Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 19
Found at i:1215895 original size:74 final size:75
Alignment explanation
Indices: 1215799--1215970 Score: 213
Period size: 74 Copynumber: 2.3 Consensus size: 75
1215789 ATTAACAAGA
* * * *
1215799 AGCAAATATTGGGGCATACTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
1215864 TA-TT-TATC
66 CACTTGTATC
* * ** *
1215872 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
1215937 ACACTTGTATT
65 ACACTTGTATC
*
1215948 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
1215971 GGCCCACAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 3 0.04
74 54 0.64
75 21 0.25
76 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:1217288 original size:22 final size:22
Alignment explanation
Indices: 1217259--1217313 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1217249 ATCTACACTC
1217259 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1217281 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1217303 TTCAAAGATGA
1 TTCAAAGATGA
1217314 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1218107 original size:76 final size:76
Alignment explanation
Indices: 1217981--1218285 Score: 538
Period size: 76 Copynumber: 4.0 Consensus size: 76
1217971 CTATTTCTCA
1217981 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1218046 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
1218057 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1218122 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
1218133 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1218198 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1218209 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
1218274 AAAGCCTTCGGG
64 AAAGCCTTCGGG
1218286 ATCTTTTTGA
Statistics
Matches: 220, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
76 208 0.95
78 12 0.05
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:1218266 original size:31 final size:31
Alignment explanation
Indices: 1218231--1218314 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
1218221 CTTCAGTGCA
1218231 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1218262 TGATGTTTCCAAAAAGCCTTCGGGATCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1218293 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
1218315 TCATCTGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 12 0.24
31 39 0.76
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:1218273 original size:107 final size:107
Alignment explanation
Indices: 1218155--1218390 Score: 413
Period size: 107 Copynumber: 2.2 Consensus size: 107
1218145 CTTCAGTGCA
*
1218155 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1218220 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
1218262 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
*
1218327 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1218369 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
1218391 TCATCTGTAA
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
105 12 0.10
107 112 0.90
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (107 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:1218342 original size:76 final size:76
Alignment explanation
Indices: 1218262--1218958 Score: 1333
Period size: 76 Copynumber: 9.2 Consensus size: 76
1218252 GGGAGCTTTT
1218262 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218327 CCTTCAGTGCA
66 CCTTCAGTGCA
1218338 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218403 CCTTCAGTGCA
66 CCTTCAGTGCA
1218414 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218479 CCTTCAGTGCA
66 CCTTCAGTGCA
1218490 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218555 CCTTCAGTGCA
66 CCTTCAGTGCA
1218566 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218631 CCTTCAGTGCA
66 CCTTCAGTGCA
1218642 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218707 CCTTCAGTGCA
66 CCTTCAGTGCA
1218718 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218783 CCTTCAGTGCA
66 CCTTCAGTGCA
*
1218794 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218859 CCTTCAGTGCA
66 CCTTCAGTGCA
* * *
1218870 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1218935 CCTTTC-GTGCA
66 CC-TTCAGTGCA
*
1218946 TGATGTTTTCAAA
1 TGATGTTTCCAAA
1218959 CATTTCCATC
Statistics
Matches: 616, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
76 613 1.00
77 3 0.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (76 bp):
TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCA
Found at i:1218462 original size:259 final size:259
Alignment explanation
Indices: 1218003--1218542 Score: 985
Period size: 259 Copynumber: 2.1 Consensus size: 259
1217993 CTTCAGTGCA
1218003 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
*
1218068 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
1218133 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
131 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1218198 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
196 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
1218262 TGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
*
1218327 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
1218392 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
131 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1218457 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTT
196 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1218521 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
1218543 TCATCTGTAA
Statistics
Matches: 272, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
257 12 0.04
259 260 0.96
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (259 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:1218598 original size:335 final size:333
Alignment explanation
Indices: 1217981--1218618 Score: 1168
Period size: 335 Copynumber: 1.9 Consensus size: 333
1217971 CTATTTCTCA
1217981 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1218046 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1218111 GATGTTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1218176 GGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1218241 AAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAA
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTCC--AAAGCCTTCGGGATCTTTTTGATGTTTTCAAA
1218306 GCCTTCGGGT
324 GCCTTCGGGT
* *
1218316 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1218381 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1218446 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
* *
1218511 GGGATCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
* *
1218576 AAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTCGGG
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAGCCTTCGGG
1218619 TCATCTGTAA
Statistics
Matches: 293, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
333 12 0.04
335 281 0.96
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (333 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGC
CTTCGGGT
Found at i:1219093 original size:3 final size:3
Alignment explanation
Indices: 1219085--1219149 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
1219075 CATTTAAATT
* * *
1219085 TTA TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
1219131 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
1219150 ATATATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1219536 original size:1 final size:1
Alignment explanation
Indices: 1219530--1219556 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1219520 ACTGAACCTG
1219530 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1219557 GAGGAGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1225501 original size:29 final size:30
Alignment explanation
Indices: 1225468--1225528 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
1225458 AAAAAACCTT
* *
1225468 AATGTATT-AAGTTCAGTGAG-GAAATTGGA
1 AATGT-TTAAAGTGCAGTGAGTGAAATAGGA
1225497 AATGTTTAAAGTGCAGTGAGTGAAATAGGA
1 AATGTTTAAAGTGCAGTGAGTGAAATAGGA
1225527 AA
1 AA
1225529 GAGAGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 16 0.57
30 10 0.36
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (30 bp):
AATGTTTAAAGTGCAGTGAGTGAAATAGGA
Found at i:1225626 original size:15 final size:15
Alignment explanation
Indices: 1225604--1225664 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
1225594 ATAATAATAA
1225604 TAAT-AAATATCAAG
1 TAATAAAATATCAAG
*
1225618 TAATAAAATATTAA-
1 TAATAAAATATCAAG
* *
1225632 TAA-AATAGATCAAG
1 TAATAAAATATCAAG
1225646 TAATTAAAATAT-AAG
1 TAA-TAAAATATCAAG
1225661 TAAT
1 TAAT
1225665 TGGAAAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
13 7 0.19
14 11 0.30
15 14 0.38
16 5 0.14
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (15 bp):
TAATAAAATATCAAG
Found at i:1225632 original size:28 final size:28
Alignment explanation
Indices: 1225592--1225657 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 28
1225582 CTCTAGACGA
*
1225592 TAATAATAATAATAAT-AAAT--ATCAAG
1 TAATAA-AATATTAATAAAATAGATCAAG
1225618 TAATAAAATATTAATAAAATAGATCAAG
1 TAATAAAATATTAATAAAATAGATCAAG
1225646 TAATTAAAATAT
1 TAA-TAAAATAT
1225658 AAGTAATTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 8 0.23
26 10 0.29
28 9 0.26
29 8 0.23
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (28 bp):
TAATAAAATATTAATAAAATAGATCAAG
Found at i:1226434 original size:22 final size:22
Alignment explanation
Indices: 1226409--1226461 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1226399 CCGCTGCTCC
* * *
1226409 CATGCAGCTTTAATTGTTGCTT
1 CATGCAGCATCAATTGCTGCTT
* *
1226431 CATGCATCATCATTTGCTGCTT
1 CATGCAGCATCAATTGCTGCTT
1226453 CATGCAGCA
1 CATGCAGCA
1226462 ATTATTACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (22 bp):
CATGCAGCATCAATTGCTGCTT
Found at i:1226696 original size:18 final size:18
Alignment explanation
Indices: 1226661--1226700 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1226651 ACATCGAGGT
*
1226661 AATTTTTTATTTTATTTA
1 AATTTTTTATTATATTTA
1226679 AATTTGTTTATTAT-TTTA
1 AATTT-TTTATTATATTTA
1226697 AATT
1 AATT
1226701 ATTAGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
AATTTTTTATTATATTTA
Found at i:1226777 original size:21 final size:21
Alignment explanation
Indices: 1226753--1226792 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1226743 GTTAATTAGT
1226753 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1226774 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1226793 CATACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1229462 original size:16 final size:16
Alignment explanation
Indices: 1229441--1229482 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1229431 ATATATAAAG
1229441 ATAAATTTGACTAGTT
1 ATAAATTTGACTAGTT
** *
1229457 ATAAATTAAACTATTT
1 ATAAATTTGACTAGTT
1229473 ATAAATTTGA
1 ATAAATTTGA
1229483 TTTAAATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (16 bp):
ATAAATTTGACTAGTT
Found at i:1229531 original size:10 final size:10
Alignment explanation
Indices: 1229512--1229552 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1229502 ATTTAAATAT
*
1229512 TTAATTATTA
1 TTAATCATTA
1229522 TTAATCATTA
1 TTAATCATTA
*
1229532 TGAAATCATTA
1 T-TAATCATTA
1229543 TTAATCATTA
1 TTAATCATTA
1229553 AATATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (10 bp):
TTAATCATTA
Found at i:1229555 original size:18 final size:17
Alignment explanation
Indices: 1229520--1229646 Score: 65
Period size: 18 Copynumber: 6.9 Consensus size: 17
1229510 ATTTAATTAT
* * *
1229520 TATTAATCATTATGAAA
1 TATTAATAATCATTAAA
*
1229537 TCATTATTAATCATTAAA
1 T-ATTAATAATCATTAAA
* * *
1229555 TATTAATAATAATTTCAT
1 TATTAATAATCA-TTAAA
1229573 TATTAATAATCATTACTAAA
1 TATTAATAATCA-T--TAAA
1229593 TCATTAATATCAAATCATTAAA
1 T-ATT-A-AT--AATCATTAAA
* * * *
1229615 TATTAATAATAAATCAT
1 TATTAATAATCATTAAA
1229632 TATTAATAATCATTA
1 TATTAATAATCATTA
1229647 CTAAATCATT
Statistics
Matches: 83, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
17 28 0.34
18 29 0.35
19 2 0.02
20 4 0.05
21 6 0.07
22 6 0.07
23 2 0.02
24 1 0.01
25 5 0.06
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.43
Consensus pattern (17 bp):
TATTAATAATCATTAAA
Found at i:1229598 original size:21 final size:20
Alignment explanation
Indices: 1229518--1229701 Score: 86
Period size: 21 Copynumber: 9.4 Consensus size: 20
1229508 ATATTTAATT
*
1229518 ATTATTAATCATTATGAAATC
1 ATTAATAATCATTAT-AAATC
*
1229539 ATTATTAATCA-T-TAAAT-
1 ATTAATAATCATTATAAATC
* * *
1229556 ATTAATAATAATT-T-CATT
1 ATTAATAATCATTATAAATC
1229574 ATTAATAATCATTACTAAATC
1 ATTAATAATCATTA-TAAATC
*
1229595 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTA-TAAATC
* * *
1229616 ATTAATAAT-A-AAT-CATT
1 ATTAATAATCATTATAAATC
1229633 ATTAATAATCATTACTAAATC
1 ATTAATAATCATTA-TAAATC
* * *
1229654 ATT-ATTATAATTTTAAAT-
1 ATTAATAATCATTATAAATC
* *
1229672 ATAAAATAATTATTATCAAATC
1 AT-TAATAATCATTAT-AAATC
1229694 ATTAATAA
1 ATTAATAA
1229702 ATCAAATCAT
Statistics
Matches: 125, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.02
17 21 0.17
18 22 0.18
19 8 0.06
20 21 0.17
21 39 0.31
22 12 0.10
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (20 bp):
ATTAATAATCATTATAAATC
Found at i:1229649 original size:59 final size:57
Alignment explanation
Indices: 1229515--1229705 Score: 213
Period size: 59 Copynumber: 3.4 Consensus size: 57
1229505 TAAATATTTA
* *
1229515 ATTATTATTAATCATTA-TGAAATCATT-ATTAATCATTAAATATTAATAATAATTTC
1 ATTATTAATAATCATTACT-AAATCATTAATTAATCATTAAATATTAATAATAATATC
1229571 ATTATTAATAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-ATC
1 ATTATTAATAATCATTACTAAATCATTAAT-T--AATCATTAAATATTAATAATAATATC
* *
1229630 ATTATTAATAATCATTACTAAATCATTATTATAAT-TTTAAATA-TAA-AATAAT-T-
1 ATTATTAATAATCATTACTAAATCATTAAT-TAATCATTAAATATTAATAATAATATC
* *
1229683 ATTA-TCA-AATCATTAATAAATCA
1 ATTATTAATAATCATTACTAAATCA
1229706 AATCATAACA
Statistics
Matches: 123, Mismatches: 6, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
51 15 0.12
52 2 0.02
53 4 0.03
54 6 0.05
55 3 0.02
56 31 0.25
57 6 0.05
58 1 0.01
59 33 0.27
60 22 0.18
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (57 bp):
ATTATTAATAATCATTACTAAATCATTAATTAATCATTAAATATTAATAATAATATC
Found at i:1230053 original size:21 final size:21
Alignment explanation
Indices: 1230023--1230113 Score: 59
Period size: 22 Copynumber: 4.4 Consensus size: 21
1230013 TAATTATTAC
1230023 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATCAAATCAT
* *
1230045 TAAATATTAATAAT-AATTTCAT
1 TAAATATTACT-ATCAA-ATCAT
* * *
1230067 T-ATTATTA--ATC--ATTAC
1 TAAATATTACTATCAAATCAT
1230083 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATCAAATCAT
1230105 TAAATATTA
1 TAAATATTA
1230114 ATAATAATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 19
0.65 0.11 0.24
Matches are distributed among these distances:
16 3 0.06
17 2 0.04
18 6 0.12
20 3 0.06
21 17 0.33
22 20 0.39
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTACTATCAAATCAT
Found at i:1230065 original size:60 final size:60
Alignment explanation
Indices: 1229997--1230141 Score: 254
Period size: 60 Copynumber: 2.4 Consensus size: 60
1229987 AATCATTATT
*
1229997 ATAATTTCATTATTACTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
*
1230057 ATAATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
* *
1230117 ATAATTTTATTATTACCAATCATTA
1 ATAATTTCATTATTACTAATCATTA
1230142 ATATCAAATC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (60 bp):
ATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
Found at i:1230202 original size:11 final size:11
Alignment explanation
Indices: 1230167--1230259 Score: 65
Period size: 11 Copynumber: 8.6 Consensus size: 11
1230157 ATATTAATAA
1230167 TAAATCATTAT
1 TAAATCATTAT
*
1230178 TAGTAATTATTAT
1 TA--AATCATTAT
1230191 TAAATCATTAT
1 TAAATCATTAT
*
1230202 T--ATAATT-T
1 TAAATCATTAT
1230210 TAAAT-A-TA-
1 TAAATCATTAT
1230218 -AAATCATTAT
1 TAAATCATTAT
1230228 TAAATCATTATT
1 TAAATCATTA-T
*
1230240 ATCAAATCATTAC
1 -T-AAATCATTAT
1230253 TAAATCA
1 TAAATCA
1230260 AATCATGTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
7 4 0.06
8 4 0.06
9 8 0.12
10 2 0.03
11 26 0.39
12 2 0.03
13 11 0.17
14 9 0.14
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (11 bp):
TAAATCATTAT
Found at i:1230202 original size:14 final size:14
Alignment explanation
Indices: 1229966--1230251 Score: 67
Period size: 14 Copynumber: 20.1 Consensus size: 14
1229956 ATTAGTAATA
1229966 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
1229980 AGTATCAAATCATT
1 ATTATTAAATCATT
1229994 ATTA-T-AAT--TT
1 ATTATTAAATCATT
* *
1230004 CATTATT-ACTAATT
1 -ATTATTAAATCATT
*
1230018 ATTACTAAATCATT
1 ATTATTAAATCATT
* *
1230032 ACTATCAAATCATT
1 ATTATTAAATCATT
* *
1230046 AAATATTAATAATAATTT
1 -ATTATT-A-AATCA-TT
* * *
1230064 CATTATT-ATTAATC
1 -ATTATTAAATCATT
*
1230078 ATTACTAAATCATT
1 ATTATTAAATCATT
* *
1230092 ACTATCAAATCATT
1 ATTATTAAATCATT
* *
1230106 AAATATTAATAATAATTTT
1 -ATTATT-A-AATCA--TT
1230125 ATTATTACCAATCATT
1 ATTATTA--AATCATT
* *
1230141 AATATCAAATCATT
1 ATTATTAAATCATT
* * *
1230155 AAATATTAATAATAAATC
1 -ATTATT-A-AAT-CATT
* *
1230173 ATTATT-AGTAATT
1 ATTATTAAATCATT
1230186 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1230200 ATTA-T-AAT-TTT
1 ATTATTAAATCATT
* *
1230211 A-AATATAAA--ATC
1 ATTAT-TAAATCATT
1230223 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1230237 ATTATCAAATCATT
1 ATTATTAAATCATT
1230251 A
1 A
1230252 CTAAATCAAA
Statistics
Matches: 197, Mismatches: 48, Indels: 54
0.66 0.16 0.18
Matches are distributed among these distances:
10 3 0.02
11 7 0.04
12 16 0.08
13 24 0.12
14 83 0.42
15 17 0.09
16 10 0.05
17 17 0.09
18 18 0.09
19 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1230555 original size:550 final size:551
Alignment explanation
Indices: 1229510--1230831 Score: 1784
Period size: 550 Copynumber: 2.4 Consensus size: 551
1229500 ATATTTAAAT
*
1229510 ATTTAATTATTATTAATCATTA-TGAAATCATTA-T-T--AATCATTAAATATTAATAATAATTT
1 ATTTCATTATTATTAATCATTACT-AAATCATTACTATCAAATCATTAAATATTAATAAT-A---
*
1229570 CATTATTAATAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATCATTAT
61 -ATT-TT-AT--T-ATTACTCAATCATTAATATCAAATCATTAAATATTAATAATAAATCATTAT
* *
1229635 TAATAATCATTACTAAATCATTATTATAATTTTAAATATAA-A--AT--A--ATTATTATCAAAT
120 TAGTAATCATTATTAAATCATTATTATAATTTTAAATATAATATTATAAATCATTATTATCAAAT
* * * * *
1229693 CATTAATAAATCAAATCATAACATTATTTTAAGCCAAACCAGTGTTCATGAATGGGTATTAGTTA
185 CATTACTAAATCAAATCATAACATCATTATAAACCAAACCAGTATTC---AATGGGTATTAGTTA
* * *
1229758 TGTAACGAAAATAAGGTTAATTTAACCACACGTCCATTCAAATTTGTTCAAGTCCTCGAATTATA
247 TGTAACGAAAATAAGGTTAATTGAACCACACGTCAATTCAAATATGTTCAAGTCCTCGAATTATA
1229823 AATGTCATATCAATTAGGTCCCTATATTTAAAAAGTCCGCTCGAATAATTTATCGACAAAAATTA
312 AATGTCATATCAATTAGGTCCCTATATTTAAAAAGTCCGCTCGAATAATTTATCGACAAAAATTA
*
1229888 CATAAATTCAACTTCAATGTGAAGATATAAAAATTTATCAAATCTTTAAATATTATTATTCCATA
377 CATAAATTCAACTTCAATGTGAAGATATAAAAATTTATCAAATCATTAAATATTATTATTCCATA
* *
1229953 ATTATTAGTAATAATTATTAAATCATTAGTATCAAATCATTATTATAATTTC-ATTATTACT-A-
442 ATTAATAATAATAATTATTAAATCATTAGTATCAAATCATTATTATAATTTCTATTATTACTAAC
1230015 ATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATA
507 ATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATA
1230060 ATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTT
1 ATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTT
*
1230125 ATTATTAC-CAATCATTAATATCAAATCATTAAATATTAATAATAAATCATTATTAGTAATTATT
66 ATTATTACTCAATCATTAATATCAAATCATTAAATATTAATAATAAATCATTATTAGTAATCATT
1230189 ATTAAATCATTATTATAATTTTAAATATAAAATCATTATTAAATCATTATTATCAAATCATTACT
131 ATTAAATCATTATTATAATTTTAAATAT--AAT-ATTA-TAAATCATTATTATCAAATCATTACT
** * * *
1230254 AAATCAAATCATGTCATCATTATAAATCAAATCAGTATTC-CTGGGTATTAGTTATGTAACGAAA
192 AAATCAAATCATAACATCATTATAAACCAAACCAGTATTCAATGGGTATTAGTTATGTAACGAAA
* *
1230318 ATAGGGTTAATTGAACCACACGTCAATTCAAATATGTTCAAGTCTTCGAATTATAAATGTCATAT
257 ATAAGGTTAATTGAACCACACGTCAATTCAAATATGTTCAAGTCCTCGAATTATAAATGTCATAT
* *
1230383 CAATTAGGTCCCTCTATTTAAAAAGTCCGTTCGAATAATTTATCGACAAAAATTACATAAATTCA
322 CAATTAGGTCCCTATATTTAAAAAGTCCGCTCGAATAATTTATCGACAAAAATTACATAAATTCA
* * *
1230448 ACTTCAATGTGAATATATAATAATTTATCAAATCATTAAATATTATTATTTCATAATTAATAATA
387 ACTTCAATGTGAAGATATAAAAATTTATCAAATCATTAAATATTATTATTCCATAATTAATAATA
1230513 ATAATTATTAAATCATTAGTATCAAATCATTATTATAATTTCATTATTATTAATTATTACTAAAT
452 ATAATTATTAAATCATTAGTATCAAATCATTATTATAATTTC--------T-ATTATTACT-AA-
* *
1230578 CATTATTATTAAATCATTACTATTAAATCATTAAATATTAATAATA
506 CATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATA
* *
1230624 ATTTCATT-TTACTAATCATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTT
1 ATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTT
* *
1230688 ATTATTACTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATT
66 ATTATTAC-------T-C--AATCATTAATATCAAATCATTAAATATTAATAATAAATCATTATT
* * *
1230753 AGTAATCATTATTAAATCATTACTATCAAATCATTAAATAT--TATTAATAAATCATTACTATCA
121 AGTAATCATTATTAAATCATTATTAT--AAT-TTTAAATATAATATT-ATAAATCATTATTATCA
1230816 AATCATTACTAAATCA
182 AATCATTACTAAATCA
1230832 TTACTATCAA
Statistics
Matches: 689, Mismatches: 38, Indels: 68
0.87 0.05 0.09
Matches are distributed among these distances:
543 80 0.12
544 5 0.01
545 3 0.00
547 3 0.00
548 2 0.00
549 4 0.01
550 278 0.40
551 2 0.00
552 2 0.00
553 1 0.00
554 71 0.10
560 9 0.01
562 1 0.00
563 62 0.09
564 51 0.07
572 35 0.05
573 2 0.00
574 67 0.10
576 3 0.00
577 8 0.01
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (551 bp):
ATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTT
ATTATTACTCAATCATTAATATCAAATCATTAAATATTAATAATAAATCATTATTAGTAATCATT
ATTAAATCATTATTATAATTTTAAATATAATATTATAAATCATTATTATCAAATCATTACTAAAT
CAAATCATAACATCATTATAAACCAAACCAGTATTCAATGGGTATTAGTTATGTAACGAAAATAA
GGTTAATTGAACCACACGTCAATTCAAATATGTTCAAGTCCTCGAATTATAAATGTCATATCAAT
TAGGTCCCTATATTTAAAAAGTCCGCTCGAATAATTTATCGACAAAAATTACATAAATTCAACTT
CAATGTGAAGATATAAAAATTTATCAAATCATTAAATATTATTATTCCATAATTAATAATAATAA
TTATTAAATCATTAGTATCAAATCATTATTATAATTTCTATTATTACTAACATTATTACTAAATC
ATTACTATCAAATCATTAAATATTAATAATA
Found at i:1230571 original size:24 final size:24
Alignment explanation
Indices: 1230553--1230599 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1230543 TATTATAATT
1230553 TCATTATTATTAATTATTACTAAA
1 TCATTATTATTAATTATTACTAAA
*
1230577 TCATTATTATTAAATCATTACTA
1 TCATTATTATT-AATTATTACTA
1230600 TTAAATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (24 bp):
TCATTATTATTAATTATTACTAAA
Found at i:1230579 original size:52 final size:54
Alignment explanation
Indices: 1230488--1230596 Score: 141
Period size: 52 Copynumber: 2.0 Consensus size: 54
1230478 AATCATTAAA
* *
1230488 TATTATTATTTCATAATTAATAATAATAATTATTAAATCATTAGTATCAAATCAT
1 TATTATAATTTCATAATTAAT-ATAATAATTACTAAATCATTAGTATCAAATCAT
* * * *
1230543 TATTATAATTTCATTATT-AT-TAATTATTACTAAATCATTATTATTAAATCAT
1 TATTATAATTTCATAATTAATATAATAATTACTAAATCATTAGTATCAAATCAT
1230595 TA
1 TA
1230597 CTATTAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 30 0.62
54 2 0.04
55 16 0.33
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (54 bp):
TATTATAATTTCATAATTAATATAATAATTACTAAATCATTAGTATCAAATCAT
Found at i:1230581 original size:38 final size:37
Alignment explanation
Indices: 1230536--1230655 Score: 113
Period size: 38 Copynumber: 3.2 Consensus size: 37
1230526 CATTAGTATC
1230536 AAATCATTATTATAATTTCATTATTATTAATTATTACT
1 AAATCATTATTATAATTTCATTATTATTAA-TATTACT
* * * *
1230574 AAATCATTATTATTAA-ATCATTACTATTAA-ATCATT
1 AAATCATTATTA-TAATTTCATTATTATTAATATTACT
* *
1230610 AAAT-ATTAATAATAATTTCATT-TTACTAATCATTACT
1 AAATCATT-ATTATAATTTCATTATTATTAAT-ATTACT
*
1230647 AAATTATTA
1 AAATCATTA
1230656 CTATCAAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
35 11 0.17
36 16 0.24
37 9 0.14
38 27 0.41
39 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (37 bp):
AAATCATTATTATAATTTCATTATTATTAATATTACT
Found at i:1230584 original size:14 final size:13
Alignment explanation
Indices: 1230516--1230610 Score: 79
Period size: 14 Copynumber: 7.1 Consensus size: 13
1230506 AATAATAATA
1230516 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1230530 AGTATCAAATCATT
1 ATTAT-AAATCATT
*
1230544 ATTATAATTTCATT
1 ATTATAA-ATCATT
*
1230558 ATTAT---TAATT
1 ATTATAAATCATT
1230568 ATTACTAAATCATT
1 ATTA-TAAATCATT
1230582 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1230596 ACTATTAAATCATT
1 ATTA-TAAATCATT
1230610 A
1 A
1230611 AATATTAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
10 8 0.12
11 1 0.01
13 3 0.04
14 56 0.82
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.47
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:1230609 original size:52 final size:53
Alignment explanation
Indices: 1230506--1230622 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 53
1230496 TTTCATAATT
* * * *
1230506 AATAATAATAATTATTAAATCATTAGTATCAAATCATTATTATAATTTCATT-
1 AATATTAATAATTACTAAATCATTAGTATCAAATCATTACTATAATATCATTA
* * * *
1230558 ATTATTAATTATTACTAAATCATTATTATTAAATCATTACTATTAA-ATCATTA
1 AATATTAATAATTACTAAATCATTAGTATCAAATCATTACTA-TAATATCATTA
1230611 AATATTAATAAT
1 AATATTAATAAT
1230623 AATTTCATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
52 40 0.75
53 13 0.25
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (53 bp):
AATATTAATAATTACTAAATCATTAGTATCAAATCATTACTATAATATCATTA
Found at i:1230656 original size:21 final size:21
Alignment explanation
Indices: 1230632--1230718 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
1230622 TAATTTCATT
1230632 TTACTAATCATTACTAAATTA
1 TTACTAATCATTACTAAATTA
* *
1230653 TTACT-ATCAAATCATTAAA-TA
1 TTACTAATC--ATTACTAAATTA
* * *
1230674 TTAATAATAATT--T-TATTA
1 TTACTAATCATTACTAAATTA
* *
1230692 TTACTAATTATTACTAAATCA
1 TTACTAATCATTACTAAATTA
1230713 TTACTA
1 TTACTA
1230719 TCAAATCATT
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
17 1 0.02
18 13 0.27
20 6 0.12
21 20 0.41
22 9 0.18
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (21 bp):
TTACTAATCATTACTAAATTA
Found at i:1230719 original size:60 final size:59
Alignment explanation
Indices: 1230633--1230859 Score: 346
Period size: 60 Copynumber: 3.8 Consensus size: 59
1230623 AATTTCATTT
* * *
1230633 TACTAATCATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTTATTAT
1 TACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA-ATCATTAT
* *
1230693 TACTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTAT
1 TACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATCATTAT
* * * *
1230752 TAGTAATCATTATTAAATCATTACTATCAAATCATTAAATATTATTAATAAATCATTAC
1 TACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATCATTAT
*
1230811 TATCAAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAA
1 TA-CTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAA
1230860 ATTAATTAAC
Statistics
Matches: 153, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
59 62 0.41
60 91 0.59
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (59 bp):
TACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATCATTAT
Found at i:1230733 original size:119 final size:119
Alignment explanation
Indices: 1230614--1230859 Score: 359
Period size: 119 Copynumber: 2.1 Consensus size: 119
1230604 ATCATTAAAT
* ** * *
1230614 ATTAATAATAATTTCATTTTACTAATCATTACTAAATTATTACTATCAAATCATTAAATATTAAT
1 ATTAATAATAAATTATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT
* * * *
1230679 AATAATTTTATTATTA-CTAATTATTACTAAATCATTACTATCAAATCATTAAAT
66 AATAA-ATCATTACTATCAAATTATTACTAAATCATTACTATCAAATCATTAAAT
* * *
1230733 ATTAATAATAAATTATTATTAGTAATCATTATTAAATCATTACTATCAAATCATTAAATATTATT
1 ATTAATAATAAATTATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT
*
1230798 AATAAATCATTACTATCAAATCATTACTAAATCATTACTATCAAATCATTAAAT
66 AATAAATCATTACTATCAAATTATTACTAAATCATTACTATCAAATCATTAAAT
1230852 ATTAATAA
1 ATTAATAA
1230860 ATTAATTAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 7 0.06
119 106 0.94
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (119 bp):
ATTAATAATAAATTATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT
AATAAATCATTACTATCAAATTATTACTAAATCATTACTATCAAATCATTAAAT
Found at i:1230763 original size:13 final size:11
Alignment explanation
Indices: 1230741--1230848 Score: 58
Period size: 14 Copynumber: 8.9 Consensus size: 11
1230731 ATATTAATAA
*
1230741 TAAATTATTAT
1 TAAATCATTAT
1230752 TAGTAATCATTAT
1 TA--AATCATTAT
1230765 TAAATCATTACT
1 TAAATCATTA-T
1230777 ATCAAATCATTA-
1 -T-AAATCATTAT
* *
1230789 -AATATTATTAA
1 TAA-ATCATTAT
1230800 TAAATCATTACT
1 TAAATCATTA-T
*
1230812 ATCAAATCATTAC
1 -T-AAATCATTAT
1230825 TAAATCATTACT
1 TAAATCATTA-T
1230837 ATCAAATCATTA
1 -T-AAATCATTA
1230849 AATATTAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
9 2 0.03
10 6 0.08
11 25 0.32
12 4 0.05
13 13 0.17
14 27 0.35
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATCATTAT
Found at i:1230785 original size:14 final size:12
Alignment explanation
Indices: 1230756--1230848 Score: 70
Period size: 14 Copynumber: 7.7 Consensus size: 12
1230746 TATTATTAGT
*
1230756 AATCATTA-TTA
1 AATCATTACATA
1230767 AATCATTACTATCA
1 AATCATTAC-AT-A
1230781 AATCATTA-A-A
1 AATCATTACATA
* *
1230791 TATTATTA-ATA
1 AATCATTACATA
1230802 AATCATTACTATCA
1 AATCATTAC-AT-A
1230816 AATCATTAC-TA
1 AATCATTACATA
1230827 AATCATTACTATCA
1 AATCATTAC-AT-A
1230841 AATCATTA
1 AATCATTA
1230849 AATATTAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.12
11 25 0.37
12 2 0.03
13 4 0.06
14 28 0.42
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (12 bp):
AATCATTACATA
Found at i:1231033 original size:21 final size:23
Alignment explanation
Indices: 1230992--1231033 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1230982 TGTAAAAAAA
1230992 ATAAATTCGACGTATTTATAAAG
1 ATAAATTCGACGTATTTATAAAG
1231015 ATAAATTCGAC-TA-TTATAA
1 ATAAATTCGACGTATTTATAA
1231034 TCTTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (23 bp):
ATAAATTCGACGTATTTATAAAG
Found at i:1234080 original size:26 final size:25
Alignment explanation
Indices: 1234058--1234108 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
1234048 ATTTGATATT
1234058 TAATGATTTAATAATAATATGATTTA
1 TAATGA-TTAATAATAATATGATTTA
*
1234084 CTAATGATTACTAATAAT-T-ATTTA
1 -TAATGATTAATAATAATATGATTTA
1234108 T
1 T
1234109 TATAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.04
24 5 0.22
25 1 0.04
26 10 0.43
27 6 0.26
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (25 bp):
TAATGATTAATAATAATATGATTTA
Found at i:1234227 original size:21 final size:20
Alignment explanation
Indices: 1234197--1234256 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
1234187 TTTTATTTTT
1234197 TTAAATATCAAACAAATTTG
1 TTAAATATCAAACAAATTTG
* * *
1234217 TTAATTAATCAATCAAATTTT
1 TTAAAT-ATCAAACAAATTTG
*
1234238 TTAAATATCAAATAAATTT
1 TTAAATATCAAACAAATTT
1234257 AAATATCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAATATCAAACAAATTTG
Found at i:1234281 original size:17 final size:17
Alignment explanation
Indices: 1234220--1234291 Score: 64
Period size: 17 Copynumber: 4.3 Consensus size: 17
1234210 AAATTTGTTA
1234220 ATTAATCAATCAAATTT
1 ATTAATCAATCAAATTT
*
1234237 TTTAAATATCAAAT-AAATTT
1 ATT--A-ATC-AATCAAATTT
1234257 A--AAT--ATCAAATTT
1 ATTAATCAATCAAATTT
1234270 ATTAATCAATCAAATTT
1 ATTAATCAATCAAATTT
1234287 ATTAA
1 ATTAA
1234292 AATTTGTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
12 2 0.05
13 7 0.16
15 5 0.11
16 1 0.02
17 16 0.36
19 1 0.02
20 9 0.20
21 3 0.07
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATCAATCAAATTT
Found at i:1234356 original size:19 final size:20
Alignment explanation
Indices: 1234325--1234364 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1234315 AAATTAAACA
1234325 AAATATATTTTAAAAACAAT
1 AAATATATTTTAAAAACAAT
*
1234345 AAATAT-TTTTAAACACAAT
1 AAATATATTTTAAAAACAAT
1234364 A
1 A
1234365 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATATTTTAAAAACAAT
Found at i:1234370 original size:17 final size:17
Alignment explanation
Indices: 1234318--1234374 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 17
1234308 AGATTATAAA
* *
1234318 TTAAACAAAATA-TATT
1 TTAAACACAATATTTTT
* *
1234334 TTAAAAACAATAAATATTT
1 TTAAACACAAT--ATTTTT
1234353 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
1234370 TTAAA
1 TTAAA
1234375 TGGGAATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 9 0.28
17 10 0.31
18 1 0.03
19 12 0.38
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:1234852 original size:44 final size:44
Alignment explanation
Indices: 1234762--1234852 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
1234752 GTTTAAACAC
* * *
1234762 ACTAACAAATTAATTAAATAATTTTTATACATATAATAACTTTA
1 ACTAACAAACTAATTAAATAATTTTTATAAATATAATAACTATA
* *
1234806 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAAT-A-TATA
1 ACTAACAAACTAATTAAATAA-TTTTTATA-AATATAATAACTATA
1234850 ACT
1 ACT
1234853 TAAACTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 24 0.60
45 9 0.22
46 7 0.17
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (44 bp):
ACTAACAAACTAATTAAATAATTTTTATAAATATAATAACTATA
Found at i:1234883 original size:27 final size:30
Alignment explanation
Indices: 1234836--1234897 Score: 103
Period size: 27 Copynumber: 2.2 Consensus size: 30
1234826 ATTTTTTATA
1234836 TAATATAATATATAACTTAAACTAA-AAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1234865 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1234893 TAATA
1 TAATA
1234898 ATTTATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 16 0.50
28 10 0.31
29 6 0.19
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1234898 original size:21 final size:21
Alignment explanation
Indices: 1234874--1234916 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1234864 CTAATATAAT
1234874 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1234895 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1234916 A
1 A
1234917 ATTAAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1235159 original size:27 final size:27
Alignment explanation
Indices: 1235128--1235179 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1235118 ACTTATTTGT
1235128 CGTTGGTGAGCTACAATCAATTTGAAC
1 CGTTGGTGAGCTACAATCAATTTGAAC
*
1235155 CGTTGGTGAGCTGCAATCAATTTGA
1 CGTTGGTGAGCTACAATCAATTTGA
1235180 GCGTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (27 bp):
CGTTGGTGAGCTACAATCAATTTGAAC
Found at i:1235505 original size:29 final size:29
Alignment explanation
Indices: 1235443--1235505 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1235433 AGGTCGTACA
* * *
1235443 GATGTCATGGCGACCTCCTTCCTCGCCCG
1 GATGCCATGACGACCTCCTTCCTCGCCAG
*
1235472 GATGCCATGACGACTTCCTTCCTCG-CAG
1 GATGCCATGACGACCTCCTTCCTCGCCAG
1235500 GCATGC
1 G-ATGC
1235506 AAAGCTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.14, C:0.38, G:0.24, T:0.24
Consensus pattern (29 bp):
GATGCCATGACGACCTCCTTCCTCGCCAG
Found at i:1235927 original size:2 final size:2
Alignment explanation
Indices: 1235920--1235962 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1235910 CACTTCACAG
* *
1235920 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1235962 T
1 T
1235963 GTTCCCACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:1235939 original size:14 final size:14
Alignment explanation
Indices: 1235920--1235962 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
1235910 CACTTCACAG
*
1235920 TCTCTCTCTCTCTC
1 TCTCTCTTTCTCTC
1235934 TCTCTCTTTCTCTC
1 TCTCTCTTTCTCTC
1235948 TCTCTCTTTCTCTC
1 TCTCTCTTTCTCTC
1235962 T
1 T
1235963 GTTCCCACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (14 bp):
TCTCTCTTTCTCTC
Found at i:1238119 original size:23 final size:24
Alignment explanation
Indices: 1238060--1238119 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
1238050 ATACTTATTG
*
1238060 TTTATTATGATTATTTGAAAAAAT
1 TTTATTATGATTATGTGAAAAAAT
* * * *
1238084 ATTA-TACGTTTATGTGTAAAAAT
1 TTTATTATGATTATGTGAAAAAAT
1238107 TTTATTATG-TTAT
1 TTTATTATGATTAT
1238120 ATTTTCGTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTATTATGATTATGTGAAAAAAT
Found at i:1243039 original size:22 final size:23
Alignment explanation
Indices: 1242991--1243040 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1242981 ATCGTGTTTA
* *
1242991 TATTTTTAAAAAAAATATTAATT
1 TATTTTTAAAAAAAATATAAATC
1243014 TATTTTTAAAAAATAA-A-AAATC
1 TATTTTTAAAAAA-AATATAAATC
1243036 TATTT
1 TATTT
1243041 GTTTAGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 14 0.58
24 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTTTTAAAAAAAATATAAATC
Found at i:1243670 original size:15 final size:15
Alignment explanation
Indices: 1243652--1243694 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1243642 AATCTTTTTA
1243652 TATTTTATCT-AATAT
1 TATTTTAT-TAAATAT
1243667 TATTTTATTAAATAT
1 TATTTTATTAAATAT
*
1243682 TA-ATTATTAAATA
1 TATTTTATTAAATA
1243695 CATAAGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTATTAAATAT
Found at i:1248333 original size:31 final size:31
Alignment explanation
Indices: 1248298--1248370 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
1248288 TTTTAACCTT
1248298 AACTTAAATATATAAATTACAATTTAAAATA
1 AACTTAAATATATAAATTACAATTTAAAATA
1248329 AACTTAAATATATAAATTACAATTTAAAATA
1 AACTTAAATATATAAATTACAATTTAAAATA
1248360 AACTTAAATAT
1 AACTTAAATAT
1248371 TATTAAAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (31 bp):
AACTTAAATATATAAATTACAATTTAAAATA
Found at i:1248372 original size:25 final size:29
Alignment explanation
Indices: 1248298--1248384 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 29
1248288 TTTTAACCTT
1248298 AACTTAAATATATAAATTACAATTTAAAATA
1 AACTT-AATATAT-AATTACAATTTAAAATA
1248329 AACTTAAATATATAAATTACAATTTAAAATA
1 AACTT-AATATAT-AATTACAATTTAAAATA
* * *
1248360 AACTTAA-ATATTATTAAAACTTAAA
1 AACTTAATATATAATTACAATTTAAA
1248385 TATTATAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.21
29 4 0.08
30 2 0.04
31 36 0.68
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (29 bp):
AACTTAATATATAATTACAATTTAAAATA
Found at i:1251462 original size:32 final size:29
Alignment explanation
Indices: 1251394--1251464 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
1251384 TCGTATGTAT
*
1251394 CACACGACAACCTCCATGGTCGCATGAAG
1 CACACGACAACCTCCATGGTCACATGAAG
* * *
1251423 CACACGACGACCTCTATGGTCACATGGAG
1 CACACGACAACCTCCATGGTCACATGAAG
*
1251452 CACACGACGACCT
1 CACACGACAACCT
1251465 GGGGTGCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.14
Consensus pattern (29 bp):
CACACGACAACCTCCATGGTCACATGAAG
Found at i:1254689 original size:16 final size:16
Alignment explanation
Indices: 1254670--1254804 Score: 56
Period size: 16 Copynumber: 7.8 Consensus size: 16
1254660 AAAATAAGTA
1254670 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
**
1254686 AAAATGAACAAAATGGTAAC
1 AAAAT--A-AAAAT-AAAAC
*
1254706 ATAAATAAAAATAAAAT
1 A-AAATAAAAATAAAAC
*
1254723 AAAACAAAAATAAAA-
1 AAAATAAAAATAAAAC
** ** *
1254738 ACAAGGAAAAATGGAAT
1 A-AAATAAAAATAAAAC
* *
1254755 TAAATAAAAAAAGAAAC
1 AAAATAAAAATA-AAAC
*
1254772 AAAAATAAATAATAATAAA
1 -AAAATAAA-AATAA-AAC
1254791 AATAATAAAAATAA
1 AA-AATAAAAATAA
1254805 TATATAATAT
Statistics
Matches: 87, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
15 1 0.01
16 35 0.40
17 5 0.06
18 21 0.24
19 17 0.20
20 4 0.05
21 4 0.05
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:1254698 original size:26 final size:26
Alignment explanation
Indices: 1254626--1254698 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
1254616 CGCACATATG
* *
1254626 AAAATAATAAACA-GAACAACAATAAA
1 AAAATAACAAA-ATGAACAAAAATAAA
* *
1254652 AAAATAATAAAAT-AAGTAAAAATAAA
1 AAAATAACAAAATGAA-CAAAAATAAA
1254678 AATAA-AACAAAATGAACAAAA
1 AA-AATAACAAAATGAACAAAA
1254699 TGGTAACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 3 0.08
26 32 0.82
27 4 0.10
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (26 bp):
AAAATAACAAAATGAACAAAAATAAA
Found at i:1254794 original size:9 final size:9
Alignment explanation
Indices: 1254757--1254806 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
1254747 AATGGAATTA
1254757 AATAAAAA-
1 AATAAAAAT
* *
1254765 AAGAAACAAA
1 AATAAA-AAT
1254775 AATAAATAAT
1 AATAAA-AAT
1254785 AATAAAAAT
1 AATAAAAAT
1254794 AATAAAAAT
1 AATAAAAAT
1254803 AATA
1 AATA
1254807 TATAATATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
8 5 0.14
9 18 0.50
10 13 0.36
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1254996 original size:2 final size:2
Alignment explanation
Indices: 1254989--1255036 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1254979 TAGGTAGTGC
1254989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1255031 AT AT AT
1 AT AT AT
1255037 GTAATAAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1255137 original size:36 final size:34
Alignment explanation
Indices: 1255084--1255164 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 34
1255074 AATTATATAG
* *
1255084 ATATACATATAGTAATATTTTAAAAAGAAAAAAGAT
1 ATATACATATAG-AA-ATATTAAAAAGAAAAAAGAA
* * *
1255120 ATATACATATCA-AAATATTAATAAGACAAATGAA
1 ATATACATAT-AGAAATATTAAAAAGAAAAAAGAA
1255154 ATATACATATA
1 ATATACATATA
1255165 TACATAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 1 0.03
34 25 0.64
35 2 0.05
36 10 0.26
37 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (34 bp):
ATATACATATAGAAATATTAAAAAGAAAAAAGAA
Found at i:1255308 original size:27 final size:26
Alignment explanation
Indices: 1255278--1255366 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
1255268 GTGTAGGTAT
1255278 ATAATATAGTATTAAATAATAATAAAA
1 ATAA-ATAGTATTAAATAATAATAAAA
* *
1255305 ATAAA-A-TAAATAAATAAATAAAATAAA
1 ATAAATAGT-ATTAAAT-AATAATA-AAA
* *
1255332 ATAAAGAGTATGTATAATGATAATAAAA
1 ATAAATAGTAT-TA-AATAATAATAAAA
1255360 ATAAATA
1 ATAAATA
1255367 AATAAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 7 0.14
27 12 0.24
28 11 0.22
29 8 0.16
30 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (26 bp):
ATAAATAGTATTAAATAATAATAAAA
Found at i:1255315 original size:9 final size:9
Alignment explanation
Indices: 1255291--1255336 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
1255281 ATATAGTATT
1255291 AAAT-AATA
1 AAATAAATA
1255299 ATAA-AAATA
1 A-AATAAATA
1255308 AAATAAAT-
1 AAATAAATA
1255316 AAATAAATA
1 AAATAAATA
1255325 AAATAAAATA
1 AAAT-AAATA
1255335 AA
1 AA
1255337 GAGTATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 11 0.33
9 15 0.45
10 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:1255327 original size:22 final size:21
Alignment explanation
Indices: 1255290--1255336 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
1255280 AATATAGTAT
1255290 TAAATAATAATAAAAATAAAA
1 TAAATAATAATAAAAATAAAA
1255311 TAAATAAATAA-ATAAAATAAAA
1 TAAAT-AATAATA-AAAATAAAA
1255333 TAAA
1 TAAA
1255337 GAGTATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAATAATAATAAAAATAAAA
Found at i:1255372 original size:14 final size:14
Alignment explanation
Indices: 1255353--1255379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1255343 GTATAATGAT
1255353 AATAAAAATAAATA
1 AATAAAAATAAATA
1255367 AATAAAAATAAAT
1 AATAAAAATAAAT
1255380 TTATATATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:1255472 original size:12 final size:13
Alignment explanation
Indices: 1255457--1255488 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1255447 TAAACAAAGT
1255457 AATAAAACAAA-A
1 AATAAAACAAACA
1255469 AATAAAACAAACA
1 AATAAAACAAACA
1255482 AATAAAA
1 AATAAAA
1255489 AAATAAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (13 bp):
AATAAAACAAACA
Found at i:1257241 original size:107 final size:107
Alignment explanation
Indices: 1257055--1257262 Score: 362
Period size: 107 Copynumber: 1.9 Consensus size: 107
1257045 TCATTCGTCG
*
1257055 TGAAGTTGAAATCCAATCTAAGAATGAATGTTGCTGGTAGACACGATATCCTTCGTTGTGAAGTT
1 TGAAGTTGAAATCCAATCTAAGAATGAATGTTGCTGGTAGACACGATATCCTTCGTCGTGAAGTT
* *
1257120 GAAATCGTGTATGACCCCTTCGTTGTGAAGTTGAGCTCATCA
66 GAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCTCATCA
* *
1257162 TGAAGTTGAAATCCAATCTAAGGATGAATGTTGCTGGTAGACACGATATCCTTCGTCGTGAATTT
1 TGAAGTTGAAATCCAATCTAAGAATGAATGTTGCTGGTAGACACGATATCCTTCGTCGTGAAGTT
*
1257227 GAAATCGTGGATGACCCATTTGTTGTGAAGTTGAGC
66 GAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGC
1257263 CTCGAATTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 95 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (107 bp):
TGAAGTTGAAATCCAATCTAAGAATGAATGTTGCTGGTAGACACGATATCCTTCGTCGTGAAGTT
GAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCTCATCA
Found at i:1260257 original size:25 final size:25
Alignment explanation
Indices: 1260194--1260257 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
1260184 TTCAATTAAA
1260194 ATTATTATATTATATAATATAGTTACGT
1 ATTA-TATATT-TATAATATAGTTAC-T
1260222 ATTATAT-TTTATAATATA-TATA-T
1 ATTATATATTTATAATATAGT-TACT
1260245 ATATATATATTTA
1 AT-TATATATTTA
1260258 CATCCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 15 0.45
26 2 0.06
27 3 0.09
28 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
ATTATATATTTATAATATAGTTACT
Found at i:1260340 original size:25 final size:24
Alignment explanation
Indices: 1260308--1260356 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1260298 CACAACAACC
*
1260308 AGTGGCCCAAACTACACGTGACCCA
1 AGTGGCCC-AACAACACGTGACCCA
*
1260333 AGTGGCCCACCAACACGTGACCCA
1 AGTGGCCCAACAACACGTGACCCA
1260357 GATTTGGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.31, C:0.39, G:0.20, T:0.10
Consensus pattern (24 bp):
AGTGGCCCAACAACACGTGACCCA
Found at i:1261381 original size:2 final size:2
Alignment explanation
Indices: 1261374--1261402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1261364 ATTAATATTA
1261374 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 A
1261403 ATTTTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1261445 original size:17 final size:17
Alignment explanation
Indices: 1261425--1261459 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1261415 TTCATTTCCC
1261425 TTATATATTTATATATT
1 TTATATATTTATATATT
* *
1261442 TTATTTATTTATTTATT
1 TTATATATTTATATATT
1261459 T
1 T
1261460 ATCTATCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATATTTATATATT
Found at i:1263290 original size:13 final size:13
Alignment explanation
Indices: 1263272--1263326 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
1263262 TGTGTCATAA
* *
1263272 ATTTATGACGCGT
1 ATTTATGACACGC
1263285 ATTTATGACACGC
1 ATTTATGACACGC
*
1263298 ATTTATGACACAC
1 ATTTATGACACGC
* *
1263311 ATTTAAGACGCGC
1 ATTTATGACACGC
1263324 ATT
1 ATT
1263327 GCGTGTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:1270792 original size:72 final size:74
Alignment explanation
Indices: 1270708--1270895 Score: 199
Period size: 72 Copynumber: 2.6 Consensus size: 74
1270698 CTCACCTGAT
* *
1270708 ATTGTTTTTCTTAAGACAGACTTTGTCTCACTTGAGACAGTTTT-ACTCGAAAGAA-G-ATTT-A
1 ATTG-TTTTCTTAAGA-AGATTTTGTCTCGCTTGAGACAGTTTTCACTCGAAAGAAGGCATTTCA
1270769 TTTCACTCAAG
64 TTTCACTCAAG
* * * * *
1270780 ATTGTTTCTCTTAA-AATAAGTTTTGTCTCGCTTGGGGCCGTTTTCACTTGAAAGAAGGCATTTC
1 ATTGTTT-TCTTAAGAA-GA-TTTTGTCTCGCTTGAGACAGTTTTCACTCGAAAGAAGGCATTTC
1270844 ATTTCACTCAAG
63 ATTTCACTCAAG
* * *
1270856 ATTGTTTT-TAAAGAAGATTTTATCTCGCTTGAGATAGTTT
1 ATTGTTTTCTTAAGAAGATTTTGTCTCGCTTGAGACAGTTT
1270896 CCCTTGAAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
70 1 0.01
71 5 0.05
72 29 0.31
73 28 0.30
74 5 0.05
75 7 0.07
76 19 0.20
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (74 bp):
ATTGTTTTCTTAAGAAGATTTTGTCTCGCTTGAGACAGTTTTCACTCGAAAGAAGGCATTTCATT
TCACTCAAG
Found at i:1270883 original size:73 final size:72
Alignment explanation
Indices: 1270747--1270886 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 72
1270737 ACTTGAGACA
* *
1270747 GTTTTACTCGAAAGAAGATTTATTTCACTCAAGATTGTTTCTCTTAAAATAAGTTTTGTCTCGCT
1 GTTTTACTCGAAAGAAGATTTATTTCACTCAAGATTGTTTCTCTTAAAAGAAGTTTTATCTCGCT
1270812 TGGGGCC
66 TGGGGCC
*
1270819 GTTTTCACTTGAAAGAAGGCATTTCATTTCACTCAAGATTG-TT-T-TT-AAAGAAGATTTTATC
1 GTTTT-ACTCGAAAGAA-G-ATTT-ATTTCACTCAAGATTGTTTCTCTTAAAAGAAG-TTTTATC
1270880 TCGCTTG
61 TCGCTTG
1270887 AGATAGTTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
72 11 0.18
73 25 0.42
74 2 0.03
75 6 0.10
76 16 0.27
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (72 bp):
GTTTTACTCGAAAGAAGATTTATTTCACTCAAGATTGTTTCTCTTAAAAGAAGTTTTATCTCGCT
TGGGGCC
Found at i:1270924 original size:37 final size:37
Alignment explanation
Indices: 1270872--1270942 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1270862 TTTAAAGAAG
* * *
1270872 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCCATTGAAACAAA
* *
1270909 ATTTTTTCTCCCTTGAGACAGTTTCTATTGAAAC
1 ATTTTATCTCCCTTGAGACAGTTTCCATTGAAAC
1270943 CTAAACATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCATTGAAACAAA
Found at i:1271006 original size:36 final size:36
Alignment explanation
Indices: 1270959--1271043 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
1270949 ATTGAAAACA
* * *
1270959 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACT-AATTTTGTCTCCCTTAAGACAG
1270995 TTTCCCTTGAAACTAATTTTGTCTCCCTTAAGACAG
1 TTTCCCTTGAAACTAATTTTGTCTCCCTTAAGACAG
*
1271031 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
1271044 ATAAACTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 43 0.98
37 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACTAATTTTGTCTCCCTTAAGACAG
Found at i:1271049 original size:101 final size:101
Alignment explanation
Indices: 1270872--1271070 Score: 301
Period size: 101 Copynumber: 2.0 Consensus size: 101
1270862 TTTAAAGAAG
* *
1270872 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTAT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCTAT
* *
1270937 TGAAACCTAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAAC-GTTCCCTTGAAATGA
* * * *
1270974 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-TAATTTTGTCTCCCTTAAGACAGTTTCTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCTAT
*
1271038 TGAAACATAAACTTTGAAAACGTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACGTTCCCTTGAAA
1271071 CACAAAATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 11 0.12
101 45 0.51
102 32 0.36
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (101 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCTAT
TGAAACATAAACATTGAAAACGTTCCCTTGAAATGA
Found at i:1271246 original size:30 final size:30
Alignment explanation
Indices: 1271177--1271256 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
1271167 GTCTCTCTTG
* *
1271177 AGACAATTTCTCTTGAAACACCAACCTTTG
1 AGACAGTTTCTCTTGAAACACCAACCTTTA
1271207 AGACAGTTTCTCTTGAAACACCAACCTTTA
1 AGACAGTTTCTCTTGAAACACCAACCTTTA
** *
1271237 AGATTGTTTCCCTTGAAACA
1 AGACAGTTTCTCTTGAAACA
1271257 AATTTCGTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (30 bp):
AGACAGTTTCTCTTGAAACACCAACCTTTA
Found at i:1271273 original size:96 final size:97
Alignment explanation
Indices: 1271107--1271291 Score: 273
Period size: 96 Copynumber: 1.9 Consensus size: 97
1271097 TGAAACAGGT
* * ** *
1271107 TTTGAGACAGTTTCCCTTAAAACACCCACATTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTC
1 TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTGTTTCCCTTGAAACAAATTTCGTCTC
* *
1271172 TCTTGAGACAA-TTTCTCTTGAAACACCAACC
66 ACTTGAGACAATTTTCCCTTGAAACACCAACC
* * *
1271203 TTTGAGACAGTTTCTCTTGAAACACCAACCTTTAAGATTGTTTCCCTTGAAACAAATTTCGTCTC
1 TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTGTTTCCCTTGAAACAAATTTCGTCTC
1271268 ACTTGAGACAATTTTCCCTTGAAA
66 ACTTGAGACAATTTTCCCTTGAAA
1271292 TAATAAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 67 0.86
97 11 0.14
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (97 bp):
TTTGAGACAGTTTCCCTTAAAACACCAACATTTAAGATTGTTTCCCTTGAAACAAATTTCGTCTC
ACTTGAGACAATTTTCCCTTGAAACACCAACC
Found at i:1273297 original size:29 final size:30
Alignment explanation
Indices: 1273255--1273325 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1273245 CCCGAAGGAC
* * **
1273255 CTATCCAGATGTCACAAAG-ACCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTCGACAA
1273284 CTATCCATAGGTCACAAAGAACCTCGACAA
1 CTATCCATAGGTCACAAAGAACCTCGACAA
*
1273314 CTTTCCATAGGT
1 CTATCCATAGGT
1273326 GTCGAAGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTCGACAA
Found at i:1274298 original size:20 final size:22
Alignment explanation
Indices: 1274273--1274330 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1274263 TTCCCCTTGA
1274273 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1274293 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1274316 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1274331 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1274396 original size:64 final size:63
Alignment explanation
Indices: 1274318--1274458 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
1274308 TCTTTAACAT
* *
1274318 GTGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACCTTCGATGTTTTCAT-TTTAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACATC-AATTACATTCGATG-TTTCATCTTTAAAG
*
1274380 G
63 A
* * * *
1274381 GATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
1274445 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1274459 ATTGAATATG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 21 0.31
64 45 0.67
65 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:1276605 original size:26 final size:23
Alignment explanation
Indices: 1276545--1276612 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 23
1276535 TATTTATATA
1276545 TTTTATTTATTTATTTATCTTTTC
1 TTTT-TTTATTTATTTATCTTTTC
* *
1276569 TTTTCTT-TTTATTTATTTTTTCC
1 TTTTTTTATTTATTTATCTTTT-C
1276592 TTTAATTTTATTTATTTATCT
1 TTT--TTTTATTTATTTATCT
1276613 ATAATGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 13 0.36
23 6 0.17
24 4 0.11
25 3 0.08
26 10 0.28
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTTTATTTATTTATCTTTTC
Found at i:1277898 original size:48 final size:48
Alignment explanation
Indices: 1277846--1277942 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
1277836 TTTTTAGTTC
*
1277846 ACTTCGGTTTAAGTAATACAATTTCTGAAATGATGGAAATGTTATTAG
1 ACTTCGGTTTAAGTAATACAATTTCTGAAACGATGGAAATGTTATTAG
*
1277894 ACTTCGGTTTAAGTAATACAATTTCTGAAACGGTGGAAATGTTATTAG
1 ACTTCGGTTTAAGTAATACAATTTCTGAAACGATGGAAATGTTATTAG
1277942 A
1 A
1277943 TATACTTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (48 bp):
ACTTCGGTTTAAGTAATACAATTTCTGAAACGATGGAAATGTTATTAG
Found at i:1278912 original size:5 final size:5
Alignment explanation
Indices: 1278902--1278932 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1278892 TTACTGAGAA
*
1278902 TATTG TATTG TATTG TATTG TATTG TCTTG T
1 TATTG TATTG TATTG TATTG TATTG TATTG T
1278933 TTGATTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.03, G:0.19, T:0.61
Consensus pattern (5 bp):
TATTG
Found at i:1283382 original size:75 final size:76
Alignment explanation
Indices: 1283259--1283475 Score: 339
Period size: 76 Copynumber: 2.9 Consensus size: 76
1283249 TAAAACATCT
* * *
1283259 TAAATCCTAATTAAAACACTTAAAA-TTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATATA
1283322 AAAATAATATCC
65 AAAATAATATCC
*
1283334 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAAATAATATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATATAA
1283399 AAATAATATCC
66 AAATAATATCC
* * * *
1283410 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATATAA
1283475 A
66 A
1283476 TATTTAAAAT
Statistics
Matches: 131, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 5 0.04
75 52 0.40
76 74 0.56
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATATAA
AAATAATATCC
Found at i:1283414 original size:13 final size:13
Alignment explanation
Indices: 1283382--1283407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1283372 AATACCTAAA
1283382 ATAAAAATAATAT
1 ATAAAAATAATAT
1283395 ATAAAAATAATAT
1 ATAAAAATAATAT
1283408 CCTAAAACTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATAATAT
Found at i:1285611 original size:5 final size:5
Alignment explanation
Indices: 1285601--1285709 Score: 51
Period size: 5 Copynumber: 20.8 Consensus size: 5
1285591 TGTTCAGAGA
* * ****
1285601 AAAAT AAAAT AAAAT -AAAT AGAAT AAAACT AAAGT TTGCT AAAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAA-AT
* * *
1285648 AAAAT GAAAAT AAAACT -GAAT AAATT GAATAT AAAAT GAAAAT AAAAT
1 AAAAT -AAAAT AAAA-T AAAAT AAAAT -AAAAT AAAAT -AAAAT AAAAT
*
1285696 AAAAT AAAAC AAAA
1 AAAAT AAAAT AAAA
1285710 AATATAACGG
Statistics
Matches: 77, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
4 5 0.06
5 50 0.65
6 21 0.27
7 1 0.01
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1285659 original size:11 final size:11
Alignment explanation
Indices: 1285643--1285704 Score: 76
Period size: 11 Copynumber: 5.8 Consensus size: 11
1285633 AGTTTGCTAA
1285643 AAAATAAAATG
1 AAAATAAAATG
1285654 AAAATAAAACTG
1 AAAATAAAA-TG
*
1285666 --AATAAATTG
1 AAAATAAAATG
*
1285675 AATATAAAATG
1 AAAATAAAATG
1285686 AAAATAAAAT-
1 AAAATAAAATG
1285696 AAAATAAAA
1 AAAATAAAA
1285705 CAAAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.05
10 15 0.34
11 25 0.57
12 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:1292404 original size:20 final size:20
Alignment explanation
Indices: 1292379--1292419 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1292369 GACCTTACTT
*
1292379 TTAGCATGTGTGGTTGTGTG
1 TTAGCATGCGTGGTTGTGTG
1292399 TTAGCATGCGTGGTTGTGTG
1 TTAGCATGCGTGGTTGTGTG
1292419 T
1 T
1292420 GCGTATGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.07, G:0.39, T:0.44
Consensus pattern (20 bp):
TTAGCATGCGTGGTTGTGTG
Found at i:1292431 original size:20 final size:20
Alignment explanation
Indices: 1292381--1292431 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1292371 CCTTACTTTT
*
1292381 AGCATGTGTGGTTGTGTGTT
1 AGCATGTGTGGTTGTGTGTG
*
1292401 AGCATGCGTGGTTGTGTGTG
1 AGCATGTGTGGTTGTGTGTG
* *
1292421 CGTATGTGTGG
1 AGCATGTGTGG
1292432 GGTGGATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.08, G:0.43, T:0.39
Consensus pattern (20 bp):
AGCATGTGTGGTTGTGTGTG
Found at i:1296894 original size:19 final size:19
Alignment explanation
Indices: 1296870--1296923 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
1296860 TGTCTTACGC
*
1296870 CTAACTTAGCCAATCCGGA
1 CTAACTTAGCCGATCCGGA
1296889 CTAACTTAGCCGATCCGGA
1 CTAACTTAGCCGATCCGGA
1296908 CTAACTTAGCCGATCC
1 CTAACTTAGCCGATCC
1296924 ATTAAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (19 bp):
CTAACTTAGCCGATCCGGA
Found at i:1297050 original size:31 final size:32
Alignment explanation
Indices: 1297015--1297102 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 32
1297005 TTTTATTAAG
1297015 TTTAAAGATCATCTTATAATATTT-TGAT-AAA
1 TTTAAAGATCAT-TTATAATATTTCTGATAAAA
* *
1297046 TTTAAAGATCATTTCTTAACATTTCTGATAAAA
1 TTTAAAGATCATTT-ATAATATTTCTGATAAAA
* *
1297079 TGTAACGATCATTTATAATCATTT
1 TTTAAAGATCATTTATAAT-ATTT
1297103 AAAAGATCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.04
31 19 0.40
32 7 0.15
33 19 0.40
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (32 bp):
TTTAAAGATCATTTATAATATTTCTGATAAAA
Found at i:1297102 original size:33 final size:31
Alignment explanation
Indices: 1297017--1297102 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 31
1297007 TTATTAAGTT
*
1297017 TAAAGATCATCTTATAAT-ATTTTGATAAATT
1 TAAAGATCAT-TTATAATCATTTTGATAAATG
*
1297048 TAAAGATCATTTCTTAA-CATTTCTGATAAAATG
1 TAAAGATCATTT-ATAATCATTT-TGAT-AAATG
*
1297081 TAACGATCATTTATAATCATTT
1 TAAAGATCATTTATAATCATTT
1297103 AAAAGATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 2 0.04
31 17 0.37
32 7 0.15
33 20 0.43
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (31 bp):
TAAAGATCATTTATAATCATTTTGATAAATG
Found at i:1299713 original size:25 final size:23
Alignment explanation
Indices: 1299668--1299718 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
1299658 CATTTAATTT
*
1299668 TAATTTTTTTAATAATAAAAATA
1 TAATTTTTTTAATAATAAAAAAA
1299691 TAATTTTTAATTAATAA-AGAAAAAA
1 TAATTTTT--TTAATAATA-AAAAAA
1299716 TAA
1 TAA
1299719 AAAAAGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 15 0.62
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATTTTTTTAATAATAAAAAAA
Found at i:1301901 original size:32 final size:33
Alignment explanation
Indices: 1301813--1301907 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 33
1301803 GTTTGTGCAC
*
1301813 TAAAATAAAAAGTTAGTAA-GTTAATAAGAACAA
1 TAAAATAAAAAGTTAG-AATGTTAGTAAGAACAA
* * *
1301846 TAAAAATAAAAAAGTCAGTATGTTAGTATGAACAA
1 T-AAAAT-AAAAAGTTAGAATGTTAGTAAGAACAA
1301881 TAAAAT-AAAAGTTAGAATGTTAGTAAG
1 TAAAATAAAAAGTTAGAATGTTAGTAAG
1301908 TTAGAAAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
32 18 0.35
33 1 0.02
34 11 0.21
35 22 0.42
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (33 bp):
TAAAATAAAAAGTTAGAATGTTAGTAAGAACAA
Found at i:1302298 original size:29 final size:29
Alignment explanation
Indices: 1302266--1302328 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1302256 ATGGTTAGAA
* *
1302266 TGAAAGAAAATAAAAGTAAGTGGTTAATT
1 TGAAAGAAAATAAAAGTAAGTAGTTAACT
** *
1302295 TGAAATTAAATAAAAGTTAGTAGTTAACT
1 TGAAAGAAAATAAAAGTAAGTAGTTAACT
1302324 TGAAA
1 TGAAA
1302329 TAAATAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (29 bp):
TGAAAGAAAATAAAAGTAAGTAGTTAACT
Found at i:1302329 original size:29 final size:28
Alignment explanation
Indices: 1302273--1302335 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
1302263 GAATGAAAGA
* *
1302273 AAATAAAAGTAAGTGGTTAATTTGAAATT
1 AAATAAAAGTAAGTAGTTAACTTGAAA-T
*
1302302 AAATAAAAGTTAGTAGTTAACTTGAAAT
1 AAATAAAAGTAAGTAGTTAACTTGAAAT
1302330 AAATAA
1 AAATAA
1302336 CATAGCAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (28 bp):
AAATAAAAGTAAGTAGTTAACTTGAAAT
Found at i:1303680 original size:61 final size:60
Alignment explanation
Indices: 1303613--1303804 Score: 147
Period size: 61 Copynumber: 3.1 Consensus size: 60
1303603 TATAACTTGG
1303613 TGTTGAAGACGAAACTGCTCATCCATGTTGAAGAGATATGATCGCTTTCAGATAAATTATT
1 TGTTGAAGACGAAACTGCTCATCCATGTTGAAGAGAT-TGATCGCTTTCAGATAAATTATT
* * * * * * * ** ** * *
1303674 TGTTGAAGATGACGA-TGTTCCTTCTTGTTGAAGA-ATTCAGCTCAATATGGAGATAATTTA-G
1 TGTTGAAGACGA-AACTGCTCATCCATGTTGAAGAGATT--GATCGCT-TTCAGATAAATTATT
** * * *
1303735 TGTTGAAGACGACTCTGCTCATCCATGTTGAAGAGATCTGGTTGCTTTCAGATAAATTGTT
1 TGTTGAAGACGAAACTGCTCATCCATGTTGAAGAGAT-TGATCGCTTTCAGATAAATTATT
1303796 TGTTGAAGA
1 TGTTGAAGA
1303805 TGACGTTGTT
Statistics
Matches: 94, Mismatches: 29, Indels: 16
0.68 0.21 0.12
Matches are distributed among these distances:
59 1 0.01
60 11 0.12
61 68 0.72
62 13 0.14
63 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (60 bp):
TGTTGAAGACGAAACTGCTCATCCATGTTGAAGAGATTGATCGCTTTCAGATAAATTATT
Found at i:1303782 original size:122 final size:122
Alignment explanation
Indices: 1303558--1303978 Score: 556
Period size: 122 Copynumber: 3.5 Consensus size: 122
1303548 GAATATTCAG
* * * * *
1303558 AGATGACAATGTTCCTTCAT-GTTGAGGACTTCGGGTCAATCTAGATATAACTTGGTGTTGAAGA
1 AGATGACGATGTTCCTTC-TCGTTGAGGAATTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
** * * *
1303622 CGAAACTGCTCATCCATGTTGAAGAGATATGATCGCTTTCAGATAAATTATTTGTTGA
65 CGACTCTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGA
* * * * * *
1303680 AGATGACGATGTTCCTTCTTGTTGAAGAATTCAGCTCAATATGGAGATAATTTAGTGTTGAAGAC
1 AGATGACGATGTTCCTTCTCGTTGAGGAATTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAC
*
1303745 GACTCTGCTCATCCATGTTGAAGAGATCTGGTTGCTTTCAGATAAATTGTTTGTTGA
66 GACTCTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGA
* * * *
1303802 AGATGACGTTGTTCCTTCTCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTGAATAT
1 AGATGACGATGTTCCTTCTCGTTGAGGAATTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAC
* * * * *
1303867 GACTCTTCACATCCGTGTTGAAGAGATCTGGTCGCTTTCAGATAAGTTGTTTATTGA
66 GACTCTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGA
* * * *
1303924 AGATGAAGTTGTTCCTTATCGTTGAGGAATTTGGGTCAATCTGGAGATAATTTGG
1 AGATGACGATGTTCCTTCTCGTTGAGGAATTCGGGTCAATCTGGAGATAATTTGG
1303979 AGACAACACA
Statistics
Matches: 262, Mismatches: 36, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
121 1 0.00
122 261 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (122 bp):
AGATGACGATGTTCCTTCTCGTTGAGGAATTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAC
GACTCTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGA
Found at i:1303826 original size:61 final size:61
Alignment explanation
Indices: 1303639--1303948 Score: 179
Period size: 61 Copynumber: 5.1 Consensus size: 61
1303629 GCTCATCCAT
* * * * *
1303639 GTTGAAGAGATATGATCGCTTTCAGATAAATTATTTGTTGAAGATGACGATGTTCCTTCTT
1 GTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTC
* * ** ** * * * * *
1303700 GTTGAAGA-ATTCAGCTCAATATGGAGAT-AATT-TAGTGTTGAAGACGAC-TCTGCTCATCCAT
1 GTTGAAGAGA-TCTGGTCGCT-TTCAGATAAATTGT-TTGTTGAAGATGACGT-TGTTCCTTC-T
1303761 -
61 C
*
1303761 GTTGAAGAGATCTGGTTGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTC
1 GTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTC
* * * ** ** * * * * *
1303822 GTTGAGGAAATCGGGTCAATCTGGAGATAATTTG-GTGTTGAATATGAC--TCTTCACATC-C
1 GTTGAAGAGATCTGGTCGCT-TTCAGATAAATTGTTTGTTGAAGATGACGTTGTTC-CTTCTC
* * * *
1303881 GTGTTGAAGAGATCTGGTCGCTTTCAGATAAGTTGTTTATTGAAGATGAAGTTGTTCCTTATC
1 --GTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTC
1303944 GTTGA
1 GTTGA
1303949 GGAATTTGGG
Statistics
Matches: 178, Mismatches: 53, Indels: 36
0.67 0.20 0.13
Matches are distributed among these distances:
59 5 0.03
60 21 0.12
61 126 0.71
62 21 0.12
63 5 0.03
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (61 bp):
GTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTC
Found at i:1304203 original size:220 final size:221
Alignment explanation
Indices: 1303814--1304493 Score: 990
Period size: 220 Copynumber: 3.1 Consensus size: 221
1303804 ATGACGTTGT
* * * * *
1303814 TCCTTCTCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTGAATATGACTCTTCACAT
1 TCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTACTCAT
* * *
1303879 CCGTGTTGAAGAGATCTGGTCGCTTTCAGATAAGTTGTTTATTGAAGATGAAGTTGTTCCTTATC
66 CCGTGTTGAAGAGATCTGGTCACTTTCAGATAAATTGTTTGTTGAAGATGAAGTTGTTCCTTATC
* *
1303944 GTTGAGGAA-TTTGGGTCAATCTGGAGATAATTTGGAGACAACACAGTTCTTTCGCGTTGAGGAA
131 GTTGAGGAAGTTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCTTTCGCGTTGAGGAA
*
1304008 GTCTGATTGTCTGAGGATGACACTAC
196 GTCTGATTGTCTGAGGATGACACTGC
* *
1304034 TCCTTCACGTTGAGGAGATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTACTCAT
1 TCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTACTCAT
* * *
1304099 CCGTGTTGAAGAGATCTGGTCACTTTCAGATAAATTGTTTGTTGAAGAAGATGATGTTCCTTATC
66 CCGTGTTGAAGAGATCTGGTCACTTTCAGATAAATTGTTTGTTGAAGATGAAGTTGTTCCTTATC
* * *
1304164 GTTGAGGAAGTTGGGGT-AATTTGGAGATAATTTGGAGACAACACGGTTCTTTCACGTTGAGGAA
131 GTTGAGGAAGTTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCTTTCGCGTTGAGGAA
* **
1304228 GTCTGATTGTCTGAGAATGTTACTGC
196 GTCTGATTGTCTGAGGATGACACTGC
* * *
1304254 TCCTTCGCGTTGAGGAGATCGGGTCAATCTAGAGATAATTTGGTGTTAAAGATAACTCTACTCAT
1 TCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTACTCAT
* * * *
1304319 CCGTGTTGAAGAGATTTGGTCATTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTTTC
66 CCGTGTTGAAGAGATCTGGTCACTTTCAGATAAATTGTTTGTTGAAGATGAAGTTGTTCCTTATC
* * *
1304384 GTTGAGGAAG-TCGGCTCAATCTGGAGATAATTTGGAGACATCATGGTT-TCTTCGCGTTGAGGA
131 GTTGAGGAAGTTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCT-TTCGCGTTGAGGA
* * *
1304447 AGTCTGATTATTTGAGGATGACATTGC
195 AGTCTGATTGTCTGAGGATGACACTGC
* *
1304474 TCATTTGCGTTGAGGAGATC
1 TCCTTCGCGTTGAGGAGATC
1304494 TGGTTGGTAG
Statistics
Matches: 412, Mismatches: 45, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
219 5 0.01
220 401 0.97
221 6 0.01
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (221 bp):
TCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTACTCAT
CCGTGTTGAAGAGATCTGGTCACTTTCAGATAAATTGTTTGTTGAAGATGAAGTTGTTCCTTATC
GTTGAGGAAGTTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCTTTCGCGTTGAGGAA
GTCTGATTGTCTGAGGATGACACTGC
Found at i:1304589 original size:139 final size:138
Alignment explanation
Indices: 1304406--1304830 Score: 490
Period size: 139 Copynumber: 3.1 Consensus size: 138
1304396 GGCTCAATCT
* * * *
1304406 GGAGATAATTTGGAGACATCATGGTTTCTTCGCGTTGAGGAAGTCTGATTATTTGAGGATGACAT
1 GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTTT-AGGATGACAT
* * * * * *
1304471 TGCTCATTTGCGTTGAGGAGATCTGGTTGGTAGACGACATTTTTCTTTCGTGTTGAAGAAGTCTA
65 TGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTTTTCCTTCGTGTTGAGGAAGTCTA
*
1304536 GCCTTTTTA
130 GCCGTTTTA
* * * * * *
1304545 GGAGATAATTTGGAGACAACAGGGTTCCTTCACGTTGATGAAGTCTGATTGTCTAAGGATGAAAC
1 GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGT-TTAGGATGACAT
* * * ** * *
1304610 TGCTCCTTCGAGTTGAGGAGATATGGTCGGCGGAATACATTTTTCCTTCATTTTGAGGAAGTCTA
65 TGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTTTTCCTTCGTGTTGAGGAAGTCTA
1304675 GCCGTTTTA
130 GCCGTTTTA
* * * *
1304684 GGAGATAATTTGGAGATAACACGGTTCGTTCGCGTTGAGGAAGTCTGGTTGTCTTATGATGACAT
1 GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGT-TTAGGATGACAT
* * * * * * * *
1304749 TGCTCCTTCGCTTTGAGGATATCTGGCCAGTGGGCGACATTTTTCCTTCGTGATGAGGAAATATA
65 TGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTTTTCCTTCGTGTTGAGGAAGTCTA
*
1304814 GTCGTTTTA
130 GCCGTTTTA
1304823 GGAGATAA
1 GGAGATAA
1304831 ATATTCTTTG
Statistics
Matches: 236, Mismatches: 49, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
139 235 1.00
140 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (138 bp):
GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTTTAGGATGACATT
GCTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTTTTCCTTCGTGTTGAGGAAGTCTAG
CCGTTTTA
Found at i:1313104 original size:32 final size:32
Alignment explanation
Indices: 1313016--1313113 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 32
1313006 TTAGTTTTTG
1313016 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTAAGAA
* * *
1313049 TAATAAAAATAAAAAAGTCAGAATGTTAGTATGAA
1 CAAT-AAAAT--AAAAGTTAGAATGTTAGTAAGAA
1313084 CAATAAAATAAAAGTTAGAATGTTAGTAAG
1 CAATAAAATAAAAGTTAGAATGTTAGTAAG
1313114 TTAGAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
32 19 0.35
33 3 0.05
34 12 0.22
35 17 0.31
36 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTAAGAA
Found at i:1313258 original size:113 final size:115
Alignment explanation
Indices: 1313129--1313425 Score: 492
Period size: 113 Copynumber: 2.6 Consensus size: 115
1313119 AAATTTAGCT
*
1313129 GTTAGTGGTTAGCAGAGTCTGGACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
1 GTTAGTGGTTAGCAGAGTCTGGACCATAATAATGTGGATCTTACCCCAGATCGGGTCACCACAAG
*
1313194 GTCAAATCGAATTATGCAAACAAATATATAAAAATAAAATAAAAT-AA-A
66 GTCAAATCGAATAATGCAAACAAATATATAAAAATAAAATAAAATAAATA
1313242 GTTAGTGGTTAGCAGAGTCTGGACCATAATAATGTGGATCTTACCCCAGATCGGGTCACCACAAG
1 GTTAGTGGTTAGCAGAGTCTGGACCATAATAATGTGGATCTTACCCCAGATCGGGTCACCACAAG
*
1313307 GTCAAATCGAATAATGTAAACAAATATATAAAAATAAAATAAAATAAAATA
66 GTCAAATCGAATAATGCAAACAAATATATAAAAATAAAATAAAAT-AAATA
* * * *
1313358 GTTAGTGGTTAGTAGAGT-TCGAACCATAATAATGTTGATCTTACCCCAGATCGAGTCACCACAA
1 GTTAGTGGTTAGCAGAGTCT-GGACCATAATAATGTGGATCTTACCCCAGATCGGGTCACCACAA
1313422 GGTC
65 GGTC
1313426 GAGGAATAAG
Statistics
Matches: 173, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
113 107 0.62
115 3 0.02
116 63 0.36
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (115 bp):
GTTAGTGGTTAGCAGAGTCTGGACCATAATAATGTGGATCTTACCCCAGATCGGGTCACCACAAG
GTCAAATCGAATAATGCAAACAAATATATAAAAATAAAATAAAATAAATA
Found at i:1313451 original size:4 final size:4
Alignment explanation
Indices: 1313442--1313466 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1313432 TAAGAGAAAC
1313442 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
1313467 CCAGTGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1313503 original size:29 final size:29
Alignment explanation
Indices: 1313468--1313525 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1313458 AATAAATAAC
1313468 CAGTGGTTAGA-ATGCAAGAAAATAAAAGT
1 CAGTGGTTA-ATATGCAAGAAAATAAAAGT
* *
1313497 CAGTGGTTAATGTGCAATAAAATAAAAGT
1 CAGTGGTTAATATGCAAGAAAATAAAAGT
1313526 TTGTAGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (29 bp):
CAGTGGTTAATATGCAAGAAAATAAAAGT
Found at i:1313534 original size:29 final size:29
Alignment explanation
Indices: 1313480--1313535 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1313470 GTGGTTAGAA
*
1313480 TGCAAGAAAATAAAAGTCAGTGGTTAATG
1 TGCAAGAAAATAAAAGTCAGTAGTTAATG
* **
1313509 TGCAATAAAATAAAAGTTTGTAGTTAA
1 TGCAAGAAAATAAAAGTCAGTAGTTAA
1313536 CTTGAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (29 bp):
TGCAAGAAAATAAAAGTCAGTAGTTAATG
Found at i:1313544 original size:29 final size:29
Alignment explanation
Indices: 1313486--1313546 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1313476 AGAATGCAAG
* *
1313486 AAAATAAAAGTCAGTGGTTAATGTGCAAT
1 AAAATAAAAGTCAGTAGTTAATGTGAAAT
**
1313515 AAAATAAAAGTTTGTAGTTAACT-TGAAAT
1 AAAATAAAAGTCAGTAGTTAA-TGTGAAAT
1313544 AAA
1 AAA
1313547 TAACATAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (29 bp):
AAAATAAAAGTCAGTAGTTAATGTGAAAT
Found at i:1316111 original size:20 final size:20
Alignment explanation
Indices: 1316082--1316119 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1316072 TTTTAGAGTG
1316082 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1316102 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1316120 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1316188 original size:45 final size:46
Alignment explanation
Indices: 1316139--1316229 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
1316129 AAACATCAAA
* *
1316139 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
1316184 TGCATTTGATGCATCGATGCACAAGATCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1316230 GCTTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1316286 original size:110 final size:110
Alignment explanation
Indices: 1316080--1316290 Score: 279
Period size: 110 Copynumber: 1.9 Consensus size: 110
1316070 TTTTTTAGAG
* *
1316080 TGATGCACCGATGCACCAATCCATGCATCGATGCACCAATTAATTTTTCAAACATCAAATGCATT
1 TGATGCACCGATGCACAAATCCATGCATCGATGCACCAATGAATTTTTCAAACATCAAATGCATT
*
1316145 TTATGCATCGATGCACATACCATGCATCGATGCACTCAGTGCATT
66 TTATGCATCGATGCACATACCATGCACCGATGCACTCAGTGCATT
* ** *
1316190 TGATGCATCGATGCACAAGAT-CATGCATCGATGCACTC-A-GGCTTTTTCAAAACATCGAATGC
1 TGATGCACCGATGCACAA-ATCCATGCATCGATGCAC-CAATGAATTTTTC-AAACATCAAATGC
1316252 ATTTTATGCATCGATGCAC-T-CTCAGTGCACCGATGCACT
63 ATTTTATGCATCGATGCACATAC-CA-TGCACCGATGCACT
1316291 GAGAGCCCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
108 1 0.01
109 9 0.10
110 76 0.85
111 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (110 bp):
TGATGCACCGATGCACAAATCCATGCATCGATGCACCAATGAATTTTTCAAACATCAAATGCATT
TTATGCATCGATGCACATACCATGCACCGATGCACTCAGTGCATT
Found at i:1318558 original size:15 final size:15
Alignment explanation
Indices: 1318538--1318567 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1318528 TTAAGCAAAA
1318538 ATCTTCTTGTCAACT
1 ATCTTCTTGTCAACT
1318553 ATCTTCTTGTCAACT
1 ATCTTCTTGTCAACT
1318568 GATTTATTAC
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:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
ATCTTCTTGTCAACT
Found at i:1320399 original size:138 final size:137
Alignment explanation
Indices: 1320143--1320442 Score: 354
Period size: 138 Copynumber: 2.2 Consensus size: 137
1320133 GTGAGGACTT
* * * ** *
1320143 AATTGAAAATTTC-CCTAAATTAAAGGACTAAAGTGATATTAAACCTAATATGGATGCTCTAGTA
1 AATTG-AAATTTCTCCT-AATTAAAGGACTAAAGTCAAATTAAACCTAAAACAGAGGCTCTAGTA
* ***
1320207 TTAAAACCTAACCAAATTTAGACAATTATTGAATCGAATAATCATTTTGGAACCTCGGGAAAAAA
64 TTAAAACCTAACCAAATTTAGACAATTATTGAATCGAATAATCAATTCAAAACCTCGGGAAAAAA
1320272 CAAGAACCA
129 CAAGAACCA
1320281 AATTGAAATTTCTCCTGAATTAAAGGACTAAAGTCAAATTAAACCTAAAACAGAGGCTCTAGTAT
1 AATTGAAATTTCTCCT-AATTAAAGGACTAAAGTCAAATTAAACCTAAAACAGAGGCTCTAGTAT
* * * *
1320346 TAAAAGCTAA-CAAATTTTA-ACCAATTATTGAATTGAATAATTAATTCAAAACCTTGGGAAAAA
65 TAAAACCTAACCAAA-TTTAGA-CAATTATTGAATCGAATAATCAATTCAAAACCTCGGGAAAAA
** *
1320409 GTAAGGACCA
128 ACAAGAACCA
* *
1320419 AATTAAAAATTCTCCTAAGTTAAA
1 AATTGAAATTTCTCCTAA-TTAAA
1320443 AGAGTTTAGG
Statistics
Matches: 138, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
137 14 0.10
138 124 0.90
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (137 bp):
AATTGAAATTTCTCCTAATTAAAGGACTAAAGTCAAATTAAACCTAAAACAGAGGCTCTAGTATT
AAAACCTAACCAAATTTAGACAATTATTGAATCGAATAATCAATTCAAAACCTCGGGAAAAAACA
AGAACCA
Found at i:1320632 original size:30 final size:29
Alignment explanation
Indices: 1320553--1320632 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
1320543 ATATAAGTGT
* *
1320553 TAAATTATAAAAATACAAAAAATTGAAGGAC
1 TAAATTAT--AAATACAAAAAATTAAAGCAC
* **
1320584 TAAAATATAAATGTAAAAAATTAAATAGCA-
1 TAAATTATAAATACAAAAAATT-AA-AGCAC
1320614 TAAATTATAAATACAAAAA
1 TAAATTATAAATACAAAAA
1320633 TTTTAAAGGG
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
29 12 0.31
30 17 0.44
31 10 0.26
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (29 bp):
TAAATTATAAATACAAAAAATTAAAGCAC
Found at i:1329261 original size:20 final size:21
Alignment explanation
Indices: 1329236--1329289 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
1329226 TTCCTTTAAA
1329236 TAGTATCGATACTC-G-GGGT
1 TAGTATCGATACTCAGAGGGT
1329255 CTAGTATCGATACTCAGAGGGT
1 -TAGTATCGATACTCAGAGGGT
*
1329277 TGGTATCGATACT
1 TAGTATCGATACT
1329290 GAGGCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 14 0.45
21 13 0.42
22 4 0.13
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (21 bp):
TAGTATCGATACTCAGAGGGT
Found at i:1331350 original size:17 final size:18
Alignment explanation
Indices: 1331330--1331369 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1331320 TAAAGTCACT
*
1331330 TTTTCAC-AATTCGTGCC
1 TTTTCACGAATACGTGCC
*
1331347 TTTTCACGAATAGGTGCC
1 TTTTCACGAATACGTGCC
1331365 TTTTC
1 TTTTC
1331370 GGGATGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (18 bp):
TTTTCACGAATACGTGCC
Found at i:1333919 original size:24 final size:24
Alignment explanation
Indices: 1333809--1333921 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
1333799 ATAATTCACA
* *
1333809 TCAAGTATCATATCAAAATCCAGG
1 TCAAGTATCATATCAGAATCCATG
* *
1333833 TCAAGTATCATATCAAAATCCAAG
1 TCAAGTATCATATCAGAATCCATG
*
1333857 TCAAGTATCAGATCAGAATCCATG
1 TCAAGTATCATATCAGAATCCATG
*
1333881 TC-AGATATCATATCAGAAGCCATG
1 TCAAG-TATCATATCAGAATCCATG
* *
1333905 TCAAGTATTAGATCAGA
1 TCAAGTATCATATCAGA
1333922 CATCAAATCA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
TCAAGTATCATATCAGAATCCATG
Found at i:1336372 original size:63 final size:63
Alignment explanation
Indices: 1336295--1336473 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 63
1336285 GAATTAAATT
*
1336295 GAACATCGAATGCATTTCATGCATCGATGCACACCATGCACCGATGCACT-GAGGAT-TTTATAA
1 GAACATCGAATGCATTTGATGCATCGATGCACACCATGCACCGATGCACTCG-GGATATTT-TAA
* *
1336358 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCGGGCTATTTTAA
1 GAACATCGAATGCATTTGATGCATCGATGCA-CA-CCATGCACCGATGCACTCGGGATATTTTAA
* * *
1336423 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCATTTGATGCATCGATGCACAC-CA-TGCACCGATGCACT
1336474 AAGGTTCCAA
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
62 1 0.01
63 32 0.31
64 44 0.43
65 22 0.21
66 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (63 bp):
GAACATCGAATGCATTTGATGCATCGATGCACACCATGCACCGATGCACTCGGGATATTTTAA
Found at i:1336441 original size:64 final size:64
Alignment explanation
Indices: 1336247--1336453 Score: 230
Period size: 64 Copynumber: 3.2 Consensus size: 64
1336237 ATTTTCAGAG
* * ** *
1336247 TGATGCACCGATGCACCAATCCATGCATCGATGCACATGA--ATTAAAT-TGAACATCGAATGCA
1 TGATGCATCGATGCACC-A-CCATGCACCGATGCAC-TGAGGATTTTATAAGAACATCGAATGCA
1336309 TT
63 TT
*
1336311 TCATGCATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATT
1 TGATGCATCGATGCACCACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATT
* *
1336374 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-TAA-AACATCGAATGCA
1 TGATGCATCGATGCACCA-CCATGCACCGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCA
*
1336436 CT
63 TT
1336438 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1336454 TCTTAGTGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
60 3 0.02
61 15 0.12
62 6 0.05
63 31 0.25
64 45 0.36
65 22 0.17
66 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (64 bp):
TGATGCATCGATGCACCACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATT
Found at i:1336453 original size:17 final size:19
Alignment explanation
Indices: 1336425--1336473 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1336415 TATTTTAAAA
1336425 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1336443 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1336462 CACCGATGCACT
1 CATCGATGCACT
1336474 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.