Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold422
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: 263912
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:186066 original size:5 final size:5
Alignment explanation
Indices: 186056--186112 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
186046 TTTAAATATT
* *
186056 TTATA TTATA TT-TA TTATA TTATT TTATA TT-TA TTA-A TTATG TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
186103 TTTATA TTAT
1 -TTATA TTAT
186113 GTTTTTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 12 0.27
5 27 0.61
6 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:186068 original size:24 final size:24
Alignment explanation
Indices: 186036--186121 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 24
186026 AAATACATCG
186036 TATTA-ATTTATT-TAAATATTTTA
1 TATTATATTTATTAT-AATATTTTA
*
186059 TATTATATTTATTATATTATTTTA
1 TATTATATTTATTATAATATTTTA
* **
186083 TATT-TATTAATTATGTTATATTTA
1 TATTATATTTATTATAATAT-TTTA
*
186107 TATTATGTTT-TTATA
1 TATTATATTTATTATA
186122 TAATGTATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
23 18 0.34
24 31 0.58
25 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTATATTTATTATAATATTTTA
Found at i:186083 original size:19 final size:18
Alignment explanation
Indices: 186056--186107 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
186046 TTTAAATATT
186056 TTATATTATATTTATTATA
1 TTATATTATATTTATTA-A
*
186075 TTATTTTATATTTATTAA
1 TTATATTATATTTATTAA
*
186093 TTATGTTATATTTAT
1 TTATATTATATTTAT
186108 ATTATGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATATTATATTTATTAA
Found at i:186122 original size:19 final size:19
Alignment explanation
Indices: 186061--186122 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
186051 ATATTTTATA
186061 TTATATTTAT-TATAT-TATT
1 TTATATTTATAT-TATGT-TT
186080 TTATATTTATTAATTATG---
1 TTATATTTA-T-ATTATGTTT
186098 TTATATTTATATTATGTTT
1 TTATATTTATATTATGTTT
186117 TTATAT
1 TTATAT
186123 AATGTATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 9 0.25
19 15 0.42
20 1 0.03
21 3 0.08
22 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTATATTTATATTATGTTT
Found at i:186127 original size:29 final size:28
Alignment explanation
Indices: 186070--186127 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
186060 ATTATATTTA
* *
186070 TTATATTATTTTATATTTATTAATTATG
1 TTATATTATATTATATTTATTAATAATG
*
186098 TTATATTTATATTATGTTT-TTATATAATG
1 TTATA-TTATATTATATTTATTA-ATAATG
186127 T
1 T
186128 ATACAAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
TTATATTATATTATATTTATTAATAATG
Found at i:190611 original size:8 final size:8
Alignment explanation
Indices: 190594--190623 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
190584 AATAACAATG
190594 TAAAAAAA
1 TAAAAAAA
*
190602 TAAAATAA
1 TAAAAAAA
190610 TAAAAAAA
1 TAAAAAAA
190618 TAAAAA
1 TAAAAA
190624 TTATTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:190792 original size:22 final size:22
Alignment explanation
Indices: 190767--190839 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
190757 AAGAGGTTAG
190767 TTCAATTAAAGTCATATGTACA
1 TTCAATTAAAGTCATATGTACA
* *
190789 TTCAATTAAAGTTATAGGTACA
1 TTCAATTAAAGTCATATGTACA
* * * *
190811 TTTAGTTATAGTCACATGTACA
1 TTCAATTAAAGTCATATGTACA
190833 TTCAATT
1 TTCAATT
190840 TTATTCGAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
TTCAATTAAAGTCATATGTACA
Found at i:191185 original size:2 final size:2
Alignment explanation
Indices: 191180--191236 Score: 71
Period size: 2 Copynumber: 27.5 Consensus size: 2
191170 TCGTTATTGT
*
191180 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA GT- TA TA GTCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -T-A TA
191222 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
191237 TTAATTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
1 1 0.02
2 44 0.90
3 3 0.06
4 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:191408 original size:22 final size:22
Alignment explanation
Indices: 191383--191425 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
191373 AGGTACATTT
* *
191383 AGTTATAGTCATATATGTATTC
1 AGTTATAATCATATATATATTC
*
191405 AGTTATAATTATATATATATT
1 AGTTATAATCATATATATATT
191426 TAATCTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (22 bp):
AGTTATAATCATATATATATTC
Found at i:191987 original size:53 final size:52
Alignment explanation
Indices: 191679--192444 Score: 762
Period size: 53 Copynumber: 14.9 Consensus size: 52
191669 AATACAAAGA
* * *
191679 TTAATATATTAAATATGTTTTTAA-TTTT-TTATTTTTAATTAGTAATTCGAGAT
1 TTAATATA--AAATAT-TTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* * *
191732 TTAATATAAAATATTTTTAAAATTTTA-T-TTTTTAAATAATAATTTAAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* *
191782 TTAATAT-AAA-A----TAATTTTTTATTATTTTTAAGTAGTAA-TTGAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* * * *
191827 TTGATAT--AAT-TTTTTTAATTTTTATTATTTTT-AATTGTAATTTCAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* * *
191875 TTAATATAAAAT-TTTTT-ATTTTTTATTATTTTTAAGTATTAATTTGAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
191925 TTAATATAAAATATTTTTAAATTTCTTATTATTTTTTAAATAGTAATTTGAGAT
1 TTAATATAAAATATTTTTAAATTT-TTATTA-TTTTTAAATAGTAATTTGAGAT
* * *
191979 TTAA-ATAAAATATTTTTGAGTTTTTATTATTTTTAAACAGTAATTT-AGGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGA-GAT
** * * *
192030 TTAATATAGTTATATATCTT-AATCTTT-TTATTTTTCAAATGGTAATTTGAGAT
1 TTAATATA-AAATAT-TTTTAAATTTTTATTATTTTT-AAATAGTAATTTGAGAT
* * * * *
192083 TTAATATAAAATATATTTTTAAATTTATATTATTTTTAGATAATATTTTGTGAT
1 TTAATAT-AAA-ATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* *
192137 TTAATATAAAATATATTTTATATTTTTATTATTTTTAAATAGTAA-TTCAGGAT
1 TTAATATAAAATAT-TTTTAAATTTTTATTATTTTTAAATAGTAATTTGA-GAT
* *
192190 TCAATATAAAATATTTTTAAA-ATTTATTATTTTTAAATAGTAATTTGAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
* * *
192241 TTAATATAAAATA-TTTT-ATTTTTTATTAGTTTTAAA-AGT-ATTTTAGGAT
1 TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGA-GAT
* * *
192290 TTAATATAAACTATTTTTTAATTTTTATTATTTTTTAAATAGTGATTTGAGAT
1 TTAATATAAAATATTTTTAAATTTTTATTA-TTTTTAAATAGTAATTTGAGAT
*
192343 TTAATATAAAATATACATTTTAAAATTTTTATTATTTTTAAATGGTAATTCT-AGAT
1 TTAATATAAAATAT---TTTT-AAATTTTTATTATTTTTAAATAGTAATT-TGAGAT
* * *
192399 TT-ATATAAAATATTTTAAAATATTTTATAATTTTTAAATAATAATT
1 TTAATATAAAATATTTTTAAAT-TTTTATTATTTTTAAATAGTAATT
192445 CAAGATTAAA
Statistics
Matches: 597, Mismatches: 73, Indels: 87
0.79 0.10 0.11
Matches are distributed among these distances:
44 10 0.02
45 13 0.02
46 12 0.02
47 6 0.01
48 34 0.06
49 37 0.06
50 86 0.14
51 89 0.15
52 67 0.11
53 126 0.21
54 62 0.10
55 19 0.03
56 24 0.04
57 12 0.02
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (52 bp):
TTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATAGTAATTTGAGAT
Found at i:192119 original size:158 final size:157
Alignment explanation
Indices: 191679--192444 Score: 713
Period size: 158 Copynumber: 5.0 Consensus size: 157
191669 AATACAAAGA
* *
191679 TTAATATATTAAATATGTTTTTAA-TTTT-TTATTTTTAATTAGTAA-TTCGAGATTTAATATAA
1 TTAATATA--AAATAT-TTTTTAATTTTTATTATTTTTAAATAGTAATTTAG-GATTTAATATAA
* * * *
191741 AATAT-TTTTAAAATTTTA-T-TTTTTAAATAATAATTTAAGATTTAATATAAAATA-A---TT-
62 TATATATTTT-AATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTA
*
191798 --TTTTATTATTTTTAAGTAGTAA-TTGAGAT
126 AATTTTATTATTTTTAAATAGTAATTTGAGAT
* *
191827 TTGATAT--AAT-TTTTTTAATTTTTATTATTTTT-AATTGTAATTTCA-GATTTAATATAA-A-
1 TTAATATAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTT-AGGATTTAATATAATAT
* * * *
191885 ATTTTTTATTTTTTATTATTTTTAAGTATTAATTTGAGATTTAATAT-AAA-ATATTTTTAAATT
65 ATATTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAAA-T
191948 TCTTATTATTTTTTAAATAGTAATTTGAGAT
129 T-TTATTA-TTTTTAAATAGTAATTTGAGAT
* * * *
191979 TTAA-ATAAAATATTTTTGAGTTTTTATTATTTTTAAACAGTAATTTAGGATTTAATATAGTTAT
1 TTAATATAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTAGGATTTAATATA-ATAT
* * *
192043 ATATCTTAATCTTT-TTATTTTTCAAATGGTAATTTGAGATTTAATATAAAATATATTTTTAAAT
65 ATATTTTAATTTTTATTATTTTT-AAATAGTAATTTGAGATTTAATATAAAATATATTTTTAAAT
* * * *
192107 TTATATTATTTTTAGATAATATTTTGTGAT
129 TT-TATTATTTTTAAATAGTAATTTGAGAT
* * * *
192137 TTAATATAAAATATATTTTATATTTTTATTATTTTTAAATAGTAATTCAGGATTCAATATAAAAT
1 TTAATATAAAATATTTTTTA-ATTTTTATTATTTTTAAATAGTAATTTAGGATTTAATATAATAT
**
192202 AT-TTTTAAAATTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATAT-TTTATT---T
65 ATATTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTT-TTAAAT
* *
192262 TTTATTAGTTTTAAA-AGT-ATTTTAGGAT
129 TTTATTATTTTTAAATAGTAATTTGA-GAT
* *
192290 TTAATATAAACTATTTTTTAATTTTTATTATTTTTTAAATAGTGATTT-GAGATTTAATATAAAA
1 TTAATATAAAATATTTTTTAATTTTTATTA-TTTTTAAATAGTAATTTAG-GATTTAATAT--AA
* * *
192354 TATACATTTTAAAATTTTTATTATTTTTAAATGGTAATTCT-AGATTT-ATATAAAATAT-TTTA
62 TATATATTTT--AATTTTTATTATTTTTAAATAGTAATT-TGAGATTTAATATAAAATATATTTT
* * *
192416 AAATATTTTATAATTTTTAAATAATAATT
124 TAA-ATTTTATTATTTTTAAATAGTAATT
192445 CAAGATTAAA
Statistics
Matches: 509, Mismatches: 60, Indels: 84
0.78 0.09 0.13
Matches are distributed among these distances:
141 9 0.02
142 17 0.03
143 49 0.10
144 13 0.03
145 2 0.00
148 6 0.01
149 2 0.00
150 6 0.01
151 15 0.03
152 24 0.05
153 50 0.10
154 32 0.06
155 28 0.06
156 4 0.01
157 26 0.05
158 124 0.24
159 36 0.07
160 61 0.12
161 2 0.00
162 3 0.01
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (157 bp):
TTAATATAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTAGGATTTAATATAATATA
TATTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAAATTT
TATTATTTTTAAATAGTAATTTGAGAT
Found at i:192204 original size:44 final size:44
Alignment explanation
Indices: 192156--192264 Score: 107
Period size: 51 Copynumber: 2.4 Consensus size: 44
192146 AATATATTTT
192156 ATATTTTTATTATTTTTAAATAGTAATTCAG-GATTCAATATAAA
1 ATATTTTTATTATTTTTAAATAGTAATT-AGAGATTCAATATAAA
* *
192200 ATATTTTTAAAATTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAA
1 ATA---TT----TTTATTATTTTTAAATAGTAATTAGAGATTCAATATAAA
192251 ATA-TTTTATT-TTTT
1 ATATTTTTATTATTTT
192265 ATTAGTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
42 4 0.07
43 6 0.11
44 3 0.05
47 3 0.05
50 1 0.02
51 38 0.69
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (44 bp):
ATATTTTTATTATTTTTAAATAGTAATTAGAGATTCAATATAAA
Found at i:192419 original size:10 final size:10
Alignment explanation
Indices: 192404--192436 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
192394 TAGATTTATA
192404 TAAAATATTT
1 TAAAATATTT
192414 TAAAATATTT
1 TAAAATATTT
*
192424 TATAAT-TTT
1 TAAAATATTT
192433 TAAA
1 TAAA
192437 TAATAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAAATATTT
Found at i:192464 original size:51 final size:53
Alignment explanation
Indices: 192347--192474 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 53
192337 TGAGATTTAA
* * ** *
192347 TATAAAATATACATTTTAAAAT-TTTTATTATTTTTAAATGGTAATTCTAGATT
1 TATAAAATAT-TATTTTAAAATATTTTATAATTTTTAAATAATAATTCAAGATT
192400 TATATAAA-A-TATTTTAAAATATTTTATAATTTTTAAATAATAATTCAAGA-T
1 TATA-AAATATTATTTTAAAATATTTTATAATTTTTAAATAATAATTCAAGATT
*
192451 TA-AAAATATTATTTAAAAAATATT
1 TATAAAATATTATTT-TAAAATATT
192475 ATTAGTCATA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
49 3 0.05
50 2 0.03
51 18 0.28
52 33 0.52
53 5 0.08
54 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (53 bp):
TATAAAATATTATTTTAAAATATTTTATAATTTTTAAATAATAATTCAAGATT
Found at i:192535 original size:20 final size:21
Alignment explanation
Indices: 192487--192535 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
192477 TAGTCATAAT
*
192487 TGTTCTT-CTCAACATGAACC
1 TGTTCTTCCTCAACATGAACA
*
192507 TTTTC-TCCTCAACATGAA-A
1 TGTTCTTCCTCAACATGAACA
192526 TGTTCTTCCT
1 TGTTCTTCCT
192536 TCAGCTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (21 bp):
TGTTCTTCCTCAACATGAACA
Found at i:193265 original size:27 final size:27
Alignment explanation
Indices: 193206--193279 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
193196 TTCAAGAATA
* **
193206 AAAAACATTTAATTAGAAATTCTATGTG
1 AAAAA-ATCTAATTAGAAATTCTATACG
193234 AAAAAATCTAATTAGAAATTCTATACG
1 AAAAAATCTAATTAGAAATTCTATACG
* * *
193261 TAAAAGTTTAATTA-AAATT
1 AAAAAATCTAATTAGAAATT
193280 TTAATGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 5 0.12
27 30 0.75
28 5 0.12
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (27 bp):
AAAAAATCTAATTAGAAATTCTATACG
Found at i:193502 original size:29 final size:29
Alignment explanation
Indices: 193471--193525 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
193461 AGTTTAGTTA
* *
193471 AAAATTTTAATTT-AGAGTTTCTATATGT
1 AAAATTCTAATTTGAGAGTTTATATATGT
*
193499 AAAATTCTAATTTGAGATTTTATATAT
1 AAAATTCTAATTTGAGAGTTTATATAT
193526 AGGAGTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (29 bp):
AAAATTCTAATTTGAGAGTTTATATATGT
Found at i:194238 original size:65 final size:65
Alignment explanation
Indices: 194155--194317 Score: 157
Period size: 65 Copynumber: 2.5 Consensus size: 65
194145 TTTCAAAAAA
* * * * * *
194155 AAAATAAATTTAAATTAAAAAGAAAATATTTAAATGATGATCTCTAAGCTCGACTTGCTT-AGAA
1 AAAATAAGTTCAACTTAAAAAGAAAATACTTAAATGATAATCTCTAAGCTCAACTTG-TTCAGAA
194219 G
65 G
* * * * * * * *
194220 AAGATAAGTTCAATTTAAAAAGAAAAGACTTAGATGGTAATCTCTAGGCTTAACTTGTTCATAAG
1 AAAATAAGTTCAACTTAAAAAGAAAATACTTAAATGATAATCTCTAAGCTCAACTTGTTCAGAAG
**
194285 AAAATAAGTTTGACTTAAAAAGAAAATAACTTA
1 AAAATAAGTTCAACTTAAAAAGAAAAT-ACTTA
194318 GATGGCAATC
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
64 2 0.03
65 71 0.91
66 5 0.06
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.30
Consensus pattern (65 bp):
AAAATAAGTTCAACTTAAAAAGAAAATACTTAAATGATAATCTCTAAGCTCAACTTGTTCAGAAG
Found at i:194720 original size:27 final size:26
Alignment explanation
Indices: 194688--194755 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
194678 TATATAAGAG
194688 TTTAATTAAAAATTTTACATGTG-AAAA
1 TTTAATTAAAAATTTT--ATGTGAAAAA
* * *
194715 TTTAATTGAGAATTTTATTTGAAAAA
1 TTTAATTAAAAATTTTATGTGAAAAA
*
194741 GTTAATTAAAAATTT
1 TTTAATTAAAAATTT
194756 CACAAAATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.12
26 16 0.47
27 14 0.41
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (26 bp):
TTTAATTAAAAATTTTATGTGAAAAA
Found at i:197377 original size:26 final size:26
Alignment explanation
Indices: 197316--197377 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
197306 AATAATATTA
* *
197316 TTTAAATTAATTAAAAATATATAAAT
1 TTTAAATAAAATAAAAATATATAAAT
* *
197342 ATTAATATAAAATAAAAATTTA-AAATT
1 TTTAA-ATAAAATAAAAATATATAAA-T
197369 TTTAAATAA
1 TTTAAATAA
197378 TGCTATAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTAAATAAAATAAAAATATATAAAT
Found at i:200711 original size:2 final size:2
Alignment explanation
Indices: 200704--200738 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
200694 TTCTTCTTCA
200704 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
200739 ATCTATATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:200753 original size:2 final size:2
Alignment explanation
Indices: 200742--200793 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
200732 TCTCTCTATC
* * *
200742 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
200784 TA TA T- TA TA T
1 TA TA TA TA TA T
200794 TAAAACACGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:207692 original size:18 final size:18
Alignment explanation
Indices: 207669--207705 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
207659 ACTGCTTTGC
207669 ATACTCATATCTCAAGCT
1 ATACTCATATCTCAAGCT
207687 ATACTCATATCTCAAGCT
1 ATACTCATATCTCAAGCT
207705 A
1 A
207706 ATGTGTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ATACTCATATCTCAAGCT
Found at i:211452 original size:33 final size:33
Alignment explanation
Indices: 211415--211481 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
211405 TTCAACGATT
211415 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
211448 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
211481 T
1 T
211482 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:211453 original size:13 final size:13
Alignment explanation
Indices: 211435--211459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211425 CATAAAATGT
211435 TGTATCGATACAA
1 TGTATCGATACAA
211448 TGTATCGATACA
1 TGTATCGATACA
211460 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:211540 original size:13 final size:13
Alignment explanation
Indices: 211522--211546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211512 ATTACTCAAA
211522 TGTATCGATACAT
1 TGTATCGATACAT
211535 TGTATCGATACA
1 TGTATCGATACA
211547 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:211648 original size:52 final size:52
Alignment explanation
Indices: 211555--211682 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
211545 CACTGATCTT
*
211555 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
211606 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
211658 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
211683 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:215580 original size:21 final size:21
Alignment explanation
Indices: 215556--215608 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
215546 AAAGTTGTTT
*
215556 TTTCATCCAAAAAATGCATTC-
1 TTTCATCCAAAAAATACA-TCA
* **
215577 TTTCATTCAACCAATACATCA
1 TTTCATCCAAAAAATACATCA
215598 TTTCATCCAAA
1 TTTCATCCAAA
215609 TACATATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (21 bp):
TTTCATCCAAAAAATACATCA
Found at i:217274 original size:9 final size:8
Alignment explanation
Indices: 217262--217309 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
217252 TTTTCGACTT
217262 TTTTTTCAA
1 TTTTTT-AA
*
217271 TTTTTTATT
1 TTTTTTA-A
217280 TTTTTTAA
1 TTTTTTAA
*
217288 TTTTTTAG
1 TTTTTTAA
*
217296 TTTTTTTA
1 TTTTTTAA
217304 TTTTTT
1 TTTTTT
217310 TAAAACGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
8 20 0.61
9 13 0.39
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTTTAA
Found at i:217282 original size:8 final size:8
Alignment explanation
Indices: 217261--217311 Score: 57
Period size: 9 Copynumber: 6.0 Consensus size: 8
217251 TTTTTCGACT
217261 TTTTTTTCA
1 TTTTTTT-A
*
217270 ATTTTTTA
1 TTTTTTTA
217278 TTTTTTTTA
1 -TTTTTTTA
*
217287 ATTTTTTA
1 TTTTTTTA
217295 GTTTTTTTA
1 -TTTTTTTA
217304 TTTTTTTA
1 TTTTTTTA
217312 AAACGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 16 0.44
9 20 0.56
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:217283 original size:17 final size:17
Alignment explanation
Indices: 217261--217311 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
217251 TTTTTCGACT
*
217261 TTTTTTTCAATTTTTTAT
1 TTTTTTT-AATTTTTTAG
217279 TTTTTTTAATTTTTTAG
1 TTTTTTTAATTTTTTAG
*
217296 TTTTTTTATTTTTTTA
1 TTTTTTTAATTTTTTA
217312 AAACGTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTTAATTTTTTAG
Found at i:218098 original size:13 final size:14
Alignment explanation
Indices: 218080--218114 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
218070 AATTGCTAAA
218080 TTTTTTTCATGA-T
1 TTTTTTTCATGAGT
218093 TTTTTTTCATGAGGT
1 TTTTTTTCATGA-GT
218108 TTTTTTT
1 TTTTTTT
218115 TTTTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.71
Consensus pattern (14 bp):
TTTTTTTCATGAGT
Found at i:218410 original size:2 final size:2
Alignment explanation
Indices: 218405--218443 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
218395 AACATTAATA
218405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218444 AGTGGATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:221415 original size:89 final size:88
Alignment explanation
Indices: 221308--221564 Score: 327
Period size: 89 Copynumber: 2.9 Consensus size: 88
221298 CTTGGAATCG
* * *
221308 GAAAGATGTGATAGATGCATATGGGTATCAGATTGCTTCTAACATGATAGAAAATATTTGACTAA
1 GAAAGATGTGACAGATGCATGTGGGTATCAGATT-CTTCTAACACGATAGAAAATATTTGACTAA
221373 TGCCTAATAAATTTCTTGAAACCC
65 TGCCTAATAAATTTCTTGAAACCC
* * * * *
221397 GAAAGATGTGACAAATGCATGCGGGTAAT-AGATTCTTTCTGACACAATAGAAAATATTGGACTA
1 GAAAGATGTGACAGATGCATGTGGGT-ATCAGATTC-TTCTAACACGATAGAAAATATTTGACTA
* *
221461 ATGCCTAATAAATTTCTTGAGACTC
64 ATGCCTAATAAATTTCTTGAAACCC
* ** * * *
221486 GAAAGATGTGACAGATACATGTAAGTATCATATTCCTTCTAACACGAAAGACAATATTTGACTAA
1 GAAAGATGTGACAGATGCATGTGGGTATCAGATT-CTTCTAACACGATAGAAAATATTTGACTAA
221551 TGCCTAATAAATTT
65 TGCCTAATAAATTT
221565 TTTGGAATCA
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
88 3 0.02
89 137 0.96
90 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (88 bp):
GAAAGATGTGACAGATGCATGTGGGTATCAGATTCTTCTAACACGATAGAAAATATTTGACTAAT
GCCTAATAAATTTCTTGAAACCC
Found at i:221711 original size:148 final size:149
Alignment explanation
Indices: 221429--221715 Score: 380
Period size: 148 Copynumber: 1.9 Consensus size: 149
221419 GGGTAATAGA
* * * *
221429 TTCTTTCTGACACAATAGAAAATATTGGACTAATGCCTAATAAATTTCTTGAGACTCGAAAGATG
1 TTCTTTCTGACACAATAAAAAATATTGAACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATG
* * * *
221494 TGACAGATACATGTAAGTATCATATTCCTTCTAACACGAAAGACAATATTTGACTAATGCCTAAT
66 TGACAGATACATGTAAGTATCAGATTCCTTCTAACACGAAAGAAAATATTTGACTAATACCTAAC
221559 AAATTTTTTGGAATCAGAT
131 AAATTTTTTGGAATCAGAT
** *
221578 TTCTTT-TGACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATG
1 TTCTTTCTGACACAATAAAAAATATTGAACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATG
* * ** * * * *
221642 TGATAGATGCATGTGGGTATCAGATTCCTTTTGACACGATAGAAAATATTTGA-TAAATATCTAA
66 TGACAGATACATGTAAGTATCAGATTCCTTCTAACACGAAAGAAAATATTTGACT-AATACCTAA
221706 CAAATTTTTT
130 CAAATTTTTT
221716 AGAACCCGAA
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
147 1 0.01
148 111 0.94
149 6 0.05
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (149 bp):
TTCTTTCTGACACAATAAAAAATATTGAACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATG
TGACAGATACATGTAAGTATCAGATTCCTTCTAACACGAAAGAAAATATTTGACTAATACCTAAC
AAATTTTTTGGAATCAGAT
Found at i:221722 original size:89 final size:89
Alignment explanation
Indices: 221571--221769 Score: 258
Period size: 89 Copynumber: 2.2 Consensus size: 89
221561 ATTTTTTGGA
* * * *
221571 ATCAGATTTCTTTTGACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGA
1 ATCAGATTCCTTTTGACACGATAAAAAATATTTAACTAATACCTAACAAATTTCTTGAAACCCGA
* *
221636 AAGATGTGATAGATGCATGTGGGT
66 AAGATGTGACAAATGCATGTGGGT
* * * *
221660 ATCAGATTCCTTTTGACACGATAGAAAATATTTGA-TAAATATCTAACAAATTT-TTTAGAACCC
1 ATCAGATTCCTTTTGACACGATAAAAAATATTTAACT-AATACCTAACAAATTTCTTGA-AACCC
221723 GAAAGATGTGACAAATGCATGTGGGT
64 GAAAGATGTGACAAATGCATGTGGGT
* *
221749 ATCAAATTCCTTCTGACACGA
1 ATCAGATTCCTTTTGACACGA
221770 CTAATTTTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
88 4 0.04
89 92 0.96
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (89 bp):
ATCAGATTCCTTTTGACACGATAAAAAATATTTAACTAATACCTAACAAATTTCTTGAAACCCGA
AAGATGTGACAAATGCATGTGGGT
Found at i:221760 original size:237 final size:237
Alignment explanation
Indices: 221334--221769 Score: 619
Period size: 237 Copynumber: 1.8 Consensus size: 237
221324 GCATATGGGT
* *
221334 ATCAGATTGCTTCTAACATGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGAAACCCGA
1 ATCAGATTGCTTCTAACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGA
*
221399 AAGATGTGACAAATGCATGCGGGTAATAGATTCTTTCTGACACAATAGAAAATATTGGACTAATG
66 AAGATGTGACAAATGCATGCGGGTAATAGATTCTTTCTGACACAATAGAAAATATTGGACTAATA
* * * *
221464 CCTAATAAATTTCTTGAGACTCGAAAGATGTGACAGATACATGTAAGTATCATATTCCTTCTAAC
131 CCTAACAAATTTCTTGAGACCCGAAAGATGTGACAAATACATGTAAGTATCAAATTCCTTCTAAC
221529 ACGAAAGACAATATTTGACTAATGCCTAATAAATTTTTTGGA
196 ACGAAAGACAATATTTGACTAATGCCTAATAAATTTTTTGGA
* * *
221571 ATCAGATTTCTTTTGACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGA
1 ATCAGATTGCTTCTAACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGA
* * * * *
221636 AAGATGTGATAGATGCATGTGGGT-ATCAGATTCCTTT-TGACACGATAGAAAATATTTGA-TAA
66 AAGATGTGACAAATGCATGCGGGTAAT-AGATT-CTTTCTGACACAATAGAAAATATTGGACT-A
* * * **
221698 ATATCTAACAAATTT-TTTAGAACCCGAAAGATGTGACAAATGCATGTGGGTATCAAATTCCTTC
128 ATACCTAACAAATTTCTTGAG-ACCCGAAAGATGTGACAAATACATGTAAGTATCAAATTCCTTC
*
221762 TGACACGA
192 TAACACGA
221770 CTAATTTTTT
Statistics
Matches: 174, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
236 7 0.04
237 163 0.94
238 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (237 bp):
ATCAGATTGCTTCTAACATGATAAAAAATATTTAACTAATGCCTAATAAATTTCTTGAAACCCGA
AAGATGTGACAAATGCATGCGGGTAATAGATTCTTTCTGACACAATAGAAAATATTGGACTAATA
CCTAACAAATTTCTTGAGACCCGAAAGATGTGACAAATACATGTAAGTATCAAATTCCTTCTAAC
ACGAAAGACAATATTTGACTAATGCCTAATAAATTTTTTGGA
Found at i:225274 original size:24 final size:25
Alignment explanation
Indices: 225226--225274 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
225216 AAAAATTAAT
* * *
225226 AATATAACTTAAAAAATTTATAAAA
1 AATATAACTTAAAAAACTAAAAAAA
225251 AATAT-ACTTAAAAAACTAAAAAAA
1 AATATAACTTAAAAAACTAAAAAAA
225275 CAAAAAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (25 bp):
AATATAACTTAAAAAACTAAAAAAA
Found at i:225807 original size:33 final size:33
Alignment explanation
Indices: 225742--225813 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
225732 ATATTATATA
**
225742 TTTATAATAAATTTTAATTTATTAATAATTTAT
1 TTTATAATAAATTTTAAAATATTAATAATTTAT
*
225775 TTTAT-ATAAATTTTAAAATATTTAT-ATTT-T
1 TTTATAATAAATTTTAAAATATTAATAATTTAT
*
225805 TATATAATA
1 TTTATAATA
225814 TTTATGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 5 0.15
31 7 0.21
32 17 0.50
33 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATAATAAATTTTAAAATATTAATAATTTAT
Found at i:226736 original size:89 final size:90
Alignment explanation
Indices: 226577--226751 Score: 264
Period size: 89 Copynumber: 2.0 Consensus size: 90
226567 TTTTACAGCC
* * *
226577 TTAACCATATAGTCAAGTAGTAATAAGCAATGGTGTTTTATCAACTGAATATCTAATTTCTCTAT
1 TTAACCATATAGTCAAGTAGTAATAAGCAATGGTGTTTCATCAACTGAATATCCAATTTCTCTAA
226642 AAGGAATTCAATA-TCTACAAAACTT
66 AAGGAATTCAATACTC-ACAAAACTT
* * * *
226667 TTAATCATATAGTCAAGTAGTAATGATCAATGGTG-TTCATCAATTGAATATCCAATTTCTCTAA
1 TTAACCATATAGTCAAGTAGTAATAAGCAATGGTGTTTCATCAACTGAATATCCAATTTCTCTAA
226731 AAGGAATTCAATACTCACAAA
66 AAGGAATTCAATACTCACAAA
226752 GTTAGGATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 43 0.56
90 34 0.44
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (90 bp):
TTAACCATATAGTCAAGTAGTAATAAGCAATGGTGTTTCATCAACTGAATATCCAATTTCTCTAA
AAGGAATTCAATACTCACAAAACTT
Found at i:233128 original size:20 final size:20
Alignment explanation
Indices: 233078--233141 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
233068 CCCTTATTTG
*
233078 TATCAATAC-ATACCAAAATG
1 TATCAATACAATA-CAAAATA
* *
233098 TATCGATACAATACACAATA
1 TATCAATACAATACAAAATA
* *
233118 TATCAATACAATATATAATA
1 TATCAATACAATACAAAATA
233138 TATC
1 TATC
233142 GACACATCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 34 0.92
21 3 0.08
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (20 bp):
TATCAATACAATACAAAATA
Found at i:233366 original size:16 final size:16
Alignment explanation
Indices: 233340--233372 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
233330 TGATATTCCA
233340 ATTTCTTTTTGTATCTC
1 ATTTCTTTTTGTA-CTC
233357 ATTT-TTTTTGTACTC
1 ATTTCTTTTTGTACTC
233372 A
1 A
233373 AATTTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.64
Consensus pattern (16 bp):
ATTTCTTTTTGTACTC
Found at i:233377 original size:17 final size:17
Alignment explanation
Indices: 233338--233378 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
233328 TGTGATATTC
233338 CAATTTCTTTTTGTATCT
1 CAATTT-TTTTTGTATCT
233356 C-ATTTTTTTTGTA-CT
1 CAATTTTTTTTGTATCT
233371 CAAATTTT
1 C-AATTTT
233379 AGTAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 9 0.43
18 1 0.05
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.61
Consensus pattern (17 bp):
CAATTTTTTTTGTATCT
Found at i:236060 original size:140 final size:138
Alignment explanation
Indices: 235816--236326 Score: 541
Period size: 140 Copynumber: 3.7 Consensus size: 138
235806 TAAATTTTTC
* * * *
235816 AAATCTCATTTC-TACCTTAATAGAAAACTAAGAAAATACGAAAAGTTTTGAAAATTTCTATAAC
1 AAAT-TCATTTCGTACCTTAATGGAAAACTAA-AAAATACAAAAAGTTTTAAAAATTTCTATACC
* ** *
235880 CATACCCAAAACCATAGGAATATAAAAATCTTGAAAAATTAAGGCAATAATTTTTATTTAATTTT
64 CTTACGAAAAACCATAGGAATATAGAAATCTTGAAAAATTAAGG-AATAATTTTTATTTAA-TTT
235945 TTTAA-TTTAAA
127 TTTAATTTTAAA
* * * * * *
235956 AAATTCATTTCGTACCTTCATGGACAACCAAAAAGATACGAAAAGTTTTAAAAATTTTTACACCC
1 AAATTCATTTCGTACCTTAATGGAAAACTAAAAA-ATACAAAAAGTTTTAAAAATTTCTATACCC
* * *
236021 TTACGAAAAATCATAAGAATATAGAAATCTTGAAAAATTAA-GACTAATTTTTATTTAATTTTTT
65 TTACGAAAAACCATAGGAATATAGAAATCTTGAAAAATTAAGGAATAATTTTTATTTAATTTTTT
236085 AATTTTAAA
130 AATTTTAAA
* * * *
236094 AAATTCATTT-GTACCTTAATGGAGAACT-AAAAAGACAAAAAGTTTTTAAGATTTCTATA-CCT
1 AAATTCATTTCGTACCTTAATGGAAAACTAAAAAATACAAAAAGTTTTAAAAATTTCTATACCCT
* * * * * *
236156 ATAAGGAAAACCATAGGAATATTAGAAATTTTGAAAAATTAAGATAATAATTTTTATCTGA-TTT
66 -TACGAAAAACCATAGGAATA-TAGAAATCTTGAAAAATTAAG-GAATAATTTTTATTTAATTTT
*
236220 TTAATTTTTATGA
128 TTAA-TTTTA-AA
* * * * *
236233 AAATTCATTTTGTACCTTAATTGAAAATCGAAAAAATACAAAAAGTTTCAAAGATTTCTATACCC
1 AAATTCATTTCGTACCTTAATGGAAAA-CTAAAAAATACAAAAAGTTTTAAAAATTTCTATACCC
* * *
236298 TTACGGATAACCATAGAAATAATAGAAAT
65 TTACGAAAAACCATAGGAAT-ATAGAAAT
236327 ATATAAAAAA
Statistics
Matches: 314, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
134 3 0.01
135 37 0.12
136 23 0.07
137 30 0.10
138 49 0.16
139 22 0.07
140 94 0.30
141 1 0.00
142 51 0.16
143 4 0.01
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (138 bp):
AAATTCATTTCGTACCTTAATGGAAAACTAAAAAATACAAAAAGTTTTAAAAATTTCTATACCCT
TACGAAAAACCATAGGAATATAGAAATCTTGAAAAATTAAGGAATAATTTTTATTTAATTTTTTA
ATTTTAAA
Found at i:237258 original size:166 final size:167
Alignment explanation
Indices: 237062--237891 Score: 590
Period size: 166 Copynumber: 5.0 Consensus size: 167
237052 GACAACATTA
* * ** *
237062 GATGAAT-TTTAAAATTTTAAATTAAGAAAAATCCCTCTGAAAACATTTATAGAACAGAAAACTC
1 GATGAATATTAAAAATTATAAACCAAGAAAAATCCCTCTGAAAACATTTATAGAAAAGAAAACTC
* *
237126 GATTTTTTGAAAACAGGAG-AATTTCAAGAAAAAAATGAAAAACTCACGAAAATAAATAAATTTT
66 GATTTTTCGAAAACAGGAGAAATTTCAAGAAAAAAATGAAAAACTCATGAAAATAAATAAATTTT
* ** * *
237190 TCAAAACTGATTTACTACACTTTAATTGGTGATATTT
131 TCAAAACTGATTTAATACAAATTAAATGATGATATTT
* * * * * * *
237227 GATGAATATTAAAAATTTTGAACCGAGAAAAA-CTCTCTCGAAAACATTTATGGAATAGAGAACT
1 GATGAATATTAAAAATTATAAACCAAGAAAAATCCCTCT-GAAAACATTTATAGAAAAGAAAACT
* * * * * *
237291 CTAGTTTTCGAAAAAAAAGG-GAAATTT-AAAAAAAAAATGAAAAACTCATGAAAAGAAATTAA-
65 CGATTTTTCG--AAAACAGGAGAAATTTCAAGAAAAAAATGAAAAACTCATGAAAATAAATAAAT
* *
237353 TTTTCAAAACTAATTTAATATAAATTAAATGATGATATTT
128 TTTTCAAAACTGATTTAATACAAATTAAATGATGATATTT
* * * * *
237393 GATGAATTTTAAAAATTATAAACTAAGAAAAAT-CCTCCTGAAAATATTTACAGAGTAAAAAAAA
1 GATGAATATTAAAAATTATAAACCAAGAAAAATCCCT-CTGAAAACATTT----A-TAGAAAAGA
* * * * *
237457 AAACTTCG-TATTTCAAAAACA-GAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAAC
60 AAAC-TCGATTTTTCGAAAACAGGAGAAATTTCAAGAAAAAAATGAAAAACTCATGAAAATAAAT
* * ** *
237520 GAATTTTTCAAAATTGATTTAATATGAATTAAATAATGATATTT
124 AAATTTTTCAAAACTGATTTAATACAAATTAAATGATGATATTT
* * * * * * * * * *
237564 GATGGATTTTAATAATTATAAACTAAGAAAAATCTCTCCGAAAATATTTACAGAGTAAAAAAAAG
1 GATGAATATTAAAAATTATAAACCAAGAAAAATCCCTCTGAAAACATTTATAGA--AAAGAAAAC
* * * * * * *
237629 TACG-TATTTCAAAAATA-AAGAAATTTCAAGAAAAAAAATGAAAAACTAATGAAAGTAAATGAA
64 T-CGATTTTTCGAAAACAGGAGAAATTTCAAG-AAAAAAATGAAAAACTCATGAAAATAAATAAA
* ** * *
237692 -TTTTCAAAA---ATTTAGTATGAATTAAATAATAATATTT
127 TTTTTCAAAACTGATTTAATACAAATTAAATGATGATATTT
* * * * * *
237729 GATGGATTTTAATAATTATAAACCAAGAAAAA-GCCTCCCGAAAACATTTATAGAATAGAAAACA
1 GATGAATATTAAAAATTATAAACCAAGAAAAATCCCT-CTGAAAACATTTATAGAAAAGAAAAC-
* * * * * *
237793 T-GATTTTTC-AAAA-A-AAAAAATTTCAA-AGAAAAAA-GAAAAATTAATGAATA-AAATGAAT
64 TCGATTTTTCGAAAACAGGAGAAATTTCAAGA-AAAAAATGAAAAACTCATGAAAATAAAT-AAA
** * * ***
237851 TTTTTTTAAACTAATTTGATGGTAATTAAATGATGATATTT
127 TTTTTCAAAACTGATTTAATACAAATTAAATGATGATATTT
237892 AAAGAATTTT
Statistics
Matches: 548, Mismatches: 87, Indels: 62
0.79 0.12 0.09
Matches are distributed among these distances:
158 4 0.01
159 15 0.03
160 13 0.02
161 12 0.02
162 5 0.01
163 32 0.06
164 3 0.01
165 84 0.15
166 121 0.22
167 36 0.07
168 56 0.10
169 43 0.08
170 30 0.05
171 90 0.16
172 4 0.01
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (167 bp):
GATGAATATTAAAAATTATAAACCAAGAAAAATCCCTCTGAAAACATTTATAGAAAAGAAAACTC
GATTTTTCGAAAACAGGAGAAATTTCAAGAAAAAAATGAAAAACTCATGAAAATAAATAAATTTT
TCAAAACTGATTTAATACAAATTAAATGATGATATTT
Found at i:237527 original size:337 final size:336
Alignment explanation
Indices: 237135--237778 Score: 775
Period size: 337 Copynumber: 1.9 Consensus size: 336
237125 CGATTTTTTG
* *
237135 AAAACAGGAGAATTTCAAGAAAAAAATGAAAAACTCACGAAAATAAATAAATTTTTCAAAACTGA
1 AAAACAGGAGAATTTCAAGAAAAAAATGAAAAACTAACGAAAATAAACAAATTTTTCAAAACTGA
* * * ** * * *
237200 TTTACTA-CACTTTAATTGGTGATATTTGATGAATATTAAAAATTTTGAACCGAGAAAAA-CTCT
66 TTTAATATCA-ATTAAATAATGATATTTGATGAATATTAAAAATTATAAACCAAGAAAAATCTCT
** * * **
237263 CTCGAAAACATTTATGGAATAGAGAACTCTA-GT-TTTCGAAAAA-AAAGGGAAATTT-AA-AAA
130 C-CGAAAACATTTACAGAATAAAAAAAACTACGTATTTC-AAAAATAAA--GAAATTTCAAGAAA
* * * *
237323 AAAAATGAAAAACTCATGAAAAG-AAATTAATTTTCAAAACTAATTTAATATAAATTAAATGATG
191 AAAAATGAAAAACTAATG-AAAGTAAATGAATTTTC-AAA--AATTTAATATAAATTAAATAATA
* * * *
237387 ATATTTGATGAATTTTAAAAATTATAAACTAAGAAAAATCCTCCTGAAAATATTTACAGAGTAAA
252 ATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAAGCCTCCCGAAAACATTTACAGAGTAAA
237452 AAAAAAAACTTCGTATTTCA
317 AAAAAAAACTTCGTATTTCA
* * * *
237472 AAAACA-GAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAACGAATTTTTCAAAATTG
1 AAAACAGGAG-AATTTCAAGAAAAAAATGAAAAACTAACGAAAATAAACAAATTTTTCAAAACTG
* * * * *
237536 ATTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAAATCTCT
65 ATTTAATATCAATTAAATAATGATATTTGATGAATATTAAAAATTATAAACCAAGAAAAATCTCT
* * *
237601 CCGAAAATATTTACAGAGTAAAAAAAAGTACGTATTTCAAAAATAAAGAAATTTCAAGAAAAAAA
130 CCGAAAACATTTACAGAATAAAAAAAACTACGTATTTCAAAAATAAAGAAATTTCAAGAAAAAAA
* *
237666 ATGAAAAACTAATGAAAGTAAATGAATTTTCAAAAATTTAGTATGAATTAAATAATAATATTTGA
195 ATGAAAAACTAATGAAAGTAAATGAATTTTCAAAAATTTAATATAAATTAAATAATAATATTTGA
* *
237731 TGGATTTTAATAATTATAAACCAAGAAAAAGCCTCCCGAAAACATTTA
260 TGAATTTTAAAAATTATAAACCAAGAAAAAGCCTCCCGAAAACATTTA
237779 TAGAATAGAA
Statistics
Matches: 258, Mismatches: 40, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
336 72 0.28
337 126 0.49
338 22 0.09
339 38 0.15
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (336 bp):
AAAACAGGAGAATTTCAAGAAAAAAATGAAAAACTAACGAAAATAAACAAATTTTTCAAAACTGA
TTTAATATCAATTAAATAATGATATTTGATGAATATTAAAAATTATAAACCAAGAAAAATCTCTC
CGAAAACATTTACAGAATAAAAAAAACTACGTATTTCAAAAATAAAGAAATTTCAAGAAAAAAAA
TGAAAAACTAATGAAAGTAAATGAATTTTCAAAAATTTAATATAAATTAAATAATAATATTTGAT
GAATTTTAAAAATTATAAACCAAGAAAAAGCCTCCCGAAAACATTTACAGAGTAAAAAAAAAAAC
TTCGTATTTCA
Found at i:237552 original size:171 final size:168
Alignment explanation
Indices: 237062--237778 Score: 657
Period size: 166 Copynumber: 4.3 Consensus size: 168
237052 GACAACATTA
* ** * * *
237062 GATGAATTTT-AAAATTTTAAATTAAGAAAAATCC-CTCTGAAAACATTT--ATAG-AACAGAAA
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCCTC-CTGAAAACATTTACAGAGTAAAAAAAA
* ** * * * *
237122 AC-TCGATTTTTTGAAAACAG-GAGAATTTCAAGAAAAAAATGAAAAACTCACGAAAATAAATAA
65 ACTTCG-TATTTCAAAAACAGAGA-AATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAATGA
* * * * **
237185 ATTTTTCAAAACTGATTTACTA-CACTTTAATTGGTGATATTT
128 A-TTTTCAAAACTGATTTAATATGA-ATTAAATAATGATATTT
* * * * * * * *
237227 GATGAATATTAAAAATTTTGAACCGAGAAAAA--CTCTCTCGAAAACATTTA-TG-G-AATAGAG
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCCTC-CT-GAAAACATTTACAGAGTAAAAAAA
* * * * *
237287 AACTCTAGT-TTTCGAAAAAAAAGGGAAATTT-AAAAAAAAAATGAAAAACTCATGAAAAG-AAA
64 AACT-TCGTATTTC--AAAAACAGAGAAATTTCAAGAAAAAAATGAAAAACTAATG-AAAGTAAA
* * * *
237349 TTAATTTTCAAAACTAATTTAATATAAATTAAATGATGATATTT
125 TGAATTTTCAAAACTGATTTAATATGAATTAAATAATGATATTT
* *
237393 GATGAATTTTAAAAATTATAAACTAAGAAAAATCCTCCTGAAAATATTTACAGAGTAAAAAAAAA
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCCTGAAAACATTTACAGAGT--AAAAAAA
*
237458 AACTTCGTATTTCAAAAACAGAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAACGAA
64 AACTTCGTATTTCAAAAACAGAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAATGAA
*
237523 TTTTTCAAAATTGATTTAATATGAATTAAATAATGATATTT
129 -TTTTCAAAACTGATTTAATATGAATTAAATAATGATATTT
* * * *
237564 GATGGATTTTAATAATTATAAACTAAGAAAAATCTCTCC-GAAAATATTTACAGAGT-AAAAAAA
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATC-CTCCTGAAAACATTTACAGAGTAAAAAAAA
* * * *
237627 AGTACGTATTTCAAAAATAAAGAAATTTCAAGAAAAAAAATGAAAAACTAATGAAAGTAAATGAA
65 ACTTCGTATTTCAAAAACAGAGAAATTTCAAG-AAAAAAATGAAAAACTAATGAAAGTAAATGAA
* *
237692 TTTTCAAAA---ATTTAGTATGAATTAAATAATAATATTT
129 TTTTCAAAACTGATTTAATATGAATTAAATAATGATATTT
* * * *
237729 GATGGATTTTAATAATTATAAACCAAGAAAAAGCCTCCCGAAAACATTTA
1 GATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCCTGAAAACATTTA
237779 TAGAATAGAA
Statistics
Matches: 471, Mismatches: 56, Indels: 50
0.82 0.10 0.09
Matches are distributed among these distances:
164 5 0.01
165 81 0.17
166 108 0.23
167 32 0.07
168 64 0.14
169 51 0.11
170 29 0.06
171 97 0.21
172 4 0.01
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (168 bp):
GATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCCTGAAAACATTTACAGAGTAAAAAAAAA
CTTCGTATTTCAAAAACAGAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAATGAATT
TTCAAAACTGATTTAATATGAATTAAATAATGATATTT
Found at i:237759 original size:165 final size:160
Alignment explanation
Indices: 237296--237853 Score: 644
Period size: 171 Copynumber: 3.4 Consensus size: 160
237286 GAACTCTAGT
* *
237296 TTTCGAAAAAAAAGGGAAATTT-AAAAAAAAAATGAAAAACTCATGAAAAG-AAATTAATTTTCA
1 TTTC-AAAAAAAA--GAAATTTCAAAAAAAAAATGAAAAACTAATG-AAAGTAAATGAATTTTC-
* * * *
237359 AAACTAATTTAATATAAATTAAATGATGATATTTGATGAATTTTAAAAATTATAAACTAAGAAAA
61 AAA--AATTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAA
237424 ATCCTCCTGAAAATATTTACAGAGTAAAAAAAAAAACTTCGTA
124 ATCCTCC-GAAAATATTTACAGAGT---AAAAAAAA--TCGTA
* * *
237467 TTTCAAAAACAGAGAAATTTCAAGAAAAAAATGAAAAACTAATGAAAGTAAACGAATTTTTCAAA
1 TTTCAAAAA-AAAGAAATTTCAAAAAAAAAATGAAAAACTAATGAAAGTAAATGAA-TTTTCAAA
237532 ATTGATTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAAAT
64 A---ATTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAAAT
237597 CTCTCCGAAAATATTTACAGAGTAAAAAAAAGTACGTA
126 C-CTCCGAAAATATTTACAGAGTAAAAAAAA-T-CGTA
237635 TTTCAAAAATAAAGAAATTTCAAGAAAAAAAATGAAAAACTAATGAAAGTAAATGAATTTTCAAA
1 TTTCAAAAA-AAAGAAATTTCAA-AAAAAAAATGAAAAACTAATGAAAGTAAATGAATTTTCAAA
* * * *
237700 AATTTAGTATGAATTAAATAATAATATTTGATGGATTTTAATAATTATAAACCAAGAAAAAGCCT
64 AATTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAAATCCT
* * * * * *
237765 CCCGAAAACATTTATAGAATAGAAAACAT-GATT
129 -CCGAAAATATTTACAGAGTAAAAAAAATCG-TA
* *
237798 TTTCAAAAAAAA-AAATTTCAAAGAAAAAA-GAAAAATTAATG-AA-TAAAATGAATTTT
1 TTTCAAAAAAAAGAAATTTCAAAAAAAAAATGAAAAACTAATGAAAGT-AAATGAATTTT
237854 TTTTAAACTA
Statistics
Matches: 348, Mismatches: 26, Indels: 39
0.84 0.06 0.09
Matches are distributed among these distances:
157 1 0.00
158 13 0.04
159 11 0.03
160 7 0.02
161 9 0.03
162 4 0.01
163 10 0.03
164 3 0.01
165 80 0.23
167 1 0.00
168 43 0.12
169 42 0.12
170 34 0.10
171 86 0.25
172 4 0.01
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (160 bp):
TTTCAAAAAAAAGAAATTTCAAAAAAAAAATGAAAAACTAATGAAAGTAAATGAATTTTCAAAAA
TTTAATATGAATTAAATAATGATATTTGATGGATTTTAATAATTATAAACTAAGAAAAATCCTCC
GAAAATATTTACAGAGTAAAAAAAATCGTA
Found at i:239137 original size:43 final size:43
Alignment explanation
Indices: 239004--239156 Score: 123
Period size: 43 Copynumber: 3.5 Consensus size: 43
238994 GATTGAATTA
* * *
239004 ATAAGTCAACAAATGATAAAAGGATTTACCCTGAGATTAAGCCG
1 ATAAGTTAACAAAAGATAAAAGGATTTACCCAG-GATTAAGCCG
* * ** * * *
239048 A-CAGGTAGACAAAAGA-AAAAAAAGTTGACCGA-GATTAAACCG
1 ATAAGTTA-ACAAAAGATAAAAGGA-TTTACCCAGGATTAAGCCG
*
239090 ATAAGTTAACAAAAGATAAAAGGATTTACCCAGGACTAAGCCG
1 ATAAGTTAACAAAAGATAAAAGGATTTACCCAGGATTAAGCCG
* * *
239133 ATAAGTAAATAAAGGATGAAAAGG
1 ATAAGTTAACAAAAGAT-AAAAGG
239157 TTGACCGAGA
Statistics
Matches: 82, Mismatches: 21, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
42 24 0.29
43 39 0.48
44 19 0.23
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18
Consensus pattern (43 bp):
ATAAGTTAACAAAAGATAAAAGGATTTACCCAGGATTAAGCCG
Found at i:239193 original size:85 final size:87
Alignment explanation
Indices: 238928--239265 Score: 284
Period size: 85 Copynumber: 4.0 Consensus size: 87
238918 CGATAAGTTG
* * ** ** *
238928 ACAAAGGGTAAAAGGATTTAGCCAG-GACTAAATCGATGGGTAAAC-AAGGATG-AAAGAATTGA
1 ACAAAGGATAAAAGGATTTACCCAGAGACTAAGCCGATAAGTAAACAAAGGATGAAAAG-GTTGA
* * * *
238990 CTGAGATTGAA-TTAATAAGTCA
65 CCGAGATTAAACTGAACAAGTCA
* * * * * * * ** *
239012 ACAAATGATAAAAGGATTTACCCTGAGATTAAGCCGACAGGTAGACAAAAGAAAAAAAAGTTGAC
1 ACAAAGGATAAAAGGATTTACCCAGAGACTAAGCCGATAAGTAAACAAAGGATGAAAAGGTTGAC
* * *
239077 CGAGATTAAACCG-ATAAGTTA
66 CGAGATTAAACTGAACAAGTCA
* *
239098 ACAAAAGATAAAAGGATTTACCCAG-GACTAAGCCGATAAGTAAATAAAGGATGAAAAGGTTGAC
1 ACAAAGGATAAAAGGATTTACCCAGAGACTAAGCCGATAAGTAAACAAAGGATGAAAAGGTTGAC
*
239162 CGAGATTGAACTGAA-AAGTCA
66 CGAGATTAAACTGAACAAGTCA
* * * * * *
239183 ATAAAGGATAAAAAGATTTA-CCTGAGACGAAGCCAAT-AGATAAACAAAGGATGAAAATGTTGA
1 ACAAAGGATAAAAGGATTTACCCAGAGACTAAGCCGATAAG-TAAACAAAGGATGAAAAGGTTGA
239246 CC-AGATTAAACT-AACAAGTC
65 CCGAGATTAAACTGAACAAGTC
239266 GACCAACTAA
Statistics
Matches: 203, Mismatches: 43, Indels: 16
0.77 0.16 0.06
Matches are distributed among these distances:
83 2 0.01
84 40 0.20
85 110 0.54
86 48 0.24
87 3 0.01
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.19
Consensus pattern (87 bp):
ACAAAGGATAAAAGGATTTACCCAGAGACTAAGCCGATAAGTAAACAAAGGATGAAAAGGTTGAC
CGAGATTAAACTGAACAAGTCA
Found at i:239209 original size:170 final size:170
Alignment explanation
Indices: 238897--239209 Score: 407
Period size: 170 Copynumber: 1.8 Consensus size: 170
238887 CAAGGGACAC
* * * * * * * *
238897 AAAAGTTAATCGAGATTGAATCGATAAGTTGACAAAGGGTAAAAGGATTTAGCCAGGACTAAATC
1 AAAAGTTAACCGAGATTAAACCGATAAGTTAACAAAAGATAAAAGGATTTACCCAGGACTAAACC
** * * * * *
238962 GATGGGTAAACAAGGATGAAAGAATTGACTGAGATTGAATTAATAAGTCAACAAATGATAAAAGG
66 GATAAGTAAAAAAGGATGAAAGAATTGACCGAGATTGAATGAATAAGTCAACAAAGGATAAAAAG
239027 ATTTACCCTGAGATTAAGCCGACAGGTAGACAAAAGAAAA
131 ATTTACCCTGAGATTAAGCCGACAGGTAGACAAAAGAAAA
* *
239067 AAAAGTTGACCGAGATTAAACCGATAAGTTAACAAAAGATAAAAGGATTTACCCAGGACTAAGCC
1 AAAAGTTAACCGAGATTAAACCGATAAGTTAACAAAAGATAAAAGGATTTACCCAGGACTAAACC
* *
239132 GATAAGTAAATAAAGGATGAAA-AGGTTGACCGAGATTGAACTGAA-AAGTCAATAAAGGATAAA
66 GATAAGTAAA-AAAGGATGAAAGA-ATTGACCGAGATTGAA-TGAATAAGTCAACAAAGGATAAA
239195 AAGATTTA-CCTGAGA
128 AAGATTTACCCTGAGA
239210 CGAAGCCAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 71 0.59
171 47 0.39
172 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.20
Consensus pattern (170 bp):
AAAAGTTAACCGAGATTAAACCGATAAGTTAACAAAAGATAAAAGGATTTACCCAGGACTAAACC
GATAAGTAAAAAAGGATGAAAGAATTGACCGAGATTGAATGAATAAGTCAACAAAGGATAAAAAG
ATTTACCCTGAGATTAAGCCGACAGGTAGACAAAAGAAAA
Found at i:240180 original size:2 final size:2
Alignment explanation
Indices: 240173--240203 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
240163 ATTCTCTTTT
240173 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
240204 ACAACTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:241514 original size:2 final size:2
Alignment explanation
Indices: 241507--241533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
241497 TCTCATCACT
241507 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
241534 TAATTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:242141 original size:29 final size:31
Alignment explanation
Indices: 242109--242167 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
242099 TATTTTTTAA
242109 TATAAATTATAATAT-AA-TAAAAAA-ATTAG
1 TATAAA-TATAATATAAACTAAAAAATATTAG
*
242138 TATAAATATGATATAAACTAAAAAATATTA
1 TATAAATATAATATAAACTAAAAAATATTA
242168 AAATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
30 7 0.27
31 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (31 bp):
TATAAATATAATATAAACTAAAAAATATTAG
Found at i:243303 original size:20 final size:21
Alignment explanation
Indices: 243271--243309 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
243261 TATTTAAAAG
243271 AATATCATTAATAT-TATTAT
1 AATATCATTAATATATATTAT
243291 AATAT-ATTAAATATATATT
1 AATATCATT-AATATATATT
243310 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATCATTAATATATATTAT
Found at i:246097 original size:23 final size:23
Alignment explanation
Indices: 246071--246143 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
246061 TTTATAGGTA
*
246071 AAATTACAGTAACTATTTGGTCT
1 AAATTACAATAACTATTTGGTCT
* *
246094 AAATTACAAT-ACT-TATAGGT-A
1 AAATTACAATAACTAT-TTGGTCT
* *
246115 AAATTACAATAAGTAATTGGTCT
1 AAATTACAATAACTATTTGGTCT
246138 AAATTA
1 AAATTA
246144 AGATACTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 11 0.28
22 13 0.33
23 15 0.38
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.36
Consensus pattern (23 bp):
AAATTACAATAACTATTTGGTCT
Found at i:246112 original size:44 final size:44
Alignment explanation
Indices: 246062--246151 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
246052 AGATATAATT
* *
246062 TTATAGGTAAAATTACAGTAACTATTTGGTCTAAATTACA-ATAC
1 TTATAGGTAAAATTACAATAACTAATTGGTCTAAATTA-AGATAC
*
246106 TTATAGGTAAAATTACAATAAGTAATTGGTCTAAATTAAGATAC
1 TTATAGGTAAAATTACAATAACTAATTGGTCTAAATTAAGATAC
246150 TT
1 TT
246152 CTTCTGGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
TTATAGGTAAAATTACAATAACTAATTGGTCTAAATTAAGATAC
Found at i:246120 original size:21 final size:21
Alignment explanation
Indices: 246062--246125 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
246052 AGATATAATT
*
246062 TTATAGGTAAAATTACAGTAAC
1 TTATAGGTAAAATTACAAT-AC
* *
246084 -TATTTGGTCTAAATTACAATAC
1 TTA-TAGGT-AAAATTACAATAC
246106 TTATAGGTAAAATTACAATA
1 TTATAGGTAAAATTACAATA
246126 AGTAATTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 13 0.38
22 10 0.29
23 11 0.32
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
TTATAGGTAAAATTACAATAC
Found at i:246510 original size:21 final size:21
Alignment explanation
Indices: 246484--246532 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
246474 TCATATGAAA
246484 AAACTTTGAATTCTTGTCTCC
1 AAACTTTGAATTCTTGTCTCC
246505 AAACTTTGAATTCTTGTCTCC
1 AAACTTTGAATTCTTGTCTCC
246526 AAACTTT
1 AAACTTT
246533 AGCCAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (21 bp):
AAACTTTGAATTCTTGTCTCC
Found at i:247171 original size:23 final size:24
Alignment explanation
Indices: 247135--247181 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
247125 GGATCGAAAA
247135 AAAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAAGTGGGCTTTCC
** *
247158 AAAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAAGTGGGCTTTCC
247182 GATTGAGTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAAAAAAAAAAAGTGGGCTTTCC
Found at i:247553 original size:11 final size:11
Alignment explanation
Indices: 247515--247555 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
247505 AAATTTAGGT
247515 AAAAAAGAAAG
1 AAAAAAGAAAG
*
247526 AAAGAAGATGAAG
1 AAAAAAGA--AAG
247539 AAAAAAGAAAG
1 AAAAAAGAAAG
247550 AAAAAA
1 AAAAAA
247556 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:255402 original size:27 final size:27
Alignment explanation
Indices: 255362--256316 Score: 1534
Period size: 27 Copynumber: 35.0 Consensus size: 27
255352 GTGGTATTTT
*
255362 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
255390 CTTTTAAGTCCACAACTCTGTGG-ACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255416 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
255444 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
255471 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255498 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255525 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255552 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
255579 CTTTTAAGTCCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
255606 CTTTTAAAGACCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
255634 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
255661 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
255689 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255716 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
255744 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255771 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
255798 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255825 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
255852 CTTTTAAAGACCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
255880 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255907 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
255934 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
255962 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
255989 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
256017 CTTTTTAGTCCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
256044 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
256071 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
256098 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
256125 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
256153 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
256180 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
256208 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
256235 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
256262 CTTTTAAGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
256289 CTTTTAAATCCACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
256316 C
1 C
256317 ATTTCAAAGC
Statistics
Matches: 861, Mismatches: 56, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
26 7 0.01
27 640 0.74
28 214 0.25
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:255848 original size:273 final size:271
Alignment explanation
Indices: 255362--256316 Score: 1556
Period size: 273 Copynumber: 3.5 Consensus size: 271
255352 GTGGTATTTT
* *
255362 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGG-ACCCTTTTAAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
255426 CCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTG
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTG
255491 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
130 TGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* *
255556 TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAAGACCACA
195 TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
255621 ACTCCGTGGCACC
259 ACTCCGTGGCACC
* *
255634 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
* * *
255698 CCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCC
65 CCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
*
255763 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTT
129 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTT
*
255828 TTAAGTCCACAACTCCGTGGCACCCTTTTAAAGACCACAACTCCGTGGCACCCTTTTAAGTCCAC
194 TTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
255893 AACTCCGTGGCACC
258 AACTCCGTGGCACC
* *
255907 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
* * *
255971 CCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTTT
65 CCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
*
256036 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACCCTT
129 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTT
* *
256101 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCAC
194 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCAC
*
256166 AACTCTGTGGCACC
258 AACTCCGTGGCACC
* *
256180 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* ** *
256245 CACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCGTCCTTTTAAATCCACAACTCTGT
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGT
*
256310 AGCACCC
131 GGCACCC
256317 ATTTCAAAGC
Statistics
Matches: 644, Mismatches: 33, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
271 42 0.07
272 94 0.15
273 439 0.68
274 69 0.11
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (271 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGT
GGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
TCCGTGGCACC
Found at i:256349 original size:32 final size:32
Alignment explanation
Indices: 256313--256806 Score: 848
Period size: 32 Copynumber: 15.4 Consensus size: 32
256303 ACTCTGTAGC
256313 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
256345 ACCCATTCCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
256377 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
256409 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
256441 ACCCATTTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCA-TTTCAAAGCCCACACAAGTCGGTGGCA
256474 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
256506 ACCCATTTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCA-TTTCAAAGCCCACACAAGTCGGTGGCA
256539 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
256571 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
256603 ACCCATTTCAAAGCCCACACAGGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
256635 ACCCA-TTCTAAAGCCCACACAAGTAGGTGGCA
1 ACCCATTTC-AAAGCCCACACAAGTCGGTGGCA
256667 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
**
256699 ACCTTTTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
256731 ACCCATTTAAAAGCCCACGA-AAGTCGGTGGCA
1 ACCCATTTCAAAGCCCAC-ACAAGTCGGTGGCA
* * *
256763 ACCCATTTAAAAGCCCACGCAAGTCAGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
256795 ACCCTTTTCAAA
1 ACCCATTTCAAA
256807 TCACCATTTT
Statistics
Matches: 441, Mismatches: 15, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
31 3 0.01
32 370 0.84
33 68 0.15
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
Found at i:256886 original size:45 final size:47
Alignment explanation
Indices: 256827--256957 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 47
256817 TGTCATCTTA
* * *
256827 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGG-CACCTTT-CT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCACCTTTCCT
* *
256872 AAGTCCAATGTCGCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCT
* * * *
256921 TAGTCCAATGTCGTTGACCTTGAAAT-GGCACATTGGC
1 AAGTCCAATGTCGCTGGCCTTG-AATCAGCACATTGGC
256958 ACTCCTCTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
45 32 0.45
47 6 0.08
48 1 0.01
49 30 0.42
50 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (47 bp):
AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCACCTTTCCT
Found at i:258077 original size:16 final size:17
Alignment explanation
Indices: 258046--258080 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
258036 AAGGAAGATG
*
258046 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
258063 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
258079 AA
1 AA
258081 ATATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:258088 original size:10 final size:10
Alignment explanation
Indices: 258052--258081 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
258042 GATGAAGAAG
*
258052 AAAGAAAGAA
1 AAAGAAAAAA
258062 AAAGAAAAAA
1 AAAGAAAAAA
258072 AAAGAAAAAA
1 AAAGAAAAAA
258082 TATGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Done.