Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 12 of 14
Found at i:2254074 original size:233 final size:230
Alignment explanation
Indices: 2253612--2254317 Score: 786
Period size: 233 Copynumber: 3.0 Consensus size: 230
2253602 ATTGCGACCA
* * * * *
2253612 GAAACAATGTTCTTAAATCATTGCTAGCTATTTCTTGATTACTTGTTGGTTGA----T-ATA-AT
1 GAAACAATGTTCTTAAATCATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAAAGAT
* *
2253671 GTCATTTGAATCTCTCCAGGCTA-GGCCATAAATAAAGTAATCATCAAGGAAAATTGTATATTGT
66 GTCATTTGAATCTCTCTAGGCTAGGGCCATAAATAAATTAATCATCAAGG-AAA-T-TATATTGT
* * * ***
2253735 TTGTTATTTGTAATTTCTATCATATTTACCTGATTCACGGGACCGCCTTTCAAGCTGCATCTGGG
128 TTGTAATATG-AA---C---CATAGTTACCTGATTCACTAAACC-CCTTTCAAGCTGCATCTGGG
*
2253800 ATCATGCCACCCCAATCA-TGGTTCTTATGTGATCCAGAATGTGGACT
185 ATCATG-CAACCCAAT-AGTGGTTCTTATGTGATCCAGAATGTGGACT
2253847 GAAACAATGTTCTTAAATCATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAAAGAT
1 GAAACAATGTTCTTAAATCATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAAAGAT
*
2253912 GTCATTTGAATCTCTATAGGCTAGGGCCATAAATAAATTAATCATCAAGTGAAA-TATATTGTTT
66 GTCATTTGAATCTCTCTAGGCTAGGGCCATAAATAAATTAATCATCAAG-GAAATTATATTGTTT
* * *
2253976 GTAATATGGACCATAGTTACCTGATTCGCTAAACCTCCTTTTCAAGCTGCATCTGGGATCATGCG
130 GTAATATGAACCATAGTTACCTGATTCACTAAACC-CC-TTTCAAGCTGCATCTGGGATCATGCA
* *
2254041 ACCACAATTGTTGTTCTTATGTGATCCAGAATGTGGACT
193 ACC-CAATAGTGGTTCTTATGTGATCCAGAATGTGGACT
* * *
2254080 GAAACAATATTCTTAAATTATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAATGAT
1 GAAACAATGTTCTTAAATCATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAAAGAT
* * * * *
2254145 GTCATTTTAGTCTTTCTAGGCTAGTGCCATAAATAAATTAATCATCAAGGACAATCGTCTATTGT
66 GTCATTTGAATCTCTCTAGGCTAGGGCCATAAATAAATTAATCATCAAGGA-AAT--TATATTGT
* * * * * **
2254210 TTGTAATGT-ATACCACAGTTACCTGATTCACTACACCACTTTCAATCTGTGTCCT-GGATCATG
128 TTGTAATATGA-ACCATAGTTACCTGATTCACTAAACCCCTTTCAAGCTGCAT-CTGGGATCATG
* * *
2254273 CAAACCCAACAGTGGTTCTTATGGGATCCAAAATGTGGACT
191 C-AACCCAATAGTGGTTCTTATGTGATCCAGAATGTGGACT
2254314 GAAA
1 GAAA
2254318 TGACCTGCCG
Statistics
Matches: 408, Mismatches: 45, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
232 26 0.06
233 164 0.40
234 53 0.13
235 56 0.14
236 38 0.09
238 1 0.00
239 17 0.04
240 2 0.00
241 23 0.06
242 27 0.07
243 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (230 bp):
GAAACAATGTTCTTAAATCATTGCTGGTTATTTCTTGATTACTAGTCGGTTGATGTTTGAAAGAT
GTCATTTGAATCTCTCTAGGCTAGGGCCATAAATAAATTAATCATCAAGGAAATTATATTGTTTG
TAATATGAACCATAGTTACCTGATTCACTAAACCCCTTTCAAGCTGCATCTGGGATCATGCAACC
CAATAGTGGTTCTTATGTGATCCAGAATGTGGACT
Found at i:2258930 original size:19 final size:18
Alignment explanation
Indices: 2258906--2258947 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2258896 ACTCGGATTT
2258906 GGTATGAGTGTTCGATACA
1 GGTATG-GTGTTCGATACA
* *
2258925 GGTAT-GTGTTTGATATA
1 GGTATGGTGTTCGATACA
2258942 GGTATG
1 GGTATG
2258948 TTTAAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.75
19 5 0.25
ACGTcount: A:0.24, C:0.05, G:0.33, T:0.38
Consensus pattern (18 bp):
GGTATGGTGTTCGATACA
Found at i:2258939 original size:17 final size:17
Alignment explanation
Indices: 2258913--2258948 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2258903 TTTGGTATGA
2258913 GTGTTCGATACAGGTAT
1 GTGTTCGATACAGGTAT
* *
2258930 GTGTTTGATATAGGTAT
1 GTGTTCGATACAGGTAT
2258947 GT
1 GT
2258949 TTAAAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (17 bp):
GTGTTCGATACAGGTAT
Found at i:2259285 original size:20 final size:20
Alignment explanation
Indices: 2259260--2259299 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2259250 TTTAATCTTC
2259260 TGATACATTTTGCAAACGAG
1 TGATACATTTTGCAAACGAG
2259280 TGATACATTTTGCAAACGAG
1 TGATACATTTTGCAAACGAG
2259300 CTCCTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TGATACATTTTGCAAACGAG
Found at i:2260297 original size:39 final size:39
Alignment explanation
Indices: 2260243--2260320 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2260233 TGCTGATAAA
2260243 TATAAGTTTGACTTCATAAGCACCGCACATGGCTAGTGG
1 TATAAGTTTGACTTCATAAGCACCGCACATGGCTAGTGG
2260282 TATAAGTTTGACTTCATAAGCACCGCACATGGCTAGTGG
1 TATAAGTTTGACTTCATAAGCACCGCACATGGCTAGTGG
2260321 CGATTAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (39 bp):
TATAAGTTTGACTTCATAAGCACCGCACATGGCTAGTGG
Found at i:2260425 original size:16 final size:17
Alignment explanation
Indices: 2260383--2260425 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2260373 TTAAATAATT
*
2260383 TTTTTTATTATTTAAAA
1 TTTTATATTATTTAAAA
* *
2260400 TATTAAATTA-TTAAAA
1 TTTTATATTATTTAAAA
2260416 TTTTATATTA
1 TTTTATATTA
2260426 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATTATTTAAAA
Found at i:2260453 original size:22 final size:21
Alignment explanation
Indices: 2260399--2260453 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
2260389 ATTATTTAAA
*
2260399 ATATTAAATTATTAAAATTTT
1 ATATTAAATTTTTAAAATTTT
* *
2260420 ATATTAATATTTTTATATTTTT
1 ATATTAA-ATTTTTAAAATTTT
2260442 ATAATTAAATTT
1 AT-ATTAAATTT
2260454 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 17 0.59
23 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAATTTTTAAAATTTT
Found at i:2261618 original size:14 final size:14
Alignment explanation
Indices: 2261599--2261627 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2261589 CCCCCGTATC
2261599 CATGTCCAGATAAG
1 CATGTCCAGATAAG
2261613 CATGTCCAGATAAG
1 CATGTCCAGATAAG
2261627 C
1 C
2261628 GTAAGGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (14 bp):
CATGTCCAGATAAG
Found at i:2266291 original size:38 final size:38
Alignment explanation
Indices: 2266236--2266324 Score: 162
Period size: 38 Copynumber: 2.4 Consensus size: 38
2266226 TCAAAATCCG
2266236 AAAG-AGAAAATAGAAAAGTTGAATGAAACCAGAGTAA
1 AAAGCAGAAAATAGAAAAGTTGAATGAAACCAGAGTAA
2266273 AAAGCAGAAAATAGAAAAGTTGAATGAAACCAGAGTAA
1 AAAGCAGAAAATAGAAAAGTTGAATGAAACCAGAGTAA
*
2266311 AAAGCAGAGAATAG
1 AAAGCAGAAAATAG
2266325 CTAAAACTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 4 0.08
38 46 0.92
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.12
Consensus pattern (38 bp):
AAAGCAGAAAATAGAAAAGTTGAATGAAACCAGAGTAA
Found at i:2269645 original size:21 final size:22
Alignment explanation
Indices: 2269607--2269662 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
2269597 ATAATATTAA
2269607 AATATTAAATATTATTTTAT-ATT
1 AATATTAAA-A-TATTTTATAATT
2269630 AATATTAAAATATTTTATAATT
1 AATATTAAAATATTTTATAATT
*
2269652 AA-ATTTAAATA
1 AATATTAAAATA
2269663 AAAAAGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 16 0.52
22 6 0.19
23 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTAAAATATTTTATAATT
Found at i:2270288 original size:42 final size:42
Alignment explanation
Indices: 2270229--2270336 Score: 207
Period size: 42 Copynumber: 2.6 Consensus size: 42
2270219 TATTGTAAAT
2270229 GTAATCGAATTGGGTCCAAACAGCTTTGACCTTTCTCAACGA
1 GTAATCGAATTGGGTCCAAACAGCTTTGACCTTTCTCAACGA
2270271 GTAATCGAATTGGGTCCAAACAGCTTTGACCTTTCTCAACGA
1 GTAATCGAATTGGGTCCAAACAGCTTTGACCTTTCTCAACGA
*
2270313 GTAATCGAATGGGGTCCAAACAGC
1 GTAATCGAATTGGGTCCAAACAGC
2270337 ATTGTAAAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
GTAATCGAATTGGGTCCAAACAGCTTTGACCTTTCTCAACGA
Found at i:2272221 original size:2 final size:2
Alignment explanation
Indices: 2272216--2272246 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2272206 TTGCAAAATA
2272216 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 A
2272247 ATAGATAGGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2273875 original size:14 final size:14
Alignment explanation
Indices: 2273856--2273883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2273846 ATCAGTCATC
2273856 CATGAGCACAACTT
1 CATGAGCACAACTT
2273870 CATGAGCACAACTT
1 CATGAGCACAACTT
2273884 GGGTACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
CATGAGCACAACTT
Found at i:2275643 original size:22 final size:22
Alignment explanation
Indices: 2275618--2275661 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2275608 AAAATTTTTG
2275618 AATTTGTATATCC-AAATTCAAA
1 AATTTGTATA-CCAAAATTCAAA
* *
2275640 AATTTTTTTACCAAAATTCAAA
1 AATTTGTATACCAAAATTCAAA
2275662 TCTCCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTTGTATACCAAAATTCAAA
Found at i:2278476 original size:29 final size:27
Alignment explanation
Indices: 2278422--2278476 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2278412 TATTTATATA
*
2278422 TTTTAATAATTAAATTTAATTAAAATT
1 TTTTAATAATTAAATGTAATTAAAATT
* *
2278449 TTTTATATTATTAAATAGTAATTCAAAT
1 TTTTA-ATAATTAAAT-GTAATTAAAAT
2278477 GATCCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 9 0.39
29 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTTAATAATTAAATGTAATTAAAATT
Found at i:2279144 original size:12 final size:12
Alignment explanation
Indices: 2279127--2279152 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2279117 AAACATATTA
2279127 GATATGTTAGGT
1 GATATGTTAGGT
2279139 GATATGTTAGGT
1 GATATGTTAGGT
2279151 GA
1 GA
2279153 GTAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (12 bp):
GATATGTTAGGT
Found at i:2283867 original size:34 final size:34
Alignment explanation
Indices: 2283769--2283870 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 34
2283759 ATCTTTATTA
*
2283769 AGTGTGTTAGGTAAACATATTAGGTGTATTAGGT
1 AGTGTGTTAGGTAAACATATTAGGTGTGTTAGGT
* * * *
2283803 GGTATGTTAAGCAAGT-AATATATTAAGTGTGTTAGGT
1 AGTGTGTT-AG---GTAAACATATTAGGTGTGTTAGGT
*
2283840 AGTGTATTAGGTAAACATATTAGGTGTGTTA
1 AGTGTGTTAGGTAAACATATTAGGTGTGTTA
2283871 AGTAAACATA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
33 2 0.04
34 22 0.42
35 2 0.04
36 2 0.04
37 23 0.43
38 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.38
Consensus pattern (34 bp):
AGTGTGTTAGGTAAACATATTAGGTGTGTTAGGT
Found at i:2283875 original size:22 final size:22
Alignment explanation
Indices: 2283840--2283926 Score: 129
Period size: 22 Copynumber: 4.0 Consensus size: 22
2283830 TGTGTTAGGT
* *
2283840 AGTGTATTAGGTAAACATATTA
1 AGTGTGTTAAGTAAACATATTA
*
2283862 GGTGTGTTAAGTAAACATATTA
1 AGTGTGTTAAGTAAACATATTA
2283884 AGTGTGTTAAGTAAACATATTA
1 AGTGTGTTAAGTAAACATATTA
* *
2283906 AGTGTGTTAAGTGAACTTATT
1 AGTGTGTTAAGTAAACATATT
2283927 TTATATAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (22 bp):
AGTGTGTTAAGTAAACATATTA
Found at i:2287036 original size:2 final size:2
Alignment explanation
Indices: 2287029--2287063 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2287019 AAAATAATGC
2287029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2287064 AAGGGATGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2289201 original size:118 final size:121
Alignment explanation
Indices: 2288933--2289238 Score: 302
Period size: 118 Copynumber: 2.5 Consensus size: 121
2288923 TTTGTTTGAA
** * * * * *
2288933 CTATTAAATTTAAGTATGCAATTAAAAATAAAAAATAACAAACTAAAGAAAAT-AAAAAAAAAAC
1 CTATTAAATTTAAACAT-CAACTAAAAAGAAAAGATAACAAACTAAAGAGAATGAAAAATAAAA-
* * * * *
2288997 TTTAGAAAAAATTAAAGAAATCTACAAATAAATAATTAATGTTTTGATAATTTGTTTAAG
64 --GAGAAAAAATTAAAAAAATCTACAAATAAATAATTAATGTTTTGACAACTTATTTAAG
* * * * *
2289057 CTATTAAATTTAAGCGTGCGACT-AAAA-AAAAGATAACAAACTAGAGAGCA-GAAAAA-AAAAG
1 CTATTAAATTTAAACAT-CAACTAAAAAGAAAAGATAACAAACTAAAGAGAATGAAAAATAAAAG
* *
2289118 AGAAAAAATTAAAAAAAT-TACAAGTAAATGATTAATGTTTTGACAACTTATTTAAAG
65 AGAAAAAATTAAAAAAATCTACAAATAAATAATTAATGTTTTGACAACTTATTT-AAG
* *
2289175 CTATTAAATTTGAATACAT-AATTAAAAAGAAAAGATAATAAACTAAAGAGAATGAAAAATAAAA
1 CTATTAAATTT-AA-ACATCAACTAAAAAGAAAAGATAACAAACTAAAGAGAATGAAAAATAAAA
2289239 ACTACAAAAA
Statistics
Matches: 152, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
117 30 0.20
118 33 0.22
119 6 0.04
120 22 0.14
121 10 0.07
122 28 0.18
123 4 0.03
124 19 0.12
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (121 bp):
CTATTAAATTTAAACATCAACTAAAAAGAAAAGATAACAAACTAAAGAGAATGAAAAATAAAAGA
GAAAAAATTAAAAAAATCTACAAATAAATAATTAATGTTTTGACAACTTATTTAAG
Found at i:2289280 original size:23 final size:22
Alignment explanation
Indices: 2289214--2289280 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 22
2289204 AAAAGATAAT
*
2289214 AAACTAAAGAGAATGAAAAATAA
1 AAACTAAAGAGAA-GAAAAAAAA
* *
2289237 AAACT--ACA-AA-AAAAAATA
1 AAACTAAAGAGAAGAAAAAAAA
2289255 AAACTAAAGAGAAGAAAAAAGAA
1 AAACTAAAGAGAAGAAAAAA-AA
2289278 AAA
1 AAA
2289281 ATTAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 11 0.32
20 4 0.12
21 4 0.12
22 6 0.18
23 9 0.26
ACGTcount: A:0.75, C:0.06, G:0.10, T:0.09
Consensus pattern (22 bp):
AAACTAAAGAGAAGAAAAAAAA
Found at i:2289292 original size:41 final size:42
Alignment explanation
Indices: 2289200--2289293 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 42
2289190 ACATAATTAA
* *
2289200 AAAGAAAAGATAATAAACTAAAGAGAATGAAAAATAAAAACT
1 AAAGAAAAAATAATAAACTAAAGAGAATGAAAAAAAAAAACT
* *
2289242 ACA-AAAAAA-AATAAAACTAAAGAGAA-GAAAAAAGAAAAAATT
1 AAAGAAAAAATAAT-AAACTAAAGAGAATG-AAAAA-AAAAAACT
2289284 AAAGAAAAAA
1 AAAGAAAAAA
2289294 ATTAAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
40 4 0.09
41 23 0.53
42 10 0.23
43 6 0.14
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (42 bp):
AAAGAAAAAATAATAAACTAAAGAGAATGAAAAAAAAAAACT
Found at i:2289293 original size:21 final size:22
Alignment explanation
Indices: 2289264--2289304 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2289254 AAAACTAAAG
2289264 AGAAGAAAAAAGAAAAAATTAA
1 AGAAGAAAAAAGAAAAAATTAA
**
2289286 AGAA-AAAAATTAAAAAATT
1 AGAAGAAAAAAGAAAAAATT
2289305 TATAAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (22 bp):
AGAAGAAAAAAGAAAAAATTAA
Found at i:2289498 original size:128 final size:126
Alignment explanation
Indices: 2289244--2289502 Score: 301
Period size: 128 Copynumber: 2.1 Consensus size: 126
2289234 TAAAAACTAC
** *
2289244 AAAAAAA-AAT-A-AAACTAAAGAGAAGAAAAAAGAAAAAATTAAAGAAAAAAATTAAAAAATTT
1 AAAAAAATAATAATAAACTAAAGAGAAGAAAAAAGAAAAAACGAAAGAAAAAAATTAAAAAATCT
* * * * * * * *
2289306 ATAAGTAAATTGTTAATGTTTTGACAGCTTTTTTAAACAATTAAATTTGAGTGTGCAATCA
66 ACAAATAAATAGTTAATATTTTAACAGCTTGTTTAAACAATTAAATTTAAGTATGCAATCA
* * *
2289367 AAAATAAATAATAATAAACTAAAGAGGAGAAAAAAGAAAAAACGAGAGAAAAAAGTTTAAAAAAT
1 AAAA-AAATAATAATAAACTAAAGAGAAGAAAAAAGAAAAAACGAAAGAAAAAA-ATTAAAAAAT
* * * *
2289432 CTACAAATAAATAGTTAATATTTTAAC-GACTTGTTTAAGCTATTAAATTTAAGTATGCGATTA
64 CTACAAATAAATAGTTAATATTTTAACAG-CTTGTTTAAACAATTAAATTTAAGTATGCAATCA
2289495 AAAAAAAT
1 AAAAAAAT
2289503 TACAAACTAA
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
123 4 0.04
124 3 0.03
125 3 0.03
126 1 0.01
127 40 0.36
128 61 0.54
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (126 bp):
AAAAAAATAATAATAAACTAAAGAGAAGAAAAAAGAAAAAACGAAAGAAAAAAATTAAAAAATCT
ACAAATAAATAGTTAATATTTTAACAGCTTGTTTAAACAATTAAATTTAAGTATGCAATCA
Found at i:2289612 original size:91 final size:91
Alignment explanation
Indices: 2289425--2289614 Score: 203
Period size: 91 Copynumber: 2.1 Consensus size: 91
2289415 AAAAAAGTTT
*
2289425 AAAAAATCTACAAATAAATAGTTAATATTTTAACGACTTGTTTAAGCTATTAAATTTAAGTATGC
1 AAAAAATCGACAAATAAATAGTTAATATTTTAACGACTTGTTTAAGCTATTAAATTTAAGTATGC
** *
2289490 GATTAAAAAAAATTACAAACTAAAAAGA
66 GAAAAAAAAAAATGACAAACT--AAAGA
* *
2289518 AAAAAAT-GACAAATAAATATTTAA-ATTTTAAC-AGTTTGTTTAAGCTATTAAATTTAAGCGCA
1 AAAAAATCGACAAATAAATAGTTAATATTTTAACGA-CTTGTTTAAGCTATTAAATTTAA--G--
2289580 TAAT-C-AAAAATAAAAAATGACAAACTAAA-A
61 T-ATGCGAAAAA-AAAAAATGACAAACTAAAGA
2289610 AAAAA
1 AAAAA
2289615 GAAAAAAAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
90 1 0.01
91 30 0.36
92 21 0.25
93 11 0.13
94 3 0.04
95 16 0.19
96 2 0.02
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (91 bp):
AAAAAATCGACAAATAAATAGTTAATATTTTAACGACTTGTTTAAGCTATTAAATTTAAGTATGC
GAAAAAAAAAAATGACAAACTAAAGA
Found at i:2289674 original size:109 final size:108
Alignment explanation
Indices: 2289518--2289792 Score: 317
Period size: 111 Copynumber: 2.5 Consensus size: 108
2289508 ACTAAAAAGA
* * * *
2289518 AAAAAATGACAAATAAATATTTAA-ATTTTAACAGTTTGTTTAAGCTATTAAATTTAAGCGCATA
1 AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCG--T-
2289582 ATCAAAAATAAAAAATGACAAACT-AA-AAAAAA-AGA-AAAAAAATT
63 AT-AAAAA-AAAAAATGACAAACTAAAGAAAAAATAGAGAAAAAAATT
* * * * *
2289626 AAAAAATTACAAATAAATAGTTAATGTTTTAATAATTTATTTTAGCTATTAAATTTAAGCGTGTA
1 AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCGTATA
* * *
2289691 ATAAAAAAAATGACAAACTAGAAGAAAAAATTAGAGAAAAGATTT
66 AAAAAAAAAATGACAAACTA-AAGAAAAAA-TAGAGAAAAAAATT
* *
2289736 AAAAAGTTTATAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTT
1 AAAAA-ATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTT
2289793 GAATATGTAA
Statistics
Matches: 142, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
104 15 0.11
105 4 0.03
106 3 0.02
107 7 0.05
108 22 0.15
109 34 0.24
110 12 0.08
111 45 0.32
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.33
Consensus pattern (108 bp):
AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCGTATA
AAAAAAAAAATGACAAACTAAAGAAAAAATAGAGAAAAAAATT
Found at i:2289776 original size:111 final size:106
Alignment explanation
Indices: 2289518--2289823 Score: 314
Period size: 111 Copynumber: 2.8 Consensus size: 106
2289508 ACTAAAAAGA
* * * *
2289518 AAAAAATGACAAATAAATATTTAA-ATTTTAACAGTTTGTTTAAGCTATTAAATTTAAGCGCATA
1 AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCG--T-
*
2289582 ATCAAAAATAAAAAATGACAAACT--AAAAAAAAAGAAAAAAAATT
63 GT-AAAAA-AAAAAATGACAAACTAGAAAAAAAAAGAAAAAAAATT
* * * *
2289626 AAAAAATTACAAATAAATAGTTAATGTTTTAATAATTTATTTTAGCTATTAAATTTAAGCGTGTA
1 AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCGTGTA
* * *
2289691 ATAAAAAAAATGACAAACTAGAAGAAAAAATTAGAGAAAAGATTT
66 AAAAAAAAAATGACAAACTAGAA-AAAAAA--AGA-AAAAAAATT
* * **
2289736 AAAAAGTTTATAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTGAA-TATG
1 AAAAA-ATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTT-AAGCGTG
* * *
2289800 TAACAAAAAAAATAACAAATTAGA
64 TAAAAAAAAAAATGACAAACTAGA
2289824 GAGGAGAAAA
Statistics
Matches: 167, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
104 15 0.09
105 4 0.02
106 3 0.02
107 7 0.04
108 22 0.13
109 34 0.20
110 12 0.07
111 68 0.41
112 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (106 bp):
AAAAAATTACAAATAAATAATTAATATTTTAACAGTTTATTTTAGCTATTAAATTTAAGCGTGTA
AAAAAAAAAATGACAAACTAGAAAAAAAAAGAAAAAAAATT
Found at i:2290238 original size:20 final size:20
Alignment explanation
Indices: 2290215--2290254 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2290205 AATCAAAAAG
*
2290215 AAAAAATGATAAACTAGAGAA
1 AAAAAAT-ACAAACTAGAGAA
2290236 AAAAAATACAAACTAGAGA
1 AAAAAATACAAACTAGAGA
2290255 GAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAAATACAAACTAGAGAA
Found at i:2290461 original size:109 final size:104
Alignment explanation
Indices: 2290267--2290486 Score: 246
Period size: 108 Copynumber: 2.1 Consensus size: 104
2290257 AGAAAAAAAT
* * * *
2290267 AGAAAAAAATAAAAAAAAAACTATAAGTAAATGGTTAATGTTTTGACAACTTTTTAAACTATTAA
1 AGAAAAAAATAAAAAAAAAACTACAAGTAAATAGTTAATATTTTAACAACTTTTTAAACTATTAA
* *
2290332 ATTTGAGCCTGTAATAAAAAATAAATGATATTAAACTAAAGAGG
66 ATTTGAACCTGCAAT-AAAAA-AAATG--A-TAAACTAAAGAGG
* * * * *
2290376 AGAAAAAAAT-TAAAGAAATCTACAAGTAAATAGTTAATATTTTAACAACTTATTTGAGCTATTA
1 AGAAAAAAATAAAAAAAAAACTACAAGTAAATAGTTAATATTTTAACAACTT-TTTAAACTATTA
* * *
2290440 AATTTGAACGTGCGATTAAAAAAATGATAAACTAAAGAGG
65 AATTTGAACCTGCAATAAAAAAAATGATAAACTAAAGAGG
2290480 A-AAAAAA
1 AGAAAAAA
2290487 TGACAAATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
103 6 0.06
104 14 0.15
105 1 0.01
107 5 0.05
108 38 0.40
109 32 0.33
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (104 bp):
AGAAAAAAATAAAAAAAAAACTACAAGTAAATAGTTAATATTTTAACAACTTTTTAAACTATTAA
ATTTGAACCTGCAATAAAAAAAATGATAAACTAAAGAGG
Found at i:2290608 original size:110 final size:110
Alignment explanation
Indices: 2290494--2290758 Score: 313
Period size: 110 Copynumber: 2.4 Consensus size: 110
2290484 AAATGACAAA
* *
2290494 TAAATAATTAATGTTTTAATAGCTTGTTTGAGCTATTAAATTTAAGCAAATAAT-AAAAAATAAC
1 TAAATAATTAATGTTTTAATAGTTTATTTGAGCTATTAAATTTAAGCAAATAATAAAAAAATAAC
2290558 AAACTAAAAAAGAAAAAAAATT-AGAAAAAAATT-AAAAAA-TTATAAG
66 AAACT---AAAG-AAAAAAATTAAGAAAAAAATTAAAAAAATTTATAAG
* * * * *** *
2290604 TAAATAGTTAATGTTTTGATAATTTATTTGAGCAATTAAATTTAAGCGTGTAATCAAAAAAATGA
1 TAAATAATTAATGTTTTAATAGTTTATTTGAGCTATTAAATTTAAGCAAATAAT-AAAAAAATAA
* *
2290669 TAAACTAGAGAAAAAAATTAGAGAAAAAAATTAAAAAAATTTATAAG
65 CAAACTAAAGAAAAAAATTA-AGAAAAAAATTAAAAAAATTTATAAG
* **
2290716 TAAATAATTAATATTTTAACGGTTTATTTGAGCTATTAAATTT
1 TAAATAATTAATGTTTTAATAGTTTATTTGAGCTATTAAATTT
2290759 GAATGCGTAA
Statistics
Matches: 130, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
108 9 0.07
109 3 0.02
110 56 0.43
111 6 0.05
112 56 0.43
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (110 bp):
TAAATAATTAATGTTTTAATAGTTTATTTGAGCTATTAAATTTAAGCAAATAATAAAAAAATAAC
AAACTAAAGAAAAAAATTAAGAAAAAAATTAAAAAAATTTATAAG
Found at i:2290692 original size:13 final size:13
Alignment explanation
Indices: 2290674--2290701 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2290664 AATGATAAAC
2290674 TAGAGAAAAAAAT
1 TAGAGAAAAAAAT
2290687 TAGAGAAAAAAAT
1 TAGAGAAAAAAAT
2290700 TA
1 TA
2290702 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (13 bp):
TAGAGAAAAAAAT
Found at i:2290769 original size:112 final size:107
Alignment explanation
Indices: 2290571--2290775 Score: 277
Period size: 112 Copynumber: 1.9 Consensus size: 107
2290561 CTAAAAAAGA
* * * *
2290571 AAAAAAATTAGAAAAAAATTAAAAAATTATAAGTAAATAGTTAATGTTTTGATAATTTATTTGAG
1 AAAAAAATTAGAAAAAAATTAAAAAATTATAAGTAAATAATTAATATTTTAACAATTTATTTGAG
2290636 CAATTAAATTTAAGCGTGTAATCAAAAAAATGATAAACTAGAG
66 CAATTAAATTTAAGCG-GTAATCAAAAAAATGATAAACTAGAG
**
2290679 AAAAAAATTAGAGAAAAAAATTAAAAAAATTTATAAGTAAATAATTAATATTTTAACGGTTTATT
1 AAAAAAATT--AGAAAAAAATT-AAAAAA-TTATAAGTAAATAATTAATATTTTAACAATTTATT
*
2290744 TGAGCTATTAAATTTGAATGC-GTAATCAAAAA
62 TGAGCAATTAAATTT-AA-GCGGTAATCAAAAA
2290776 GAAAAGATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
108 9 0.11
110 11 0.13
111 6 0.07
112 54 0.64
113 2 0.02
114 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (107 bp):
AAAAAAATTAGAAAAAAATTAAAAAATTATAAGTAAATAATTAATATTTTAACAATTTATTTGAG
CAATTAAATTTAAGCGGTAATCAAAAAAATGATAAACTAGAG
Found at i:2290965 original size:116 final size:113
Alignment explanation
Indices: 2290843--2291155 Score: 353
Period size: 118 Copynumber: 2.7 Consensus size: 113
2290833 AGAGAAGGAA
* * * * *
2290843 AGAAAAAACTAGAGAAAAAATTAAAGAAATCTATAATTAAATAGTTAATTTTTTGATAACTTGTT
1 AGAAAAAACTAGAGAAAAAATTAAA-AAATATATAAATAAATAATTAATGTTTTGATAACTTATT
* *
2290908 T-AACTATTAAATTTAAGCGTGCAATTAAAAATAAAAAATAACAAACTAGAGA-
65 TGAGCTATTAAATTTAA-CGTGCAACT---AA-AAAAAATAACAAACTAGAGAG
* * * * *
2290960 A-AAAAAATTGGAGAAAAAATAAAAAAATATACAAATAAATAATTAATGTTTTAATAACTTATTT
1 AGAAAAAACTAGAGAAAAAATTAAAAAATATATAAATAAATAATTAATGTTTTGATAACTTATTT
* * *
2291024 GAGCTATTAAATTTTAACGTGTAACTAAAAAAAATGATAAACTAGAGAGG
66 GAGCTATTAAA-TTTAACGTGCAACTAAAAAAAATAACAAACTAGAGA-G
* *
2291074 AGAAAAAAGCGAAAGAAAAAATTTAAAAATATATATAAATAAATAATTAATGTTTTGATAACTTA
1 AGAAAAAA-CTAGAGAAAAAA-TTAAAAA-ATATATAAATAAATAATTAATGTTTTGATAACTTA
2291139 TTTGAGCTATTAAATTT
63 TTTGAGCTATTAAATTT
2291156 TAAATAAATT
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
112 18 0.11
113 2 0.01
114 1 0.01
115 39 0.23
116 44 0.27
117 15 0.09
118 47 0.28
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (113 bp):
AGAAAAAACTAGAGAAAAAATTAAAAAATATATAAATAAATAATTAATGTTTTGATAACTTATTT
GAGCTATTAAATTTAACGTGCAACTAAAAAAAATAACAAACTAGAGAG
Found at i:2291286 original size:21 final size:23
Alignment explanation
Indices: 2291244--2291287 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2291234 CAAACTAAAA
2291244 AGAAGAAAAAATTAGAAAAAATT
1 AGAAGAAAAAATTAGAAAAAATT
2291267 AGAA-AAAAAATTA-AAAAAATT
1 AGAAGAAAAAATTAGAAAAAATT
2291288 TATAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AGAAGAAAAAATTAGAAAAAATT
Found at i:2291456 original size:126 final size:125
Alignment explanation
Indices: 2291260--2291488 Score: 284
Period size: 126 Copynumber: 1.8 Consensus size: 125
2291250 AAAAATTAGA
* * * * *
2291260 AAAAATTAGAAAAAAAATTAAAAAAATTTATAAGTAAAGGATTAATGTTTTAAAAGCTTATTTTA
1 AAAAATGAGAAAAAAAATTAAAAAAATCTATAAGTAAAAGATTAATATTTTAAAAGATTATTTTA
*
2291325 ACTATTAAATTTGAGTATGCAATTAAAAATAAATGATAATAAACTATAAAAGAGAAAAAAG
66 ACTATTAAATTTGAGCATGCAATTAAAAA-AAATGATAATAAACTATAAAAGAGAAAAAAG
* * *
2291386 AAAAATGAGAAAAAAAATTAAAGAAATCTATAAGTAAATAG-TTAATATTTT-GACGATT-TGTT
1 AAAAATGAGAAAAAAAATTAAAAAAATCTATAAGTAAA-AGATTAATATTTTAAAAGATTAT-TT
* * * *
2291448 TGAGCTATTAAATTTGAGCGTGCGATTAAAAAAAATTATAA
64 T-AACTATTAAATTTGAGCATGCAATTAAAAAAAATGATAA
2291489 ACTAGAGAGA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
124 1 0.01
125 15 0.17
126 70 0.80
127 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (125 bp):
AAAAATGAGAAAAAAAATTAAAAAAATCTATAAGTAAAAGATTAATATTTTAAAAGATTATTTTA
ACTATTAAATTTGAGCATGCAATTAAAAAAAATGATAATAAACTATAAAAGAGAAAAAAG
Found at i:2291667 original size:17 final size:17
Alignment explanation
Indices: 2291625--2291668 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
2291615 GAAGAAAAAT
2291625 AAAAAAAAA-ACTAGAG
1 AAAAAAAAAGACTAGAG
2291641 AAAAAAAAAGACTAGAG
1 AAAAAAAAAGACTAGAG
2291658 AAAAAAAAAGA
1 AAAAAAAAAGA
2291669 TGACAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAGACTAGAG
Found at i:2291703 original size:13 final size:13
Alignment explanation
Indices: 2291685--2291715 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2291675 ACTAGAGAGG
2291685 AGAAAAAAATTAA
1 AGAAAAAAATTAA
2291698 AGAAAAAAATTAA
1 AGAAAAAAATTAA
2291711 A-AAAA
1 AGAAAA
2291716 TTTATAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (13 bp):
AGAAAAAAATTAA
Found at i:2291821 original size:14 final size:14
Alignment explanation
Indices: 2291802--2291835 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2291792 ATAAATTAGA
2291802 AGAGAAAAAAAATT
1 AGAGAAAAAAAATT
2291816 AGAG-AAAAAAATT
1 AGAGAAAAAAAATT
*
2291829 AAAGAAA
1 AGAGAAA
2291836 TTTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AGAGAAAAAAAATT
Found at i:2291823 original size:425 final size:420
Alignment explanation
Indices: 2290909--2291849 Score: 961
Period size: 425 Copynumber: 2.2 Consensus size: 420
2290899 TAACTTGTTT
* * * *
2290909 AACTATTAAATTT-AAGCGTGCAATTAAAAATAAAAAATAACAAAC--T---AGAGAAAAAAAAT
1 AACTATTAAATTTGAA-CATGCAATAAAAAATAAATAATAATAAACTATAAAAGAGAAAAAAAAT
* * * * *
2290968 T-G-GAGAAAAAA-TAAAAAAATATACAAATAAATAATTAATGTTTTAATAACTTATTTGAGCTA
65 TAGAGAAAAAAAATTAAAGAAATATATAAATAAATAATTAATATTTTAACAACTTATTTGAGCTA
* *
2291030 TTAAATTTTAACGTGTAACTAAAAAAAATGATAAACTAGAGAGGAGAAAAAAGCGAAAGAAAAAA
130 TTAAATTTGAACGTGCAACTAAAAAAAATGATAAACTAGAGAGGAGAAAAAA--GAAAGAAAAAA
*
2291095 TTTAAAAATATATATAAATAAATAATTAATGTTTTGATAACTTATTTGAGCTATTAAATTTTAAA
193 TTTAAAAATATATACAAATAAATAATTAATGTTTTGATAACTTATTTGAGCTATTAAATTTTAAA
* * *
2291160 TAAATTATCAAAAAAGAAAAAATGATAAACTAGAGAGGAGGAAAAATAAAAAAGTAAAAAAAAAA
258 TAAATAATCAAAAAAGAAAAAATGATAAACTAGAAAGGAAGAAAAATAAAAAAG-AAAAAAAAAA
* * * ** *
2291225 GAAAAGAAACAAACTAAAAAGAAGAAAAAATTAGAAAAAATTAGAAAAAAAATTAAAAAAATTTA
322 AAAAAGAAACAAACAAAAAAGAACAAAAAAGGAGAAAAAATTAAAAAAAAAATTAAAAAAATTTA
** * *
2291290 TAAGTAAAGGATTAATGTTTTAAAAGCTTATTTT
387 TAAGTAAAGGACAAATATTTTAAAAGCTTATTTG
** * * *
2291324 AACTATTAAATTTGAGTATGCAATTAAAAATAAATGATAATAAACTATAAAAGAGAAAAAAGAAA
1 AACTATTAAATTTGAACATGCAATAAAAAATAAATAATAATAAACTATAAAAGAGAAAAAA-AAT
* * * * * * * *
2291389 AATGAGAAAAAAAATTAAAGAAATCTATAAGTAAATAGTTAATATTTTGACGATTTGTTTGAGCT
65 TA-GAGAAAAAAAATTAAAGAAATATATAAATAAATAATTAATATTTTAACAACTTATTTGAGCT
* * * *
2291454 ATTAAATTTGAGCGTGCGATTAAAAAAAATTATAAACTAGAGA-GA-AAAAAA-AAGAGAAAAAA
129 ATTAAATTTGAACGTGCAACTAAAAAAAATGATAAACTAGAGAGGAGAAAAAAGAA-AGAAAAAA
* * * ** *
2291516 TTTAAAAA-ATCTACCAATAAATTATTAATGTTTTGATAGTTTATTTGAGTTATTAAA-TTTAAA
193 TTTAAAAATATATACAAATAAATAATTAATGTTTTGATAACTTATTTGAGCTATTAAATTTTAAA
** *
2291579 TACGTAAT-TAAAAAGAAAAAATGATAAACTAGAAAGGAAGAAAAATAAAAAA-AAAACTAGAGA
258 TAAATAATCAAAAAAGAAAAAATGATAAACTAGAAAGGAAGAAAAATAAAAAAGAAAA--A-A-A
*
2291642 AAAAAAAAGACTAGAGAAA-AAAAAAGATGACAAACTAGAGAGGAGAAAAAAATTAAAGAAAAAA
319 AAAAAAAAGA--A-ACAAACAAAAAAGA--ACAAA--A-A-AGGAG-AAAAAATTAAA-AAAAAA
** * * * *
2291706 ATTAAAAAAATTTATAAGTAAATTACAAATATTTTGACAGTTTGTTTG
373 ATTAAAAAAATTTATAAGTAAAGGACAAATATTTTAAAAGCTTATTTG
* * * * *
2291754 AGCTATTAAATTTGAACGTGTAATAAAAAATAAA-AATGATAAA-T-TAGAAGAGAAAAAAAATT
1 AACTATTAAATTTGAACATGCAATAAAAAATAAATAATAATAAACTATAAAAGAGAAAAAAAATT
*
2291816 AGAG-AAAAAAATTAAAGAAATTTATAAATAAATA
66 AGAGAAAAAAAATTAAAGAAATATATAAATAAATA
2291850 TCTTATTTAG
Statistics
Matches: 430, Mismatches: 69, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
415 37 0.09
416 5 0.01
417 1 0.00
418 42 0.10
419 12 0.03
420 64 0.15
421 18 0.04
422 8 0.02
423 11 0.03
424 42 0.10
425 79 0.18
426 4 0.01
427 14 0.03
428 4 0.01
429 17 0.04
430 72 0.17
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.26
Consensus pattern (420 bp):
AACTATTAAATTTGAACATGCAATAAAAAATAAATAATAATAAACTATAAAAGAGAAAAAAAATT
AGAGAAAAAAAATTAAAGAAATATATAAATAAATAATTAATATTTTAACAACTTATTTGAGCTAT
TAAATTTGAACGTGCAACTAAAAAAAATGATAAACTAGAGAGGAGAAAAAAGAAAGAAAAAATTT
AAAAATATATACAAATAAATAATTAATGTTTTGATAACTTATTTGAGCTATTAAATTTTAAATAA
ATAATCAAAAAAGAAAAAATGATAAACTAGAAAGGAAGAAAAATAAAAAAGAAAAAAAAAAAAAA
AGAAACAAACAAAAAAGAACAAAAAAGGAGAAAAAATTAAAAAAAAAATTAAAAAAATTTATAAG
TAAAGGACAAATATTTTAAAAGCTTATTTG
Found at i:2292474 original size:21 final size:21
Alignment explanation
Indices: 2292448--2292487 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2292438 TATTAAAAAT
2292448 TATTTTAT-ATTAATATTTACA
1 TATTTTATAATTAA-ATTTACA
2292469 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2292488 AATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATTAAATTTACA
Found at i:2301667 original size:16 final size:15
Alignment explanation
Indices: 2301642--2301690 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
2301632 TAACTTCTCC
*
2301642 TTCTTTTTCTTTTCT
1 TTCTTTTTCTCTTCT
2301657 TTCTGTTTTCTCTTCT
1 TTCT-TTTTCTCTTCT
2301673 TTCTTTTCCTCTCTTCT
1 TTCTTTT--TCTCTTCT
2301690 T
1 T
2301691 CTCTCTCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 14 0.47
17 9 0.30
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (15 bp):
TTCTTTTTCTCTTCT
Found at i:2301694 original size:10 final size:10
Alignment explanation
Indices: 2301667--2301729 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
2301657 TTCTGTTTTC
*
2301667 TCTTCTTTCT
1 TCTTCTCTCT
2301677 T-TTCCTCTCT
1 TCTT-CTCTCT
2301687 TCTTCTCTCT
1 TCTTCTCTCT
*
2301697 CCTTCTCT-T
1 TCTTCTCTCT
2301706 TCCTTCTCCTCT
1 T-CTTCT-CTCT
2301718 TCTTCTC-CT
1 TCTTCTCTCT
2301727 TCT
1 TCT
2301730 CTTTCCTCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
9 8 0.18
10 26 0.58
11 9 0.20
12 2 0.04
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (10 bp):
TCTTCTCTCT
Found at i:2301695 original size:27 final size:27
Alignment explanation
Indices: 2301664--2301780 Score: 109
Period size: 27 Copynumber: 4.3 Consensus size: 27
2301654 TCTTTCTGTT
* *
2301664 TTCTCT-TCTTTCT-TTTCCTCTCTTC
1 TTCTCTCTCCTTCTCTTTCCTCTCCTC
2301689 TTCTCTCTCCTTCTCTTTCCTTCTCCTC
1 TTCTCTCTCCTTCTCTTTCC-TCTCCTC
*
2301717 TTCT-TCTCCTTCTCTTTCCTCCTCCTT
1 TTCTCTCTCCTTCTCTTTCCT-CTCCTC
*
2301744 TTCCTTTCCCTCTCTTCTCTTT-CTCTCCTC
1 TT-C--TCTCTC-CTTCTCTTTCCTCTCCTC
2301774 TTC-CTCT
1 TTCTCTCT
2301781 TCCTCCTCCT
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
25 6 0.08
26 10 0.13
27 27 0.35
28 11 0.14
29 1 0.01
30 8 0.10
31 5 0.06
32 9 0.12
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (27 bp):
TTCTCTCTCCTTCTCTTTCCTCTCCTC
Found at i:2301715 original size:6 final size:6
Alignment explanation
Indices: 2301694--2301768 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
2301684 TCTTCTTCTC
*
2301694 TCTCCT TCT-CT T-TCCT TCTCC- TCTTCT TCTCCT TCT-CT T-TCCT
1 TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT
* * * *
2301737 CCTCCT TTTCCT T-TCCC TCT-CT TCTCTT TCTC
1 TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTC
2301769 TCCTCTTCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 23 0.43
6 29 0.54
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTCCT
Found at i:2301855 original size:21 final size:21
Alignment explanation
Indices: 2301813--2301856 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2301803 CTCCTCCACC
*
2301813 TCCGAATACTCTGAATCGGAT
1 TCCGAATACTCAGAATCGGAT
* * *
2301834 TCCGAATAGTCAGACTCTGAT
1 TCCGAATACTCAGAATCGGAT
2301855 TC
1 TC
2301857 GGATTCTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCCGAATACTCAGAATCGGAT
Found at i:2313488 original size:4 final size:4
Alignment explanation
Indices: 2313471--2313500 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2313461 CAATCTAAAA
*
2313471 TTAT TTAG TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2313501 CAATTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:2313858 original size:24 final size:23
Alignment explanation
Indices: 2313811--2313858 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2313801 TTTACTGTTT
* *
2313811 ATTTAATAAAAATATTTATTTAA
1 ATTTAATAAAAATATTAATATAA
*
2313834 ATTTAATTATAAATATTAATATAA
1 ATTTAA-TAAAAATATTAATATAA
2313858 A
1 A
2313859 AATATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATAAAAATATTAATATAA
Found at i:2314459 original size:21 final size:20
Alignment explanation
Indices: 2314428--2314467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2314418 TTAAATTTAA
*
2314428 ATAAAAATAATTTTTATTAT
1 ATAAAAATAATTTATATTAT
2314448 ATAAATAATAATTTATATTA
1 ATAAA-AATAATTTATATTA
2314468 AGTCAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATAATTTATATTAT
Found at i:2314590 original size:27 final size:27
Alignment explanation
Indices: 2314560--2314615 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2314550 TAAAGTAATG
* ** *
2314560 AAAAGTAAATATATGTTATGAGTTTTA
1 AAAAATAAATATATGCCATGAATTTTA
2314587 AAAAATAAATATATGCCATGAATTTTA
1 AAAAATAAATATATGCCATGAATTTTA
2314614 AA
1 AA
2314616 TATGTCTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (27 bp):
AAAAATAAATATATGCCATGAATTTTA
Found at i:2318636 original size:19 final size:19
Alignment explanation
Indices: 2318599--2318636 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2318589 TCTAAATCAT
*
2318599 TTATCTTGAATAAAATAAA
1 TTATCTTGAAAAAAATAAA
2318618 TTATCTT-AAAAAAACTAAA
1 TTATCTTGAAAAAAA-TAAA
2318637 ATTGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (19 bp):
TTATCTTGAAAAAAATAAA
Found at i:2318723 original size:4 final size:4
Alignment explanation
Indices: 2318714--2318743 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2318704 TTATTTTAGA
2318714 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
2318744 GATTTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:2320094 original size:2 final size:2
Alignment explanation
Indices: 2320081--2320118 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2320071 GCGATAGGTT
*
2320081 TA TA TA TT 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
2320119 AATCTAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2320722 original size:29 final size:27
Alignment explanation
Indices: 2320685--2320825 Score: 90
Period size: 29 Copynumber: 5.0 Consensus size: 27
2320675 TCTAACTTTT
* *
2320685 TTAT-TTAAACAAATTTTTATATTTTTA
1 TTATATTAAATAAATTTTTA-ATTATTA
2320712 TTATATCTAAATAAATTTTTAATTATTA
1 TTATAT-TAAATAAATTTTTAATTATTA
* *
2320740 TTTTATTCAAATAAATTTTGAACTT-TTAA
1 TTATATT-AAATAAATTTTTAA-TTATT-A
* * *
2320769 TTATTTTCAAATAAGTTATTAACTT-TTA
1 TTATATT-AAATAAATTTTTAA-TTATTA
* *
2320797 TTTTAAACTTAAATAAAATTTTAATTATT
1 --TTATA-TTAAATAAATTTTTAATTATT
2320826 TTAATATAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.05
28 28 0.31
29 40 0.44
30 16 0.18
31 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (27 bp):
TTATATTAAATAAATTTTTAATTATTA
Found at i:2320741 original size:28 final size:28
Alignment explanation
Indices: 2320685--2320758 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
2320675 TCTAACTTTT
* *
2320685 TTAT-TTAAACAAATTTTTATATTTTTA
1 TTATATTAAATAAATTTTTATATTATTA
2320712 TTATATCTAAATAAATTTTTA-ATTATTA
1 TTATAT-TAAATAAATTTTTATATTATTA
*
2320740 TTTTATTCAAATAAATTTT
1 TTATATT-AAATAAATTTT
2320759 GAACTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.12
28 23 0.56
29 13 0.32
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATATTAAATAAATTTTTATATTATTA
Found at i:2320856 original size:30 final size:29
Alignment explanation
Indices: 2320821--2320879 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2320811 AAAATTTTAA
*
2320821 TTATTTTAATATAAATTAAAAGATAAAATT
1 TTATTTTAATAT-AATAAAAAGATAAAATT
*
2320851 TTATTTTAATATAATAAAAATATAAAATT
1 TTATTTTAATATAATAAAAAGATAAAATT
2320880 CTGTTAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TTATTTTAATATAATAAAAAGATAAAATT
Found at i:2321532 original size:4 final size:4
Alignment explanation
Indices: 2321523--2321548 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2321513 AAAGCAACAT
2321523 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
2321549 CTTTCATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2322174 original size:49 final size:48
Alignment explanation
Indices: 2322099--2322201 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 48
2322089 TTAAATATTT
*
2322099 TTTTCTAATTGATTTTTTCTATTTTTTAAATAGATACTTTAAAAGTATATA
1 TTTT-TAATTAATTTTTTCTATTTTTTAAATAGAT-C-TTAAAAGTATATA
* * * *
2322150 TTTTTAATTAATTTTTT-TATTTTTTATATATATCTTAAAATTGTATA
1 TTTTTAATTAATTTTTTCTATTTTTTAAATAGATCTTAAAAGTATATA
2322197 TTTTT
1 TTTTT
2322202 TCAAATTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 16 0.34
48 1 0.02
49 14 0.30
50 12 0.26
51 4 0.09
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (48 bp):
TTTTTAATTAATTTTTTCTATTTTTTAAATAGATCTTAAAAGTATATA
Found at i:2322782 original size:21 final size:21
Alignment explanation
Indices: 2322758--2322801 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2322748 ATCATAAGTA
*
2322758 AAATTAATTTAATTTTATATT
1 AAATTAATTTAATTATATATT
* *
2322779 AAATTTATTTAATTATATTTT
1 AAATTAATTTAATTATATATT
2322800 AA
1 AA
2322802 TTGATTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTAATTTAATTATATATT
Found at i:2322800 original size:15 final size:15
Alignment explanation
Indices: 2322782--2322874 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 15
2322772 TTATATTAAA
*
2322782 TTTATTTAATTATAT
1 TTTATATAATTATAT
*
2322797 TTTA-ATTGATTGAT-T
1 TTTATA-TAATT-ATAT
2322812 TATTA-ATAATTA-A-
1 T-TTATATAATTATAT
* *
2322825 TATATATAAATATAT
1 TTTATATAATTATAT
*
2322840 TTAATTATAATTATAT
1 TTTA-TATAATTATAT
*
2322856 TTTATATAATTATAG
1 TTTATATAATTATAT
2322871 TTTA
1 TTTA
2322875 AAAAAATAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
12 2 0.03
13 7 0.12
14 2 0.03
15 30 0.50
16 19 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTATATAATTATAT
Found at i:2322854 original size:16 final size:15
Alignment explanation
Indices: 2322828--2322875 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2322818 TAATTAATAT
*
2322828 ATATAAATATATTTA
1 ATATAATTATATTTA
*
2322843 ATTATAATTATATTTT
1 A-TATAATTATATTTA
2322859 ATATAATTATAGTTTA
1 ATATAATTATA-TTTA
2322875 A
1 A
2322876 AAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATAATTATATTTA
Found at i:2323842 original size:9 final size:9
Alignment explanation
Indices: 2323828--2323861 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2323818 AAGTTAAATT
2323828 TTAAAAAAA
1 TTAAAAAAA
2323837 TTAAAAAAA
1 TTAAAAAAA
* *
2323846 TTATAAATA
1 TTAAAAAAA
2323855 TTAAAAA
1 TTAAAAA
2323862 TTAAATCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:2324169 original size:29 final size:29
Alignment explanation
Indices: 2324118--2324203 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
2324108 AAAAAAAATC
* * * *
2324118 TTAATTTTAATATTTTATTTAAATGAGTTT
1 TTAATTTTTA-ATTATATTTAAATAAATTT
2324148 TTAATTTTTAATTATATTTAAATAAATTT
1 TTAATTTTTAATTATATTTAAATAAATTT
*
2324177 TTAATTTTTAATTTAAATTTAAATAAA
1 TTAATTTTTAA-TTATATTTAAATAAA
2324204 ATTTAAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
TTAATTTTTAATTATATTTAAATAAATTT
Found at i:2324269 original size:29 final size:30
Alignment explanation
Indices: 2324211--2324273 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2324201 AAAATTTAAA
* * *
2324211 TATTTTGATATAGATCAAAAGATAGAATTT
1 TATTTTGATATAAATAAAAAGATAAAATTT
*
2324241 TATTTTGATA-AAATAAAAATATAAAATTT
1 TATTTTGATATAAATAAAAAGATAAAATTT
2324270 TATT
1 TATT
2324274 AGAGTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (30 bp):
TATTTTGATATAAATAAAAAGATAAAATTT
Found at i:2325194 original size:11 final size:11
Alignment explanation
Indices: 2325175--2325217 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2325165 ATAAGTAAAA
2325175 TTATTTTAATT
1 TTATTTTAATT
* *
2325186 TTATATTAAAT
1 TTATTTTAATT
2325197 TTA-TTTAATT
1 TTATTTTAATT
*
2325207 ATATTTTAATT
1 TTATTTTAATT
2325218 GATTGATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:2325203 original size:21 final size:22
Alignment explanation
Indices: 2325170--2325215 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2325160 TTATCATAAG
*
2325170 TAAAATTATTTTAATTTTATAT
1 TAAAATTATTTTAATTATATAT
* *
2325192 TAAATTTA-TTTAATTATATTT
1 TAAAATTATTTTAATTATATAT
2325213 TAA
1 TAA
2325216 TTGATTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAAAATTATTTTAATTATATAT
Found at i:2325281 original size:16 final size:15
Alignment explanation
Indices: 2325244--2325292 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
2325234 ATAATTAATA
*
2325244 TATATAAATATATTT
1 TATATAATTATATTT
*
2325259 AATTATAATTATGATTT
1 TA-TATAATTAT-ATTT
*
2325276 TATATAATTATAATT
1 TATATAATTATATTT
2325291 TA
1 TA
2325293 AAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TATATAATTATATTT
Found at i:2325995 original size:2 final size:2
Alignment explanation
Indices: 2325988--2326013 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2325978 ATTAATAGTG
2325988 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
2326014 CTAAGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2326299 original size:20 final size:21
Alignment explanation
Indices: 2326276--2326314 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2326266 TACAAAAAGT
* *
2326276 TAAATTTTGAAAA-AAAATTA
1 TAAATATTAAAAATAAAATTA
2326296 TAAATATTAAAAATAAAAT
1 TAAATATTAAAAATAAAAT
2326315 CACAACCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAATATTAAAAATAAAATTA
Found at i:2326675 original size:29 final size:29
Alignment explanation
Indices: 2326641--2326700 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
2326631 AATTATTATT
* *
2326641 TTATATTCAAATGAGTTTTTAATTTTTAA
1 TTATATTCAAATAAGTTATTAATTTTTAA
* *
2326670 TTATATTTAAATAAGTTATTACTTTTTAA
1 TTATATTCAAATAAGTTATTAATTTTTAA
2326699 TT
1 TT
2326701 TCAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (29 bp):
TTATATTCAAATAAGTTATTAATTTTTAA
Found at i:2326710 original size:30 final size:29
Alignment explanation
Indices: 2326606--2326713 Score: 87
Period size: 30 Copynumber: 3.7 Consensus size: 29
2326596 AGTTTATATA
* *
2326606 TTTT-ATTATATCTAAATAAATT-TTAAAT
1 TTTTAATTATATTTAAATAAGTTATT-AAT
* * * * *
2326634 TATTATTTTATATTCAAATGAGTTTTTAAT
1 TTTTA-ATTATATTTAAATAAGTTATTAAT
*
2326664 TTTTAATTATATTTAAATAAGTTATTACT
1 TTTTAATTATATTTAAATAAGTTATTAAT
2326693 TTTTAATT-TCAATTTAAATAA
1 TTTTAATTAT--ATTTAAATAA
2326714 AATTTTAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.06
29 27 0.43
30 30 0.48
31 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTAATTATATTTAAATAAGTTATTAAT
Found at i:2328647 original size:16 final size:16
Alignment explanation
Indices: 2328626--2328669 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
2328616 TATATATATA
2328626 TATATATTTAATTATAAT
1 TATA-ATTTAA-TATAAT
*
2328644 TATAATTTTATATAAT
1 TATAATTTAATATAAT
2328660 TATAATTTAA
1 TATAATTTAA
2328670 AGTAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.62
17 5 0.21
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAATTTAATATAAT
Found at i:2329102 original size:17 final size:18
Alignment explanation
Indices: 2329058--2329095 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2329048 ATTTATATAA
*
2329058 TTAATATTTTTTAATTAT
1 TTAATAATTTTTAATTAT
*
2329076 TTAATAATTTTTATTTAT
1 TTAATAATTTTTAATTAT
2329094 TT
1 TT
2329096 TTAATTTAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATAATTTTTAATTAT
Found at i:2329663 original size:18 final size:18
Alignment explanation
Indices: 2329625--2329667 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2329615 CATATATAAT
* *
2329625 AATATATATTAAAATTTTA
1 AATA-ATATTAAAAATATA
2329644 AATAATATTAAAAATATA
1 AATAATATTAAAAATATA
2329662 AA-AATA
1 AATAATA
2329668 ATTTTCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATATTAAAAATATA
Found at i:2332893 original size:13 final size:13
Alignment explanation
Indices: 2332875--2332913 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2332865 AAAAAATTTT
2332875 AAAAATATAATTA
1 AAAAATATAATTA
*
2332888 AAAAATTAAAATTA
1 AAAAA-TATAATTA
2332902 AAAAATAATAAT
1 AAAAAT-ATAAT
2332914 ATAAGTAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATATAATTA
Found at i:2336826 original size:153 final size:152
Alignment explanation
Indices: 2336544--2336829 Score: 437
Period size: 153 Copynumber: 1.9 Consensus size: 152
2336534 ACTGGCCTTT
*
2336544 TTTCCTCTCCCACGAGTCTCCATGACCTCTTGTGTCTGGTTTTCTACTTAAGACACCATCTCTAC
1 TTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGTTTTCTACTTAAGACACCATCTCTAC
** * * *
2336609 GATTAGTACCTTCATGAAACAAGAGCTCTGATATCAACTGTCACGAGCTTGGACTTTAGTCTAGC
66 GATTAGTACCTTCACAAAACAAGAGCTCTGATATCAACTGTCACGAGCCTGAACTTTAGCCTAGC
2336674 AAACCGCGTGGCCTTAGGTCTC
131 AAACCGCGTGGCCTTAGGTCTC
* * * * *
2336696 TTTCCTCTTCCATGAGTCTCCAGGACCTCTTGTGTTTGGTTTTCTGCTTGAGACAGCCATCTCTA
1 TTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGTTTTCTACTTAAGACA-CCATCTCTA
* * *
2336761 CGATTAGTACCTTCACAAAACAGGAGCTCTGATATTAATTGTCACGAGCCTGAACTTTAGCCTAG
65 CGATTAGTACCTTCACAAAACAAGAGCTCTGATATCAACTGTCACGAGCCTGAACTTTAGCCTAG
2336826 CAAA
130 CAAA
2336830 TCGTGCGACC
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
152 49 0.41
153 70 0.59
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (152 bp):
TTTCCTCTCCCACGAGTCTCCAGGACCTCTTGTGTCTGGTTTTCTACTTAAGACACCATCTCTAC
GATTAGTACCTTCACAAAACAAGAGCTCTGATATCAACTGTCACGAGCCTGAACTTTAGCCTAGC
AAACCGCGTGGCCTTAGGTCTC
Found at i:2338609 original size:12 final size:14
Alignment explanation
Indices: 2338577--2338616 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2338567 ATAAAAATGA
*
2338577 ATATATTAAAATTT
1 ATATAATAAAATTT
2338591 ATATAATAAAA-TT
1 ATATAATAAAATTT
2338604 AT-TAAT-AAATTT
1 ATATAATAAAATTT
2338616 A
1 A
2338617 AATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 7 0.29
13 4 0.17
14 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:2341189 original size:14 final size:14
Alignment explanation
Indices: 2341170--2341196 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2341160 TGTTTGGTAG
2341170 AAAATAATTTTTAA
1 AAAATAATTTTTAA
2341184 AAAATAATTTTTA
1 AAAATAATTTTTA
2341197 TATATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATAATTTTTAA
Found at i:2342455 original size:159 final size:157
Alignment explanation
Indices: 2341582--2342495 Score: 488
Period size: 159 Copynumber: 5.7 Consensus size: 157
2341572 TTTCGATAAG
* * * * * * * *
2341582 TGATTTAGCTACAGTTTCTTTTCATGTTTCATACGAGATTGATG-AAAAACTTGTAAGGGAGTCA
1 TGATTTAGTTACTGTTTCTTTTCAAGTTT-ATACGAGATTGACGAAAAAAATTATAAGGAAGTTA
* * *** * * *
2341646 AATTAAAGAAAAAAT--ATA-TTTAGCCATGTGAAAAAATAATATCAATACAACCTGTCTTAATT
65 AATTAAAGCAAAAATGCA-AGTCTAGTTGTGTGGAAAAATAATATCAAT---A-TTTTCTTAATT
* * * *
2341708 TAAGAGATTGTTTTATAATA-GTTTTGTTTTG-TT
125 TAACAGATTATTTTCTAATACG-TTCG-TTTGATT
* * * * * ** *
2341741 TGATTTAGTTA-TAGTTTCTTTTTATGTTTTATATGAGATCGATGATGAAAATTGTGAAGG-AGT
1 TGATTTAGTTACT-GTTTCTTTTCAAG-TTTATACGAGATTGACGAAAAAAATTAT-AAGGAAGT
* * * * * * ** **
2341804 TATATTAAAGAAAAAATGCACGTGTAGTCGTGTGAAAAAATAATATTGATATTCCCTTAATTTAA
63 TAAATTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATCAATATTTTCTTAATTTAA
* * * **
2341869 AAGATTACTTTCTAATATC-TTCATTCCATT
128 CAGATTATTTTCTAATA-CGTTCGTTTGATT
* * ** * * * * * *
2341899 TCATTTAGCTACAATTTCTTTTTATGTTTCATACGAAATTGACGAAGAAAATTATGAGGGAGTTA
1 TGATTTAGTTACTGTTTCTTTTCAAGTTT-ATACGAGATTGACGAAAAAAATTATAAGGAAGTTA
** * * * * *
2341964 AATTAAAGTTAAAATGCAAGTCTATTTACT-TCGAAAAATAATATTAATACAATTCATCTTAATT
65 AATTAAAGCAAAAATGCAAGTCTAGTT-GTGTGGAAAAATAATATCAAT---ATT-TTCTTAATT
* * * * * * *
2342028 TCAGAAATTGCTTTT-TGATA-GCTTC-ATT--CT
125 TAACAGATT-ATTTTCTAATACG-TTCGTTTGATT
* * * * * * * *
2342058 TGATCTAGTT-GTAATTTCCTGTCATGTTTCAT-CAGAGATTGA-TAAAGAAAATTACGAA-GAA
1 TGATTTAGTTACT-GTTTCTTTTCAAGTTT-ATAC-GAGATTGACGAAA-AAAATTA-TAAGGAA
* * * *
2342119 GTCAAATCAAAGCAAAATTGCAAGTCTAGTTGTGTAGAAAAATAATATCAATATAATTTGTCTTA
61 GTTAAATTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATC-A-AT-ATTT-TCTTA
*
2342184 ATTTAAGAGATTATTTTCTAATACGTTCGTTTGATT
122 ATTTAACAGATTATTTTCTAATACGTTCGTTTGATT
* * * * *
2342220 TGATTTAGTTACTGTTTCTTTTCAAGTTTATACGAGATTGATGTAGAAAATTGTAAGGGAGTTAA
1 TGATTTAGTTACTGTTTCTTTTCAAGTTTATACGAGATTGACGAAAAAAATTATAAGGAAGTTAA
* * **
2342285 ACTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATCGATATTTTCTTAATTTAACTT
66 ATTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATCAATATTTTCTTAATTTAACAG
*
2342350 ATTGCTTTT-TAATA-GTTTCGTTTGATT
131 ATT-ATTTTCTAATACG-TTCGTTTGATT
* * *
2342377 TGATTTAGTCA-TAGTTTTTTTTTCATA-TTTCATACGAGATTGCCGAAAAAAATTATAAGGAAG
1 TGATTTAGTTACT-G-TTTCTTTTCA-AGTTT-ATACGAGATTGACGAAAAAAATTATAAGGAAG
** *
2342440 TTAAATTAAAGCAAAAATGCAAGTCTAGTCATGTGAAAAAATAATATCAATATTTT
62 TTAAATTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATCAATATTTT
2342496 GTTTATCATA
Statistics
Matches: 586, Mismatches: 125, Indels: 88
0.73 0.16 0.11
Matches are distributed among these distances:
156 2 0.00
157 49 0.08
158 136 0.23
159 220 0.38
160 35 0.06
161 72 0.12
162 68 0.12
163 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (157 bp):
TGATTTAGTTACTGTTTCTTTTCAAGTTTATACGAGATTGACGAAAAAAATTATAAGGAAGTTAA
ATTAAAGCAAAAATGCAAGTCTAGTTGTGTGGAAAAATAATATCAATATTTTCTTAATTTAACAG
ATTATTTTCTAATACGTTCGTTTGATT
Found at i:2344328 original size:161 final size:158
Alignment explanation
Indices: 2343976--2344605 Score: 502
Period size: 162 Copynumber: 3.9 Consensus size: 158
2343966 TCAATATTTC
* * * *
2343976 CTTAATTTAAAGGATTGCTTTCTAATAACTTTGTTCCATTTGATTTAACTACAATTTTTTTTCA-
1 CTTAATTTAAAGAATTGCTTTCTAATAGCTTCGTT-CATTTGATTTAACTA-TATTTTTTTTCAT
* * * * * * *
2344040 CTTTCATATGAGATTGTCAAAGAAAATTAT-GACGGGTCAAATTAAAACAAAAGTGTAAGTCTAG
64 ATTTCATATGAGATTGACAAA-AAAATTATAAACGAGTCAAATTAAAGCAAAAATGCAAGTCTAG
* **
2344104 TCATGTGAAAAAAATAATATCAATACAATCCGC
128 TCATGTG-GAAAAATAATATCAATAC-ATCCAT
* * * *
2344137 CTTAATTTGAGGAATTGCATTT-TGATAGCTTCGTTCATTTGATTTAGCTATATTTTCTTTTCAT
1 CTTAATTTAAAGAATTGC-TTTCTAATAGCTTCGTTCATTTGATTTAACTATATTTT-TTTTCAT
* * * *
2344201 GTTTCATATGAGATTGACAAAAAAATTTATAAACGAATCAAATTAAACCAAAAATGCAAGTTTAG
64 ATTTCATATGAGATTGACAAAAAAA-TTATAAACGAGTCAAATTAAAGCAAAAATGCAAGTCTAG
2344266 TCATGTGGAAAAATAATATCAATACAGTCCAT
128 TCATGTGGAAAAATAATATCAATACA-TCCAT
* * * * * * * *
2344298 CATAATTTAAAGCATTG-TCTTCTAATAGCTTTGTTTCGTTCGATTTAACTACAATTTCTTTTCG
1 CTTAATTTAAAGAATTGCT-TTCTAATAGCTTCG-TTCATTTGATTTAACTA-TATTTTTTTTCA
* * * * * * ** * *
2344362 TATTTCATACGAAATTGATGAAGAAACTTGTAAGGGAGTTAAATTAAAGCAAAATTGCAAGTCTA
63 TATTTCATATGAGATTGA-CAAAAAAATTATAAACGAGTCAAATTAAAGCAAAAATGCAAGTCTA
** * *
2344427 GTTTTGTGGAAAAATAATATCGATAC-T--TT
127 GTCATGTGGAAAAATAATATCAATACATCCAT
* * * * * * *
2344456 CTTAATTTAAGGTATTGCTTTCCAATTGCTTCGTT-ATGTTTGATTTAGCTGTAGTTTTTTTCAT
1 CTTAATTTAAAGAATTGCTTTCTAATAGCTTCGTTCA--TTTGATTTAACTATATTTTTTTTCA-
* * * * * * *
2344520 TATTTCATAAGAGATTGACGAAGAAAATTGTGAATGAGTCAAATTGAAGCAAAAATGTAAGTCTA
63 TATTTCATATGAGATTGAC-AAAAAAATTATAAACGAGTCAAATTAAAGCAAAAATGCAAGTCTA
* *
2344585 GCCGTGTGGAAAAAATAATAT
127 GTCATGTGG-AAAAATAATAT
2344606 TGATATTTAT
Statistics
Matches: 374, Mismatches: 78, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
157 10 0.03
158 95 0.25
159 18 0.05
160 28 0.07
161 90 0.24
162 124 0.33
163 9 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (158 bp):
CTTAATTTAAAGAATTGCTTTCTAATAGCTTCGTTCATTTGATTTAACTATATTTTTTTTCATAT
TTCATATGAGATTGACAAAAAAATTATAAACGAGTCAAATTAAAGCAAAAATGCAAGTCTAGTCA
TGTGGAAAAATAATATCAATACATCCAT
Found at i:2345911 original size:20 final size:20
Alignment explanation
Indices: 2345871--2345907 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2345861 TTATATGTTT
*
2345871 AATTCTTATAATTAATATAA
1 AATTATTATAATTAATATAA
2345891 AATTATTAT-ATTAATAT
1 AATTATTATAATTAATAT
2345908 TAAAGATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTATTATAATTAATATAA
Found at i:2346370 original size:11 final size:11
Alignment explanation
Indices: 2346356--2346410 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
2346346 ATATGAGTGT
*
2346356 AATATAATATA
1 AATATAATACA
*
2346367 AATATGAGTACA
1 AATAT-AATACA
*
2346379 ATATATAATGCA
1 A-ATATAATACA
2346391 AATATAATACA
1 AATATAATACA
2346402 AATATAATA
1 AATATAATA
2346411 AATATTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 23 0.62
12 10 0.27
13 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (11 bp):
AATATAATACA
Found at i:2346393 original size:24 final size:22
Alignment explanation
Indices: 2346356--2346410 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
2346346 ATATGAGTGT
* *
2346356 AATATAATATAAATATGAGTACA
1 AATATAATACAAATAT-AATACA
*
2346379 ATATATAATGCAAATATAATACA
1 A-ATATAATACAAATATAATACA
2346402 AATATAATA
1 AATATAATA
2346411 AATATTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.26
23 7 0.26
24 13 0.48
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (22 bp):
AATATAATACAAATATAATACA
Found at i:2346550 original size:39 final size:39
Alignment explanation
Indices: 2346507--2346586 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
2346497 TATAACGATA
*
2346507 ATAAAAATTATTTTTTGTATAATAATATATAATAAAAAT
1 ATAAAAACTATTTTTTGTATAATAATATATAATAAAAAT
2346546 ATAAAAACTATTTTTTGTATAATAATATATAATAAAAAT
1 ATAAAAACTATTTTTTGTATAATAATATATAATAAAAAT
2346585 AT
1 AT
2346587 GAAATTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (39 bp):
ATAAAAACTATTTTTTGTATAATAATATATAATAAAAAT
Found at i:2351083 original size:41 final size:41
Alignment explanation
Indices: 2351036--2351117 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2351026 TCCTGGAATT
2351036 TACATAATTGTGTGACCACTTTGCAAGTCCAAATTTTCGGC
1 TACATAATTGTGTGACCACTTTGCAAGTCCAAATTTTCGGC
*
2351077 TACATAATTGTGTGACCACTTTGCAGGTCCAAATTTTCGGC
1 TACATAATTGTGTGACCACTTTGCAAGTCCAAATTTTCGGC
2351118 CTTCTTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (41 bp):
TACATAATTGTGTGACCACTTTGCAAGTCCAAATTTTCGGC
Found at i:2351655 original size:12 final size:12
Alignment explanation
Indices: 2351640--2351682 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
2351630 TTATATTTTT
2351640 AAAAAAATAAAG
1 AAAAAAATAAAG
2351652 AAAAAAATTAAAG
1 AAAAAAA-TAAAG
* *
2351665 AAAAAAATTATG
1 AAAAAAATAAAG
2351677 AAAAAA
1 AAAAAA
2351683 TCAAAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATAAAG
Found at i:2351682 original size:13 final size:13
Alignment explanation
Indices: 2351640--2351674 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2351630 TTATATTTTT
2351640 AAAAAAA-TAAAG
1 AAAAAAATTAAAG
2351652 AAAAAAATTAAAG
1 AAAAAAATTAAAG
2351665 AAAAAAATTA
1 AAAAAAATTA
2351675 TGAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAATTAAAG
Found at i:2352463 original size:21 final size:22
Alignment explanation
Indices: 2352428--2352468 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2352418 AATCAAAATA
2352428 TATTATTATTATAATTTTAATT
1 TATTATTATTATAATTTTAATT
*
2352450 TATTTTTA-TATAATTTTAA
1 TATTATTATTATAATTTTAA
2352469 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTATTATAATTTTAATT
Found at i:2352471 original size:22 final size:23
Alignment explanation
Indices: 2352423--2352471 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2352413 TGAAGAATCA
*
2352423 AAATATATTATTATTATAATTTT
1 AAATTTATTATTATTATAATTTT
*
2352446 -AATTTATTTTTA-TATAATTTT
1 AAATTTATTATTATTATAATTTT
2352467 AAATT
1 AAATT
2352472 AAATTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATTTATTATTATTATAATTTT
Found at i:2352478 original size:21 final size:21
Alignment explanation
Indices: 2352437--2352479 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2352427 ATATTATTAT
* **
2352437 TATAATTTTAATTTATTTTTA
1 TATAATTTTAAATTAAATTTA
2352458 TATAATTTTAAATTAAATTTA
1 TATAATTTTAAATTAAATTTA
2352479 T
1 T
2352480 GTTATTTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATAATTTTAAATTAAATTTA
Found at i:2356519 original size:16 final size:16
Alignment explanation
Indices: 2356498--2356535 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2356488 AAAATGATCG
* *
2356498 AATTTAAATTTATTTA
1 AATTTAAAATAATTTA
2356514 AATTTAAAATAATTTA
1 AATTTAAAATAATTTA
2356530 AATTTA
1 AATTTA
2356536 CGTGTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:2357081 original size:32 final size:33
Alignment explanation
Indices: 2357045--2357112 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2357035 AAATATTAAA
*
2357045 ATATTTTAAAAATT-A-TTTATATAAATATTTTT
1 ATATTTT-AAAATTAACTTTAAATAAATATTTTT
* *
2357077 ATATTTTATAATTAACTTTAAATAAATTTTTTT
1 ATATTTTAAAATTAACTTTAAATAAATATTTTT
2357110 ATA
1 ATA
2357113 AATTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 8 0.26
33 18 0.58
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
ATATTTTAAAATTAACTTTAAATAAATATTTTT
Found at i:2358456 original size:16 final size:16
Alignment explanation
Indices: 2358437--2358526 Score: 62
Period size: 15 Copynumber: 5.8 Consensus size: 16
2358427 ATCAAAATTC
2358437 AAATAATTTAAACTTA
1 AAATAATTTAAACTTA
*
2358453 AAATAATCTGAAA-TTA
1 AAATAAT-TTAAACTTA
* * * *
2358469 AAGTGACTTAAATTTA
1 AAATAATTTAAACTTA
* *
2358485 AAAT-ATTCAAAATTA
1 AAATAATTTAAACTTA
*
2358500 AAATAATATAAAC-TA
1 AAATAATTTAAACTTA
2358515 AAA-AATATTAAA
1 AAATAAT-TTAAA
2358527 AAAATTAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
14 3 0.05
15 25 0.44
16 25 0.44
17 4 0.07
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAATTTAAACTTA
Found at i:2358456 original size:32 final size:30
Alignment explanation
Indices: 2358413--2358518 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 30
2358403 CAGATTCATC
2358413 TAAACTAAAAATGAATCAAAATTCAAATAATT
1 TAAACTAAAAAT-AATCAAAATT-AAATAATT
* * * *
2358445 TAAACTTAAAATAATCTGAAATTAAAGTGACT
1 TAAACTAAAAATAATC-AAAATTAAA-TAATT
* * * *
2358477 TAAATTTAAAATATTCAAAATTAAAATAATA
1 TAAACTAAAAATAATCAAAATT-AAATAATT
2358508 TAAACTAAAAA
1 TAAACTAAAAA
2358519 ATATTAAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
31 23 0.39
32 36 0.61
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (30 bp):
TAAACTAAAAATAATCAAAATTAAATAATT
Found at i:2363789 original size:14 final size:14
Alignment explanation
Indices: 2363767--2363797 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2363757 CAGACAAACT
*
2363767 AAAACAAAAAAAGA
1 AAAAAAAAAAAAGA
2363781 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
2363795 AAA
1 AAA
2363798 GAAACAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:2365394 original size:22 final size:21
Alignment explanation
Indices: 2365361--2365401 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2365351 TATTAAAAAT
*
2365361 TATTTTATATTAATATTTATA
1 TATTTTATATTAAAATTTATA
2365382 TATTTATATATTAAAATTTA
1 TATTT-TATATTAAAATTTA
2365402 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATATTAAAATTTATA
Found at i:2381327 original size:2 final size:2
Alignment explanation
Indices: 2381320--2381349 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2381310 AGTGAATTTG
2381320 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
2381350 CTATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2381661 original size:11 final size:11
Alignment explanation
Indices: 2381647--2381705 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
2381637 TAATACAATT
2381647 ATATTATATAA
1 ATATTATATAA
2381658 ATATT-TGATAAA
1 ATATTAT-AT-AA
* *
2381670 AAATAATATAA
1 ATATTATATAA
2381681 ATATTATATAA
1 ATATTATATAA
*
2381692 ATATATAAATAA
1 ATAT-TATATAA
2381704 AT
1 AT
2381706 TAAAATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.03
11 22 0.56
12 15 0.38
13 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATTATATAA
Found at i:2381691 original size:23 final size:24
Alignment explanation
Indices: 2381652--2381705 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2381642 CAATTATATT
2381652 ATATAAATATTTGATAAA-AAATA
1 ATATAAATATTTGATAAATAAATA
*
2381675 ATATAAATATTAT-ATAAATATATA
1 ATATAAATATT-TGATAAATAAATA
2381699 A-ATAAAT
1 ATATAAAT
2381706 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATATAAATATTTGATAAATAAATA
Found at i:2381701 original size:28 final size:27
Alignment explanation
Indices: 2381665--2381733 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
2381655 TAAATATTTG
*
2381665 ATAAAAAATAATAT-AAATATTATATAA
1 ATAAAAAATAATATAAAAT-TTATAAAA
*
2381692 ATATATAAATAA-ATTAAAATTTATAAAA
1 ATA-AAAAATAATA-TAAAATTTATAAAA
2381720 ATAAAAAATAATAT
1 ATAAAAAATAATAT
2381734 GATAGAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
27 12 0.34
28 19 0.54
29 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAAAAAATAATATAAAATTTATAAAA
Found at i:2390004 original size:2 final size:2
Alignment explanation
Indices: 2389997--2390040 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2389987 ACTAATAAAG
* *
2389997 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GT GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2390039 GA
1 GA
2390041 CCATAATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:2396377 original size:17 final size:17
Alignment explanation
Indices: 2396345--2396387 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2396335 TAGACACGAC
2396345 AAAATATGAAAAATAAAA
1 AAAATAT-AAAAATAAAA
* *
2396363 AAAATATAAATATAATA
1 AAAATATAAAAATAAAA
*
2396380 TAAATATA
1 AAAATATA
2396388 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAATAAAA
Found at i:2396787 original size:13 final size:13
Alignment explanation
Indices: 2396769--2396795 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2396759 AGCCTTTATT
2396769 CAAAAAAGTGAAG
1 CAAAAAAGTGAAG
2396782 CAAAAAAGTGAAG
1 CAAAAAAGTGAAG
2396795 C
1 C
2396796 CTAAGCGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.11, G:0.22, T:0.07
Consensus pattern (13 bp):
CAAAAAAGTGAAG
Found at i:2398058 original size:25 final size:25
Alignment explanation
Indices: 2398030--2398079 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2398020 TAATTATTTT
2398030 CTTTCATCATTG-ATTTTTATTTCCA
1 CTTTCATCATTGTATTTTT-TTTCCA
* *
2398055 CTTTCTTCCTTGTATTTTTTTTCCA
1 CTTTCATCATTGTATTTTTTTTCCA
2398080 ATAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.14, C:0.22, G:0.04, T:0.60
Consensus pattern (25 bp):
CTTTCATCATTGTATTTTTTTTCCA
Found at i:2398988 original size:18 final size:19
Alignment explanation
Indices: 2398965--2399002 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2398955 AATATTAAAA
* *
2398965 AAAGCT-TTTTTTTTTTGT
1 AAAGCTATTTCTTTTATGT
2398983 AAAGCTATTTCTTTTATGT
1 AAAGCTATTTCTTTTATGT
2399002 A
1 A
2399003 TTGATAGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (19 bp):
AAAGCTATTTCTTTTATGT
Found at i:2399343 original size:26 final size:26
Alignment explanation
Indices: 2399292--2399343 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2399282 GTCTCATCTT
* *
2399292 TAAATTATATAATATATTATATTATA
1 TAAAATATATAATATATTATAATATA
*
2399318 TAAAATATAT-ATAATATTGTAATATA
1 TAAAATATATAAT-ATATTATAATATA
2399344 AATAATAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAAATATATAATATATTATAATATA
Found at i:2399350 original size:26 final size:24
Alignment explanation
Indices: 2399292--2399350 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
2399282 GTCTCATCTT
* *
2399292 TAAATTATATAATATATTATATTA
1 TAAATAATATAATATATTATAATA
*
2399316 TATAA-AATATATATAATATTGTAATA
1 TA-AATAATATA-AT-ATATTATAATA
2399342 TAAATAATA
1 TAAATAATA
2399351 ACAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.25
25 6 0.21
26 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAATAATATAATATATTATAATA
Found at i:2399509 original size:20 final size:21
Alignment explanation
Indices: 2399465--2399524 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
2399455 AATTATTTAT
* *
2399465 AAATTTAAAATAACATAAA-TA
1 AAATATAAAA-AATATAAATTA
2399486 AAATATAAAAAAT-TAAATTA
1 AAATATAAAAAATATAAATTA
* *
2399506 AAATTTAATAAATATAAAT
1 AAATATAAAAAATATAAAT
2399525 ATATTTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 14 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATATAAAAAATATAAATTA
Found at i:2400056 original size:50 final size:50
Alignment explanation
Indices: 2399964--2400060 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
2399954 AATTATTAAT
* * * * *
2399964 TATTTTTCACTAACCTTTGACAATTGAGAGAGGTGACCATAATTGTTGAC
1 TATTATTCACCAACCTTTGACAATAGAGAAAAGTGACCATAATTGTTGAC
* **
2400014 TATTATTCACCAACCTTTGACAATAGATAAAAGTGATTATAATTGTT
1 TATTATTCACCAACCTTTGACAATAGAGAAAAGTGACCATAATTGTT
2400061 AACTCTAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (50 bp):
TATTATTCACCAACCTTTGACAATAGAGAAAAGTGACCATAATTGTTGAC
Found at i:2403271 original size:543 final size:533
Alignment explanation
Indices: 2402234--2403303 Score: 1663
Period size: 543 Copynumber: 2.0 Consensus size: 533
2402224 TGGGTAGAAA
* * * *
2402234 CAGTCAAGACCGCATGTTATGTGATAAATCGGACTTCATCTACAGCAATTACACTGAAGACTCCA
1 CAGTCAAGACCACATGCTATGTGATAAATCAGACTCCATCTACAGCAATTACACTGAAGACTCCA
* *
2402299 ATGAAAATATGGACAAGTAAGCCAGTTGATTACTTTAATCTCCATATATTTGGATGTCCTACATA
66 ATGAAAATATGGACAAGTAAGCCAGTTGATTACTCTAATCTCCACATATTTGGATGTCCTACATA
2402364 TGTAATGTATAATGCCCAAGAAAGAACAAAGTTGGATCCAAAATCCAAAAAATGTATATTCTTGG
131 TGTAATGTATAATGCCCAAGAAAGAACAAAGTTGGATCCAAAATCCAAAAAATGTATATTCTTGG
*
2402429 GATATGCTGATGGAGTAAAAGGGTATCGCTTGTGGGATCTCACTGACCACAAGCTAGTCATCAGT
196 GATATGCTGATGGAGTAAAAGGGTATCGCTTGTGGGATCTCACTGACCACAAGCTAGTCATCAGC
* * * * *
2402494 AGAGATGTTATCTTCGTAGAATATCAATTATAAAAAAAAGATGTAGATAGTAGTACTTCGAGAGA
261 AGAAATGTTATCTTCGTAAAACATCAATTACAAAAAAAAGATGTAGATAGTAGTACTTCAAGAGA
*
2402559 AAAGTCAGAGACTATAATAGTTTTGACTGAAAATAATTAAGAACAAGAAAAGTCAAATTCTTCTG
326 AAAGTCAGAGACTACAATAGTTTTGACTGAAAATAATTAAGAACAAGAAAAGTCAAATTCTTCTG
* * *
2402624 AAGCTGCACCAGAGCACGAGGAATAAGAACCAGTTGAGTCTGAGGCTCCGGGGGTTCGTCGCTCA
391 AAGCTGCACCAGAGCACAAGGAACAAGAACCAGTTGAATCTGAGGCTCCGGGGGTTCGTCGCTCA
* * * * * *
2402689 ACTCGTGAGAGATGACTACCATCGTGGCAGTCGGATTATGTTATGGAGAGCAATGTTGCATACTG
456 AATCGTGAGAGACGACTACCATCATGGCACTCAGATTATGTTATGAAGAGCAATGTTGCATACTG
*
2402754 TTTTTTACATATG
521 TCTTTTACATATG
**
2402767 CAGTCAAGACCACATGCTATGTGATAAATCAGACTCCATCTACAGCAATTGGACTGAAGACTCCA
1 CAGTCAAGACCACATGCTATGTGATAAATCAGACTCCATCTACAGCAATTACACTGAAGACTCCA
* *
2402832 ATTAAAATATGGACAAGTAAGCCAGTTGATTACTCTAATCTCCACATATTTGGATGTCCTATATA
66 ATGAAAATATGGACAAGTAAGCCAGTTGATTACTCTAATCTCCACATATTTGGATGTCCTACATA
* * * * *
2402897 TGTAATGTATAATGCCCAAGAAAGAATAAAGTTTGATCCAAAATCTAGAAGATGTATATTCTTGG
131 TGTAATGTATAATGCCCAAGAAAGAACAAAGTTGGATCCAAAATCCAAAAAATGTATATTCTTGG
* *
2402962 GGTATGCTGATGGAGTAAAGGGGTATCGCTTGTGGTCGCTTGTGGGATCTCACTGACCACAAGCT
196 GATATGCTGATGGAGTAAAAGGGTA----------TCGCTTGTGGGATCTCACTGACCACAAGCT
* * *
2403027 AGTCATCAGCATAAATGTTATCTTTGTAAAACATCAATTACAAAAGAAAGATGTAGATAGTAGTA
251 AGTCATCAGCAGAAATGTTATCTTCGTAAAACATCAATTACAAAAAAAAGATGTAGATAGTAGTA
*
2403092 CTTCAAGAGAAAAGTCAGAGACTACAATAGTTTTGACTGAAAATAATTAAGAACAAGAAAAGTTA
316 CTTCAAGAGAAAAGTCAGAGACTACAATAGTTTTGACTGAAAATAATTAAGAACAAGAAAAGTCA
*
2403157 GATTCTTCTGAAGCTGCACCAGAGCACAAGGAACAAGAACCAGTTGAATCTGAGGCTCCGGGGGT
381 AATTCTTCTGAAGCTGCACCAGAGCACAAGGAACAAGAACCAGTTGAATCTGAGGCTCCGGGGGT
* * * *
2403222 TCGTTGCTTAAATCGTTAGAGACGACTATCATCATGGCACTCAGATTATGTTATGAAGAGCAATG
446 TCGTCGCTCAAATCGTGAGAGACGACTACCATCATGGCACTCAGATTATGTTATGAAGAGCAATG
2403287 TTGCATACTGTCTTTTA
511 TTGCATACTGTCTTTTA
2403304 ACAGAGGATA
Statistics
Matches: 484, Mismatches: 43, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
533 203 0.42
543 281 0.58
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (533 bp):
CAGTCAAGACCACATGCTATGTGATAAATCAGACTCCATCTACAGCAATTACACTGAAGACTCCA
ATGAAAATATGGACAAGTAAGCCAGTTGATTACTCTAATCTCCACATATTTGGATGTCCTACATA
TGTAATGTATAATGCCCAAGAAAGAACAAAGTTGGATCCAAAATCCAAAAAATGTATATTCTTGG
GATATGCTGATGGAGTAAAAGGGTATCGCTTGTGGGATCTCACTGACCACAAGCTAGTCATCAGC
AGAAATGTTATCTTCGTAAAACATCAATTACAAAAAAAAGATGTAGATAGTAGTACTTCAAGAGA
AAAGTCAGAGACTACAATAGTTTTGACTGAAAATAATTAAGAACAAGAAAAGTCAAATTCTTCTG
AAGCTGCACCAGAGCACAAGGAACAAGAACCAGTTGAATCTGAGGCTCCGGGGGTTCGTCGCTCA
AATCGTGAGAGACGACTACCATCATGGCACTCAGATTATGTTATGAAGAGCAATGTTGCATACTG
TCTTTTACATATG
Found at i:2405066 original size:50 final size:50
Alignment explanation
Indices: 2404982--2405165 Score: 260
Period size: 50 Copynumber: 3.7 Consensus size: 50
2404972 GCAAAGTGAT
* *
2404982 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACTGTAATTG
* * * * *
2405032 TTGACTATTTTTTACTAACCTTTGATAATAGAGAGAGGTGGCTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACTGTAATTG
* *
2405082 TTGACTATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACTGTAATTG
* * *
2405132 TTAACTATTATTCACCAACCTTTAACAATAGAGA
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGA
2405166 AATATGATCA
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 115 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACTGTAATTG
Found at i:2405162 original size:100 final size:100
Alignment explanation
Indices: 2404982--2405165 Score: 296
Period size: 100 Copynumber: 1.8 Consensus size: 100
2404972 GCAAAGTGAT
* * *
2404982 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTTTTAC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
* * *
2405047 TAACCTTTGATAATAGAGAGAGGTGGCTGTAATTG
66 CAACCTTTAACAATAGAGAGAGGTGGCTGTAATTG
* *
2405082 TTGACTATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACTGTAATTGTTAACTATTATTCAC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
2405147 CAACCTTTAACAATAGAGA
66 CAACCTTTAACAATAGAGA
2405166 AATATGATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
CAACCTTTAACAATAGAGAGAGGTGGCTGTAATTG
Found at i:2405180 original size:100 final size:100
Alignment explanation
Indices: 2404982--2405187 Score: 279
Period size: 100 Copynumber: 2.1 Consensus size: 100
2404972 GCAAAGTGAT
* * *
2404982 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTTTTAC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
* * * * * *
2405047 TAACCTTTGATAATAGAGAGAGGTGGCTGTAATTG
66 CAACCTTTAACAATAGAGAAAGATGGCTATAATTG
* *
2405082 TTGACTATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACTGTAATTGTTAACTATTATTCAC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
* *
2405147 CAACCTTTAACAATAGAGAAATAT-GATCATAATTG
66 CAACCTTTAACAATAGAGAAAGATGGCT-ATAATTG
2405182 TTGACT
1 TTGACT
2405188 CTAAGCATCT
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 2 0.02
100 90 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTAACTATTATTCAC
CAACCTTTAACAATAGAGAAAGATGGCTATAATTG
Found at i:2405571 original size:17 final size:19
Alignment explanation
Indices: 2405533--2405575 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
2405523 ATTTATTACA
2405533 TTTAAATTGTTTGAATTGT
1 TTTAAATTGTTTGAATTGT
*
2405552 TTTAAATT-TTT-AATTTT
1 TTTAAATTGTTTGAATTGT
2405569 TTTAAAT
1 TTTAAAT
2405576 ATTTGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTAAATTGTTTGAATTGT
Found at i:2406160 original size:25 final size:25
Alignment explanation
Indices: 2406131--2406217 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
2406121 AATTATTGTC
2406131 TAATTAATAAAATATATTTTTTATT
1 TAATTAATAAAATATATTTTTTATT
* *
2406156 TAATTTAATTATAAA-ATA-TATATA-T
1 TAA-TTAA-TA-AAATATATTTTTTATT
2406181 TAA-T-ATAAAATAATATTTTATTATT
1 TAATTAATAAAAT-ATATTTT-TTATT
2406206 T-ATTAA-AAAATA
1 TAATTAATAAAATA
2406218 GAATATAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 21
0.66 0.05 0.29
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 4 0.08
23 3 0.06
24 4 0.08
25 15 0.31
26 9 0.19
27 5 0.10
28 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATTAATAAAATATATTTTTTATT
Found at i:2406189 original size:19 final size:19
Alignment explanation
Indices: 2406160--2406196 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2406150 TTTATTTAAT
2406160 TTAATTATAAAATATATATA
1 TTAATTATAAAATA-ATATA
2406180 TTAA-TATAAAATAATAT
1 TTAATTATAAAATAATAT
2406197 TTTATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATTATAAAATAATATA
Found at i:2412021 original size:12 final size:12
Alignment explanation
Indices: 2412001--2412033 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2411991 TGGGTGAATA
2412001 TTATTTTTTCCC
1 TTATTTTTTCCC
*
2412013 TT-TTTTTTTCC
1 TTATTTTTTCCC
2412024 TTATTTTTTC
1 TTATTTTTTC
2412034 AACTAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTTTTCCC
Found at i:2419431 original size:18 final size:19
Alignment explanation
Indices: 2419408--2419444 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2419398 TTAATATTTT
2419408 AAAAAATCAAT-TTTTTAA
1 AAAAAATCAATCTTTTTAA
2419426 AAAAAATCAATCTTTTTAA
1 AAAAAATCAATCTTTTTAA
2419445 TGCATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATCAATCTTTTTAA
Found at i:2420349 original size:3 final size:3
Alignment explanation
Indices: 2420341--2420381 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2420331 TAACCCTATC
2420341 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2420382 CAACTTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2420580 original size:8 final size:8
Alignment explanation
Indices: 2420569--2420638 Score: 56
Period size: 8 Copynumber: 8.5 Consensus size: 8
2420559 ATTTATATAA
2420569 ATTTTAAT
1 ATTTTAAT
2420577 ATTTTAAT
1 ATTTTAAT
*
2420585 AATTT-AT
1 ATTTTAAT
2420592 ATTATATAAT
1 ATT-T-TAAT
*
2420602 -TTTAATAT
1 ATTTTA-AT
2420610 ATTATTAAT
1 ATT-TTAAT
2420619 ATTTTATAT
1 ATTTTA-AT
2420628 ATTTT-AT
1 ATTTTAAT
2420635 ATTT
1 ATTT
2420639 ATATAATCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 11 0.22
8 19 0.37
9 17 0.33
10 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2420629 original size:9 final size:9
Alignment explanation
Indices: 2420556--2420636 Score: 66
Period size: 9 Copynumber: 9.3 Consensus size: 9
2420546 CTCTTATAAT
2420556 TATATTTATA
1 TATATTT-TA
*
2420566 TAAATTTTA
1 TATATTTTA
2420575 -ATATTTTA
1 TATATTTTA
*
2420583 -ATA-ATT-
1 TATATTTTA
*
2420589 TATATTATA
1 TATATTTTA
2420598 TA-ATTTTAA
1 TATATTTT-A
2420607 TATATTATTA
1 TATATT-TTA
2420617 -ATATTTTA
1 TATATTTTA
2420625 TATATTTTA
1 TATATTTTA
2420634 TAT
1 TAT
2420637 TTATATAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.09
8 18 0.31
9 23 0.40
10 10 0.17
11 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTTA
Done.