Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 6 of 135
Found at i:1792223 original size:16 final size:16
Alignment explanation
Indices: 1792204--1792265 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1792194 GTTATAATAG
1792204 AATAAAACTGTAATGA
1 AATAAAACTGTAATGA
* ** * *
1792220 AATAGAGTTATAATGT
1 AATAAAACTGTAATGA
*
1792236 AATAAAGCTGTAATGA
1 AATAAAACTGTAATGA
*
1792252 AATAAGACTGTAAT
1 AATAAAACTGTAAT
1792266 AAAAAATTCA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (16 bp):
AATAAAACTGTAATGA
Found at i:1792240 original size:32 final size:32
Alignment explanation
Indices: 1792194--1792255 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1792184 CGTTTAGTTT
1792194 GTTATAATAGAATAAAACTGTAATGAAATAGA
1 GTTATAATAGAATAAAACTGTAATGAAATAGA
*
1792226 GTTATAAT-GTAATAAAGCTGTAATGAAATA
1 GTTATAATAG-AATAAAACTGTAATGAAATA
1792256 AGACTGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (32 bp):
GTTATAATAGAATAAAACTGTAATGAAATAGA
Found at i:1792487 original size:58 final size:57
Alignment explanation
Indices: 1792420--1792586 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 57
1792410 AATTATTGTT
1792420 ATTAAATTTTAATAAGATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATAA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * * * * *
1792478 ATTATATTTTTATGTAATTATTATGAAATACAATTTAAT-AAAATAATATATAATTTA
1 ATTAAATTTTAAT-AAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* *
1792535 A-TAACATTTTTAATATAATTATTATTAAGATATGAA-TTAGTAAAAATTATAA
1 ATTAA-A-TTTTAATA-AATTATTATTAA-ATAT-AATTTAATAAAAATAATAA
1792587 TATATAATAT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
56 2 0.02
57 19 0.22
58 49 0.56
59 8 0.09
60 10 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (57 bp):
ATTAAATTTTAATAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:1798075 original size:47 final size:47
Alignment explanation
Indices: 1798024--1798119 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
1798014 ATAAATTTTG
1798024 TATATATATATAATTAGTTTATTAAGTTTTGGTTTTAATGTTGTTCT
1 TATATATATATAATTAGTTTATTAAGTTTTGGTTTTAATGTTGTTCT
1798071 TATATATATATAATTAGTTTATTAAGTTTTGGTTTTAATGTTGTTCT
1 TATATATATATAATTAGTTTATTAAGTTTTGGTTTTAATGTTGTTCT
1798118 TA
1 TA
1798120 AAATACTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.57
Consensus pattern (47 bp):
TATATATATATAATTAGTTTATTAAGTTTTGGTTTTAATGTTGTTCT
Found at i:1799950 original size:29 final size:29
Alignment explanation
Indices: 1799918--1799998 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
1799908 GACTTTTGAG
* *
1799918 GGGTAAAATGATAATTTTGGAAAAATT-TA
1 GGGTAAAAAGATAATTTT-GAAAAATTCGA
*
1799947 GGGTTAAAAAAGA-AATTTT-AGAAATTCGA
1 GGG-T-AAAAAGATAATTTTGAAAAATTCGA
*
1799976 GGGTAAAACGATAATTTTTGAAA
1 GGGTAAAAAGATAA-TTTTGAAA
1799999 GTTTCAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
27 6 0.15
28 9 0.22
29 11 0.27
30 9 0.22
31 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (29 bp):
GGGTAAAAAGATAATTTTGAAAAATTCGA
Found at i:1799989 original size:58 final size:58
Alignment explanation
Indices: 1799916--1800347 Score: 163
Period size: 59 Copynumber: 7.3 Consensus size: 58
1799906 TGGACTTTTG
* * * *
1799916 AGGGGTAAAATGATAATTTTGGAAAAATTT-AGGGTTAAAAAAGAAATTTTAGAAATTC
1 AGGGGTAAAACGATAATTTTGG-AAAATTTCAAGATCAAAAAAGAAATTTTAGAAATTC
* * * * *
1799974 -GAGGGTAAAACGATAATTTTTGAAAGTTTCAAGATCAAAAATGGAATTTTAGACATTC
1 AG-GGGTAAAACGATAATTTTGGAAAATTTCAAGATCAAAAAAGAAATTTTAGAAATTC
* * ** * * *
1800032 AGGGGTAAAACGGTAATTTTCAGAAAGA--TCGGGATCAAAAATAGAATTTTTGGATATTC
1 AGGGGTAAAACGATAATTTT-GGAAA-ATTTCAAGATCAAAAA-AGAAATTTTAGAAATTC
* * * * ** * * * *
1800091 GGGGGTAAAATGGTAATTTTTAGAAGAA--TCGGGATCAAAAATGGAATTTTTGGACATTC
1 AGGGGTAAAACGATAA-TTTTGGAA-AATTTCAAGATCAAAAA-AGAAATTTTAGAAATTC
* * * * * * *
1800150 GGGGGTAAAATGGTAAATTTTAGAAGAA--TCGAA-ATCAAAAATAGAATTTTTTTGGACATTC
1 AGGGGTAAAACGAT-AATTTTGGAA-AATTTC-AAGATCAAAAA-AGAA--ATTTTAGAAATTC
* * * * * * *
1800211 AAGGGTAAAATGGTAATTTTTAGAAGAA--TCAGGATCAAAAATA-AAATATTTGGACATTC
1 AGGGGTAAAACGATAA-TTTTGGAA-AATTTCAAGATCAAAAA-AGAAAT-TTTAGAAATTC
* * * * * *
1800270 AGGGGTAAAATGGTAATTTTGGAAGAA--TCGAGATCAAAAATGGAATTTTTAGATATTC
1 AGGGGTAAAACGATAATTTTGGAA-AATTTCAAGATCAAAAA-AGAAATTTTAGAAATTC
*
1800328 GGGGGTAAAACGATAATTTT
1 AGGGGTAAAACGATAATTTT
1800348 TAGAAAAATC
Statistics
Matches: 317, Mismatches: 41, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
57 7 0.02
58 117 0.37
59 133 0.42
60 12 0.04
61 48 0.15
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (58 bp):
AGGGGTAAAACGATAATTTTGGAAAATTTCAAGATCAAAAAAGAAATTTTAGAAATTC
Found at i:1800100 original size:29 final size:29
Alignment explanation
Indices: 1800068--1800469 Score: 89
Period size: 30 Copynumber: 13.6 Consensus size: 29
1800058 GATCGGGATC
* *
1800068 AAAAATAGAATTTTTGGATATTCGGGGGT
1 AAAAATGGAATTTTTGGACATTCGGGGGT
* * * *
1800097 -AAAATGGTAATTTTTAGAAGAATC-GGGAT
1 AAAAATGG-AATTTTT-GGACATTCGGGGGT
1800126 CAAAAATGGAATTTTTGGACATTCGGGGGT
1 -AAAAATGGAATTTTTGGACATTCGGGGGT
* * * * ***
1800156 -AAAATGGTAAATTTTAGAAGAATC-GAAAT
1 AAAAATGG--AATTTTTGGACATTCGGGGGT
* **
1800185 CAAAAATAGAATTTTTTTGGACATTCAAGGGT
1 -AAAAATGGAA--TTTTTGGACATTCGGGGGT
* * * * *
1800217 -AAAATGGTAATTTTTAGAAGAATC-AGGAT
1 AAAAATGG-AATTTTT-GGACATTCGGGGGT
** * *
1800246 CAAAAATAAAATATTTGGACATTCAGGGGT
1 -AAAAATGGAATTTTTGGACATTCGGGGGT
* * * *
1800276 -AAAATGGTAA-TTTTGGAAGAATC-GAGAT
1 AAAAATGG-AATTTTTGG-ACATTCGGGGGT
* *
1800304 CAAAAATGGAATTTTTAGATATTCGGGGGT
1 -AAAAATGGAATTTTTGGACATTCGGGGGT
* * * * *
1800334 AAAACGAT--AATTTTTAGAAAAATC-GAGAT
1 AAAA--ATGGAATTTTT-GGACATTCGGGGGT
* *
1800363 CAAAAATGGAATTTTCGGACATCCGGGAGGT
1 -AAAAATGGAATTTTTGGACATTCGGG-GGT
1800394 -AAAATGGTAA-TTTTGGA-AGTGTC-GGGGT
1 AAAAATGG-AATTTTTGGACA-T-TCGGGGGT
* * **
1800422 AAAAAATAGAATTTTTGGAAATTTAGGGGT
1 -AAAAATGGAATTTTTGGACATTCGGGGGT
* *
1800452 AAAAGTGTAATTTTTGGA
1 AAAAATGGAATTTTTGGA
1800470 AGTTTTGGGG
Statistics
Matches: 264, Mismatches: 70, Indels: 78
0.64 0.17 0.19
Matches are distributed among these distances:
28 32 0.12
29 98 0.37
30 99 0.38
31 34 0.13
32 1 0.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGACATTCGGGGGT
Found at i:1800429 original size:237 final size:233
Alignment explanation
Indices: 1799952--1800467 Score: 635
Period size: 237 Copynumber: 2.2 Consensus size: 233
1799942 ATTTAGGGTT
* * * * **
1799952 AAAAA-AGAAATTTTAGAAATTCGAGGGTAAAACGATAATTTTTGAAAGTTTCAAGATCAAAAAT
1 AAAAATAGAATTTTTGGAAATTCAAGGGTAAAA-GGTAATTTTTG-AAGAATCAAGATCAAAAAT
** *
1800016 GGAATTTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAAAGATCGGGATCAAAAATAGAATTT
64 AAAATTTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAAAGATCGAGATCAAAAATAGAATTT
* * * * * *
1800081 TTGGATATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCAAAAATGGAATTTTTGGAC
129 TTAGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGAGATCAAAAATGGAATTTTCGGAC
* *
1800146 ATTCGGGGGTAAAATGGTAAATTTTAGAAGAATCGAAATC
194 ATCCGGGGGTAAAATGGTAAATTTTAGAAGAATCGAAATA
* *
1800186 AAAAATAGAATTTTTTTGGACATTCAAGGGTAAAATGGTAATTTTTAGAAGAATCAGGATCAAAA
1 AAAAATAGAA--TTTTTGGAAATTCAAGGGTAAAA-GGTAATTTTT-GAAGAATCAAGATCAAAA
* * * *
1800251 ATAAAATATTTGGACATTCAGGGGTAAAATGGTAATTTT--GGAAGAATCGAGATCAAAAATGGA
62 ATAAAAT-TTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAAAG-ATCGAGATCAAAAATAGA
1800314 ATTTTTAGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGAGATCAAAAATGGAATTTTC
125 ATTTTTAGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGAGATCAAAAATGGAATTTTC
* ** ***
1800379 GGACATCCGGGAGGTAAAATGGT-AATTTTGGAAGTGTCGGGGTA
190 GGACATCCGGG-GGTAAAATGGTAAATTTTAGAAGAATCGAAATA
* *
1800423 AAAAATAGAATTTTTGGAAATTTAGGGGTAAAAGTGTAATTTTTG
1 AAAAATAGAATTTTTGGAAATTCAAGGGTAAAAG-GTAATTTTTG
1800468 GAAGTTTTGG
Statistics
Matches: 241, Mismatches: 33, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
234 7 0.03
235 33 0.14
236 4 0.02
237 156 0.65
238 41 0.17
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (233 bp):
AAAAATAGAATTTTTGGAAATTCAAGGGTAAAAGGTAATTTTTGAAGAATCAAGATCAAAAATAA
AATTTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAAAGATCGAGATCAAAAATAGAATTTTT
AGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGAGATCAAAAATGGAATTTTCGGACAT
CCGGGGGTAAAATGGTAAATTTTAGAAGAATCGAAATA
Found at i:1800468 original size:59 final size:59
Alignment explanation
Indices: 1800006--1800498 Score: 521
Period size: 59 Copynumber: 8.4 Consensus size: 59
1799996 AAAGTTTCAA
* * * *
1800006 GATCAAAAATGGAA-TTTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAA-AGATCGG
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGA-ATCGG
* *
1800064 GATCAAAAATAGAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGG
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
* * * *
1800123 GATCAAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAAATTTTAGAAGAATCGA
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
* * *
1800182 AATCAAAAATAGAATTTTTTTGGACATTCAAGGGTAAAATGGTAATTTTTAGAAGAATCAG
1 GATCAAAAATAGAA--TTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
* * * *
1800243 GATCAAAAATAAAATATTTGGACATTCAGGGGTAAAATGGTAA-TTTTGGAAGAATCGA
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
* * * * * * * *
1800301 GATCAAAAATGGAATTTTTAGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGA
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
* * * * * **
1800360 GATCAAAAATGGAATTTTCGGACATCCGGGAGGTAAAATGGTAA-TTTTGGAAGTGTCGG
1 GATCAAAAATAGAATTTTTGGACATTCAGG-GGTAAAATGGTAATTTTTAGAAGAATCGG
* * * * * ** *
1800419 GGTAAAAAATAGAATTTTTGGAAATTTAGGGGTAAAA-GTGTAATTTTTGGAAGTTTTGG
1 GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATG-GTAATTTTTAGAAGAATCGG
* *
1800478 GGTC-AAAATATAATTTTTGGA
1 GATCAAAAATAGAATTTTTGGA
1800499 TAGTTTAGGG
Statistics
Matches: 370, Mismatches: 57, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
57 1 0.00
58 87 0.24
59 218 0.59
60 12 0.03
61 52 0.14
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (59 bp):
GATCAAAAATAGAATTTTTGGACATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGG
Found at i:1800470 original size:29 final size:29
Alignment explanation
Indices: 1800404--1800509 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
1800394 AAAATGGTAA
* * * *
1800404 TTTTGGAAGTGTCGGGGTAAAAAATAGAAT
1 TTTTGGAAGTTTAGGGGT-CAAAATATAAT
* *
1800434 TTTTGGAAATTTAGGGGT-AAAAGTGTAAT
1 TTTTGGAAGTTTAGGGGTCAAAA-TATAAT
*
1800463 TTTTGGAAGTTTTGGGGTCAAAATATAAT
1 TTTTGGAAGTTTAGGGGTCAAAATATAAT
1800492 TTTTGGATAGTTTAGGGG
1 TTTTGGA-AGTTTAGGGG
1800510 CCTTCAGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.06
29 32 0.50
30 28 0.44
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTCAAAATATAAT
Found at i:1800485 original size:118 final size:116
Alignment explanation
Indices: 1799893--1800471 Score: 565
Period size: 117 Copynumber: 4.9 Consensus size: 116
1799883 ATCTGGGGGC
* * * * ** * *
1799893 AAAATGGTAATTTTGGACTTTTGAGGGGTAAAATGATAATTTTGGAAAAATTTAGGGTTAAAAA-
1 AAAATGG-AATTTTGGAC-ATTCAGGGGTAAAATGGTAATTTTGGAAGAATCGA-GATCAAAAAT
* * * * * ** **
1799957 AGAAATTTTAGAAATTC-GAGGGTAAAACGATAATTTTT-GAAAGTTTCAAGATCA
63 AGAATTTTTGGATATTCAG-GGGTAAAATGGTAATTTTTAG-AAGAATCGGGATCA
* * * *
1800011 AAAATGGAATTTTAGACATTCAGGGGTAAAACGGTAATTTTCAGAA-AGATCGGGATCAAAAATA
1 AAAATGGAATTTTGGACATTCAGGGGTAAAATGGTAATTTT-GGAAGA-ATCGAGATCAAAAATA
*
1800075 GAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCA
64 GAATTTTTGGATATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCA
* * *
1800128 AAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAAATTTTAGAAGAATCGAAATCAAAAATA
1 AAAATGGAA-TTTTGGACATTCAGGGGTAAAATGGT-AATTTTGGAAGAATCGAGATCAAAAATA
* * *
1800193 GAATTTTTTTGGACATTCAAGGGTAAAATGGTAATTTTTAGAAGAATCAGGATCA
64 GAA--TTTTTGGATATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCA
** *
1800248 AAAATAAAATATTTGGACATTCAGGGGTAAAATGGTAATTTTGGAAGAATCGAGATCAAAAATGG
1 AAAATGGAAT-TTTGGACATTCAGGGGTAAAATGGTAATTTTGGAAGAATCGAGATCAAAAATAG
* * * * * *
1800313 AATTTTTAGATATTCGGGGGTAAAACGATAATTTTTAGAAAAATCGAGATCA
65 AATTTTTGGATATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCA
* * ** * * *
1800365 AAAATGGAATTTTCGGACATCCGGGAGGTAAAATGGTAATTTTGGAAGTGTCGGGGTAAAAAATA
1 AAAATGGAATTTT-GGACATTCAGG-GGTAAAATGGTAATTTTGGAAGAATCGAGATCAAAAATA
* * *
1800430 GAATTTTTGGAAATTTAGGGGTAAAA-GTGTAATTTTTGGAAG
64 GAATTTTTGGATATTCAGGGGTAAAATG-GTAATTTTTAGAAG
1800472 TTTTGGGGTC
Statistics
Matches: 386, Mismatches: 61, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
116 31 0.08
117 123 0.32
118 119 0.31
119 36 0.09
120 77 0.20
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (116 bp):
AAAATGGAATTTTGGACATTCAGGGGTAAAATGGTAATTTTGGAAGAATCGAGATCAAAAATAGA
ATTTTTGGATATTCAGGGGTAAAATGGTAATTTTTAGAAGAATCGGGATCA
Found at i:1801365 original size:13 final size:13
Alignment explanation
Indices: 1801347--1801371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1801337 CTTCTTTTTA
1801347 TTTCATTTTTATG
1 TTTCATTTTTATG
1801360 TTTCATTTTTAT
1 TTTCATTTTTAT
1801372 CTTAAAAAAA
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:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTCATTTTTATG
Found at i:1801808 original size:19 final size:19
Alignment explanation
Indices: 1801784--1801820 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1801774 TTTTAATAAC
*
1801784 ATTATTATTAATAATATTT
1 ATTATTATAAATAATATTT
*
1801803 ATTATTATAAATAGTATT
1 ATTATTATAAATAATATT
1801821 GTTAATAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATTATAAATAATATTT
Found at i:1801815 original size:16 final size:16
Alignment explanation
Indices: 1801776--1801809 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1801766 AATAACGCTT
*
1801776 TTAATAACA-TTATTA
1 TTAATAATATTTATTA
1801791 TTAATAATATTTATTA
1 TTAATAATATTTATTA
1801807 TTA
1 TTA
1801810 TAAATAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATAATATTTATTA
Found at i:1802370 original size:19 final size:19
Alignment explanation
Indices: 1802343--1802385 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1802333 GCTTATAGCA
*
1802343 GTGGCGGTGCAACTTGCTG
1 GTGGTGGTGCAACTTGCTG
1802362 GTGGTGGTGCAACTTGCTG
1 GTGGTGGTGCAACTTGCTG
*
1802381 TTGGT
1 GTGGT
1802386 CAATGCTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.42, T:0.33
Consensus pattern (19 bp):
GTGGTGGTGCAACTTGCTG
Found at i:1802623 original size:17 final size:17
Alignment explanation
Indices: 1802582--1802621 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1802572 TTTTAAATGT
1802582 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
1802599 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
1802615 ATTTAAA
1 ATTTAAA
1802622 ATCAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:1802628 original size:27 final size:27
Alignment explanation
Indices: 1802585--1802637 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1802575 TAAATGTATT
* *
1802585 TAAATTTAAAACAAATTTAAATTTAAA
1 TAAATTTAAAACAAATTCAAACTTAAA
1802612 TAAATTTAAAATC-AATTCAAACTTAA
1 TAAATTTAAAA-CAAATTCAAACTTAA
1802638 TTTAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTTAAAACAAATTCAAACTTAAA
Found at i:1803131 original size:39 final size:39
Alignment explanation
Indices: 1803088--1803192 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
1803078 GTTGATGGTG
*
1803088 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTAT-A
* * *
1803127 ATCTGCCCCAGGCTCGGGTTAAGAGATCGAATGGCTATT
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTATA
*
1803166 ATCTGCCCCAGACTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
1803193 TGACTAACGG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 58 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTATA
Found at i:1803490 original size:69 final size:69
Alignment explanation
Indices: 1803400--1803534 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
1803390 TTACTGCAAC
*
1803400 TTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTTAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1803465 AAAT
66 AAAT
*
1803469 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1803534 A
66 A
1803535 GACTTGTTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (69 bp):
TTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
AAAT
Found at i:1803606 original size:161 final size:161
Alignment explanation
Indices: 1803336--1803626 Score: 476
Period size: 161 Copynumber: 1.8 Consensus size: 161
1803326 TGGTGCCGAA
* * *
1803336 GCTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGTCTTGCTATCCAACTTTACTGCAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
1803401 TCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTTAGAGAGATAAA
66 TCAAGAGGATAAGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAA
1803466 AATTTCAAGAGGATAGGAATTGATGTTTGAT
131 AATTTCAAGAGGATAGGAATTGATGTTTGAT
*
1803497 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
1803562 TTAAGAGGATAAGAATTGATGTTTGATA-CTTTATCTTACTCTTACTACAACTTCAGAGGGATAA
66 TCAAGAGGATAAGAATTGATGTTTGA-AGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAA
1803626 A
130 A
1803627 GACTTGCTAT
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
161 118 0.99
162 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (161 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAAGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAA
AATTTCAAGAGGATAGGAATTGATGTTTGAT
Found at i:1803629 original size:92 final size:92
Alignment explanation
Indices: 1803469--1804282 Score: 1385
Period size: 92 Copynumber: 8.8 Consensus size: 92
1803459 AGATAAAAAT
1803469 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
*
1803534 AGACTTGTTATCCAACTTTACTACAAC
66 AGACTTGCTATCCAACTTTACTACAAC
* * * * * *
1803561 TTTAAGAGGATAAGAATTGATGTTTGATACTTTATCTTACTCTTACTACAACTTCAGAGGGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
*
1803626 AGACTTGCTATCCAACTTTACTGCAAC
66 AGACTTGCTATCCAACTTTACTACAAC
*
1803653 TTCAAGAGGATAGGAATTGATATTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
*
1803718 TGACTTGCTATCCAACTTTACTACAAC
66 AGACTTGCTATCCAACTTTACTACAAC
* *
1803745 TTTAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTTTTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1803810 AGACTTGCTATCCAACTTTACTACAAC
66 AGACTTGCTATCCAACTTTACTACAAC
* * *
1803837 TTCAAGAGGATAGAAATTGATGTTTCATGCTTCATCTTGCTCTTACTACAACTTCAGAGGGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
*
1803902 AGACTTGCTATCCAACTTTACTGCAAC
66 AGACTTGCTATCCAACTTTACTACAAC
*
1803929 TTCAAGAGGATAGGAATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTC-AGAGAGATA
1803994 AAGACTTGCTATCCAACTTTACTACAAC
65 AAGACTTGCTATCCAACTTTACTACAAC
* *
1804022 TTTAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1804087 AGACTTGCTATCCAACTTTACTACAAC
66 AGACTTGCTATCCAACTTTACTACAAC
1804114 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
* *
1804179 AGACTTGTTATCCAACTTTACTACAAT
66 AGACTTGCTATCCAACTTTACTACAAC
* * *
1804206 TTCAAGAGGATAGGAATTGATGTTCGATGCTTCATCTTGCTATTACTATAACTTCAAGAGAGATA
1 TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTC-AGAGAGATA
*
1804271 AAGACTAGCTAT
65 AAGACTTGCTAT
1804283 TTTGATTTGA
Statistics
Matches: 676, Mismatches: 44, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
92 570 0.84
93 106 0.16
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (92 bp):
TTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAA
AGACTTGCTATCCAACTTTACTACAAC
Found at i:1804029 original size:41 final size:40
Alignment explanation
Indices: 1803971--1804217 Score: 138
Period size: 40 Copynumber: 5.5 Consensus size: 40
1803961 CATCTTGCTC
1803971 TTACTACAACTTCAAGAGAGATAAAGACTTGCTATCCAACT
1 TTACTACAACTTCAAGAG-GATAAAGACTTGCTATCCAACT
* * ***
1804012 TTACTACAACTTTAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCT
1 TTACTACAACTTCAAGAGGATA--AA--GA---CT--TGC-T-ATCCAACT
1804063 ATTACTACAACTTC-AGAGAGATAAAGACTTGCTATCCAACT
1 -TTACTACAACTTCAAGAG-GATAAAGACTTGCTATCCAACT
* ***
1804104 TTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCT
1 TTACTACAACTTCAAGAGGATA--AA--GA---CT--TGC-T-ATCCAACT
*
1804155 CTTACTACAACTTC-AGAGAGATAAAGACTTGTTATCCAACT
1 -TTACTACAACTTCAAGAG-GATAAAGACTTGCTATCCAACT
*
1804196 TTACTACAATTTCAAGAGGATA
1 TTACTACAACTTCAAGAGGATA
1804218 GGAATTGATG
Statistics
Matches: 158, Mismatches: 20, Indels: 57
0.67 0.09 0.24
Matches are distributed among these distances:
40 37 0.23
41 35 0.22
42 6 0.04
43 5 0.03
44 4 0.03
45 2 0.01
47 2 0.01
48 4 0.03
49 6 0.04
50 6 0.04
51 18 0.11
52 33 0.21
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (40 bp):
TTACTACAACTTCAAGAGGATAAAGACTTGCTATCCAACT
Found at i:1804114 original size:277 final size:277
Alignment explanation
Indices: 1803472--1804282 Score: 1428
Period size: 277 Copynumber: 2.9 Consensus size: 277
1803462 TAAAAATTTC
*
1803472 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGA
1 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
* * * * *
1803537 CTTGTTATCCAACTTTACTACAACTTTAAGAGGATA-AGAATTGATGTTTGATACTTTATCTTAC
66 CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGA-AATTGATGTTTGATGCTTCATCTTGC
1803601 TCTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAG
130 TCTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAG
* * *
1803666 GAATTGATATTTGATGCTTCATCTTGCTCTTACTACAACTTC-AGAGAGATAATGACTTGCTATC
195 GAATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATAAAGACTTGCTATC
1803730 CAACTTTACTACAACTTT
260 CAACTTTACTACAACTTT
*
1803748 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTTTTACTACAACTTCAGAGAGATAAAGA
1 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
*
1803813 CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTCATGCTTCATCTTGCT
66 CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTTGCT
1803878 CTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGG
131 CTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGG
1803943 AATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATAAAGACTTGCTATCC
196 AATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATAAAGACTTGCTATCC
1804008 AACTTTACTACAACTTT
261 AACTTTACTACAACTTT
1804025 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
1 AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
*
1804090 CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCT
66 CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTTGCT
* * * *
1804155 CTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTACAATTTCAAGAGGATAGG
131 CTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGG
* * *
1804220 AATTGATGTTCGATGCTTCATCTTGCTATTACTATAACTTCAAGAGAGATAAAGACTAGCTAT
196 AATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATAAAGACTTGCTAT
1804283 TTTGATTTGA
Statistics
Matches: 513, Mismatches: 20, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
276 225 0.44
277 288 0.56
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (277 bp):
AAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
CTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTTGCT
CTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGG
AATTGATGTTCGATGCTTCATCTTGCTCTTACTACAACTTCAAGAGAGATAAAGACTTGCTATCC
AACTTTACTACAACTTT
Found at i:1804663 original size:100 final size:100
Alignment explanation
Indices: 1804442--1804681 Score: 272
Period size: 100 Copynumber: 2.4 Consensus size: 100
1804432 TTTTTTTCAA
* * *
1804442 GGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATC--TTTGCGATATTAAATCCACTGTTAC
1 GGTCCG-CGTTGCGACTTAGACCTTT--CTTTTTTATCTTTTTGCGATACTAAATCCACCGTTAC
* * *
1804505 GGTTTTAGATCTTTTCCGTTGTGTCTTCTGAGGTACAC
63 GGTTTTAGATATTTCCCGTCGTGTCTTCTGAGGTACAC
* * ** *
1804543 GGTCCGCTGTTACGACTTAGACCTTTCTTTTTTATCTTTTTGCGGTACTGGATCCACCGTTGCGG
1 GGTCCGC-GTTGCGACTTAGACCTTTCTTTTTTATCTTTTTGCGATACTAAATCCACCGTTACGG
*
1804608 -TTTAGATATTTCCCGTCGTGTCTTCTGAGGTACAT
65 TTTTAGATATTTCCCGTCGTGTCTTCTGAGGTACAC
* *
1804643 GGTCCGTCGTTGCGAGTTAGACCTTT-TCCTTTTATCTTT
1 GGTCCG-CGTTGCGACTTAGACCTTTCT-TTTTTATCTTT
1804682 GCTTGGTACT
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
99 10 0.08
100 64 0.54
101 45 0.38
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (100 bp):
GGTCCGCGTTGCGACTTAGACCTTTCTTTTTTATCTTTTTGCGATACTAAATCCACCGTTACGGT
TTTAGATATTTCCCGTCGTGTCTTCTGAGGTACAC
Found at i:1805418 original size:96 final size:100
Alignment explanation
Indices: 1805240--1805419 Score: 242
Period size: 98 Copynumber: 1.8 Consensus size: 100
1805230 AGGCGAATGA
* *
1805240 AATTTGATTGGAGGCAAAGCTCTCTCATGAATAAAAATGACTCATATTGGTCAAAGAATATGCCA
1 AATTTGATTGGAGGCAAAGCTCTCTCATGAATAAAAATGACCCATATTGGTCAAAG-AGATGCCA
1805305 AACACAAAGTGAGCAAAGAATAGGATTAGGTGGATG
65 AACACAAAGTGAGCAAAGAATAGGATTAGGTGGATG
* * * *
1805341 AATTTTATTGGAGGCAAAGCTC-GT-ATGAA-AAAAGTGACCCATATTGGTCAAAG-GATGCCGA
1 AATTTGATTGGAGGCAAAGCTCTCTCATGAATAAAAATGACCCATATTGGTCAAAGAGATGCCAA
* * *
1805402 ATATAGAGTGAGCAAAGA
66 ACACAAAGTGAGCAAAGA
1805420 GTATCGTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
96 21 0.30
98 22 0.31
99 5 0.07
100 1 0.01
101 21 0.30
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (100 bp):
AATTTGATTGGAGGCAAAGCTCTCTCATGAATAAAAATGACCCATATTGGTCAAAGAGATGCCAA
ACACAAAGTGAGCAAAGAATAGGATTAGGTGGATG
Found at i:1805999 original size:18 final size:16
Alignment explanation
Indices: 1805967--1806016 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
1805957 ACCTCTCCCT
1805967 TTTTTATTTTACTTTTC
1 TTTTT-TTTTACTTTTC
*
1805984 TTCTTGTTTTTGCTTTTC
1 TT-TT-TTTTTACTTTTC
*
1806002 TTTTTTTTTTCTTTT
1 TTTTTTTTTACTTTT
1806017 TTTGCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
18 14 0.48
19 1 0.03
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTACTTTTC
Found at i:1808997 original size:19 final size:19
Alignment explanation
Indices: 1808973--1809009 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1808963 TTTTAATAAC
*
1808973 ATTATTATTAATAATATTT
1 ATTATTATAAATAATATTT
*
1808992 ATTATTATAAATAGTATT
1 ATTATTATAAATAATATT
1809010 GTTAATAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATTATAAATAATATTT
Found at i:1809004 original size:16 final size:16
Alignment explanation
Indices: 1808965--1808998 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1808955 AATAACGCTT
*
1808965 TTAATAACA-TTATTA
1 TTAATAATATTTATTA
1808980 TTAATAATATTTATTA
1 TTAATAATATTTATTA
1808996 TTA
1 TTA
1808999 TAAATAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATAATATTTATTA
Found at i:1809560 original size:19 final size:19
Alignment explanation
Indices: 1809533--1809575 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1809523 GCTTGTAGCA
*
1809533 GTGGCGGTGCAACTTGCTG
1 GTGGTGGTGCAACTTGCTG
1809552 GTGGTGGTGCAACTTGCTG
1 GTGGTGGTGCAACTTGCTG
*
1809571 CTGGT
1 GTGGT
1809576 CAATGCTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.42, T:0.30
Consensus pattern (19 bp):
GTGGTGGTGCAACTTGCTG
Found at i:1809801 original size:17 final size:17
Alignment explanation
Indices: 1809760--1809799 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1809750 TTTTAAATGT
1809760 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
1809777 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
1809793 ATTTAAA
1 ATTTAAA
1809800 ATCAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:1809806 original size:27 final size:27
Alignment explanation
Indices: 1809763--1809815 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1809753 TAAATGTATT
* *
1809763 TAAATTTAAAACAAATTTAAATTTAAA
1 TAAATTTAAAACAAATTCAAACTTAAA
1809790 TAAATTTAAAATC-AATTCAAACTTAA
1 TAAATTTAAAA-CAAATTCAAACTTAA
1809816 TTTAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTTAAAACAAATTCAAACTTAAA
Found at i:1814115 original size:12 final size:12
Alignment explanation
Indices: 1814050--1814194 Score: 62
Period size: 12 Copynumber: 12.4 Consensus size: 12
1814040 AAACTAATAA
1814050 ATTAAATTATAT
1 ATTAAATTATAT
*
1814062 ATTAATTTATAT
1 ATTAAATTATAT
* *
1814074 TTTAATAATAATTAT
1 ATT-A-AATTA-TAT
*
1814089 ATTAAA-AATATT
1 ATTAAATTATA-T
1814101 ATTAAATTATAT
1 ATTAAATTATAT
1814113 ATT--ATT-T-T
1 ATTAAATTATAT
1814121 ATTAAATTATAT
1 ATTAAATTATAT
*
1814133 -TTAATAATAATTAT
1 ATT-A-AATTA-TAT
* *
1814147 GTTAAAATATA-
1 ATTAAATTATAT
1814158 ATTAAA-T-TA-
1 ATTAAATTATAT
*
1814167 ATTAATATT-TTT
1 ATTAA-ATTATAT
1814179 ATTAAATTATAT
1 ATTAAATTATAT
1814191 -TTAA
1 ATTAA
1814195 TAATAATCAT
Statistics
Matches: 104, Mismatches: 12, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
8 4 0.04
9 8 0.08
10 8 0.08
11 19 0.18
12 37 0.36
13 13 0.12
14 8 0.08
15 7 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (12 bp):
ATTAAATTATAT
Found at i:1814140 original size:58 final size:58
Alignment explanation
Indices: 1814061--1814201 Score: 205
Period size: 58 Copynumber: 2.4 Consensus size: 58
1814051 TTAAATTATA
* * *
1814061 TATTAATTTATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATTA-TTT
1 TATTAAATTATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAATATTTT
*
1814120 TATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAATATTTT
1 TATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTTT
1814178 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
1814202 CATTAAAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
57 19 0.25
58 46 0.61
59 11 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (58 bp):
TATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTTT
Found at i:1814152 original size:26 final size:26
Alignment explanation
Indices: 1814120--1814201 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 26
1814110 TATATTATTT
1814120 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
* * * *
1814146 TGTTAAAATATAATTAAATTAATTAATATTTT
1 TATT-AAAT-T-A-T-ATTTAA-TAATAATTA
1814178 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
1814202 CATTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
26 9 0.21
27 9 0.21
28 2 0.05
29 2 0.05
30 2 0.05
31 9 0.21
32 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:1817979 original size:4 final size:4
Alignment explanation
Indices: 1817970--1817995 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1817960 GCTCAAAGAG
1817970 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1817996 TAAGAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1818772 original size:43 final size:43
Alignment explanation
Indices: 1818719--1818811 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
1818709 TAGTTTGTAG
* *
1818719 CTTAACTCGACCCGACTCATGAAATACTGGTTAACTTTGTTAC
1 CTTAATTCGACCCGACTCATGAAATACTGGTTAAATTTGTTAC
*
1818762 CTTAATTCGACCCGACTCATGAAATATTGGTTAAATTTGTTAC
1 CTTAATTCGACCCGACTCATGAAATACTGGTTAAATTTGTTAC
1818805 CTTAATT
1 CTTAATT
1818812 TGTTGTTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (43 bp):
CTTAATTCGACCCGACTCATGAAATACTGGTTAAATTTGTTAC
Found at i:1819204 original size:20 final size:21
Alignment explanation
Indices: 1819179--1819219 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1819169 CGAACTCACA
1819179 CTTAGG-AAATATGTGTTAAT
1 CTTAGGAAAATATGTGTTAAT
1819199 CTTAGGATAAAATATGTGTTA
1 CTTAGG--AAAATATGTGTTA
1819220 GCATATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
23 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
CTTAGGAAAATATGTGTTAAT
Found at i:1819951 original size:2 final size:2
Alignment explanation
Indices: 1819944--1819977 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1819934 AGTTGATACA
1819944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1819978 GATTATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1823198 original size:3 final size:3
Alignment explanation
Indices: 1823157--1823187 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1823147 CTTATTTCTC
1823157 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1823188 GAACATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1826287 original size:3 final size:3
Alignment explanation
Indices: 1826279--1826312 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1826269 CTTATTTCTC
1826279 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1826313 GCACATACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1827807 original size:14 final size:14
Alignment explanation
Indices: 1827788--1827818 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1827778 AGAATAGATT
1827788 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
1827802 TTTAATTAATTAAA
1 TTTAATTAAATAAA
1827816 TTT
1 TTT
1827819 TTTAAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:1832738 original size:25 final size:23
Alignment explanation
Indices: 1832710--1832755 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1832700 GTTGAATCCA
1832710 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAATT-T-AAAAAATAATTAG
*
1832735 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
1832756 CTTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTAG
Found at i:1833820 original size:11 final size:11
Alignment explanation
Indices: 1833806--1833832 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1833796 TTTCTTTTTC
1833806 TTTTTTTCAAT
1 TTTTTTTCAAT
1833817 TTTTTTTCAAT
1 TTTTTTTCAAT
1833828 TTTTT
1 TTTTT
1833833 CTTTTCGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:1834799 original size:17 final size:17
Alignment explanation
Indices: 1834779--1834817 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1834769 AGTGCATAAT
*
1834779 TAAAATAAAATTAAAAA
1 TAAAATAAAACTAAAAA
1834796 TAAAATAAAACTAAAAA
1 TAAAATAAAACTAAAAA
1834813 TAAAA
1 TAAAA
1834818 ATGAAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAATAAAACTAAAAA
Found at i:1834812 original size:7 final size:6
Alignment explanation
Indices: 1834780--1834834 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
1834770 GTGCATAATT
* * * *
1834780 AAAATA AAATTA AAAAT- AAAATA AAACTA AAAATA AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1834827 AAAATA AA
1 AAAATA AA
1834835 TATGCTACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:1834893 original size:4 final size:4
Alignment explanation
Indices: 1834884--1834910 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1834874 CATGAAAGTA
1834884 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1834911 AATAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1837700 original size:25 final size:26
Alignment explanation
Indices: 1837658--1837706 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1837648 AAAAGGGAAA
* *
1837658 AAAAATTAAAATAGATAAATTAAATT
1 AAAAATGAAAATAGATAAAATAAATT
1837684 AAAAATGAAAATA-ATAAAATAAA
1 AAAAATGAAAATAGATAAAATAAA
1837707 AATAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAAATGAAAATAGATAAAATAAATT
Found at i:1837708 original size:14 final size:15
Alignment explanation
Indices: 1837685--1837723 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1837675 AATTAAATTA
*
1837685 AAAATGAAAAT-AAT
1 AAAATAAAAATAAAT
1837699 AAAATAAAAATAAAT
1 AAAATAAAAATAAAT
1837714 AATAATAAAA
1 AA-AATAAAA
1837724 TGGCTAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 5 0.23
16 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATAAAAATAAAT
Found at i:1837708 original size:21 final size:21
Alignment explanation
Indices: 1837659--1837724 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
1837649 AAAGGGAAAA
* * *
1837659 AAAATTAAAATAGATAA-ATT
1 AAAATAAAAATAAATAATAAT
* *
1837679 AAATTAAAAATGAA-AATAAT
1 AAAATAAAAATAAATAATAAT
1837699 AAAATAAAAATAAATAATAAT
1 AAAATAAAAATAAATAATAAT
1837720 AAAAT
1 AAAAT
1837725 GGCTAAAGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.05
20 24 0.65
21 11 0.30
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAATAAAAATAAATAATAAT
Found at i:1837712 original size:26 final size:26
Alignment explanation
Indices: 1837658--1837712 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1837648 AAAAGGGAAA
* * *
1837658 AAAAATTAAAATAGATAAATTAAATT
1 AAAAATGAAAATAGATAAATAAAAAT
1837684 AAAAATGAAAATA-ATAAAATAAAAAT
1 AAAAATGAAAATAGAT-AAATAAAAAT
1837710 AAA
1 AAA
1837713 TAATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAAATGAAAATAGATAAATAAAAAT
Found at i:1838816 original size:25 final size:23
Alignment explanation
Indices: 1838788--1838833 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1838778 GTTGGATCTA
1838788 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
1838813 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
1838834 CTTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:1843202 original size:2 final size:2
Alignment explanation
Indices: 1843195--1843222 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1843185 CCCCACTTGT
1843195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1843223 AAAGCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1844058 original size:78 final size:78
Alignment explanation
Indices: 1843936--1844090 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
1843926 TGTGTTGTGT
* *
1843936 TGTTTTGTTATTACCTGTTTTCTTCAGGCAAATTCAAGAAGCCATAGCTATGTTTTTCTTGACTA
1 TGTTTTGTTATTACCTGTTTTCTTCAGGCAAATTCAAGAAGCCATAGCCATGTTTTTATTGACTA
1844001 CTTTCAGTTGTTC
66 CTTTCAGTTGTTC
* *
1844014 TGTTTTGTTTTTACTTGTTTTCTTCAGGCAAATTCAAGAAGCCATAGCCATGTTTTTATTGACTA
1 TGTTTTGTTATTACCTGTTTTCTTCAGGCAAATTCAAGAAGCCATAGCCATGTTTTTATTGACTA
*
1844079 CTTTGAGTTGTT
66 CTTTCAGTTGTT
1844091 TGTAATAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (78 bp):
TGTTTTGTTATTACCTGTTTTCTTCAGGCAAATTCAAGAAGCCATAGCCATGTTTTTATTGACTA
CTTTCAGTTGTTC
Found at i:1849365 original size:83 final size:85
Alignment explanation
Indices: 1849207--1849365 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
1849197 GAATCCTCGA
* *
1849207 TGTACTTGTATCGATTAGGCTTATTTCTTTTTTTTTTAACACACCTCAGTCTTAAGTCATTCATA
1 TGTACTTGTATCGATTAGGCCTATTTCTTTTTTTTTTAACACA-CTCAGTCTTAAATCATTCATA
1849272 ACATAAGATACTCGAAGTATT
65 ACATAAGATACTCGAAGTATT
1849293 TGTA-TTGTATCGATTAGGCCTATTTCTTTTTTTTTTAACACA-TCAGTCTTAAATCATTCATAA
1 TGTACTTGTATCGATTAGGCCTATTTCTTTTTTTTTTAACACACTCAGTCTTAAATCATTCATAA
*
1849356 TATAAGATAC
66 CATAAGATAC
1849366 GTACATGTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 29 0.41
85 37 0.53
86 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (85 bp):
TGTACTTGTATCGATTAGGCCTATTTCTTTTTTTTTTAACACACTCAGTCTTAAATCATTCATAA
CATAAGATACTCGAAGTATT
Found at i:1855298 original size:38 final size:39
Alignment explanation
Indices: 1855227--1855303 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
1855217 TAACTGAACC
1855227 AGTAGACACCCTATTAAGATTTTAAATATCAGGAAATGA
1 AGTAGACACCCTATTAAGATTTTAAATATCAGGAAATGA
1855266 AGTAGACACCCTATTAAGA-TTTAAATATCAGGAAATGA
1 AGTAGACACCCTATTAAGATTTTAAATATCAGGAAATGA
1855304 CCCTGAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 19 0.50
39 19 0.50
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (39 bp):
AGTAGACACCCTATTAAGATTTTAAATATCAGGAAATGA
Found at i:1856772 original size:43 final size:43
Alignment explanation
Indices: 1856711--1856798 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
1856701 CAGAGGGAAT
1856711 GGCTAAATTTTGAGACAAAATCACAGACAAGTATATAAAAGCA
1 GGCTAAATTTTGAGACAAAATCACAGACAAGTATATAAAAGCA
1856754 GGCTAAATTTTGAGACAAAATCACAGACAAGTATATAAAAGCA
1 GGCTAAATTTTGAGACAAAATCACAGACAAGTATATAAAAGCA
1856797 GG
1 GG
1856799 AAAAAGGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (43 bp):
GGCTAAATTTTGAGACAAAATCACAGACAAGTATATAAAAGCA
Found at i:1859114 original size:2 final size:2
Alignment explanation
Indices: 1859107--1859136 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1859097 CAGTTAAAAC
1859107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1859137 CTGGAATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1866331 original size:20 final size:19
Alignment explanation
Indices: 1866306--1866347 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1866296 TTTCACTATG
*
1866306 ATTAAAATATAATAAATAGA
1 ATTAAAA-ATAATAAAAAGA
1866326 ATT--AAATAATAAAAAGA
1 ATTAAAAATAATAAAAAGA
1866343 ATTAA
1 ATTAA
1866348 TAGAATTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
17 14 0.74
18 2 0.11
20 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATTAAAAATAATAAAAAGA
Found at i:1866336 original size:17 final size:17
Alignment explanation
Indices: 1866314--1866347 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1866304 TGATTAAAAT
*
1866314 ATAATAAATAGAATTAA
1 ATAATAAAAAGAATTAA
1866331 ATAATAAAAAGAATTAA
1 ATAATAAAAAGAATTAA
1866348 TAGAATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
ATAATAAAAAGAATTAA
Found at i:1883247 original size:27 final size:25
Alignment explanation
Indices: 1883190--1883240 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1883180 ACCCTGATAG
1883190 AATAGACCATTTTTTTAACAATCTC
1 AATAGACCATTTTTTTAACAATCTC
*
1883215 AATAGACCCTTTTTTTAACAATCTC
1 AATAGACCATTTTTTTAACAATCTC
1883240 A
1 A
1883241 TTATAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (25 bp):
AATAGACCATTTTTTTAACAATCTC
Found at i:1883442 original size:2 final size:2
Alignment explanation
Indices: 1883435--1883464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1883425 GGGTGTAGTT
1883435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1883465 AAACACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1885104 original size:23 final size:26
Alignment explanation
Indices: 1885074--1885124 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1885064 GTCAAATTAT
*
1885074 ATATATTA-A-ATTTTA-AATATAAA
1 ATATATTATATATTTTATAATAAAAA
1885097 ATATATTATATATTTTATAATAAAAA
1 ATATATTATATATTTTATAATAAAAA
1885123 AT
1 AT
1885125 TGCATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 6 0.25
26 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATATTATATATTTTATAATAAAAA
Found at i:1888122 original size:17 final size:16
Alignment explanation
Indices: 1888097--1888130 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1888087 TTATCCGAAA
*
1888097 TACTTATTTTTTAAAT
1 TACTTATTTTTAAAAT
1888113 TACTTGATTTTTAAAAT
1 TACTT-ATTTTTAAAAT
1888130 T
1 T
1888131 TAATTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (16 bp):
TACTTATTTTTAAAAT
Found at i:1889860 original size:5 final size:5
Alignment explanation
Indices: 1889850--1889874 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1889840 TCATCCTCAA
1889850 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
1889875 CTCTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1893901 original size:2 final size:2
Alignment explanation
Indices: 1893894--1893964 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1893884 TCTCATAAAT
1893894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1893936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1893965 TTTAAAACAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1905944 original size:9 final size:9
Alignment explanation
Indices: 1905930--1905960 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
1905920 GAAGTTGCAT
1905930 AAGAAGGAG
1 AAGAAGGAG
1905939 AAGAAGGAG
1 AAGAAGGAG
1905948 AAGAAGGAG
1 AAGAAGGAG
1905957 AAGA
1 AAGA
1905961 GAGAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (9 bp):
AAGAAGGAG
Found at i:1905969 original size:18 final size:18
Alignment explanation
Indices: 1905930--1905970 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1905920 GAAGTTGCAT
*
1905930 AAGAAGGAGAAGAAGGAG
1 AAGAAGGAGAAGAAGGAA
1905948 AAGAAGGAGAAG-AGAGAA
1 AAGAAGGAGAAGAAG-GAA
1905966 AAGAA
1 AAGAA
1905971 AGAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGAAGGAGAAGAAGGAA
Found at i:1913023 original size:18 final size:17
Alignment explanation
Indices: 1912979--1913031 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1912969 TTTTGAAATC
*
1912979 ATAAAAA-AAACATAAA
1 ATAAAAATAAAAATAAA
1912995 ATAAAAATAAAAATAAA
1 ATAAAAATAAAAATAAA
*
1913012 A-AAGAAACTAAAAACAAA
1 ATAA-AAA-TAAAAATAAA
1913030 AT
1 AT
1913032 GAAGAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 9 0.29
17 12 0.39
18 10 0.32
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (17 bp):
ATAAAAATAAAAATAAA
Found at i:1915180 original size:11 final size:11
Alignment explanation
Indices: 1915164--1915201 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1915154 GGAAATGATG
*
1915164 AAAAAAGGGAA
1 AAAAAAGAGAA
1915175 AAAAAAGAGAA
1 AAAAAAGAGAA
1915186 AAAAAA-AGAA
1 AAAAAAGAGAA
1915196 AAAAAA
1 AAAAAA
1915202 AATACAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:1915201 original size:10 final size:10
Alignment explanation
Indices: 1915172--1915202 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1915162 TGAAAAAAGG
1915172 GAAAAAAAAGA
1 GAAAAAAAA-A
1915183 GAAAAAAAAA
1 GAAAAAAAAA
1915193 GAAAAAAAAA
1 GAAAAAAAAA
1915203 ATACAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:1916855 original size:45 final size:45
Alignment explanation
Indices: 1916805--1916902 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
1916795 TTTCCTCTGT
* * * *
1916805 GATGCTTGCCATCAGAAGATCTTGACCTTGACCTCTTTCTATCCC
1 GATGCTTACCATCAGAAGATCTTGACCTCGACCGCCTTCTATCCC
* *
1916850 GATGCTTACCATTAGCAGATCTTGACCTCGACCGCCTTCTATCCC
1 GATGCTTACCATCAGAAGATCTTGACCTCGACCGCCTTCTATCCC
1916895 GATGCTTA
1 GATGCTTA
1916903 GATTTCTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (45 bp):
GATGCTTACCATCAGAAGATCTTGACCTCGACCGCCTTCTATCCC
Found at i:1917744 original size:42 final size:42
Alignment explanation
Indices: 1917620--1917778 Score: 169
Period size: 42 Copynumber: 3.8 Consensus size: 42
1917610 AGACCTCCTC
* * *
1917620 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCGATAACTAATCGGTGATCTTGACTTTGACCTTGAT
* * * *
1917661 CTTTCGCCTATAAATGATCGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCGATAACTAATCGGTGATCTTGACTTTGACCTTGAT
* *
1917704 CTTCGCCGATAACTAATCGGTGATCTAGACTTTGATCTTGAT
1 CTTCGCCGATAACTAATCGGTGATCTTGACTTTGACCTTGAT
* * ** *
1917746 CTTCTCCGGTAACTAAGGGGTGATTTTGA-TTTG
1 CTTCGCCGATAACTAATCGGTGATCTTGACTTTG
1917779 GATCTTGACC
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
41 5 0.05
42 95 0.94
43 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (42 bp):
CTTCGCCGATAACTAATCGGTGATCTTGACTTTGACCTTGAT
Found at i:1929526 original size:22 final size:21
Alignment explanation
Indices: 1929487--1929532 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
1929477 TCTCTTCTTC
*
1929487 TTTATTTTATTTTATCTT-AA
1 TTTATATTATTTTATCTTCAA
1929507 TTTATATTATATTTATTCTTCAA
1 TTTATATTAT-TTTA-TCTTCAA
1929530 TTT
1 TTT
1929533 TTTGAAGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 4 0.18
23 5 0.23
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATTATTTTATCTTCAA
Found at i:1930982 original size:6 final size:6
Alignment explanation
Indices: 1930971--1930999 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1930961 ACATCTTCTG
1930971 ATCCAA ATCCAA ATCCAA ATCCAA ATCCA
1 ATCCAA ATCCAA ATCCAA ATCCAA ATCCA
1931000 GTCTCCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
ATCCAA
Found at i:1933161 original size:34 final size:33
Alignment explanation
Indices: 1933122--1933196 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 33
1933112 TAGATGCAAC
* *
1933122 TTAACAAATAAATATCTCTAAAATAATAACAAAA
1 TTAACAAA-AAATACCCCTAAAATAATAACAAAA
1933156 TTAAC---AAATACCCCTAAAATAATAACAAAA
1 TTAACAAAAAATACCCCTAAAATAATAACAAAA
1933186 TTAACAAAAAA
1 TTAACAAAAAA
1933197 ATAAGTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 28 0.78
33 3 0.08
34 5 0.14
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.23
Consensus pattern (33 bp):
TTAACAAAAAATACCCCTAAAATAATAACAAAA
Found at i:1938872 original size:29 final size:29
Alignment explanation
Indices: 1938819--1938904 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
1938809 GTTGAATTAG
*
1938819 AGATTCAGTTACAGATGCA-ATCATG-TAAT
1 AGATACAGTTACAGATGCAGA-CATGAT-AT
* *
1938848 AGATATAGTTACAGATGTAGACATGATAT
1 AGATACAGTTACAGATGCAGACATGATAT
* *
1938877 AGATACAGTTATAAATGCAGACATGATA
1 AGATACAGTTACAGATGCAGACATGATA
1938905 CCCCCACCTG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (29 bp):
AGATACAGTTACAGATGCAGACATGATAT
Found at i:1939700 original size:2 final size:2
Alignment explanation
Indices: 1939633--1939690 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1939623 CAAACAGTTT
*
1939633 AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1939675 AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC
1939691 CTTGACACAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1939740 original size:42 final size:43
Alignment explanation
Indices: 1939680--1939765 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
1939670 CACACACACA
* *
1939680 CACACACACACCTTGACACACCCCCGTGTGCCAGCTCGCGTGC
1 CACACACACACCTGGACACACCCCCGTGTGCCAACTCGCGTGC
* *
1939723 CACACACAC-CCTGGACACACCCCTGTGTGCCAACTCGTGTGC
1 CACACACACACCTGGACACACCCCCGTGTGCCAACTCGCGTGC
1939765 C
1 C
1939766 TTCGAACAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 30 0.77
43 9 0.23
ACGTcount: A:0.21, C:0.45, G:0.19, T:0.15
Consensus pattern (43 bp):
CACACACACACCTGGACACACCCCCGTGTGCCAACTCGCGTGC
Found at i:1941818 original size:107 final size:107
Alignment explanation
Indices: 1941632--1941841 Score: 411
Period size: 107 Copynumber: 2.0 Consensus size: 107
1941622 TGCAATGTCA
1941632 AATGCTGAGACTAAGTCCAATAATTAAGTGTGAATGGGGACATAAGACTAAGAATAAATGATCCA
1 AATGCTGAGACTAAGTCCAATAATTAAGTGTGAATGGGGACATAAGACTAAGAATAAATGATCCA
*
1941697 TGCTTTATTACTAAGAGGTTTAATATATATATATATATATAT
66 TGCTTTATGACTAAGAGGTTTAATATATATATATATATATAT
1941739 AATGCTGAGACTAAGTCCAATAATTAAGTGTGAATGGGGACATAAGACTAAGAATAAATGATCCA
1 AATGCTGAGACTAAGTCCAATAATTAAGTGTGAATGGGGACATAAGACTAAGAATAAATGATCCA
1941804 TGCTTTATGACTAAGAGGTTTAATATATATATATATAT
66 TGCTTTATGACTAAGAGGTTTAATATATATATATATAT
1941842 TTTAAGGTAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 102 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (107 bp):
AATGCTGAGACTAAGTCCAATAATTAAGTGTGAATGGGGACATAAGACTAAGAATAAATGATCCA
TGCTTTATGACTAAGAGGTTTAATATATATATATATATATAT
Found at i:1944886 original size:3 final size:3
Alignment explanation
Indices: 1944878--1944932 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1944868 TATCTCATCC
* * * * * *
1944878 TAT TAT TAT TAT TAT TAT TGT TGT TGT TGT TGT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1944926 TAT TAT T
1 TAT TAT T
1944933 CCTTGTTGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1947152 original size:72 final size:71
Alignment explanation
Indices: 1947028--1947229 Score: 244
Period size: 72 Copynumber: 2.8 Consensus size: 71
1947018 ATTTTATTTG
* ** * * *
1947028 GATGCATCTTATAACGATTTGAGTGGCCCAATTCCAAACTCGTTAT-GCAATATGAGTGAATTTA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAA-TTGTT-TGGCAATATGAGTGAACTAA
*
1947092 GCACTTTT
64 ACACTTTT
* * *
1947100 GATGTATCTTATAATAATTGGAGTGGCCCAATTCCAAATTGTTTGGATAATATGAGTCAACTAAA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGG-CAATATGAGTGAACTAAA
*
1947165 CATTTTT
65 CACTTTT
* *
1947172 GATGTATCTTATAATAATTTGAGTGGTCCAACTCCAAATTGTTTGGGCAATATGAGTG
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTT-GGCAATATGAGTG
1947230 CTCTCACTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 5 0.05
72 103 0.93
73 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (71 bp):
GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGGCAATATGAGTGAACTAAAC
ACTTTT
Found at i:1949816 original size:3 final size:3
Alignment explanation
Indices: 1949808--1949836 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1949798 TATATTTTTG
1949808 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1949837 CCTTGTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1952053 original size:72 final size:72
Alignment explanation
Indices: 1951934--1952273 Score: 511
Period size: 72 Copynumber: 4.7 Consensus size: 72
1951924 ATTTGGACGC
* * * * * * *
1951934 ATCTTGTAACAATTTGAGTGGCCCAATTCCAAACTGGTTATG-CAATATGAGTCAATTAAACATT
1 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTT-GGACAATATGAGTCAACTAAACACT
1951998 TTTGATGT
65 TTTGATGT
* *
1952006 ATCTTATAATAATTTGAGTGGCTCAATTCCAAATTGCTTGGATAATATGAGTCAACTAAACACTT
1 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACTAAACACTT
1952071 TTGATGT
66 TTGATGT
* *
1952078 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATTAGTCAACTAGACACTT
1 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACTAAACACTT
1952143 TTGATGT
66 TTGATGT
* * *
1952150 CTCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGGACAATATGAGTCAACTAGACACTT
1 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACTAAACACTT
1952215 TTGATGT
66 TTGATGT
* * *
1952222 ATCTTATAATAATTTGAGTGGCCCAATTCTAAATTGTTTGGGCAATATGAGT
1 ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGT
1952274 GCACTGACTT
Statistics
Matches: 248, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
71 1 0.00
72 247 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (72 bp):
ATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACTAAACACTT
TTGATGT
Found at i:1958613 original size:22 final size:21
Alignment explanation
Indices: 1958574--1958619 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
1958564 TCTCTTCTTC
*
1958574 TTTATTTTATTTTATCTT-AA
1 TTTATATTATTTTATCTTCAA
1958594 TTTATATTATATTTATTCTTCAA
1 TTTATATTAT-TTTA-TCTTCAA
1958617 TTT
1 TTT
1958620 TTTGAAGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 4 0.18
23 5 0.23
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATTATTTTATCTTCAA
Found at i:1960905 original size:8 final size:8
Alignment explanation
Indices: 1960882--1960923 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1960872 ATAAAATGCC
1960882 AAAGACTT
1 AAAGACTT
*
1960890 AAACACTT
1 AAAGACTT
*
1960898 TAAGACTT
1 AAAGACTT
1960906 -AAGACTT
1 AAAGACTT
*
1960913 AAAGACAT
1 AAAGACTT
1960921 AAA
1 AAA
1960924 AGGTGGGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (8 bp):
AAAGACTT
Found at i:1962463 original size:3 final size:3
Alignment explanation
Indices: 1962455--1962480 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1962445 TCCTATCATT
1962455 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1962481 TTGATGCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1964631 original size:72 final size:72
Alignment explanation
Indices: 1964535--1964951 Score: 635
Period size: 72 Copynumber: 5.8 Consensus size: 72
1964525 ATTTTATTTG
* *
1964535 GATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGGTTAT-G-CAATATGAGTCAACTA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAA-TGGTT-TGGACAATATGAGTCAACTA
*
1964598 AACACTTTT
64 AACATTTTT
1964607 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAACTGGTTAT-G-CAATATGAGTCAACTA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAA-TGGTT-TGGACAATATGAGTCAACTA
*
1964670 AACACTTTT
64 AACATTTTT
* *
1964679 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGGACAATATAAGTCAACTAAA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATGGTTTGGACAATATGAGTCAACTAAA
*
1964744 TATTTTT
66 CATTTTT
* *
1964751 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGGACAATATAAGTCAACTAAA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATGGTTTGGACAATATGAGTCAACTAAA
*
1964816 TATTTTT
66 CATTTTT
*
1964823 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATTGTTTGGACAATATGAGTCAACTAAA
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATGGTTTGGACAATATGAGTCAACTAAA
1964888 CATTTTT
66 CATTTTT
* * * *
1964895 GATGTATCTTATAATAATTTGAGTGGTCCAACTCCAAATTGTTTGGGCAATATGAGT
1 GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATGGTTTGGACAATATGAGT
1964952 GCTCTCACTT
Statistics
Matches: 332, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
70 1 0.00
71 5 0.02
72 326 0.98
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (72 bp):
GATGTATCTTATAATAATTTGAGTGGCCCAATTCCAAATGGTTTGGACAATATGAGTCAACTAAA
CATTTTT
Found at i:1968288 original size:30 final size:27
Alignment explanation
Indices: 1968218--1968279 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1968208 GCAAATGGAG
1968218 TGGAACATTATTCATATAAAACAAAGA
1 TGGAACATTATTCATATAAAACAAAGA
1968245 TGGAACATTATTCATATAAAACAAAGA
1 TGGAACATTATTCATATAAAACAAAGA
1968272 TGGAACAT
1 TGGAACAT
1968280 CATTATTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (27 bp):
TGGAACATTATTCATATAAAACAAAGA
Found at i:1976035 original size:32 final size:33
Alignment explanation
Indices: 1975998--1976063 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1975988 ATTTAACACA
* *
1975998 ACAGTCACTCAAC-TT-TGAAAACGTGACAAAAC
1 ACAGTCACT-AACATTATCAAAAAGTGACAAAAC
1976030 ACAGTCACTAACATTATCAAAAAGTGACAAAAC
1 ACAGTCACTAACATTATCAAAAAGTGACAAAAC
1976063 A
1 A
1976064 GTCGCTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 3 0.10
32 11 0.37
33 16 0.53
ACGTcount: A:0.48, C:0.23, G:0.11, T:0.18
Consensus pattern (33 bp):
ACAGTCACTAACATTATCAAAAAGTGACAAAAC
Found at i:1977161 original size:176 final size:178
Alignment explanation
Indices: 1976947--1977304 Score: 585
Period size: 176 Copynumber: 2.0 Consensus size: 178
1976937 TTTTCATTTT
*
1976947 GAATCTAAACAGAAAAAAAAAAAAAACAAGAAAGAAAGTAATGAATATTATGAATTAAAATTTAA
1 GAATCTAAACAGAAAAAAAAAAAAAACAAGAAAGAAAGTAATGAATAATATGAATTAAAATTTAA
** ** * *
1977012 GTTTTGATTTCTATACTTTAAAATTAAAAATTTAATATTTTTACTTTTTCAATTTTAAAATCAAG
66 AATTTGATCCCTATACTTTAAAATTAAAAATTTAATATTTTTACTTTTTCAATTTAAAAATCAAA
*
1977077 CTAAATCTTTTTACATTTAATTTAAAA-TTTTGTACATTAAATCAATA
131 CTAAATCTTTTTACATTTAATTTAAAATTTTTATACATTAAATCAATA
* *
1977124 GAATCTAAACAG-AGAAAAAAAAAAACAAGAAAGAAAGTAATGAATAATATGACTTAAAATTTAA
1 GAATCTAAACAGAAAAAAAAAAAAAACAAGAAAGAAAGTAATGAATAATATGAATTAAAATTTAA
1977188 AATTTGATCCCTATACTTTAAAATTAAAAATTTAATATTTTTACTTTTTCAATTTAAAAATCAAA
66 AATTTGATCCCTATACTTTAAAATTAAAAATTTAATATTTTTACTTTTTCAATTTAAAAATCAAA
* * *
1977253 CTAAATTTTTTTACATTTAATTTAAAATTTTTATACATTGAATCATTA
131 CTAAATCTTTTTACATTTAATTTAAAATTTTTATACATTAAATCAATA
1977301 GAAT
1 GAAT
1977305 GTCCGATCGA
Statistics
Matches: 167, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 134 0.80
177 33 0.20
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (178 bp):
GAATCTAAACAGAAAAAAAAAAAAAACAAGAAAGAAAGTAATGAATAATATGAATTAAAATTTAA
AATTTGATCCCTATACTTTAAAATTAAAAATTTAATATTTTTACTTTTTCAATTTAAAAATCAAA
CTAAATCTTTTTACATTTAATTTAAAATTTTTATACATTAAATCAATA
Found at i:1979266 original size:21 final size:22
Alignment explanation
Indices: 1979242--1979290 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1979232 AATTTAAAAA
1979242 TTAATCT-AAATCTTTT-TACAT
1 TTAATCTAAAAT-TTTTGTACAT
*
1979263 TTAATTTAAAATTTTTGTACAT
1 TTAATCTAAAATTTTTGTACAT
*
1979285 TGAATC
1 TTAATC
1979291 ATCAGAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (22 bp):
TTAATCTAAAATTTTTGTACAT
Found at i:1984487 original size:18 final size:18
Alignment explanation
Indices: 1984456--1984501 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
1984446 ATTCGAAAAA
1984456 AATTCGAGTTGACTCGAAT
1 AATTCGA-TTGACTCGAAT
1984475 AATTCGATTGACTCGAAT
1 AATTCGATTGACTCGAAT
*
1984493 AACTCGATT
1 AATTCGATT
1984502 CATTTTACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
AATTCGATTGACTCGAAT
Found at i:1985435 original size:16 final size:17
Alignment explanation
Indices: 1985408--1985444 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1985398 TCGTTCTATT
1985408 TTTTTCTATTTT-TGGAG
1 TTTTTCTATTTTCTGG-G
1985425 TTTTTCT-TTTTCTGGG
1 TTTTTCTATTTTCTGGG
1985441 TTTT
1 TTTT
1985445 CTGTCTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.05, C:0.08, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTTTCTATTTTCTGGG
Found at i:1990173 original size:30 final size:31
Alignment explanation
Indices: 1990146--1990203 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1990136 TTTTTTTGAT
*
1990146 AAAAAAAAAA-AAAACAATCCATGTTTTGTC
1 AAAAAAAAAATAAAAAAATCCATGTTTTGTC
1990176 AAAAAAAAAATAAAAAAATCCATGTTTT
1 AAAAAAAAAATAAAAAAATCCATGTTTT
1990204 AGATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.24
Consensus pattern (31 bp):
AAAAAAAAAATAAAAAAATCCATGTTTTGTC
Found at i:1991515 original size:19 final size:19
Alignment explanation
Indices: 1991491--1991527 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1991481 CCTTTCTTCT
1991491 TTCTCT-TCTCATCCTCCCC
1 TTCTCTATCTCAT-CTCCCC
1991510 TTCTCTATCTCATCTCCC
1 TTCTCTATCTCATCTCCC
1991528 AAAGCAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.08, C:0.49, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCTCTATCTCATCTCCCC
Found at i:1995887 original size:47 final size:47
Alignment explanation
Indices: 1995818--1995912 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1995808 GCAATTCCTT
1995818 AACTAAACAGCAGGAGTGGTGACACAGTGAGTGTGTTTTTGCTATGC
1 AACTAAACAGCAGGAGTGGTGACACAGTGAGTGTGTTTTTGCTATGC
1995865 AACTAAACAGCAGGAGTGGTGACACAGTGAGTGTGTTTTTGCTATGC
1 AACTAAACAGCAGGAGTGGTGACACAGTGAGTGTGTTTTTGCTATGC
1995912 A
1 A
1995913 GTATTCTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (47 bp):
AACTAAACAGCAGGAGTGGTGACACAGTGAGTGTGTTTTTGCTATGC
Found at i:1996770 original size:3 final size:3
Alignment explanation
Indices: 1996762--1996823 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1996752 ACTAATAGCT
1996762 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1996810 TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TC
1996824 CTTTGCTGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2010226 original size:222 final size:222
Alignment explanation
Indices: 2009809--2010265 Score: 641
Period size: 222 Copynumber: 2.1 Consensus size: 222
2009799 ACCTTACTGA
* * * * * *
2009809 ATTTCCAGAATTCATTAAAAGACAAGACAAGTTGGGTTATCTAGATCTTTCTAACAACCATATCC
1 ATTTCCGGAGTTCATCAAAACACAAGACAAGCTGGGTTATCTAGATCTTTCCAACAACCATATCC
* * * * *
2009874 ATGGTTTTGTGCCCAATTGGTTGTGGAAGAGCAGTCTTTCATGGGTAGACCTTTCTTTCAATGTG
66 ATGGTGTTGTGCCCAATTGGTTGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTG
*
2009939 ATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATT
131 ATTCATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATT
* **
2010004 GTAT-TTGAGATTCTGTAACATAAGTGC
196 GTATCTGGA-AGCCTGTAACATAAGTGC
*
2010031 ATTTCCGGAGTTCATCAAAACACAAGACAAGCT-GGTTGAGT-TAGATCTTTCCAACAATCATAT
1 ATTTCCGGAGTTCATCAAAACACAAGACAAGCTGGGTT-A-TCTAGATCTTTCCAACAACCATAT
* *
2010094 CCATGGTGTTGTGCCTAATTGGTTGTGGAATAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATG
64 CCATGGTGTTGTGCCCAATTGGTTGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATG
* * * * *
2010159 TGATTCATTTTCCAAAACAGCTTCCCTTGAGTGATGCAAACTTCTCTTTTTCTATGTTGAGGGAA
129 TGATTCATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAA
*
2010224 TTGTATCTGGAAGCCTGTAACATAAGTTC
194 TTGTATCTGGAAGCCTGTAACATAAGTGC
*
2010253 ATTCCCGGAGTTC
1 ATTTCCGGAGTTC
2010266 TTAAAGAGTC
Statistics
Matches: 207, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
221 4 0.02
222 199 0.96
223 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (222 bp):
ATTTCCGGAGTTCATCAAAACACAAGACAAGCTGGGTTATCTAGATCTTTCCAACAACCATATCC
ATGGTGTTGTGCCCAATTGGTTGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTG
ATTCATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATT
GTATCTGGAAGCCTGTAACATAAGTGC
Found at i:2010345 original size:222 final size:222
Alignment explanation
Indices: 2009895--2010347 Score: 470
Period size: 222 Copynumber: 2.0 Consensus size: 222
2009885 CCCAATTGGT
* * * * *
2009895 TGTGGAAGAGCAGTCTTTCATGGGTAGACCTTTCTTTCAATGTGATTGATTTTCCAAAACAGCTT
1 TGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTGATTCATTTTCCAAAACAGCTT
* **
2009960 CCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATTGTATTTGAGATTCTGTAACAT
66 CCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATTGTATTGGAGAGCCTGTAACAT
* * ** *
2010025 AAGTGCATTTCCGGAGTTCATCAAAACACAAGACAAGCTGGTTGAGTTAGATCTTTCCAACAATC
131 AAGTGCATTCCCGGAGTTCATCAAAACACAAGAAAAGCTGAATGAGTTAGACCTTTCCAACAATC
* * *** * * * *
2010090 ATATCCATGGTGTTGTGCCTAATTGGT
196 AAATCAATGGTGCAATACCAAACTGGG
*
2010117 TGTGGAATAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTGATTCATTTTCCAAAACAGCTT
1 TGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTGATTCATTTTCCAAAACAGCTT
* * * * *
2010182 CCCTTGAGTGATGCAAACTTCTCTTTTTCTATGTTGAGGGAATTGTATCTGGA-AGCCTGTAACA
66 CCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATTGTAT-TGGAGAGCCTGTAACA
* * ** ** *
2010246 TAAGTTCATTCCCGGAGTTC-TTAAAGAGTCAAGAAAATTTAGAAT-A-TCTCGACCTTT-CAAG
130 TAAGTGCATTCCCGGAGTTCATCAAA-ACACAAGAAAAGCT-GAATGAGT-TAGACCTTTCCAA-
*
2010307 TAA-CAAAAT-AAGTGGTGCAATACCAAACTGGG
191 CAATC-AAATCAA-TGGTGCAATACCAAACTGGG
2010339 TGTGGAAGA
1 TGTGGAAGA
2010348 AAAGTTTGCG
Statistics
Matches: 187, Mismatches: 37, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
221 10 0.05
222 172 0.92
223 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (222 bp):
TGTGGAAGAGCACTCTTTCAAGGGTAAACCTTTCCTTCAATGTGATTCATTTTCCAAAACAGCTT
CCCTTAAGTGATGCAAACTTCTCTTTCTCAATGTTAACGGAATTGTATTGGAGAGCCTGTAACAT
AAGTGCATTCCCGGAGTTCATCAAAACACAAGAAAAGCTGAATGAGTTAGACCTTTCCAACAATC
AAATCAATGGTGCAATACCAAACTGGG
Found at i:2010657 original size:72 final size:72
Alignment explanation
Indices: 2010487--2010663 Score: 196
Period size: 72 Copynumber: 2.5 Consensus size: 72
2010477 CACTCAGTGC
* * *
2010487 ATCTCATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAAGCAATATGAGTCAACTCAATTACT
1 ATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAAGCAAAATGAGTCAACTCAATGACT
*
2010552 TCTATGT
66 TCGATGT
* * * * * * **
2010559 ATCTAATAATAAATTT-AGCGGCCCAATTCCAAATTGCTTATGCAAAATGAGTCTACTTAGTGGT
1 ATCTAATAA-CAATTTGAGTGGCCCAATTCCAAATTGCTTAAGCAAAATGAGTCAACTCAATGAC
2010623 TTCGATGCT
65 TTCGATG-T
* *
2010632 -TCTTATAACAATTTGAGTGGTCCAATTCCAAA
1 ATCTAATAACAATTTGAGTGGCCCAATTCCAAA
2010664 ATGTTTTGGC
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
71 5 0.06
72 75 0.87
73 6 0.07
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (72 bp):
ATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAAGCAAAATGAGTCAACTCAATGACT
TCGATGT
Found at i:2015758 original size:21 final size:22
Alignment explanation
Indices: 2015732--2015773 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2015722 CAAAACGACG
2015732 TAATTTT-ATCTTTTAA-TTTAA
1 TAATTTTGA-CTTTTAACTTTAA
2015753 TAATTTTGACTTTTAACTTTA
1 TAATTTTGACTTTTAACTTTA
2015774 GAAAAGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TAATTTTGACTTTTAACTTTAA
Found at i:2016631 original size:13 final size:13
Alignment explanation
Indices: 2016613--2016678 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
2016603 CTTAAACCAA
2016613 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
2016626 ACTTTTCAAAATT
1 ACTTTTCAAAAGT
* *
2016639 ACTTTTCCAAAGC
1 ACTTTTCAAAAGT
* *
2016652 ACTTTTTAAAAAT
1 ACTTTTCAAAAGT
2016665 A-TTTCTCAAAAGT
1 ACTTT-TCAAAAGT
2016678 A
1 A
2016679 ATGCTAAACT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
12 3 0.07
13 39 0.93
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:2023115 original size:222 final size:223
Alignment explanation
Indices: 2022795--2023433 Score: 890
Period size: 222 Copynumber: 2.9 Consensus size: 223
2022785 TTAGGTTCTC
* * * * *
2022795 TAGATCTTTCTAACAACCATATCCATGGTTTTATGCCCAATTGGTTATGGAAGAGCAGTCTTACA
1 TAGATCTTTCTAACAACCATATCCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCAGTCTTTCA
* * * *
2022860 TGGCTAGACCTTTCTTTCAATGTAATTGATTTTCCAAAACAACTTCCTTTAAGTGATGCAAACTT
66 TGGGTAGACCTTTCTTTTAATGTGATTGATTTTCCAAAACAACTTCCCTTAAGTGATGCAAACTT
* * *
2022925 CTCTTTTCC-AATGTTGAGGGTATTGTATCTGGGATTCTGCAACATAAGTTCATTTCCAGAGTTC
131 CTC-TTTCCTAATGTTGAGGGAATTGTATTTGGGATTCTGTAACATAAGTTCATTTCCAGAGTTC
* * *
2022989 ATCAA-AACATAAGACGAGTTGGTTGAGT
195 ATCAAGAACACAAGACAAGTTGGTTAAGT
** ** *
2023017 TAGATCTTTCTAACAACCATATCCATGGTGTTGTGCCTAATTATTTGTAAAAGAGCAATCTTTCA
1 TAGATCTTTCTAACAACCATATCCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCAGTCTTTCA
*
2023082 TGGGTAGACCTTTCTTTTAATGTGATTGATTTTCCAAAACAACTTCCCTTAAGTGATGTAAACTT
66 TGGGTAGACCTTTCTTTTAATGTGATTGATTTTCCAAAACAACTTCCCTTAAGTGATGCAAACTT
* * *
2023147 CTCTTTCCTAATGTTGATGGAATTGTATTTGAGA-TCTTATAACATAAGTTCATTTCCAGAGTT-
131 CTCTTTCCTAATGTTGAGGGAATTGTATTTGGGATTC-TGTAACATAAGTTCATTTCCAGAGTTC
* *
2023210 TTTAAGAACACAAGACAAGTTGGTTAAGT
195 ATCAAGAACACAAGACAAGTTGGTTAAGT
* *
2023239 TATATCTTTTCTAACAACCATATCCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGTAGTCTTTC
1 TAGATC-TTTCTAACAACCATATCCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCAGTCTTTC
* * * *
2023304 ATGGGTAAACCTTTCTTTTAATGTGATTGATTTTCCAAAAGAGCTTCCCTTAAGTGATTCAAACT
65 ATGGGTAGACCTTTCTTTTAATGTGATTGATTTTCCAAAACAACTTCCCTTAAGTGATGCAAACT
* * * * *
2023369 TTTCTTTCCTAATGTTGAGGGGATTGAATTTGGGATCCTGTAACATAAGTTCATTTCCAAAGTTC
130 TCTCTTTCCTAATGTTGAGGGAATTGTATTTGGGATTCTGTAACATAAGTTCATTTCCAGAGTTC
2023434 TTAAAAAGTC
Statistics
Matches: 365, Mismatches: 46, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
221 10 0.03
222 188 0.52
223 166 0.45
224 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (223 bp):
TAGATCTTTCTAACAACCATATCCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCAGTCTTTCA
TGGGTAGACCTTTCTTTTAATGTGATTGATTTTCCAAAACAACTTCCCTTAAGTGATGCAAACTT
CTCTTTCCTAATGTTGAGGGAATTGTATTTGGGATTCTGTAACATAAGTTCATTTCCAGAGTTCA
TCAAGAACACAAGACAAGTTGGTTAAGT
Found at i:2023671 original size:72 final size:70
Alignment explanation
Indices: 2023582--2023781 Score: 204
Period size: 72 Copynumber: 2.8 Consensus size: 70
2023572 TTTCACTTCT
* * * * **
2023582 ATGTATCTAATAATAATTTGAGCGGACCAATTCCAAATTGCTTATGCAATATGAGTTAACTTGTC
1 ATGTATCT-ATAATAATTTGAGTGG-CCAATTCCAAATTGCTTAGGCAATATGAGTCAAATTCAC
2023647 GAATTCG
64 GAATTCG
*
2023654 ATGTATCATATAATAATTTGAGTGGCTCGATTCCAAATTGCTT-GGACAATATGAGTCAAATTCA
1 ATGTATC-TATAATAATTTGAGTGGC-CAATTCCAAATTGCTTAGG-CAATATGAGTCAAATTCA
* **
2023718 GGTTTTCG
63 CGAATTCG
* * * *
2023726 ATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATAGTTTAGGCAATATGAGT
1 ATGTATC-TATAATAATTTGAGTGG-CCAATTCCAAATTGCTTAGGCAATATGAGT
2023782 GCTTTGAGTT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
71 2 0.02
72 101 0.94
73 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (70 bp):
ATGTATCTATAATAATTTGAGTGGCCAATTCCAAATTGCTTAGGCAATATGAGTCAAATTCACGA
ATTCG
Found at i:2037331 original size:30 final size:29
Alignment explanation
Indices: 2037295--2037352 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2037285 TTTTTAAAAG
*
2037295 TTCAAGGGTAAAATTGTAATTTTTGGAAGA
1 TTCAAGGGTAAAA-TATAATTTTTGGAAGA
2037325 TTCAAGGGTAAAATATAATTTTTGGAAG
1 TTCAAGGGTAAAATATAATTTTTGGAAG
2037353 TTTGAGGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (29 bp):
TTCAAGGGTAAAATATAATTTTTGGAAGA
Found at i:2037397 original size:30 final size:29
Alignment explanation
Indices: 2037270--2037478 Score: 167
Period size: 30 Copynumber: 7.1 Consensus size: 29
2037260 TAGAACATTT
* *
2037270 GGGGTTAAAATGTTATTTTTAAAAGTTCA
1 GGGGTTAAAATGTAATTTTTAAAAGTTTA
* ** *
2037299 AGGG-TAAAATTGTAATTTTTGGAAGATTCA
1 GGGGTTAAAA-TGTAATTTTTAAAAG-TTTA
* * **
2037329 AGGG-TAAAATATAATTTTTGGAAGTTT-
1 GGGGTTAAAATGTAATTTTTAAAAGTTTA
* * *
2037356 GAGGTCCAAAATGTAATTTTCTTAAAGTTTA
1 GGGGT-TAAAATGTAATTTT-TAAAAGTTTA
* *
2037387 GGGGTTAAAATGTGAGTTTTAGAAAGTTT-
1 GGGGTTAAAATGTAATTTTTA-AAAGTTTA
2037416 GGCGGTTAAAATGTAATTTTTGAAAAGTTTA
1 GG-GGTTAAAATGTAATTTTT-AAAAGTTTA
2037447 GGGGTTAAAAT-TAAATTTTTAAAAAGTTTA
1 GGGGTTAAAATGT-AATTTTT-AAAAGTTTA
2037477 GG
1 GG
2037479 ATCATAATCA
Statistics
Matches: 149, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 7 0.05
29 45 0.30
30 88 0.59
31 7 0.05
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTTAAAAGTTTA
Found at i:2037491 original size:29 final size:30
Alignment explanation
Indices: 2037430--2037495 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2037420 GTTAAAATGT
* * * *
2037430 AATTTTTGAAAAGTTTAGGGGTTAAAATTA
1 AATTTTTAAAAAGTTTAGGGATCAAAATCA
*
2037460 AATTTTTAAAAAGTTTA-GGATCATAATCA
1 AATTTTTAAAAAGTTTAGGGATCAAAATCA
2037489 AATTTTT
1 AATTTTT
2037496 GGATAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (30 bp):
AATTTTTAAAAAGTTTAGGGATCAAAATCA
Found at i:2038857 original size:209 final size:208
Alignment explanation
Indices: 2038358--2038869 Score: 579
Period size: 209 Copynumber: 2.4 Consensus size: 208
2038348 TATCTCTTGG
* * * * * *
2038358 TCTACTTCTTTGTATCTCATCAGGAAGGTGACCGCCTTATTGTTTCGACCCACTCCTCTGTATCT
1 TCTACTTCTCTGTATCTCATTAAGAAGGTGACCGCTTTATTGCTTCGA-CCACTTCTCTGTATCT
* ** * * *
2038423 CATTAGGGTGATGGGGTTGGAAATTTCA-CTCACATTGAGCTTATGTTTCATTGAATTGGTCTTC
65 CATCAGGAAGATGGGGTTTGAAATTTCACCTCACATTGAGCTTA-GCTTCATTAAATTGGTCTTC
* * * *
2038487 TTCTCTGTATCTCATTAAGAAAATGACCGCTTCGTTTATTTAATCCAATTCTTTGTATTTCATCA
129 TTCTCTGTATCTCATTAAGAAAATGACCGCTTCATTGATTGAATCCAATTCTTTGTATCTCATCA
*
2038552 AGAAGACGAATTTGG
194 AGAAGACGAATTTGA
* * * ** *
2038567 TCAATTTCTCTGTATCTCATTAAGAAGCTGACCTTTTTATTGCTTTGACTCACTTCT-TAGTATC
1 TCTACTTCTCTGTATCTCATTAAGAAGGTGACCGCTTTATTGCTTCGAC-CACTTCTCT-GTATC
* * **
2038631 TTATCAGGAAGATGGGGTTTGAAGTTTCACCT-ATGTTGAGCCTTA-CTTCATTAAATTGGTCTT
64 TCATCAGGAAGATGGGGTTTGAAATTTCACCTCACATTGAG-CTTAGCTTCATTAAATTGGTCTT
* * * *
2038694 CTTCTCTGTATCTTA-TCAGAAAGATGACCGCCTT-ATTGATTGATTCCACTT-TTCTGTATCTC
128 CTTCTCTGTATCTCATTAAGAAA-ATGACCG-CTTCATTGATTGAATCCAATTCTT-TGTATCTC
2038756 ATCAAGAAGACGAATTTTGA
190 ATCAAGAAGACGAA-TTTGA
* *
2038776 TCTACTTCTCTATATCTCATTAAGAAGGTGACCGCTTTATTGCTTCGACCAAATTCTCTGTATCT
1 TCTACTTCTCTGTATCTCATTAAGAAGGTGACCGCTTTATTGCTTCGACC-ACTTCTCTGTATCT
*
2038841 CATCAGGAAGATGGGGTTTGAATTTTCAC
65 CATCAGGAAGATGGGGTTTGAAATTTCAC
2038870 TCTTTCCTAT
Statistics
Matches: 252, Mismatches: 41, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
207 8 0.03
208 73 0.29
209 164 0.65
210 7 0.03
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (208 bp):
TCTACTTCTCTGTATCTCATTAAGAAGGTGACCGCTTTATTGCTTCGACCACTTCTCTGTATCTC
ATCAGGAAGATGGGGTTTGAAATTTCACCTCACATTGAGCTTAGCTTCATTAAATTGGTCTTCTT
CTCTGTATCTCATTAAGAAAATGACCGCTTCATTGATTGAATCCAATTCTTTGTATCTCATCAAG
AAGACGAATTTGA
Found at i:2039127 original size:3 final size:3
Alignment explanation
Indices: 2039119--2039144 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2039109 TCTAGTTCAT
2039119 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2039145 TAGGTTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2043328 original size:25 final size:25
Alignment explanation
Indices: 2043294--2043345 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2043284 GTATGAGTAT
2043294 GAGTGTATTTTGTCAAATTGGACAA
1 GAGTGTATTTTGTCAAATTGGACAA
2043319 GAGTGTATTTTGTCAAATTGGACAA
1 GAGTGTATTTTGTCAAATTGGACAA
2043344 GA
1 GA
2043346 ATTTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (25 bp):
GAGTGTATTTTGTCAAATTGGACAA
Found at i:2050692 original size:59 final size:59
Alignment explanation
Indices: 2050629--2050810 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 59
2050619 AATTTTTGGG
*** *
2050629 AGTTTAAGGGCCAAAATGTAATTTT-TTTAAGTTTAGTGGTTAAAATATGATTTTTGAAA
1 AGTTTAAGGGCCAAAATGTAATTTTAGGAAAGTTTAGAGGTTAAAATAT-ATTTTTGAAA
* * * *
2050688 AGTTTGAGGGTCAAAATGTGATTTTAGGAAATTTTAGAGGTTAAAATATATTTTTGAAA
1 AGTTTAAGGGCCAAAATGTAATTTTAGGAAAGTTTAGAGGTTAAAATATATTTTTGAAA
* ** * * *
2050747 AGTTT-GGGGTTAAAATATAATTTTTA-GAAAGTTTA-AGGGTTAAAAT-TAAATTTTAAAA
1 AGTTTAAGGGCCAAAATGTAA-TTTTAGGAAAGTTTAGA-GGTTAAAATAT-ATTTTTGAAA
2050805 AGTTTA
1 AGTTTA
2050811 GGGTTAAAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.02
58 41 0.40
59 42 0.41
60 18 0.17
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (59 bp):
AGTTTAAGGGCCAAAATGTAATTTTAGGAAAGTTTAGAGGTTAAAATATATTTTTGAAA
Found at i:2050704 original size:30 final size:29
Alignment explanation
Indices: 2050657--2050820 Score: 172
Period size: 30 Copynumber: 5.6 Consensus size: 29
2050647 TAATTTTTTT
*
2050657 AAGTTTAGTGGTTAAAATATGATTTTTGAA
1 AAGTTTAG-GGTTAAAATATAATTTTTGAA
* * * * *
2050687 AAGTTTGAGGGTCAAAATGTGATTTTAGGA
1 AAGTTT-AGGGTTAAAATATAATTTTTGAA
*
2050717 AATTTTAGAGGTTAAAATAT-ATTTTTGAA
1 AAGTTTAG-GGTTAAAATATAATTTTTGAA
*
2050746 AAGTTTGGGGTTAAAATATAATTTTT-AGA
1 AAGTTTAGGGTTAAAATATAATTTTTGA-A
* *
2050775 AAGTTTAAGGGTTAAAAT-TAAATTTTAAA
1 AAGTTT-AGGGTTAAAATATAATTTTTGAA
2050804 AAGTTTAGGGTTAAAAT
1 AAGTTTAGGGTTAAAAT
2050821 CAAATTTATA
Statistics
Matches: 115, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
28 23 0.20
29 42 0.37
30 48 0.42
31 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.40
Consensus pattern (29 bp):
AAGTTTAGGGTTAAAATATAATTTTTGAA
Found at i:2050791 original size:58 final size:59
Alignment explanation
Indices: 2050657--2050820 Score: 192
Period size: 58 Copynumber: 2.8 Consensus size: 59
2050647 TAATTTTTTT
* * * * *
2050657 AAGTTTAGTGGTTAAAATATGATTTTTGAAAAGTTTGAGGGTCAAAATGTGATTTTAGGA
1 AAGTTTAGAGGTTAAAATATAATTTTTGAAAAGTTTG-GGGTTAAAATATAATTTTAGGA
*
2050717 AATTTTAGAGGTTAAAATAT-ATTTTTGAAAAGTTTGGGGTTAAAATATAATTTTTA-GA
1 AAGTTTAGAGGTTAAAATATAATTTTTGAAAAGTTTGGGGTTAAAATATAA-TTTTAGGA
* * *
2050775 AAGTTTA-AGGGTTAAAAT-TAAATTTTAAAAAGTTTAGGGTTAAAAT
1 AAGTTTAGA-GGTTAAAATATAATTTTTGAAAAGTTTGGGGTTAAAAT
2050821 CAAATTTATA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
57 2 0.02
58 51 0.55
59 21 0.23
60 18 0.20
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.40
Consensus pattern (59 bp):
AAGTTTAGAGGTTAAAATATAATTTTTGAAAAGTTTGGGGTTAAAATATAATTTTAGGA
Found at i:2051317 original size:17 final size:17
Alignment explanation
Indices: 2051281--2051327 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2051271 GGACATTCTT
*
2051281 TTTAAATTT-AAGTAAA
1 TTTAAATTTAAAATAAA
*
2051297 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
2051314 TTTAAATTTAAAAT
1 TTTAAATTTAAAAT
2051328 TGAGTTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2051967 original size:25 final size:23
Alignment explanation
Indices: 2051939--2051999 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 23
2051929 ATAGATAATA
2051939 TATAATTAATATAAAAATAATATAT
1 TATAATTAAT-TAAAAAT-ATATAT
*
2051964 TATATTTATTGAATTATAAATATATAT
1 TATA---ATT-AATTAAAAATATATAT
2051991 TATAATTAA
1 TATAATTAA
2052000 AACTTGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 4 0.13
27 10 0.32
28 9 0.29
29 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAATTAATTAAAAATATATAT
Found at i:2055116 original size:6 final size:6
Alignment explanation
Indices: 2055105--2055150 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
2055095 CTTTACATAC
* *
2055105 TTTTAG TTTTAG TTTTAA TTTTAA TTTTAA TTTTAA TTTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTT
2055151 CAAAACCCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:2055928 original size:21 final size:22
Alignment explanation
Indices: 2055886--2055933 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2055876 ATACATATAC
2055886 TTATATTTTATACCACTTTTTT
1 TTATATTTTATACCACTTTTTT
2055908 TTATATTTTATACCA-TTTTTT
1 TTATATTTTATACCACTTTTTT
2055929 TTATA
1 TTATA
2055934 ATTGCTACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATATTTTATACCACTTTTTT
Found at i:2056417 original size:6 final size:6
Alignment explanation
Indices: 2056406--2056435 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2056396 TATAATGTGA
2056406 TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC
1 TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC
2056436 CTTTGCTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
TGTTTC
Found at i:2073905 original size:32 final size:33
Alignment explanation
Indices: 2073861--2073941 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
2073851 AAGCTTAGTC
* * *
2073861 AAAATTGTTTATTTTATTAATTTTATTTTGA-T
1 AAAATTATTTATTTTACTAATTTCATTTTGACT
* *
2073893 TAAATT-TGTTATTTTCCTAATTTCATTTTGACT
1 AAAATTAT-TTATTTTACTAATTTCATTTTGACT
2073926 AAAATTATTTATTTTA
1 AAAATTATTTATTTTA
2073942 AGTAAATAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 1 0.03
32 25 0.62
33 13 0.32
34 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (33 bp):
AAAATTATTTATTTTACTAATTTCATTTTGACT
Found at i:2083053 original size:20 final size:20
Alignment explanation
Indices: 2083028--2083070 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2083018 GTAAATATAA
*
2083028 AAATATGTTTAATAATTTTT
1 AAATATATTTAATAATTTTT
*
2083048 AAATATATTTTATAATTTTT
1 AAATATATTTAATAATTTTT
2083068 AAA
1 AAA
2083071 ATTAGAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATATATTTAATAATTTTT
Done.