Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 31
Found at i:2804320 original size:2 final size:2
Alignment explanation
Indices: 2804315--2804349 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2804305 AAATAAAAGA
2804315 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 A
2804350 ATAATTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2804382 original size:13 final size:13
Alignment explanation
Indices: 2804359--2804420 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
2804349 AATAATTTGT
2804359 AAATAAATAAATAA
1 AAAT-AATAAATAA
*
2804373 AAGTAATAAAGTAA
1 AAATAATAAA-TAA
*
2804387 AAATAA-AAAAATA
1 AAATAATAAATA-A
* *
2804400 AAATATTATATAA
1 AAATAATAAATAA
2804413 AAATAATA
1 AAATAATA
2804421 TTAATATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 1 0.03
13 23 0.61
14 14 0.37
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:2804390 original size:28 final size:26
Alignment explanation
Indices: 2804359--2804418 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
2804349 AATAATTTGT
*
2804359 AAATAAATAAATAAAAGTAATAAAGTAA
1 AAATAAAAAAATAAAA-TAATAAA-TAA
* *
2804387 AAATAAAAAAATAAAATATTATATAA
1 AAATAAAAAAATAAAATAATAAATAA
2804413 AAATAA
1 AAATAA
2804419 TATTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 9 0.31
27 5 0.17
28 15 0.52
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (26 bp):
AAATAAAAAAATAAAATAATAAATAA
Found at i:2804401 original size:14 final size:14
Alignment explanation
Indices: 2804359--2804402 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2804349 AATAATTTGT
*
2804359 AAATAAATAAATAA
1 AAATAAAAAAATAA
* * *
2804373 AAGTAATAAAGTAA
1 AAATAAAAAAATAA
2804387 AAATAAAAAAATAA
1 AAATAAAAAAATAA
2804401 AA
1 AA
2804403 TATTATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:2804422 original size:16 final size:18
Alignment explanation
Indices: 2804401--2804438 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2804391 AAAAAAATAA
2804401 AATATT-ATA-TAAAAAT
1 AATATTAATATTAAAAAT
*
2804417 AATATTAATATTGAAAAT
1 AATATTAATATTAAAAAT
2804435 AATA
1 AATA
2804439 ATAACAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 3 0.16
18 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AATATTAATATTAAAAAT
Found at i:2805635 original size:17 final size:17
Alignment explanation
Indices: 2805613--2805646 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2805603 AATTAATAAA
2805613 TATATATATATA-TTTAT
1 TATATA-ATATAGTTTAT
2805630 TATATAATATAGTTTAT
1 TATATAATATAGTTTAT
2805647 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TATATAATATAGTTTAT
Found at i:2812167 original size:4 final size:4
Alignment explanation
Indices: 2812158--2812298 Score: 73
Period size: 4 Copynumber: 34.5 Consensus size: 4
2812148 ATGTGCATAT
* *
2812158 AATA AATA AATA AATA AATA AATA AATA AA-G AAT- AATA AATA AAGA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * *
2812204 GATAA AATA AAT- -ATA AAGGA AATAA AAGTA AGATAA AGATA AAGAA AATA
1 AAT-A AATA AATA AATA AA-TA AAT-A AA-TA A-AT-A A-ATA AA-TA AATA
*
2812254 AATA TAAT- AA-A AATAA AATA AAT- -ATA AATA AATA TAAAA AATA AA
1 AATA -AATA AATA AAT-A AATA AATA AATA AATA AATA -AATA AATA AA
2812299 AACAAAGAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
2 4 0.04
3 9 0.08
4 61 0.56
5 27 0.25
6 7 0.06
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:2812226 original size:15 final size:14
Alignment explanation
Indices: 2812161--2812318 Score: 67
Period size: 15 Copynumber: 10.8 Consensus size: 14
2812151 TGCATATAAT
*
2812161 AAATAAATAAATAAAT
1 AAATAAAT--ATAAAA
2812177 AAATAAATA-AAGAA
1 AAATAAATATAA-AA
* *
2812191 TAATAAATAAAGAGATA
1 AAATAAATATA-A-A-A
*
2812208 AAATAAATATAAAGG
1 AAATAAATATAAA-A
*
2812223 AAATAAA-AGTAAGA
1 AAATAAATA-TAAAA
* * *
2812237 TAA-AGATA-AAGA
1 AAATAAATATAAAA
2812249 AAATAAATATAATAA
1 AAATAAATATAA-AA
2812264 AAATAAA-ATAAATA
1 AAATAAATATAAA-A
2812278 TAAATAAATAT-AAA
1 -AAATAAATATAAAA
* *
2812292 AAATAAAAACAAAGA
1 AAATAAATATAAA-A
2812307 AAATAAAATATA
1 AAAT-AAATATA
2812319 TATATATATA
Statistics
Matches: 110, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
12 6 0.05
13 17 0.15
14 24 0.22
15 34 0.31
16 19 0.17
17 10 0.09
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAAATATAAAA
Found at i:2812239 original size:26 final size:28
Alignment explanation
Indices: 2812195--2812313 Score: 91
Period size: 28 Copynumber: 4.2 Consensus size: 28
2812185 AAAGAATAAT
* *
2812195 AAATAAAGAGATAAAATAAATATAAAGG
1 AAATAAAGAGATAAAATAAAGATAAAGA
*
2812223 AAATAAA-AG-TAAGATAAAGATAAAGA
1 AAATAAAGAGATAAAATAAAGATAAAGA
* * *
2812249 AAATAAATATAATAAAAATAAA-ATAAATA
1 AAATAAAGA-GAT-AAAATAAAGATAAAGA
* * * * *
2812278 TAAATAAATATAAAAAATAAAAACAAAGA
1 -AAATAAAGAGATAAAATAAAGATAAAGA
2812307 AAATAAA
1 AAATAAA
2812314 ATATATATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
26 21 0.28
27 3 0.04
28 22 0.29
29 13 0.17
30 16 0.21
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (28 bp):
AAATAAAGAGATAAAATAAAGATAAAGA
Found at i:2812316 original size:20 final size:19
Alignment explanation
Indices: 2812207--2812316 Score: 62
Period size: 20 Copynumber: 5.6 Consensus size: 19
2812197 ATAAAGAGAT
** *
2812207 AAAATAAATATAAAGGAAAT
1 AAAATAAA-ATAAAAAAAAG
* *
2812227 AAAAGTAAGATAAAGATAAAG
1 AAAA-TAAAATAAA-AAAAAG
* *
2812248 AAAATAAATATAATAAAAAT
1 AAAATAAA-ATAAAAAAAAG
* *
2812268 AAAAT-AAATATAAATAAAT
1 AAAATAAAATA-AAAAAAAG
*
2812287 ATAA-AAAATAAAAACAAAG
1 AAAATAAAATAAAAA-AAAG
2812306 AAAATAAAATA
1 AAAATAAAATA
2812317 TATATATATA
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
18 6 0.09
19 22 0.32
20 27 0.39
21 14 0.20
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAAAAAAAAG
Found at i:2812321 original size:2 final size:2
Alignment explanation
Indices: 2812314--2812339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2812304 AGAAAATAAA
2812314 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
2812340 TAATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2812382 original size:2 final size:2
Alignment explanation
Indices: 2812375--2812472 Score: 116
Period size: 2 Copynumber: 51.0 Consensus size: 2
2812365 AAAGGAAAAG
* * * *
2812375 TA TA TA TA TA TA TA TA -A TA -A TA TG TA GTA TT TA AA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
2812415 TA -A TA TA -A 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
2812455 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
2812473 CATGAAAATA
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
1 5 0.06
2 76 0.92
3 2 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2812409 original size:60 final size:59
Alignment explanation
Indices: 2812311--2812459 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 59
2812301 CAAAGAAAAT
*
2812311 AAAATATATATATATATATATATATATATTAATGTTAAAATAAATTAA-ATAAATAAAGG
1 AAAATATATATATATATATATATATATATTAATGTT-AAATAAAATAATATAAATAAAGG
* *
2812370 AAAAGTATATATATATATATA-ATA-ATATGTAGTAT-TTAAATAAAATAATATAATATATA-T
1 AAAA-TATATATATATATATATATATATAT-TA--ATGTTAAATAAAATAATATAA-ATAAAGG
*
2812430 ATATATATATATATATATATATATATATAT
1 A-AAATATATATATATATATATATATATAT
2812460 ATATATATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
58 4 0.05
59 19 0.25
60 39 0.51
61 11 0.14
62 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (59 bp):
AAAATATATATATATATATATATATATATTAATGTTAAATAAAATAATATAAATAAAGG
Found at i:2813755 original size:9 final size:9
Alignment explanation
Indices: 2813741--2813766 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2813731 GAAATCGGTT
2813741 AATTAACCG
1 AATTAACCG
2813750 AATTAACCG
1 AATTAACCG
2813759 AATTAACC
1 AATTAACC
2813767 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:2813892 original size:17 final size:17
Alignment explanation
Indices: 2813870--2813908 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2813860 TGAATCAAAT
2813870 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2813887 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2813904 -AATTA
1 TAATTA
2813909 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:2818712 original size:20 final size:20
Alignment explanation
Indices: 2818687--2818733 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2818677 ATGCATATGT
2818687 CATAGACTAAATCCTAATGA
1 CATAGACTAAATCCTAATGA
2818707 CATAGACTAAATCCTAATGA
1 CATAGACTAAATCCTAATGA
2818727 CATAGAC
1 CATAGAC
2818734 GGAGATTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (20 bp):
CATAGACTAAATCCTAATGA
Found at i:2823343 original size:117 final size:117
Alignment explanation
Indices: 2823161--2823462 Score: 457
Period size: 117 Copynumber: 2.6 Consensus size: 117
2823151 TTTTATATAT
* ***
2823161 TTCCCC-GAAACATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGTTGAGGA
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGA
* *
2823224 GCCTGCAGTAATAACGTCTCCATCCAGTCGCTTCC-ATAACTACAATGTGTAGG
65 GCCTGCAGTAATAACGTCCCCATCCAGTCAC-TCCAATAACTACAATGTGTAGG
* * *
2823277 TTCCCCAGTACCATACACCCACCTGCACACCAGTAAGGACTTACCTTAAGCACACAGCAAATGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
* *
2823342 CCTGCAGTAATAACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGG
66 CCTGCAGTAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
*
2823394 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
2823459 CCTG
66 CCTG
2823463 AAATACTTCC
Statistics
Matches: 168, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
116 10 0.06
117 158 0.94
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (117 bp):
TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
CCTGCAGTAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
Found at i:2824428 original size:29 final size:31
Alignment explanation
Indices: 2824392--2824518 Score: 90
Period size: 29 Copynumber: 4.4 Consensus size: 31
2824382 CATTTTACAG
*
2824392 AAATAGCACCCCTTTT-AAAAT-AATTACCA
1 AAATAGCACCCATTTTCAAAATAAATTACCA
* *
2824421 AAATAGCA--CATTTTCAAATTAAATTCCCA
1 AAATAGCACCCATTTTCAAAATAAATTACCA
* * * *
2824450 AAATAGCA-CC-TTTACGAATTAAATTCCCA
1 AAATAGCACCCATTTTCAAAATAAATTACCA
* * * *
2824479 GAATAGCACCCA-TTTC-GAATTAATTCCCA
1 AAATAGCACCCATTTTCAAAATAAATTACCA
*
2824508 AAATATCACCC
1 AAATAGCACCC
2824519 GGTCAACGGT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
27 5 0.06
28 4 0.05
29 66 0.81
30 6 0.07
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (31 bp):
AAATAGCACCCATTTTCAAAATAAATTACCA
Found at i:2824500 original size:30 final size:29
Alignment explanation
Indices: 2824413--2824518 Score: 126
Period size: 29 Copynumber: 3.7 Consensus size: 29
2824403 CTTTTAAAAT
* ** *
2824413 AATTACCAAAATAGCACATTTTCAAATTA
1 AATTCCCAAAATAGCACCCTTTCGAATTA
2824442 AATTCCCAAAATAGCA-CCTTTACGAATTA
1 AATTCCCAAAATAGCACCCTTT-CGAATTA
*
2824471 AATTCCCAGAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATAGCACCC-TTTCGAATTA
*
2824500 AATTCCCAAAATATCACCC
1 AATTCCCAAAATAGCACCC
2824519 GGTCAACGGT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
28 3 0.04
29 53 0.79
30 8 0.12
31 3 0.04
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCCTTTCGAATTA
Found at i:2824544 original size:19 final size:19
Alignment explanation
Indices: 2824520--2824556 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2824510 ATATCACCCG
2824520 GTCAACGGTCGGGTCAACA
1 GTCAACGGTCGGGTCAACA
2824539 GTCAACGGTCGGGTCAAC
1 GTCAACGGTCGGGTCAAC
2824557 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.16
Consensus pattern (19 bp):
GTCAACGGTCGGGTCAACA
Found at i:2824563 original size:13 final size:12
Alignment explanation
Indices: 2824539--2824568 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2824529 CGGGTCAACA
2824539 GTCAACGGTCGG
1 GTCAACGGTCGG
2824551 GTCAACGGGTCGG
1 GTCAAC-GGTCGG
2824564 GTCAA
1 GTCAA
2824569 AACCGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (12 bp):
GTCAACGGTCGG
Found at i:2830389 original size:117 final size:117
Alignment explanation
Indices: 2830209--2830510 Score: 432
Period size: 117 Copynumber: 2.6 Consensus size: 117
2830199 TTTTATATAT
* * **
2830209 TTCCCC-GAAACATACACCCACCTGCACACCAGTAAGGACTTATCCTAA-G-CACGAAGCTGAGG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGGACAC-AA-CAAAGG
* * * *
2830271 AGCCTGCAGTAATAACGTCTCCATCCAGTCGCTTCC-ATAACTACAATGTGTATG
64 AGCCTGCAGTAATAACATCCCCATCCAGTCAC-TCCAATAACTACAATGTGTAGG
*
2830325 TTCCCCAGTACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGGACACAACAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGGACACAACAAAGGAG
*
2830390 CCTGCAGTAATAACATCCCCATCCAGTCACTCCAATCACTACAATGTGTAGG
66 CCTGCAGTAATAACATCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
* * *
2830442 TTCCCCAGAACCATACACCCATCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGGACACAACAAAGGAG
2830507 CCTG
66 CCTG
2830511 AAATACTTCC
Statistics
Matches: 168, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
116 9 0.05
117 153 0.91
118 3 0.02
119 3 0.02
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (117 bp):
TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGGACACAACAAAGGAG
CCTGCAGTAATAACATCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
Found at i:2831106 original size:8 final size:8
Alignment explanation
Indices: 2831093--2831118 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2831083 ATAAATAATC
2831093 AAAATATT
1 AAAATATT
2831101 AAAATATT
1 AAAATATT
2831109 AAAATATT
1 AAAATATT
2831117 AA
1 AA
2831119 GCCTTTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:2831520 original size:29 final size:30
Alignment explanation
Indices: 2831445--2831514 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
2831435 CAGAAGTAAT
* *
2831445 AATTACCAAAATAGCA-CCTTTTCGAATTA
1 AATTCCCAAAATAGCACCCATTTCGAATTA
*
2831474 AATTCCCAGAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATAGCACCCATTTCGAATTA
2831503 AATTCCCAAAAT
1 AATTCCCAAAAT
2831515 GTCACCGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (30 bp):
AATTCCCAAAATAGCACCCATTTCGAATTA
Found at i:2837734 original size:77 final size:78
Alignment explanation
Indices: 2837621--2837768 Score: 174
Period size: 77 Copynumber: 1.9 Consensus size: 78
2837611 GTTTAGGCGC
* ** * * * * *
2837621 AACTTAAAATATTATTTTTTTCCTAACATTTTCGGTTG-AACTGAAAATGTTACATTCTT-AGTA
1 AACTGAAAATATTACATTATTCCTAAAATTTCCGGTTGAAACCGAAAATGATACATTCTTCA-TA
2837684 ATATTTTTCGATTG
65 ATATTTTTCGATTG
* *
2837698 AACTGAAAATATTACATTATTCGTAAAATTTCCGGTTGACAACCGAAAATGATACCTTCTTCATA
1 AACTGAAAATATTACATTATTCCTAAAATTTCCGGTTGA-AACCGAAAATGATACATTCTTCATA
2837763 ATATTT
65 ATATTT
2837769 CAGCTTCAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
77 31 0.53
79 26 0.45
80 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (78 bp):
AACTGAAAATATTACATTATTCCTAAAATTTCCGGTTGAAACCGAAAATGATACATTCTTCATAA
TATTTTTCGATTG
Found at i:2843754 original size:147 final size:148
Alignment explanation
Indices: 2843476--2843772 Score: 578
Period size: 147 Copynumber: 2.0 Consensus size: 148
2843466 CCTAATAAAC
2843476 TCCTGACAACTTTTTGCCTCTTCCTCGGTAATGGTGATACGCCCTCAATCTAATTACCACTCACT
1 TCCTGACAACTTTTTGCCTCTTCCTCGGTAATGGTGATACGCCCTCAATCTAATTACCACTCACT
2843541 TCGGCGATCTCGTTGCCGTAAATAATCCTGAAACCGTCTTCAGCATTCAGTTATGGCTCAACATT
66 TCGGCGATCTCGTTGCCGTAAATAATCCTGAAACCGTCTTCAGCATTCAGTTATGGCTCAACATT
2843606 TATATTATATATATTTAT
131 TATATTATATATATTTAT
2843624 TCCTGACAAC-TTTTGCCTCTTCCTCGGTAATGGTGATACGCCCTCAATCTAATTACCACTCACT
1 TCCTGACAACTTTTTGCCTCTTCCTCGGTAATGGTGATACGCCCTCAATCTAATTACCACTCACT
*
2843688 TCGGCGATCTCGTTGCCGTAAATAATCCTGAAACTGTCTTCAGCATTCAGTTATGGCTCAACATT
66 TCGGCGATCTCGTTGCCGTAAATAATCCTGAAACCGTCTTCAGCATTCAGTTATGGCTCAACATT
2843753 TATATTATATATATTTAT
131 TATATTATATATATTTAT
2843771 TC
1 TC
2843773 ACGCGTTTAT
Statistics
Matches: 148, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
147 138 0.93
148 10 0.07
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (148 bp):
TCCTGACAACTTTTTGCCTCTTCCTCGGTAATGGTGATACGCCCTCAATCTAATTACCACTCACT
TCGGCGATCTCGTTGCCGTAAATAATCCTGAAACCGTCTTCAGCATTCAGTTATGGCTCAACATT
TATATTATATATATTTAT
Found at i:2845945 original size:67 final size:67
Alignment explanation
Indices: 2845837--2845974 Score: 249
Period size: 67 Copynumber: 2.1 Consensus size: 67
2845827 ACCACAAAAT
2845837 ACCTGCAAGCATTTCTTAGGATTGAAAAGACTTAAGCCTCTCAAAGTAAACTACTCATCTCGATA
1 ACCTGCAAGCATTTCTTAGGATTGAAAAGACTTAAGCCTCTCAAAGTAAACTACTCATCTCGATA
*
2845902 AG
66 AA
* *
2845904 ACCTGCAAGCATTTCTTAGGATTGAAGAGACTTAAGCCTCTCAAAGTAAACTACTCATCTTGATA
1 ACCTGCAAGCATTTCTTAGGATTGAAAAGACTTAAGCCTCTCAAAGTAAACTACTCATCTCGATA
2845969 AA
66 AA
2845971 ACCT
1 ACCT
2845975 TGTATTTGTC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (67 bp):
ACCTGCAAGCATTTCTTAGGATTGAAAAGACTTAAGCCTCTCAAAGTAAACTACTCATCTCGATA
AA
Found at i:2848753 original size:25 final size:25
Alignment explanation
Indices: 2848718--2848776 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
2848708 ATTGATTATC
*
2848718 TAATTTCGCACCCCCTAAAATTTTA
1 TAATTTCGCACCCCCTAAAACTTTA
* *
2848743 TAATTTTGCACCCCTTAAAACTTTAA
1 TAATTTCGCACCCCCTAAAACTTT-A
2848769 TATATTTC
1 TA-ATTTC
2848777 TTTAGTTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 21 0.75
26 3 0.11
27 4 0.14
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (25 bp):
TAATTTCGCACCCCCTAAAACTTTA
Found at i:2849258 original size:3 final size:3
Alignment explanation
Indices: 2849250--2849327 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
2849240 GTAAATTTAC
* * * *
2849250 AAG AAG AAG AAG AAG AAC AAG AAG AAG AAG AAG GAG GAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
2849298 AAG AAG AATG -AG AAG AAG AAG AAA AAG AAG
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG
2849328 GAGGAGGAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 1 0.02
3 63 0.97
4 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:2849338 original size:12 final size:12
Alignment explanation
Indices: 2849250--2849338 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
2849240 GTAAATTTAC
*
2849250 AAGAAGAAGAAG
1 AAGAAGAAGGAG
* *
2849262 AAGAACAAGAAG
1 AAGAAGAAGGAG
2849274 AAGAAGAAGGAG
1 AAGAAGAAGGAG
*
2849286 GAGAAGAAGGAG
1 AAGAAGAAGGAG
*
2849298 AAGAAGAATGAG
1 AAGAAGAAGGAG
* *
2849310 AAGAAGAAGAAA
1 AAGAAGAAGGAG
*
2849322 AAGAAGGAGGAG
1 AAGAAGAAGGAG
*
2849334 GAGAA
1 AAGAA
2849339 TGAGAAAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 64 1.00
ACGTcount: A:0.61, C:0.01, G:0.37, T:0.01
Consensus pattern (12 bp):
AAGAAGAAGGAG
Found at i:2850097 original size:211 final size:206
Alignment explanation
Indices: 2849409--2850995 Score: 1570
Period size: 211 Copynumber: 7.8 Consensus size: 206
2849399 TTGCCTACAA
* * * * * * * *
2849409 GGTCAAACATGCTAAGTCAACTTGTTTAACGAGCCAAGTCAACATTCCGTTACTGTAATAACATT
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * * *
2849474 GAGTGAGTAATTTGTTATATTTCAATAATGTCAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
* * * * * * * * *
2849539 GGGAAACAAAAACTTACTTCATGAAGAAGAAAAAAAAGAAGAAGAGTCAAACGATTAGTCGAAGG
131 GGAAAACGAAAACTTAC-TCA--AACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGG
*
2849604 GTGTCCCGCCCGCTT
193 GTGTCCCG-CCGCAT
* * * * * *
2849619 GGTCAAACATGCTAATTCAGTTGGTTTAACATTCCACGTCAACATTTCGTTACTGCAATAATGCC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * * * * *
2849684 GAGTGAATGATTTTTTATAAGTCGATAATGTTAGTGACTTATTTGTTACTTTTAAAACTTTAGTG
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
*
2849749 GGAAAAATGAAAACTTACTCAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGGT
131 GG-AAAACGAAAACTTACTCAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGGT
2849814 GTCCCGCCTGCAT
195 GTCCCGCC-GCAT
* ** * * * *
2849827 GGTCAAACGTGCTAAGTCATATGGTTTAACGTGCCATGTCAACATTTAGTTACTGCAATAATGTT
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
*
2849892 GAGTGACTGATTTGTTATAAGTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTT
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAG-T
* * * *
2849957 GGGAAAACGAAAACTTACTCAACATCATGAAGATGAAGAAGAAAAGTCAAAATGGTCGGTCAAAG
130 GGGAAAACGAAAACTTACTCAA-A-CATGAAGAAGAAGAAGAAGAGTC-AAACGGTTGGTCAAAG
* * *
2850022 GGTTTCCTGTGCGCAT
192 GGTGTCCCG-CCGCAT
* *
2850038 GGTCAAACGTGCTAAGTCAGCTGGTTTAACGTGTCACGTCAACATTTCGTTACTGCAATAACGTC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* *
2850103 GAGTAACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTA
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
* * * *
2850168 GGAGAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAGTCAAACGGTAGGACAAAG
131 GGA-AAACGAAAACTTACTCAAACATGAAGAAG---AAGAAGAAGAGTCAAACGGTTGGTCAAAG
** *
2850233 GGTGTCCCGGATGTAT
192 GGTGTCCC-GCCGCAT
* * * * *
2850249 GGTCAAACATGCTAAGTTAGTTGGTTTAACGCGCCACGTCAACATTTTGTTACTGCAATAACATC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * ** * * *
2850314 AAGTGACTAATTTAATATAATTCGATAATATTAGTGACTAATTTGTTACTTTTAAAACTTCAATG
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT-
* * * * * *
2850379 GGGAAAACAAAAAATGACTCAAACAT------GAAGAAGAAGAGTCAAACAGTCGGTC--A--CT
130 GGGAAAACGAAAACTTACTCAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGGT
2850434 -T------GCAT
195 GTCCCGCCGCAT
** * * *
2850439 GGTCAAACATATTAAGTCAGCTGATTTAACGTGCCACATCAACATTTTGTTACTGCAATAAC-TC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * *
2850503 TAAGTGACTGATTTGTTATAATTCGATAATTTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT
66 -GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT
* * * ****
2850568 AGGGAAAATGAAAACTTACTCAAACAT---GAAGAAGAA-TA-A-TCAAACAGTCAACCAAAGGG
130 -GGGAAAACGAAAACTTACTCAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGG
*
2850627 TGTCCCGCCCGCTT
194 TGTCCCG-CCGCAT
* * * * * * * *
2850641 GGTCAAACATGCTAAGTCAGTTGGTTTAACGCGCCATGTCAATATTTTGTTATTGTAATAATGTC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * * *
2850706 AAGTGACTGATTTGTTATAATTCGATAATGTTTGTGACTAATTTGTTACTTTTAAAACTTTAGTG
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
* * * **
2850771 GAGAAAATGAAAACTTA-TCCAAACAT------GAAG-A-AA-AGTCAAATGATCAGTCAAAGGG
131 G-GAAAACGAAAACTTACT-CAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGG
* *
2850826 TGTCCCACCCCCAT
194 TGTCCC-GCCGCAT
* * * * *
2850840 GGTCAAATATGCTAAGTTAACTGGTTTAACGTGCCACGTCAACATTTCGTTACTACAATAATGTC
1 GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
* * *
2850905 GAGTGACTGATTAGTTATAAATCGATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTTC-GT
66 GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAAC-TTCAGT
* * * *
2850969 AGGAAAAAAGAAATCTTACTCCAACAT
130 -GGGAAAACGAAAACTTACTCAAACAT
2850996 TAGTGACCGT
Statistics
Matches: 1169, Mismatches: 171, Indels: 85
0.82 0.12 0.06
Matches are distributed among these distances:
189 2 0.00
190 150 0.13
191 1 0.00
192 2 0.00
193 6 0.01
194 1 0.00
195 1 0.00
197 1 0.00
198 4 0.00
199 157 0.13
200 6 0.01
201 3 0.00
202 158 0.14
203 2 0.00
205 1 0.00
207 2 0.00
208 177 0.15
209 14 0.01
210 138 0.12
211 327 0.28
212 16 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (206 bp):
GGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTACTGCAATAACGTC
GAGTGACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
GGAAAACGAAAACTTACTCAAACATGAAGAAGAAGAAGAAGAGTCAAACGGTTGGTCAAAGGGTG
TCCCGCCGCAT
Found at i:2850375 original size:422 final size:416
Alignment explanation
Indices: 2849409--2850995 Score: 1741
Period size: 401 Copynumber: 3.9 Consensus size: 416
2849399 TTGCCTACAA
* * * ** *
2849409 GGTCAAACATGCTAAGTCAACTT-GTTTAACGAGCCAAGTCAACATTCCGTTACTGTAATAACAT
1 GGTCAAACATGCTAAGTC-AGTTGGTTTAACGCGCCATGTCAACATTTTGTTACTGCAATAACAT
** * * *
2849473 TGAGTGAGTAATTTGTTATATTTCAATAATGTCAGTGACTAATTTGTTACTTTTAAAACTTCAGT
65 CAAGTGACTAATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT
* * * ** * * * *
2849538 GGGGAAACAAAAACTTACTTCATGA-AGAAGAAAAAAAAGAAGAAGAGTCAAACGATTAGTCGAA
130 GGGAAAACAAAAACTTAC-TCA--ACACATG-AAATGAAGAAGAAAAGTCAAATGATCAGTCAAA
* * * * *
2849602 GGGTGTCCCGCCCGCTTGGTCAAACATGCTAATTCAGTTGGTTTAACATTCCACGTCAACATTTC
191 GGGTGTCCCGCCCGCATGGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTC
* * * * *
2849667 GTTACTGCAATAATGCCGAGTGAA-TGATTTTTTATAAGTCGATAATGTTAGTGACTTATTTGTT
256 GTTACTGCAATAACGTCGAGT-AACTGATTTGTTATAATTCGATAATGTTAGTGACTAATTTGTT
* * *
2849731 ACTTTTAAAACTTTAGTGGGAAAAATGAAAACTTACTCAAACATGAAGAAG---AAGAAGAAGAG
320 ACTTTTAAAACTTCAGTAGGAAAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAG
*
2849793 TCAAACGGTTGGTCAAAGGGTGTCCCGCCTGCAT
385 TCAAACGG-TGG-CAAAGGGTGTCCCGCCTGTAT
* * * **
2849827 GGTCAAACGTGCTAAGTCA-TATGGTTTAACGTGCCATGTCAACATTTAGTTACTGCAATAATGT
1 GGTCAAACATGCTAAGTCAGT-TGGTTTAACGCGCCATGTCAACATTTTGTTACTGCAATAACAT
** * *
2849891 TGAGTGACTGATTTGTTATAAGTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT
65 CAAGTGACTAATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAG-
* * *
2849956 TGGGAAAACGAAAACTTACTCAACATCATGAAGATGAAGAAGAAAAGTCAAAATGGTCGGTCAAA
129 TGGGAAAACAAAAACTTACTCAACA-CATGAA-ATGAAGAAGAAAAGTC-AAATGATCAGTCAAA
* * ** * *
2850021 GGGTTTCCTGTGCGCATGGTCAAACGTGCTAAGTCAGCTGGTTTAACGTGTCACGTCAACATTTC
191 GGGTGTCCCGCCCGCATGGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTC
*
2850086 GTTACTGCAATAACGTCGAGTAACTGATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTA
256 GTTACTGCAATAACGTCGAGTAACTGATTTGTTATAATTCGATAATGTTAGTGACTAATTTGTTA
*
2850151 CTTTTAAAACTTCAGTAGGAGAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAGT
321 CTTTTAAAACTTCAGTAGGAAAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAGT
**
2850216 CAAACGGTAGGACAAAGGGTGTCCCGGATGTAT
386 CAAACGGT-GG-CAAAGGGTGTCCCGCCTGTAT
* *
2850249 GGTCAAACATGCTAAGTTAGTTGGTTTAACGCGCCACGTCAACATTTTGTTACTGCAATAACATC
1 GGTCAAACATGCTAAGTCAGTTGGTTTAACGCGCCATGTCAACATTTTGTTACTGCAATAACATC
** * * *
2850314 AAGTGACTAATTTAATATAATTCGATAATATTAGTGACTAATTTGTTACTTTTAAAACTTCAATG
66 AAGTGACTAATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGT-
* *
2850379 GGGAAAACAAAAAATGACTCAA-ACATG-AA-GAAGAAG---AGTC-AA--A-CAGTC-----G-
130 GGGAAAACAAAAACTTACTCAACACATGAAATGAAGAAGAAAAGTCAAATGATCAGTCAAAGGGT
* ** ** * * *
2850428 GT--CACTTGCATGGTCAAACATATTAAGTCAGCTGATTTAACGTGCCACATCAACATTTTGTTA
195 GTCCCGCCCGCATGGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTA
* * *
2850491 CTGCAATAAC-TCTAAGTGACTGATTTGTTATAATTCGATAATTTTAGTGACTAATTTGTTACTT
260 CTGCAATAACGTC-GAGTAACTGATTTGTTATAATTCGATAATGTTAGTGACTAATTTGTTACTT
* * *
2850555 TTAAAACTTCAGTAGGGAAAATGAAAACTTACTCAAACATGAAGAAGAATAATCA-AACAGTC-A
324 TTAAAACTTCAGTAGGAAAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAGTCAA
*
2850618 AC-----CAAAGGGTGTCCCGCCCGCT-T
389 ACGGTGGCAAAGGGTGTCCCGCCTG-TAT
* * * **
2850641 GGTCAAACATGCTAAGTCAGTTGGTTTAACGCGCCATGTCAATATTTTGTTATTGTAATAATGTC
1 GGTCAAACATGCTAAGTCAGTTGGTTTAACGCGCCATGTCAACATTTTGTTACTGCAATAACATC
* * * *
2850706 AAGTGACTGATTTGTTATAATTCGATAATGTTTGTGACTAATTTGTTACTTTTAAAACTTTAGTG
66 AAGTGACTAATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
** *
2850771 GAGAAAATGAAAACTTA-TC--CA-A--ACAT---GAAGAAAAGTCAAATGATCAGTCAAAGGGT
131 G-GAAAACAAAAACTTACTCAACACATGAAATGAAGAAGAAAAGTCAAATGATCAGTCAAAGGGT
* * * * *
2850827 GTCCCACCCCCATGGTCAAATATGCTAAGTTAACTGGTTTAACGTGCCACGTCAACATTTCGTTA
195 GTCCCGCCCGCATGGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTA
* * * * *
2850892 CTACAATAATGTCGAGTGACTGATTAGTTATAAATCGATAATGTTAGTGACTAATTTGTTACTTT
260 CTGCAATAACGTCGAGTAACTGATTTGTTATAATTCGATAATGTTAGTGACTAATTTGTTACTTT
* * *
2850957 TAAAACTTTC-GTAGGAAAAAAGAAATCTTACTCCAACAT
325 TAAAAC-TTCAGTAGGAAAAATGAAAACTTACTCAAACAT
2850996 TAGTGACCGT
Statistics
Matches: 997, Mismatches: 135, Indels: 91
0.82 0.11 0.07
Matches are distributed among these distances:
386 4 0.00
388 1 0.00
389 5 0.01
390 3 0.00
391 4 0.00
392 143 0.14
393 6 0.01
398 1 0.00
399 5 0.01
400 8 0.01
401 295 0.30
402 5 0.01
403 1 0.00
404 1 0.00
409 4 0.00
412 2 0.00
414 4 0.00
416 2 0.00
417 12 0.01
418 131 0.13
419 185 0.19
420 4 0.00
421 3 0.00
422 167 0.17
423 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (416 bp):
GGTCAAACATGCTAAGTCAGTTGGTTTAACGCGCCATGTCAACATTTTGTTACTGCAATAACATC
AAGTGACTAATTTGTTATAATTCAATAATGTTAGTGACTAATTTGTTACTTTTAAAACTTCAGTG
GGAAAACAAAAACTTACTCAACACATGAAATGAAGAAGAAAAGTCAAATGATCAGTCAAAGGGTG
TCCCGCCCGCATGGTCAAACATGCTAAGTCAGCTGGTTTAACGTGCCACGTCAACATTTCGTTAC
TGCAATAACGTCGAGTAACTGATTTGTTATAATTCGATAATGTTAGTGACTAATTTGTTACTTTT
AAAACTTCAGTAGGAAAAATGAAAACTTACTCAAACATGAAGAAGAATAATAAGAAGAGTCAAAC
GGTGGCAAAGGGTGTCCCGCCTGTAT
Found at i:2856986 original size:17 final size:16
Alignment explanation
Indices: 2856964--2856997 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2856954 TAAAAACAGT
2856964 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2856981 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2856997 A
1 A
2856998 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2857516 original size:24 final size:24
Alignment explanation
Indices: 2857472--2857521 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2857462 ATAAAGAACC
*
2857472 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2857496 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
2857520 AA
1 AA
2857522 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2867245 original size:17 final size:16
Alignment explanation
Indices: 2867225--2867258 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2867215 TAAAAACAGT
2867225 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2867242 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2867258 A
1 A
2867259 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2867777 original size:24 final size:24
Alignment explanation
Indices: 2867733--2867782 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2867723 ATAAAGAACC
*
2867733 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2867757 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
2867781 AA
1 AA
2867783 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2871450 original size:22 final size:21
Alignment explanation
Indices: 2871408--2871447 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2871398 GAGATTATTT
*
2871408 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2871429 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2871448 ATAATTTCTC
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:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2873467 original size:47 final size:48
Alignment explanation
Indices: 2873410--2873514 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
2873400 ATGGATAAAA
* *
2873410 TGCATTCGATGTTTT-A-AAATAGCCTGAGTGCATCGATGCATGGCT-TG
1 TGCATTCGATGTTTTCATAAA-AACCGGAGTGCATCGATGCATGG-TATG
*
2873457 TGCATTCGATGTTTTCATAAAAATCGGAGTGCATCGATGCATGGTATG
1 TGCATTCGATGTTTTCATAAAAACCGGAGTGCATCGATGCATGGTATG
2873505 TGCA-TCGATG
1 TGCATTCGATG
2873515 CATAAAATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
47 22 0.42
48 27 0.52
49 3 0.06
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (48 bp):
TGCATTCGATGTTTTCATAAAAACCGGAGTGCATCGATGCATGGTATG
Found at i:2874722 original size:17 final size:17
Alignment explanation
Indices: 2874700--2874740 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2874690 TATAATAAAC
2874700 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
2874717 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
2874734 ATATGAT
1 TTATGAT
2874741 TATTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:2874768 original size:51 final size:52
Alignment explanation
Indices: 2874710--2874807 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
2874700 TTATGATAAT
* *
2874710 TAAATTATTATGATAATTAAATTAATATGATTA-TTTTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTAAAATTTTATCA
2874761 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTAAAATTT
1 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTAAAATTT
2874808 AGTTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 32 0.73
52 12 0.27
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTAAAATTTTATCA
Found at i:2875652 original size:20 final size:20
Alignment explanation
Indices: 2875626--2875679 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2875616 AACCCTTACA
**
2875626 AATATCAAGTAGAAACAAAC
1 AATATCAAAAAGAAACAAAC
* *
2875646 GATATCAAAAAGAAGCAAAC
1 AATATCAAAAAGAAACAAAC
*
2875666 AATATCAAACAGAA
1 AATATCAAAAAGAA
2875680 TAAAGCAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.13
Consensus pattern (20 bp):
AATATCAAAAAGAAACAAAC
Found at i:2875854 original size:13 final size:13
Alignment explanation
Indices: 2875836--2875861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2875826 AAAGAAGACA
2875836 GAATCTCCAATTC
1 GAATCTCCAATTC
2875849 GAATCTCCAATTC
1 GAATCTCCAATTC
2875862 AAATGATTTT
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:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
GAATCTCCAATTC
Found at i:2878306 original size:23 final size:23
Alignment explanation
Indices: 2878257--2878314 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2878247 TCTTATATGG
*
2878257 CACTACGGTGCAATTCTACGCAA
1 CACTTCGGTGCAATTCTACGCAA
* *
2878280 CACTTTGGTGCAATTCTACGTC-G
1 CACTTCGGTGCAATTCTACG-CAA
2878303 CACTTCGGTGCA
1 CACTTCGGTGCA
2878315 TTTATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCAA
Found at i:2885268 original size:23 final size:23
Alignment explanation
Indices: 2885219--2885276 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2885209 TCTTATATGG
*
2885219 CACTACGGTGCAATTCTACGCAA
1 CACTTCGGTGCAATTCTACGCAA
* *
2885242 CACTTTGGTGCAATTCTACGTC-G
1 CACTTCGGTGCAATTCTACG-CAA
2885265 CACTTCGGTGCA
1 CACTTCGGTGCA
2885277 TTTATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCAA
Found at i:2891091 original size:64 final size:65
Alignment explanation
Indices: 2890983--2891143 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 65
2890973 ATTATTCAAG
* * * *
2890983 GTGTATCGATGCACATGAAGTGCATCGATGCACTAATTTAAAATAAAAATATCGAAT-GCCA-TC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTAACTTAAAATAAAAACATCGAATAG-CATTC
2891046 A
65 A
* * *
2891047 GTGTATCGATGCACAAGTAGTGCATCGATGCA-TCACCCTT-AAATACAAACATCGAATAGGATT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACT-A-ACTTAAAATAAAAACATCGAATAGCATT
*
2891110 TA
64 CA
*
2891112 -TGTATCGATGCA-TAGATAGTGCATCGATGCAC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCAC
2891144 CCGTCAAGGG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
63 3 0.04
64 74 0.90
65 5 0.06
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (65 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACTAACTTAAAATAAAAACATCGAATAGCATTCA
Found at i:2891838 original size:23 final size:23
Alignment explanation
Indices: 2891786--2891846 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2891776 CAATCTTATA
*
2891786 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*** *
2891809 CAACACTTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
2891832 TGGCACTTCAGTGCA
1 TGGCACTTCGGTGCA
2891847 TTTATATGAG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2893829 original size:31 final size:31
Alignment explanation
Indices: 2893792--2894380 Score: 766
Period size: 31 Copynumber: 19.3 Consensus size: 31
2893782 TACATTACAT
* *
2893792 CAATAAACCATTACATAATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
2893823 CAATAAACCAGTACATAATTTATATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
2893854 TAATAAACCA-TACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
*
2893884 CAATAAACCAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2893915 CAATAAACCAGTACATAATTAACATCAATAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2893946 CAATAAATCAGTACATAATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2893977 CAATAAACCAGTACATAATGTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
2894008 CAATAAACCAGCACATCATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
*
2894039 CAATAAACCAGTACATCATTTACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
2894070 CAAT-----A--A-ATCA-TTACTTCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2894092 CAATAAACCAGTACATAATTAACATCAACAT
1 CAATAAACCAGTACATCATTTACATCAACAG
*
2894123 CAATAAACCAGAACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2894154 CAATAAGCCAGTACATAATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* *
2894185 CAATAAATCAGTACATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2894216 CAATAAACCAGTACATCATTTGCATTAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
2894247 CAATAAACCAGTACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
2894278 CAATAAACCAGTACATCATTTACATCAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2894309 TAATAAACCAGTACATTATTTACATTAACAG
1 CAATAAACCAGTACATCATTTACATCAACAG
* * *
2894340 CAATAAACCATTATATCATTTACATCAACAA
1 CAATAAACCAGTACATCATTTACATCAACAG
2894371 CAATAAACCA
1 CAATAAACCA
2894381 ATATATATAT
Statistics
Matches: 495, Mismatches: 53, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.03
23 4 0.01
24 1 0.00
26 1 0.00
27 1 0.00
29 1 0.00
30 30 0.06
31 443 0.89
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (31 bp):
CAATAAACCAGTACATCATTTACATCAACAG
Found at i:2894025 original size:16 final size:16
Alignment explanation
Indices: 2893973--2894056 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
2893963 ATTTACATCA
*
2893973 ACATCAATAAACCAGT
1 ACATCAATAAACCAGC
** *
2893989 ACAT-AATGTA-CATC
1 ACATCAATAAACCAGC
2894003 AACATCAATAAACCAGC
1 -ACATCAATAAACCAGC
** *
2894020 ACATC-ATTTA-CATC
1 ACATCAATAAACCAGC
*
2894034 AACATCAATAAACCAGT
1 -ACATCAATAAACCAGC
2894051 ACATCA
1 ACATCA
2894057 TTTACATCAA
Statistics
Matches: 48, Mismatches: 14, Indels: 12
0.65 0.19 0.16
Matches are distributed among these distances:
14 5 0.10
15 16 0.33
16 22 0.46
17 5 0.10
ACGTcount: A:0.48, C:0.26, G:0.05, T:0.21
Consensus pattern (16 bp):
ACATCAATAAACCAGC
Found at i:2894088 original size:22 final size:23
Alignment explanation
Indices: 2894053--2894098 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2894043 AAACCAGTAC
*
2894053 ATCATTTACATCAACATCAATAA
1 ATCATTTACATCAACAACAATAA
*
2894076 ATCA-TTACTTCAACAACAATAA
1 ATCATTTACATCAACAACAATAA
2894098 A
1 A
2894099 CCAGTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (23 bp):
ATCATTTACATCAACAACAATAA
Found at i:2894624 original size:7 final size:7
Alignment explanation
Indices: 2894612--2894669 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
2894602 GTTTAAAATA
2894612 GTTTAGG
1 GTTTAGG
2894619 GTTTAGG
1 GTTTAGG
2894626 GTTTAGG
1 GTTTAGG
**
2894633 GTTTATA
1 GTTTAGG
*
2894640 TTTTAGG
1 GTTTAGG
2894647 GTTTAGG
1 GTTTAGG
*
2894654 GTTTA-A
1 GTTTAGG
2894660 GTTTAGG
1 GTTTAGG
2894667 GTT
1 GTT
2894670 AGTTAGGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:2894644 original size:21 final size:20
Alignment explanation
Indices: 2894619--2894669 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
2894609 ATAGTTTAGG
2894619 GTTTAGGGTTTAGGGTTTATA
1 GTTTAGGGTTTAGGGTTTA-A
*
2894640 TTTTAGGGTTTAGGGTTTAA
1 GTTTAGGGTTTAGGGTTTAA
2894660 GTTTAGGGTT
1 GTTTAGGGTT
2894670 AGTTAGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (20 bp):
GTTTAGGGTTTAGGGTTTAA
Found at i:2894708 original size:17 final size:18
Alignment explanation
Indices: 2894686--2894719 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2894676 GGTTAGGGTC
2894686 TGGGTTC-AGTTTGGATA
1 TGGGTTCGAGTTTGGATA
*
2894703 TGGGTTCGGGTTTGGAT
1 TGGGTTCGAGTTTGGAT
2894720 TTGGATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (18 bp):
TGGGTTCGAGTTTGGATA
Found at i:2899050 original size:23 final size:23
Alignment explanation
Indices: 2898987--2899069 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
2898977 TATAAATTTA
2898987 CACCGAAGTGCCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAA-TTG
* *
2899011 TC-CCGAA-TGACCGCGTAGAAATG
1 -CACCGAAGTG-CCACGTAGAATTG
2899034 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
2899057 CACCGTAGTGCCA
1 CACCGAAGTGCCA
2899070 TATAATATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 32 0.64
24 16 0.32
25 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:2899347 original size:30 final size:30
Alignment explanation
Indices: 2899313--2899374 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2899303 TTATATCGCG
*
2899313 TAGACATATTATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
*
2899343 TAGACATATCATTTTCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
2899373 TA
1 TA
2899375 ACTCATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:2906566 original size:16 final size:16
Alignment explanation
Indices: 2906545--2906575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2906535 GGAGAAAGAA
2906545 AGTATAAACAATATGG
1 AGTATAAACAATATGG
*
2906561 AGTATAGACAATATG
1 AGTATAAACAATATG
2906576 ACAAAAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
AGTATAAACAATATGG
Found at i:2907298 original size:20 final size:20
Alignment explanation
Indices: 2907252--2907306 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
2907242 GTACCACATG
* **
2907252 AACAGTATCGAAACTGTTCA
1 AACAGTATCGATACTGTAAA
* *
2907272 TATAGTATCGATACTGTAAA
1 AACAGTATCGATACTGTAAA
*
2907292 AACAGTATCAATACT
1 AACAGTATCGATACT
2907307 TTATACGTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (20 bp):
AACAGTATCGATACTGTAAA
Found at i:2907584 original size:24 final size:24
Alignment explanation
Indices: 2907557--2907606 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2907547 GGAAAATGTT
* *
2907557 AAAGCTCCCCTTTTGTCATTGAGA
1 AAAGCTCCCCATTTATCATTGAGA
*
2907581 AAAGTTCCCCATTTATCATTGAGA
1 AAAGCTCCCCATTTATCATTGAGA
2907605 AA
1 AA
2907607 TTGAAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (24 bp):
AAAGCTCCCCATTTATCATTGAGA
Found at i:2910230 original size:161 final size:162
Alignment explanation
Indices: 2909951--2910282 Score: 486
Period size: 161 Copynumber: 2.1 Consensus size: 162
2909941 CTATGTGTAC
* * * * *
2909951 TATCGACACTAAGTGTGTAACCCACGGAATTCATTATATGTTAATGAACGACTGTATCGACACTA
1 TATCGGCACAAAGTGTGTAACCCACAGAATTCATAATATGTTAATGAACGACCGTATCGACACTA
* ** * * *
2910016 AGTGTGTAACCCACGTAATTCATCATATATTGATGAACGACCGTATTGGCACTAAGTGTGTAA-C
66 AGTGTGCAACCCACAAAATTCATCATATATTGATAAACGACCGTATAGGCACTAAGTGTGCAACC
* * *
2910080 CACGGAATTCATAATGTGTTTATGAACGGCCA
131 CACAGAATTCATAATATGTTTATGAACGACCA
* * *
2910112 TATCGGCACAAAGTGTGTAACTCACAGAATTCATAATGTGTTTATGAACGACCGTATCGACACTA
1 TATCGGCACAAAGTGTGTAACCCACAGAATTCATAATATGTTAATGAACGACCGTATCGACACTA
*
2910177 AGTGTGCAACCCACAAAATTCATCATATATTGATAAACTACCGTATAGGCACTAAGTGTGCAACC
66 AGTGTGCAACCCACAAAATTCATCATATATTGATAAACGACCGTATAGGCACTAAGTGTGCAACC
*
2910242 CACAGAATTCATAATATGTTTATGAACGACCG
131 CACAGAATTCATAATATGTTTATGAACGACCA
2910274 TATCGGCAC
1 TATCGGCAC
2910283 TATGTGTGCA
Statistics
Matches: 151, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
161 113 0.75
162 38 0.25
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (162 bp):
TATCGGCACAAAGTGTGTAACCCACAGAATTCATAATATGTTAATGAACGACCGTATCGACACTA
AGTGTGCAACCCACAAAATTCATCATATATTGATAAACGACCGTATAGGCACTAAGTGTGCAACC
CACAGAATTCATAATATGTTTATGAACGACCA
Found at i:2910292 original size:54 final size:54
Alignment explanation
Indices: 2909951--2910290 Score: 405
Period size: 54 Copynumber: 6.3 Consensus size: 54
2909941 CTATGTGTAC
* * * * *
2909951 TATCGACACTAAGTGTGTAACCCACGGAATTCATTATATGTTAATGAACGACTG
1 TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
2910005 TATCGACACTAAGTGTGTAACCCAC-GTAATTCATCATATATTGATGAACGACCG
1 TATCGGCACTAAGTGTGTAACCCACAG-AATTCATAATATGTTTATGAACGACCG
* * * * *
2910059 TATTGGCACTAAGTGTGTAA-CCACGGAATTCATAATGTGTTTATGAACGGCCA
1 TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
2910112 TATCGGCACAAAGTGTGTAACTCACAGAATTCATAATGTGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * * * * * *
2910166 TATCGACACTAAGTGTGCAACCCACAAAATTCATCATATATTGATAAACTACCG
1 TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
2910220 TATAGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
2910274 TATCGGCACTATGTGTG
1 TATCGGCACTAAGTGTG
2910291 CATCTCAAAG
Statistics
Matches: 244, Mismatches: 39, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
53 44 0.18
54 200 0.82
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGACCG
Found at i:2916584 original size:53 final size:54
Alignment explanation
Indices: 2916521--2916706 Score: 232
Period size: 54 Copynumber: 3.5 Consensus size: 54
2916511 CTATGTGTAC
* * *
2916521 TATCGGCACTAAGTGTGCGACCCACGAAACTCATCATATATTGATAAACGA-CAG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACGATC-G
* * * * *
2916575 TATC-GCACTAAGTGTGCAACCCACGGAATTCATAATGTGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACGATCG
* * * *
2916628 TATCGGCACTAAGTGTGGAACACATGAAATTCATCATATATTGATGAACTATCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACGATCG
*
2916682 TATAGGCACTAAGTGTGCAACCCAC
1 TATCGGCACTAAGTGTGCAACCCAC
2916707 AGAACATAAT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
53 43 0.39
54 66 0.61
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACGATCG
Found at i:2916750 original size:106 final size:106
Alignment explanation
Indices: 2916521--2916750 Score: 277
Period size: 107 Copynumber: 2.2 Consensus size: 106
2916511 CTATGTGTAC
* * *
2916521 TATCGGCACTAAGTGTGCG-ACCCACGAAACTCATCATATATTGATAAACGACAGTATCGCACTA
1 TATCGACACTAAGTGTG-GAACACATGAAACTCATCATATATTGATAAACGACAGTATCGCACTA
* * * *
2916585 AGTGTGCAACCCACGGAATTCATAATGTGTTTATGAACGATCG
65 AGTGTGCAACCCACAGAA-TCATAATATGTTTATGAACAACCG
* * * * *
2916628 TATCGGCACTAAGTGTGGAACACATGAAATTCATCATATATTGATGAACTATC-GTATAGGCACT
1 TATCGACACTAAGTGTGGAACACATGAAACTCATCATATATTGATAAACGA-CAGTAT-CGCACT
*
2916692 AAGTGTGCAACCCACAGAA-CATAATATTTTTATGAACAACCG
64 AAGTGTGCAACCCACAGAATCATAATATGTTTATGAACAACCG
*
2916734 TATCGACACTACGTGTG
1 TATCGACACTAAGTGTG
2916751 CATCTCAAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
106 35 0.33
107 48 0.45
108 24 0.22
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (106 bp):
TATCGACACTAAGTGTGGAACACATGAAACTCATCATATATTGATAAACGACAGTATCGCACTAA
GTGTGCAACCCACAGAATCATAATATGTTTATGAACAACCG
Found at i:2925121 original size:18 final size:18
Alignment explanation
Indices: 2925100--2925136 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2925090 CATCCCTTGG
2925100 AGTTTTTACATGGTCAAT
1 AGTTTTTACATGGTCAAT
2925118 AGTTTTTACATGGTCAAT
1 AGTTTTTACATGGTCAAT
2925136 A
1 A
2925137 TTTGTGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (18 bp):
AGTTTTTACATGGTCAAT
Found at i:2927712 original size:3 final size:3
Alignment explanation
Indices: 2927704--2927749 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
2927694 AAATTATTTT
2927704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
2927748 TA
1 TA
2927750 TTTTTTTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2932487 original size:14 final size:14
Alignment explanation
Indices: 2932468--2932501 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2932458 TGCACAAGCT
2932468 AGTAATATCCTAAA
1 AGTAATATCCTAAA
2932482 AGTAATATCCTAAA
1 AGTAATATCCTAAA
2932496 ATGTAA
1 A-GTAA
2932502 AGGAAGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (14 bp):
AGTAATATCCTAAA
Found at i:2937278 original size:2 final size:2
Alignment explanation
Indices: 2937271--2937297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2937261 AATATTAGAT
2937271 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 T
2937298 TGCAGCCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2940190 original size:83 final size:85
Alignment explanation
Indices: 2940095--2940276 Score: 233
Period size: 83 Copynumber: 2.2 Consensus size: 85
2940085 GACTGATAGT
*
2940095 CCTTCTCGCCTTGAGTTATACTATAAATTTGATATGCCCTTCAGCTGAATGTAATCAAACTCG-A
1 CCTTCTCGCCTTGAGTTATACTATAAATTTGATATGCCATTCAGCTGAATGTAATCAAACTCGAA
* *
2940159 GG-GTTTGTTGACATATAAC
66 GGTATTTGTTAACATATAAC
** * * * * * * *
2940178 CCTTCTCGCCTTGAGTTATGTTGTAAATTTGGTATTCGATTGAGCTGAATGTAATCGAACTTGAA
1 CCTTCTCGCCTTGAGTTATACTATAAATTTGATATGCCATTCAGCTGAATGTAATCAAACTCGAA
2940243 GGTATTTGTTAACATATAAC
66 GGTATTTGTTAACATATAAC
*
2940263 CCTTTTCGCCTTGA
1 CCTTCTCGCCTTGA
2940277 TCTATATTGT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 53 0.63
84 3 0.04
85 28 0.33
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (85 bp):
CCTTCTCGCCTTGAGTTATACTATAAATTTGATATGCCATTCAGCTGAATGTAATCAAACTCGAA
GGTATTTGTTAACATATAAC
Found at i:2948590 original size:14 final size:13
Alignment explanation
Indices: 2948552--2948594 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2948542 TCCCTCTCAT
2948552 TTTTAACTTTTTC
1 TTTTAACTTTTTC
* *
2948565 TTTT-TCTCTTTC
1 TTTTAACTTTTTC
2948577 ATTTTAACTTTTTC
1 -TTTTAACTTTTTC
2948591 TTTT
1 TTTT
2948595 CCTATCTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAACTTTTTC
Found at i:2948604 original size:26 final size:26
Alignment explanation
Indices: 2948546--2948606 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2948536 CCAATTTCCC
* *
2948546 TCTCATTTTTAACTTTTTCTTTTTCTC
1 TCTCA-TTTTAACTTTTTCTTTTCCTA
*
2948573 TTTCATTTTAACTTTTTCTTTTCCTA
1 TCTCATTTTAACTTTTTCTTTTCCTA
2948599 TCTCATTT
1 TCTCATTT
2948607 CTTCATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (26 bp):
TCTCATTTTAACTTTTTCTTTTCCTA
Found at i:2948919 original size:15 final size:15
Alignment explanation
Indices: 2948899--2948928 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2948889 TTACTCCAGT
2948899 ATCTCTAAGCTGAAC
1 ATCTCTAAGCTGAAC
2948914 ATCTCTAAGCTGAAC
1 ATCTCTAAGCTGAAC
2948929 CAACACTCCA
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:0.13, T:0.27
Consensus pattern (15 bp):
ATCTCTAAGCTGAAC
Found at i:2952134 original size:22 final size:22
Alignment explanation
Indices: 2952109--2952152 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2952099 ATGATGATTC
2952109 GAACCCCACCATGACTTAACCT
1 GAACCCCACCATGACTTAACCT
2952131 GAACCCCACCATGACTTAACCT
1 GAACCCCACCATGACTTAACCT
2952153 TATTTGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.41, G:0.09, T:0.18
Consensus pattern (22 bp):
GAACCCCACCATGACTTAACCT
Found at i:2957963 original size:33 final size:31
Alignment explanation
Indices: 2957877--2957961 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
2957867 CATCAGGATA
* * *
2957877 TTGAATTCCCAAAGATGCCCCAATATTCGATG
1 TTGAA-TCTCAAAGATGCCCCAACATTCAATG
* *
2957909 TTGAATCTCAAAAAATGCCCCAACATTTAATG
1 TTGAATCTC-AAAGATGCCCCAACATTCAATG
*
2957941 TTGAATATTCAAAGATGCCCC
1 TTGAAT-CTCAAAGATGCCCC
2957962 CATTGTTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 3 0.07
32 39 0.89
33 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (31 bp):
TTGAATCTCAAAGATGCCCCAACATTCAATG
Found at i:2959041 original size:12 final size:13
Alignment explanation
Indices: 2959026--2959091 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 13
2959016 TTTTCTTCAC
2959026 TTTTTC-CTTTGTT
1 TTTTTCTCTTTG-T
*
2959039 TTTGTTTCTCTTTTT
1 TTT--TTCTCTTTGT
2959054 TATTTTCTCTTTGT
1 T-TTTTCTCTTTGT
2959068 TTTTT-TCTTTGTT
1 TTTTTCTCTTTG-T
2959081 TTTTTCTCTTT
1 TTTTTCTCTTT
2959092 TTTCTTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.13
13 13 0.29
14 15 0.33
15 5 0.11
16 6 0.13
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTCTCTTTGT
Found at i:2959066 original size:24 final size:23
Alignment explanation
Indices: 2959039--2959102 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 23
2959029 TTCCTTTGTT
2959039 TTTGTTTCTCTTTTTTATTTTCTC
1 TTTGTTTCTCTTTTTT-TTTTCTC
*
2959063 TTTGTTTTTTTCTTTGTTTTTTTCTC
1 TTTG--TTTCTCTTT-TTTTTTTCTC
2959089 TTT-TTTCTTCTTTT
1 TTTGTTTC-TCTTTT
2959103 CTCTTTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 4 0.12
24 9 0.26
26 18 0.53
27 3 0.09
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (23 bp):
TTTGTTTCTCTTTTTTTTTTCTC
Found at i:2959094 original size:12 final size:13
Alignment explanation
Indices: 2959037--2959094 Score: 73
Period size: 14 Copynumber: 4.4 Consensus size: 13
2959027 TTTTCCTTTG
*
2959037 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
2959050 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
2959064 TTGTTTTTTTCT-T
1 TT-TTTTTTTCTCT
*
2959077 TGTTTTTTTCTCT
1 TTTTTTTTTCTCT
2959090 TTTTT
1 TTTTT
2959095 CTTCTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.23
13 12 0.31
14 15 0.38
15 3 0.08
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:2959109 original size:24 final size:23
Alignment explanation
Indices: 2959012--2959109 Score: 63
Period size: 24 Copynumber: 4.0 Consensus size: 23
2959002 CGTCTTGTCT
* *
2959012 TCTTTTTTCTTCACTTTTTCCTTTG
1 TCTTTTTTCTT--CTTTTTCTTTTC
* *
2959037 TTTTTGTTTC-TCTTTTTTATTTTC
1 TCTTT-TTTCTTC-TTTTTCTTTTC
* *
2959061 TCTTTGTTTTTTTCTTTGTTTTTTTC
1 TC-TT-TTTTCTTCTTT-TTCTTTTC
2959087 TCTTTTTTCTTCTTTTCTCTTTT
1 TCTTTTTTCTTCTTTT-TCTTTT
2959110 TGTTCTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
23 2 0.04
24 24 0.42
25 15 0.26
26 16 0.28
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (23 bp):
TCTTTTTTCTTCTTTTTCTTTTC
Found at i:2959115 original size:16 final size:17
Alignment explanation
Indices: 2959075--2959115 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2959065 TGTTTTTTTC
*
2959075 TTTGTTTTTTTCTCTTT
1 TTTGTTCTTTTCTCTTT
*
2959092 TTTCTTCTTTTCTC-TT
1 TTTGTTCTTTTCTCTTT
2959108 TTTGTTCT
1 TTTGTTCT
2959116 GATTGGATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTGTTCTTTTCTCTTT
Found at i:2961311 original size:44 final size:44
Alignment explanation
Indices: 2961254--2961341 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
2961244 CCTACTCGGA
*
2961254 CATGATCTGTACCCCGCATGTTAATTTTGAACAAGTCCTAACCG
1 CATGATCTCTACCCCGCATGTTAATTTTGAACAAGTCCTAACCG
2961298 CATGATCTCTACCCCGCATGTTAATTTTGAACAAGTCCTAACCG
1 CATGATCTCTACCCCGCATGTTAATTTTGAACAAGTCCTAACCG
2961342 ACCATTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (44 bp):
CATGATCTCTACCCCGCATGTTAATTTTGAACAAGTCCTAACCG
Found at i:2973105 original size:60 final size:60
Alignment explanation
Indices: 2973010--2973155 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 60
2973000 TTATATGTCT
* * * *
2973010 CCAAACTAT-AACATTCATTTTAAATTAATCCTTAAACTTTTAAATATTCTAATTTCACCC
1 CCAAACTATGACCA-TCATTCTAAATTAATCATTAAACTTTTAAACATTCTAATTTCACCC
* * * *
2973070 CCAAATTATGACTC-TCATTCTAAATTAGTCATTAAACTTTTGAACATTCTAATTTCATCC
1 CCAAACTATGAC-CATCATTCTAAATTAATCATTAAACTTTTAAACATTCTAATTTCACCC
* *
2973130 CTAAACTATGACCATCTTTCTAAATT
1 CCAAACTATGACCATCATTCTAAATT
2973156 GCTCCCTAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 69 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.40
Consensus pattern (60 bp):
CCAAACTATGACCATCATTCTAAATTAATCATTAAACTTTTAAACATTCTAATTTCACCC
Found at i:2973392 original size:61 final size:59
Alignment explanation
Indices: 2973317--2973490 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 59
2973307 TATGTACGTG
2973317 TAGTTT-GGGATGAAATTAGAATATTCAAAAAGTTTGGGGACCAATTTAGAATGA-AGGTCA
1 TAGTTTAGGGATGAAATT-GAATATTC-AAAAGTTTGGGGACCAATTTAGAATGATA-GTCA
* * * * * *
2973377 TATTTTGGGGATGAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAGAATGATAGTTA
1 TAGTTTAGGGATGAAATTG-AATATTCAAAAGTTTGGGGACCAATTTAGAATGATAGTCA
* * * * *
2973437 TAGTTTAGGGATGAAATTGGAACATTTAAAAGTTTAGGTACCAATTTAAAATGA
1 TAGTTTAGGGATGAAATT-GAATATTCAAAAGTTTGGGGACCAATTTAGAATGA
2973491 GTCTCATACT
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
60 76 0.80
61 19 0.20
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (59 bp):
TAGTTTAGGGATGAAATTGAATATTCAAAAGTTTGGGGACCAATTTAGAATGATAGTCA
Found at i:2975317 original size:38 final size:38
Alignment explanation
Indices: 2975249--2975326 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
2975239 TGTTTAATCC
2975249 TTATATGATCTAAAGAGACAAGTTTATTGTGTCAATAG
1 TTATATGATCTAAAGAGACAAGTTTATTGTGTCAATAG
* * *
2975287 TTATATGATCTCAAGTGACTAA-TTTTTTGTGTCAATAG
1 TTATATGATCTAAAGAGAC-AAGTTTATTGTGTCAATAG
2975325 TT
1 TT
2975327 TCTAGCGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 34 0.94
39 2 0.06
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (38 bp):
TTATATGATCTAAAGAGACAAGTTTATTGTGTCAATAG
Found at i:2980672 original size:60 final size:60
Alignment explanation
Indices: 2980608--2980753 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
2980598 AGTCTCTAAG
* * * *
2980608 CTTTTGAATATTTTAATTTAATCCCCAAACTATGACTCC-CATTCTAAAATAGTCCTTAAA
1 CTTTTGAATATTCTAATATAATCCCCAAACTATGAC-CCTCATTCTAAAATAATCCTCAAA
* * * * * * *
2980668 CTTTTGAACATTCCAAAATCATCCTCAAACTATGACCCTTATTCTAAATTAATCCTCAAA
1 CTTTTGAATATTCTAATATAATCCCCAAACTATGACCCTCATTCTAAAATAATCCTCAAA
2980728 CTTTTGAATATTCTAATA-ATATCCCC
1 CTTTTGAATATTCTAATATA-ATCCCC
2980754 CTAAATAATT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
59 2 0.03
60 66 0.97
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (60 bp):
CTTTTGAATATTCTAATATAATCCCCAAACTATGACCCTCATTCTAAAATAATCCTCAAA
Found at i:2980680 original size:29 final size:28
Alignment explanation
Indices: 2980647--2980751 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
2980637 CTATGACTCC
*
2980647 CATTCTAAAATAGTCCTTAAACTTTTGAA
1 CATTCTAAAATA-TCCTCAAACTTTTGAA
* * *
2980676 CATTCCAAAATCATCCTCAAAC-TATGACC
1 CATTCTAAAAT-ATCCTCAAACTTTTGA-A
*
2980705 CTTATTCTAAATTAATCCTCAAACTTTTGAA
1 C--ATTCTAAAAT-ATCCTCAAACTTTTGAA
*
2980736 TATTCTAATAATATCC
1 CATTCTAA-AATATCC
2980752 CCCTAAATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.07
29 30 0.51
30 3 0.05
31 18 0.31
32 4 0.07
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (28 bp):
CATTCTAAAATATCCTCAAACTTTTGAA
Found at i:2981450 original size:60 final size:60
Alignment explanation
Indices: 2981377--2981501 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
2981367 ATTGAGTGAT
* * * ** *
2981377 CATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGTAACACCCTATAGTTGAA-GGAC
1 CATTTTGCAACTTTTAATAATCGAGGGACTCAACAAAACAACACCCTATAG-TCAAGGGAC
*
2981437 CATTTTGCAACTTTTAATAATCGAGGGACTCAACAAAACATCACCCTATAGTCAAGGGAC
1 CATTTTGCAACTTTTAATAATCGAGGGACTCAACAAAACAACACCCTATAGTCAAGGGAC
2981497 CATTT
1 CATTT
2981502 GTACACTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (60 bp):
CATTTTGCAACTTTTAATAATCGAGGGACTCAACAAAACAACACCCTATAGTCAAGGGAC
Found at i:2982338 original size:60 final size:60
Alignment explanation
Indices: 2982213--2982343 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
2982203 CACGTGTCCT
* * * * * *
2982213 CAAAATATGACTCTTATTTTAAATTGATCCCTAAACTTTTAAAATTTCTAATTTTATCAG
1 CAAACTATGACTATCATTTTAAATTGATCCCTAAAATTTTAAAATTTCTAATTTCATCAC
* * * *
2982273 TAAACTATGACTATCATTTTAAATT-AGTCCTTAAAATTTTGAACATTTC-AATTTCATCCC
1 CAAACTATGACTATCATTTTAAATTGA-TCCCTAAAATTTT-AAAATTTCTAATTTCATCAC
2982333 CAAACTATGAC
1 CAAACTATGAC
2982344 CTGTATTCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 50 0.86
61 7 0.12
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (60 bp):
CAAACTATGACTATCATTTTAAATTGATCCCTAAAATTTTAAAATTTCTAATTTCATCAC
Found at i:2982637 original size:61 final size:60
Alignment explanation
Indices: 2982561--2982695 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 60
2982551 GTCTTGGGAC
* * * * * *
2982561 TAATTTAAAAAGAGGGTCATAGTTTAGAGATGAAATTAGAATTTTTAAAAAATTTAAAGAT
1 TAATTTAAAATGAGGGTCATAATTTAGAGATGAAAGTA-AAATATTAAAAAATTAAAAGAT
* *
2982622 TAATTTAAAATGAGGGTCATAATTTAGGGATGAAAGTAAAATATTCAAAAATTAAAAGAT
1 TAATTTAAAATGAGGGTCATAATTTAGAGATGAAAGTAAAATATTAAAAAATTAAAAGAT
*
2982682 AAATTTAAAATGAG
1 TAATTTAAAATGAG
2982696 AATTATAACT
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 31 0.48
61 34 0.52
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (60 bp):
TAATTTAAAATGAGGGTCATAATTTAGAGATGAAAGTAAAATATTAAAAAATTAAAAGAT
Found at i:2983389 original size:60 final size:60
Alignment explanation
Indices: 2983290--2983418 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
2983280 ATATGTCCTT
* * * * * *
2983290 AAACTATGATTCGCATTCTAAATTGGTCACTAAATTTTTGAATATTTCAGTTTTATCATC
1 AAACTATGATTCGCATTCTAAATTAGTCACTAAACTTTTGAACATTCCAATTTCATCATC
* *
2983350 AAACTATGATAT-TCATTCTAAATTAGTC-CTTAAACTTTTGAACATTCCAATTTCATCCTC
1 AAACTATGAT-TCGCATTCTAAATTAGTCAC-TAAACTTTTGAACATTCCAATTTCATCATC
*
2983410 AAAGTATGA
1 AAACTATGA
2983419 CCCTTATTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
59 1 0.02
60 56 0.97
61 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (60 bp):
AAACTATGATTCGCATTCTAAATTAGTCACTAAACTTTTGAACATTCCAATTTCATCATC
Found at i:2983782 original size:3 final size:3
Alignment explanation
Indices: 2983774--2983798 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2983764 CAATTAACTC
2983774 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2983799 GTTTAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2987363 original size:59 final size:60
Alignment explanation
Indices: 2987251--2987364 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
2987241 ACTATAGGGT
** * * *
2987251 GTTACTTTGTTGAGTCCTTTGACTATTAAAAGTTATAAAATAATTCATTGACTATAAGAC
1 GTTACTTTGTTGAGTCCTCCGAATATTAAAAGTCATAAAATAATTCATCGACTATAAGAC
*
2987311 GTTATTTTGTTGAGT-CTCCGAATATTAAAAGTCATAAAATAA-TCACTCGACTAT
1 GTTACTTTGTTGAGTCCTCCGAATATTAAAAGTCATAAAATAATTCA-TCGACTAT
2987365 TCATATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 3 0.06
59 30 0.64
60 14 0.30
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (60 bp):
GTTACTTTGTTGAGTCCTCCGAATATTAAAAGTCATAAAATAATTCATCGACTATAAGAC
Found at i:2991981 original size:2 final size:2
Alignment explanation
Indices: 2991974--2992011 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2991964 TATAAAACTA
2991974 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
2992012 TTAGGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2993620 original size:3 final size:3
Alignment explanation
Indices: 2993614--2993703 Score: 94
Period size: 3 Copynumber: 30.0 Consensus size: 3
2993604 AATGGGCCTG
* ** * * *
2993614 TAA TAA TAA TTA TTT TAA TAA TAA TAA TAA TAT TAA TAT TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2993662 TAA TAAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -ACA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
2993704 ATAAAAAGGG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 3 0.04
3 66 0.90
4 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2994036 original size:123 final size:123
Alignment explanation
Indices: 2993817--2994441 Score: 842
Period size: 123 Copynumber: 5.1 Consensus size: 123
2993807 ATTAAGACGA
** ** ** * * ** *
2993817 AAATGTTGATAATGCTCTATCTTTTTCTGTAATAGAATTGAGCAAAAGGTTTAATAAGTTCTTCA
1 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
* * *
2993882 GATTATGAACTTATCCTTCATCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGG
66 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGG
* *
2993940 AAATGTTGATGCTGCTCTATCTCCTTCTGGGATAGGGTCGAGCAAAAACTTGAATAAGTTCTTCA
1 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
*
2994005 GATTATGAAGTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT-TCTTCTGG
66 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT-TTCTGG
* * * *
2994063 AAATGTTGATGCTGCTCTATCTCCTTCTACGATATAGCCGAGCAAAAGCTTGAATAAGTTCTTCA
1 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
*
2994128 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAACT-TCTTCTGG
66 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT-TTCTGG
* ** ** *
2994186 AAATGTTGATGTTGCTCTATCTTTTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTTA
1 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
* * * *
2994251 GATTATGAACTTCTTTTTCCTCTTTAGATGAGTTCTTCTTATTAAGAACTCCTTCTGG
66 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGG
* * * *
2994309 AAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGTAAAAAGTTGAATAAGTTTTTCA
1 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
* * * *
2994374 GATTATGAACTTCTTATTCCTCTTCAGATGAGTT-TCTCTTATGACGAACTCCTTATGG
66 GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT-TCTTATTACGAACTCTTTCTGG
2994432 AAATGTTGAT
1 AAATGTTGAT
2994442 CCCTCAAGTG
Statistics
Matches: 452, Mismatches: 47, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
122 2 0.00
123 450 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (123 bp):
AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAACTTGAATAAGTTCTTCA
GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGG
Found at i:2996150 original size:7 final size:7
Alignment explanation
Indices: 2996138--2996192 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
2996128 TAGTAACTTT
2996138 TTTTTTC
1 TTTTTTC
2996145 TTTTTTCC
1 TTTTTT-C
*
2996153 TTTTTCC
1 TTTTTTC
2996160 TTTTTTC
1 TTTTTTC
*
2996167 -TTTCTC
1 TTTTTTC
2996173 TTTTTT-
1 TTTTTTC
2996179 TTCTTTTC
1 TT-TTTTC
2996187 TTTTTT
1 TTTTTT
2996193 GCTATTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 7 0.17
7 25 0.62
8 8 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:2996156 original size:15 final size:14
Alignment explanation
Indices: 2996138--2996192 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
2996128 TAGTAACTTT
2996138 TTTTTTCTTTTTTCC
1 TTTTTTCTTTTTT-C
*
2996153 TTTTTCCTTTTTTC
1 TTTTTTCTTTTTTC
*
2996167 -TTTCTCTTTTTT-
1 TTTTTTCTTTTTTC
2996179 TTCTTTTCTTTTTT
1 TT-TTTTCTTTTTT
2996193 GCTATTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.32
14 11 0.32
15 12 0.35
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:2996380 original size:61 final size:61
Alignment explanation
Indices: 2996276--2996392 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
2996266 ATATAATATT
* *
2996276 ATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGATGATTAACCAATTACTTTAAGGGC
1 ATAACAGGCTAGCTGAATATTATCCATAAAGCCGAGATGATTAACCAATTACTTTAAGGGC
* * * * *
2996337 ATAACAGGCTAGTTGAATATTATTCATAAAGCCAGAGCT-ATTAACCAGTTGCTTTA
1 ATAACAGGCTAGCTGAATATTATCCATAAAGCC-GAGATGATTAACCAATTACTTTA
2996393 GGGGGACAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 45 0.94
62 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (61 bp):
ATAACAGGCTAGCTGAATATTATCCATAAAGCCGAGATGATTAACCAATTACTTTAAGGGC
Found at i:2998668 original size:23 final size:23
Alignment explanation
Indices: 2998638--2998683 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2998628 TACCAATTAA
2998638 TGGAAAGAAAAGAGCATATCTAC
1 TGGAAAGAAAAGAGCATATCTAC
2998661 TGGAAAGAAAAGAGCATATCTAC
1 TGGAAAGAAAAGAGCATATCTAC
2998684 CATGATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (23 bp):
TGGAAAGAAAAGAGCATATCTAC
Found at i:2999344 original size:26 final size:25
Alignment explanation
Indices: 2999315--2999365 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
2999305 TAAAAATAAT
2999315 AAAGAATAAAAAATTGAAAGAAATCA
1 AAAGAATAAAAAATT-AAAGAAATCA
* * *
2999341 AAAGAATTACAAATTAAATAAATCA
1 AAAGAATAAAAAATTAAAGAAATCA
2999366 GAATTCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAGAATAAAAAATTAAAGAAATCA
Found at i:3000145 original size:172 final size:172
Alignment explanation
Indices: 2999833--3000151 Score: 414
Period size: 172 Copynumber: 1.8 Consensus size: 172
2999823 ATTCTAAGAA
** * *
2999833 AAAATATATTAAAATGATTTTTATAAAACTAATATATATATATAGGGTTTTATAAATAGGGTATT
1 AAAATATATTAAAATGATTTAAATAAAACTAATAAACATATATAGGGTTTTATAAATAGGG---T
*
2999898 TATTTATTTAAAAATATCAGAAAAAAAAACATTTAGTTACTTTAAGACAAACCCTTTCTTAATAT
63 TATTTATTTAAAAATATCAG-AAAAAAAACATCTAGTTACTTTAAGACAAACCCTTTCTTAATAT
2999963 AAATAAATAAATAAATAATAATAAAAATATGATAATTTTTCTTAAG
127 AAATAAATAAATAAATAATAATAAAAATATGATAATTTTTCTTAAG
** *
3000009 AAAATCATATTAAAATGATTTAAATAAAACTAAAGTAAACATATATA-TTTTTTATAAGTAGGG-
1 AAAAT-ATATTAAAATGATTTAAATAAAACT-AA-TAAACATATATAGGGTTTTATAAATAGGGT
* ** *
3000072 TATTTATTTAAAAATATTAG-AAAAGTACATCTAGTTACTTTAAGAC-ATCCTCTTTCTTAATAT
63 TATTTATTTAAAAATATCAGAAAAAAAACATCTAGTTACTTTAAGACAAACC-CTTTCTTAATA-
3000135 TAAA-AAATAAATAAATA
126 TAAATAAATAAATAAATA
3000152 TCATCCTTAA
Statistics
Matches: 126, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
171 3 0.02
172 47 0.37
173 4 0.03
174 19 0.15
176 5 0.04
177 23 0.18
178 15 0.12
179 10 0.08
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (172 bp):
AAAATATATTAAAATGATTTAAATAAAACTAATAAACATATATAGGGTTTTATAAATAGGGTTAT
TTATTTAAAAATATCAGAAAAAAAACATCTAGTTACTTTAAGACAAACCCTTTCTTAATATAAAT
AAATAAATAAATAATAATAAAAATATGATAATTTTTCTTAAG
Found at i:3000182 original size:20 final size:20
Alignment explanation
Indices: 3000157--3000196 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3000147 AAATATCATC
* *
3000157 CTTAAATATATCAAATTATA
1 CTTAAAAATATAAAATTATA
3000177 CTTAAAAATATAAAATTATA
1 CTTAAAAATATAAAATTATA
3000197 GGATTAAATT
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:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
CTTAAAAATATAAAATTATA
Found at i:3001534 original size:13 final size:13
Alignment explanation
Indices: 3001518--3001551 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3001508 AGAACTTGCA
3001518 TGTAATAATTATT
1 TGTAATAATTATT
*
3001531 TGTAATTATTATT
1 TGTAATAATTATT
3001544 T-TAATAAT
1 TGTAATAAT
3001552 AATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
TGTAATAATTATT
Found at i:3001551 original size:3 final size:3
Alignment explanation
Indices: 3001545--3001594 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
3001535 ATTATTATTT
3001545 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA -AA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3001589 TAA TAA
1 TAA TAA
3001595 CTAAAAAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3001561 original size:25 final size:25
Alignment explanation
Indices: 3001545--3001594 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3001535 ATTATTATTT
3001545 TAATAATAATAAATAATAATAATAA
1 TAATAATAATAAATAATAATAATAA
3001570 TAATAATAAT-AATAA-AA-AATAA
1 TAATAATAATAAATAATAATAATAA
3001592 TAA
1 TAA
3001595 CTAAAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 5 0.20
25 10 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
TAATAATAATAAATAATAATAATAA
Found at i:3014114 original size:139 final size:136
Alignment explanation
Indices: 3013735--3014244 Score: 463
Period size: 139 Copynumber: 3.7 Consensus size: 136
3013725 TTAATTAGGA
* * * * * * *
3013735 AATTTTAAATTTGGTCATCACTTTTGCCCAAGGTTCCATTTTAATTATTAGAATCACATAATTAA
1 AATTTTTAATTTGGTCCTCGCTTTTGCTCGA-GTTCTATTTTAATTATTAGAATCA-ATAATTAG
*
3013800 TT-AAATTGACTAGGTTAATAATTAGAGCCTTCATCTTAGGCTTAATTTCAAACTTAGTCCTTAA
64 TTAAAATTGACTAGGTTAATAATTAGAGCC-TCATTTTAGGCTTAATTTCAAACTTAGTCCTTAA
3013864 ATTTAGAGG
128 ATTTAGAGG
* * *
3013873 AATTTTTAATTTGGTCCTCGCTTTTGCTCGAGTTGTTATTTTAATTATTCGAATCAAATAATTGG
1 AATTTTTAATTTGGTCCTCGCTTTTGCTCGAGTT-CTATTTTAATTATTAGAATC-AATAATTAG
* * * *
3013938 TTAAAATTGACTAGGTTAACAAATAGAGCATCAATTTTAGGCTTAATTTCACACTTAGTCCTTAA
64 TTAAAATTGACTAGGTTAATAATTAGAGCCTC-ATTTTAGGCTTAATTTCAAACTTAGTCCTTAA
*
3014003 ATTTAGTGG
128 ATTTAGAGG
* * *
3014012 AATTTTTAATTTGGTCCTCGTTTTTGCTCGAGATTCTATTTTAATTATTTGAATCAATTAAATAG
1 AATTTTTAATTTGGTCCTCGCTTTTGCTCGAG-TTCTATTTTAATTATTAGAATCAA-TAATTAG
* * * ** * * * *
3014077 TTAAAATTAATTAGGATAATTTTTAGAGCCTACATTTTTATGTTTAATTTCATAGC-TAGTGCTT
64 TTAAAATTGACTAGGTTAATAATTAGAGCCT-CA-TTTTAGGCTTAATTTCA-AACTTAGTCCTT
* *
3014141 TAATCTAG-GAG
126 AAATTTAGAG-G
* ** * * * * * * * *
3014152 ACTTTTCGATTTTGTCCTCGCTTGTGCTCGAGGTTCTCTTTTGACTATTCGATTCAATAATTTAC
1 AATTTTTAATTTGGTCCTCGCTTTTGCTCGA-GTTCTATTTTAATTATTAGAATCAATAA-TTAG
*
3014217 TAAAAATTGA-TCAGAGTTAAT-ATTAGAG
64 TTAAAATTGACT-AG-GTTAATAATTAGAG
3014245 ACTATATTTT
Statistics
Matches: 305, Mismatches: 53, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
137 3 0.01
138 55 0.18
139 146 0.48
140 94 0.31
141 7 0.02
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (136 bp):
AATTTTTAATTTGGTCCTCGCTTTTGCTCGAGTTCTATTTTAATTATTAGAATCAATAATTAGTT
AAAATTGACTAGGTTAATAATTAGAGCCTCATTTTAGGCTTAATTTCAAACTTAGTCCTTAAATT
TAGAGG
Found at i:3015558 original size:24 final size:23
Alignment explanation
Indices: 3015531--3015617 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 23
3015521 TCATATAATT
3015531 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAG-GCCACGTAGAATA
* *
3015555 TGCATCGAAGGGCCACGTAG-ATT
1 TGCACCGAA-GGCCACGTAGAATA
*
3015578 TGTC-CCGAAGGACCACGTAGAATT
1 TG-CACCGAAGG-CCACGTAGAATA
3015602 TGTC-CCGAAGGACCAC
1 TG-CACCGAAGG-CCAC
3015618 ATAAAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.04
23 16 0.29
24 37 0.66
25 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGGCCACGTAGAATA
Found at i:3015611 original size:47 final size:47
Alignment explanation
Indices: 3015535--3015672 Score: 145
Period size: 47 Copynumber: 2.9 Consensus size: 47
3015525 ATAATTTGCA
* * * *
3015535 CCGAAGTG-CCACGTAGAATATG-CATCGAAGGGCCACGTAGATTTGTC
1 CCGAAG-GACCACGTAGAATTTGTC-CCGAAGGACCACGTAGATTTATC
* *
3015582 CCGAAGGACCACGTAGAATTTGTCCCGAAGGACCACATAAAAATTTATC
1 CCGAAGGACCACGTAGAATTTGTCCCGAAGGACCACGT--AGATTTATC
* *
3015631 CCGAAGGACCACGTAGAAATTTATCCCGAAGGACCGCGTAGA
1 CCGAAGGACCACGTAG-AATTTGTCCCGAAGGACCACGTAGA
3015673 ACCCTCAACT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
46 1 0.01
47 30 0.39
48 3 0.04
49 23 0.30
50 19 0.25
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (47 bp):
CCGAAGGACCACGTAGAATTTGTCCCGAAGGACCACGTAGATTTATC
Found at i:3015671 original size:25 final size:25
Alignment explanation
Indices: 3015560--3015673 Score: 153
Period size: 25 Copynumber: 4.7 Consensus size: 25
3015550 GAATATGCAT
* *
3015560 CGAAGGGCCACGTAG--ATTTGTCC
1 CGAAGGACCACGTAGAAATTTATCC
*
3015583 CGAAGGACCACGTAG-AATTTGTCC
1 CGAAGGACCACGTAGAAATTTATCC
* *
3015607 CGAAGGACCACATAAAAATTTATCC
1 CGAAGGACCACGTAGAAATTTATCC
3015632 CGAAGGACCACGTAGAAATTTATCC
1 CGAAGGACCACGTAGAAATTTATCC
*
3015657 CGAAGGACCGCGTAGAA
1 CGAAGGACCACGTAGAA
3015674 CCCTCAACTC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 14 0.17
24 21 0.26
25 47 0.57
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (25 bp):
CGAAGGACCACGTAGAAATTTATCC
Found at i:3016542 original size:21 final size:20
Alignment explanation
Indices: 3016501--3016549 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
3016491 TTCCTCTTGA
3016501 TATCGATACCTTCACATCAG
1 TATCGATACCTTCACATCAG
3016521 TATCGATACTGCTTCA-ATCAG
1 TATCGATAC--CTTCACATCAG
3016542 TATCGATA
1 TATCGATA
3016550 TTGTTCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATACCTTCACATCAG
Found at i:3016679 original size:23 final size:24
Alignment explanation
Indices: 3016642--3016686 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3016632 TAATTAACCC
**
3016642 ATTTCACTTCGATCT-TTACCCAA
1 ATTTCACTTAAATCTCTTACCCAA
3016665 ATTTCACTTAAATCTCTTACCC
1 ATTTCACTTAAATCTCTTACCC
3016687 TTAACTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTCACTTAAATCTCTTACCCAA
Found at i:3021738 original size:24 final size:24
Alignment explanation
Indices: 3021706--3021779 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 24
3021696 TGCCACATAG
*
3021706 ATTTGTCCCGAAGGACTGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
* *
3021730 ATTTTTCCCGAAGGACCACGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAG-A
3021755 ATTTGTCCCGAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
3021779 A
1 A
3021780 CCTTAACTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 22 0.50
25 22 0.50
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
ATTTGTCCCGAAGGACCGCGTAGA
Found at i:3021763 original size:25 final size:25
Alignment explanation
Indices: 3021706--3021779 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
3021696 TGCCACATAG
*
3021706 ATTTGTCCCGAAGGACTGCGTAG-A
1 ATTTGTCCCGAAGGACCGCGTAGAA
* *
3021730 ATTTTTCCCGAAGGACCACGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAGAA
3021755 ATTTGTCCCGAAGGACCGCGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAGAA
3021780 CCTTAACTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 20 0.45
25 24 0.55
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCGCGTAGAA
Found at i:3022780 original size:23 final size:24
Alignment explanation
Indices: 3022749--3022793 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3022739 TAATTCACCC
*
3022749 ATTTCACTTTAATCT-TTACCCAA
1 ATTTCACTTAAATCTCTTACCCAA
*
3022772 ATTTTACTTAAATCTCTTACCC
1 ATTTCACTTAAATCTCTTACCC
3022794 TTAACTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTCACTTAAATCTCTTACCCAA
Found at i:3025149 original size:33 final size:34
Alignment explanation
Indices: 3025112--3025178 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3025102 TTTATTTTTA
* *
3025112 CTTTTCTACA-CATTTGTAGTTGAAATTTGTGCT
1 CTTTTCTACATCATTTGTAATTGAAATTTATGCT
* **
3025145 CTTTTCTGCATGTTTTGTAATTGAAATTTATGCT
1 CTTTTCTACATCATTTGTAATTGAAATTTATGCT
3025179 TGGAAGCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (34 bp):
CTTTTCTACATCATTTGTAATTGAAATTTATGCT
Found at i:3026555 original size:28 final size:29
Alignment explanation
Indices: 3026477--3026553 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
3026467 TTTTCTCTTC
3026477 TATTTTATTCACTGAACTTTAAAAGTTTTT
1 TATTTT-TTCACTGAACTTTAAAAGTTTTT
* *
3026507 AATTTTTTCACTAAACTTTAAAAGTTTTT
1 TATTTTTTCACTGAACTTTAAAAGTTTTT
*
3026536 TATTTTTCCACTGAACTT
1 TATTTTTTCACTGAACTT
3026554 AATACATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 37 0.88
30 5 0.12
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTTTTTCACTGAACTTTAAAAGTTTTT
Found at i:3030281 original size:27 final size:27
Alignment explanation
Indices: 3030250--3030303 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3030240 ATTCCTAATG
*
3030250 TAATT-TTTGATATTTTTTAAATAAAAT
1 TAATTGTTT-ATATTTTTTAAAAAAAAT
*
3030277 TAATTGTTTCTATTTTTTAAAAAAAAT
1 TAATTGTTTATATTTTTTAAAAAAAAT
3030304 ATAGATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (27 bp):
TAATTGTTTATATTTTTTAAAAAAAAT
Found at i:3030407 original size:39 final size:39
Alignment explanation
Indices: 3030364--3030443 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
3030354 CAGATTTGTT
3030364 GTTACGCAGATATAATAAATGTCATTGTATCAGTTGAAA
1 GTTACGCAGATATAATAAATGTCATTGTATCAGTTGAAA
3030403 GTTACGCAGATATAATAAATGTCATTGTATCAGTTGAAA
1 GTTACGCAGATATAATAAATGTCATTGTATCAGTTGAAA
3030442 GT
1 GT
3030444 CAAAGAAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (39 bp):
GTTACGCAGATATAATAAATGTCATTGTATCAGTTGAAA
Found at i:3030713 original size:38 final size:37
Alignment explanation
Indices: 3030667--3030953 Score: 218
Period size: 38 Copynumber: 7.7 Consensus size: 37
3030657 AATATAGTAT
3030667 AGTTTTTGAAAACATATAATATATAGTTTTTAGAAAAC
1 AGTTTTTGAAAACATATAATATATAGTTTTTA-AAAAC
*
3030705 AGTTTTTGAAAGCATATAATATATAGTTTTTTAAAAATC
1 AGTTTTTGAAAACATATAATATATAG-TTTTTAAAAA-C
* * * * *
3030744 GGTTTTTGAAAATATAT-ATA-ACATGGTTTTGAAAAC
1 AGTTTTTGAAAACATATAATATATA-GTTTTTAAAAAC
* * *
3030780 ACGTTTTTGAAAACGTATAATATA-AATTTTGAAAATAC
1 A-GTTTTTGAAAACATATAATATATAGTTTTTAAAA-AC
*
3030818 A-TTTTTG-AAA-ATATAATATATAATGTTTTAAAAAC
1 AGTTTTTGAAAACATATAATATATAGT-TTTTAAAAAC
* * *
3030853 GGATTTTGAAAACGTATATAATATA-A--TTTTGAAAAC
1 AGTTTTTGAAAAC--ATATAATATATAGTTTTTAAAAAC
* *
3030889 A-TATTTTAAAAACATATATAGATATAGTTATTT-AAAAC
1 AGT-TTTTGAAAACATATA-ATATATAGTT-TTTAAAAAC
* *
3030927 AATTTTTAAAAACATATATAATATATA
1 AGTTTTTGAAAAC--ATATAATATATA
3030954 TAATTTTTGA
Statistics
Matches: 202, Mismatches: 24, Indels: 45
0.75 0.09 0.17
Matches are distributed among these distances:
34 14 0.07
35 12 0.06
36 38 0.19
37 33 0.16
38 57 0.28
39 33 0.16
40 15 0.07
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (37 bp):
AGTTTTTGAAAACATATAATATATAGTTTTTAAAAAC
Found at i:3030823 original size:36 final size:36
Alignment explanation
Indices: 3030669--3030906 Score: 159
Period size: 36 Copynumber: 6.4 Consensus size: 36
3030659 TATAGTATAG
* * *
3030669 TTTTTGAAAACATATAATATATAGTTTTTAGAAAACA
1 TTTTTGAAAACGTATAATATATAATTTTGA-AAAACA
* * * * *
3030706 GTTTTTGAAAGCATATAATATATAGTTTTTTAAAAATCGG
1 -TTTTTGAAAACGTATAATATATA-ATTTTGAAAAA-C-A
* ** *
3030746 TTTTTGAAAA--TATATATAACATGGTTTTGAAAACACG
1 TTTTTGAAAACGTATA-AT-ATATAATTTTGAAAA-ACA
3030783 TTTTTGAAAACGTATAATATA-AATTTTGAAAATACA
1 TTTTTGAAAACGTATAATATATAATTTTGAAAA-ACA
*
3030819 TTTTTGAAAA--TATAATATATAATGTTTTAAAAACGGA
1 TTTTTGAAAACGTATAATATATAAT-TTTGAAAAAC--A
3030856 -TTTTGAAAACGTAT-ATAATATAATTTTG-AAAACA
1 TTTTTGAAAACGTATAAT-ATATAATTTTGAAAAACA
* *
3030890 TATTTTAAAAACATATA
1 T-TTTTGAAAACGTATA
3030907 TAGATATAGT
Statistics
Matches: 165, Mismatches: 17, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
34 10 0.06
35 5 0.03
36 54 0.33
37 23 0.14
38 49 0.30
39 24 0.15
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (36 bp):
TTTTTGAAAACGTATAATATATAATTTTGAAAAACA
Found at i:3030832 original size:73 final size:72
Alignment explanation
Indices: 3030669--3030908 Score: 217
Period size: 72 Copynumber: 3.2 Consensus size: 72
3030659 TATAGTATAG
* * * *
3030669 TTTTTGAAAACATATA-ATATATAGTTTTTAGAAAACA-GTTTTTGAAAGCATATAATATATAGT
1 TTTTTGAAAATATATATATA-AT-G-TTTT-GAAAACACGTTTTTGAAAACGTATAATATATA-A
* *
3030732 TTTTTAAAAATCGG
61 TTTTGAAAAA-C-A
3030746 TTTTTGAAAATATATATA-ACATGGTTTTGAAAACACGTTTTTGAAAACGTATAATATA-AATTT
1 TTTTTGAAAATATATATATA-AT-GTTTTGAAAACACGTTTTTGAAAACGTATAATATATAATTT
3030809 TGAAAATACA
64 TGAAAA-ACA
*
3030819 TTTTTGAAAATATAATATATAATGTTTT-AAAA-ACGGATTTTGAAAACGTAT-ATAATATAATT
1 TTTTTGAAAATAT-ATATATAATGTTTTGAAAACAC-GTTTTTGAAAACGTATAAT-ATATAATT
3030881 TTG-AAAACA
63 TTGAAAAACA
* *
3030890 TATTTTAAAAACATATATA
1 T-TTTTGAAAATATATATA
3030909 GATATAGTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
71 13 0.09
72 35 0.24
73 25 0.17
74 16 0.11
75 10 0.07
76 24 0.17
77 19 0.13
78 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (72 bp):
TTTTTGAAAATATATATATAATGTTTTGAAAACACGTTTTTGAAAACGTATAATATATAATTTTG
AAAAACA
Found at i:3030907 original size:36 final size:36
Alignment explanation
Indices: 3030795--3030988 Score: 144
Period size: 36 Copynumber: 5.1 Consensus size: 36
3030785 TTTGAAAACG
* *
3030795 TATAATATAAATTTTGAAAATACAT-TTTTGAAAATATA
1 TATAATAT-AATTTTG-AAA-ACATATTTTAAAAACATA
* ** * *
3030833 -AT-ATATAATGTTTTAAAAACGGATTTTGAAAACGTA
1 TATAATATAA--TTTTGAAAACATATTTTAAAAACATA
3030869 TATAATATAATTTTGAAAACATATTTTAAAAACATA
1 TATAATATAATTTTGAAAACATATTTTAAAAACATA
* *
3030905 TATAGATATAGTTATTTAAAACA-ATTTTTAAAAACATATA
1 TATA-ATATAATT-TTGAAAACATA-TTTTAAAAAC--ATA
*
3030945 TAATATATATAATTTTTGAAAACATATTTTAAAAAAATAA
1 T-ATA-ATATAA-TTTTGAAAACATATTTTAAAAACAT-A
3030985 TATA
1 TATA
3030989 TGTTATATAA
Statistics
Matches: 126, Mismatches: 16, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
35 4 0.03
36 43 0.34
37 16 0.13
38 24 0.19
39 5 0.04
40 6 0.05
41 25 0.20
42 3 0.02
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (36 bp):
TATAATATAATTTTGAAAACATATTTTAAAAACATA
Found at i:3030984 original size:28 final size:28
Alignment explanation
Indices: 3030922--3030985 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
3030912 ATAGTTATTT
*
3030922 AAAACAATTTTTAAAAACATATATAATA
1 AAAATAATTTTTAAAAACATATATAATA
* * * *
3030950 TATATAATTTTTGAAAACATATTTTAA-A
1 AAAATAATTTTTAAAAACATA-TATAATA
3030978 AAAATAAT
1 AAAATAAT
3030986 ATATGTTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATAATTTTTAAAAACATATATAATA
Found at i:3030988 original size:42 final size:40
Alignment explanation
Indices: 3030868--3031002 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 40
3030858 TTGAAAACGT
3030868 ATATAATATAATTTTGAAAACATATTTTAAAAACATATATA
1 ATAT-ATATAATTTTGAAAACATATTTTAAAAACATATATA
3030909 GATATAGT-T-A-TTT-AAAACA-ATTTTTAAAAACATATATA
1 -ATATA-TATAATTTTGAAAACATA-TTTTAAAAACATATATA
*
3030947 ATATATATAATTTTTGAAAACATATTTTAAAAAAATA-ATA
1 ATATATATAA-TTTTGAAAACATATTTTAAAAACATATATA
*
3030987 TATGTTATATAATTTT
1 -AT-ATATATAATTTT
3031003 TTTATTATAT
Statistics
Matches: 81, Mismatches: 2, Indels: 21
0.78 0.02 0.20
Matches are distributed among these distances:
36 1 0.01
37 7 0.09
38 24 0.30
39 3 0.04
40 7 0.09
41 26 0.32
42 13 0.16
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (40 bp):
ATATATATAATTTTGAAAACATATTTTAAAAACATATATA
Done.