
TCTGCTCCACTGTAACCTCAGGGAGATAAGAACTGATGCGATCTACTCCGCTGTAACCTCAGGGA
GATAAGATCTATTCTTCAA
Found at i:3277395 original size:6 final size:6
Alignment explanation
Indices: 3277386--3277421 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
3277376 TCCATTTTAC
3277386 TTTTCA TTTTTCA TTTTCA TTTTTCA TTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA -TTTTCA TTTTCA TTTT
3277422 TTTTGACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:3277398 original size:7 final size:7
Alignment explanation
Indices: 3277386--3277422 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
3277376 TCCATTTTAC
3277386 TTTTCAT
1 TTTTCAT
3277393 TTTTCA-
1 TTTTCAT
3277399 TTTTCAT
1 TTTTCAT
3277406 TTTTCA-
1 TTTTCAT
3277412 TTTTCAT
1 TTTTCAT
3277419 TTTT
1 TTTT
3277423 TTTGACTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTCAT
Found at i:3277402 original size:13 final size:13
Alignment explanation
Indices: 3277386--3277422 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
3277376 TCCATTTTAC
3277386 TTTTCATTTTTCA
1 TTTTCATTTTTCA
3277399 TTTTCATTTTTCA
1 TTTTCATTTTTCA
3277412 TTTTCATTTTT
1 TTTTCATTTTT
3277423 TTTGACTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:3278367 original size:6 final size:6
Alignment explanation
Indices: 3278334--3278475 Score: 53
Period size: 6 Copynumber: 23.7 Consensus size: 6
3278324 GATTTCTCTT
* * * * *
3278334 TTTTCA TTCTTC- TTTTCT TTTCTCA TTTTCA TTTTGA TCTTGA TTTTGA
1 TTTTCA TT-TTCA TTTTCA TTT-TCA TTTTCA TTTTCA TTTTCA TTTTCA
* ** * *
3278383 TTTT-- TTCTTCT TTCTTC- TTTTTG TTTT-- TTTTTA TTTTGA TTTTTTCA
1 TTTTCA TT-TTCA TT-TTCA TTTTCA TTTTCA TTTTCA TTTTCA -TTTT-CA
* * * * *
3278430 TTTTCA TTTTCA TTTTCA TTTTGA CTTTGA TTTTGA TTTTGA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
3278476 TCTTTTTTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.05
5 7 0.06
6 79 0.69
7 22 0.19
8 1 0.01
ACGTcount: A:0.11, C:0.12, G:0.06, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:3278368 original size:19 final size:20
Alignment explanation
Indices: 3278325--3278368 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3278315 TTTTATCTAG
*
3278325 ATTTCTCTTTTTTCATTCTTC
1 ATTT-TCTTTTCTCATTCTTC
3278346 -TTTTCTTTTCTCATT-TTC
1 ATTTTCTTTTCTCATTCTTC
3278364 ATTTT
1 ATTTT
3278369 GATCTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 15 0.71
20 3 0.14
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTCTTTTCTCATTCTTC
Found at i:3278398 original size:51 final size:51
Alignment explanation
Indices: 3278282--3278398 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 51
3278272 TGGCCTCTCC
* * *
3278282 TTTTCTT-TTTCTTTTCTTTTTCATTTTGATTTTTTTTATCTAGATTTCTCTT
1 TTTTCTTCTTTCTTTTCTTTTTCATTTTCA--TTTTTGATCTAGATTTCTATT
*
3278334 TTTTCATTC-TTCTTTTCTTTTCTCATTTTCA-TTTTGATCTTGATTT-TGATT
1 TTTTC-TTCTTTCTTTTCTTTT-TCATTTTCATTTTTGATCTAGATTTCT-ATT
3278385 TTTTCTTCTTTCTT
1 TTTTCTTCTTTCTT
3278399 CTTTTTGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
50 4 0.07
51 25 0.45
52 5 0.09
53 14 0.25
54 8 0.14
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.71
Consensus pattern (51 bp):
TTTTCTTCTTTCTTTTCTTTTTCATTTTCATTTTTGATCTAGATTTCTATT
Found at i:3278439 original size:12 final size:12
Alignment explanation
Indices: 3278424--3278475 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
3278414 TATTTTGATT
3278424 TTTTCATTTTCA
1 TTTTCATTTTCA
3278436 TTTTCATTTTCA
1 TTTTCATTTTCA
* * *
3278448 TTTTGACTTTGA
1 TTTTCATTTTCA
* *
3278460 TTTTGATTTTGA
1 TTTTCATTTTCA
3278472 TTTT
1 TTTT
3278476 TCTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.15, C:0.10, G:0.08, T:0.67
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:3279911 original size:5 final size:5
Alignment explanation
Indices: 3279901--3279962 Score: 83
Period size: 5 Copynumber: 12.2 Consensus size: 5
3279891 TAATTATGTT
3279901 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATA TTATTA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA
3279951 TTATA TATATA T
1 TTATA T-TATA T
3279963 GACAAAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 33 0.63
6 15 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:3279917 original size:3 final size:3
Alignment explanation
Indices: 3279904--3279954 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
3279894 TTATGTTTTA
*
3279904 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3279946 TAT TAT TAT
1 TAT TAT TAT
3279955 ATATATATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
2 12 0.29
3 29 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3280028 original size:40 final size:40
Alignment explanation
Indices: 3279971--3280066 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
3279961 ATGACAAAGA
3279971 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
3280012 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
3280052 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
3280067 AAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:3284984 original size:20 final size:21
Alignment explanation
Indices: 3284938--3284984 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
3284928 AAACAGACCT
*
3284938 AACCCAAAACAATAAAATTAC
1 AACCCAAAACAATAAAATTAA
*
3284959 AGCCCAAAA-AGA-AAAATTAA
1 AACCCAAAACA-ATAAAATTAA
3284979 AACCCA
1 AACCCA
3284985 GCCCAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.62, C:0.23, G:0.04, T:0.11
Consensus pattern (21 bp):
AACCCAAAACAATAAAATTAA
Found at i:3286103 original size:3 final size:3
Alignment explanation
Indices: 3286097--3286174 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
3286087 TTTAGCATTT
* * * * *
3286097 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
3286142 TTA TTA TTG TTA TTA TTA GTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
3286175 TCCTCATCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 6 0.10
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3286315 original size:47 final size:45
Alignment explanation
Indices: 3286224--3286335 Score: 102
Period size: 47 Copynumber: 2.4 Consensus size: 45
3286214 ATAGCGTATG
* * * * **
3286224 TTTTATAATATATATATACATATGTAAATTTTTTATTTTTTTTATTA
1 TTTTACAA-ATATATATACATATCTAAATATTTTATATAGTTTA-TA
3286271 TTTTTACAAATATATATACATA-CTAATATATTTTATATAGTTTATA
1 -TTTTACAAATATATATACATATCTAA-ATATTTTATATAGTTTATA
* *
3286317 -TGTACATATATATATACAT
1 TTTTACAAATATATATACAT
3286336 GCGCATGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
44 17 0.31
46 5 0.09
47 26 0.47
48 7 0.13
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (45 bp):
TTTTACAAATATATATACATATCTAAATATTTTATATAGTTTATA
Found at i:3286950 original size:106 final size:108
Alignment explanation
Indices: 3286746--3286952 Score: 256
Period size: 109 Copynumber: 1.9 Consensus size: 108
3286736 AAGGAAAATT
* * *
3286746 TTTCAAAGTAAGGTAATATTTTGCATTTAGAAATTCGAGAAAACGTGCCTTAAGGTGCTGGGTGC
1 TTTCAAAATAAGGCAATATTTTGCATTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGC
**
3286811 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
66 CGA-TTTTCTCGTTCAACCAAATGGCCAAATATCCTTTTAAAAA
* * * * * * **
3286855 TTTCAAAATATGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCATTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGC
* *
3286919 CGA-TTTCTCGTTTAACCAAATTGCCAAATATCCT
66 CGATTTTCTCGTTCAACCAAATGGCCAAATATCCT
3286953 CCTGAATTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 27 0.33
108 23 0.28
109 33 0.40
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATATTTTGCATTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGC
CGATTTTCTCGTTCAACCAAATGGCCAAATATCCTTTTAAAAA
Found at i:3288483 original size:28 final size:29
Alignment explanation
Indices: 3288398--3288484 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 29
3288388 AATTGGTAAT
* * *
3288398 TAAATTATATTGTTTTTCACATCTTGATACT
1 TAAACTATATT-TTTTTCACA-ATTGATACC
* *
3288429 TAAACT-T-TTTTTATCACAATTGGTACC
1 TAAACTATATTTTTTTCACAATTGATACC
*
3288456 TAAACTATATTTTTTTCA-AGTTGATACC
1 TAAACTATATTTTTTTCACAATTGATACC
3288484 T
1 T
3288485 TTGTTAGTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
27 12 0.26
28 18 0.39
29 10 0.22
30 1 0.02
31 5 0.11
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (29 bp):
TAAACTATATTTTTTTCACAATTGATACC
Found at i:3301490 original size:3 final size:3
Alignment explanation
Indices: 3301475--3301508 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3301465 AGGAACTATT
* *
3301475 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3301509 GGAAAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3301509 original size:15 final size:15
Alignment explanation
Indices: 3301482--3301510 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3301472 ATTCTGCTGT
3301482 TGCTGCTGCTGCGGC
1 TGCTGCTGCTGCGGC
3301497 TGCTGCTGCTGCGG
1 TGCTGCTGCTGCGG
3301511 AAAGTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (15 bp):
TGCTGCTGCTGCGGC
Found at i:3301543 original size:15 final size:15
Alignment explanation
Indices: 3301525--3301564 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3301515 TGATGAGGAG
*
3301525 GAGGGTGAGGAAAGC
1 GAGGGAGAGGAAAGC
*
3301540 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGC
*
3301555 GAAGGAGAGG
1 GAGGGAGAGG
3301565 GAGAGGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05
Consensus pattern (15 bp):
GAGGGAGAGGAAAGC
Found at i:3301564 original size:21 final size:21
Alignment explanation
Indices: 3301540--3301580 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3301530 TGAGGAAAGC
*
3301540 GAGGGAGAGGAAAGTGAAGGA
1 GAGGGAGAGGAAAGGGAAGGA
*
3301561 GAGGGAGAGGAGAGGGAAGG
1 GAGGGAGAGGAAAGGGAAGG
3301581 GATGAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (21 bp):
GAGGGAGAGGAAAGGGAAGGA
Found at i:3307787 original size:3 final size:3
Alignment explanation
Indices: 3307781--3307818 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3307771 AAACAAATTT
*
3307781 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3307819 TTGCATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3327518 original size:210 final size:210
Alignment explanation
Indices: 3327154--3328203 Score: 1665
Period size: 210 Copynumber: 5.0 Consensus size: 210
3327144 CAATCTATAA
* *
3327154 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
*
3327219 G-TTCC-CACAGCGAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCT
66 GTTTCCTCACA--GAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCT
* * *
3327282 GACAATTTATCCC-ATTCTGGTTTATACATGAGTGATGAAATTCATGAAAATTCACAAGTGGAAT
129 GACAATTTA-CCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAAT
*
3327346 CTGTCATCAGTAATCCAT
193 CTGTCATCAGTGATCCAT
* * *
3327364 TTGAATCCTCTGCCTCATCCAATATCATTTTAAGCGATGAGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * * *
3327429 GTTTCCTCGCAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* * *
3327494 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGGGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3327559 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* *
3327574 TTGAATCCTCTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
3327639 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3327704 CAATTTTCCCTATACTGATTTATACATGAGTGGTGAAATTCATAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3327769 TCATTAGTGATCCAT
196 TCATCAGTGATCCAT
3327784 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * *
3327849 GTTTCCTCACAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3327914 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
* *
3327979 TCAGCAATGATCCAT
196 TCATCAGTGATCCAT
* * *
3327994 TTGAATCCTTTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
3328059 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* * ** *
3328124 CAATTTTCCCTATACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3328189 TCATCAGTCATCCAT
196 TCATCAGTGATCCAT
3328204 CATCATCCTC
Statistics
Matches: 771, Mismatches: 66, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
209 3 0.00
210 761 0.99
211 4 0.01
212 3 0.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (210 bp):
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT
Found at i:3332989 original size:57 final size:57
Alignment explanation
Indices: 3332920--3333033 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
3332910 TATAAGAAAA
3332920 AGAAACCATTGATCAGCATGTACCCATCATTTCATGCATCTAGTAGTGGAATTCACT
1 AGAAACCATTGATCAGCATGTACCCATCATTTCATGCATCTAGTAGTGGAATTCACT
3332977 AGAAACCATTGATCAGCATGTACCCATCATTTCATGCATCTAGTAGTGGAATTCACT
1 AGAAACCATTGATCAGCATGTACCCATCATTTCATGCATCTAGTAGTGGAATTCACT
3333034 CTTTTCTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (57 bp):
AGAAACCATTGATCAGCATGTACCCATCATTTCATGCATCTAGTAGTGGAATTCACT
Found at i:3337899 original size:31 final size:30
Alignment explanation
Indices: 3337864--3337923 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3337854 GGAGGTGGGA
*
3337864 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
3337895 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
3337924 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:3342955 original size:31 final size:32
Alignment explanation
Indices: 3342920--3342981 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3342910 TGATAATTCA
**
3342920 GTGACTTA-AATAAAAACTTTTGAATAGTTTC
1 GTGACTTAGAATAAAAACTTTCAAATAGTTTC
*
3342951 GTGACTTAGAATGAAAACTTTCAAATAGTTT
1 GTGACTTAGAATAAAAACTTTCAAATAGTTT
3342982 AATAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (32 bp):
GTGACTTAGAATAAAAACTTTCAAATAGTTTC
Found at i:3344237 original size:9 final size:9
Alignment explanation
Indices: 3344223--3344254 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3344213 AACTTGGTGC
3344223 ATTTTGTTT
1 ATTTTGTTT
3344232 ATTTTGTTT
1 ATTTTGTTT
3344241 ATTTTGTTT
1 ATTTTGTTT
3344250 ATTTT
1 ATTTT
3344255 AATATTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:3344364 original size:23 final size:23
Alignment explanation
Indices: 3344331--3344379 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3344321 ATTGAAACAA
*
3344331 CATAATGATAGCTAATATGCTTT
1 CATAATAATAGCTAATATGCTTT
3344354 CATAATAATAGCTAATATGCTTT
1 CATAATAATAGCTAATATGCTTT
3344377 CAT
1 CAT
3344380 CTTTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (23 bp):
CATAATAATAGCTAATATGCTTT
Found at i:3348719 original size:9 final size:9
Alignment explanation
Indices: 3348705--3348736 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3348695 AACTTGGTGC
3348705 ATTTTGTTT
1 ATTTTGTTT
3348714 ATTTTGTTT
1 ATTTTGTTT
3348723 ATTTTGTTT
1 ATTTTGTTT
3348732 ATTTT
1 ATTTT
3348737 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:3348847 original size:23 final size:23
Alignment explanation
Indices: 3348814--3348862 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3348804 ATTGAAACAA
*
3348814 CATAATGATAGCTAATATGCTTT
1 CATAATAATAGCTAATATGCTTT
3348837 CATAATAATAGCTAATATGCTTT
1 CATAATAATAGCTAATATGCTTT
3348860 CAT
1 CAT
3348863 CTTTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (23 bp):
CATAATAATAGCTAATATGCTTT
Found at i:3353250 original size:48 final size:48
Alignment explanation
Indices: 3353179--3353313 Score: 234
Period size: 48 Copynumber: 2.8 Consensus size: 48
3353169 TAACAGAAGT
* * * *
3353179 GATAAAATGAACATAAATTTCATTTCCATAACATAATTTGTGGTAATA
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3353227 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3353275 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
3353314 ATTACAATAG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (48 bp):
GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
Found at i:3357926 original size:737 final size:742
Alignment explanation
Indices: 3356509--3357929 Score: 2242
Period size: 743 Copynumber: 1.9 Consensus size: 742
3356499 TCAAGACTAA
* * * *
3356509 GCTACAGTATAATTTTTTAATAAAGATCAGCAATCTCGGCCGAAAGATGGTGAATATTTATATAA
1 GCTACAGTAAAATGTTTGAATAAAGATCAGCAATCTCAGCCGAAAGATGGTGAATATTTATATAA
* *
3356574 TCATCATAAGACACATCAGGTTTGATGATTCATTTTCATCATAGATTGCAGCAACTGACAAAAAA
66 TCATCATAACACAAATCAGGTTTGATGATTCATTTTCATCATAGATTGCAGCAACTGACAAAAAA
* * * *
3356639 AGGAGGAAAAAAACAGTTATATCAATTAAAATTTGACCCCAAATTCCCAGAAAATTAAACAAAAT
131 ACGAGGAAAAAAACAATTAAATCAATTAAAATTTGACCCCAAATTCCCAGAAAAGTAAACAAAAT
3356704 ATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCATCATTCAAATGCAGAAATGATGGATA
196 ATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCATCATTCAAATGCAGAAATGATGGATA
* *
3356769 AGTATCATCACACCTCCTTGCATATCTTAAGAAAATCAAATCCTATGAAGCATAAAGAAGTAGAA
261 AGTATCATCACACCTCCTTGCATATCTTAAGAAAATCAAATCCTATGAAGCATAAAAAACTAGAA
*
3356834 CCATTAACTCATAGCAATTTCTGTTTGGCAAATTAACAAATTGAAAATAATCATAAAAAGAGAAT
326 CCATTAACT-ATAG-AATTTCTGTTTGGCAAATTAACAAAATGAAAATAATCATAAAAAGAGAAT
3356899 ATTTTACAGGTTACACCCCATTGGAGTAATGGTAAATGGATCAGATAGTCGATCGCTAATGTCTC
389 ATTTTACAGGTTACACCCCATTGGAGTAATGGTAAATGGATCAGATAGTCGATCGCTAATGTCTC
*
3356964 AGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTCATATCCACATTCAATCAAATTTTA
454 AGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTCATATCCACATTCAATCAAATTTAA
*
3357029 AAAAAATAAGATTTTAGACAAAATTTTGCAAACAAGTGAAGCTGCAGACAATAATTACAAGTGGA
519 AAAAAATAAGATTTTAAACAAAATTTTGCAAACAAGTGAAGCTGCAGACAATAATTACAAGTGGA
* *
3357094 AATCAGATAAAAAAGTCAATCACCAATTTTGCATATGAAGACATTATTATATGCAAAGTAAGACT
584 AATCAGATAAAAAAGTCAATCACCAATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACT
*
3357159 GGGGCGACAATAACTGTCATCATGTTCCCTTTTTCCCTTGAAAAACATAGCTCAAACAAAAACAT
649 GGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCTTGAAAAACATAGCTCAAACAAAAACAT
3357224 TTGACCTATATCATTAATTTTAGGACTGG
714 TTGACCTATATCATTAATTTTAGGACTGG
* *
3357253 GCTACATTAAAATGTTTGAATAAAGATCAGCAATCTCAGCCGAAAGATGGTGATTATTTATATAA
1 GCTACAGTAAAATGTTTGAATAAAGATCAGCAATCTCAGCCGAAAGATGGTGAATATTTATATAA
* * **
3357318 TCATCATAACATAAATCAGGTTTGATTATTCATTTTCATCATAGATTGCAGCAACTGAC-GGAAA
66 TCATCATAACACAAATCAGGTTTGATGATTCATTTTCATCATAGATTGCAGCAACTGACAAAAAA
* * *
3357382 ACGAGGCAAAAAACAATTAAATCAATTAAAATTTGACCCCCAATTCCCA-AAAAGGTAAAGAAAA
131 ACGAGGAAAAAAACAATTAAATCAATTAAAATTTGACCCCAAATTCCCAGAAAA-GTAAACAAAA
*
3357446 TATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTTTTCATCATTCAAATGCAGAAATGATGGAT
195 TATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCATCATTCAAATGCAGAAATGATGGAT
* ** * *
3357511 AAGTTTCATCACACCTCCTTGCATATCTTTTGAAGAATCAAATCTTATTAAGCAATAAAAAACTA
260 AAGTATCATCACACCTCCTTGCATATCTTAAGAA-AATCAAATCCTATGAAGC-ATAAAAAACTA
* *
3357576 G-AGC-TT-A-T-T-G-ATTT-T-TTTTGCAAA-TAA-AAGAAT-AAAATATAGTCA-ATAAAAG
323 GAACCATTAACTATAGAATTTCTGTTTGGCAAATTAACAA-AATGAAAATA-A-TCATA-AAAAG
* * *
3357628 TGAATATTTTACAGTTTACACCCCTCATTGGAGTAATGGTAGATGGATCAGATAGTCGATCGCTA
384 AGAATATTTTACAGGTTACA-CCC-CATTGGAGTAATGGTAAATGGATCAGATAGTCGATCGCTA
*
3357693 ATGTCTCAGCATATTGCAACTCAGACTGGGTGTCAAATATCTATCTTCATATCCACATTCAATCA
447 ATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTCATATCCACATTCAATCA
* *
3357758 AATTTAAAAAAAATAAGATTTTTAAATAAAATTTTGCAAACAAGTGAAGCTGCAGACGATAATTA
512 AATTTAAAAAAAATAAGA-TTTTAAACAAAATTTTGCAAACAAGTGAAGCTGCAGACAATAATTA
*
3357823 CAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATACGAAGACATTAATATATGCAAA
576 CAAGTGGAAATCAGATAAAAAAGTCAATCACCAATTTTGCATACGAAGACATTAATATATGCAAA
*
3357888 GTAAGACTGGGGCGACAATAACTATCATCATTTTCCCTTTTT
641 GTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTT
3357930 TTTCTCAAAA
Statistics
Matches: 624, Mismatches: 43, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
732 8 0.01
733 7 0.01
734 34 0.05
735 4 0.01
736 124 0.20
737 145 0.23
738 1 0.00
739 1 0.00
741 1 0.00
742 5 0.01
743 152 0.24
744 132 0.21
745 10 0.02
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (742 bp):
GCTACAGTAAAATGTTTGAATAAAGATCAGCAATCTCAGCCGAAAGATGGTGAATATTTATATAA
TCATCATAACACAAATCAGGTTTGATGATTCATTTTCATCATAGATTGCAGCAACTGACAAAAAA
ACGAGGAAAAAAACAATTAAATCAATTAAAATTTGACCCCAAATTCCCAGAAAAGTAAACAAAAT
ATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCATCATTCAAATGCAGAAATGATGGATA
AGTATCATCACACCTCCTTGCATATCTTAAGAAAATCAAATCCTATGAAGCATAAAAAACTAGAA
CCATTAACTATAGAATTTCTGTTTGGCAAATTAACAAAATGAAAATAATCATAAAAAGAGAATAT
TTTACAGGTTACACCCCATTGGAGTAATGGTAAATGGATCAGATAGTCGATCGCTAATGTCTCAG
CATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTCATATCCACATTCAATCAAATTTAAAA
AAAATAAGATTTTAAACAAAATTTTGCAAACAAGTGAAGCTGCAGACAATAATTACAAGTGGAAA
TCAGATAAAAAAGTCAATCACCAATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACTGG
GGCGACAATAACTATCATCATGTTCCCTTTTTCCCTTGAAAAACATAGCTCAAACAAAAACATTT
GACCTATATCATTAATTTTAGGACTGG
Found at i:3358494 original size:30 final size:31
Alignment explanation
Indices: 3358458--3358525 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
3358448 TTCTTTTACA
3358458 TTCATTTTAGTCACTCAACTTTAAT-AAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
*
3358488 TTCATTTTAGTCACTCAATTTTAATAAAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
3358519 TT-ATTTT
1 TTCATTTT
3358526 GATCACTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 29 0.81
31 7 0.19
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.51
Consensus pattern (31 bp):
TTCATTTTAGTCACTCAACTTTAATAAAATT
Found at i:3359005 original size:42 final size:42
Alignment explanation
Indices: 3358944--3359030 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
3358934 TCTTGATAAT
3358944 AAGGGAAAACTTGGATTTTCCGGTGAACTACTTGGGTTTTAA
1 AAGGGAAAACTTGGATTTTCCGGTGAACTACTTGGGTTTTAA
*
3358986 AAGGGAAAA-TTTGAGTTTTCCGGTGAACTACTTGGGTTTTAA
1 AAGGGAAAACTTGGA-TTTTCCGGTGAACTACTTGGGTTTTAA
3359028 AAG
1 AAG
3359031 TTTCATCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.33
Consensus pattern (42 bp):
AAGGGAAAACTTGGATTTTCCGGTGAACTACTTGGGTTTTAA
Found at i:3359024 original size:21 final size:21
Alignment explanation
Indices: 3358952--3359025 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
3358942 ATAAGGGAAA
*
3358952 ACTTGGATTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
** *
3358973 ACTTGGGTTTTAAAAGG-GAA-A
1 ACTTGGGTTTT--CCGGTGAACT
* *
3358994 ATTTGAGTTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
3359015 ACTTGGGTTTT
1 ACTTGGGTTTT
3359026 AAAAGTTTCA
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 28 0.74
22 3 0.08
23 2 0.05
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (21 bp):
ACTTGGGTTTTCCGGTGAACT
Found at i:3361760 original size:38 final size:38
Alignment explanation
Indices: 3361709--3361787 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
3361699 TGTTATAAAC
3361709 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
*
3361747 ACATAGGCATGCATACAAAAGAACTGTAGCAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
3361785 ACA
1 ACA
3361788 ATGCCCAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (38 bp):
ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
Found at i:3368041 original size:23 final size:23
Alignment explanation
Indices: 3368014--3370032 Score: 1176
Period size: 23 Copynumber: 88.1 Consensus size: 23
3368004 TTGTACACCA
* * *
3368014 CAATTTGCAGCACTTAAACTCTT
1 CAATTTACAGCATTTAAACACTT
* * * *
3368037 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
* *
3368060 CAATTTACAACAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3368083 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3368106 CAACTTACAACACTTT-AACA-TCC
1 CAATTTACAGCA-TTTAAACACT-T
* * * *
3368129 CAATTAACAACATTTATACACCT
1 CAATTTACAGCATTTAAACACTT
*
3368152 CAA-TTACAACGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* ** *
3368173 CAATTTTCAGCAACTAAACAATT
1 CAATTTACAGCATTTAAACACTT
* * *
3368196 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3368220 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
** *
3368243 CAATTTGTAGCACTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* * * *
3368266 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
* *
3368289 CAATTTACAGGAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
3368312 CAATTTACAACATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3368335 CAACTTACAACACTTT-AACA-TC
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3368357 CTAATTAACACCATTTATACACCT
1 C-AATTTACAGCATTTAAACACTT
3368381 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* ** *
3368402 CAATTTCCAGCAACTAAACAATT
1 CAATTTACAGCATTTAAACACTT
* * *
3368425 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
* *
3368449 CAATTTATAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
3368472 CAATTTGCAGCACTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* * * *
3368495 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
*
3368518 CAATTTACAGCAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3368541 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3368564 CAACTTACAACACTTT-AACA-TCC
1 CAATTTACAGCA-TTTAAACACT-T
* * * *
3368587 CAATTAACAACATTTATACACCT
1 CAATTTACAGCATTTAAACACTT
3368610 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* **
3368631 CAATTTTCAGCAACTAAACTA-TT
1 CAATTTACAGCATTTAAAC-ACTT
* * *
3368654 CAA-TTGCAGTACTTAAAACACTTTT
1 CAATTTACAGCA-TTTAAACAC--TT
*
3368679 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* **
3368702 CAATTTGCAGCACCTAAACAC-T
1 CAATTTACAGCATTTAAACACTT
* * * *
3368724 CTAATTTACATCATTTGAGCACCT
1 C-AATTTACAGCATTTAAACACTT
* *
3368748 CAATTTATAGCAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
**
3368771 CAATTTACAGCATTTAAACACCC
1 CAATTTACAGCATTTAAACACTT
* * *
3368794 CAACTTACAACACTTT-AACA-TC
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3368816 CTAATTAACACCATTTATACACCT
1 C-AATTTACAGCATTTAAACACTT
3368840 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* ** *
3368861 CAATTTCCAGCAACTAAACAATT
1 CAATTTACAGCATTTAAACACTT
* * *
3368884 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3368908 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3368931 CAATTTGCAGCACTTT-AACACTT
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3368954 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
*
3368977 CAATTTACAGCAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369000 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3369023 CAACTTACAACACTTT-AACA-TCC
1 CAATTTACAGCA-TTTAAACACT-T
* * * *
3369046 CAATTAACAACATTTATACACCT
1 CAATTTACAGCATTTAAACACTT
3369069 CAA-TTACAGCGA--TAAACATCTT
1 CAATTTACAGC-ATTTAAACA-CTT
* **
3369091 -AATTTCCAGCAACTAAACGA-TT
1 CAATTTACAGCATTTAAAC-ACTT
* * *
3369113 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3369137 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369160 CAATTTGCAGCACTTT-AACACTT
1 CAATTTACAGCA-TTTAAACACTT
* *
3369183 CAATTTACATCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* *
3369206 CAATTTACAACAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369229 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3369252 CAACTTACAACACTTT-AACA-TCC
1 CAATTTACAGCA-TTTAAACACT-T
* * * *
3369275 CAATTAACAACATTTATACACCT
1 CAATTTACAGCATTTAAACACTT
3369298 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* **
3369319 CAATTTCCAGCAACTAAACGA-TT
1 CAATTTACAGCATTTAAAC-ACTT
* *
3369342 CAATTTACAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3369366 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* ** *
3369389 CAATTTGCAGCACCTAAACACTC
1 CAATTTACAGCATTTAAACACTT
* * * *
3369412 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
* *
3369435 CAATTTATAGCAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
3369458 CAATTTACAGCATTTAAACGCCT
1 CAATTTACAGCATTTAAACACTT
* * *
3369481 CAACTTACAACACTTT-AACA-TC
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3369503 CTAATTAACACCATTTATACACCT
1 C-AATTTACAGCATTTAAACACTT
3369527 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* ** *
3369548 CAATTTCCAGCAACTAAGCGA-TT
1 CAATTTACAGCATTTAAAC-ACTT
* * *
3369571 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
* *
3369595 CAATTTACAACATTTAAATACTT
1 CAATTTACAGCATTTAAACACTT
* **
3369618 CAATTTGCAGCACCTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* * * *
3369641 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCATTTAAACACTT
* *
3369664 CAATTTATAGCAATTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369687 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCATTTAAACACTT
* * *
3369710 CAACTTACAACACTTT-AACA-TC
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3369732 CTAATTAACACCATTTATACACCT
1 C-AATTTACAGCATTTAAACACTT
*
3369756 CAA-TTACAACGA--TAAACA-TCT
1 CAATTTACAGC-ATTTAAACACT-T
* * ** *
3369777 CAGTTTCCAGCAACTAAACAATT
1 CAATTTACAGCATTTAAACACTT
* * *
3369800 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3369824 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369847 CAATTTGCAGCACTTT-AACACTT
1 CAATTTACAGCA-TTTAAACACTT
* * * *
3369870 CAATTCACAACATTTAAATACCT
1 CAATTTACAGCATTTAAACACTT
*
3369893 CAATTTGCAGCACTTT-AACACTT
1 CAATTTACAGCA-TTTAAACACTT
*
3369916 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
*
3369939 CAATTTGCAGCACTTT-AACA-TCT
1 CAATTTACAGCA-TTTAAACACT-T
* * * *
3369962 CTATTAACAACATTTATACACCTT
1 CAATTTACAGCATTTAAACA-CTT
* * *
3369986 -AA-TTACAACAATAAAACA-TCT
1 CAATTTACAGCATTTAAACACT-T
* **
3370007 CAATTTTCAGCAACTAAACACTT
1 CAATTTACAGCATTTAAACACTT
3370030 CAA
1 CAA
3370033 ATTGCAGTAC
Statistics
Matches: 1513, Mismatches: 368, Indels: 230
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.00
21 78 0.05
22 159 0.11
23 1090 0.72
24 166 0.11
25 14 0.01
26 5 0.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (23 bp):
CAATTTACAGCATTTAAACACTT
Found at i:3368415 original size:229 final size:229
Alignment explanation
Indices: 3368014--3370047 Score: 3453
Period size: 229 Copynumber: 8.9 Consensus size: 229
3368004 TTGTACACCA
* *
3368014 CAATTTGCAGCACTTAAACTCTTCAATTTACATCATTTGAGCACCTCAATTTACAACAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
*
3368079 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3368144 ATACACCTCAATTACAACGATAAACATCTCAATTTTCAGCAACTAAACAATTCAATTTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
3368209 TTAAAACACTTCAATTTACAACATTTAAACACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
* *
3368243 CAATTTGTAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGGAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
* *
3368308 ACTTCAATTTACAACATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACACCATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
3368373 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
*
3368438 TTAAAACACTTCAATTTATAACATTTAAACACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
3368472 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
*
3368537 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3368602 ATACACCTCAATTACAGCGATAAACATCTCAATTTTCAGCAACTAAACTATTCAA-TTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
3368666 TTAAAACACTTTTCAATTTACAACATTTAAACACTT
196 TTAAAACAC--TTCAATTTACAACATTTAAACACTT
* *
3368702 CAATTTGCAGCACCTAAACAC-TCTAATTTACATCATTTGAGCACCTCAATTTATAGCAATTAAA
1 CAATTTGCAGCACTTAAACACTTC-AATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAA
* *
3368766 CACTTCAATTTACAGCATTTAAACACCCCAACTTACAACACTTTAACATCCTAATTAACACCATT
65 CACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATT
3368831 TATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTA
130 TATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTA
3368896 CTTAAAACACTTCAATTTACAACATTTAAACACTT
195 CTTAAAACACTTCAATTTACAACATTTAAACACTT
*
3368931 CAATTTGCAGCACTTTAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
*
3368996 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3369061 ATACACCTCAATTACAGCGATAAACATCTTAATTTCCAGCAACTAAACGATTCAATTTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
3369126 TTAAAACACTTCAATTTACAACATTTAAACACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
* * * *
3369160 CAATTTGCAGCACTTTAACACTTCAATTTACATCATTTAAACACCTCAATTTACAACAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
*
3369225 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3369290 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACGATTCAATTTACAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
3369355 TTAAAACACTTCAATTTACAACATTTAAACACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
* * *
3369389 CAATTTGCAGCACCTAAACACTCCAATTTACATCATTTGAGCACCTCAATTTATAGCAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
* *
3369454 ACTTCAATTTACAGCATTTAAACGCCTCAACTTACAACACTTTAACATCCTAATTAACACCATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3369519 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAGCGATTCAATTTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
*
3369584 TTAAAACACTTCAATTTACAACATTTAAATACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
* *
3369618 CAATTTGCAGCACCTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTATAGCAATTAAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
*
3369683 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACACCATTT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
* *
3369748 ATACACCTCAATTACAACGATAAACATCTCAGTTTCCAGCAACTAAACAATTCAATTTGCAGTAC
131 ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
3369813 TTAAAACACTTCAATTTACAACATTTAAACACTT
196 TTAAAACACTTCAATTTACAACATTTAAACACTT
* * * * ** * * *
3369847 CAATTTGCAGCACTTTAACACTTCAATTCACAACATTTAAATACCTCAATTTGCAGCACTTTAAC
1 CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
* * * * *
3369912 ACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACATCTCT-ATTAACAACATT
66 ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATC-CTAATTAACAACATT
* * * * * *
3369976 TATACACCTTAATTACAACAATAAAACATCTCAATTTTCAGCAACTAAACACTTCAAATTGCAGT
130 TATACACCTCAATTACAGCGAT-AAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGT
3370041 ACTTAAA
194 ACTTAAA
3370048 CAGGGCTTTA
Statistics
Matches: 1717, Mismatches: 81, Indels: 13
0.95 0.04 0.01
Matches are distributed among these distances:
228 18 0.01
229 1433 0.83
230 248 0.14
231 18 0.01
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (229 bp):
CAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAATTAAAC
ACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTT
ATACACCTCAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGTAC
TTAAAACACTTCAATTTACAACATTTAAACACTT
Found at i:3387697 original size:23 final size:23
Alignment explanation
Indices: 3387647--3387709 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3387637 ATTGACAAGT
*
3387647 ATTTTATAAATATATA--ATAAG
1 ATTTTAAAAATATATATGATAAG
*
3387668 ATATTAAAAATATATATGATGAA-
1 ATTTTAAAAATATATATGAT-AAG
* *
3387691 ATTTTAAAATTATTTATGA
1 ATTTTAAAAATATATATGA
3387710 AATAAAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.41
23 18 0.53
24 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
ATTTTAAAAATATATATGATAAG
Found at i:3390887 original size:23 final size:23
Alignment explanation
Indices: 3390861--3390954 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
3390851 AAGTTAGAAG
3390861 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
3390884 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
3390907 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
3390930 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
3390953 AG
1 AG
3390955 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:3395391 original size:23 final size:23
Alignment explanation
Indices: 3395365--3395458 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
3395355 AAGTTAGAAG
3395365 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
3395388 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
3395411 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
3395434 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
3395457 AG
1 AG
3395459 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:3404367 original size:38 final size:38
Alignment explanation
Indices: 3404324--3404399 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
3404314 TTTAAGTATG
*
3404324 TCAAGAAA-ACTGGTGAGCATATAGGTATTTAAGGCAAT
1 TCAAGAAACA-TGATGAGCATATAGGTATTTAAGGCAAT
* *
3404362 TCAAGAAACATTATGAGCATATAGGTATTTGAGGCAAT
1 TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
3404400 CCAGATGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (38 bp):
TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
Found at i:3412205 original size:52 final size:52
Alignment explanation
Indices: 3412127--3412230 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
3412117 TATGTCATAG
3412127 AGTTGGATTAGAAATTTTCTTTAATGTATAAAGTTCTGGTTGATACTTGATA
1 AGTTGGATTAGAAATTTTCTTTAATGTATAAAGTTCTGGTTGATACTTGATA
3412179 AGTTGGATTAGAAATTTTCTTTAATGTATAAAGTTCTGGTTGATACTTGATA
1 AGTTGGATTAGAAATTTTCTTTAATGTATAAAGTTCTGGTTGATACTTGATA
3412231 GCGGCATCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (52 bp):
AGTTGGATTAGAAATTTTCTTTAATGTATAAAGTTCTGGTTGATACTTGATA
Found at i:3417892 original size:22 final size:20
Alignment explanation
Indices: 3417857--3417900 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
3417847 AGAAGGGTTA
3417857 TGGCGCGTGAGGTGGTTAATGC
1 TGGCGCGTGAGGT-GTTAA-GC
3417879 TGGCGCGT-ATGGTGTTAAGC
1 TGGCGCGTGA-GGTGTTAAGC
3417899 TG
1 TG
3417901 ACGGAGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.30
Consensus pattern (20 bp):
TGGCGCGTGAGGTGTTAAGC
Found at i:3418286 original size:17 final size:18
Alignment explanation
Indices: 3418260--3418294 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3418250 CATGTTTTTA
*
3418260 TTTAATAATTTGATTAAT
1 TTTAATAATTAGATTAAT
3418278 TTTAA-AATTAGATTAAT
1 TTTAATAATTAGATTAAT
3418295 ATACTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTAATAATTAGATTAAT
Found at i:3429427 original size:23 final size:23
Alignment explanation
Indices: 3429390--3429434 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3429380 TAAAAAATAT
3429390 TATTGTTTTATTAATATTTTTAA
1 TATTGTTTTATTAATATTTTTAA
*
3429413 TATT-TTTTATATAATTTTTTTA
1 TATTGTTTTAT-TAATATTTTTA
3429435 GGTGATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTGTTTTATTAATATTTTTAA
Found at i:3431833 original size:13 final size:14
Alignment explanation
Indices: 3431817--3431849 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3431807 TTTTTTTCTT
3431817 AATAATT-AATATC
1 AATAATTAAATATC
*
3431830 AATAATTAAATATG
1 AATAATTAAATATC
3431844 AATAAT
1 AATAAT
3431850 CACTTATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
AATAATTAAATATC
Found at i:3437251 original size:31 final size:33
Alignment explanation
Indices: 3437192--3437254 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
3437182 CTCCTTATTT
3437192 GGAGCAATCCTTCCATATTTATAAGGCACGGTAG
1 GGAGCAATCCTTCCATA-TTATAAGGCACGGTAG
3437226 GGAGCAATCCTTCCATA-T-TAAGGCACGGT
1 GGAGCAATCCTTCCATATTATAAGGCACGGT
3437255 TTTTGATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 11 0.38
32 1 0.03
34 17 0.59
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (33 bp):
GGAGCAATCCTTCCATATTATAAGGCACGGTAG
Found at i:3438272 original size:15 final size:16
Alignment explanation
Indices: 3438240--3438276 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3438230 AAAGTATGAT
*
3438240 ATAAAAAATACAAGAA
1 ATAAAAAATACAAAAA
3438256 ATAAAAAATA-AAAAA
1 ATAAAAAATACAAAAA
3438271 ATAAAA
1 ATAAAA
3438277 TTTTTTACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
ATAAAAAATACAAAAA
Found at i:3461341 original size:276 final size:276
Alignment explanation
Indices: 3460848--3461403 Score: 1031
Period size: 276 Copynumber: 2.0 Consensus size: 276
3460838 AGAAGACTTT
* *
3460848 AGTGAGAGCAGAGTTGTTGAAAAGGTCATCACCACTCTCCCTGAGAAGTTTGAGTCAAAGATTTC
1 AGTGAGAACAGAGTTGTTGAAAAGGTCATCACCACTCTCCCGGAGAAGTTTGAGTCAAAGATTTC
* *
3460913 ATCACTTGAGGACTCGAAAGACTTGTCAGCTATCTCATTGTCTGAGCTGATAAACTCTCTGTATG
66 ATCACTTGAGGACTCGAAAAAATTGTCAGCTATCTCATTGTCTGAGCTGATAAACTCTCTGTATG
3460978 CACTTGAGCAAAGGAGGGTCAATAGGCAGGAAGAGTATCCTGAAGGAGCTTTCTAGGCAAAGGTC
131 CACTTGAGCAAAGGAGGGTCAATAGGCAGGAAGAGTATCCTGAAGGAGCTTTCTAGGCAAAGGTC
3461043 AAAGTAGGCTCAGGTTCAAATCTGAAAGGGAAGAAGCCTTGGCTCGATAAAAGGGAAAACAAGGA
196 AAAGTAGGCTCAGGTTCAAATCTGAAAGGGAAGAAGCCTTGGCTCGATAAAAGGGAAAACAAGGA
*
3461108 GAGATACAGGTAAGAA
261 GAGATACAGGCAAGAA
*
3461124 AGTGAGAACAGAGTTGTTGAAAAGGTTATCACCACTCTCCCGGAGAAGTTTGAGTCAAAGATTTC
1 AGTGAGAACAGAGTTGTTGAAAAGGTCATCACCACTCTCCCGGAGAAGTTTGAGTCAAAGATTTC
* *
3461189 ATCACTTGAGGACTCGAAAAAATTGTCAGCTATCTCATTGTCTGAGCTGATAAATTCTTTGTATG
66 ATCACTTGAGGACTCGAAAAAATTGTCAGCTATCTCATTGTCTGAGCTGATAAACTCTCTGTATG
3461254 CACTTGAGCAAAGGAGGGTCAATAGGCAGGAAGAGTATCCTGAAGGAGCTTTCTAGGCAAAGGTC
131 CACTTGAGCAAAGGAGGGTCAATAGGCAGGAAGAGTATCCTGAAGGAGCTTTCTAGGCAAAGGTC
3461319 AAAGTAGGCTCAGGTTCAAATCTGAAAGGGAAGAAGCCTTGGCTCGATAAAAGGGAAAACAAGGA
196 AAAGTAGGCTCAGGTTCAAATCTGAAAGGGAAGAAGCCTTGGCTCGATAAAAGGGAAAACAAGGA
*
3461384 GAGATGCAGGCAAGAA
261 GAGATACAGGCAAGAA
3461400 AGTG
1 AGTG
3461404 TTCCCACCAT
Statistics
Matches: 271, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
276 271 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (276 bp):
AGTGAGAACAGAGTTGTTGAAAAGGTCATCACCACTCTCCCGGAGAAGTTTGAGTCAAAGATTTC
ATCACTTGAGGACTCGAAAAAATTGTCAGCTATCTCATTGTCTGAGCTGATAAACTCTCTGTATG
CACTTGAGCAAAGGAGGGTCAATAGGCAGGAAGAGTATCCTGAAGGAGCTTTCTAGGCAAAGGTC
AAAGTAGGCTCAGGTTCAAATCTGAAAGGGAAGAAGCCTTGGCTCGATAAAAGGGAAAACAAGGA
GAGATACAGGCAAGAA
Found at i:3471629 original size:34 final size:35
Alignment explanation
Indices: 3471591--3471657 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3471581 CAGTAAAATA
*
3471591 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3471625 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3471658 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3471631 original size:20 final size:20
Alignment explanation
Indices: 3471606--3471645 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3471596 CGTAAAATGA
*
3471606 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3471626 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3471646 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3471661 original size:14 final size:15
Alignment explanation
Indices: 3471585--3471661 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3471575 GATTGCCAGT
* *
3471585 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
3471599 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3471613 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3471633 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3471648 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3471662 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3475109 original size:62 final size:62
Alignment explanation
Indices: 3475033--3475158 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
3475023 CAAAAAGAAA
3475033 AAGTGATAGAATGCAACACGATTCTTTTGAAAATTTGACTCTATTTGCTACAGTTGCACATT
1 AAGTGATAGAATGCAACACGATTCTTTTGAAAATTTGACTCTATTTGCTACAGTTGCACATT
3475095 AAGTGATAGAATGCAACACGATTCTTTTGAAAATTTGACTCTATTTGCTACAGTTGCACATT
1 AAGTGATAGAATGCAACACGATTCTTTTGAAAATTTGACTCTATTTGCTACAGTTGCACATT
3475157 AA
1 AA
3475159 CAAAAGCATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (62 bp):
AAGTGATAGAATGCAACACGATTCTTTTGAAAATTTGACTCTATTTGCTACAGTTGCACATT
Found at i:3477759 original size:20 final size:20
Alignment explanation
Indices: 3477714--3477762 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
3477704 TAATGACAGC
* *
3477714 AAAAAAACAACAATAATGAT
1 AAAAAAATAACAATAATAAT
3477734 AGAAAAAATAAC-ATAATAAGT
1 A-AAAAAATAACAATAATAA-T
3477755 AAAAAAAT
1 AAAAAAAT
3477763 GACGAGGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (20 bp):
AAAAAAATAACAATAATAAT
Found at i:3477760 original size:21 final size:21
Alignment explanation
Indices: 3477714--3477761 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3477704 TAATGACAGC
*
3477714 AAAAAAACAACAATAATGATA
1 AAAAAAACAACAATAATAATA
* *
3477735 GAAAAAATAAC-ATAATAAGTA
1 AAAAAAACAACAATAATAA-TA
3477756 AAAAAA
1 AAAAAA
3477762 TGACGAGGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAAAACAACAATAATAATA
Found at i:3479649 original size:13 final size:14
Alignment explanation
Indices: 3479626--3479654 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3479616 TTAAAGTATT
3479626 TAAAAATTAAAAAA
1 TAAAAATTAAAAAA
3479640 TAAAAA-TAAAAAA
1 TAAAAATTAAAAAA
3479653 TA
1 TA
3479655 TATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAATTAAAAAA
Found at i:3496423 original size:17 final size:18
Alignment explanation
Indices: 3496391--3496426 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3496381 TTTTATTTTA
*
3496391 AATATTATAGATTTAAAT
1 AATATTATAAATTTAAAT
3496409 AATATTA-AAATTTAAAT
1 AATATTATAAATTTAAAT
3496426 A
1 A
3496427 TTTTAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AATATTATAAATTTAAAT
Found at i:3497010 original size:30 final size:30
Alignment explanation
Indices: 3496970--3497031 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3496960 ATTTATAAAT
*
3496970 AATTAATATTT-AT-TACTTAAAAATATTTAC
1 AATTAATATTTCATATA-TT-AAAATATTAAC
*
3497000 AATTTATATTTCATATATTAAAATATTAAC
1 AATTAATATTTCATATATTAAAATATTAAC
3497030 AA
1 AA
3497032 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 22 0.79
31 4 0.14
32 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTAAC
Found at i:3497222 original size:13 final size:13
Alignment explanation
Indices: 3497206--3497230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3497196 ATCAAATTTT
3497206 TCAAAAGTACTTC
1 TCAAAAGTACTTC
3497219 TCAAAAGTACTT
1 TCAAAAGTACTT
3497231 TTCCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TCAAAAGTACTTC
Found at i:3504186 original size:33 final size:33
Alignment explanation
Indices: 3504123--3504186 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3504113 TTTTATTAAA
* *
3504123 ATAATATTTTAATTACCTATTATTTTATTTTAGG
1 ATAATATTTTAATTA-CTAGTAGTTTATTTTAGG
3504157 ATAATACTTTTAATT-CTAGTAGTTTATTTT
1 ATAATA-TTTTAATTACTAGTAGTTTATTTT
3504187 TTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 13 0.48
34 6 0.22
35 8 0.30
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (33 bp):
ATAATATTTTAATTACTAGTAGTTTATTTTAGG
Found at i:3517946 original size:59 final size:60
Alignment explanation
Indices: 3517829--3517947 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 60
3517819 AAATTATCAC
* * * *
3517829 TTTTAAAGAAAAATATTTGGTATATTGTTAATGAAATTTTTAGACTTCACAAATAATATA
1 TTTTAAAGAAAAATATTTAGTATATGGTCAATGAAATTTTTAGACTTCACAAACAATATA
* * *
3517889 TTTTAACG-AAAATATTTAGTATATGGTCAATGAAATTTTTAGACTTTATAAACAATATA
1 TTTTAAAGAAAAATATTTAGTATATGGTCAATGAAATTTTTAGACTTCACAAACAATATA
3517948 GGAATTGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
59 45 0.87
60 7 0.13
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (60 bp):
TTTTAAAGAAAAATATTTAGTATATGGTCAATGAAATTTTTAGACTTCACAAACAATATA
Found at i:3519494 original size:3 final size:3
Alignment explanation
Indices: 3519486--3519510 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3519476 ATAATTAAAA
3519486 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
3519511 CGTAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3530842 original size:18 final size:18
Alignment explanation
Indices: 3530821--3530863 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3530811 GTGGTGGTGG
3530821 TGGTGATGGTCATGGCCA
1 TGGTGATGGTCATGGCCA
* *
3530839 TGGTCATGGTGATGGCCA
1 TGGTGATGGTCATGGCCA
3530857 TGGTGAT
1 TGGTGAT
3530864 CATTGGAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.40, T:0.30
Consensus pattern (18 bp):
TGGTGATGGTCATGGCCA
Found at i:3530853 original size:12 final size:12
Alignment explanation
Indices: 3530821--3530863 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3530811 GTGGTGGTGG
3530821 TGGTGATGGTCA
1 TGGTGATGGTCA
**
3530833 TGGCCATGGTCA
1 TGGTGATGGTCA
*
3530845 TGGTGATGGCCA
1 TGGTGATGGTCA
3530857 TGGTGAT
1 TGGTGAT
3530864 CATTGGAAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.40, T:0.30
Consensus pattern (12 bp):
TGGTGATGGTCA
Found at i:3531188 original size:46 final size:46
Alignment explanation
Indices: 3531127--3531219 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
3531117 TGACCAGCTT
3531127 TTTTTCTTGTATGTGATGACTTGACATATATACTTAGATATTTTTG
1 TTTTTCTTGTATGTGATGACTTGACATATATACTTAGATATTTTTG
*
3531173 TTTTTCTTGTCTGTGATGACTTGACATATATACTTAGATATTTTTG
1 TTTTTCTTGTATGTGATGACTTGACATATATACTTAGATATTTTTG
3531219 T
1 T
3531220 ACGGTTGGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (46 bp):
TTTTTCTTGTATGTGATGACTTGACATATATACTTAGATATTTTTG
Found at i:3535458 original size:16 final size:16
Alignment explanation
Indices: 3535427--3535460 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3535417 TTTAATTTTT
3535427 TATAAAAAAATATTAA
1 TATAAAAAAATATTAA
3535443 TATATAAAAAAT-TTAA
1 TATA-AAAAAATATTAA
3535459 TA
1 TA
3535461 CAGTCAGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAAAAATATTAA
Found at i:3539408 original size:17 final size:18
Alignment explanation
Indices: 3539382--3539415 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3539372 AATTTTGATG
3539382 AATAATTAATTAAATAAA
1 AATAATTAATTAAATAAA
*
3539400 AATAA-TAATTAGATAA
1 AATAATTAATTAAATAA
3539416 TTTATTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AATAATTAATTAAATAAA
Found at i:3546548 original size:16 final size:17
Alignment explanation
Indices: 3546527--3546562 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
3546517 CTTCGCGTGG
3546527 GGACATTTGA-ATCTAT
1 GGACATTTGATATCTAT
3546543 GGACATTTGATTATCTAT
1 GGACATTTGA-TATCTAT
3546561 GG
1 GG
3546563 GTTGCTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (17 bp):
GGACATTTGATATCTAT
Found at i:3548956 original size:25 final size:25
Alignment explanation
Indices: 3548925--3548974 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3548915 TAGAAAGCAA
3548925 ATAAATATTTAAAAACCCAGACAAT
1 ATAAATATTTAAAAACCCAGACAAT
3548950 ATAAATATTTAAAAACCCAGACAAT
1 ATAAATATTTAAAAACCCAGACAAT
3548975 CTTTTACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (25 bp):
ATAAATATTTAAAAACCCAGACAAT
Found at i:3548993 original size:18 final size:18
Alignment explanation
Indices: 3548970--3549007 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3548960 AAAAACCCAG
*
3548970 ACAATCTTTTACTTATCT
1 ACAATCTTTTACTTACCT
3548988 ACAATCTTTTACTTACCT
1 ACAATCTTTTACTTACCT
3549006 AC
1 AC
3549008 GAGAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (18 bp):
ACAATCTTTTACTTACCT
Found at i:3555760 original size:17 final size:16
Alignment explanation
Indices: 3555738--3555769 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3555728 ATTTAATTAA
3555738 ATAAATTAATAAAATAT
1 ATAAATTAA-AAAATAT
3555755 ATAAATTAAAAAATA
1 ATAAATTAAAAAATA
3555770 AATTCTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATTAAAAAATAT
Found at i:3559138 original size:14 final size:14
Alignment explanation
Indices: 3559107--3559157 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3559097 ACATATTATT
3559107 TTAATATTTTA-A-C
1 TTAA-ATTTTAGACC
3559120 TTAAATTTTAGACC
1 TTAAATTTTAGACC
**
3559134 TTAAATTCAAGACC
1 TTAAATTTTAGACC
*
3559148 TTAAAATTTA
1 TTAAATTTTA
3559158 AATAGTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 20 0.65
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (14 bp):
TTAAATTTTAGACC
Found at i:3562903 original size:49 final size:49
Alignment explanation
Indices: 3562849--3562949 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
3562839 CATGTCATTG
3562849 TCCTTCTCACTGGTTTCTTGACTAAATATCTTGTTTCATGTGTAAACTT
1 TCCTTCTCACTGGTTTCTTGACTAAATATCTTGTTTCATGTGTAAACTT
3562898 TCCTTCTCACTGGTTTCTTGACTAAATATCTTGTTTCATGTGTAAACTT
1 TCCTTCTCACTGGTTTCTTGACTAAATATCTTGTTTCATGTGTAAACTT
3562947 TCC
1 TCC
3562950 ATCTACGGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (49 bp):
TCCTTCTCACTGGTTTCTTGACTAAATATCTTGTTTCATGTGTAAACTT
Found at i:3570687 original size:59 final size:59
Alignment explanation
Indices: 3570621--3570738 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
3570611 TATTATCCTA
3570621 AAATGTTATTTCTCTTGCTAATTAACTATAGATGCATAACCAACATGATTTTAAAAATT
1 AAATGTTATTTCTCTTGCTAATTAACTATAGATGCATAACCAACATGATTTTAAAAATT
*
3570680 AAATGTTATTTCTCTTGCTAATTAACTATAGATGCATAATCAACATGATTTTAAAAATT
1 AAATGTTATTTCTCTTGCTAATTAACTATAGATGCATAACCAACATGATTTTAAAAATT
3570739 TTAAGGTCTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (59 bp):
AAATGTTATTTCTCTTGCTAATTAACTATAGATGCATAACCAACATGATTTTAAAAATT
Found at i:3570957 original size:11 final size:11
Alignment explanation
Indices: 3570941--3570974 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
3570931 CCAATAATTT
3570941 AGGTGTTGAAA
1 AGGTGTTGAAA
3570952 AGGTGTTGAAA
1 AGGTGTTGAAA
3570963 AGGTGTTGAAA
1 AGGTGTTGAAA
3570974 A
1 A
3570975 AACCAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (11 bp):
AGGTGTTGAAA
Found at i:3572505 original size:20 final size:20
Alignment explanation
Indices: 3572480--3572517 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3572470 TTTTGAAGAT
3572480 AAAATA-TACTTATTAAAATC
1 AAAATATTA-TTATTAAAATC
3572500 AAAATATTATTATTAAAA
1 AAAATATTATTATTAAAA
3572518 GTAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTATTATTAAAATC
Found at i:3573865 original size:29 final size:29
Alignment explanation
Indices: 3573827--3573884 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3573817 TGTTTAAAAT
3573827 TGTTTAAGATGTGAATATGAATATTTGAA
1 TGTTTAAGATGTGAATATGAATATTTGAA
*
3573856 TGTTTCAGATGTGAATATGAATATTTGAA
1 TGTTTAAGATGTGAATATGAATATTTGAA
3573885 CATTGATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (29 bp):
TGTTTAAGATGTGAATATGAATATTTGAA
Found at i:3576918 original size:98 final size:98
Alignment explanation
Indices: 3576747--3576943 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
3576737 GTGCAATAAA
* *
3576747 ACTTTAAAAGAACATCCACTTATCCAAGCTTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
3576812 CCTCTAAAATCCCAAACTCGGAAGATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAAGATTTCCTTT
3576845 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
3576910 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAAGATTTCCTTT
3576943 A
1 A
3576944 TTATTTTTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAAGATTTCCTTT
Found at i:3577606 original size:20 final size:20
Alignment explanation
Indices: 3577578--3577625 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3577568 ATATATGTGT
* *
3577578 ATATATATATAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
3577598 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
3577618 ATATATAT
1 ATATATAT
3577626 GTACATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:3579041 original size:44 final size:44
Alignment explanation
Indices: 3578939--3579391 Score: 280
Period size: 44 Copynumber: 10.5 Consensus size: 44
3578929 CTTCAATCTA
* * *
3578939 CTCCTCTGCAACTTCAGGGAGATAAGATTTGAT-ATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTGAT-TT-AGTCTG
*
3578984 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTATTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTGATTTAGTCTG
**
3579028 CTCCACTGCAACTTCAGGGAGATAAGAC-TG--GA-TGCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTGATTTAG-TCTG
* * * * *
3579069 CT-CTCTACAACTTCAGAGAGATAAGA--T-CTAAGATTCTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCT--GATT-TAGTCTG
* * * * *
3579112 CTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTGATTTAGTCTG
* * * *
3579156 CTACACTGCAACTTCAGAGAGATAAGACTTGCCGATTTCAGTCTT
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTGATTT-AGTCTG
* * *
3579201 CCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG
1 CTCCACTGCAACTTCAGGGA-GATAAGACTTGCTGATTTAGTCTG
* * **
3579245 CTCCACTGCAACTTCAGGGAGATAAGACTAGATG--CGA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTGATTTAGTCTG
* * ** * * *
3579286 CT-CTCTGCAACTTCAGAGAGATAAGA-TCTGAGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-TGCTGATTTAGTCTG
* * * * * **
3579329 C-CCACTGCAACTTCAGCGAGATAGGA-TTACCGGCTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTGATTTAGTCTG
3579372 CTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGA
3579392 AGTAGAATTA
Statistics
Matches: 324, Mismatches: 57, Indels: 55
0.74 0.13 0.13
Matches are distributed among these distances:
39 2 0.01
40 48 0.15
41 13 0.04
42 5 0.02
43 44 0.14
44 137 0.42
45 72 0.22
46 2 0.01
47 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCTGATTTAGTCTG
Found at i:3579050 original size:89 final size:87
Alignment explanation
Indices: 3578939--3579273 Score: 305
Period size: 89 Copynumber: 3.8 Consensus size: 87
3578929 CTTCAATCTA
* * *
3578939 CTCCTCTGCAACTTCAGGGAGATAAGATTTGATATCTTCAGTCTGCCT-CACTGCAACTTCAG-G
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGAT-GCTT-AGTCTG-CTACACTGCAACTTCAGAG
*
3579002 AGGATAAGACTTGCTTATTTAGTCTG
63 A-GATAAGACTTGCTGATTTAGTCTG
* * * *
3579028 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGC-GA-TCTGCT-CTCTACAACTTCAGAGAGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATGCTTAGTCTGCTACACTGCAACTTCAGAGAGA
* *
3579090 TAAGA--T-CTAAGATTCTAATCCG
66 TAAGACTTGCT--GATT-TAGTCTG
* *
3579112 CTCCACTGCAACTTCAGGGAGATAGGA-TT-ATCGGCTTTAATCTGCTACACTGCAACTTCAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGAT--GC-TTAGTCTGCTACACTGCAACTTCAGAG
* *
3579175 AGATAAGACTTGCCGATTTCAGTCTT
63 AGATAAGACTTGCTGATTT-AGTCTG
* * * * *
3579201 CCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGA-GATAAGACTTG-ATGCTTAGTCTGCTACACTGCAACTTCAGAGA
3579265 GATAAGACT
64 GATAAGACT
3579274 AGATGCGATC
Statistics
Matches: 202, Mismatches: 26, Indels: 36
0.77 0.10 0.14
Matches are distributed among these distances:
81 2 0.01
82 3 0.01
83 4 0.02
84 54 0.27
85 6 0.03
86 2 0.01
87 6 0.03
88 27 0.13
89 92 0.46
90 4 0.02
91 1 0.00
92 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (87 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGATGCTTAGTCTGCTACACTGCAACTTCAGAGAGA
TAAGACTTGCTGATTTAGTCTG
Found at i:3579328 original size:217 final size:216
Alignment explanation
Indices: 3578944--3579388 Score: 721
Period size: 217 Copynumber: 2.1 Consensus size: 216
3578934 ATCTACTCCT
* * * *
3578944 CTGCAACTTCAGGGAGATAAGATTTGATATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGAGAGATAAGACTTGAGATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAA
* *
3579009 GACTTGCTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
*
3579074 TACAACTTCAGAGAGATAAGATCTAAGATTCTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
131 TACAACTTCAGAGAGATAAGATCTAAGATTCTAATCCGC-CCACTGCAACTTCAGCGAGATAGGA
* *
3579139 TTATCGGCTTTAATCTGCTACA
195 TTACCGGCTTTAACCTGCTACA
* *
3579161 CTGCAACTTCAGAGAGATAAGACTTGCCGAT-TTCAGTCTTCCCCACTGCAACTTCAGGAGGATA
1 CTGCAACTTCAGAGAGATAAGACTTG-AGATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATA
3579225 AGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCT
65 AGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCT
* * * *
3579290 CTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGA
130 CTACAACTTCAGAGAGATAAGATCTAAGATTCTAATCCGCCCACTGCAACTTCAGCGAGATAGGA
*
3579355 TTACCGGCTTTAACCTGCTCCA
195 TTACCGGCTTTAACCTGCTACA
3579377 CTGCAACTTCAG
1 CTGCAACTTCAG
3579389 GGAAGTAGAA
Statistics
Matches: 211, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
216 55 0.26
217 154 0.73
218 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (216 bp):
CTGCAACTTCAGAGAGATAAGACTTGAGATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAA
GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
TACAACTTCAGAGAGATAAGATCTAAGATTCTAATCCGCCCACTGCAACTTCAGCGAGATAGGAT
TACCGGCTTTAACCTGCTACA
Found at i:3579540 original size:132 final size:131
Alignment explanation
Indices: 3579386--3579995 Score: 970
Period size: 132 Copynumber: 4.6 Consensus size: 131
3579376 ACTGCAACTT
* * *
3579386 CAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTATAACCACAGAGAGGTAAAATCTGCCAT
1 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
*
3579451 CTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
66 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
3579516 TA
131 -A
* * * * *
3579518 CAGGGAAGTAGAATTACGGGCTTAAATGTACTCCACTATAACCATAGGGAGGTAAAATACACCAT
1 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
* ** *
3579583 CTTCGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTTCAATCTTCAATCTATTCTACTGTTG
66 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
3579648 A
131 A
* * *
3579649 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCATAGGGAGGTAAAATCTGCCA
1 -CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCA
3579714 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
65 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
3579779 -A
130 GA
*
3579780 CCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGAGAGGTAAAATCCGCC
1 --CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCC
* *
3579845 ATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCGATCTATTCCACTGT
64 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGT
*
3579910 TGC
129 TGA
* *
3579913 CTAGGAAAGTAGAATTACTGGCTTCAATGTACTTCACTATAACCACAGGGAGGTAAAATCCGCCA
1 C-AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCA
3579978 TCTTCGATCTGCTCCACT
65 TCTTCGATCTGCTCCACT
3579996 GTCAATGCAG
Statistics
Matches: 441, Mismatches: 33, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
131 3 0.01
132 438 0.99
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (131 bp):
CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
A
Found at i:3583618 original size:24 final size:24
Alignment explanation
Indices: 3583590--3583635 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3583580 ATCATTTTTT
* *
3583590 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
3583614 GCTGCTCATGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
3583636 GGATTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:3585405 original size:98 final size:98
Alignment explanation
Indices: 3585234--3585430 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
3585224 GTGCAATAAA
*
3585234 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
3585299 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
3585332 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
3585397 CTTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
3585430 A
1 A
3585431 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:3586116 original size:110 final size:112
Alignment explanation
Indices: 3585958--3586162 Score: 288
Period size: 110 Copynumber: 1.8 Consensus size: 112
3585948 ATAAAGAAAA
* * * * *
3585958 ATATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATATACGTACATATTTATGTAA
1 ATATATATAGAAATTATAAAAAGATGGATAGAAAGTATAATATATATACGTACAGATATATATAA
* * *
3586023 GTTAATAAATATAGAC-CATAAAGATAATGATTGCATTTATGTGTAT
66 GGTAACAAATATAGACACATAAACATAATGATTGCATTTATGTGTAT
* * *
3586069 ATATATATATAAATTAT-AAAAGATGTATAGAAAGTATGATATATATACGTACAGATATATATAA
1 ATATATATAGAAATTATAAAAAGATGGATAGAAAGTATAATATATATACGTACAGATATATATAA
3586133 GGTAACAAATATAGACATCATAAACATAAT
66 GGTAACAAATATAGACA-CATAAACATAAT
3586163 AATTACACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 54 0.67
111 16 0.20
112 11 0.14
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (112 bp):
ATATATATAGAAATTATAAAAAGATGGATAGAAAGTATAATATATATACGTACAGATATATATAA
GGTAACAAATATAGACACATAAACATAATGATTGCATTTATGTGTAT
Found at i:3592855 original size:17 final size:19
Alignment explanation
Indices: 3592820--3592856 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3592810 AATTTTGGAA
*
3592820 ATTTTATAAATATTTTTTT
1 ATTTTATAAATATTATTTT
3592839 ATTTTA-AAA-ATTATTTT
1 ATTTTATAAATATTATTTT
3592856 A
1 A
3592857 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATAAATATTATTTT
Found at i:3592861 original size:19 final size:20
Alignment explanation
Indices: 3592780--3592862 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 20
3592770 TTTTTTTTGA
3592780 AAATTTTATAATATATTTTTT
1 AAATTTTATAA-ATATTTTTT
** **
3592801 AAA-AATAT-AA-ATTTTGG
1 AAATTTTATAAATATTTTTT
3592818 AAATTTTATAAATATTTTTT
1 AAATTTTATAAATATTTTTT
*
3592838 -TATTTTA-AAA-ATTATTTT
1 AAATTTTATAAATATT-TTTT
3592856 AAATTTT
1 AAATTTT
3592863 TTTGTAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
17 11 0.23
18 11 0.23
19 14 0.30
20 8 0.17
21 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AAATTTTATAAATATTTTTT
Found at i:3596985 original size:17 final size:19
Alignment explanation
Indices: 3596951--3596987 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3596941 TTTCTCCTTC
*
3596951 TCTCTCCCCTTCCTCTTTT
1 TCTCTCCCCATCCTCTTTT
3596970 TCTCT-CCCATCC-CTTTT
1 TCTCTCCCCATCCTCTTTT
3596987 T
1 T
3596988 TTTCTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (19 bp):
TCTCTCCCCATCCTCTTTT
Found at i:3596988 original size:19 final size:20
Alignment explanation
Indices: 3596951--3596995 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3596941 TTTCTCCTTC
* *
3596951 TCTCTCCCCTTCC-TCTTTT
1 TCTCTCCCATCCCTTCTTTT
*
3596970 TCTCTCCCATCCCTTTTTTT
1 TCTCTCCCATCCCTTCTTTT
3596990 TCTCTC
1 TCTCTC
3596996 TGAGATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (20 bp):
TCTCTCCCATCCCTTCTTTT
Found at i:3603778 original size:18 final size:19
Alignment explanation
Indices: 3603755--3603805 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3603745 CCTCAGCAAA
*
3603755 ACTTTTTAAAAAA-GAAAT
1 ACTTTTTAAAAAATAAAAT
3603773 ACTTTTTACAAAAATAAAAT
1 ACTTTTTA-AAAAATAAAAT
*
3603793 ATTTTCTTAAAAA
1 ACTTT-TTAAAAA
3603806 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.29
19 5 0.18
20 12 0.43
21 3 0.11
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (19 bp):
ACTTTTTAAAAAATAAAAT
Done.