Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 39
Found at i:2379549 original size:21 final size:21
Alignment explanation
Indices: 2379523--2379634 Score: 156
Period size: 21 Copynumber: 5.3 Consensus size: 21
2379513 TATGTCATCT
*
2379523 CCGCAGGGTTACATTCCAAGC
1 CCGCAGGGTTACATTCCTAGC
2379544 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
2379565 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCTAGC
*
2379586 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
2379607 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
2379628 CCGCAGG
1 CCGCAGG
2379635 ATTTTATACC
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
20 4 0.05
21 73 0.90
22 4 0.05
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:2379575 original size:42 final size:42
Alignment explanation
Indices: 2379529--2379634 Score: 176
Period size: 42 Copynumber: 2.5 Consensus size: 42
2379519 ATCTCCGCAG
2379529 GGTTACATTCCAAGCCCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCAAGCCCGCAGGGTTACATTCCTAGCCCGCCA
* *
2379571 GGTTACATTCCGAGCCCGCAGGGTTATATTCCTAGCCCGCCA
1 GGTTACATTCCAAGCCCGCAGGGTTACATTCCTAGCCCGCCA
* *
2379613 GGTTACATGCCTAGCCCGCAGG
1 GGTTACATTCCAAGCCCGCAGG
2379635 ATTTTATACC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.22
Consensus pattern (42 bp):
GGTTACATTCCAAGCCCGCAGGGTTACATTCCTAGCCCGCCA
Found at i:2380261 original size:34 final size:34
Alignment explanation
Indices: 2380156--2380262 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
2380146 ATAAATGTTT
*
2380156 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
* *
2380190 TAAAAATAAAAATAATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
* * * *
2380224 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
2380258 TTAAA
1 TTAAA
2380263 TTTCAACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCAAAATTTAAAA
Found at i:2380886 original size:128 final size:128
Alignment explanation
Indices: 2380658--2381386 Score: 1226
Period size: 128 Copynumber: 5.7 Consensus size: 128
2380648 ACAATCCATC
2380658 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
2380723 AGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
2380786 TAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTTTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
2380851 GGAAGGCGCGTCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
2380914 CAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
2380979 GGAAGGCGCGCCCCCGGGAACACGCCTTCAAGTACCTTGAGAAATAATAGGTACTGATATGAT
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
2381042 TAGTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
2381107 GGAAGGCGC-CCTCCGGGAACGCGTCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
2381169 TAGTGTCCCCGAGGGACATGAGTGCCATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
2381234 GAAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
2381297 TAGTGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
2381362 GGAATGCGCGCCCCCGGGAACGCGC
66 GGAAGGCGCGCCCCCGGGAACGCGC
2381387 GTCCCCGGGA
Statistics
Matches: 556, Mismatches: 44, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
127 117 0.21
128 439 0.79
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:2381250 original size:255 final size:254
Alignment explanation
Indices: 2380658--2381386 Score: 1208
Period size: 255 Copynumber: 2.9 Consensus size: 254
2380648 ACAATCCATC
2380658 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
2380723 -AGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAAT
66 GA-AAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAAT
* * *
2380787 AGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTTTGACAAAATAATG
130 AGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG
* *
2380852 GAAGGCGCGTCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAA
195 GAAGGCGC--CCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
2380914 CAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * *
2380979 GGAAGGCGCGCCCCCGGGAACACGCCTTCAAGTACCTTGAGAAATAATAGGTACTGATATGATTA
66 GAAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
*
2381044 GTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
*
2381109 AAGGCGCCCTCCGGGAACGCGTCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
196 AAGGCGCCC-CCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
2381169 TAGTGTCCCCGAGGGACATGAGTGCCATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
2381234 GAAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GAAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
*
2381299 GTGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
2381364 AATGCGCGCCCCCGGGAACGCGC
196 AA-G-GCGCCCCCGGGAACGCGC
2381387 GTCCCCGGGA
Statistics
Matches: 439, Mismatches: 30, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
254 2 0.00
255 231 0.53
256 200 0.46
257 6 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (254 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GAAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
AAGGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:2381373 original size:383 final size:384
Alignment explanation
Indices: 2380658--2381382 Score: 1256
Period size: 383 Copynumber: 1.9 Consensus size: 384
2380648 ACAATCCATC
*
2380658 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
2380723 AGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
66 AGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
* * * * *
2380788 GTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTTTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGA
** *
2380853 AAGGCGCGTCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAACAGT
196 AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAACAGT
*
2380918 GTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAATGGAA
261 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAATGGAA
2380983 GGCGCGCCCCCGGGAACACGCCTTCAAGTACCTTGAGAAATAATAGGTACTGATATGAT
326 GGCGCGCCCCCGGGAACACGCCTTCAAGTACCTTGAGAAATAATAGGTACTGATATGAT
2381042 TAGTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
2381107 GGAAGGCGC-CCTCC-GGGAACGCGTCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAAT
66 AGAAGGCGCGCC-CCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAAT
*
2381170 AGTGTCCCCGAGGGACATGAGTGCCATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATG
130 AGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATG
* *
2381235 AAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAG
195 AAAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAACAG
* *
2381300 TGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGA
260 TGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAATGGA
*
2381365 ATGCGCGCCCCCGGGAAC
325 AGGCGCGCCCCCGGGAAC
2381383 GCGCGTCCCC
Statistics
Matches: 321, Mismatches: 19, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
383 247 0.77
384 74 0.23
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (384 bp):
TAGTGTCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
AGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAATA
GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGA
AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAACAGT
GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATACTCTCTGACAAAATAATGGAA
GGCGCGCCCCCGGGAACACGCCTTCAAGTACCTTGAGAAATAATAGGTACTGATATGAT
Found at i:2381386 original size:16 final size:16
Alignment explanation
Indices: 2381362--2381402 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2381352 ACAAAATAAT
*
2381362 GGAATGCGCGCCCCCG
1 GGAACGCGCGCCCCCG
*
2381378 GGAACGCGCGTCCCCG
1 GGAACGCGCGCCCCCG
*
2381394 GGATCGCGC
1 GGAACGCGC
2381403 ATTCATGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.41, G:0.39, T:0.07
Consensus pattern (16 bp):
GGAACGCGCGCCCCCG
Found at i:2381516 original size:8 final size:8
Alignment explanation
Indices: 2381488--2381520 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2381478 TCATAAGCTT
2381488 TCAAATTC
1 TCAAATTC
*
2381496 TCAAACTC
1 TCAAATTC
2381504 T-AAATTC
1 TCAAATTC
2381511 TCAAATTC
1 TCAAATTC
2381519 TC
1 TC
2381521 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (8 bp):
TCAAATTC
Found at i:2386424 original size:30 final size:30
Alignment explanation
Indices: 2386346--2386425 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
2386336 AATAGTGACT
* *
2386346 AAAATGTAAGTTTTGAAAGTTTGAGAGATA
1 AAAATGTAATTTTTAAAAGTTTGAGAGATA
* * *
2386376 AAGTAT-AAACTTTATAAAAGTTT-AGAGATCA
1 AA-AATGTAA-TTTTTAAAAGTTTGAGAGAT-A
2386407 AAAATGTAATTTTTAAAAG
1 AAAATGTAATTTTTAAAAG
2386426 CTATAGATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTAAAAGTTTGAGAGATA
Found at i:2387693 original size:14 final size:12
Alignment explanation
Indices: 2387665--2387689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2387655 TTTAATTTAT
2387665 ATAAATTTTAAA
1 ATAAATTTTAAA
2387677 ATAAATTTTAAA
1 ATAAATTTTAAA
2387689 A
1 A
2387690 AATATGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAATTTTAAA
Found at i:2390171 original size:13 final size:13
Alignment explanation
Indices: 2390153--2390178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2390143 TTTAGTCGCG
2390153 TGATGATGAGAAA
1 TGATGATGAGAAA
2390166 TGATGATGAGAAA
1 TGATGATGAGAAA
2390179 GACCGTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
TGATGATGAGAAA
Found at i:2392332 original size:18 final size:17
Alignment explanation
Indices: 2392309--2392347 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
2392299 ATTATTATTG
*
2392309 TTATTATAATTTTGGTTA
1 TTATTATAAGTTTGG-TA
2392327 TTATTATAAGTTTGGTA
1 TTATTATAAGTTTGGTA
2392344 TTAT
1 TTAT
2392348 GTAGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
TTATTATAAGTTTGGTA
Found at i:2398816 original size:2 final size:2
Alignment explanation
Indices: 2398809--2398849 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2398799 ATCCCTTCAA
2398809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2398850 CTCCTTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2399124 original size:14 final size:14
Alignment explanation
Indices: 2399086--2399138 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2399076 ATGTAAAAAA
2399086 AAAGAAAAAAAATTGG
1 AAAG-AAAAAAA-TGG
2399102 AAATGAAAAAAATGG
1 AAA-GAAAAAAATGG
*
2399117 AAACAAAAAGAA-GG
1 AAAGAAAAA-AATGG
2399131 AAAGAAAA
1 AAAGAAAA
2399139 CTCACCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 14 0.42
15 8 0.24
16 10 0.30
17 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAGAAAAAAATGG
Found at i:2401865 original size:36 final size:37
Alignment explanation
Indices: 2401784--2401866 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
2401774 AAAATCAATC
* *
2401784 TTAAGCCTTTACCGAAGAGTAGTGAAGCAAGTCGATT
1 TTAAGCCTTCACCAAAGAGTAGTGAAGCAAGTCGATT
* * *
2401821 TTAAGCCTTCACTAAAGAGTAGTGAAGTAATTC-ATT
1 TTAAGCCTTCACCAAAGAGTAGTGAAGCAAGTCGATT
2401857 TTAAGCCTTC
1 TTAAGCCTTC
2401867 TCAGAAGAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 13 0.32
37 28 0.68
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (37 bp):
TTAAGCCTTCACCAAAGAGTAGTGAAGCAAGTCGATT
Found at i:2401875 original size:36 final size:37
Alignment explanation
Indices: 2401784--2401876 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 37
2401774 AAAATCAATC
*
2401784 TTAAGCCTT-TACCGAAGAGTAGTGAAGCAAGTCGATT
1 TTAAGCCTTCT-CAGAAGAGTAGTGAAGCAAGTCGATT
* * *
2401821 TTAAGCCTTCACTA-AAGAGTAGTGAAGTAATTC-ATT
1 TTAAGCCTTCTC-AGAAGAGTAGTGAAGCAAGTCGATT
2401857 TTAAGCCTTCTCAGAAGAGT
1 TTAAGCCTTCTCAGAAGAGT
2401877 GTTGGAGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
35 1 0.02
36 20 0.42
37 27 0.56
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
TTAAGCCTTCTCAGAAGAGTAGTGAAGCAAGTCGATT
Found at i:2402279 original size:54 final size:54
Alignment explanation
Indices: 2402147--2402543 Score: 388
Period size: 54 Copynumber: 7.3 Consensus size: 54
2402137 TAGTGAAGCA
* * *
2402147 AAGAAGATTATTCTAGTTCCATACTCCTTAAAGAAAGAGGGAGCGAACCCGT---
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
** * * * *
2402199 TTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCATAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * * *
2402253 AAGAAGATGTTCGAGTTCCCTACTCCCTAGAGAAAGAAGGAGCAAACCCGTAAA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * *
2402307 AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGTGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * **
2402361 AAGAAGATGTTCGAGTTCCATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * **
2402416 TAGAAGAT-TATCCGAGTTCTATACTTCCTGAAAGAAAGAGGAAGCGAACCCATTCG
1 AAGAAGATGT-T-CGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * *
2402472 CATAAGATTATTCGAGTTCCATACTCCCTAAAGAAAGAGTGAGCGAACCTGTAGG
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
2402527 AAGAAGATTGTTCGAGT
1 AAGAAGA-TGTTCGAGT
2402544 CTTATACTCT
Statistics
Matches: 285, Mismatches: 52, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
51 37 0.13
52 5 0.02
54 118 0.41
55 63 0.22
56 59 0.21
57 2 0.01
58 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:2402588 original size:55 final size:55
Alignment explanation
Indices: 2402529--2403500 Score: 1293
Period size: 55 Copynumber: 17.8 Consensus size: 55
2402519 CCTGTAGGAA
* * *
2402529 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGAGAGCAGACGCGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
*
2402584 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* *
2402639 GAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * * *
2402694 GAAGATTATTCGAGTCTTATACTCTCTGAATG-AATAGAGAGTAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGACACGATTATT
* * *
2402749 GAAGATTATTCGAGTCTTATACTCTCTAAAAAAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * * * * *
2402804 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAACAGATATGA-TGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * *
2402858 GAAGATTGTTCGAGTCTTATACTTTCTGAAAAAATAGGGAGCATACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * * * **
2402913 GAAGATTATTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGCA-AGCCCGTTTACA
1 GAAGATTGTTCGAGTCT-TATACTCT-CTG-AAGAAATAGGGAGCAGA-CACGATTATT
* * *
2402969 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGA-TGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* *
2403023 GAAGATTGTTCGAGTCTTATA--CTCTGAAAAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * * *
2403076 AAAGATTATTCGAGTCTTATACTCTCTGAAAAAATAGGGAGTAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * *
2403131 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
*
2403186 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* *
2403241 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* * * *
2403296 GAAGATTGTTCGAGTGTTATACTCTCTGAAGGAATATGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
* *
2403351 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
** *
2403406 GAAGATTGTTCGAGTCTTATACTCTCTGAAG-AATACAGAGCAGAGACG-TTAGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA-TT
* * * *
2403460 GAAGATTGTGCGAGT-TCCATACACCCTGAA-AAATAGGGAGC
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGC
2403501 GAACCCGCTG
Statistics
Matches: 825, Mismatches: 76, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
52 26 0.03
53 26 0.03
54 115 0.14
55 612 0.74
56 44 0.05
57 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATT
Found at i:2406762 original size:33 final size:33
Alignment explanation
Indices: 2406714--2406804 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
2406704 AGTTAAAGAA
2406714 ACTTTCGATGACAGCAACAATTGTTCAACAATT
1 ACTTTCGATGACAGCAACAATTGTTCAACAATT
* *
2406747 ACTTTCGGTGGCAGCAACAATTGTTCAACAATT
1 ACTTTCGATGACAGCAACAATTGTTCAACAATT
* *
2406780 GCTTTCGATGCCAGCAACAATTGTT
1 ACTTTCGATGACAGCAACAATTGTT
2406805 GAATTTGGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (33 bp):
ACTTTCGATGACAGCAACAATTGTTCAACAATT
Found at i:2412598 original size:40 final size:40
Alignment explanation
Indices: 2412542--2412618 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2412532 AGGAAGAATA
* * **
2412542 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
1 GAAATAGAGTGACAAGAACAACAACACTGCTAGAAGAGCG
2412582 GAAATAGAGTGACAAGAACAACAACACTGCTAGAAGA
1 GAAATAGAGTGACAAGAACAACAACACTGCTAGAAGA
2412619 TCAGATCAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.45, C:0.16, G:0.27, T:0.12
Consensus pattern (40 bp):
GAAATAGAGTGACAAGAACAACAACACTGCTAGAAGAGCG
Found at i:2415733 original size:12 final size:12
Alignment explanation
Indices: 2415713--2415746 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2415703 GTGGGAAATG
*
2415713 AGAGATTTCTCC
1 AGAGCTTTCTCC
2415725 AGAGCTTTCTCC
1 AGAGCTTTCTCC
*
2415737 GGAGCTTTCT
1 AGAGCTTTCT
2415747 TCTTTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (12 bp):
AGAGCTTTCTCC
Found at i:2419318 original size:22 final size:22
Alignment explanation
Indices: 2419290--2419380 Score: 155
Period size: 22 Copynumber: 4.1 Consensus size: 22
2419280 GATAATGCTC
2419290 AATCCACTAATATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
2419312 AATCCACTAATATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
*
2419334 AATCCACTAATATTGAGTGCTA
1 AATCCACTAATATTGAGTGTTA
**
2419356 AATCCACTAGCATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
2419378 AAT
1 AAT
2419381 GCATGAGGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (22 bp):
AATCCACTAATATTGAGTGTTA
Found at i:2420834 original size:22 final size:23
Alignment explanation
Indices: 2420781--2420834 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2420771 TTTTCTCTTT
*
2420781 TCTTCTCTCCACGTATGGCTTCTC
1 TCTTC-CTCCACGTATGACTTCTC
2420805 TCTTTTCCT-CACGTATGACTTCTC
1 TC--TTCCTCCACGTATGACTTCTC
2420829 TCTTCC
1 TCTTCC
2420835 CCCTCCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
24 18 0.67
25 2 0.07
26 3 0.11
ACGTcount: A:0.09, C:0.37, G:0.09, T:0.44
Consensus pattern (23 bp):
TCTTCCTCCACGTATGACTTCTC
Found at i:2421025 original size:3 final size:3
Alignment explanation
Indices: 2421017--2421088 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
2421007 AGTGCTTGAG
*
2421017 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2421065 TAC TAA TAA TAA TATT TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TA
2421089 TTTTTTGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
3 60 0.97
4 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2421613 original size:36 final size:36
Alignment explanation
Indices: 2421559--2422079 Score: 302
Period size: 36 Copynumber: 14.6 Consensus size: 36
2421549 AAAGGTTTTA
*
2421559 TGTTTCAAGGGAAACTGTCTCAAAGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTC-AAGGAGACAAAATTT
* *
2421596 TGTTTCAA-GGAAACTGTCTCACAGGAGACAAAACTTA
1 TGTTTCAAGGGAAACTATCTCA-AGGAGACAAAA-TTT
*
2421633 T-TTT-AAGGGAAACTGAT-TCAA--AG----ATTTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGAGACAAAATTT
*
2421661 GTGTTTCAAGGGAAACGT-TTTCAA--AG------TTT
1 -TGTTTCAAGGGAAAC-TATCTCAAGGAGACAAAATTT
* * *
2421690 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TT
1 -TGTTTCAAGGGAAACTATCTCAA-GGAGACAAAATTT
2421727 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGACAAAATTT
* * *
2421763 CGTTCCAAGGGAAACTATCTCAAAAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTC-AAGGAGACAAAATTT
* *
2421799 CGTTTCAAGGGAAACGT-TTTCAA--AG------TTT
1 TGTTTCAAGGGAAAC-TATCTCAAGGAGACAAAATTT
* *
2421827 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 -TGTTTCAAGGGAAACTATCTCAA-GGAGACAAAATTT
2421864 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATATTT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGAC-AAA-ATTT
* * * *
2421903 TGTTTCGA-GGATACTATCTCATGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGACAAAA--TTT
* * *
2421941 TATTTCGAGGGAAACTATCTTC-AGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATC-TCAAG-GAGACAAAA--TTT
* *
2421980 TGTTTCGAGGGAAACTATCTCAAGCG-GATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGACAAAA--TTT
*
2422018 TGTTTCAAGGGAAACTATCTCAAGCGAGACGAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAG-GAGAC-AAA-ATTT
*
2422057 TGTTTAAAGGGAAACTATCTCAA
1 TGTTTCAAGGGAAACTATCTCAA
2422080 ACGAGATACA
Statistics
Matches: 404, Mismatches: 34, Indels: 90
0.77 0.06 0.17
Matches are distributed among these distances:
28 6 0.01
29 41 0.10
30 4 0.01
31 15 0.04
32 5 0.01
33 4 0.01
35 8 0.02
36 141 0.35
37 25 0.06
38 67 0.17
39 83 0.21
40 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGGAGACAAAATTT
Found at i:2421957 original size:77 final size:77
Alignment explanation
Indices: 2421866--2422079 Score: 306
Period size: 77 Copynumber: 2.8 Consensus size: 77
2421856 ACAAAATTTG
* * * *
2421866 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATATTTTGTTTCGA-GGATACTATCTCATGCGAG
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCG-G
2421930 ATAAAATCTTTTA
65 ATAAAATCTTTTA
* *
2421943 TTTCGAGGGAAACTATCTTC-AGCGAGATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGG
1 TTTCAAGGGAAACTATC-TCAAGCGAGACAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGG
*
2422007 ATAAAATCTTTTG
65 ATAAAATCTTTTA
* **
2422020 TTTCAAGGGAAACTATCTCAAGCGAGACGAAATCTTTTGTTTAAAGGGAAACTATCTCAA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTTTGTTTCGAGGGAAACTATCTCAA
2422080 ACGAGATACA
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
76 2 0.02
77 103 0.84
78 17 0.14
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (77 bp):
TTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGGA
TAAAATCTTTTA
Found at i:2421969 original size:39 final size:39
Alignment explanation
Indices: 2421828--2422087 Score: 316
Period size: 39 Copynumber: 6.8 Consensus size: 39
2421818 TCAAAGTTTA
* * * *
2421828 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA---TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* * *
2421864 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATATTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* * *
2421903 TGTTTCGA-GGATACTATCTCATGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* *
2421941 TATTTCGAGGGAAACTATCTTC-AGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATC-TCAAGCGAGATAAAATCTTT
*
2421980 TGTTTCGAGGGAAACTATCTCAAGCG-GATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
**
2422018 TGTTTCAAGGGAAACTATCTCAAGCGAGACGAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* *
2422057 TGTTTAAAGGGAAACTATCTCAAACGAGATA
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATA
2422088 CAATGTTCTT
Statistics
Matches: 197, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
36 31 0.16
38 71 0.36
39 93 0.47
40 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
Found at i:2422239 original size:76 final size:75
Alignment explanation
Indices: 2422158--2422319 Score: 184
Period size: 75 Copynumber: 2.1 Consensus size: 75
2422148 TCAAGCGAGA
* * * **
2422158 AAAAACAATCTTGAGTGAAAT-AAATCTTCATGTTTTTAGTGAAAAATGTCTCAAGCGAGA-AAA
1 AAAAACAATCTTGAGTCAAATGAAAT-GTCATCTTTCGAGT-AAAAATGTCTCAAGCGAGACAAA
2422221 ATCTTCTTTTAAG
64 ATC-TCTTTTAAG
* ** * *
2422234 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAATCTGTCTCAAGGGAGACAAAGT
1 AAAAACAATCTTGAGTCAAATGAAATGTCATCTTTCGAGTAAAAATGTCTCAAGCGAGACAAAAT
*
2422299 CTGTTTTAAG
66 CTCTTTTAAG
2422309 AAAAACAATCT
1 AAAAACAATCT
2422320 CAAGTAAGAT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
75 35 0.48
76 34 0.47
77 4 0.05
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (75 bp):
AAAAACAATCTTGAGTCAAATGAAATGTCATCTTTCGAGTAAAAATGTCTCAAGCGAGACAAAAT
CTCTTTTAAG
Found at i:2429867 original size:3 final size:3
Alignment explanation
Indices: 2429859--2429888 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2429849 AGTGCTTGAC
2429859 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
2429889 TTTTTTGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2436695 original size:441 final size:441
Alignment explanation
Indices: 2435830--2436705 Score: 1452
Period size: 441 Copynumber: 2.0 Consensus size: 441
2435820 GAAAGTTTTA
* *
2435830 TCTGTTTTATTTCAAATAATTTCATATATTTCCATATTTTATTTATTTGTTCTCACCTTTAATAT
1 TCTGTTTTATTTCAAATAATTTCATATATTTCAATATTTTATCTATTTGTTCTCACCTTTAATAT
* * *
2435895 TACTGCATCACTAAGTTGTACTTAGCACGTGATGATTTTCGTACGTAGGTCCTGATTGAGACACA
66 TAATGCATCACTAAGTTATACTTAGCACGTGATGATTTTCATACGTAGGTCCTGATTGAGACACA
* * * *
2435960 TATGTCTTGTGAGGAGCCTCCCAAGCATCGTGTGTAGATCATCTATAATATTAATATCAGTAAGA
131 GACGTCTTGTGAGGAGCCTCCCAAGCATCGTGTGCAGATCATCTATAATATCAATATCAGTAAGA
*
2436025 CATCATCGATGTTCCTTCTGACTAGCAGTGGCATGTATAATTATGTTTATTAGACTACCTTATCA
196 CATCATCGATGTTCCTTCTGACTAGCAGTGACATGTATAATTATGTTTATTAGACTACCTTATCA
*
2436090 GTTATGACTAAATGGTCAGTAATAGTAAATTAGGATTGTTTAATGTGACTAGTTTCGGTTAGCAA
261 GTTATGACTAAATGGTCAGTAATAGTAAATTAGGATTGTTTAATGTGACTAATTTCGGTTAGCAA
* *
2436155 TATTTAATATGCCTATTATATATAATAGATAAAATATTATGTTTTTAAAATGGTACTTAAGTTTA
326 TATTTAATATGCCTAATATATATAATAGATAAAATATTATGTTTTTAAAATGGTACTGAAGTTTA
2436220 AGTAAATATAAATAGTTTTAAAAGTTGAAAATATGAAATGTTTTAACTTTCC
391 AGTAAATATAAATAGTTTTAAAAGTTGAAAATATG-AATGTTTTAACTTTCC
* * *
2436272 TCTGTTTTATTTTAAATAATTTCGTATATTTCAATA-TTTATCTATTTGTTCTCGCCTTTAATAT
1 TCTGTTTTATTTCAAATAATTTCATATATTTCAATATTTTATCTATTTGTTCTCACCTTTAATAT
* **
2436336 TAATGCATCACTAAGTTATACTTAGCGCGTGATGATTTTCATACGTAGGTTTTGATTG-GCACAC
66 TAATGCATCACTAAGTTATACTTAGCACGTGATGATTTTCATACGTAGGTCCTGATTGAG-ACAC
* *
2436400 AGACGTTTTGTGAGGAGCCTCCCAAGCATCGTGTGCAGATCATCTATAATATCAGTATCAGTAAG
130 AGACGTCTTGTGAGGAGCCTCCCAAGCATCGTGTGCAGATCATCTATAATATCAATATCAGTAAG
* * *
2436465 ACATCATCGATGTTCCTTTTGACTAGTAGTGACATGTATAATTATGTTTATTAGCCTACCTTATC
195 ACATCATCGATGTTCCTTCTGACTAGCAGTGACATGTATAATTATGTTTATTAGACTACCTTATC
* *
2436530 AGTTATGACTAAATGGTCAGTAATAGTAAATTATGATTGTTTAATTTGACTAATTTCGGTTAGCA
260 AGTTATGACTAAATGGTCAGTAATAGTAAATTAGGATTGTTTAATGTGACTAATTTCGGTTAGCA
2436595 ATATTTAATATGCCTAATATATATAATAGATAAAATATTATGTTTTTAAAATGGT-CATGAAGTT
325 ATATTTAATATGCCTAATATATATAATAGATAAAATATTATGTTTTTAAAATGGTAC-TGAAGTT
* *
2436659 TAAGTAGATATGAATAGTTTTAAAAGTTGAAAATATGAATGTTTTAA
389 TAAGTAAATATAAATAGTTTTAAAAGTTGAAAATATGAATGTTTTAA
2436706 AAGAAACAAA
Statistics
Matches: 404, Mismatches: 28, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
440 12 0.03
441 359 0.89
442 33 0.08
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (441 bp):
TCTGTTTTATTTCAAATAATTTCATATATTTCAATATTTTATCTATTTGTTCTCACCTTTAATAT
TAATGCATCACTAAGTTATACTTAGCACGTGATGATTTTCATACGTAGGTCCTGATTGAGACACA
GACGTCTTGTGAGGAGCCTCCCAAGCATCGTGTGCAGATCATCTATAATATCAATATCAGTAAGA
CATCATCGATGTTCCTTCTGACTAGCAGTGACATGTATAATTATGTTTATTAGACTACCTTATCA
GTTATGACTAAATGGTCAGTAATAGTAAATTAGGATTGTTTAATGTGACTAATTTCGGTTAGCAA
TATTTAATATGCCTAATATATATAATAGATAAAATATTATGTTTTTAAAATGGTACTGAAGTTTA
AGTAAATATAAATAGTTTTAAAAGTTGAAAATATGAATGTTTTAACTTTCC
Found at i:2436716 original size:24 final size:25
Alignment explanation
Indices: 2436666--2436716 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
2436656 GTTTAAGTAG
**
2436666 ATATGAATAGTTTTAAAAGTTGAAA
1 ATATGAATAGTTTTAAAAGTAAAAA
2436691 ATATGAAT-GTTTTAAAAG-AAACAA
1 ATATGAATAGTTTTAAAAGTAAA-AA
2436715 AT
1 AT
2436717 TTTTAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.61
25 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (25 bp):
ATATGAATAGTTTTAAAAGTAAAAA
Found at i:2438023 original size:2 final size:2
Alignment explanation
Indices: 2438016--2438045 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2438006 TTTATTTATT
2438016 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
2438046 GTATCTTCTG
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:2438473 original size:2 final size:2
Alignment explanation
Indices: 2438466--2438521 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
2438456 TTTTATTGAT
2438466 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
2438508 TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA T
2438522 TTATCTTCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2439605 original size:2 final size:2
Alignment explanation
Indices: 2439598--2439636 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2439588 AAATAGATTT
2439598 TA TA TA TA TA 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 TA TA TA TA TA T
2439637 TCCTCATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2439680 original size:28 final size:28
Alignment explanation
Indices: 2439640--2439705 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
2439630 TATATATTCC
2439640 TCATTAAATTTAAAAGTTCTAATCTTTA
1 TCATTAAATTTAAAAGTTCTAATCTTTA
2439668 TCATTAAATTTAAAAGTTCTAATCTTTA
1 TCATTAAATTTAAAAGTTCTAATCTTTA
2439696 TCATTAAATT
1 TCATTAAATT
2439706 CAGTTGATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (28 bp):
TCATTAAATTTAAAAGTTCTAATCTTTA
Found at i:2444917 original size:12 final size:12
Alignment explanation
Indices: 2444889--2444925 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
2444879 TTTGGTAATC
2444889 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
2444902 CCCGCCCCGATA
1 CCCGCCCCGATA
*
2444914 CCCGACCCGATA
1 CCCGCCCCGATA
2444926 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:2444986 original size:24 final size:25
Alignment explanation
Indices: 2444959--2445019 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
2444949 ATATATATAT
2444959 ATAATATTA-ATAAATTTAATTTAA
1 ATAATATTATATAAATTTAATTTAA
* *
2444983 ATAA-AATATATATATTTAATTTAA
1 ATAATATTATATAAATTTAATTTAA
2445007 AT-ATATATATATA
1 ATAATAT-TATATA
2445020 CCCGACCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 21 0.68
25 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAATATTATATAAATTTAATTTAA
Found at i:2445001 original size:19 final size:19
Alignment explanation
Indices: 2444977--2445016 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2444967 AATAAATTTA
2444977 ATTTAAATAAAATATATAT
1 ATTTAAATAAAATATATAT
* *
2444996 ATTTAATTTAAATATATAT
1 ATTTAAATAAAATATATAT
2445015 AT
1 AT
2445017 ATACCCGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAAATATATAT
Found at i:2445048 original size:23 final size:23
Alignment explanation
Indices: 2445021--2445068 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2445011 ATATATATAC
* *
2445021 CCGACCCGATTCCCGGCCCAATA
1 CCGACCCAATACCCGGCCCAATA
2445044 CCGACCCAATACCCGGCCCAATA
1 CCGACCCAATACCCGGCCCAATA
2445067 CC
1 CC
2445069 CGTTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.50, G:0.15, T:0.10
Consensus pattern (23 bp):
CCGACCCAATACCCGGCCCAATA
Found at i:2445065 original size:12 final size:12
Alignment explanation
Indices: 2445017--2445070 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
2445007 ATATATATAT
*
2445017 ATACCCGACCCG
1 ATACCCGACCCA
* *
2445029 ATTCCCGGCCCA
1 ATACCCGACCCA
2445041 ATA-CCGACCCA
1 ATACCCGACCCA
*
2445052 ATACCCGGCCCA
1 ATACCCGACCCA
2445064 ATACCCG
1 ATACCCG
2445071 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:2454959 original size:15 final size:15
Alignment explanation
Indices: 2454939--2454968 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2454929 TCTCACCCAC
2454939 AAGGAAGTCTCCCTA
1 AAGGAAGTCTCCCTA
2454954 AAGGAAGTCTCCCTA
1 AAGGAAGTCTCCCTA
2454969 GTGATACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (15 bp):
AAGGAAGTCTCCCTA
Found at i:2462990 original size:30 final size:30
Alignment explanation
Indices: 2462955--2463020 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2462945 AGAACCGGAA
*
2462955 GAACCGGCTGAAAA-TCGGGAAAACCGGGGT
1 GAACCGGCTGAAAACT-GGCAAAACCGGGGT
**
2462985 GAACCGGCTGAAAACTGGCAAAACCGGTTT
1 GAACCGGCTGAAAACTGGCAAAACCGGGGT
2463015 GAACCG
1 GAACCG
2463021 CTGGTTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.32, T:0.12
Consensus pattern (30 bp):
GAACCGGCTGAAAACTGGCAAAACCGGGGT
Found at i:2469311 original size:21 final size:20
Alignment explanation
Indices: 2469277--2469315 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2469267 AACTTGGATG
2469277 TTATATAAGCTTAAGAAAAGC
1 TTATATAAGCTTAA-AAAAGC
2469298 TTATATAA-CATTAAAAAA
1 TTATATAAGC-TTAAAAAA
2469316 CAAGACGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (20 bp):
TTATATAAGCTTAAAAAAGC
Found at i:2469522 original size:20 final size:21
Alignment explanation
Indices: 2469494--2469533 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2469484 AAGATTTAAG
2469494 TGTTCAAAGT-GAAATTGTGA
1 TGTTCAAAGTAGAAATTGTGA
* *
2469514 TGTTTAAAGTAGTAATTGTG
1 TGTTCAAAGTAGAAATTGTG
2469534 CACAAGTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.40
Consensus pattern (21 bp):
TGTTCAAAGTAGAAATTGTGA
Found at i:2469843 original size:54 final size:53
Alignment explanation
Indices: 2469780--2469902 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 53
2469770 TGAAGGATGA
* ** *
2469780 TATCGATACCCTT-AAATCATTGAATGTAATTTCGGTATCAGTACCTTGAGGAAG
1 TATCGATACCCTTGAAA-CATCGAACCTAATTTCGGTATCAGTA-CATGAGGAAG
* * * *
2469834 TATCGATACCCTTGAAACATCGAACCTTATTTCGGTATCGGTACATGCGGAGG
1 TATCGATACCCTTGAAACATCGAACCTAATTTCGGTATCAGTACATGAGGAAG
*
2469887 TATCGATACCCCTGAA
1 TATCGATACCCTTGAA
2469903 GGGTGGTATC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
53 22 0.37
54 34 0.58
55 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (53 bp):
TATCGATACCCTTGAAACATCGAACCTAATTTCGGTATCAGTACATGAGGAAG
Found at i:2469927 original size:20 final size:21
Alignment explanation
Indices: 2469885--2469937 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2469875 TACATGCGGA
2469885 GGTATCGATACCCCTGAAGGGT
1 GGTATCGATA-CCCTGAAGGGT
*
2469907 GGTATCGATACCCT-TAGGGT
1 GGTATCGATACCCTGAAGGGT
*
2469927 GGTACCGATAC
1 GGTATCGATAC
2469938 TTCCAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.52
21 4 0.14
22 10 0.34
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (21 bp):
GGTATCGATACCCTGAAGGGT
Found at i:2469963 original size:20 final size:20
Alignment explanation
Indices: 2469925--2469964 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2469915 TACCCTTAGG
**
2469925 GTGGTACCGATACTTCCAAA
1 GTGGTACCGATACCACCAAA
2469945 GTGGTACCGATACCACCAAA
1 GTGGTACCGATACCACCAAA
2469965 CATGAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (20 bp):
GTGGTACCGATACCACCAAA
Found at i:2470336 original size:21 final size:21
Alignment explanation
Indices: 2470310--2470355 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2470300 TATGGAAATA
2470310 TGAACTTTGAACAAGTGAATG
1 TGAACTTTGAACAAGTGAATG
*
2470331 TGAACTTTGAACCAGTGAATG
1 TGAACTTTGAACAAGTGAATG
2470352 TGAA
1 TGAA
2470356 TATACTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (21 bp):
TGAACTTTGAACAAGTGAATG
Found at i:2471599 original size:54 final size:53
Alignment explanation
Indices: 2471505--2471628 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 53
2471495 CTAAAGGATT
* * ** * * *
2471505 GTATCGATACCCTTAAAACATCGAATGTAATTTTGGTATCGGTACCTTGAGGAG
1 GTATCGATACCCTTGAAACATCAAACCTAATTTCGATATCGGTA-CATGAGGAG
* *
2471559 GTATCGATACCCTTGAAACATCAAACCTTATTTCGATATCGGTACATGCGGAG
1 GTATCGATACCCTTGAAACATCAAACCTAATTTCGATATCGGTACATGAGGAG
* *
2471612 GTATTGATACCCCTGAA
1 GTATCGATACCCTTGAA
2471629 GGGTGGTATC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
53 22 0.37
54 37 0.63
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (53 bp):
GTATCGATACCCTTGAAACATCAAACCTAATTTCGATATCGGTACATGAGGAG
Found at i:2471636 original size:22 final size:21
Alignment explanation
Indices: 2471611--2471663 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2471601 TACATGCGGA
*
2471611 GGTATTGATACCCCTGAAGGGT
1 GGTATCGATACCCCT-AAGGGT
*
2471633 GGTATCGGTA-CCCTAAGGGT
1 GGTATCGATACCCCTAAGGGT
2471653 GGTATCGATAC
1 GGTATCGATAC
2471664 TTCCAAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.56
21 4 0.15
22 8 0.30
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (21 bp):
GGTATCGATACCCCTAAGGGT
Found at i:2477452 original size:63 final size:63
Alignment explanation
Indices: 2477353--2477476 Score: 248
Period size: 63 Copynumber: 2.0 Consensus size: 63
2477343 ATGTTTTCAA
2477353 CAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTGAAATCAAAAAC
1 CAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTGAAATCAAAAAC
2477416 CAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTGAAATCAAAA
1 CAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTGAAATCAAAA
2477477 CCGACGTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (63 bp):
CAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAAGATTTTGAAATCAAAAAC
Found at i:2478152 original size:12 final size:12
Alignment explanation
Indices: 2478135--2478163 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2478125 TTGTTGTGCT
2478135 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2478147 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2478159 TGCTC
1 TGCTC
2478164 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:2479876 original size:20 final size:20
Alignment explanation
Indices: 2479847--2479884 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2479837 CCCCTTCAAA
*
2479847 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2479867 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2479885 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2483692 original size:22 final size:21
Alignment explanation
Indices: 2483650--2483689 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2483640 GAATTTATTT
*
2483650 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2483671 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2483690 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2489684 original size:13 final size:13
Alignment explanation
Indices: 2489666--2489690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2489656 TTGAAAATTA
2489666 ATATTATATATTG
1 ATATTATATATTG
2489679 ATATTATATATT
1 ATATTATATATT
2489691 TTATTGGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATTATATATTG
Found at i:2494232 original size:101 final size:102
Alignment explanation
Indices: 2494052--2494267 Score: 407
Period size: 101 Copynumber: 2.1 Consensus size: 102
2494042 TAATGTCCAT
*
2494052 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTGGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACA-ATACTAGGGATCAAGTATGTGTCTCACCA
2494117 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2494155 AAGGACCACATATCATTCCTTAAGAATCATATAC-ATACTAGGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATACAATACTAGGGATCAAGTATGTGTCTCACCAG
2494219 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2494256 AAGGACCACATA
1 AAGGACCACATA
2494268 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
101 78 0.70
103 34 0.30
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACAATACTAGGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2498810 original size:23 final size:23
Alignment explanation
Indices: 2498776--2498836 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2498766 GCTATATAAA
*
2498776 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
2498799 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
2498822 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2498837 TGTATAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:2499029 original size:98 final size:97
Alignment explanation
Indices: 2498851--2499058 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 97
2498841 TAATGTCCAT
2498851 AAGGACCACATATCATTCCTTAAGAATCATATACATATATGGGATCAAGTATGTGTCTCACCAGA
1 AAGGACCACATATCATTCCTTAAGAATCA-ATACATATATGGGATCAAG-ATGTGTCTCACCAGA
2498916 CTTCACACATGTTCCAAAGAATACATATATGT-CCG
64 CTTCACACATGTTCCAAAGAAT--ATATATGTCCCG
*
2498951 AAGGACCACATATCATTCCTTAAGAATC-ATACATATACTAGGGATCAA-ATGTGTCTCACTAGA
1 AAGGACCACATATCATTCCTTAAGAATCAATACATATA-T-GGGATCAAGATGTGTCTCACCAGA
2499014 CTTCACACATGTTCCAAAGAATATATATGTCCCG
64 CTTCACACATGTTCCAAAGAATATATATGTCCCG
2499048 AA-GACCACATA
1 AAGGACCACATA
2499059 GACCTCGACT
Statistics
Matches: 104, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
96 17 0.16
97 5 0.05
98 45 0.43
99 1 0.01
100 36 0.35
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (97 bp):
AAGGACCACATATCATTCCTTAAGAATCAATACATATATGGGATCAAGATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATATATATGTCCCG
Found at i:2501989 original size:70 final size:70
Alignment explanation
Indices: 2501876--2502032 Score: 192
Period size: 70 Copynumber: 2.2 Consensus size: 70
2501866 TAGTAAAACA
* * ** *
2501876 TCCGTTCTAGTTGAATCGAAAGTGTGATGCCTCCTTTTGTTCGACTTGCATC-ATAAGTGCGATA
1 TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGA-AAGTGCGATA
2501940 CTTCCT
65 CTTCCT
* * * **
2501946 TCCGTTCTACTTGGATTGAAAATGTGATGCCTTCTTTCATTCGACTTGAATCGAAAGTGCGATGT
1 TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGAAAGTGCGATAC
2502011 TTCCT
66 TTCCT
2502016 TCCGTT-TAACTTGAATC
1 TCCGTTCT-ACTTGAATC
2502033 TATGCAAACT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
69 1 0.01
70 71 0.97
71 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (70 bp):
TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGAAAGTGCGATAC
TTCCT
Found at i:2504448 original size:151 final size:153
Alignment explanation
Indices: 2504174--2504479 Score: 573
Period size: 151 Copynumber: 2.0 Consensus size: 153
2504164 TGATATTTAA
2504174 ATATTAAAAGAAAATGTTAAAAGTAATTAAGGAAGATACTTTTATTAGGATTGGAAGTTATACTA
1 ATATTAAAAGAAAATGTTAAAAGTAATTAAGGAAGATACTTTTATTAGGATTGGAAGTTATACTA
2504239 AAGTAAAATAATTAAATGTGAACTAAATCGAAAGATATTATTAGAACTTTAACTCGTATAA-TAA
66 AAGTAAAATAATTAAATGTGAACTAAATCGAAAGATATTATTAGAACTTTAACTCGTATAATTAA
2504303 ATTAAATT-AAAAATAGTTATAC
131 ATTAAATTAAAAAATAGTTATAC
2504325 ATATTAAAAGAAAATGTTAAAAGTAATTAAAGGAAGATACTTTTATTAGGATTGGAAGTTATACT
1 ATATTAAAAGAAAATGTTAAAAGTAATT-AAGGAAGATACTTTTATTAGGATTGGAAGTTATACT
2504390 AAAGT-AAATAATTAAATGTGAACTAAATCGAAAGATATTATTAGAACTTTAACTCGTATAATTA
65 AAAGTAAAATAATTAAATGTGAACTAAATCGAAAGATATTATTAGAACTTTAACTCGTATAATTA
2504454 AATTAAATTAAAAAAATAGTTATAC
130 AATTAAATT-AAAAAATAGTTATAC
2504479 A
1 A
2504480 AAGATTTAAT
Statistics
Matches: 151, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
151 84 0.56
152 52 0.34
154 15 0.10
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.33
Consensus pattern (153 bp):
ATATTAAAAGAAAATGTTAAAAGTAATTAAGGAAGATACTTTTATTAGGATTGGAAGTTATACTA
AAGTAAAATAATTAAATGTGAACTAAATCGAAAGATATTATTAGAACTTTAACTCGTATAATTAA
ATTAAATTAAAAAATAGTTATAC
Found at i:2507632 original size:17 final size:17
Alignment explanation
Indices: 2507612--2507647 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2507602 ACTCGAGTCA
*
2507612 AGTTCGAGCTCGAGTTG
1 AGTTCAAGCTCGAGTTG
*
2507629 AGTTCAAGCTTGAGTTG
1 AGTTCAAGCTCGAGTTG
2507646 AG
1 AG
2507648 ACAATTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (17 bp):
AGTTCAAGCTCGAGTTG
Found at i:2508120 original size:2 final size:2
Alignment explanation
Indices: 2508115--2508160 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2508105 TAGAGTTAAC
2508115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2508157 AT AT
1 AT AT
2508161 TAGTAATAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2509192 original size:29 final size:30
Alignment explanation
Indices: 2509136--2509205 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 30
2509126 AACAAAATTC
*
2509136 ATAATTTGGTGGTAAAAAAGAACTATCCCT
1 ATAATTTAGTGGTAAAAAAGAACTATCCCT
2509166 ATAATTTAGTGGT-AAAAAGAACTATCCCT
1 ATAATTTAGTGGTAAAAAAGAACTATCCCT
2509195 ATAATTTAGTG
1 ATAATTTAGTG
2509206 ACTATACATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (30 bp):
ATAATTTAGTGGTAAAAAAGAACTATCCCT
Found at i:2509368 original size:30 final size:31
Alignment explanation
Indices: 2509299--2509387 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
2509289 GTATCTAACA
2509299 TTTTTGGGTCAAAATAAGTACATAAAGTTATC
1 TTTTT-GGTCAAAATAAGTACATAAAGTTATC
* *
2509331 TTTTTGGTCAAAATATGTACTTAAAGTTATC
1 TTTTTGGTCAAAATAAGTACATAAAGTTATC
* *
2509362 -TTTTGGTCAAAATAAGAACCTAAAGT
1 TTTTTGGTCAAAATAAGTACATAAAGT
2509388 ATTTTATGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 23 0.44
31 24 0.46
32 5 0.10
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (31 bp):
TTTTTGGTCAAAATAAGTACATAAAGTTATC
Found at i:2509921 original size:2 final size:2
Alignment explanation
Indices: 2509914--2509945 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2509904 CTTGTTCTAC
2509914 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
2509946 TGTCTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2513678 original size:18 final size:19
Alignment explanation
Indices: 2513647--2513682 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2513637 TTTGACCATA
2513647 TAAAAAATAATAAAATATG
1 TAAAAAATAATAAAATATG
*
2513666 TAAAAAAT-TTAAAATAT
1 TAAAAAATAATAAAATAT
2513683 ATATCTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAAATAATAAAATATG
Found at i:2514071 original size:17 final size:17
Alignment explanation
Indices: 2514045--2514079 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2514035 CTTTTGAAAA
2514045 TTTTAAATTTTAAATTT
1 TTTTAAATTTTAAATTT
*
2514062 TTTTATATTTTAAATTT
1 TTTTAAATTTTAAATTT
2514079 T
1 T
2514080 CTTGTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAAATTTTAAATTT
Found at i:2518523 original size:24 final size:24
Alignment explanation
Indices: 2518496--2518542 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2518486 AAATTAGATC
2518496 AATTAGTA-TCAAAATATTATAAAT
1 AATTA-TACTCAAAATATTATAAAT
* *
2518520 AATTATACTTAAAATTTTATAAA
1 AATTATACTCAAAATATTATAAA
2518543 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTATACTCAAAATATTATAAAT
Found at i:2521077 original size:17 final size:17
Alignment explanation
Indices: 2521039--2521077 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2521029 AATTTTATAT
* *
2521039 AAATAAAAATATATTTT
1 AAATAAAAATATATCTA
*
2521056 TAATAAAAATATATCTA
1 AAATAAAAATATATCTA
2521073 AAATA
1 AAATA
2521078 TATAAAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAAAAATATATCTA
Found at i:2524503 original size:24 final size:23
Alignment explanation
Indices: 2524475--2524519 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2524465 ATTTAGAACT
*
2524475 AAAATTTAAAAAATTAATATTAAA
1 AAAATATAAAAAA-TAATATTAAA
*
2524499 AAAATATCAAAAATAATATTA
1 AAAATATAAAAAATAATATTA
2524520 CATGAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATATAAAAAATAATATTAAA
Found at i:2525270 original size:21 final size:20
Alignment explanation
Indices: 2525203--2525341 Score: 89
Period size: 21 Copynumber: 6.8 Consensus size: 20
2525193 AAATGACCAA
***
2525203 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** * *
2525223 CAGAATCGCAAATCAATTTC
1 CAAAATCGCAACGCGATTTT
2525243 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2525264 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2525285 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2525305 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2525326 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2525342 ACACATAAAT
Statistics
Matches: 90, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
20 44 0.49
21 46 0.51
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2525373 original size:20 final size:20
Alignment explanation
Indices: 2525308--2525597 Score: 275
Period size: 20 Copynumber: 14.5 Consensus size: 20
2525298 CGATTTTCCA
* ** *
2525308 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
2525328 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
2525348 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
2525368 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
2525388 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
2525408 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
2525428 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
2525448 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
2525468 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
2525488 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
2525508 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
2525528 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
2525548 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
2525568 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
2525588 AAATCACAAC
1 AAATCGCAAC
2525598 ACTGAAATTT
Statistics
Matches: 231, Mismatches: 29, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
20 230 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:2525579 original size:40 final size:40
Alignment explanation
Indices: 2525328--2525597 Score: 339
Period size: 40 Copynumber: 6.8 Consensus size: 40
2525318 GCGAATATGA
* * *
2525328 AAATCGCAACGCGAA-CACATAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGAT-AATCCGT
* * * * *
2525368 ATATCGCAACGCGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
2525408 AAATCGCAATGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
2525448 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
2525488 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
2525528 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
2525568 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
2525598 ACTGAAATTT
Statistics
Matches: 213, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.00
40 210 0.99
41 1 0.00
42 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:2525590 original size:60 final size:60
Alignment explanation
Indices: 2525328--2525597 Score: 319
Period size: 60 Copynumber: 4.5 Consensus size: 60
2525318 GCGAATATGA
* * * * * *
2525328 AAATCGCAACGCGAA-CACATAAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * * * * *
2525388 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* * * * *
2525448 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
2525508 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
2525568 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
2525598 ACTGAAATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
59 1 0.01
60 182 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:2526315 original size:24 final size:24
Alignment explanation
Indices: 2526276--2526322 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2526266 AAATTTGGTC
2526276 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2526300 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2526323 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2528867 original size:19 final size:19
Alignment explanation
Indices: 2528827--2528924 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2528817 GATTCTCTCG
2528827 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2528847 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2528866 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2528880 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2528899 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2528918 TTGCGAT
1 TTGCGAT
2528925 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2528921 original size:52 final size:53
Alignment explanation
Indices: 2528808--2528924 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
2528798 GAAATGAAAA
2528808 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2528861 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2528913 TCGCATTGCGAT
1 TCGCATTGCGAT
2528925 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2529050 original size:14 final size:14
Alignment explanation
Indices: 2529031--2529067 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2529021 CATCAATTAC
2529031 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2529045 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2529059 ACAAATCAA
1 ACAAATCAA
2529068 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2531011 original size:20 final size:19
Alignment explanation
Indices: 2530986--2531050 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
2530976 TAGTTTACTT
*
2530986 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
2531006 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
2531024 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
2531043 TCGCAACG
1 TCGCAACG
2531051 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 16 0.40
19 11 0.28
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:2531045 original size:19 final size:19
Alignment explanation
Indices: 2530986--2531119 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2530976 TAGTTTACTT
* *
2530986 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2531006 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
2531024 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2531043 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2531057 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2531076 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2531090 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2531109 TCGCAATGCGA
1 TCGCAACGCGA
2531120 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
18 16 0.17
19 29 0.31
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2531060 original size:14 final size:14
Alignment explanation
Indices: 2531041--2531097 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2531031 GCGAAATGAA
*
2531041 AATCGCAACGACAG
1 AATCGCAACGAAAG
2531055 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2531072 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2531088 AATCGCAACG
1 AATCGCAACG
2531098 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2531068 original size:33 final size:33
Alignment explanation
Indices: 2530986--2531114 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
2530976 TAGTTTACTT
* * *
2530986 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAA-TGAAAATCGCAA--CGAAA--GAA
*
2531024 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
2531057 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
2531090 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
2531115 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.68
35 4 0.05
37 11 0.13
38 12 0.14
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:2531137 original size:19 final size:19
Alignment explanation
Indices: 2531115--2531243 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2531105 AAAATCGCAA
2531115 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2531134 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2531148 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2531167 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2531181 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2531200 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2531219 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2531239 TGCGA
1 TGCGA
2531244 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2531157 original size:33 final size:33
Alignment explanation
Indices: 2531115--2531206 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2531105 AAAATCGCAA
2531115 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2531148 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2531181 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2531207 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2531446 original size:93 final size:93
Alignment explanation
Indices: 2531287--2531571 Score: 522
Period size: 93 Copynumber: 3.1 Consensus size: 93
2531277 TTGAATGGAT
*
2531287 AAATTTACTTTCAACCAAAAGACAAAACAAAGATAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2531352 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2531380 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2531445 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2531473 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTT--CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2531535 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2531563 AAATTTACT
1 AAATTTACT
2531572 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
90 53 0.28
92 21 0.11
93 114 0.61
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.24
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2533283 original size:14 final size:14
Alignment explanation
Indices: 2533264--2533353 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2533254 TTGAAATGAA
2533264 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2533278 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2533295 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2533311 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2533330 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2533344 AATCGCAACG
1 AATCGCAACG
2533354 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2533301 original size:33 final size:33
Alignment explanation
Indices: 2533256--2533370 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2533246 TCTTTTGGTT
2533256 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
2533289 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2533322 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2533355 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2533371 TGCGATTTGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2533302 original size:19 final size:18
Alignment explanation
Indices: 2533263--2533375 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
2533253 GTTGAAATGA
2533263 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
2533278 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
2533295 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
2533311 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
2533328 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
2533344 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
2533361 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
2533376 TTTGGTTTCG
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:2533405 original size:14 final size:14
Alignment explanation
Indices: 2533386--2533440 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2533376 TTTGGTTTCG
2533386 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2533400 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2533419 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2533433 CGTTGCGA
1 CGTTGCGA
2533441 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2533448 original size:33 final size:33
Alignment explanation
Indices: 2533381--2533462 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2533371 TGCGATTTGG
***
2533381 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2533414 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2533447 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2533463 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2533467 original size:20 final size:20
Alignment explanation
Indices: 2533393--2533481 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2533383 TCGCGTTGCG
2533393 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2533413 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2533426 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2533446 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2533466 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2533482 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2533608 original size:33 final size:33
Alignment explanation
Indices: 2533561--2533631 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2533551 AATACTAACT
* *
2533561 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2533594 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2533627 TGAAA
1 TGAAA
2533632 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2533864 original size:22 final size:22
Alignment explanation
Indices: 2533812--2533866 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2533802 TGGTTGTGAG
**
2533812 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2533834 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2533856 GGATTTCTTCG
1 GGATTTCTTCG
2533867 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2534037 original size:20 final size:20
Alignment explanation
Indices: 2534012--2534185 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
2534002 CTTTAAATAT
2534012 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2534032 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2534054 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2534073 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2534093 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2534113 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2534133 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2534153 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
2534173 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2534186 TGGAAAATCG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2534177 original size:60 final size:60
Alignment explanation
Indices: 2534014--2534185 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
2534004 TTAAATATCG
** *
2534014 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
2534075 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
2534135 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
2534186 TGGAAAATCG
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:2534202 original size:21 final size:21
Alignment explanation
Indices: 2534172--2534295 Score: 108
Period size: 21 Copynumber: 6.0 Consensus size: 21
2534162 ATTTATGTGT
*
2534172 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * *
2534193 TCGCAATGCGATTTT-CATAT
1 TCGCATTGCGATTTTGGAAAA
*
2534213 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2534234 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2534255 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2534276 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2534296 CTGATTTGCG
Statistics
Matches: 77, Mismatches: 23, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
20 16 0.21
21 59 0.77
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2534216 original size:41 final size:43
Alignment explanation
Indices: 2534171--2534269 Score: 152
Period size: 41 Copynumber: 2.4 Consensus size: 43
2534161 GATTTATGTG
2534171 TTCGCGTTGCGATTTTGGAAAATCGCAATGCG-ATTT-T-CATA
1 TTCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTAC-TA
2534212 TTCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTACTA
1 TTCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTACTA
*
2534255 -TCGCATTGCGATTTT
1 TTCGCGTTGCGATTTT
2534270 CAAGAATCGC
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
41 32 0.59
42 18 0.33
43 3 0.06
44 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TTCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTACTA
Found at i:2534222 original size:20 final size:19
Alignment explanation
Indices: 2534153--2534227 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
2534143 TTTACGGATA
* *
2534153 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
* *
2534173 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT--ATATT
**
2534194 CGCAATGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
2534214 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
2534228 GGAAAATCGC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 28 0.67
21 13 0.31
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:2536785 original size:7 final size:7
Alignment explanation
Indices: 2536773--2536860 Score: 54
Period size: 7 Copynumber: 12.3 Consensus size: 7
2536763 CTAAATTGAT
2536773 AACCTTA
1 AACCTTA
2536780 AACCTTA
1 AACCTTA
*
2536787 AACCAT-
1 AACCTTA
*
2536793 AACCTCA
1 AACCTTA
2536800 TAACCTCTA
1 -AACCT-TA
2536809 AACCTTA
1 AACCTTA
* *
2536816 AATCAT-
1 AACCTTA
*
2536822 AACCTCA
1 AACCTTA
2536829 TAACCTCTA
1 -AACCT-TA
*
2536838 AATCTTA
1 AACCTTA
*
2536845 AACCCTA
1 AACCTTA
*
2536852 AACATTA
1 AACCTTA
2536859 AA
1 AA
2536861 TCCTAAATTA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
6 7 0.12
7 32 0.53
8 19 0.32
9 2 0.03
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
AACCTTA
Found at i:2536804 original size:21 final size:22
Alignment explanation
Indices: 2536771--2536827 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
2536761 CACTAAATTG
*
2536771 ATAACCTTA-AACCT-TAAACC
1 ATAACCTCATAACCTCTAAACC
2536791 ATAACCTCATAACCTCTAAACC
1 ATAACCTCATAACCTCTAAACC
* *
2536813 TTAA-ATCATAACCTC
1 ATAACCTCATAACCTC
2536828 ATAACCTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.25
21 15 0.47
22 9 0.28
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAACCTCATAACCTCTAAACC
Found at i:2536810 original size:29 final size:29
Alignment explanation
Indices: 2536771--2536848 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
2536761 CACTAAATTG
2536771 ATAACCT-TAAACCTTAAACCATAACCTC
1 ATAACCTCTAAACCTTAAACCATAACCTC
*
2536799 ATAACCTCTAAACCTTAAATCATAACCTC
1 ATAACCTCTAAACCTTAAACCATAACCTC
*
2536828 ATAACCTCTAAATCTTAAACC
1 ATAACCTCTAAACCTTAAACC
2536849 CTAAACATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (29 bp):
ATAACCTCTAAACCTTAAACCATAACCTC
Found at i:2536833 original size:21 final size:22
Alignment explanation
Indices: 2536797--2536862 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
2536787 AACCATAACC
2536797 TCATAACCTCTAAACCT-TAAA
1 TCATAACCTCTAAACCTCTAAA
2536818 TCATAACCTC-ATAACCTCTAAA
1 TCATAACCTCTA-AACCTCTAAA
* *
2536840 TCTTAAACC-CTAAACAT-TAAA
1 TCAT-AACCTCTAAACCTCTAAA
2536861 TC
1 TC
2536863 CTAAATTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 1 0.03
21 21 0.54
22 12 0.31
23 5 0.13
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (22 bp):
TCATAACCTCTAAACCTCTAAA
Found at i:2540430 original size:28 final size:28
Alignment explanation
Indices: 2540398--2540452 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2540388 GTCCCTTCAA
*
2540398 ATTTGAAAATATACAT-TAAACGTTAAGT
1 ATTTGAAAATATA-ATGTAAAAGTTAAGT
*
2540426 ATTTGAAAGTATAATGTAAAAGTTAAG
1 ATTTGAAAATATAATGTAAAAGTTAAG
2540453 CATATGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (28 bp):
ATTTGAAAATATAATGTAAAAGTTAAGT
Found at i:2544512 original size:34 final size:34
Alignment explanation
Indices: 2544438--2544550 Score: 145
Period size: 35 Copynumber: 3.3 Consensus size: 34
2544428 GCAAAAGTCC
* *
2544438 TCAATTTTATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAA-TAAT
* *
2544473 TCAATTTCATTCTAAACCCTAAATTCCAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAATAAT
* * *
2544507 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTC-CAAATAAT
2544542 TCAATTTAA
1 TCAATTTAA
2544551 GGTTTAGAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
34 27 0.40
35 41 0.60
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAATAAT
Found at i:2546363 original size:32 final size:34
Alignment explanation
Indices: 2546305--2546412 Score: 139
Period size: 35 Copynumber: 3.2 Consensus size: 34
2546295 TCTAAACCTT
* *
2546305 AAATTGAAGTATTTAGAATTTGGGGTTTAGAATT
1 AAATTGAAGTATTTGGAATTTGGGGTTTAGAATG
* *
2546339 TAATTGAA-T-TTTGGAATTTAGGGTTTAGAATG
1 AAATTGAAGTATTTGGAATTTGGGGTTTAGAATG
* *
2546371 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAAGTA-TTTGGAATTTGGGGTTTAGAATG
2546406 AAATTGA
1 AAATTGA
2546413 GGATTGTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
32 27 0.42
33 2 0.03
34 7 0.11
35 28 0.44
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (34 bp):
AAATTGAAGTATTTGGAATTTGGGGTTTAGAATG
Found at i:2546991 original size:15 final size:15
Alignment explanation
Indices: 2546971--2547000 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2546961 AATGATAATT
2546971 ACAATACTAATTGTG
1 ACAATACTAATTGTG
2546986 ACAATACTAATTGTG
1 ACAATACTAATTGTG
2547001 TAACACGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
ACAATACTAATTGTG
Found at i:2548140 original size:38 final size:36
Alignment explanation
Indices: 2548105--2548174 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
2548095 TACAAATTGT
*
2548105 AAAATATTTATATATTTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
2548142 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
2548175 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:2552172 original size:42 final size:42
Alignment explanation
Indices: 2552119--2552204 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
2552109 AAATCCCTAT
2552119 ATAACTTTTTAAGTACAATCGAAAATGTTACAAATTTATATA
1 ATAACTTTTTAAGTACAATCGAAAATGTTACAAATTTATATA
* * *
2552161 ATAATTTTTTAATTACAATCGAAAATGTTATAAATTTATATA
1 ATAACTTTTTAAGTACAATCGAAAATGTTACAAATTTATATA
2552203 AT
1 AT
2552205 CTTTAAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (42 bp):
ATAACTTTTTAAGTACAATCGAAAATGTTACAAATTTATATA
Found at i:2558896 original size:36 final size:35
Alignment explanation
Indices: 2558824--2558947 Score: 105
Period size: 35 Copynumber: 3.5 Consensus size: 35
2558814 ATATATATTC
* *
2558824 TAAAA-TATATAATATATATATTTC-AAAAATTATTTT
1 TAAAATTATAT-AT-TATAT-TTTCAAAAAAATGTTTT
* *
2558860 AAAATATTATATGTT-T-TTTTCAAAAAAAATGTTTT
1 TAAA-ATTATATATTATATTTTC-AAAAAAATGTTTT
*
2558895 TAAAATTATATATTATATTTTCCAAAAAATGATTTT
1 TAAAATTATATATTATATTTTCAAAAAAATG-TTTT
*
2558931 TAAAACTATAT-TTATAT
1 TAAAATTATATATTATAT
2558948 CATTTTTCAA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
33 4 0.05
34 10 0.14
35 29 0.40
36 23 0.32
37 2 0.03
38 5 0.07
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (35 bp):
TAAAATTATATATTATATTTTCAAAAAAATGTTTT
Found at i:2558960 original size:36 final size:34
Alignment explanation
Indices: 2558885--2559085 Score: 163
Period size: 36 Copynumber: 5.6 Consensus size: 34
2558875 TTTTTCAAAA
* * *
2558885 AAAATGTTTTTAAAATTATATAT-TATATTTTCC
1 AAAATGTTTTAAAAACTATATATATATATTTTTC
* *
2558918 AAAAAATGATTTTTAAAACTATATTTATATCATTTTTC
1 --AAAATG-TTTTAAAAACTATATATATAT-ATTTTTC
* * *
2558956 AAAATATTTAAAAAACTATACTATATA-AGTTTTC
1 AAAATGTTTTAAAAACTATA-TATATATATTTTTC
*
2558990 AAATTGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATAT-ATATAT--AT-TTTTC
* * *
2559028 AAAATGTTTTCAAAACTATATATTATATATATTTA
1 AAAATGTTTTAAAAACTATATA-TATATATTTTTC
* *
2559063 AAAATATTTTCAAAAATTATATA
1 AAAATGTTTT-AAAAACTATATA
2559086 AAATTTTAAA
Statistics
Matches: 136, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
33 1 0.01
34 28 0.21
35 30 0.22
36 37 0.27
37 5 0.04
38 35 0.26
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (34 bp):
AAAATGTTTTAAAAACTATATATATATATTTTTC
Found at i:2559034 original size:11 final size:11
Alignment explanation
Indices: 2559018--2559042 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2559008 TATAATATAT
2559018 AAATGTTTTCA
1 AAATGTTTTCA
2559029 AAATGTTTTCA
1 AAATGTTTTCA
2559040 AAA
1 AAA
2559043 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2559036 original size:38 final size:37
Alignment explanation
Indices: 2558920--2559056 Score: 149
Period size: 38 Copynumber: 3.8 Consensus size: 37
2558910 TATTTTCCAA
* *
2558920 AAAATGATTTTTAAAACTATAT-TTATATCAT-TTTTC
1 AAAATG-TTTTAAAAACTATATATTATATAATGTTTTC
* * *
2558956 AAAATATTTAAAAAAC--TATACTATATAA-GTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAATGTTTTC
* *
2558990 AAATTGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATATATTATAT-AATGTTTTC
*
2559028 AAAATGTTTTCAAAACTATATATTATATA
1 AAAATGTTTTAAAAACTATATATTATATA
2559057 TATTTAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
33 3 0.04
34 24 0.29
35 8 0.10
36 14 0.17
37 3 0.04
38 31 0.37
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATAATGTTTTC
Found at i:2560160 original size:165 final size:165
Alignment explanation
Indices: 2559906--2561015 Score: 1777
Period size: 165 Copynumber: 6.7 Consensus size: 165
2559896 TGGGGGGTCT
* * * * * **
2559906 TTGGCAGATAGCCCTTCTCGAATTAAGCTATGCTGCAAATGATGTGTCGT-TGAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
* *
2559970 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGGGCCT
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
*
2560035 TGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTGG
131 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2560070 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
* * *
2560135 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATATGCCT
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
2560200 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
131 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2560235 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAA-CTGAGTGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AAAGCTGAGTGTA
*
2560299 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCC
65 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
2560364 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
130 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2560400 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAA-CTGAGTGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AAAGCTGAGTGTA
* *
2560464 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGGGCC
65 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
2560529 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
130 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
*
2560565 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTTCAAATGATGTGCCCTCGAAA-CTGAGTGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AAAGCTGAGTGTA
2560629 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
65 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
2560694 GTT-GAGCTGAGCGTAGTCGAACTCAAATGTCTTTTGG
130 -TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGG
* * * * * ** *
2560731 -TCGCAGATAACCCTTATAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
*
2560795 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCG
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-
2560860 TT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
130 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGG
** * * * * * * *
2560896 -TCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTGA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
2560960 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
2561016 AGTTTGTTTA
Statistics
Matches: 907, Mismatches: 34, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
164 47 0.05
165 850 0.94
166 10 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
Found at i:2564495 original size:18 final size:19
Alignment explanation
Indices: 2564454--2564498 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2564444 AGTTAATGTG
2564454 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
2564473 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
2564491 AATGCAAA
1 AATGCAAA
2564499 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2565139 original size:17 final size:17
Alignment explanation
Indices: 2565113--2565145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2565103 TGCAAACGAT
*
2565113 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
2565130 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
2565146 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:2567840 original size:38 final size:38
Alignment explanation
Indices: 2567798--2568008 Score: 186
Period size: 38 Copynumber: 5.6 Consensus size: 38
2567788 TTTTTTTCAA
* * *
2567798 AAAAAATGTTTTTAAAATTATATATTATATAATTTTCC
1 AAAAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
2567836 AAAAAATGATTTTTAAAACTATATATTATATCATTTTTC
1 AAAAAATG-TTTTAAAAACTATATATTATATAATTTTTC
** * *
2567875 AAAAATAT-TTAAAAAAACTATATACTATATAAGTTTTC
1 AAAAA-ATGTTTTAAAAACTATATATTATATAATTTTTC
* *
2567913 --AAATTGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAAAATGTTTTAAAAACTATATATTATAT-AAT-TTTTC
* *
2567951 --AAAATGTTTTCAAAACTATATATTATAT-ATATTT-
1 AAAAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
2567985 AAAAATAT-TTTCAAAAATTATATA
1 AAAAA-ATGTTTTAAAAACTATATA
2568009 AAATTTTCAA
Statistics
Matches: 144, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
35 4 0.03
36 40 0.28
37 4 0.03
38 62 0.43
39 32 0.22
40 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (38 bp):
AAAAAATGTTTTAAAAACTATATATTATATAATTTTTC
Found at i:2567957 original size:11 final size:11
Alignment explanation
Indices: 2567941--2567965 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2567931 TATAATATAT
2567941 AAATGTTTTCA
1 AAATGTTTTCA
2567952 AAATGTTTTCA
1 AAATGTTTTCA
2567963 AAA
1 AAA
2567966 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2568001 original size:74 final size:72
Alignment explanation
Indices: 2567799--2568009 Score: 192
Period size: 74 Copynumber: 2.8 Consensus size: 72
2567789 TTTTTTCAAA
* * * * *
2567799 AAAAATGTTTTTAAAATTATATATTATATAATTTTCCAAAAAATGATTTTTAAAACTATATATTA
1 AAAAATGTTTTAAAAACTATATATTATATAAGTTT---AAAAAT-ATTTTAAAAACTATATAATA
*
2567864 TATCATTTTTC
62 TATAATTTTTC
* * * * * *
2567875 AAAAATATTTAAAAAAACTATATACTATATAAGTTTTCAAATTGTTTTAAAAACTATATAATATA
1 AAAAATGTTT-TAAAAACTATATATTATATAAG-TTTAAAAATATTTTAAAAACTATATAATATA
2567940 TAAATGTTTTC
64 T-AAT-TTTTC
* *
2567951 -AAAATGTTTTCAAAACTATATATTATATATA-TTTAAAAATATTTTCAAAAATTATATAA
1 AAAAATGTTTTAAAAACTATATATTATATA-AGTTTAAAAATATTTT-AAAAACTATATAA
2568010 AATTTTCAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
73 11 0.10
74 49 0.45
75 15 0.14
76 14 0.13
77 17 0.16
78 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (72 bp):
AAAAATGTTTTAAAAACTATATATTATATAAGTTTAAAAATATTTTAAAAACTATATAATATATA
ATTTTTC
Found at i:2571048 original size:69 final size:70
Alignment explanation
Indices: 2570901--2571058 Score: 189
Period size: 69 Copynumber: 2.2 Consensus size: 70
2570891 ACAAGCAAAT
* *
2570901 ATATCCAATCAATACTAGTACACTTAATTGCAGAAGTAACAAGTGCGTAATAAATACACTTCTGT
1 ATATCCAAACAATA-TAGT--A-TTAATTGCAGAAGTAACAAGTGCGTAATAAATACACTTCAGT
2570966 AGCTAAACA
62 AGCTAAACA
*
2570975 ATAT-CAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAAATACA-TCTCAAGTA-
1 ATATCCAAACAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAAATACACT-TC-AGTAG
*
2571037 TTAAGAC-
64 CTAA-ACA
2571044 ATATCCAAACAATAT
1 ATATCCAAACAATAT
2571059 TCATAATTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
68 1 0.01
69 44 0.59
70 15 0.20
72 4 0.05
73 7 0.09
74 4 0.05
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (70 bp):
ATATCCAAACAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAAATACACTTCAGTAGCT
AAACA
Found at i:2571086 original size:186 final size:186
Alignment explanation
Indices: 2570772--2571115 Score: 688
Period size: 186 Copynumber: 1.8 Consensus size: 186
2570762 AAGAATATTA
2570772 ACTTCTGTAGCTAAACAATATCAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAA
1 ACTTCTGTAGCTAAACAATATCAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAA
2570837 ATACATCTCAAGTATTAAGACATATCCAAACAATATTCATAATTATGTAACACGACAAGCAAATA
66 ATACATCTCAAGTATTAAGACATATCCAAACAATATTCATAATTATGTAACACGACAAGCAAATA
2570902 TATCCAATCAATACTAGTACACTTAATTGCAGAAGTAACAAGTGCGTAATAAATAC
131 TATCCAATCAATACTAGTACACTTAATTGCAGAAGTAACAAGTGCGTAATAAATAC
2570958 ACTTCTGTAGCTAAACAATATCAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAA
1 ACTTCTGTAGCTAAACAATATCAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAA
2571023 ATACATCTCAAGTATTAAGACATATCCAAACAATATTCATAATTATGTAACACGACAAGCAAATA
66 ATACATCTCAAGTATTAAGACATATCCAAACAATATTCATAATTATGTAACACGACAAGCAAATA
2571088 TATCCAATCAATACTAGTACACTTAATT
131 TATCCAATCAATACTAGTACACTTAATT
2571116 TAGTAGTCTG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 158 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (186 bp):
ACTTCTGTAGCTAAACAATATCAAAGAATATAGTATTAATTGCAGAAGTAACAAGTGCGTAATAA
ATACATCTCAAGTATTAAGACATATCCAAACAATATTCATAATTATGTAACACGACAAGCAAATA
TATCCAATCAATACTAGTACACTTAATTGCAGAAGTAACAAGTGCGTAATAAATAC
Done.