Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 9
Found at i:303741 original size:3 final size:3
Alignment explanation
Indices: 303733--303778 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
303723 GTATGAGTTT
303733 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
303779 GGCTTATGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:305745 original size:3 final size:3
Alignment explanation
Indices: 305739--305806 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
305729 TCATTTAAAT
** * *
305739 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
305787 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
305807 AATATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:306230 original size:11 final size:11
Alignment explanation
Indices: 306214--306249 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
306204 TGCAAAACAA
306214 AAAAAAAAGAG
1 AAAAAAAAGAG
* *
306225 AGAAAAAAGAA
1 AAAAAAAAGAG
306236 AAAAAAAAGAG
1 AAAAAAAAGAG
306247 AAA
1 AAA
306250 GCACGAACAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:307172 original size:3 final size:3
Alignment explanation
Indices: 307153--307217 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
307143 TTATTTCCTT
* * *
307153 TTA TTT TTA TTA TTTA TTA TTA TTA TTT TTA TTG TT- TTAA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
307199 TT- TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
307218 TATAAAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:307250 original size:18 final size:19
Alignment explanation
Indices: 307225--307267 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
307215 ATTTATAAAA
307225 ATAAATAAATATATATATAT
1 ATAAATAAATA-ATATATAT
307245 ATATAATAAATAATATATAT
1 ATA-AATAAATAATATATAT
307265 ATA
1 ATA
307268 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATAAATAATATATAT
Found at i:307521 original size:27 final size:25
Alignment explanation
Indices: 307491--307546 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
307481 TCCTTTTCTA
*
307491 ATATTCTAAATAATAAATATTTTATTT
1 ATATTCTAAAT-ATAAATATATT-TTT
* *
307518 ATATTTTATATATAAATATATTTTT
1 ATATTCTAAATATAAATATATTTTT
307543 ATAT
1 ATAT
307547 AATTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 10 0.38
27 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTCTAAATATAAATATATTTTT
Found at i:307547 original size:16 final size:17
Alignment explanation
Indices: 307517--307558 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
307507 ATATTTTATT
307517 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
307534 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
307550 TATAATTTT
1 TAT-ATTTT
307559 GAAATAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:307552 original size:26 final size:26
Alignment explanation
Indices: 307503--307553 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
307493 ATTCTAAATA
* *
307503 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
307529 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
307554 ATTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:312191 original size:7 final size:7
Alignment explanation
Indices: 312147--312198 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
312137 CTCATCCAGC
312147 AAAGAAA
1 AAAGAAA
*
312154 GAAGAAA
1 AAAGAAA
312161 AAA-AAA
1 AAAGAAA
*
312167 AAACAAA
1 AAAGAAA
312174 ACAA-AAA
1 A-AAGAAA
312181 AAAGAAA
1 AAAGAAA
312188 AAAGGAAA
1 AAA-GAAA
312196 AAA
1 AAA
312199 TTGAATCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 8 0.21
7 22 0.56
8 9 0.23
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:314203 original size:92 final size:92
Alignment explanation
Indices: 314040--314299 Score: 448
Period size: 92 Copynumber: 2.8 Consensus size: 92
314030 AAGGAGACCC
*
314040 AATAGCATCTTCTCGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
314105 TCATTGAATTTGGAAGATGAATGTGCT
66 TCATTGAATTTGGAAGAGGAATGTGCT
* *
314132 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
314197 TTATTGAATTTGGAAGAGGAATGTGCT
66 TCATTGAATTTGGAAGAGGAATGTGCT
* *
314224 AATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGTAGGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
314289 TCATTGGAATT
66 TCATT-GAATT
314300 AAAAGATGAA
Statistics
Matches: 157, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 152 0.97
93 5 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (92 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
TCATTGAATTTGGAAGAGGAATGTGCT
Found at i:316706 original size:22 final size:22
Alignment explanation
Indices: 316681--316757 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
316671 ATCTACATTC
316681 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
316703 TTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
316725 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
316747 TTCAAAGATGA
1 TTCAAAGATGA
316758 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:317623 original size:76 final size:76
Alignment explanation
Indices: 317436--318528 Score: 1992
Period size: 76 Copynumber: 14.4 Consensus size: 76
317426 CTATTTCCCA
*
317436 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
317500 AGCCTTCGGGT
66 AGCCTTCGGGT
317511 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
317576 AGCCTTCGGGT
66 AGCCTTCGGGT
*
317587 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
317652 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
317663 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
317728 AGCCTTAGGGT
66 AGCCTTCGGGT
*
317739 CATCTGTAAGTCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
317804 AGCCTTCGGGT
66 AGCCTTCGGGT
*
317815 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
317880 AGCCTTAGGGT
66 AGCCTTCGGGT
*
317891 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGCTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
317956 AGCCTTAGGGT
66 AGCCTTCGGGT
*
317967 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAGAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
318032 AGCCTTCGGGT
66 AGCCTTCGGGT
*
318043 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
318107 AGCCTTAGGGT
66 AGCCTTCGGGT
318118 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
318183 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
318194 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
318259 AGCCTTCGGGT
66 AGCCTTCGGGT
318270 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
318335 AGCCTTCGGGT
66 AGCCTTCGGGT
318346 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
318411 AGCCTTCAGGT
66 AGCCTTCGGGT
318422 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
318487 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
318499 CATCTGTAAGCCCTTCAGTGCCTGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
318529 TCAACATTTC
Statistics
Matches: 985, Mismatches: 30, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
75 135 0.14
76 811 0.82
77 39 0.04
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:318666 original size:3 final size:3
Alignment explanation
Indices: 318660--318724 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
318650 TCATTTAAAT
** *
318660 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
318708 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
318725 AATATTACAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:318682 original size:12 final size:12
Alignment explanation
Indices: 318665--318731 Score: 71
Period size: 12 Copynumber: 5.3 Consensus size: 12
318655 TAAATTTATT
318665 ATTATTATTAAA
1 ATTATTATTAAA
**
318677 ATTATTATTATT
1 ATTATTATTAAA
*
318689 ATTATTATTATA
1 ATTATTATTAAA
*
318701 ATTATTATTATAT
1 ATTATTATTA-AA
318714 ATTATTTATTAAA
1 ATTA-TTATTAAA
318727 TATTA
1 -ATTA
318732 CAAAGCCCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 31 0.67
13 5 0.11
14 10 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:318692 original size:24 final size:24
Alignment explanation
Indices: 318660--318731 Score: 108
Period size: 24 Copynumber: 2.9 Consensus size: 24
318650 TCATTTAAAT
318660 TTATTATTATTATTAAAATTATTA
1 TTATTATTATTATTAAAATTATTA
*
318684 TTATTATTATTATTATAATTATTA
1 TTATTATTATTATTAAAATTATTA
318708 TTATATATTATTTATTAAATATTA
1 TTAT-TATTA-TTATTAAA-ATTA
318732 CAAAGCCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
24 27 0.63
25 5 0.12
26 7 0.16
27 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTATTATTATTAAAATTATTA
Found at i:319163 original size:20 final size:21
Alignment explanation
Indices: 319125--319166 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
319115 CGGATCCTTC
*
319125 AAAACAAAAAAAAGGAGAGAA
1 AAAACAAAAAAAAGAAGAGAA
*
319146 AAAAGAAAAAAAA-AAGAGAA
1 AAAACAAAAAAAAGAAGAGAA
319166 A
1 A
319167 GCACGAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAACAAAAAAAAGAAGAGAA
Found at i:320076 original size:3 final size:3
Alignment explanation
Indices: 320063--320120 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
320053 ATATTTTTAT
*
320063 TTA TT- TTA TTA TTA TTA TT- TT- TTA TTG TT- TTAA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
320104 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
320121 TATAAAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
2 10 0.20
3 37 0.76
4 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:320179 original size:22 final size:21
Alignment explanation
Indices: 320131--320169 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
320121 TATAAAAATA
320131 AATAAATATATATATATATAT
1 AATAAATATATATATATATAT
320152 AATAAATA-ATATATATAT
1 AATAAATATATATATATAT
320170 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAAATATATATATATATAT
Found at i:320455 original size:16 final size:17
Alignment explanation
Indices: 320425--320466 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
320415 ATATTTTATT
320425 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
320442 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
320458 TATAATTTT
1 TAT-ATTTT
320467 GAAATAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:320460 original size:26 final size:26
Alignment explanation
Indices: 320411--320461 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
320401 TTCTAAATAA
* *
320411 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
320437 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
320462 ATTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:321627 original size:19 final size:19
Alignment explanation
Indices: 321586--321627 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
321576 ATGACCAACA
* *
321586 AATTCGCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
*
321605 AATTCGCAACGTGAACTCC
1 AATTCGCAACGCGAACTCC
321624 AATT
1 AATT
321628 TTGTAACACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:321797 original size:20 final size:20
Alignment explanation
Indices: 321731--321789 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
321721 TTTTCCAAAT
321731 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
321751 TCGCAACACGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
*
321771 TCGCAACGCGAATTTGTAA
1 TCGCAACGCGAATATGTAA
321790 TTTGCAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:321815 original size:40 final size:41
Alignment explanation
Indices: 321726--321816 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 41
321716 CATGATTTTC
**
321726 CAAATTCGCAACGCGAATATGTAAATCGCAACACGAATCTGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACAC-AATAAGT
* * * *
321768 -AAA-TCGCAACGCGAATTTGTAATTTGCAACA-TATAAGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACACAATAAGT
321806 CAAATTCGCAA
1 CAAATTCGCAA
321817 AGCGCGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
38 4 0.10
39 3 0.07
40 31 0.76
41 3 0.07
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATATGTAAATCGCAACACAATAAGT
Found at i:321989 original size:22 final size:22
Alignment explanation
Indices: 321964--322010 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
321954 TCACTCTCTA
** *
321964 CGGCGACATTTGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
321986 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
322008 CGG
1 CGG
322011 TGACCCCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.43, G:0.21, T:0.21
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:322419 original size:20 final size:20
Alignment explanation
Indices: 322382--322420 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
322372 TTATTTTCGC
* * *
322382 GTTGCGAATTTCATTTTCAT
1 GTTGCAAATTTAAGTTTCAT
322402 GTTGCAAATTTAAGTTTCA
1 GTTGCAAATTTAAGTTTCA
322421 AAAACTACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (20 bp):
GTTGCAAATTTAAGTTTCAT
Found at i:324532 original size:21 final size:21
Alignment explanation
Indices: 324506--324560 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
324496 ATTCACCTGT
*
324506 CATCGTTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
324527 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
324548 CACCGTTCAAGAG
1 CATCGTTCAAGAG
324561 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:325932 original size:13 final size:13
Alignment explanation
Indices: 325909--325940 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
325899 TTTAGATGTA
325909 TTGTCTTAATTGAT
1 TTGT-TTAATTGAT
325923 TTGTTTAATTGAT
1 TTGTTTAATTGAT
325936 TTGTT
1 TTGTT
325941 GTAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.19, C:0.03, G:0.16, T:0.62
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:325979 original size:16 final size:16
Alignment explanation
Indices: 325960--326039 Score: 61
Period size: 16 Copynumber: 4.6 Consensus size: 16
325950 AATTATTTTT
325960 TTGTTTAATTGATTTG
1 TTGTTTAATTGATTTG
* *
325976 TTGTTTAATTTCAATCTG
1 TTGTTTAA-TT-GATTTG
* * *
325994 CATTATGTTGAATTGTTTTT
1 ---T-TGTTTAATTGATTTG
326014 TTGTTTAATTGATTTG
1 TTGTTTAATTGATTTG
326030 TTGTTTAATT
1 TTGTTTAATT
326040 TTAATCTGCA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
16 30 0.62
17 3 0.06
18 4 0.08
20 2 0.04
21 3 0.06
22 6 0.12
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (16 bp):
TTGTTTAATTGATTTG
Found at i:326019 original size:54 final size:54
Alignment explanation
Indices: 325949--326059 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
325939 TTGTAAATAA
325949 GAATTATTTTTTTGTTTAATTGATTTGTTGTTTAATTTCAATCTGCATTATGTT
1 GAATTATTTTTTTGTTTAATTGATTTGTTGTTTAATTTCAATCTGCATTATGTT
* *
326003 GAATTGTTTTTTTGTTTAATTGATTTGTTGTTTAATTTTAATCTGCATTATGTT
1 GAATTATTTTTTTGTTTAATTGATTTGTTGTTTAATTTCAATCTGCATTATGTT
326057 GAA
1 GAA
326060 GGCAAAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.59
Consensus pattern (54 bp):
GAATTATTTTTTTGTTTAATTGATTTGTTGTTTAATTTCAATCTGCATTATGTT
Found at i:326143 original size:20 final size:20
Alignment explanation
Indices: 326121--326184 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
326111 GTGTTGCGAT
* *
326121 TTTCACATTGCGAATTTGAT
1 TTTCACGTTGCGAATTTGAC
*
326141 TTTCGCGTTGC-AACTTTGAC
1 TTTCACGTTGCGAA-TTTGAC
* *
326161 TTTCATGTTTCGAATTTGAC
1 TTTCACGTTGCGAATTTGAC
326181 TTTC
1 TTTC
326185 GCAATAATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTCACGTTGCGAATTTGAC
Found at i:329516 original size:14 final size:15
Alignment explanation
Indices: 329480--329517 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
329470 GAAATCATTG
329480 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
329495 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
329510 AAAAATTA
1 AAAAATTA
329518 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:329712 original size:40 final size:40
Alignment explanation
Indices: 329657--329816 Score: 137
Period size: 40 Copynumber: 4.0 Consensus size: 40
329647 AAACATTTGT
*
329657 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAATAAAATTCGTGTTGCGAATTCGAAAATCGA
* *** * * *
329697 GTTGCGAAAACAAAATTCGTGTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAATAAAATTCGTGTTGCGAATTCGAAAATCGA
* *
329737 GTTGCGAAAA-AGAAATTTGCT-TTGCGAATTC-AGAAATCAA
1 GTTGCGAAAATA-AAATTCG-TGTTGCGAATTCGA-AAATCGA
** * *
329777 GTTGCGAATTTGAAATTCCGTGTTGCGAATTTGAAAATCG
1 GTTGCGAAAATAAAATT-CGTGTTGCGAATTCGAAAATCG
329817 CGATACGAAT
Statistics
Matches: 91, Mismatches: 22, Indels: 13
0.72 0.17 0.10
Matches are distributed among these distances:
39 2 0.02
40 72 0.79
41 16 0.18
42 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (40 bp):
GTTGCGAAAATAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:329726 original size:20 final size:20
Alignment explanation
Indices: 329655--329746 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
329645 CAAAACATTT
**
329655 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAAACAAAATTC
**
329675 GTGTTGCGAATTCGAAAA-TC
1 GTGTTGCGAAAAC-AAAATTC
*
329695 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAAACAAAATTC
* *
329715 GTGTTGCGAAAAGGAAACTT-
1 GTGTTGCGAAAA-CAAAATTC
329735 GTGTTGCGAAAA
1 GTGTTGCGAAAA
329747 AGAAATTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.07
20 48 0.79
21 9 0.15
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (20 bp):
GTGTTGCGAAAACAAAATTC
Found at i:329751 original size:20 final size:19
Alignment explanation
Indices: 329697--329753 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
329687 CGAAAATCGA
329697 GTTGCGAAAACA-AAATTCGT
1 GTTGCGAAAA-AGAAATT-GT
*
329717 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAAAGAAA-TTGT
329737 GTTGCGAAAAAGAAATT
1 GTTGCGAAAAAGAAATT
329754 TGCTTTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTGCGAAAAAGAAATTGT
Found at i:329761 original size:20 final size:20
Alignment explanation
Indices: 329697--329764 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
329687 CGAAAATCGA
329697 GTTGCGAAAACA-AAA-TTCGT
1 GTTGCGAAAA-AGAAACTT-GT
*
329717 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAAAGAAACTTGT
*
329737 GTTGCGAAAAAGAAATTTGCT
1 GTTGCGAAAAAGAAACTTG-T
329758 -TTGCGAA
1 GTTGCGAA
329765 TTCAGAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAAAGAAACTTGT
Found at i:329793 original size:80 final size:81
Alignment explanation
Indices: 329653--329805 Score: 188
Period size: 80 Copynumber: 1.9 Consensus size: 81
329643 CCCAAAACAT
* *
329653 TTGTGTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATT-CGT
1 TTGTGTTGCGAAATAAAAATTCGTGTTGCGAATTCGAAAATCAAGTTGCGAAAACAAAATTCCGT
329717 GTTGCGAAAAGGAAAC
66 GTTGCGAAAAGGAAAC
* ****
329733 TTGTGTTGCGAAA-AAGAAATTTGCT-TTGCGAATTC-AGAAATCAAGTTGCGAATTTGAAATTC
1 TTGTGTTGCGAAATAA-AAATTCG-TGTTGCGAATTCGA-AAATCAAGTTGCGAAAACAAAATTC
329795 CGTGTTGCGAA
63 CGTGTTGCGAA
329806 TTTGAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 2 0.03
80 48 0.77
81 12 0.19
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (81 bp):
TTGTGTTGCGAAATAAAAATTCGTGTTGCGAATTCGAAAATCAAGTTGCGAAAACAAAATTCCGT
GTTGCGAAAAGGAAAC
Found at i:329803 original size:21 final size:21
Alignment explanation
Indices: 329777--329866 Score: 112
Period size: 21 Copynumber: 4.3 Consensus size: 21
329767 CAGAAATCAA
* *
329777 GTTGCGAATTT-GAAATTCCGT
1 GTTGCGAATTTGGAAAAT-CGC
329798 GTTGCGAATTT-GAAAATCGC
1 GTTGCGAATTTGGAAAATCGC
* *
329818 GATACGAATTTGGAAAATCGC
1 GTTGCGAATTTGGAAAATCGC
*
329839 GTTGCGAATTTGGAAAATCGT
1 GTTGCGAATTTGGAAAATCGC
329860 GTTGCGA
1 GTTGCGA
329867 TCGCAGAAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.18
21 50 0.82
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (21 bp):
GTTGCGAATTTGGAAAATCGC
Found at i:329815 original size:41 final size:42
Alignment explanation
Indices: 329770--329866 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 42
329760 GCGAATTCAG
* * *
329770 AAATCAAGTTGCGAATTT-GAAATTCCGTGTTGCGAATTT-GA
1 AAATCGAGTTGCGAATTTGGAAAAT-CGCGTTGCGAATTTGGA
* * *
329811 AAATCGCGATACGAATTTGGAAAATCGCGTTGCGAATTTGGA
1 AAATCGAGTTGCGAATTTGGAAAATCGCGTTGCGAATTTGGA
*
329853 AAATCGTGTTGCGA
1 AAATCGAGTTGCGA
329867 TCGCAGAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 27 0.60
42 18 0.40
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (42 bp):
AAATCGAGTTGCGAATTTGGAAAATCGCGTTGCGAATTTGGA
Found at i:331909 original size:2 final size:2
Alignment explanation
Indices: 331902--331942 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
331892 TTCAACTATT
331902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
331943 TTGTGATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:332448 original size:2 final size:2
Alignment explanation
Indices: 332394--332429 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
332384 TGAAGAGACG
332394 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
332430 GAATGAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:333652 original size:13 final size:13
Alignment explanation
Indices: 333634--333662 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
333624 ATTTTTTTAA
333634 AATTATTAAAATT
1 AATTATTAAAATT
333647 AATTATTAAAATT
1 AATTATTAAAATT
333660 AAT
1 AAT
333663 AAATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTAAAATT
Found at i:346028 original size:24 final size:24
Alignment explanation
Indices: 346001--346046 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
345991 GTGACATGAT
* *
346001 TTTTCTCTGCTCTTGTGGCACGCA
1 TTTTCTCTACTATTGTGGCACGCA
346025 TTTTCTCTACTATTGTGGCACG
1 TTTTCTCTACTATTGTGGCACG
346047 ATCCTCATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTTCTCTACTATTGTGGCACGCA
Found at i:346395 original size:34 final size:37
Alignment explanation
Indices: 346351--346452 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
346341 TTTCGTCCTA
346351 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
346386 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
346421 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
346453 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:346436 original size:37 final size:35
Alignment explanation
Indices: 346351--346486 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
346341 TTTCGTCCTA
346351 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
346386 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
346421 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
346458 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
346487 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:346881 original size:18 final size:17
Alignment explanation
Indices: 346842--346884 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
346832 ATTATATGGA
346842 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
346858 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
346876 TATTATTAT
1 TATTATTAT
346885 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:347191 original size:30 final size:29
Alignment explanation
Indices: 347132--347193 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
347122 TAACTTTATA
* *
347132 TATTTATTATTTTTTATTATTTTCGTTTTT
1 TATTCATTATTTTATATTATTTTC-TTTTT
347162 TATTCATTATTATTATATTATTATT-TTTTT
1 TATTCATTATT-TTATATTATT-TTCTTTTT
347192 TA
1 TA
347194 AAAACCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 17 0.61
31 9 0.32
32 2 0.07
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (29 bp):
TATTCATTATTTTATATTATTTTCTTTTT
Found at i:350516 original size:15 final size:14
Alignment explanation
Indices: 350498--350588 Score: 65
Period size: 16 Copynumber: 5.9 Consensus size: 14
350488 AATCAAGAAC
350498 AAAAAAGAAAAGAAG
1 AAAAAAGAAAA-AAG
*
350513 AAAAAAAGCAAAAAAA
1 -AAAAAAG-AAAAAAG
350529 AAACAAAGAAAAAGAG
1 AAA-AAAGAAAAA-AG
*
350545 AAACAAGAACAAAAG
1 AAAAAAGAA-AAAAG
*
350560 AAAAAAAGAGCAAAAAT
1 -AAAAAAGA--AAAAAG
*
350577 CAAAAAGAAAAA
1 AAAAAAGAAAAA
350589 GGGAGGAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.06
15 15 0.24
16 34 0.55
17 8 0.13
18 1 0.02
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:350547 original size:32 final size:34
Alignment explanation
Indices: 350492--350565 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 34
350482 AGATCCAATC
*
350492 AAGAACAAA-AAAGAAAAGAAGAAA-AA-AAGCAA
1 AAGAAAAAACAAAGAAAAGAAGAAACAAGAA-CAA
350524 AA-AAAAAACAAAGAAAA-AGAGAAACAAGAACAA
1 AAGAAAAAACAAAGAAAAGA-AGAAACAAGAACAA
350557 AAGAAAAAA
1 AAGAAAAAA
350566 AGAGCAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
31 6 0.17
32 15 0.42
33 7 0.19
34 8 0.22
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (34 bp):
AAGAAAAAACAAAGAAAAGAAGAAACAAGAACAA
Found at i:350573 original size:16 final size:16
Alignment explanation
Indices: 350492--350574 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 16
350482 AGATCCAATC
*
350492 AAGAACAAAAAAG-AA
1 AAGAAAAAAAAAGCAA
350507 AAGAAGAAAAAAAGCAA
1 AAGAA-AAAAAAAGCAA
*
350524 AA-AAAAAACAAAGAAA
1 AAGAAAAAA-AAAGCAA
*
350540 AAGAGAAACAAGAA-CAA
1 AAGA-AAA-AAAAAGCAA
*
350557 AAGAAAAAAAGAGCAA
1 AAGAAAAAAAAAGCAA
350573 AA
1 AA
350575 ATCAAAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 12 0.22
16 25 0.45
17 11 0.20
18 5 0.09
19 2 0.04
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAGCAA
Found at i:350574 original size:8 final size:8
Alignment explanation
Indices: 350498--350568 Score: 74
Period size: 8 Copynumber: 9.0 Consensus size: 8
350488 AATCAAGAAC
350498 AAAAAAGA
1 AAAAAAGA
*
350506 AAAGAAGA
1 AAAAAAGA
350514 AAAAAAGCA
1 AAAAAAG-A
350523 AAAAAA-A
1 AAAAAAGA
*
350530 AACAAAGA
1 AAAAAAGA
*
350538 AAAAGAG-
1 AAAAAAGA
*
350545 AAACAAGA
1 AAAAAAGA
*
350553 ACAAAAGA
1 AAAAAAGA
350561 AAAAAAGA
1 AAAAAAGA
350569 GCAAAAATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 11 0.22
8 32 0.64
9 7 0.14
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:350580 original size:23 final size:23
Alignment explanation
Indices: 350499--350589 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 23
350489 ATCAAGAACA
* *
350499 AAAAAGAAAAGAAGAAAAAAAGC
1 AAAAACAAAAGAAGAAAAAGAGC
* *
350522 AAAAAAAAAACAAAGAAAAAGAGAAAC
1 AAAAACAAAA-GAAGAAAAAGAG---C
*
350549 AAGAACAAAAGAA-AAAAAGAGC
1 AAAAACAAAAGAAGAAAAAGAGC
350571 AAAAATC-AAA-AAGAAAAAG
1 AAAAA-CAAAAGAAGAAAAAG
350590 GGAGGAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
21 2 0.04
22 14 0.25
23 10 0.18
24 10 0.18
25 8 0.15
26 2 0.04
27 9 0.16
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAACAAAAGAAGAAAAAGAGC
Found at i:351251 original size:22 final size:22
Alignment explanation
Indices: 351226--351296 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
351216 CCATCAATCT
*
351226 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
351248 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
351270 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
351292 TTTGA
1 TTTGA
351297 CCAAACACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:352270 original size:36 final size:36
Alignment explanation
Indices: 352227--352508 Score: 303
Period size: 36 Copynumber: 8.0 Consensus size: 36
352217 ACTAGAAGAG
352227 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
352263 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
352299 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
352335 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
352371 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
352400 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
352437 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
352472 TTTTCGTTTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
352509 ACCTTTGAAT
Statistics
Matches: 204, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 141 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:352270 original size:71 final size:73
Alignment explanation
Indices: 352185--352508 Score: 230
Period size: 72 Copynumber: 4.6 Consensus size: 73
352175 GTTTTTCTTA
* * * * * *
352185 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
352247 TTTCCCTTG
65 TTTCCCTTG
* *
352256 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
352320 TTCCCTTG
66 TTCCCTTG
* * * * *
352328 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
352384 TTTTCTTTG
65 TTTCCCTTG
** * ** * * * * *
352393 AAACAAATTCCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
352457 TTTCTCTTG
65 TTTCCCTTG
* * * *
352466 AAAC-AATTTTCGTTTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
352509 ACCTTTGAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.01
65 45 0.22
66 5 0.02
70 8 0.04
71 25 0.12
72 77 0.38
73 38 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:352468 original size:102 final size:102
Alignment explanation
Indices: 352283--352471 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
352273 CTTGAGACAG
* *
352283 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
352348 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
352385 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
352449 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
352472 TTTTCGTTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 33 0.42
102 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:352500 original size:138 final size:137
Alignment explanation
Indices: 352247--352571 Score: 427
Period size: 138 Copynumber: 2.4 Consensus size: 137
352237 CTTGAGACAG
*
352247 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
352312 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
352377 GAATATG
131 GAATATA
* * ** * * * * *
352384 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
352449 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTTTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
352513 TTGAATTTA
129 TTGAATATA
* * * *
352522 TTTCCCCTAAAACAAATTTTTTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
352572 CAAAATCTTC
Statistics
Matches: 158, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
137 49 0.31
138 109 0.69
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:352601 original size:67 final size:68
Alignment explanation
Indices: 352483--352639 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
352473 TTTCGTTTAT
* **
352483 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
352544 CTCC
66 -TCC
* * *
352548 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
352613 TCC
66 TCC
* *
352616 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
352640 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:353466 original size:105 final size:105
Alignment explanation
Indices: 353278--354319 Score: 1648
Period size: 105 Copynumber: 10.0 Consensus size: 105
353268 GCACTCGAGG
* * ** * *
353278 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAAATTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
353343 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
353384 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCATCAATAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
353449 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
353489 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGGT-AACAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTT-GTCAACAACAACTTCTCAATTTCAG
* *
353553 AGCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
353594 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
353659 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
353699 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
353764 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
353804 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
353869 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
353909 CAAAGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
353974 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
354014 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
354079 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
354119 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
354179 TTCAATTTCAACTTCATAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * ** *
354219 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCA
* * *
354283 GAGCCAATTTCAACTTCACGACGGAGAATATTGGACT
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
354320 TGGAACAATG
Statistics
Matches: 880, Mismatches: 47, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
99 2 0.00
100 80 0.09
101 3 0.00
102 3 0.00
103 4 0.00
104 5 0.01
105 710 0.81
106 73 0.08
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:354910 original size:34 final size:36
Alignment explanation
Indices: 354866--354965 Score: 161
Period size: 34 Copynumber: 2.8 Consensus size: 36
354856 TTTCGTCCTA
354866 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
354901 -TAGGATTCAAACTCCTAAAAATAGGATAACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAACATTTT
354936 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
354966 TAGTTCTACT
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.48
35 3 0.05
37 28 0.46
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAACATTTT
Found at i:354951 original size:37 final size:35
Alignment explanation
Indices: 354866--355001 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
354856 TTTCGTCCTA
354866 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
354901 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
* *
354936 GCTAGGATTCAAACTCCTAAAAATAGGATATAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
354973 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
355002 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:355395 original size:18 final size:17
Alignment explanation
Indices: 355356--355398 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
355346 ATTATATGGA
355356 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
355372 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
355390 TATTATTAT
1 TATTATTAT
355399 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:355673 original size:15 final size:15
Alignment explanation
Indices: 355647--355701 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
355637 CTTTATATAT
*
355647 TTATATTATTTTTTA
1 TTATTTTATTTTTTA
*
355662 TTATTTTGTTTTTTA
1 TTATTTTATTTTTTA
*
355677 TTCATTATTATTATATTA
1 TT-ATT-TTATT-TTTTA
355695 TTATTTT
1 TTATTTT
355702 TTTAAAACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 15 0.45
16 5 0.15
17 7 0.21
18 6 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTATTTTATTTTTTA
Found at i:355983 original size:14 final size:14
Alignment explanation
Indices: 355964--355993 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
355954 TCTTACTTAC
*
355964 TTATTTTATTTATT
1 TTATTTAATTTATT
355978 TTATTTAATTTATT
1 TTATTTAATTTATT
355992 TT
1 TT
355994 TCCCTTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTAATTTATT
Found at i:357903 original size:43 final size:43
Alignment explanation
Indices: 357845--357942 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
357835 AAATTATTTT
* *
357845 AAATTAGGACCAATTTAGTAGAACGTGTTAGTTTTAAGGATTA
1 AAATTAGGACCAATTTAGCAGAACGTGTAAGTTTTAAGGATTA
* *
357888 AAATTAGGATCAATTTAGCAGAATGTGTAAGTTTTAAGGATTA
1 AAATTAGGACCAATTTAGCAGAACGTGTAAGTTTTAAGGATTA
357931 AAATTAGGACCA
1 AAATTAGGACCA
357943 CTTTGACTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (43 bp):
AAATTAGGACCAATTTAGCAGAACGTGTAAGTTTTAAGGATTA
Found at i:358939 original size:50 final size:50
Alignment explanation
Indices: 358885--358982 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
358875 TCATGTGTCT
** *
358885 TCTTCTTCTTCTTCTTCAACTTCTGCTAAAACTGTCTTAAGTCTTAACGG
1 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAACTGTCATAAGTCTTAACGG
*
358935 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAATTGTCATAAGTCTTAAC
1 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAACTGTCATAAGTCTTAAC
358983 ATAAGCACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.23, C:0.24, G:0.08, T:0.44
Consensus pattern (50 bp):
TCTTCTTCTTCTTCTAAAACTTCTGCTAAAACTGTCATAAGTCTTAACGG
Found at i:361967 original size:3 final size:3
Alignment explanation
Indices: 361959--362001 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
361949 GATTCACATG
* *
361959 TCT TCT TCT TAT TCTT TCT TCT TCT TCT TCT TCG TCT TCT TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
362002 AAAATTGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:362032 original size:50 final size:50
Alignment explanation
Indices: 361975--362073 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
361965 TCTTATTCTT
**** * * *
361975 TCTTCTTCTTCTTCTTCGTCTTCTTCTAAAATTGTCTTAAGTCTTAACAG
1 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAATTGTCGTAAGTCCTAACAG
362025 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAATTGTCGTAAGTCCTAACA
1 TCTTCTTCTTCTTCTAAAACTTCTGCTAAAATTGTCGTAAGTCCTAACA
362074 TAAGCACCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.45
Consensus pattern (50 bp):
TCTTCTTCTTCTTCTAAAACTTCTGCTAAAATTGTCGTAAGTCCTAACAG
Found at i:363360 original size:33 final size:33
Alignment explanation
Indices: 363323--363388 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
363313 TCACCCCCAT
*
363323 TTTCTTTACTTTCTTACCAAAGTCATAATCAAA
1 TTTCTTTACTTTCTTAACAAAGTCATAATCAAA
363356 TTTCTTTACTTTCTTAACAAAGTCATAATCAAA
1 TTTCTTTACTTTCTTAACAAAGTCATAATCAAA
363389 ACCTCTCTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (33 bp):
TTTCTTTACTTTCTTAACAAAGTCATAATCAAA
Found at i:365392 original size:19 final size:20
Alignment explanation
Indices: 365327--365380 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
365317 CGTTGAAACC
365327 CAAAGTTTCGAAA-TCTTGT
1 CAAAGTTTCGAAACTCTTGT
365346 CAAAGTTTCGAAACTCTTGT
1 CAAAGTTTCGAAACTCTTGT
365366 CAAAGTTTCGAAACT
1 CAAAGTTTCGAAACT
365381 TTTGCGAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
CAAAGTTTCGAAACTCTTGT
Found at i:367264 original size:19 final size:20
Alignment explanation
Indices: 367216--367262 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
367206 AGGGATATAT
367216 CGATACCCTATAGGGGGTAC
1 CGATACCCTATAGGGGGTAC
367236 CGATACCCTATAGGGGGTAC
1 CGATACCCTATAGGGGGTAC
367256 CGATACC
1 CGATACC
367263 TACTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (20 bp):
CGATACCCTATAGGGGGTAC
Found at i:374746 original size:20 final size:20
Alignment explanation
Indices: 374721--374777 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
374711 TGTTGAAACC
* *
374721 CAAAGTTTTGAAACTCTTGT
1 CAAAGTTTCGAAACTCCTGT
374741 CAAAGTTTCGAAACTCCTGT
1 CAAAGTTTCGAAACTCCTGT
374761 CAAAGTTTCGAAACTCC
1 CAAAGTTTCGAAACTCC
374778 AAAGTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (20 bp):
CAAAGTTTCGAAACTCCTGT
Found at i:379765 original size:21 final size:21
Alignment explanation
Indices: 379652--379763 Score: 161
Period size: 21 Copynumber: 5.3 Consensus size: 21
379642 CCGAGTTACC
* *
379652 CGCAATAGCTCCCGCGACGGT
1 CGCAATAGCGCCAGCGACGGT
* *
379673 CGCAATAGCTCCTGCGACGGT
1 CGCAATAGCGCCAGCGACGGT
*
379694 CGCAATAGCGCAAGCGACGGT
1 CGCAATAGCGCCAGCGACGGT
379715 CGCAATAGCGCCAGCGACGGT
1 CGCAATAGCGCCAGCGACGGT
* *
379736 CGCAATAACGCCAGCGACAGT
1 CGCAATAGCGCCAGCGACGGT
379757 CGCAATA
1 CGCAATA
379764 ACACATGCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.26, C:0.33, G:0.29, T:0.12
Consensus pattern (21 bp):
CGCAATAGCGCCAGCGACGGT
Found at i:380099 original size:15 final size:15
Alignment explanation
Indices: 380079--380109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
380069 TTTATCTTTT
*
380079 TCAAATATATATATA
1 TCAAATATAAATATA
380094 TCAAATATAAATATA
1 TCAAATATAAATATA
380109 T
1 T
380110 TTGATATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TCAAATATAAATATA
Found at i:382353 original size:26 final size:24
Alignment explanation
Indices: 382291--382353 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
382281 CATTTTAATC
382291 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
382315 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
382338 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
382354 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:382355 original size:22 final size:23
Alignment explanation
Indices: 382325--382371 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
382315 AAAATATATT
382325 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
382348 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
382370 TA
1 TA
382372 AACTAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:382520 original size:27 final size:28
Alignment explanation
Indices: 382473--382559 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 28
382463 AATTTCATTG
*
382473 AAATAATATTATTAAATTA-TTAATAAT
1 AAATAATACTATTAAATTATTTAATAAT
* *
382500 AAATAATACTATT-TATATATTTAATATT
1 AAATAATACTATTAAAT-TATTTAATAAT
382528 AATATAATA--ATCTAATATTATTT--TAAT
1 AA-ATAATACTAT-TAA-ATTATTTAATAAT
382555 AAATA
1 AAATA
382560 TATTTAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
26 5 0.10
27 21 0.43
28 10 0.20
29 11 0.22
30 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATAATACTATTAAATTATTTAATAAT
Found at i:382577 original size:23 final size:23
Alignment explanation
Indices: 382551--382595 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
382541 AATATTATTT
382551 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
382574 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
382596 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:382983 original size:15 final size:15
Alignment explanation
Indices: 382947--383005 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 15
382937 TTCCAGAAAT
* *
382947 GTAATTCATTTTCTA
1 GTAATTCAATTTCCA
*
382962 G-AATTCAAATTCCA
1 GTAATTCAATTTCCA
*
382976 GTAATTCATTTTCCA
1 GTAATTCAATTTCCA
382991 -TAATTCAATTTCCA
1 GTAATTCAATTTCCA
383005 G
1 G
383006 AAAACCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCAATTTCCA
Found at i:382995 original size:29 final size:29
Alignment explanation
Indices: 382947--383005 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
382937 TTCCAGAAAT
*
382947 GTAATTCATTTTCTAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
* *
382976 GTAATTCATTTTCCATAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
383005 G
1 G
383006 AAAACCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:385699 original size:12 final size:12
Alignment explanation
Indices: 385684--385708 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
385674 TTTTACTAAC
385684 TTTTTCTTTCTT
1 TTTTTCTTTCTT
385696 TTTTTCTTTCTT
1 TTTTTCTTTCTT
385708 T
1 T
385709 ACTTTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:390838 original size:201 final size:201
Alignment explanation
Indices: 390370--390840 Score: 518
Period size: 201 Copynumber: 2.3 Consensus size: 201
390360 AGCATAACTT
* * * * **
390370 AAGTCAAGAAAAGTTATC-AACAAACCAAATCTTTCAAGTTCGATTTTACTCAACTCGAGAGCAC
1 AAGTCAAGAAGAGCTATCTATC-AACCAAAGCTTTCAAGTTCGATTCCACTCAACTCGAGAGCAC
* *
390434 ATCGACTTCATGGTGGCAACGAGGAACCATCTTCCAATCAAAATTCAAACTAAGGTCTTCAAGTC
65 ATTGACATCATGGTGGCAACGAGGAACCATCTTCCAATCAAAATTCAAACTAAGGTCTTCAAGTC
* * *
390499 TAGAAGAAGACCCAAATCGACTGCGATTTAGCAACGAAAAACTATCAATCAGCCTAGATTTTGAC
130 TAGAAGAAGACCCAAATCGACTGCGATTTAGCAACCAAAAACTATCAATAAGCCTAAATTTTGAC
*
390564 ATAGCTT
195 ATAGCTC
* ** *
390571 AAGTCGAGAAGAGCTATCTATCAACTGAAGCTTTCAAGTTTGATTCCACTCAACTCGAGAGCACA
1 AAGTCAAGAAGAGCTATCTATCAACCAAAGCTTTCAAGTTCGATTCCACTCAACTCGAGAGCACA
* * * * * * * *
390636 TTGACCAT-ATGGTGGTAATGAGGAACCATCTTCTAGTTAAATTTTAAACTCAGAG-CTTCAAGT
66 TTGA-CATCATGGTGGCAACGAGGAACCATCTTCCAATCAAAATTCAAACTAAG-GTCTTCAAGT
* * * * ** **
390699 CTAGAAGAA-AGCCCAAATTGTCTGTGATTTAGTAACCACGAACTATCTCTAAGCCTAAATTTTG
129 CTAGAAGAAGA-CCCAAATCGACTGCGATTTAGCAACCAAAAACTATCAATAAGCCTAAATTTTG
* *
390763 ACGTGGCTC
193 ACATAGCTC
* * * * * *
390772 AAGTCAAGAAGAGGTATTTGTCAACCAAAGCTTTTAAGTTCGGTTCCACTGAACTCGAGAGCACA
1 AAGTCAAGAAGAGCTATCTATCAACCAAAGCTTTCAAGTTCGATTCCACTCAACTCGAGAGCACA
390837 TTGA
66 TTGA
390841 TTGTATGATA
Statistics
Matches: 222, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
200 1 0.00
201 216 0.97
202 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (201 bp):
AAGTCAAGAAGAGCTATCTATCAACCAAAGCTTTCAAGTTCGATTCCACTCAACTCGAGAGCACA
TTGACATCATGGTGGCAACGAGGAACCATCTTCCAATCAAAATTCAAACTAAGGTCTTCAAGTCT
AGAAGAAGACCCAAATCGACTGCGATTTAGCAACCAAAAACTATCAATAAGCCTAAATTTTGACA
TAGCTC
Found at i:392048 original size:18 final size:16
Alignment explanation
Indices: 392017--392052 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
392007 AAGGTAATTC
392017 TTTTCTTTTTCTTATT
1 TTTTCTTTTTCTTATT
392033 TTTTCCTTTGTTCTTATT
1 TTTT-CTTT-TTCTTATT
392051 TT
1 TT
392053 ATTTAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCTTATT
Found at i:392968 original size:16 final size:16
Alignment explanation
Indices: 392947--392981 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
392937 TATCTTTTTG
392947 TGTATATTTTATATAT
1 TGTATATTTTATATAT
*
392963 TGTATATTTTTTATAT
1 TGTATATTTTATATAT
392979 TGT
1 TGT
392982 TTTCTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (16 bp):
TGTATATTTTATATAT
Found at i:397763 original size:13 final size:13
Alignment explanation
Indices: 397745--397770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
397735 TACATGGCGT
397745 CTCAAGGGGTTTA
1 CTCAAGGGGTTTA
397758 CTCAAGGGGTTTA
1 CTCAAGGGGTTTA
397771 TTGTTAGTTG
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:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
CTCAAGGGGTTTA
Found at i:405299 original size:2 final size:2
Alignment explanation
Indices: 405292--405342 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
405282 TAATAATTTC
405292 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
405334 AT AT AT AT A
1 AT AT AT AT A
405343 ACTCAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:407039 original size:14 final size:14
Alignment explanation
Indices: 407017--407048 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
407007 CGTTCATGAA
*
407017 CGTTCGGTTATGTT
1 CGTTAGGTTATGTT
407031 CGTTAGGTTATGTT
1 CGTTAGGTTATGTT
407045 CGTT
1 CGTT
407049 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTAGGTTATGTT
Found at i:408061 original size:16 final size:16
Alignment explanation
Indices: 408036--408090 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
408026 GTCTCTAACG
408036 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
408052 TTTATATTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
408068 TTTATGTTCGTGCTCG
1 TTTATGTTCGTGTTCA
408084 TTTATGT
1 TTTATGT
408091 CGAACATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:408403 original size:2 final size:2
Alignment explanation
Indices: 408396--408444 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
408386 AGCTTGAGAT
408396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408438 TA TA TA T
1 TA TA TA T
408445 TCATGCTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:415156 original size:21 final size:19
Alignment explanation
Indices: 415119--415174 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
415109 GGATAAAAGA
*
415119 TTATTAAAT-TTTA-AAAT
1 TTATTAAATAATTATAAAT
415136 TTATTAAAATAATTACTAAAT
1 TTATT-AAATAATTA-TAAAT
*
415157 TTATTGAATAATTATAAA
1 TTATTAAATAATTATAAA
415175 ACTATGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 7 0.21
20 8 0.24
21 9 0.27
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TTATTAAATAATTATAAAT
Found at i:416889 original size:3 final size:3
Alignment explanation
Indices: 416872--416922 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
416862 TACCAAAAAA
*
416872 TAT TAT T-T TATT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
416918 TAT TA
1 TAT TA
416923 ATTACATATC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:417443 original size:30 final size:30
Alignment explanation
Indices: 417409--417735 Score: 165
Period size: 30 Copynumber: 11.2 Consensus size: 30
417399 AATAGCATTA
*
417409 TAGTCCCTTAAGTTTTTGTTTTTGATATTT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* * * * * *
417439 TAGTCCTTTAAATGTCTATTTTTGTTATTT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* * * * *
417469 TAGTCCTTTAAATATTTGTATTTACTA-TT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* *
417498 TAGACCCTTAAGTTTTTGGTTTTGCTATTT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* * *
417528 T-G-CCCTTTAAGTTTCT-ATTTTGCCATTT
1 TAGTCCC-TTAAGTTTTTGTTTTTGCTATTT
*** * * *
417556 TAGTTTTTTAA-ATTTAGATTTTTACTATTT
1 TAGTCCCTTAAGTTTTTG-TTTTTGCTATTT
* * *
417586 TAG-CCCTTTAAGTTTATGTTTTTTCCATTT
1 TAGTCCC-TTAAGTTTTTGTTTTTGCTATTT
* * * *
417616 TATTCCTTTAA-TTTTT-TTGTTG---TGT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* * * * *
417641 TAGTGCTTTAAGTTTCTATTTTTTCTATTT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* * *
417671 TAGTCCCTTAAATTTCTATTTTTGCTATTT
1 TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
* *
417701 TA-ACCCTTTAAGTTTATGTTTTTGCTATTT
1 TAGTCCC-TTAAGTTTTTGTTTTTGCTATTT
*
417731 AAGTC
1 TAGTC
417736 ATTTAAATCG
Statistics
Matches: 220, Mismatches: 61, Indels: 31
0.71 0.20 0.10
Matches are distributed among these distances:
25 11 0.05
26 4 0.02
27 4 0.02
28 20 0.09
29 44 0.20
30 131 0.60
31 6 0.03
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.58
Consensus pattern (30 bp):
TAGTCCCTTAAGTTTTTGTTTTTGCTATTT
Found at i:417473 original size:60 final size:61
Alignment explanation
Indices: 417409--417743 Score: 243
Period size: 60 Copynumber: 5.7 Consensus size: 61
417399 AATAGCATTA
* * * *
417409 TAGTCCC-TTAAGTTTTTGTTTTTGATATTTTAGTCCTTTAAATGTCTATTTTTGTTATTT
1 TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
* * * * * * * **
417469 TAGT-CCTTTAAATATT-TGTATTTACTA-TTTAGACCCTTAAGTTTTTGGTTTTGCTATTT
1 TAGTCCCTTTAAGT-TTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
* * * ** ** *
417528 T-G-CCCTTTAAGTTTCT-ATTTTGCCATTTTAGTTTTTTAAATTTAGATTTTTACTATTT
1 TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
* * * *
417586 TAG-CCCTTTAAGTTTATGTTTTTTCCATTTTATTCCTTT-AATTT-T-TTTGTTG---TGT
1 TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTT-TTGCTATTT
* * * * *
417641 TAGT-GCTTTAAGTTTCTATTTTTTCTATTTTAGTCCCTTAAATTTCTATTTTTGCTATTT
1 TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
* * *
417701 TA-ACCCTTTAAGTTTATGTTTTTGCTATTTAAGTCATTTAAAT
1 TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAAT
417744 CGAATATGAT
Statistics
Matches: 208, Mismatches: 51, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
55 34 0.16
56 5 0.02
57 14 0.07
58 38 0.18
59 46 0.22
60 69 0.33
61 2 0.01
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (61 bp):
TAGTCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
Found at i:417547 original size:20 final size:20
Alignment explanation
Indices: 417522--417561 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
417512 TTTGGTTTTG
*
417522 CTATTTTGCCCTTTAAGTTT
1 CTATTTTGCCATTTAAGTTT
*
417542 CTATTTTGCCATTTTAGTTT
1 CTATTTTGCCATTTAAGTTT
417562 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (20 bp):
CTATTTTGCCATTTAAGTTT
Found at i:417741 original size:115 final size:114
Alignment explanation
Indices: 417532--417741 Score: 285
Period size: 115 Copynumber: 1.8 Consensus size: 114
417522 CTATTTTGCC
*** *
417532 CTTTAAGTTTCTATTTTGCCATTTTAGTTTTTTAAATTTAGATTTTTACTATTTTAGCCCTTTAA
1 CTTTAAGTTTCTATTTTGCCATTTTAGTCCCTTAAATTTAGATTTTTACTATTTTAACCCTTTAA
* * * *
417597 GTTTATGTTTTTTCCATTTTATTCCTTTAATTTTTTTGTTGTGTTAGTG
66 GTTTATGTTTTTGCCATTTAAGTCATTTAATTTTTTTGTTGTGTTAGTG
* * ** *
417646 CTTTAAGTTTCTATTTTTTCTATTTTAGTCCCTTAAATTTCTATTTTTGCTATTTTAACCCTTTA
1 CTTTAAGTTTCTA-TTTTGCCATTTTAGTCCCTTAAATTTAGATTTTTACTATTTTAACCCTTTA
*
417711 AGTTTATGTTTTTGCTATTTAAGTCATTTAA
65 AGTTTATGTTTTTGCCATTTAAGTCATTTAA
417742 ATCGAATATG
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
114 13 0.16
115 68 0.84
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (114 bp):
CTTTAAGTTTCTATTTTGCCATTTTAGTCCCTTAAATTTAGATTTTTACTATTTTAACCCTTTAA
GTTTATGTTTTTGCCATTTAAGTCATTTAATTTTTTTGTTGTGTTAGTG
Found at i:419452 original size:24 final size:24
Alignment explanation
Indices: 419425--419474 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
419415 TGGTGGTTGA
*
419425 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
419449 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
419473 TT
1 TT
419475 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:420430 original size:12 final size:12
Alignment explanation
Indices: 420413--420441 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
420403 ATATTTTTGT
420413 TTTATTTTCAGG
1 TTTATTTTCAGG
420425 TTTATTTTCAGG
1 TTTATTTTCAGG
420437 TTTAT
1 TTTAT
420442 CAGATTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (12 bp):
TTTATTTTCAGG
Found at i:426737 original size:24 final size:24
Alignment explanation
Indices: 426710--426759 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
426700 TGGTGGTTGA
*
426710 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
426734 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
426758 TT
1 TT
426760 GGTTCTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:430226 original size:20 final size:20
Alignment explanation
Indices: 430203--430257 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
430193 CCTTATAGGA
*
430203 GTATCGATACTGAGGG-TTAG
1 GTATCGAGACTGAGGGCTT-G
*
430223 GTATCGAGACCGAGGGGCTTG
1 GTATCGAGACTGA-GGGCTTG
430244 GTATCGAGACTGAG
1 GTATCGAGACTGAG
430258 ATTTCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
21 16 0.53
22 2 0.07
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (20 bp):
GTATCGAGACTGAGGGCTTG
Found at i:435363 original size:20 final size:21
Alignment explanation
Indices: 435317--435377 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
435307 TTCCCCTGTG
435317 GGGGGAATCGGTTCCCTTTCAAA
1 GGGGGAATCGGTTCCC--TCAAA
435340 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
435360 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
435378 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
23 16 0.44
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:441821 original size:21 final size:21
Alignment explanation
Indices: 441788--441832 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
441778 TGATTTTGAA
* * *
441788 AAAATTGAAAGTTTAGATATT
1 AAAACTGAAAGTTTAAATACT
*
441809 AAAACTGATAGTTTAAATACT
1 AAAACTGAAAGTTTAAATACT
441830 AAA
1 AAA
441833 CACATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (21 bp):
AAAACTGAAAGTTTAAATACT
Found at i:444111 original size:207 final size:207
Alignment explanation
Indices: 443727--444141 Score: 670
Period size: 207 Copynumber: 2.0 Consensus size: 207
443717 TTGAAATAAT
* * *
443727 CCCAAATGAATAGTTGAGAAATCAGGTTCTCTTAGTTTATTAGGATTTCTTATCGAAAAGGATTG
1 CCCAAATGAATAGTTGAGAAATCAGGTACTCCTAGTTTATTAGGATTTCTTATCGAAAAAGATTG
*
443792 TACTTTGTATCTTACCTGGTTTTGTGCAATGGAAAAAGTAACTAAATATTTGCCAGCAAACCCTT
66 TACTTTGTATCTTACCTGGTTTTGTGCAATGGAAAAAGTAACGAAATATTTGCCAGCAAACCCTT
* * *
443857 GCGCTCGTATGATCGTCTGCTTGTATTCCATCTTACCTCTCGTAGGGTTACGACTTCTTTCCAGT
131 GCACTCGTATGATCGTCTGCTTATATTCAATCTTACCTCTCGTAGGGTTACGACTTCTTTCCAGT
*
443922 CTTTGTATTAAG
196 CATTGTATTAAG
443934 CCCAAATGAATAGTTGAGAAATCAGGTACTCCTAGTTTATTAGGATTTCTTATCGAAAAAGATTG
1 CCCAAATGAATAGTTGAGAAATCAGGTACTCCTAGTTTATTAGGATTTCTTATCGAAAAAGATTG
** * * *
443999 TACTTTGTATCTTACCTGGTTTTGTGCCTTGGAAAAAGTAACGAAATATTTGCCGGCTAACGCTT
66 TACTTTGTATCTTACCTGGTTTTGTGCAATGGAAAAAGTAACGAAATATTTGCCAGCAAACCCTT
* * *
444064 GCACTCGTGTGATCAG-CTGCTTATATTCAATCTTCCCTCTGGTAGGGTTACGACTTCTTTCCAG
131 GCACTCGTATGATC-GTCTGCTTATATTCAATCTTACCTCTCGTAGGGTTACGACTTCTTTCCAG
444128 TCATTGTATTAAG
195 TCATTGTATTAAG
444141 C
1 C
444142 TCATCCAGCA
Statistics
Matches: 191, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
207 190 0.99
208 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (207 bp):
CCCAAATGAATAGTTGAGAAATCAGGTACTCCTAGTTTATTAGGATTTCTTATCGAAAAAGATTG
TACTTTGTATCTTACCTGGTTTTGTGCAATGGAAAAAGTAACGAAATATTTGCCAGCAAACCCTT
GCACTCGTATGATCGTCTGCTTATATTCAATCTTACCTCTCGTAGGGTTACGACTTCTTTCCAGT
CATTGTATTAAG
Found at i:444553 original size:14 final size:14
Alignment explanation
Indices: 444534--444577 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
444524 TAACAGACTT
444534 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
444548 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
444564 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
444578 AAAATCCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:444566 original size:16 final size:16
Alignment explanation
Indices: 444534--444577 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
444524 TAACAGACTT
444534 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
444548 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
444564 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
444578 AAAATCCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:445554 original size:90 final size:93
Alignment explanation
Indices: 445449--445615 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 93
445439 TTTTAACGTT
*
445449 TTTTTTGTTGATTA-TTTTCTGTTCT-T-TTTTTACC-TTTAAATGAATATCTACTCTTATTTCA
1 TTTTTTGTTGATTATTTTTCTGTTCTCTCTTTTT-CCTTTTAAATGAATATCTACTATTATTTCA
445510 TTTTAACCTTCCTCCTTTTAGGTTGGTGA
65 TTTTAACCTTCCTCCTTTTAGGTTGGTGA
* * *
445539 TTTTTTGTTGCTTATTTTTCTGTTCTCTCTTTTTCCTTTTATATGAATATCTGCTATTATTTCAT
1 TTTTTTGTTGATTATTTTTCTGTTCTCTCTTTTTCCTTTTAAATGAATATCTACTATTATTTCAT
*
445604 TTTAATCTTCCT
66 TTTAACCTTCCT
445616 TTTAGGTTGC
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
90 13 0.19
91 11 0.16
92 3 0.04
93 41 0.60
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (93 bp):
TTTTTTGTTGATTATTTTTCTGTTCTCTCTTTTTCCTTTTAAATGAATATCTACTATTATTTCAT
TTTAACCTTCCTCCTTTTAGGTTGGTGA
Found at i:465064 original size:105 final size:105
Alignment explanation
Indices: 464855--465079 Score: 279
Period size: 105 Copynumber: 2.1 Consensus size: 105
464845 GATTGTCCAT
* * * * *
464855 AAGGACCACATATATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCA
1 AAGGACCACGTAGA-AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCA
464920 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
65 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * * *
464961 AAGGATCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCGCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAA
* * * * * * *
465026 AGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
465066 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
465080 CCCTAGACCC
Statistics
Matches: 100, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
105 89 0.89
106 11 0.11
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAA
AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:465886 original size:21 final size:21
Alignment explanation
Indices: 465861--465903 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
465851 TCTGGTTCGT
*
465861 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
465882 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
465903 T
1 T
465904 AGCCCAGAAA
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:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:474949 original size:21 final size:21
Alignment explanation
Indices: 474923--474962 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
474913 CAGAACCCTA
*
474923 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
474944 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
474963 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:489060 original size:28 final size:28
Alignment explanation
Indices: 489029--489085 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
489019 ATTTATCATA
*
489029 AAAATAATATTA-TTATTTTTAAAATATT
1 AAAATAAT-TTATTTATTATTAAAATATT
489057 AAAATAATTTATTTATTATTAAAATATT
1 AAAATAATTTATTTATTATTAAAATATT
489085 A
1 A
489086 TTTTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATAATTTATTTATTATTAAAATATT
Found at i:489091 original size:20 final size:20
Alignment explanation
Indices: 489039--489092 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
489029 AAAATAATAT
*
489039 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
489061 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
489081 TATTATTTTTAT
1 TATTATTTTTAT
489093 ATTTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:489109 original size:48 final size:48
Alignment explanation
Indices: 489009--489111 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
488999 TAAATACAAT
489009 AAATAATATTATTTATCATAAAAATAATATTATTATTTTTAAAATATTA
1 AAATAATATTATTTATCATAAAAATAATATTATTATTTTTAAAATA-TA
* * * * *
489058 AAATAAT-TTATTTATTATTAAAATATTATTTTTATATTTTATTAATA-A
1 AAATAATATTATTTATCATAAAAATAATATTATTAT-TTTTA-AAATATA
489106 AAATAA
1 AAATAA
489112 AAATATTGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 31 0.66
49 12 0.26
50 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
AAATAATATTATTTATCATAAAAATAATATTATTATTTTTAAAATATA
Found at i:489219 original size:22 final size:23
Alignment explanation
Indices: 489181--489254 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
489171 TAATAGTGTT
*
489181 ATATATTTTAAAAATATTAATTA
1 ATATATTTTAAATATATTAATTA
*
489204 ATATA-TTTAAATATATTTATTA
1 ATATATTTTAAATATATTAATTA
* *
489226 AAATATTATTAGAT-TATTATATTA
1 ATATATT-TTAAATATATTA-ATTA
489250 ATATA
1 ATATA
489255 AATATATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
22 19 0.45
23 10 0.24
24 13 0.31
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATATATTTTAAATATATTAATTA
Found at i:489287 original size:19 final size:18
Alignment explanation
Indices: 489220--489287 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
489210 TTAAATATAT
489220 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATT--A
* *
489239 TTATTATATTAATATAAATA
1 TTATTA-A-TAATATTATTA
*
489259 -TATAAATAATATTATTCA
1 TTATTAATAATATTATT-A
489277 TTATTAATAAT
1 TTATTAATAAT
489288 TTAATAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 19 0.50
20 2 0.05
22 7 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TTATTAATAATATTATTA
Found at i:489323 original size:18 final size:18
Alignment explanation
Indices: 489300--489337 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
489290 AATAATATTT
489300 ATATGAAATTAATAAATA
1 ATATGAAATTAATAAATA
* *
489318 ATATGAAATTTATTAATA
1 ATATGAAATTAATAAATA
489336 AT
1 AT
489338 TATTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATGAAATTAATAAATA
Found at i:489424 original size:22 final size:23
Alignment explanation
Indices: 489399--489445 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
489389 TTGATTATTT
489399 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
489421 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
489444 TA
1 TA
489446 AATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:489450 original size:22 final size:22
Alignment explanation
Indices: 489407--489467 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
489397 TTTATTATAA
*
489407 TATTAAAAATA-TAATATTATAT
1 TATTAAAAATATTAATA-AATAT
*
489429 TATTAGAAATATTAATAAATAT
1 TATTAAAAATATTAATAAATAT
* *
489451 TTTTAAATAT-TTAATAA
1 TATTAAAAATATTAATAA
489468 TTAATATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 7 0.21
22 21 0.64
23 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTAAAAATATTAATAAATAT
Found at i:489452 original size:54 final size:53
Alignment explanation
Indices: 489328--489453 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 53
489318 ATATGAAATT
*
489328 TATTAATAATTATTATATATTATTAAAATAAAAATATAATATCTTATATTATTATA
1 TATTAATAATTATT-T-TATTATTAAAATAAAAATATAATA-CTTATATTATTAAA
* *
489384 TA-TAATTGATTATTTTATTA-TAATATTAAAAATATAATA-TTATATTATTAGAAA
1 TATTAA-TAATTATTTTATTATTAA-AATAAAAATATAATACTTATATTATT--AAA
*
489438 TATTAATAAATATTTT
1 TATTAATAATTATTTT
489454 TAAATATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
52 10 0.17
53 3 0.05
54 31 0.52
55 7 0.12
56 9 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (53 bp):
TATTAATAATTATTTTATTATTAAAATAAAAATATAATACTTATATTATTAAA
Found at i:491607 original size:18 final size:18
Alignment explanation
Indices: 491586--491620 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
491576 GATGAAATAT
491586 AAATGGCGTTGTCGTGGC
1 AAATGGCGTTGTCGTGGC
*
491604 AAATGGTGTTGTCGTGG
1 AAATGGCGTTGTCGTGG
491621 TAAGTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.40, T:0.31
Consensus pattern (18 bp):
AAATGGCGTTGTCGTGGC
Found at i:496616 original size:29 final size:29
Alignment explanation
Indices: 496581--496638 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
496571 TTGTTTAATC
*
496581 GGTTTCTAATTTGTATCTTTTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
*
496610 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
496639 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:497829 original size:20 final size:20
Alignment explanation
Indices: 497804--497841 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
497794 CTATATGAGT
497804 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
497824 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
497842 AAATGTATAA
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:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:500503 original size:151 final size:151
Alignment explanation
Indices: 500186--500492 Score: 555
Period size: 151 Copynumber: 2.0 Consensus size: 151
500176 GAGTCGAGGG
* * * *
500186 TTCTACGCGGTCATTCAGG--ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGGCA
1 TTCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTAAAGTCTTGTAAGACA
*
500249 CATACTTGATCCCTAGTATATGTATATTATTCTTAAGGAATAATATGTGGTCCTTATGGACATTA
66 CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTA
500314 TTATATGGCACTACGGTGCAA
131 TTATATGGCACTACGGTGCAA
500335 TTCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTAAAGTCTTGTAAGACA
1 TTCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTAAAGTCTTGTAAGACA
500400 CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTA
66 CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTA
500465 TTATATGGCACTACGGTGCAA
131 TTATATGGCACTACGGTGCAA
500486 TTCTACG
1 TTCTACG
500493 TGGCACTTCG
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 17 0.11
151 134 0.89
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (151 bp):
TTCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTAAAGTCTTGTAAGACA
CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTA
TTATATGGCACTACGGTGCAA
Done.