Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2641994 original size:84 final size:83
Alignment explanation
Indices: 2641874--2642066 Score: 278
Period size: 84 Copynumber: 2.3 Consensus size: 83
2641864 CTTTCAGATG
* * *
2641874 AGTTCTTCTCATTATGAACATTTCTGGAAATGTTGATGTTGATCCATCTACTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
*
2641939 TAAACAAAAGGTTAAACA
66 CAAACAAAAGGTTAAACA
*
2641957 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTAATTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAG
** *
2642022 TCATGCAAAAGGTTGAACA
65 TCAAACAAAAGGTTAAACA
**
2642041 AACTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTT-TTCT
2642067 TCCTTCTTCA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 21 0.21
84 76 0.78
85 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (83 bp):
AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
CAAACAAAAGGTTAAACA
Found at i:2642404 original size:113 final size:111
Alignment explanation
Indices: 2642131--2642726 Score: 780
Period size: 113 Copynumber: 5.3 Consensus size: 111
2642121 TGATTAAACT
*
2642131 AAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
2642196 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATT--TGCA
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGTG-A
* * * *
2642241 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
* ** * *
2642306 TGAACTCTACCTGGTAATA-CTGAAT-CATCTAA-TGATGAATTCAAGTGA
66 TGAACTTTTTCTGG-AAAAGCTG-ATCCATC-AAGTGATGGATT--AGTGA
*
2642354 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
2642419 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATT--TGCA
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGTG-A
* * *
2642464 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
2642529 ATGAACTCTACCTGGTAATA-CTGAAT-CATCGAA-TGATGAATTCAAGCGA
65 ATGAACTTTTTCTGG-AAAAGCTG-ATCCATC-AAGTGATGGATT--AGTGA
2642578 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
* * *
2642643 TGAACTTTTTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCA
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGTG-A
2642690 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 AAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTC
2642727 AGATAAATTC
Statistics
Matches: 421, Mismatches: 41, Indels: 45
0.83 0.08 0.09
Matches are distributed among these distances:
109 2 0.00
110 90 0.21
111 93 0.22
112 25 0.06
113 204 0.48
114 6 0.01
115 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (111 bp):
AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGTGA
Found at i:2642566 original size:224 final size:224
Alignment explanation
Indices: 2642131--2642724 Score: 1109
Period size: 224 Copynumber: 2.6 Consensus size: 224
2642121 TGATTAAACT
*
2642131 AAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
2642196 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGC-AAAGGTTGAACAAATTCTTC
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
2642260 TCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATA
131 TCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATA
* *
2642325 CTGAATCATCTAATGATGAATTCAAGTGA
196 CTGAATCATCGAATGATGAATTCAAGCGA
*
2642354 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
2642419 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
2642484 TCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATA
131 TCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATA
2642549 CTGAATCATCGAATGATGAATTCAAGCGA
196 CTGAATCATCGAATGATGAATTCAAGCGA
2642578 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
*
2642643 TGAACTTTTTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTT--GCAAAAGGTTGAACAAATTCT
*
2642708 TCTCATTATGAACTTCT
129 TCTCATTATGAATTTCT
2642725 TCAGATAAAT
Statistics
Matches: 361, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
223 107 0.30
224 217 0.60
226 37 0.10
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (224 bp):
AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
TCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATA
CTGAATCATCGAATGATGAATTCAAGCGA
Found at i:2642710 original size:337 final size:324
Alignment explanation
Indices: 2642026--2642775 Score: 870
Period size: 337 Copynumber: 2.3 Consensus size: 324
2642016 ATAGAGTCAT
*
2642026 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
* *
2642091 ATTATGAACTTTCTCTGGAAAAGTTGATGTTGATTAAACTAAAGTCGAACAAATTCTTCTCATTA
66 ATTATGAACTTTCTCTGGAAAAGTTCATGTTGATTAAACAAAAGTCGAACAAATTCTTCTCATTA
* * * **
2642156 TGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATC
131 TGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTGATC
* * * *
2642221 CATCAAGTGATGGATTTGCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTCCTTCCTTCTT
196 CATCAAGTGATGAATTAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTCCTTCTT
*
2642286 CAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATACTGAATCATCTAATGATGAATTCAA
261 CAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAAAACTGAATCATCTAATGATGAATTCAA
* * * * *
2642350 GTGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCT
* ** *
2642414 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATT-TGCAAAAGGTTGAACAAA
65 CATTATGAACTTTCTCTGGAAAAG-T--T-CAT---GT--T-GATTAAACAAAA-GTCGAACAAA
*
2642478 TTCTTCTCATTATGAATTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
119 TTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
*
2642543 GTAATA-CTGAAT-CATCGAA-TGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATG
184 G-AAAAGCTG-ATCCATC-AAGTGATGAATT--AGC-AAAAGTTGAACAAATTCTTCTCATTATG
* * * ** *
2642605 AACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG-AAAAGTTG-ATC
243 AACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAAAA-CTGAAT-
* **
2642668 CATC-AAGTGATGGATTTGA
306 CATCTAA-TGATGAATTCAA
2642687 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA----------CTTCTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
* *
2642742 ATTATGAACTTTCTATGGAAAAGTTGATGTTGAT
66 ATTATGAACTTTCTCTGGAAAAGTTCATGTTGAT
2642776 CTATCTACTT
Statistics
Matches: 363, Mismatches: 41, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
317 3 0.01
318 1 0.00
320 2 0.01
323 2 0.01
324 77 0.21
325 5 0.01
326 1 0.00
327 41 0.11
328 2 0.01
331 2 0.01
333 5 0.01
334 88 0.24
335 7 0.02
336 13 0.04
337 114 0.31
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (324 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTCATGTTGATTAAACAAAAGTCGAACAAATTCTTCTCATTA
TGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTGATC
CATCAAGTGATGAATTAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTCCTTCTT
CAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAAAACTGAATCATCTAATGATGAATTCAA
Found at i:2643343 original size:22 final size:22
Alignment explanation
Indices: 2643318--2643396 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
2643308 GATAAAACTT
* *
2643318 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
2643340 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* *
2643362 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
2643384 TCATCTTTAAAAA
1 TCATCTTTAAAAA
2643397 ATGTAGATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:2646001 original size:114 final size:115
Alignment explanation
Indices: 2645837--2646063 Score: 384
Period size: 114 Copynumber: 2.0 Consensus size: 115
2645827 GATCATGCAG
* * * *
2645837 TTCATCTTTTTAATTCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
2645902 AACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
*
2645952 TTCATC-TTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
2646016 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCA
2646064 CATGGCACTT
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 99 0.94
115 6 0.06
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (115 bp):
TTCATCTTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2648335 original size:15 final size:16
Alignment explanation
Indices: 2648315--2648344 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2648305 CTTGATTCAA
2648315 TTTTCTT-TTTCTTTT
1 TTTTCTTATTTCTTTT
2648330 TTTTCTTATTTCTTT
1 TTTTCTTATTTCTTT
2648345 GCTGGATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTATTTCTTTT
Found at i:2648645 original size:2 final size:2
Alignment explanation
Indices: 2648638--2648688 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2648628 ACAACAAAGG
2648638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2648680 AT AT AT AT A
1 AT AT AT AT A
2648689 AAGGATAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2653319 original size:16 final size:15
Alignment explanation
Indices: 2653284--2653338 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
2653274 ATTCTTGAAT
*
2653284 ATAATAAATA-AATA
1 ATAATAAAAATAATA
2653298 A-AATAAAAATAATA
1 ATAATAAAAATAATA
2653312 ATATATAAAAATAATA
1 ATA-ATAAAAATAATA
2653328 AGTAATAAAAA
1 A-TAATAAAAA
2653339 AAAATTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 7 0.19
14 6 0.17
15 1 0.03
16 20 0.56
17 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:2655468 original size:3 final size:3
Alignment explanation
Indices: 2655460--2655529 Score: 104
Period size: 3 Copynumber: 22.7 Consensus size: 3
2655450 TTATTTATTA
* *
2655460 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
2655507 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
2655530 AATGAATCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2660154 original size:29 final size:29
Alignment explanation
Indices: 2660117--2660214 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
2660107 TTTAAATTGG
2660117 TCCTTAAACTTTTGAATATTCTAATTTCA
1 TCCTTAAACTTTTGAATATTCTAATTTCA
* * * *
2660146 TCCTCAAAC-TATGACTCTCATTCTAAATT-A
1 TCCTTAAACTTTTGA--AT-ATTCTAATTTCA
* *
2660176 GTCCTTAAACTTTTGGACATTCTAATTTCA
1 -TCCTTAAACTTTTGAATATTCTAATTTCA
*
2660206 TCATTAAAC
1 TCCTTAAAC
2660215 AATGACCTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
28 4 0.08
29 25 0.48
30 3 0.06
31 17 0.33
32 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TCCTTAAACTTTTGAATATTCTAATTTCA
Found at i:2660181 original size:60 final size:60
Alignment explanation
Indices: 2660088--2660268 Score: 211
Period size: 60 Copynumber: 3.0 Consensus size: 60
2660078 ATCATATATA
* * * *
2660088 CTCAAACTATTACTTTCATTTTAAATTGGTCCTTAAACTTTTGAATATTCTAATTTCATC
1 CTCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
* *
2660148 CTCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGGACATTCTAATTTCATC
1 CTCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
* * * * * * * * *
2660208 ATTAAACAATGAC-CTTTATTCTAAATTAGTCCATAAACTTTGGAATCTTCCAATTTTATC
1 CTCAAACTATGACTC-TCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
2660268 C
1 C
2660269 CCTATTTAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 101 0.99
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.42
Consensus pattern (60 bp):
CTCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
Found at i:2660186 original size:31 final size:31
Alignment explanation
Indices: 2660091--2660186 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
2660081 ATATATACTC
* * * *
2660091 AAACTATTACTTTCATTTTAAATTGGTCCTT
1 AAACTATGACTATCATTCTAAATTAGTCCTT
* * *
2660122 AAACTTTTGA--AT-ATTCTAATTTCA-TCCTC
1 AAAC-TATGACTATCATTCTAAATT-AGTCCTT
*
2660151 AAACTATGACTCTCATTCTAAATTAGTCCTT
1 AAACTATGACTATCATTCTAAATTAGTCCTT
2660182 AAACT
1 AAACT
2660187 TTTGGACATT
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
28 4 0.08
29 16 0.33
30 3 0.06
31 22 0.46
32 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (31 bp):
AAACTATGACTATCATTCTAAATTAGTCCTT
Found at i:2666886 original size:31 final size:31
Alignment explanation
Indices: 2666800--2666886 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
2666790 TAATATTTAA
* *
2666800 TTTTAGATAAAATGTCAATTTAATCATTAAAC
1 TTTTAAATAAAATGTCAATTTAA-CTTTAAAC
* * * * * *
2666832 -ATTAAAGAAAATATTAATTTAACTTTTACC
1 TTTTAAATAAAATGTCAATTTAACTTTAAAC
2666862 TTTTAAATAAAATGTCAATTTAACT
1 TTTTAAATAAAATGTCAATTTAACT
2666887 CTTGAATTCA
Statistics
Matches: 42, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (31 bp):
TTTTAAATAAAATGTCAATTTAACTTTAAAC
Found at i:2667318 original size:11 final size:11
Alignment explanation
Indices: 2667302--2667341 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
2667292 CCCTATTAGC
2667302 TAAATAATATA
1 TAAATAATATA
2667313 TAAATAATATA
1 TAAATAATATA
2667324 T--ATAATATA
1 TAAATAATATA
2667333 TTAAATAAT
1 -TAAATAAT
2667342 TAATAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 12 0.46
12 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATAATATA
Found at i:2674302 original size:131 final size:131
Alignment explanation
Indices: 2674049--2674411 Score: 327
Period size: 131 Copynumber: 2.8 Consensus size: 131
2674039 ATAATTTTAA
* * * * * * * *
2674049 GAGTGAAAACGATAATATCTAATTATTTCCAATAAAGAATAAATGATCTTTTGTGCATTAAAACA
1 GAGTAAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTTATACCTTAAAGCA
* * * * *** * *
2674114 GTCATTTATTACCCCAATTGAAATAAAGAGATATTAATATTTTGTCTTAAAATTCAATATCGATT
66 ATCATTTATTACCCCAATCGAAATAAAGAGATATCAACATTCCATCCTAAAATTCAATATCAATT
2674179 C
131 C
*
2674180 GAGTAAAAACGATAATATCTAATTATTTCCAATCAATAATAAATGACCTCTTATACCTTAAAGCA
1 GAGTAAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTTATACCTTAAAGCA
* * * * * * *
2674245 ATCATTTATTGCTCCAATCGAACTGAAGAGATATCACCATTCCATCCTAAGAA-TCAATGTTAAT
66 ATCATTTATTACCCCAATCGAAATAAAGAGATATCAACATTCCATCCTAA-AATTCAATATCAAT
*
2674309 TT
130 TC
* * * * * *
2674311 G-GGAGAAAACG-TCAATATCAAATCATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAG
1 GAGTA-AAAACGAT-AATATCTAATTATTTCCAATCAAGAATAAATGACCTCTTATACCTTAAAG
* * * * * * *
2674374 CAACCATTTATCACTCAAAACGAAATAAAAATATATCA
64 CAATCATTTATTACCCCAATCGAAATAAAGAGATATCA
2674412 CTACTCTCAA
Statistics
Matches: 187, Mismatches: 42, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
130 3 0.02
131 182 0.97
132 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (131 bp):
GAGTAAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTTATACCTTAAAGCA
ATCATTTATTACCCCAATCGAAATAAAGAGATATCAACATTCCATCCTAAAATTCAATATCAATT
C
Found at i:2675773 original size:73 final size:72
Alignment explanation
Indices: 2675647--2675785 Score: 235
Period size: 73 Copynumber: 1.9 Consensus size: 72
2675637 TCCAAATGTT
2675647 ACCATATATCATGGTATATGGTTTGACAACCATACCATATCGACTAAGCCACTATGTCATATACA
1 ACCATATATCATGGTATATGGTTTGACAACCATACCATATCGACTAAGCCACTATGTCATATACA
2675712 AAAAATG
66 AAAAATG
* *
2675719 ACCATATATCATGGTATATGGTTTTGGCAACCATACCATATTGACTAA-CTCACTATGTCATATA
1 ACCATATATCATGGTATATGG-TTTGACAACCATACCATATCGACTAAGC-CACTATGTCATATA
2675783 CAA
64 CAA
2675786 TCATCTCGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 22 0.35
73 41 0.65
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (72 bp):
ACCATATATCATGGTATATGGTTTGACAACCATACCATATCGACTAAGCCACTATGTCATATACA
AAAAATG
Found at i:2676876 original size:36 final size:35
Alignment explanation
Indices: 2676800--2676877 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
2676790 TTTAAACTCT
* *
2676800 AAATTAAAGTATTTTAGAATTTAGGGTTTAGAACG
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAAAACG
* * * * *
2676835 TAATTGAATTATTTTGGAATTTGGGAGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTAGG-GTTTAAAACG
2676871 AAATTGA
1 AAATTGA
2676878 GGACTGTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAGGGTTTAAAACG
Found at i:2678394 original size:20 final size:20
Alignment explanation
Indices: 2678369--2678406 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2678359 TGGATTATGG
2678369 GTTGCTTGAATTGGGCCCAA
1 GTTGCTTGAATTGGGCCCAA
2678389 GTTGCTTGAATTGGGCCC
1 GTTGCTTGAATTGGGCCC
2678407 GAGTCTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GTTGCTTGAATTGGGCCCAA
Found at i:2678509 original size:3 final size:3
Alignment explanation
Indices: 2678485--2678606 Score: 74
Period size: 3 Copynumber: 39.3 Consensus size: 3
2678475 AAAAATAAAT
*
2678485 ATA AT- ATA AT- ATA A-A GATA ATA ATA GA-A ATA ATT ATA ATTA GATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA A-TA -ATA
* * *
2678530 ATA ATA CTA ATTA ATA TTA ATA ATA ATA GA-A ATA ATT ATA ATTA GATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA -ATA
* *
2678578 ATA ATA CTA ATTA ATA TTA ATA ATA ATA A
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA A
2678607 AATTGACAAG
Statistics
Matches: 93, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
2 7 0.08
3 67 0.72
4 17 0.18
5 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2678562 original size:48 final size:48
Alignment explanation
Indices: 2678501--2678609 Score: 211
Period size: 48 Copynumber: 2.3 Consensus size: 48
2678491 TAATATAAAG
2678501 ATAATAATAGAAATAATTATAATTAGATAATAATACTAATTAATATTA
1 ATAATAATAGAAATAATTATAATTAGATAATAATACTAATTAATATTA
2678549 ATAATAATAGAAATAATTATAATTAGATAATAATACTAATTAATATTA
1 ATAATAATAGAAATAATTATAATTAGATAATAATACTAATTAATATTA
2678597 ATAATAATA-AAAT
1 ATAATAATAGAAAT
2678610 TGACAAGATC
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 4 0.07
48 57 0.93
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (48 bp):
ATAATAATAGAAATAATTATAATTAGATAATAATACTAATTAATATTA
Found at i:2684653 original size:19 final size:19
Alignment explanation
Indices: 2684629--2684671 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2684619 CTCCTCGGAT
2684629 TCAAAC-TTAAAAAAGATAA
1 TCAAACATTAAAAAAGA-AA
*
2684648 TCAAACATTTAAAAAGAAA
1 TCAAACATTAAAAAAGAAA
2684667 TCAAA
1 TCAAA
2684672 GGAACTTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (19 bp):
TCAAACATTAAAAAAGAAA
Found at i:2685622 original size:24 final size:24
Alignment explanation
Indices: 2685592--2685650 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
2685582 ATTTAGAAAT
2685592 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
2685616 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
2685640 TCAATTGAAGC
1 TCAATTGAAGC
2685651 GAAAGAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
TCAATTGAAGCCTAAAATTTGAGC
Found at i:2687715 original size:30 final size:30
Alignment explanation
Indices: 2687675--2687734 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2687665 ATAGCAGAAA
2687675 ATTAATTGAACCGTAAGAAATAGATAAAAT
1 ATTAATTGAACCGTAAGAAATAGATAAAAT
* *
2687705 ATTAGTTGAACTGTAAGAAATAGATAAAAT
1 ATTAATTGAACCGTAAGAAATAGATAAAAT
2687735 CACGACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.28
Consensus pattern (30 bp):
ATTAATTGAACCGTAAGAAATAGATAAAAT
Found at i:2689893 original size:24 final size:20
Alignment explanation
Indices: 2689836--2689893 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2689826 TTCCCCTTGA
*
2689836 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
2689856 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
2689879 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2689894 CTAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:2693682 original size:30 final size:29
Alignment explanation
Indices: 2693614--2693682 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
2693604 CATAGATCTT
2693614 ATCACTTAACTTATCCTTTATACTCATTTA
1 ATCACTTAACTTAT-CTTTATACTCATTTA
**
2693644 ATTTCTTAACTTAT-TTTATATTCTC-TTATA
1 ATCACTTAACTTATCTTTATA--CTCATT-TA
2693674 ATCACTTAA
1 ATCACTTAA
2693683 TAGTGTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 24 0.75
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (29 bp):
ATCACTTAACTTATCTTTATACTCATTTA
Found at i:2696827 original size:15 final size:15
Alignment explanation
Indices: 2696807--2696837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2696797 CAACAAATAG
2696807 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2696822 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
2696837 A
1 A
2696838 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2697029 original size:20 final size:20
Alignment explanation
Indices: 2696990--2697029 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2696980 ATAATCCTAT
* **
2696990 TCACTGATAATCTTTTATTC
1 TCACCGATAATCTTACATTC
2697010 TCACCGATAATCTTACATTC
1 TCACCGATAATCTTACATTC
2697030 AATTAACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (20 bp):
TCACCGATAATCTTACATTC
Found at i:2704555 original size:3 final size:3
Alignment explanation
Indices: 2704549--2704573 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2704539 CAATACTGGA
2704549 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2704574 GAAAACTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2707267 original size:225 final size:226
Alignment explanation
Indices: 2706868--2707312 Score: 763
Period size: 225 Copynumber: 2.0 Consensus size: 226
2706858 GTAAATTATC
* *
2706868 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
*
2706933 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
2706998 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
130 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
2707063 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
2707096 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTA-TA-TTTGGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTACTTTAGT
*
2707159 TAATATTGTTAAATTTAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAAT-ATAATT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-ATT
* *
2707222 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
2707287 GAAACATAAATTACATAACTTTAAAA
194 GAAACATAAATTACATAACTTTAAAA
2707313 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
224 6 0.03
225 113 0.54
226 35 0.17
228 38 0.18
229 16 0.08
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:2707400 original size:20 final size:19
Alignment explanation
Indices: 2707377--2707422 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
2707367 CGATATACCA
2707377 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2707397 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2707417 GGTAAA
1 GGTAAA
2707423 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2707591 original size:17 final size:18
Alignment explanation
Indices: 2707544--2707594 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 18
2707534 CGATATAACA
2707544 GGTAAAATATGATAAAACC
1 GGTAAAA-ATGATAAAACC
2707563 GGTAACAAAATGATAAAACC
1 GGT-A-AAAATGATAAAACC
2707583 GGT-AAAATGATA
1 GGTAAAAATGATA
2707595 CCGGATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.30
19 3 0.10
20 15 0.50
21 3 0.10
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.20
Consensus pattern (18 bp):
GGTAAAAATGATAAAACC
Found at i:2709854 original size:21 final size:21
Alignment explanation
Indices: 2709807--2709871 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2709797 AAGACAATCA
* *
2709807 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2709829 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2709849 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2709870 AG
1 AG
2709872 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2709947 original size:33 final size:33
Alignment explanation
Indices: 2709905--2709970 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2709895 AAATAGATGG
*
2709905 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2709938 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2709971 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2711779 original size:19 final size:19
Alignment explanation
Indices: 2711755--2711803 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2711745 AATGTCGAGT
2711755 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2711774 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2711793 TATTTTTGTAT
1 TAATTTTGTAT
2711804 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2712387 original size:197 final size:199
Alignment explanation
Indices: 2711920--2713082 Score: 2114
Period size: 198 Copynumber: 5.9 Consensus size: 199
2711910 CAATATGACC
* * *
2711920 AACAGGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
2711984 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
* *
2712049 AGAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCATAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
2712113 ATGGAA
194 ATGGAA
* *
2712119 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
2712184 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
2712247 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
2712312 TGGAA
195 TGGAA
2712317 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2712382 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
2712447 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCATAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
2712512 GGAA
196 GGAA
*
2712516 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2712581 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2712645 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
2712709 GGAA
196 GGAA
2712713 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2712778 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
2712843 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-CTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
2712907 GGAA
196 GGAA
2712911 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2712976 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2713040 AATATGTCTAAATAATGTGTCGACAC---TATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2713083 CTAATTTAAA
Statistics
Matches: 946, Mismatches: 13, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
194 17 0.02
197 259 0.27
198 405 0.43
199 242 0.26
200 23 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GGAA
Found at i:2714554 original size:18 final size:18
Alignment explanation
Indices: 2714533--2714600 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
2714523 AGCGGTCGCA
2714533 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
2714551 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
2714572 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
2714593 GAAGATGA
1 GAAGATGA
2714601 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:2714557 original size:6 final size:6
Alignment explanation
Indices: 2714533--2714630 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
2714523 AGCGGTCGCA
* * * * * *
2714533 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
2714581 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
2714629 GA
1 GA
2714631 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:2714568 original size:3 final size:3
Alignment explanation
Indices: 2714548--2714634 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
2714538 TGAAGCTGAC
* * * * * ** *
2714548 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
2714596 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2714635 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:2714583 original size:42 final size:42
Alignment explanation
Indices: 2714536--2714626 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
2714526 GGTCGCAGAA
*
2714536 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
2714578 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
2714620 GATGAAG
1 GATGAAG
2714627 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:2714634 original size:18 final size:18
Alignment explanation
Indices: 2714533--2714630 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
2714523 AGCGGTCGCA
* *
2714533 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
2714551 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
2714569 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
2714587 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
2714605 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
2714623 GAAGATGA
1 GAAGATGA
2714631 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:2716128 original size:181 final size:183
Alignment explanation
Indices: 2715823--2716329 Score: 887
Period size: 181 Copynumber: 2.8 Consensus size: 183
2715813 CAAAGTTTTC
* * * *
2715823 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
2715888 AAAAAAGTGTCG--ATTGAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAAT
66 AAAAAAGTGTCGACATT--TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAAT
*
2715951 ATAACCGGTATAAATATACCGGTTTTATGAGCG-ATAGGTCTACAACCTATATCG
129 ATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
2716005 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAG-AAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
2716069 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
2716134 AACCGGTATAAAAATACCGGTTTTATGATCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
2716187 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
2716252 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
2716317 AACCGGTATAAAA
131 AACCGGTATAAAA
2716330 TGTGTCGATA
Statistics
Matches: 312, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
181 107 0.34
182 104 0.33
183 101 0.32
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:2716368 original size:23 final size:23
Alignment explanation
Indices: 2716323--2716368 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2716313 ATATAACCGG
2716323 TATAAAATGTGTCGATACCTTTT
1 TATAAAATGTGTCGATACCTTTT
* *
2716346 TATAAAA-GTGTCTATACTTTTT
1 TATAAAATGTGTCGATACCTTTT
2716368 T
1 T
2716369 CACTGTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (23 bp):
TATAAAATGTGTCGATACCTTTT
Found at i:2717482 original size:647 final size:654
Alignment explanation
Indices: 2716035--2717560 Score: 2846
Period size: 647 Copynumber: 2.4 Consensus size: 654
2716025 GGTACTTTAT
* *
2716035 GTCCAGATTGGAAG-AAAATGTGTCGATACCATTTAAAAAAGTGTCGACA-TTTACACATCGGAA
1 GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA
* * *
2716098 CCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAAATACCGGTTTTATGAT
66 CCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTTTTATGAT
*
2716163 CGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGG
130 CGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTTCAGATTGG
2716228 AAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATA
195 AAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATA
2716293 ATGTAATAGATAATTTTGTAATATAACCGGTATAAAATGTGTCGATACCTTTTTATAAAAGTGTC
260 ATGTAATAGATAATTTTGTAATATAACCGGTATAAAATGTGTCGATACCTTTTTATAAAAGTGTC
2716358 TATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTA
325 TATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTA
2716423 ATTTAGTAATTATAGGCGTCTAATGATTAATTTTTTACGTTACGGTATATATTATTATTAAATTA
390 ATTTAGTAATTATAGGCGTCTAATGATTAATTTTTTACGTTACGGTATATATTATTATTAAATTA
2716488 AAAATTCTTAATATTATTTTATAAAATATCAAAACAATCAACTAATTTTTTGTGCAAATGAAATT
455 AAAATTCTTAATATTATTTTATAAAATATCAAAACAATCAACTAATTTTTTGTGCAAATGAAATT
2716553 ATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAATATTGAAACATAAATTACA
520 ATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAATATTGAAACATAAATTACA
2716618 TATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAACATATTATAATAA
585 TATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAACATATTATAATAA
2716683 AATAG
650 AATAG
2716688 GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA
1 GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA
2716753 CCCATAATTATAATGTAATAGATAATTTTG---TATAACCGGTATAATATACCGGTTTTATGATC
66 CCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTTATGATC
2716815 GAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTTCAGATTGGA
131 GAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTTCAGATTGGA
2716880 AGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAA
196 AGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAA
*
2716945 TGTAATAGATAATTTTGTAATATAACTGGTATAAAAATGTGTCGATACCTTTTTAT-AAAGTGTC
261 TGTAATAGATAATTTTGTAATATAACCGGTAT-AAAATGTGTCGATACCTTTTTATAAAAGTGTC
2717009 TATACTTTTTTCACTGTGG-AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTA
325 TATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTA
2717073 ATTTAGTAATTATAGGCGTCTAATGATTAATTTTTTACGTTACGGTATAT-TTATTATTAAATTA
390 ATTTAGTAATTATAGGCGTCTAATGATTAATTTTTTACGTTACGGTATATATTATTATTAAATTA
2717137 AAAATTCTTAATATTATTTTATAAAATATCAAAACAATC-ACTAA-TTTTTGTGCAAATGAAATT
455 AAAATTCTTAATATTATTTTATAAAATATCAAAACAATCAACTAATTTTTTGTGCAAATGAAATT
2717200 ATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAATATTGAAACATAAATTACA
520 ATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAATATTGAAACATAAATTACA
2717265 TATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAACATATTATAATAA
585 TATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAACATATTATAATAA
2717330 AATAG
650 AATAG
2717335 GTCCATATTGGAAGAAAAATGTGTCGATACGATTT-AAAAAGTGTCGACATTTTACACATCGGAA
1 GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA
*
2717399 CCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTTATGAGC
66 CCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTTATGATC
*
2717464 G-A-AGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATG-TCCGATTGGA
131 GAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTTCAGATTGGA
*
2717526 ATAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
196 AGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
2717561 GTAATTTGAA
Statistics
Matches: 857, Mismatches: 10, Indels: 19
0.97 0.01 0.02
Matches are distributed among these distances:
646 102 0.12
647 239 0.28
648 6 0.01
649 85 0.10
650 95 0.11
651 206 0.24
652 35 0.04
653 13 0.02
654 34 0.04
655 42 0.05
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (654 bp):
GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA
CCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAATATACCGGTTTTATGATC
GAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTTCAGATTGGA
AGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAA
TGTAATAGATAATTTTGTAATATAACCGGTATAAAATGTGTCGATACCTTTTTATAAAAGTGTCT
ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAA
TTTAGTAATTATAGGCGTCTAATGATTAATTTTTTACGTTACGGTATATATTATTATTAAATTAA
AAATTCTTAATATTATTTTATAAAATATCAAAACAATCAACTAATTTTTTGTGCAAATGAAATTA
TTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAATATTGAAACATAAATTACAT
ATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAACATATTATAATAAA
ATAG
Found at i:2720221 original size:18 final size:18
Alignment explanation
Indices: 2720200--2720236 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2720190 GTAATTGGAG
2720200 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2720218 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2720236 T
1 T
2720237 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2720244 original size:24 final size:24
Alignment explanation
Indices: 2720192--2720238 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2720182 TTTCATATGT
* *
2720192 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2720216 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2720239 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2720534 original size:39 final size:39
Alignment explanation
Indices: 2720491--2720577 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2720481 TCCGATGCTC
*
2720491 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
2720530 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2720569 ATCAAAATC
1 ATCAAAATC
2720578 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2720958 original size:21 final size:22
Alignment explanation
Indices: 2720912--2720958 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2720902 AAATTACATA
2720912 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
2720934 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
2720954 ACTTT
1 ACTTT
2720959 CAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:2721007 original size:23 final size:23
Alignment explanation
Indices: 2720976--2721039 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
2720966 ATAGGTAAAC
*
2720976 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
2720999 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2721022 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2721040 TGGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2721046 original size:23 final size:23
Alignment explanation
Indices: 2720976--2721048 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
2720966 ATAGGTAAAC
* **
2720976 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
2720999 ATATAATGTAATATGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2721022 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2721045 ATAT
1 ATAT
2721049 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2721434 original size:23 final size:23
Alignment explanation
Indices: 2721403--2721466 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2721393 ATAGGTAAAC
*
2721403 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2721426 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2721449 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2721467 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2721473 original size:23 final size:23
Alignment explanation
Indices: 2721403--2721475 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2721393 ATAGGTAAAC
* **
2721403 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2721426 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2721449 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2721472 ATAT
1 ATAT
2721476 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2721851 original size:23 final size:23
Alignment explanation
Indices: 2721825--2721888 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2721815 AATGGTAAAC
*
2721825 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2721848 ATATAATGTAATAGGTATCTTTT
1 ATATAATGTAATAGGTAGCCCTT
2721871 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2721889 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2721951 original size:422 final size:428
Alignment explanation
Indices: 2720685--2722165 Score: 2740
Period size: 422 Copynumber: 3.5 Consensus size: 428
2720675 TCAAGTGTTC
2720685 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
2720750 TTTTTTACGTTACG-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCA
66 TTTTTTACGTTACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCA
2720814 AAACAATCAAATAATTTTTTGTGCAAATTAAATTATTAAATTAATA-TGTAGGTGGAAAACATGA
131 AAACAATCAAATAATTTTTTGTGCAAA-TAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
2720878 AACACTGTT-AAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTAT
195 AACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTAT
2720942 -AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAAT
260 AAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAAT
*
2721006 GTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTA
325 GTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTA
2721071 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAAT
390 TAAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAAT
2721111 TTAAGG-TATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
2721174 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATC
66 TTTTTTACGTTACGA-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATC
2721239 AAAACAATCAAATAA-TTTTTGTGCAAATGAAATTATT-AATTAATATTGTAGGTGGAAAACATG
130 AAAACAATCAAATAATTTTTTGTGCAAAT-AAATTATTAAATTAATATTGTAGGTGGAAAACATG
2721302 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTA
194 AAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTA
2721367 TAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAA
259 TAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAA
2721432 TGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTT
324 TGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTT
2721497 ATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAAT
389 ATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAAT
2721537 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
*
2721602 -TTTTTACGTTACG-ATATATTATTATTAAATT-AAAATTCTAAATATTA-TTTATAAAATATAA
66 TTTTTTACGTTACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCA
2721663 AAACAATCAAATAATTTTTTGTGCAAA-AAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
131 AAACAATCAAATAATTTTTTGTGCAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
*
2721727 ACACTGTTAAAAAAATTAAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATA
196 ACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATA
2721792 AAAAGTATGGACACTTTCAATATAAT-GGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
261 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
2721856 TAATAGGTATCTTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
326 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
2721921 AAAAGTGTTCATACTTTTTCACTGTGGAAAACATTAAT
391 AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAAT
2721959 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
1 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
2722024 TTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTA-TTTATAAAATATC
66 TTTTTTACGTTACGA-ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATC
* *
2722088 AAAACAATCAAATAATTTTTTTGTGCAAATGAATTATTAAATTAATATTGTAGGTGAAAAACATG
130 AAAACAATCAAATAA-TTTTTTGTGCAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATG
2722153 AAACACTGTTAAA
194 AAACACTGTTAAA
2722166 GTATCGATCC
Statistics
Matches: 1031, Mismatches: 8, Indels: 30
0.96 0.01 0.03
Matches are distributed among these distances:
422 212 0.21
423 158 0.15
424 104 0.10
425 87 0.08
426 198 0.19
427 173 0.17
428 99 0.10
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (428 bp):
TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
TTTTTTACGTTACGAATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCA
AAACAATCAAATAATTTTTTGTGCAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
ACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAAT
Found at i:2723504 original size:23 final size:23
Alignment explanation
Indices: 2723456--2723504 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2723446 AACGTGCCAC
* * *
2723456 AAAACATAGATAAACGTGTAATA
1 AAAACAAAGATAAACATGTAACA
*
2723479 AAAACAAAGATAAACATGTTACA
1 AAAACAAAGATAAACATGTAACA
2723502 AAA
1 AAA
2723505 TATATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (23 bp):
AAAACAAAGATAAACATGTAACA
Found at i:2725153 original size:31 final size:31
Alignment explanation
Indices: 2725096--2725154 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2725086 ATTTGGTATC
* **
2725096 TATTTTTCAAACATTACACATTTGATTCTTG
1 TATTTTTCAAACAGTACACAAATGATTCTTG
2725127 TATTTTTC-AACAGTACACAAAATGATTC
1 TATTTTTCAAACAGTACAC-AAATGATTC
2725155 ATGTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (31 bp):
TATTTTTCAAACAGTACACAAATGATTCTTG
Found at i:2725481 original size:2 final size:2
Alignment explanation
Indices: 2725474--2725500 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2725464 TAATTTTTAG
2725474 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
2725501 TTGAAAAAAA
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:2727774 original size:30 final size:30
Alignment explanation
Indices: 2727740--2727814 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
2727730 AAAGTAAGAA
*
2727740 ATGTTCTTGGTGTTTTTCTAAGTTCAAGCG
1 ATGTTCTTGGTGTTCTTCTAAGTTCAAGCG
2727770 ATGTTCTTGGTGTTCTTCTAAGTTCAAGCG
1 ATGTTCTTGGTGTTCTTCTAAGTTCAAGCG
*
2727800 ATGTACTTGGTGTTC
1 ATGTTCTTGGTGTTC
2727815 CTCAAAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (30 bp):
ATGTTCTTGGTGTTCTTCTAAGTTCAAGCG
Found at i:2730988 original size:3 final size:3
Alignment explanation
Indices: 2730976--2731023 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
2730966 TTTTTTATCG
* * *
2730976 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTTA CTA -TA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2731021 TTA
1 TTA
2731024 CATTTACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2731143 original size:25 final size:25
Alignment explanation
Indices: 2731110--2731211 Score: 186
Period size: 25 Copynumber: 4.1 Consensus size: 25
2731100 CAATCAACCC
*
2731110 ATCATATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2731135 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2731160 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
2731185 AACAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2731210 AT
1 AT
2731212 GTTCCAGCCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:2739119 original size:4 final size:4
Alignment explanation
Indices: 2739110--2739164 Score: 96
Period size: 4 Copynumber: 14.2 Consensus size: 4
2739100 TCGAGAAAAG
2739110 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
2739156 TACA TACA T
1 TACA TACA T
2739165 GATACATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
4 47 0.96
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:2739804 original size:105 final size:105
Alignment explanation
Indices: 2739617--2739855 Score: 294
Period size: 105 Copynumber: 2.3 Consensus size: 105
2739607 TGAGAATTTT
* * *
2739617 AAAACAAATTGCGTCTCGCTTGAGATATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
2739682 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
66 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * *
2739722 AAAACAAATTGCGTCTCGTTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* * *
2739787 TT-AAACAAAGTTGATCTCA-CTTGAGATCG-T-TTTC--TC
65 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC
* *
2739823 AAAAACAAACTT-TGTCTCGCTTGAGACAATTTC
1 -AAAACAAA-TTGCGTCTCGCTTGAGACATTTTC
2739856 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 6 0.05
104 4 0.03
105 78 0.66
106 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (105 bp):
AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:2739846 original size:36 final size:36
Alignment explanation
Indices: 2739801--2739885 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
2739791 ACAAAGTTGA
**
2739801 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
2739837 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
2739873 TCTCATTTGAGAC
1 TCTCACTTGAGAC
2739886 TGTATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:2740211 original size:29 final size:28
Alignment explanation
Indices: 2740157--2740434 Score: 217
Period size: 28 Copynumber: 9.6 Consensus size: 28
2740147 TCTTGAGACA
*
2740157 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* *
2740185 GTTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
* *
2740214 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
*
2740242 GTTTCTTTTG-AAAAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* * ***
2740269 ATTTATTTT-AAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTTTTGAAAA-AAA--------TCT-TTGAGTTT
*
2740306 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* * *
2740334 GTTCCTTTTGAATAAAATCTTGGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* * *
2740362 GTTCCTTTTGAATAAATATCTTTGAG-TC
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
2740390 GTTTCTTTTG--AAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
*
2740416 GTTTCTTTGGAAACAAAAT
1 GTTTCTTTTGAAA-AAAAT
2740435 TTTTTTCTCT
Statistics
Matches: 201, Mismatches: 30, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
25 12 0.06
26 22 0.11
27 12 0.06
28 76 0.38
29 57 0.28
36 3 0.01
37 15 0.07
38 4 0.02
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTTT
Found at i:2740281 original size:26 final size:26
Alignment explanation
Indices: 2740168--2740281 Score: 81
Period size: 29 Copynumber: 4.2 Consensus size: 26
2740158 TTTCTCTTGA
*
2740168 AAAAAATCTTTGAGTT-TGTTCCTTTTG
1 AAAAAATCTTTGAGTTAT-TT-ATTTTG
* *
2740195 AATAAAAATCTTGGAGTT-TGTTCCTTTTG
1 -A-AAAAATCTTTGAGTTAT-TT-ATTTTG
* *
2740224 AATAAATATCTTTGAGTTGTTTCTTTTG
1 AA-AAA-ATCTTTGAGTTATTTATTTTG
2740252 AAAAAATCTTTGAGTCTATTTATTTT-
1 AAAAAATCTTTGAGT-TATTTATTTTG
2740278 AAAA
1 AAAA
2740282 CAAAGTTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
26 14 0.18
27 12 0.16
28 13 0.17
29 37 0.48
30 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAAATCTTTGAGTTATTTATTTTG
Found at i:2740398 original size:148 final size:149
Alignment explanation
Indices: 2740145--2740495 Score: 553
Period size: 148 Copynumber: 2.3 Consensus size: 149
2740135 ACGATTTTTG
2740145 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
1 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
*
2740210 GTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTTTGAGTCTATTTAT
66 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTG-AAAAATCTTTGAGTCTATTTAT
*
2740275 TTTAAAAC-AAAGTTTTGTC
130 TTGAAAACAAAAGTTTTGTC
2740294 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAAT-AAAATCTTGGA
1 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
* * *
2740358 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTTTGTTTCTT
66 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTCTATTTATT
* * *
2740423 TGGAAACAAAATTTTTTTC
131 TGAAAACAAAAGTTTTGTC
* * * *
2740442 TCTCTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAA
1 TCTCTTGAGACAGTTTCTCTTG-AA-AAAAATCTTTGAGTTTGTTCCTTTTGAA
2740496 ACAAAATTTT
Statistics
Matches: 187, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
147 25 0.13
148 80 0.43
149 55 0.29
150 27 0.14
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (149 bp):
TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTTGAAAAATCTTTGAGTCTATTTATT
TGAAAACAAAAGTTTTGTC
Found at i:2740414 original size:54 final size:56
Alignment explanation
Indices: 2740313--2740434 Score: 151
Period size: 54 Copynumber: 2.2 Consensus size: 56
2740303 ACAGTTTCTC
*
2740313 TTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAAATCTTTGAGTTCGTTCCTTTTGAATAAAATCTTGGAGTTTGTTCCTT
* * * *
2740369 TTGAATAAATATCTTTGAG-TCGTTTCTTTTG-A-AAAATCTTTGAGTTTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTCGTTCCTTTTGAATAAAATCTTGGAGTTTGTTCCTT
*
2740423 TGGAAACAAAAT
1 TTGAAA-AAAAT
2740435 TTTTTTCTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
53 1 0.02
54 28 0.49
55 1 0.02
56 15 0.26
57 12 0.21
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (56 bp):
TTGAAAAAAATCTTTGAGTTCGTTCCTTTTGAATAAAATCTTGGAGTTTGTTCCTT
Found at i:2740940 original size:60 final size:62
Alignment explanation
Indices: 2740821--2740989 Score: 161
Period size: 63 Copynumber: 2.7 Consensus size: 62
2740811 AGACAATTTC
*
2740821 TTTTGGAAAAAATCTTTGAGTCTATTTTACTTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTTGGAAAAAATCTTTGAGTCTAGTTTACTTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
* * * *
2740883 TTTTGTGAAAAAATCTTTGGGT-T-GTTTCCTTTGAAACGAA-TTTTGTCTCT-TTCGAGACAGT
1 TTTTG-GAAAAAATCTTTGAGTCTAGTTTACTTTGAAACAAAGTTTTGTCTCTCTT-GAGACA-A
*
2740944 TGCTTTGGAAAAACTTATCTTTGAGTTTA-TTTCAC-TTGAAACAAAG
1 T--TTTGGAAAAA---ATCTTTGAGTCTAGTTT-ACTTTGAAACAAAG
2740990 CAAATATCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
59 2 0.02
60 16 0.18
61 15 0.17
62 12 0.14
63 19 0.22
65 9 0.10
66 13 0.15
67 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (62 bp):
TTTTGGAAAAAATCTTTGAGTCTAGTTTACTTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
Found at i:2741235 original size:43 final size:43
Alignment explanation
Indices: 2741126--2741379 Score: 178
Period size: 43 Copynumber: 5.8 Consensus size: 43
2741116 TTATCCCTAG
* * *
2741126 AGATAACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC-AT
** * * * *
2741172 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
* *
2741215 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC-AT
** * * * * * **
2741261 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
* * *
2741304 AG---ACCAGATCTCCACATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
2741344 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGT
2741380 TATCACCTTT
Statistics
Matches: 160, Mismatches: 38, Indels: 23
0.72 0.17 0.10
Matches are distributed among these distances:
40 32 0.20
42 2 0.01
43 58 0.36
44 5 0.03
45 3 0.02
46 58 0.36
47 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
Found at i:2741277 original size:89 final size:89
Alignment explanation
Indices: 2741126--2741298 Score: 337
Period size: 89 Copynumber: 1.9 Consensus size: 89
2741116 TTATCCCTAG
2741126 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
2741191 TCACGTATGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCAACCAT
*
2741215 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
2741280 TCACGTATGAGCCGTGTCA
66 TCACGTATGAGCCGTGTCA
2741299 TCCCCAGACC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (89 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCAACCAT
Found at i:2741598 original size:3 final size:3
Alignment explanation
Indices: 2741586--2741633 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
2741576 TTTTTTATCG
* * *
2741586 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTTA CTA -TA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2741631 TTA
1 TTA
2741634 CATTTTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2741640 original size:24 final size:23
Alignment explanation
Indices: 2741596--2741646 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2741586 TTATTTTTAT
* *
2741596 TATTATTATTATTATTATTTACTA
1 TATTATTAATATTAATATTTAC-A
2741620 TATTATTAATATTACAT-TTTACA
1 TATTATTAATATTA-ATATTTACA
2741643 TATT
1 TATT
2741647 TTGCAGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTATTAATATTAATATTTACA
Found at i:2741694 original size:20 final size:22
Alignment explanation
Indices: 2741671--2741711 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2741661 CAATACAACA
2741671 AGGCCC-A-CCCGAAGCCCAAT
1 AGGCCCAATCCCGAAGCCCAAT
*
2741691 AGGCCCAATCCCGGAGCCCAA
1 AGGCCCAATCCCGAAGCCCAA
2741712 CAATCAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.29, C:0.44, G:0.22, T:0.05
Consensus pattern (22 bp):
AGGCCCAATCCCGAAGCCCAAT
Found at i:2741755 original size:25 final size:25
Alignment explanation
Indices: 2741722--2741823 Score: 186
Period size: 25 Copynumber: 4.1 Consensus size: 25
2741712 CAATCAACCC
*
2741722 ATCATATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2741747 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2741772 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
2741797 AACAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
2741822 AT
1 AT
2741824 GTTCCAGCCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:2749147 original size:23 final size:24
Alignment explanation
Indices: 2749101--2749151 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2749091 TTTTGTAGGG
*
2749101 TATTGTTTTGGTGAATTTTTTAAT
1 TATTGTTTTAGTGAATTTTTTAAT
*
2749125 TATTGTTTTATTGAA-TTTTTAAT
1 TATTGTTTTAGTGAATTTTTTAAT
2749148 TATT
1 TATT
2749152 AAAAGTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (24 bp):
TATTGTTTTAGTGAATTTTTTAAT
Found at i:2749509 original size:55 final size:56
Alignment explanation
Indices: 2749412--2749516 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 56
2749402 TGAGCGATTA
2749412 TTTTATAATTTTTAATAATTAAAAGATTCAACAAAATAATATTATATAATTTATTT
1 TTTTATAATTTTTAATAATTAAAAGATTCAACAAAATAATATTATATAATTTATTT
* **
2749468 TTTTATAATTTTTAATAA-TCAGGGATTCAACAAAATAATATTATATAAT
1 TTTTATAATTTTTAATAATTAAAAGATTCAACAAAATAATATTATATAAT
2749517 CGAGAGAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 28 0.61
56 18 0.39
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (56 bp):
TTTTATAATTTTTAATAATTAAAAGATTCAACAAAATAATATTATATAATTTATTT
Found at i:2764601 original size:31 final size:31
Alignment explanation
Indices: 2764566--2764626 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2764556 TCGCGAGCCT
* * *
2764566 AAAATTTTCAAGCTCGACTCGAACTCGAAAG
1 AAAATATTCAAACTCGACCCGAACTCGAAAG
* *
2764597 AAAATATTGAAACTTGACCCGAACTCGAAA
1 AAAATATTCAAACTCGACCCGAACTCGAAA
2764627 ATGTTCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACCCGAACTCGAAAG
Found at i:2765870 original size:21 final size:21
Alignment explanation
Indices: 2765846--2765904 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2765836 TGAGATTTGA
2765846 GATTTAAGGTTTATGGTTTAT
1 GATTTAAGGTTTATGGTTTAT
* *
2765867 GATTTATA-ATTTATAGTTTAT
1 GATTTA-AGGTTTATGGTTTAT
* *
2765888 AATTTAGGGTTTATGGT
1 GATTTAAGGTTTATGGT
2765905 ATAATCTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
GATTTAAGGTTTATGGTTTAT
Found at i:2765872 original size:14 final size:14
Alignment explanation
Indices: 2765846--2765902 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
2765836 TGAGATTTGA
*
2765846 GATTTAAGGTTTAT
1 GATTTATGGTTTAT
* *
2765860 GGTTTATGATTTAT
1 GATTTATGGTTTAT
* *
2765874 AATTTATAGTTTAT
1 GATTTATGGTTTAT
* *
2765888 AATTTAGGGTTTAT
1 GATTTATGGTTTAT
2765902 G
1 G
2765903 GTATAATCTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (14 bp):
GATTTATGGTTTAT
Found at i:2766010 original size:21 final size:21
Alignment explanation
Indices: 2765986--2766052 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
2765976 GGGTTTAGGG
* *
2765986 TTTATAACTTAGAGTTTATAA
1 TTTATAATTTAGGGTTTATAA
* **
2766007 TTTATGATTTAGGGTTTAGGA
1 TTTATAATTTAGGGTTTATAA
*
2766028 TTTATAATTTAGGGTTTATAG
1 TTTATAATTTAGGGTTTATAA
2766049 TTTA
1 TTTA
2766053 GAGTTTAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (21 bp):
TTTATAATTTAGGGTTTATAA
Found at i:2766058 original size:14 final size:14
Alignment explanation
Indices: 2765978--2766083 Score: 76
Period size: 14 Copynumber: 7.6 Consensus size: 14
2765968 TGGATTAAGG
*
2765978 GTTTAGGGTTTATA
1 GTTTAGAGTTTATA
**
2765992 ACTTAGAGTTTATA
1 GTTTAGAGTTTATA
* **
2766006 ATTTATGA-TTTAGG
1 GTTTA-GAGTTTATA
2766020 GTTTAG-GATTTATA
1 GTTTAGAG-TTTATA
* *
2766034 ATTTAGGGTTTATA
1 GTTTAGAGTTTATA
2766048 GTTTAGAGTTTA-A
1 GTTTAGAGTTTATA
*
2766061 GATTTAGGGTTTA-A
1 G-TTTAGAGTTTATA
2766075 GTTTAGAGT
1 GTTTAGAGT
2766084 ATAATCTAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
13 10 0.14
14 60 0.82
15 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (14 bp):
GTTTAGAGTTTATA
Found at i:2766059 original size:21 final size:20
Alignment explanation
Indices: 2765994--2766059 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
2765984 GGTTTATAAC
* *
2765994 TTAGAGTTTATAATTTATGAT
1 TTAGGGTTTATAGTTTA-GAT
* *
2766015 TTAGGGTTTA-GGATTTATAAT
1 TTAGGGTTTATAG-TTTA-GAT
2766036 TTAGGGTTTATAGTTTAGAGT
1 TTAGGGTTTATAGTTTAGA-T
2766057 TTA
1 TTA
2766060 AGATTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (20 bp):
TTAGGGTTTATAGTTTAGAT
Found at i:2767326 original size:42 final size:42
Alignment explanation
Indices: 2767279--2767368 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 42
2767269 CCACTAGGGG
2767279 CACTGAATATTTGTCCCGAAGGACCACT-ATA-TCCCGAAGGAC
1 CACTGAATA--TGTCCCGAAGGACCACTGATAGTCCCGAAGGAC
*
2767321 CACTG-ATATGTCCCGAAGGACCACTGATATGTCTCGAAGGAC
1 CACTGAATATGTCCCGAAGGACCACTGATA-GTCCCGAAGGAC
2767363 CACTGA
1 CACTGA
2767369 TAATCCCTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
39 17 0.40
40 3 0.07
41 3 0.07
42 20 0.47
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (42 bp):
CACTGAATATGTCCCGAAGGACCACTGATAGTCCCGAAGGAC
Found at i:2767336 original size:21 final size:21
Alignment explanation
Indices: 2767290--2767370 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
2767280 ACTGAATATT
2767290 TGTCCCGAAGGACCACT-ATA
1 TGTCCCGAAGGACCACTGATA
2767310 --TCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
2767329 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
*
2767350 TGTCTCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
2767371 ATCCCTCGAC
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
18 15 0.26
19 3 0.05
21 39 0.68
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:2769045 original size:18 final size:19
Alignment explanation
Indices: 2769006--2769045 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2768996 GGGTATATCA
2769006 ATGCACTCCCTATGCATCG
1 ATGCACTCCCTATGCATCG
2769025 ATGCACT-CCT-TGCATTCG
1 ATGCACTCCCTATGCA-TCG
2769043 ATG
1 ATG
2769046 TTCATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGCACTCCCTATGCATCG
Found at i:2772505 original size:21 final size:21
Alignment explanation
Indices: 2772463--2772522 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2772453 ACTGAATATT
2772463 TGTCCCGAAGGACCAC---TA
1 TGTCCCGAAGGACCACTGATA
*
2772481 TGTCCCGAAAGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
2772502 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTGATA
2772523 ATCCCTCGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 15 0.41
21 22 0.59
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:2781555 original size:13 final size:13
Alignment explanation
Indices: 2781539--2781570 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2781529 GCCCCGATTA
2781539 CCCGATTACCCGC
1 CCCGATTACCCGC
2781552 CCCGATTACCCGC
1 CCCGATTACCCGC
2781565 CCCGAT
1 CCCGAT
2781571 ACCGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:2781706 original size:12 final size:12
Alignment explanation
Indices: 2781682--2781727 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
2781672 CGATTCCCAG
2781682 CCCAATA-CCGA
1 CCCAATACCCGA
2781693 CCCAATACCCGA
1 CCCAATACCCGA
* *
2781705 CCCAATACCTGG
1 CCCAATACCCGA
2781717 CCCAATACCCG
1 CCCAATACCCG
2781728 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:2781708 original size:23 final size:24
Alignment explanation
Indices: 2781682--2781727 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2781672 CGATTCCCAG
2781682 CCCAATACC-GACCCAATACCCGA
1 CCCAATACCTGACCCAATACCCGA
*
2781705 CCCAATACCTGGCCCAATACCCG
1 CCCAATACCTGACCCAATACCCG
2781728 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (24 bp):
CCCAATACCTGACCCAATACCCGA
Found at i:2781984 original size:2 final size:2
Alignment explanation
Indices: 2781977--2782010 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2781967 TTTGATTTTA
2781977 AT AT AT AT -T 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
2782011 ACATAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2782294 original size:17 final size:17
Alignment explanation
Indices: 2782272--2782306 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2782262 CAGTTTTATT
2782272 ACGTTAAAAAATAAATC
1 ACGTTAAAAAATAAATC
2782289 ACGTTAAAAAATAAATC
1 ACGTTAAAAAATAAATC
2782306 A
1 A
2782307 AATGGTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (17 bp):
ACGTTAAAAAATAAATC
Found at i:2788350 original size:42 final size:42
Alignment explanation
Indices: 2788303--2788443 Score: 246
Period size: 42 Copynumber: 3.4 Consensus size: 42
2788293 GAACTTCGAC
*
2788303 TATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATT
1 TATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATT
* *
2788345 TATTCCAAATTCGTTGTGATAGTCGAAGTTCGTGTTGCGATT
1 TATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATT
*
2788387 TATTCCAAATTCGTTGCGATAGTCGAAGTTTGCGTTGCGATT
1 TATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATT
2788429 TATTCCAAATTCGTT
1 TATTCCAAATTCGTT
2788444 TCTTAAGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (42 bp):
TATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATT
Found at i:2788443 original size:21 final size:19
Alignment explanation
Indices: 2788303--2788443 Score: 93
Period size: 21 Copynumber: 6.8 Consensus size: 19
2788293 GAACTTCGAC
2788303 TATTCCAAATTCGTTGCGA
1 TATTCCAAATTCGTTGCGA
* *
2788322 TAGTCCAAGTTCGCGTTGCGA
1 TATTCCAAATT--CGTTGCGA
*
2788343 TTTATTCCAAATTCGTTGTGA
1 --TATTCCAAATTCGTTGCGA
* * *
2788364 TAGTCGAAGTTCGTGTTGCGA
1 TATTCCAAATTC--GTTGCGA
2788385 TTTATTCCAAATTCGTTGCGA
1 --TATTCCAAATTCGTTGCGA
* * *
2788406 TAGTCGAAGTTTGCGTTGCGA
1 TATTCCAA-ATT-CGTTGCGA
2788427 TTTATTCCAAATTCGTT
1 --TATTCCAAATTCGTT
2788444 TCTTAAGAAT
Statistics
Matches: 92, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
19 24 0.26
20 2 0.02
21 40 0.43
22 2 0.02
23 24 0.26
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (19 bp):
TATTCCAAATTCGTTGCGA
Found at i:2789017 original size:12 final size:12
Alignment explanation
Indices: 2789002--2789040 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2788992 TCTCGTCTCG
2789002 GGTCGTGGTAGT
1 GGTCGTGGTAGT
*
2789014 GGTCGTGGTCGT
1 GGTCGTGGTAGT
2789026 GGTCGTGGTAGT
1 GGTCGTGGTAGT
2789038 GGT
1 GGT
2789041 AGTACGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.10, G:0.51, T:0.33
Consensus pattern (12 bp):
GGTCGTGGTAGT
Found at i:2789021 original size:6 final size:6
Alignment explanation
Indices: 2789002--2789040 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2788992 TCTCGTCTCG
* *
2789002 GGTCGT GGTAGT GGTCGT GGTCGT GGTCGT GGTAGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2789041 AGTACGTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.10, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2789787 original size:21 final size:21
Alignment explanation
Indices: 2789761--2789805 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2789751 ATCTTCATTC
2789761 AATGTCTAAAATTTTCATATA
1 AATGTCTAAAATTTTCATATA
2789782 AATGTCTAAAATTTTCATATA
1 AATGTCTAAAATTTTCATATA
2789803 AAT
1 AAT
2789806 AAAATTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (21 bp):
AATGTCTAAAATTTTCATATA
Found at i:2793145 original size:108 final size:109
Alignment explanation
Indices: 2792971--2793355 Score: 568
Period size: 108 Copynumber: 3.6 Consensus size: 109
2792961 ATATCTTCGT
* * * * * *
2792971 CAATCGTGTCTACTCCCTA-TT-TTCAGAGAGTATAAG-CTCGAACGAT-TCTCGATAATCGTGC
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGT
2793032 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCA
65 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCA
* *
2793077 CAATCGTGTCTGTTCCCTATTT-GTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
2793141 TGCTCCCTATTTCTTC--AGAGTATGAGACTCGAACAATCTTCAA
66 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC-A
* *
2793184 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATTGTGTA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
*
2793249 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTTAA
66 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATC-TTCA
** *
2793294 CAATTATGTCTGCTCCCTATTTCTTAAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
2793356 TGGGAAACCT
Statistics
Matches: 254, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
106 42 0.17
107 37 0.15
108 91 0.36
109 1 0.00
110 81 0.32
111 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (109 bp):
CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCA
Found at i:2793241 original size:55 final size:55
Alignment explanation
Indices: 2792971--2793355 Score: 579
Period size: 55 Copynumber: 7.1 Consensus size: 55
2792961 ATATCTTCGT
* * * *
2792971 CAATCGTGTCTACTCCCTA-TT-TTCAGAGAGTATAAG-CTCGAACGAT-TCTCGA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAA
* *
2793023 TAATCGTGCCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC-A
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* *
2793077 CAATCGTGTCTGTTCCCTATTT-GTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
2793131 CAATCGTGTCTGCTCCCTATTTCTTC--AGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
2793184 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* * *
2793239 CAATTGTGTATGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTTAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
** *
2793294 CAATTATGTCTGCTCCCTATTTCTTAAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
2793349 CAATCGT
1 CAATCGT
2793356 TGGGAAACCT
Statistics
Matches: 305, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
52 16 0.05
53 84 0.28
54 56 0.18
55 148 0.49
56 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (55 bp):
CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
Found at i:2794288 original size:12 final size:12
Alignment explanation
Indices: 2794268--2794303 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2794258 CATCTTGAAC
*
2794268 CCTTCTTTTTTT
1 CCTTTTTTTTTT
2794280 CCTTTTTTTTTT
1 CCTTTTTTTTTT
*
2794292 CATTTTTTTTTT
1 CCTTTTTTTTTT
2794304 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
CCTTTTTTTTTT
Found at i:2794297 original size:8 final size:8
Alignment explanation
Indices: 2794285--2794328 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
2794275 TTTTTCCTTT
2794285 TTTTTTTCA
1 TTTTTTT-A
*
2794294 TTTTTTTT
1 TTTTTTTA
2794302 TTTTTTTA
1 TTTTTTTA
2794310 TTTTTTTA
1 TTTTTTTA
*
2794318 TTTTTTCA
1 TTTTTTTA
2794326 TTT
1 TTT
2794329 CACTCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2794303 original size:16 final size:16
Alignment explanation
Indices: 2794282--2794328 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
2794272 CTTTTTTTCC
2794282 TTTTTTTTTTCATTTT
1 TTTTTTTTTTCATTTT
*
2794298 TTTTTTTTTTTATTTT
1 TTTTTTTTTTCATTTT
*
2794314 TTTATTTTTTCATTT
1 TTTTTTTTTTCATTT
2794329 CACTCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTTCATTTT
Found at i:2807930 original size:31 final size:31
Alignment explanation
Indices: 2807890--2807949 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2807880 GACATTTAAT
*
2807890 TTACGGAATGTAAGATTAATTTGAAAATAAA
1 TTACGGAATGTAACATTAATTTGAAAATAAA
* * *
2807921 TTACTGAATGTAACTTTAATTTGAGAATA
1 TTACGGAATGTAACATTAATTTGAAAATA
2807950 TCGTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
TTACGGAATGTAACATTAATTTGAAAATAAA
Done.