Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 294 of 427
Found at i:85006496 original size:20 final size:19
Alignment explanation
Indices: 85006460--85006498 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85006450 TGATTCATGT
85006460 TTTTAAAATTTAGTATTAA
1 TTTTAAAATTTAGTATTAA
* *
85006479 TTTTACAATTATATTATTAA
1 TTTTAAAATT-TAGTATTAA
85006499 AGAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTTAGTATTAA
Found at i:85009281 original size:6 final size:6
Alignment explanation
Indices: 85009270--85009314 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
85009260 GGTTAAACTA
*
85009270 TTTATT TTTATT TTTATT ATTTCTTT ATTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT -TTT-ATT -TTTATT TTTATT TTTATT
85009315 ATTTCTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 24 0.69
7 5 0.14
8 6 0.17
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:85009291 original size:15 final size:15
Alignment explanation
Indices: 85009271--85009318 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
85009261 GTTAAACTAT
85009271 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
* *
85009286 TTA--TTTCTTTAT-
1 TTATTTTTATTTTTA
85009298 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
85009313 TTATTT
1 TTATTT
85009319 CTTTCCCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 3 0.12
13 7 0.27
14 7 0.27
15 9 0.35
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:85009306 original size:27 final size:27
Alignment explanation
Indices: 85009268--85009322 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
85009258 AGGGTTAAAC
85009268 TATTTATTTTTATTTTTATTATTTCTT
1 TATTTATTTTTATTTTTATTATTTCTT
85009295 TATTTATTTTTATTTTTATTATTTCTT
1 TATTTATTTTTATTTTTATTATTTCTT
85009322 T
1 T
85009323 CCCTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (27 bp):
TATTTATTTTTATTTTTATTATTTCTT
Found at i:85009329 original size:27 final size:27
Alignment explanation
Indices: 85009272--85009338 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
85009262 TTAAACTATT
**
85009272 TATTTTTATTTTTATTATTTCTTTATT
1 TATTTTTATTTTTATTATTTCTTTACC
*
85009299 TATTTTTATTTTTATTATTTCTTTCCC
1 TATTTTTATTTTTATTATTTCTTTACC
*
85009326 TATTATTTCTTTT
1 TATT-TTTATTTT
85009339 CTTTTTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (27 bp):
TATTTTTATTTTTATTATTTCTTTACC
Found at i:85009353 original size:17 final size:17
Alignment explanation
Indices: 85009276--85009368 Score: 63
Period size: 17 Copynumber: 5.6 Consensus size: 17
85009266 ACTATTTATT
*
85009276 TTTATTTTTATTAT-TTC
1 TTTATTTTTCTT-TCTTC
*
85009293 TTTATTTATT-TTTATT-
1 TTTATTT-TTCTTTCTTC
*
85009309 TTTATTATTTCTTTC-CC
1 TTTATT-TTTCTTTCTTC
*
85009326 TATTATTTCT-TTTCTT-
1 T-TTATTTTTCTTTCTTC
*
85009342 TTTCTTTTTCTTTCTTC
1 TTTATTTTTCTTTCTTC
85009359 TTTATTTTTC
1 TTTATTTTTC
85009369 AGCAACCCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
15 6 0.10
16 20 0.33
17 27 0.45
18 7 0.12
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTCTTTCTTC
Found at i:85010408 original size:13 final size:14
Alignment explanation
Indices: 85010380--85010427 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
85010370 CATAAAAGAG
*
85010380 ATAAATATCATAAA
1 ATAAATAACATAAA
85010394 ATAAATAAC-TAAA
1 ATAAATAACATAAA
85010407 ATAAATAAACAATAAA
1 ATAAAT-AAC-ATAAA
85010423 ATAAA
1 ATAAA
85010428 CAAACAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.33
14 11 0.37
16 9 0.30
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAATAACATAAA
Found at i:85010424 original size:16 final size:16
Alignment explanation
Indices: 85010389--85010439 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
85010379 GATAAATATC
85010389 ATAAAATAAAT-AAC-
1 ATAAAATAAATAAACA
85010403 -TAAAATAAATAAACA
1 ATAAAATAAATAAACA
*
85010418 ATAAAATAAACAAACA
1 ATAAAATAAATAAACA
85010434 ACTAAA
1 A-TAAA
85010440 CCAATTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 10 0.31
14 3 0.09
16 15 0.47
17 4 0.12
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (16 bp):
ATAAAATAAATAAACA
Found at i:85011065 original size:16 final size:16
Alignment explanation
Indices: 85011044--85011074 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
85011034 TAAAAGACGA
85011044 CCTAGTTACATCAAAT
1 CCTAGTTACATCAAAT
85011060 CCTAGTTACATCAAA
1 CCTAGTTACATCAAA
85011075 CCCCTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (16 bp):
CCTAGTTACATCAAAT
Found at i:85012958 original size:276 final size:281
Alignment explanation
Indices: 85012411--85012968 Score: 707
Period size: 288 Copynumber: 2.0 Consensus size: 281
85012401 TCAAACCAGA
* * **
85012411 CAATCGGGTCGTGTATGGGGTGTTACAACAATAATGACTTTATATGTACAATCTATTACCCGGGG
1 CAATCGGGTCATGTATGGGGTGTTACAACAATAATGAATTTATATGTACAATCTACCACCCGGGG
* *
85012476 TTGCTCAAAAATGATGGTTTCTAATAAATATCTTGACCATATGGCATGCCAACTAGGGGTGAGAA
66 TTCCTCAAAAATGATGGTTTCTAATAAATATCTTGACCATATGACATGCCAACTAGGGGTGAGAA
* *
85012541 AAACTAAATTTGATTCGAAAAAATTGGAAAAAAATCAAATTTTGAGTTCATCCAATAGGGCTATT
131 AAACTAAA--T-ATTCG----AATTGAAAAAAAATCAAATTTTGAGTTCATCCAATAGAGCTATT
* * * *
85012606 TGAGTACACTCGGATAAGTAATTTGAATTTTGAATTCGAGTCGAGTTAAAATTTGTAATTCAAAT
189 TGAGTAAACTCGGATAAGTAATTTCAATTTCGAATTCGAGTCAAGTTAAAATTTGTAATTCAAAT
* *
85012671 GACTCGAATAATTTGAATAACAAATTGG
254 AACTCGAATAATTCGAATAACAAATTGG
* * *
85012699 CAATCGGGTCATGTATGGGGTGTTACAGCAATGATGAATTTATATGTACAATCTACCACCTGGGG
1 CAATCGGGTCATGTATGGGGTGTTACAACAATAATGAATTTATATGTACAATCTACCACCCGGGG
* * * * *
85012764 TTCCTGAGAAATGATGGTTTCTAATCAATATCTTGACCCTATGACATGCCAATTA-GGGTGAGAA
66 TTCCTCAAAAATGATGGTTTCTAATAAATATCTTGACCATATGACATGCCAACTAGGGGTGAGAA
* * *
85012828 AAACT-CA-ATTCG-ATT-AAAAAAAATTAAATTTTGAGTTCATCCAATCA-AGTTATTTGAGTA
131 AAACTAAATATTCGAATTGAAAAAAAATCAAATTTTGAGTTCATCCAAT-AGAGCTATTTGAGTA
* * * * * *
85012888 AACTCGGATAAGTAA-TTCAAGTTTCGAGTTTGAGTCAAGTTAAATTTTGTAATTCAATTAATTT
195 AACTCGGATAAGTAATTTCAA-TTTCGAATTCGAGTCAAGTTAAAATTTGTAATTCAAATAACTC
85012952 GAATAATTCGAATAACA
259 GAATAATTCGAATAACA
85012969 GATTATTGTA
Statistics
Matches: 237, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
275 4 0.02
276 103 0.43
277 4 0.02
282 5 0.02
286 1 0.00
287 14 0.06
288 106 0.45
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (281 bp):
CAATCGGGTCATGTATGGGGTGTTACAACAATAATGAATTTATATGTACAATCTACCACCCGGGG
TTCCTCAAAAATGATGGTTTCTAATAAATATCTTGACCATATGACATGCCAACTAGGGGTGAGAA
AAACTAAATATTCGAATTGAAAAAAAATCAAATTTTGAGTTCATCCAATAGAGCTATTTGAGTAA
ACTCGGATAAGTAATTTCAATTTCGAATTCGAGTCAAGTTAAAATTTGTAATTCAAATAACTCGA
ATAATTCGAATAACAAATTGG
Found at i:85013072 original size:20 final size:20
Alignment explanation
Indices: 85013049--85013100 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
85013039 TTATAAAAAC
* *
85013049 AATTCAAATTGATTTTCAAA
1 AATTCAAAATAATTTTCAAA
85013069 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
*
85013089 AAGTTCTAAATA
1 AA-TTCAAAATA
85013101 TATATGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:85013222 original size:33 final size:33
Alignment explanation
Indices: 85013180--85013251 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
85013170 ATGGTTCAAG
*
85013180 TTTATTATACTAAAGTATCTTATTTTTTATTAT
1 TTTACTATACTAAAGTATCTTATTTTTTATTAT
85013213 TTTACTATACTAAAGTATCTTATTTTTTATTAT
1 TTTACTATACTAAAGTATCTTATTTTTTATTAT
85013246 TTTACT
1 TTTACT
85013252 TTGAAAAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (33 bp):
TTTACTATACTAAAGTATCTTATTTTTTATTAT
Found at i:85016334 original size:90 final size:90
Alignment explanation
Indices: 85016181--85016363 Score: 312
Period size: 90 Copynumber: 2.0 Consensus size: 90
85016171 GTTAAATAAT
* *
85016181 TAAATCATTAATTATACAAAAATATATAGAAGAGTACAAAATCATTTTTAACTTTAAAGTTTAAG
1 TAAATCATTAATTATACAAAAATATATAGAAGAGTACAAAACCATTTTTAACTTTAAAGTTTAAA
*
85016246 AACCAATTTAAAATGAGAATTACAG
66 AACCAATTTAAAATGAAAATTACAG
*
85016271 TAAATCATTAATTATATAAAAATATATAGAAGAGTACAAAACCATTTTTAACTTTAAAGTTTAAA
1 TAAATCATTAATTATACAAAAATATATAGAAGAGTACAAAACCATTTTTAACTTTAAAGTTTAAA
* *
85016336 AATCAATTTAAAATGAAAATTATAG
66 AACCAATTTAAAATGAAAATTACAG
85016361 TAA
1 TAA
85016364 TTAACTTTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (90 bp):
TAAATCATTAATTATACAAAAATATATAGAAGAGTACAAAACCATTTTTAACTTTAAAGTTTAAA
AACCAATTTAAAATGAAAATTACAG
Found at i:85020088 original size:21 final size:21
Alignment explanation
Indices: 85020050--85020089 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
85020040 TAAAAACATC
* * *
85020050 AAACCCGAAATTTGAAATTAG
1 AAACCCAAAATCTCAAATTAG
85020071 AAACCCAAAATCTCAAATT
1 AAACCCAAAATCTCAAATT
85020090 TAAACTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (21 bp):
AAACCCAAAATCTCAAATTAG
Found at i:85021985 original size:29 final size:29
Alignment explanation
Indices: 85021922--85021987 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
85021912 AAAGTTTAAG
*
85021922 TTAAAAAATTATTAAAATTATGATAATGA
1 TTAAAAAATTATTAAAATTATGATAATAA
*
85021951 TATAAAAAA-TATTAAAA-TATTATTAAATAA
1 T-TAAAAAATTATTAAAATTATGA-T-AATAA
85021981 TTAAAAA
1 TTAAAAA
85021988 GAGATGTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.12
29 16 0.50
30 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAAAAAATTATTAAAATTATGATAATAA
Found at i:85022502 original size:20 final size:21
Alignment explanation
Indices: 85022467--85022515 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
85022457 CACATTAATA
* *
85022467 TAATATTTAC-TTTTTATGAT
1 TAATATTTACAATTTAATGAT
*
85022487 TAATATTTACAATTTAATTAT
1 TAATATTTACAATTTAATGAT
85022508 TAA-ATTTA
1 TAATATTTA
85022516 TTAATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TAATATTTACAATTTAATGAT
Found at i:85023864 original size:12 final size:11
Alignment explanation
Indices: 85023847--85023891 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
85023837 ATTAGAGAAA
85023847 AATAAAATGAAT
1 AATAAAAT-AAT
85023859 AATAAAATAAAT
1 AATAAAAT-AAT
*
85023871 AATAACAATAAC
1 AATAA-AATAAT
85023883 AATAAAATA
1 AATAAAATA
85023892 GACATCAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 4 0.13
12 23 0.77
13 3 0.10
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:85024222 original size:3 final size:3
Alignment explanation
Indices: 85024214--85024282 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
85024204 AAAAGAAAGT
85024214 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
85024262 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
85024283 TCTAAATTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:85026140 original size:44 final size:45
Alignment explanation
Indices: 85026068--85026178 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 45
85026058 ATTCCAACCT
* * * *
85026068 ACTGTAACTTCAAGGTTATAGGAATTGTT-GCTTTAATATGCTCC
1 ACTGCAACTTCAAGGATATAAGAATTGTTAGCTTTAACATGCTCC
* * ** *
85026112 ACTGCATCTTCAAGGATATAAGACTTGTTATTTTTAACCTGCTCC
1 ACTGCAACTTCAAGGATATAAGAATTGTTAGCTTTAACATGCTCC
* *
85026157 ATTGCAACTTCAAGGAGATAAG
1 ACTGCAACTTCAAGGATATAAG
85026179 GTTTGGCTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 24 0.44
45 30 0.56
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (45 bp):
ACTGCAACTTCAAGGATATAAGAATTGTTAGCTTTAACATGCTCC
Found at i:85026265 original size:51 final size:51
Alignment explanation
Indices: 85026210--85026370 Score: 147
Period size: 51 Copynumber: 3.3 Consensus size: 51
85026200 TCTGACATAT
*
85026210 TGCAACTTCAGAGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCTCCAC
* * * * * * ***
85026261 TGCAACTTTAGGGAAATGAA-AT---T--CAT-TATCTTTAGTCTGCTTTGC
1 TGCAACTTCAGGGAGAT-AAGATCCGTAACTTGTAGCTTCAATCTGCTCCAC
*
85026306 TGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCTCCAC
* *
85026357 TACAACTTTAGGGA
1 TGCAACTTCAGGGA
85026371 AATGAGATTC
Statistics
Matches: 80, Mismatches: 22, Indels: 16
0.68 0.19 0.14
Matches are distributed among these distances:
44 2 0.03
45 29 0.36
46 2 0.03
48 2 0.03
50 2 0.03
51 41 0.51
52 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (51 bp):
TGCAACTTCAGGGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCTCCAC
Found at i:85026422 original size:96 final size:96
Alignment explanation
Indices: 85026209--85026423 Score: 326
Period size: 96 Copynumber: 2.2 Consensus size: 96
85026199 ATCTGACATA
* *
85026209 TTGCAACTTC-AGAGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGG
1 TTGCAACTTCAAG-GAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCCACTACAACTTTAGG
* *
85026273 GAAATGAAATTCATTATCTTTAGTCTGCTTTG
65 GAAATGAAATTCACTATCTTCAGTCTGCTTTG
* *
85026305 CTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCCACTACAACTTTAGGG
1 TTGCAACTTCAAGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCCACTACAACTTTAGGG
* *
85026370 AAATGAGATTCGCTATCTTCAGTCTGCTCTT-
66 AAATGAAATTCACTATCTTCAGTCTGCT-TTG
85026401 TTGCAACTTCAAGGAGATAAGGT
1 TTGCAACTTCAAGGAGATAAGGT
85026424 TGGTGGTTTC
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
96 104 0.97
97 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (96 bp):
TTGCAACTTCAAGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCCACTACAACTTTAGGG
AAATGAAATTCACTATCTTCAGTCTGCTTTG
Found at i:85026515 original size:143 final size:143
Alignment explanation
Indices: 85026335--85026610 Score: 328
Period size: 143 Copynumber: 1.9 Consensus size: 143
85026325 GGTCCGTAAC
* * *
85026335 TTGTAGCTTCAATCTGCTCCACTACAACTTTAGGGAAATGAGATTCGCTATCTTCAG-TCTGCTC
1 TTGTAGCTTCAATCTGCTCCACTACAACGTTAAGGAAATAAGATTCGCTATCTTCAGCT-TGCTC
**** * *
85026399 TTTTGCAACTTCAAGG-AGATAAGG-TTGGTGGTTTCAATCTGCTCCACTACAACTTTAAGAAGA
65 CGCAGCAACTTC-AGGAAGATAAGGCTT-GTGGCTTCAATCTGCTCCACTACAACTTCAAGAAGA
85026462 TAAGATTTTCCATAAT
128 TAAGATTTTCCATAAT
* * *
85026478 TTGTAGC-TCTAATCTG-TCCCACTGCAACGTTAAGGAAATAAGATTTGCTGTCTTCAGCTTGCT
1 TTGTAGCTTC-AATCTGCT-CCACTACAACGTTAAGGAAATAAGATTCGCTATCTTCAGCTTGCT
* * * *
85026541 CCGCAGTAACTTCAGGAAGATAAGGCTTTTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT
64 CCGCAGCAACTTCAGGAAGATAAGGCTTGTGGCTTCAATCTGCTCCACTACAACTTCAAGAAGAT
85026606 AAGAT
129 AAGAT
85026611 CCGCCATCTT
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
142 6 0.05
143 103 0.92
144 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (143 bp):
TTGTAGCTTCAATCTGCTCCACTACAACGTTAAGGAAATAAGATTCGCTATCTTCAGCTTGCTCC
GCAGCAACTTCAGGAAGATAAGGCTTGTGGCTTCAATCTGCTCCACTACAACTTCAAGAAGATAA
GATTTTCCATAAT
Found at i:85026686 original size:44 final size:46
Alignment explanation
Indices: 85026573--85026687 Score: 130
Period size: 45 Copynumber: 2.6 Consensus size: 46
85026563 AGGCTTTTGG
* * * *
85026573 CTTCAATCTGCTCCACTGCAAC-TTCAGGAAGATAAGATCCGCCAT
1 CTTCAATCTGCTCCACTGCTACTTTAAGGAAGATAAGATCCGACAA
* * *
85026618 CTTCGATCTACTCCACTG-TAACTTTAAGG-AGATAAGAT-CTACAA
1 CTTCAATCTGCTCCACTGCT-ACTTTAAGGAAGATAAGATCCGACAA
85026662 CTTCAATCTGCTCCACTGCTACTTTA
1 CTTCAATCTGCTCCACTGCTACTTTA
85026688 GAGAGATGGG
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
44 25 0.43
45 28 0.48
46 5 0.09
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.30
Consensus pattern (46 bp):
CTTCAATCTGCTCCACTGCTACTTTAAGGAAGATAAGATCCGACAA
Found at i:85027288 original size:65 final size:65
Alignment explanation
Indices: 85027178--85027301 Score: 176
Period size: 65 Copynumber: 1.9 Consensus size: 65
85027168 AATGATGGAC
* * * * * * *
85027178 AAGAAGGAAATTGATTGAGAGTATAGCTCTAGACGAATAATTTAATCAAAGATGGCAAATACAAT
1 AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAACAAATTAATCAAAGATAGCAAATACAAT
*
85027243 AAGAAAGAAATTGATTGAGAGCATAGCTCGAAATGAACAAATTAATCAAAGATAGCAAA
1 AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAACAAATTAATCAAAGATAGCAAA
85027302 CTTTGCTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (65 bp):
AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAACAAATTAATCAAAGATAGCAAATACAAT
Found at i:85029556 original size:52 final size:49
Alignment explanation
Indices: 85029373--85029565 Score: 200
Period size: 47 Copynumber: 4.0 Consensus size: 49
85029363 TGCACATAGT
* ** * *
85029373 CACATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
85029421 CACATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
85029468 CACATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
85029515 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
85029566 ATCACATTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
46 25 0.20
47 54 0.44
48 11 0.09
49 1 0.01
52 31 0.25
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:85031459 original size:7 final size:7
Alignment explanation
Indices: 85031444--85031494 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
85031434 TGGCCTCTCC
85031444 TTTTT-T
1 TTTTTCT
85031450 TTTTTCT
1 TTTTTCT
85031457 TTTTTCT
1 TTTTTCT
*
85031464 TTTCT-T
1 TTTTTCT
85031470 TTTTTC-
1 TTTTTCT
*
85031476 TTTTCCT
1 TTTTTCT
85031483 TTTTTCT
1 TTTTTCT
85031490 TTTTT
1 TTTTT
85031495 TTTGAAGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 15 0.39
7 23 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:85031466 original size:13 final size:13
Alignment explanation
Indices: 85031443--85031497 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
85031433 TTGGCCTCTC
85031443 CTTTTTT-TTTTT
1 CTTTTTTCTTTTT
85031455 CTTTTTTC-TTTT
1 CTTTTTTCTTTTT
*
85031467 CTTTTTTTCTTTTC
1 C-TTTTTTCTTTTT
85031481 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
85031494 -TTTT
1 CTTTT
85031498 GAAGTGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 16 0.42
13 18 0.47
14 4 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:85031473 original size:26 final size:25
Alignment explanation
Indices: 85031444--85031497 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
85031434 TGGCCTCTCC
85031444 TTTTTTT-TTTT-CTTTTTTCTTTT
1 TTTTTTTCTTTTCCTTTTTTCTTTT
85031467 CTTTTTTTCTTTTCCTTTTTTCTTTT
1 -TTTTTTTCTTTTCCTTTTTTCTTTT
85031493 TTTTT
1 TTTTT
85031498 GAAGTGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.25
25 9 0.32
26 12 0.43
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (25 bp):
TTTTTTTCTTTTCCTTTTTTCTTTT
Found at i:85036582 original size:16 final size:15
Alignment explanation
Indices: 85036561--85036590 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
85036551 CAATTAGAGA
85036561 AAAATAAATGAATAAT
1 AAAATAAAT-AATAAT
85036577 AAAATAAATAATAA
1 AAAATAAATAATAA
85036591 CAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATAAATAATAAT
Found at i:85036748 original size:3 final size:3
Alignment explanation
Indices: 85036740--85036786 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
85036730 AAAATAGTTT
85036740 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
85036787 NCAAGCATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:85038403 original size:29 final size:29
Alignment explanation
Indices: 85038361--85038444 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
85038351 AGTGCCGTTT
**
85038361 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
*
85038390 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
85038419 TTTCCAGCACGCACACTTAGTGCCAA
1 TTTCCAGCACGCACACTTAGTGCCAA
85038445 TCCGTCACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCAAATA
Found at i:85046404 original size:29 final size:29
Alignment explanation
Indices: 85046371--85046502 Score: 210
Period size: 29 Copynumber: 4.6 Consensus size: 29
85046361 CCTCCGAACT
** * *
85046371 CGCACACCCAGTGCCATATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
85046400 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
85046429 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
85046458 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
85046487 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
85046503 ATCTCGTCAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:85046413 original size:58 final size:56
Alignment explanation
Indices: 85046351--85046475 Score: 133
Period size: 58 Copynumber: 2.2 Consensus size: 56
85046341 TCGAACACAC
* * **
85046351 AGTGCCATACCCTCCGAACTCGCACACCCAGTGCCATATTTTTCCAGCTTGCACACTT
1 AGTGCCATA-CCTCC-AACACGCACACCCAGTGCCATATATTTCCAGCACGCACACTT
** * **
85046409 AGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACACTT
1 AGTGCC--ATACCTCCAACACGCACACCCAGTGCCATATATTTCCAGCACGCACACTT
85046467 AGTGCCATA
1 AGTGCCATA
85046476 TATTTCCAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.05
58 47 0.84
59 3 0.05
60 3 0.05
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (56 bp):
AGTGCCATACCTCCAACACGCACACCCAGTGCCATATATTTCCAGCACGCACACTT
Found at i:85058277 original size:16 final size:16
Alignment explanation
Indices: 85058256--85058291 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
85058246 AATGAATCAA
85058256 GAAAAGCCAAAATGCC
1 GAAAAGCCAAAATGCC
**
85058272 GAAAAGCTGAAATGCC
1 GAAAAGCCAAAATGCC
85058288 GAAA
1 GAAA
85058292 GTTGGGCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.08
Consensus pattern (16 bp):
GAAAAGCCAAAATGCC
Found at i:85058510 original size:29 final size:27
Alignment explanation
Indices: 85058463--85058574 Score: 82
Period size: 29 Copynumber: 4.0 Consensus size: 27
85058453 TGAGTATAAT
* *
85058463 ATGATTTGGGCCTAATGGGCCATATGA
1 ATGAATTGGGCCTAGTGGGCCATATGA
* *
85058490 AGGTGAATTGGGCCTAGTGGGCCAAAAGAA
1 A--TGAATTGGGCCTAGTGGGCCATATG-A
* * *
85058520 TATGAACTAGGCC-AGATGGGCCATTTGA
1 -ATGAATTGGGCCTAG-TGGGCCATATGA
* *
85058548 ATAAGATTGGGCCTAGTGGGCTATATG
1 ATGA-ATTGGGCCTAGTGGGCCATATG
85058575 CATGTATGTA
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
27 4 0.06
28 18 0.28
29 40 0.62
30 1 0.02
31 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (27 bp):
ATGAATTGGGCCTAGTGGGCCATATGA
Found at i:85058884 original size:27 final size:25
Alignment explanation
Indices: 85058833--85058886 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
85058823 AAACCATAAT
* * *
85058833 TAAGGGAAAATTACCGAAATGCCCC
1 TAAGGGAAAATGACCAAAATACCCC
85058858 TAAGGGAGAATATGACCAAAATACCCC
1 TAAGGGA-AA-ATGACCAAAATACCCC
85058885 TA
1 TA
85058887 GGTGTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 15 0.62
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.17
Consensus pattern (25 bp):
TAAGGGAAAATGACCAAAATACCCC
Found at i:85058915 original size:15 final size:15
Alignment explanation
Indices: 85058895--85058925 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
85058885 TAGGTGTTGA
85058895 ATGTAAGTTTTATGG
1 ATGTAAGTTTTATGG
85058910 ATGTAAGTTTTATGG
1 ATGTAAGTTTTATGG
85058925 A
1 A
85058926 GGTGACATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
ATGTAAGTTTTATGG
Found at i:85066255 original size:41 final size:42
Alignment explanation
Indices: 85066166--85066321 Score: 113
Period size: 41 Copynumber: 3.6 Consensus size: 42
85066156 GTCCTGGATG
** * * *
85066166 TGGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCGGATA
1 TGGTCTTACATG-AATTCAGTATCGATGCCGATGCCCCAGACA
*
85066209 GGGTCTTACATG-ATTCAGATAT-GATGCCGATGCCCCAGACA
1 TGGTCTTACATGAATTCAG-TATCGATGCCGATGCCCCAGACA
* * * *
85066250 TGGTCTTACATGTAAATCTCA-AATCGAGGCCTATGTCCCAGACA
1 TGGTCTTACATG--AAT-TCAGTATCGATGCCGATGCCCCAGACA
* *
85066294 CGGTCTTACACGATATCTCAG-ATCGATG
1 TGGTCTTACATGA-AT-TCAGTATCGATG
85066322 ACAACGTTCC
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
41 31 0.34
42 4 0.04
43 25 0.27
44 28 0.31
45 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
TGGTCTTACATGAATTCAGTATCGATGCCGATGCCCCAGACA
Found at i:85075845 original size:20 final size:20
Alignment explanation
Indices: 85075822--85075865 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
85075812 TTATTCTGTA
85075822 ACTTACCTTTTTCAACTCAT
1 ACTTACCTTTTTCAACTCAT
85075842 ACTTACCTTTTTCAACTCAT
1 ACTTACCTTTTTCAACTCAT
85075862 ACTT
1 ACTT
85075866 TTCATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (20 bp):
ACTTACCTTTTTCAACTCAT
Found at i:85076245 original size:43 final size:43
Alignment explanation
Indices: 85076198--85076342 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
85076188 TCCTAGATAG
**
85076198 GGTCTTACATGAAATCGATTAACGATGCTGATGTCCCAAACAT
1 GGTCTTACATGAAATCGATTAACGATGCCAATGTCCCAAACAT
* * * * * *
85076241 GGTCTTACACGTAATCG-TATAATGATGCCAATATCTCGAACAT
1 GGTCTTACATGAAATCGAT-TAACGATGCCAATGTCCCAAACAT
* * * *
85076284 GGTCTTACA-GATAATCACAGT-ACAATGCCAATGTCCCAGACAT
1 GGTCTTACATGA-AATC-GATTAACGATGCCAATGTCCCAAACAT
*
85076327 GGTCTTACATGTAATC
1 GGTCTTACATGAAATC
85076343 TCATCTGGGT
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
42 2 0.03
43 75 0.95
44 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGAAATCGATTAACGATGCCAATGTCCCAAACAT
Found at i:85077489 original size:8 final size:8
Alignment explanation
Indices: 85077476--85077503 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
85077466 CTGTAAACCT
85077476 TAATAAAA
1 TAATAAAA
85077484 TAATAAAA
1 TAATAAAA
85077492 TAATAAAA
1 TAATAAAA
85077500 TAAT
1 TAAT
85077504 TATTTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TAATAAAA
Found at i:85089966 original size:47 final size:47
Alignment explanation
Indices: 85089897--85090081 Score: 325
Period size: 47 Copynumber: 3.9 Consensus size: 47
85089887 GATGAAGTGA
* *
85089897 TGTTAAATTTGTTCTTACTATTTCCGGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTATTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
*
85089944 TGTTAAATTTGTTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTATTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
*
85089991 TGTTAAATTTATTCTTACTATTTCCGGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTATTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
*
85090038 TGTTAAATTTATTATTAATATTTCCGGATAAGTTACTTAGTTAA
1 TGTTAAATTTATTCTTAATATTTCCGGATAAGTTACTTAGTTAA
85090082 AGAAAATAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.47
Consensus pattern (47 bp):
TGTTAAATTTATTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
Found at i:85090694 original size:45 final size:45
Alignment explanation
Indices: 85090625--85090827 Score: 297
Period size: 45 Copynumber: 4.6 Consensus size: 45
85090615 CGTACAGTAT
* *
85090625 TATTTGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTAATATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTAATATAC
* *
85090670 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTAATATAC
* *
85090715 TATTCGGGCCTTCGAGCCTAGCAAGCTATAATGCCGGTGATATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTAATATAC
*
85090760 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCTGGTGAA-ATGA-
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGT-AATAT-AC
85090805 TA-TCGGG-CTTCGAGCCTAGCAGG
1 TATTCGGGCCTTCGAGCCTAGCAGG
85090828 TGAAATACCG
Statistics
Matches: 149, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
43 16 0.11
44 5 0.03
45 126 0.85
46 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (45 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTAATATAC
Found at i:85097859 original size:40 final size:40
Alignment explanation
Indices: 85097778--85097954 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
85097768 CAACCAAGTA
** *
85097778 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
85097817 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
85097857 CCTTCGGGATTTAG-CCAGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
85097896 CCTTCGGGACTTAGCCCAGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
85097936 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
85097955 TTATCATCCG
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 47 0.38
40 76 0.62
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:85097909 original size:79 final size:79
Alignment explanation
Indices: 85097778--85097951 Score: 251
Period size: 79 Copynumber: 2.2 Consensus size: 79
85097768 CAACCAAGTA
* * * * * **
85097778 CCTTCGGGGTTTAGCCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGT
1 CCTTCGGGATTTAGCCAGAAATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCAGAAATAGT
*
85097843 AACTCGCACAATTG
66 AACTCGCACAAATG
85097857 CCTTCGGGATTTAGCCAGAAATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCAGAAATAG
1 CCTTCGGGATTTAGCCAGAAATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCAGAAATAG
85097921 TAACTCGCACAAATG
65 TAACTCGCACAAATG
*
85097936 CCTTCGGGACTTAGCC
1 CCTTCGGGATTTAGCC
85097952 CGGTTATCAT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.01
79 84 0.99
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CCTTCGGGATTTAGCCAGAAATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCAGAAATAGT
AACTCGCACAAATG
Found at i:85099394 original size:27 final size:27
Alignment explanation
Indices: 85098865--85099392 Score: 641
Period size: 27 Copynumber: 19.6 Consensus size: 27
85098855 AAAGTACTCC
*
85098865 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
85098892 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
** *
85098919 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
85098946 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
85098973 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
85099000 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
85099027 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* * **
85099054 TGATTTACAAAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
85099081 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
85099108 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
85099135 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
85099162 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
85099189 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * * *
85099216 TAATTTACATAATTACCATTTTACCCC
1 CGATTTACAGAATTACCGTTTTACCCT
* *
85099243 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
85099270 CGATTTAAAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
85099297 CGATTTATAGAA-TACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
85099323 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
85099350 TGATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
85099377 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
85099393 TAAAATACCC
Statistics
Matches: 436, Mismatches: 58, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
26 28 0.06
27 405 0.93
28 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:85106257 original size:24 final size:26
Alignment explanation
Indices: 85106221--85106282 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
85106211 TGGTTATGTT
* * *
85106221 AGAAAGAATAGAATA-ATG-AAAGAA
1 AGAAAAAAAAGAATAGATGAAAACAA
85106245 AGAAAAAAAAGAATATGATGAAAACAA
1 AGAAAAAAAAGAATA-GATGAAAACAA
85106272 AGGAAAAAAAA
1 A-GAAAAAAAA
85106283 ATGCGTCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 13 0.42
26 3 0.10
27 6 0.19
28 9 0.29
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.10
Consensus pattern (26 bp):
AGAAAAAAAAGAATAGATGAAAACAA
Found at i:85107434 original size:29 final size:29
Alignment explanation
Indices: 85107363--85107436 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
85107353 GTTGTGAGAT
* *
85107363 TGGCACTAAGTGTACGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATACA
*
85107392 TGGCACTAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TACA
85107421 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
85107437 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATACA
Found at i:85113739 original size:30 final size:30
Alignment explanation
Indices: 85113698--85113755 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
85113688 AAATTCACAT
* *
85113698 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
85113728 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
85113756 TGCTCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:85121867 original size:55 final size:55
Alignment explanation
Indices: 85121753--85121886 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
85121743 GTGCCCTTAG
* * * ** * *
85121753 CCCGTGTGCAACACTAACTTTAAAACATGGCCATGATGCACGCCCATGTGTCCTG
1 CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCATGTGGCCTA
* * * *
85121808 CCCGTGTACAACACCGACTTTAAAACACGGCTATGACACATGCCCGTGTGGCCTA
1 CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCATGTGGCCTA
85121863 CCCGTGTACAACACTGACTTTAAA
1 CCCGTGTACAACACTGACTTTAAA
85121887 TTTTAAGTGC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (55 bp):
CCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCATGTGGCCTA
Found at i:85122711 original size:49 final size:48
Alignment explanation
Indices: 85122637--85122855 Score: 202
Period size: 49 Copynumber: 4.6 Consensus size: 48
85122627 GATATGTTGT
* *
85122637 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTATCA-TCATTGAGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCACTCATTGAGGC
* * * * * ** *
85122686 TGATGTCATGTCCCAGATATGGTCTTATACTAGCTCT-AGTCTATACATGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCACTC-ATTGAGGC
*
85122736 TGATGCATGTCCCAGACATGTCTTACACTAGC-A-CAACTC-TT-A-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTATC-ACTCATTGAGGC
* * *
85122780 CGATGCATGTCCCAGACACGTCTTACACTAGCTATCA-TCGTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTATCACTCATTGAGGC
85122827 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
85122856 GGTACACAAG
Statistics
Matches: 142, Mismatches: 19, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
44 34 0.24
45 4 0.03
46 3 0.02
47 30 0.21
48 16 0.11
49 45 0.32
50 10 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTATCACTCATTGAGGC
Found at i:85126570 original size:18 final size:19
Alignment explanation
Indices: 85126547--85126582 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
85126537 ATTAAACATA
*
85126547 AAATAAATTAAAT-GAAAT
1 AAATAAATAAAATAGAAAT
85126565 AAATAAATAAAATAGAAA
1 AAATAAATAAAATAGAAA
85126583 AAGAACAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAATAAATAAAATAGAAAT
Found at i:85130083 original size:14 final size:14
Alignment explanation
Indices: 85130064--85130092 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
85130054 ATAGGGACAA
85130064 ATTGATTTTAGTTG
1 ATTGATTTTAGTTG
85130078 ATTGATTTTAGTTG
1 ATTGATTTTAGTTG
85130092 A
1 A
85130093 ATGAAATTCT
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:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (14 bp):
ATTGATTTTAGTTG
Found at i:85132316 original size:39 final size:39
Alignment explanation
Indices: 85132273--85132410 Score: 159
Period size: 39 Copynumber: 3.5 Consensus size: 39
85132263 AACATGTTTT
*
85132273 TGAGTATTGCAATATATGCTTGGATGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGGATGTTATGTGATTATA
* * * * *
85132312 TGAGTATTGCGATGTGTGATTGGACGTTATGTAATTATA
1 TGAGTATTGCGATATATGCTTGGATGTTATGTGATTATA
* * **
85132351 TGAATATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGGATGTTATGTGATTATA
* * *
85132390 TGTGTAATGTGATATATGCTT
1 TGAGTATTGCGATATATGCTT
85132411 AAAAGTGAAT
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.44
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGGATGTTATGTGATTATA
Found at i:85134171 original size:25 final size:25
Alignment explanation
Indices: 85134097--85134173 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
85134087 TGGTTTCTCG
* *
85134097 CACAAAGGTTTCCTAAACAATTCAC
1 CACAAAGATTTCCCAAACAATTCAC
* * * ** *
85134122 CACAAGGGCTTT-ACAAATGACTCAC
1 CACAA-AGATTTCCCAAACAATTCAC
85134147 CACAAAGATTTCCCAAACAATTCAC
1 CACAAAGATTTCCCAAACAATTCAC
85134172 CA
1 CA
85134174 TAAGGGTTTT
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
24 4 0.11
25 29 0.78
26 4 0.11
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (25 bp):
CACAAAGATTTCCCAAACAATTCAC
Found at i:85134240 original size:25 final size:25
Alignment explanation
Indices: 85134189--85134248 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
85134179 GTTTTATAGA
* * *
85134189 ACAAAGGCTTCCCAAATGACTTGCC
1 ACAAAGGCTTCCCAAATCAATTACC
85134214 ACAAAGGCTTCCCAAA-CAATTCACC
1 ACAAAGGCTTCCCAAATCAATT-ACC
*
85134239 ACAAAAGCTT
1 ACAAAGGCTT
85134249 GGTTTGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (25 bp):
ACAAAGGCTTCCCAAATCAATTACC
Found at i:85134806 original size:4 final size:4
Alignment explanation
Indices: 85134797--85134843 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
85134787 CACAGAGAGC
*
85134797 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
85134844 ACTTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:85136383 original size:19 final size:19
Alignment explanation
Indices: 85136359--85136426 Score: 100
Period size: 19 Copynumber: 3.4 Consensus size: 19
85136349 ATTTAGCTAT
85136359 CAAGCACACATCATTTGTG
1 CAAGCACACATCATTTGTG
85136378 CAAGCACACATCATTTGTG
1 CAAGCACACATCATTTGTG
85136397 CAAGCACCAAAACATCATTTGTG
1 CAAGCA-C---ACATCATTTGTG
85136420 CAAGCAC
1 CAAGCAC
85136427 CAAAACATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
19 25 0.56
20 1 0.02
22 1 0.02
23 18 0.40
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (19 bp):
CAAGCACACATCATTTGTG
Found at i:85136415 original size:23 final size:23
Alignment explanation
Indices: 85136366--85136434 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
85136356 TATCAAGCAC
85136366 ACATCATTTGTGCAAGCA-C---
1 ACATCATTTGTGCAAGCACCAAA
85136385 ACATCATTTGTGCAAGCACCAAA
1 ACATCATTTGTGCAAGCACCAAA
85136408 ACATCATTTGTGCAAGCACCAAA
1 ACATCATTTGTGCAAGCACCAAA
85136431 ACAT
1 ACAT
85136435 ACATACATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.39
20 1 0.02
23 27 0.59
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
ACATCATTTGTGCAAGCACCAAA
Found at i:85140671 original size:14 final size:14
Alignment explanation
Indices: 85140648--85140684 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
85140638 TATGTAATTT
*
85140648 TATTTTAATTATTA
1 TATTTAAATTATTA
*
85140662 TATTTAAATTATTT
1 TATTTAAATTATTA
85140676 TATTTAAAT
1 TATTTAAAT
85140685 ATATAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTAAATTATTA
Found at i:85144282 original size:13 final size:13
Alignment explanation
Indices: 85144264--85144294 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
85144254 TGCAGGGGAC
85144264 ACACGGCCTAACT
1 ACACGGCCTAACT
85144277 ACACGGCCTAACT
1 ACACGGCCTAACT
85144290 ACACG
1 ACACG
85144295 CCCATGTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.39, G:0.16, T:0.13
Consensus pattern (13 bp):
ACACGGCCTAACT
Found at i:85146091 original size:44 final size:46
Alignment explanation
Indices: 85145841--85146152 Score: 187
Period size: 47 Copynumber: 6.7 Consensus size: 46
85145831 TGATTTGTGC
* * ** *
85145841 GCCAGTGTAAGACATGTCTAGGACATGCTTTGGCCACATTATGAG--A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCA-TA-GAGATA
* *
85145887 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACATC-CAGACGA-A
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CCTCATAGA-GATA
* * * * *
85145934 GGCTAGTGTAAGTCATATCTGGGACATGCTTCAACCAT-ATTATGAG-T-
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCAGCC-TCA-TA-GAGATA
*
85145981 GCCAGAGTAAGACATGTCTGGGACATGCATCAGCCTCGATAGAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTC-ATAGAGATA
* * * * *
85146028 GCCAGTGTAAGACGTGTCTGGGACACGCATC-GGCT-A-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCATAGAGAT-A
* * * *
85146072 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CATAGA-GATA
* *
85146120 GCCAGTATAAGACCATGTCTGGGATATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
85146153 GATAATTTAT
Statistics
Matches: 205, Mismatches: 37, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
43 5 0.02
44 29 0.14
45 8 0.04
46 54 0.26
47 59 0.29
48 29 0.14
49 16 0.08
50 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCATAGAGATA
Found at i:85148669 original size:27 final size:25
Alignment explanation
Indices: 85148633--85148705 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
85148623 CTCGCACACC
85148633 CAGTGCCGTATTTTTCCAGCTTGCACA
1 CAGTGCCGTATTTTTCCAGC--GCACA
85148660 CAGTGCCGTA-TTTTCCAGCGCACA
1 CAGTGCCGTATTTTTCCAGCGCACA
* *
85148684 CTTAGTGCCATATATTTCCAGC
1 C--AGTGCCGTATTTTTCCAGC
85148706 ACGCACACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.15
26 17 0.41
27 18 0.44
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.32
Consensus pattern (25 bp):
CAGTGCCGTATTTTTCCAGCGCACA
Found at i:85148714 original size:29 final size:27
Alignment explanation
Indices: 85148567--85148722 Score: 95
Period size: 29 Copynumber: 5.6 Consensus size: 27
85148557 TACTCGATTT
* *
85148567 CGCACACTTAGTGCCACGTAATTT-AAGCC
1 CGCACACTTAGTGCCA--TATTTTCCAG-C
** ***
85148596 CGCACACACAGTGCCATACCCTCCGAGC
1 CGCACACTTAGTGCCATATTTTCC-AGC
** *
85148624 TCGCACACCCAGTGCCGTATTTTTCCAGC
1 -CGCACACTTAGTGCCATA-TTTTCCAGC
* *
85148653 TTGCACAC--AGTGCCGTATTTTCCAG-
1 -CGCACACTTAGTGCCATATTTTCCAGC
85148678 CGCACACTTAGTGCCATATATTTCCAGC
1 CGCACACTTAGTGCCATAT-TTTCCAGC
85148706 ACGCACACTTAGTGCCA
1 -CGCACACTTAGTGCCA
85148723 ATCTCGTCAC
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
24 6 0.06
26 17 0.16
27 19 0.18
28 1 0.01
29 58 0.56
30 3 0.03
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (27 bp):
CGCACACTTAGTGCCATATTTTCCAGC
Found at i:85156588 original size:29 final size:29
Alignment explanation
Indices: 85156560--85156660 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
85156550 CCTCCGAGCT
** * *
85156560 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATTTTTCCAGCA
*
85156589 TGCACACTTAGTG-CATA-TTTTCCAGCA
1 CGCACACTTAGTGCCATATTTTTCCAGCA
*
85156616 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATTTTTCCAGCA
85156645 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
85156661 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
27 21 0.33
28 7 0.11
29 35 0.56
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATTTTTCCAGCA
Found at i:85164532 original size:29 final size:28
Alignment explanation
Indices: 85164500--85164567 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
85164490 ATACCCTCCG
* *
85164500 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTG-CATATATTTCC
* **
85164529 AGCTTGCACACTTAGTGCATATATTTCC
1 AGCTCGCACACCCAGTGCATATATTTCC
*
85164557 AGCACGCACAC
1 AGCTCGCACAC
85164568 TTAGTGCCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (28 bp):
AGCTCGCACACCCAGTGCATATATTTCC
Found at i:85166948 original size:16 final size:17
Alignment explanation
Indices: 85166922--85166954 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
85166912 GTTTTCATAA
85166922 ATCATTTTTCTTGTATT
1 ATCATTTTTCTTGTATT
85166939 ATCA-TTTTCTTGTATT
1 ATCATTTTTCTTGTATT
85166955 TCAAACGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (17 bp):
ATCATTTTTCTTGTATT
Found at i:85173241 original size:15 final size:16
Alignment explanation
Indices: 85173207--85173242 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
85173197 TGTTTTCTGA
85173207 TTCATTTAATTAAATT
1 TTCATTTAATTAAATT
*
85173223 TTCATTTAA-TAACTT
1 TTCATTTAATTAAATT
85173238 TTCAT
1 TTCAT
85173243 CTTTCCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCATTTAATTAAATT
Found at i:85180977 original size:24 final size:24
Alignment explanation
Indices: 85180950--85180997 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
85180940 ATTCAGATTG
85180950 ATCCAAGATTTACAACAGAGCCTA
1 ATCCAAGATTTACAACAGAGCCTA
85180974 ATCCAAGATTTACAACAGAGCCTA
1 ATCCAAGATTTACAACAGAGCCTA
85180998 CTCCTCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCCAAGATTTACAACAGAGCCTA
Found at i:85182616 original size:28 final size:28
Alignment explanation
Indices: 85182555--85182652 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
85182545 TCACAAATTG
** * *
85182555 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
85182584 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
85182612 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
85182640 GCACTAAGTGTGC
1 GCACTAAGTGTGC
85182653 GGGCTTATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:85190287 original size:28 final size:28
Alignment explanation
Indices: 85190226--85190323 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
85190216 TCACAAATTG
** * *
85190226 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
85190255 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
85190283 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
85190311 GCACTAAGTGTGC
1 GCACTAAGTGTGC
85190324 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:85192214 original size:21 final size:22
Alignment explanation
Indices: 85192185--85192225 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
85192175 TACAAGAGGC
**
85192185 GTCTCGCCTTTCCTCAGTCTCA
1 GTCTCGCCTCCCCTCAGTCTCA
85192207 GTCT-GCCTCCCCTCAGTCT
1 GTCTCGCCTCCCCTCAGTCT
85192226 GACCAACACC
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:0.07, C:0.44, G:0.15, T:0.34
Consensus pattern (22 bp):
GTCTCGCCTCCCCTCAGTCTCA
Found at i:85196686 original size:48 final size:47
Alignment explanation
Indices: 85196630--85196744 Score: 126
Period size: 46 Copynumber: 2.4 Consensus size: 47
85196620 CACAGTAAGT
* *
85196630 TCTTACACTAGCTTGCATATCTCGAGGCCGATGCATGTCCCAGACATG
1 TCTTACACTAGC-TGCATATCTCAAGGCCGATGCATGTCCCAGACATA
* * * *
85196678 TCTTACACTGGCT-C-TCATCTCAATGTCGATGCATGTCCTAGACATA
1 TCTTACACTAGCTGCAT-ATCTCAAGGCCGATGCATGTCCCAGACATA
*
85196724 TCTTACACTAGCACGCATATC
1 TCTTACACTAGC-TGCATATC
85196745 ACCCAAATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
45 1 0.02
46 37 0.67
47 1 0.02
48 15 0.27
49 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (47 bp):
TCTTACACTAGCTGCATATCTCAAGGCCGATGCATGTCCCAGACATA
Found at i:85197422 original size:20 final size:21
Alignment explanation
Indices: 85197397--85197436 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
85197387 ACAATTTCAA
*
85197397 TTATTTCACAGA-TTTACAAC
1 TTATTTCACAAACTTTACAAC
*
85197417 TTATTTTACAAACTTTACAA
1 TTATTTCACAAACTTTACAA
85197437 AATAGCCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATTTCACAAACTTTACAAC
Found at i:85199351 original size:15 final size:14
Alignment explanation
Indices: 85199318--85199387 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 14
85199308 AGAGATGGTA
* *
85199318 AGAAAACCAAGAAAA
1 AGAAATCCAA-AAAG
85199333 AGAAATCCAAAACAG
1 AGAAATCCAAAA-AG
* * *
85199348 AGAAATCTAGAATG
1 AGAAATCCAAAAAG
*
85199362 AAGAGATCCAAAATAG
1 -AGAAATCCAAAA-AG
85199378 AGAAATCCAA
1 AGAAATCCAA
85199388 GATACGATAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 3 0.07
15 38 0.90
16 1 0.02
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (14 bp):
AGAAATCCAAAAAG
Found at i:85204542 original size:17 final size:17
Alignment explanation
Indices: 85204520--85204561 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
85204510 CTATTCAAGT
*
85204520 GCGGCCCAATCAATGCA
1 GCGGCCCAATAAATGCA
*
85204537 GCGGCCCAGTAAATGCA
1 GCGGCCCAATAAATGCA
*
85204554 GTGGCCCA
1 GCGGCCCA
85204562 CACCTAGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.29, T:0.12
Consensus pattern (17 bp):
GCGGCCCAATAAATGCA
Found at i:85209490 original size:19 final size:19
Alignment explanation
Indices: 85209456--85209494 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
85209446 GATTTCGTAC
*
85209456 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCAGTTTCTC-GTT
85209476 TTTGGCCC-GTTTCTCGTT
1 TTTGGCCCAGTTTCTCGTT
85209494 T
1 T
85209495 CTTTCGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.03, C:0.26, G:0.18, T:0.54
Consensus pattern (19 bp):
TTTGGCCCAGTTTCTCGTT
Found at i:85214237 original size:49 final size:47
Alignment explanation
Indices: 85214179--85214353 Score: 174
Period size: 49 Copynumber: 3.6 Consensus size: 47
85214169 TGTCTAAGTC
85214179 GATGCCATGTCCCAGACAGGTCTTACACTTACTTTCATATATCGAGGCT
1 GATGCCATGTCCCAGACAGGTCTTACACTTA-TTTCATATATCGAGG-T
** * * * *
85214228 GATGCCATGTTGCAGATAGGTCTTACACTGGATCTCATCTATCG-GTGT
1 GATGCCATGTCCCAGACAGGTCTTACACT-TATTTCATATATCGAG-GT
* * *
85214276 CGATGCCATGTCCCAGACAGGTCTTACACTAGATTGCATATTTCGAGGTT
1 -GATGCCATGTCCCAGACAGGTCTTACACT-TATTTCATATATCGAGG-T
* *
85214326 GATG-CATGTCTCAGACATGTCTTACACT
1 GATGCCATGTCCCAGACAGGTCTTACACT
85214354 AGCACACATA
Statistics
Matches: 105, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
48 24 0.23
49 78 0.74
50 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (47 bp):
GATGCCATGTCCCAGACAGGTCTTACACTTATTTCATATATCGAGGT
Found at i:85214299 original size:98 final size:97
Alignment explanation
Indices: 85214176--85214353 Score: 261
Period size: 98 Copynumber: 1.8 Consensus size: 97
85214166 ACATGTCTAA
* *
85214176 GTCGATGCCATGTCCCAGACAGGTCTTACACTTA-CTTTCATATATCGAGGCTGATGCCATGT-T
1 GTCGATGCCATGTCCCAGACAGGTCTTACAC-TAGATTGCATATATCGAGGCTGATG-CATGTCT
*
85214239 GCAGATAGGTCTTACACTGGATCTCATCTATCGGT
64 -CAGACAGGTCTTACACTGGATCTCATCTATCGGT
* *
85214274 GTCGATGCCATGTCCCAGACAGGTCTTACACTAGATTGCATATTTCGAGGTTGATGCATGTCTCA
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTAGATTGCATATATCGAGGCTGATGCATGTCTCA
*
85214339 GACATGTCTTACACT
66 GACAGGTCTTACACT
85214354 AGCACACATA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
97 22 0.31
98 50 0.69
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (97 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTAGATTGCATATATCGAGGCTGATGCATGTCTCA
GACAGGTCTTACACTGGATCTCATCTATCGGT
Found at i:85217884 original size:44 final size:42
Alignment explanation
Indices: 85217818--85217958 Score: 146
Period size: 44 Copynumber: 3.3 Consensus size: 42
85217808 TATGTGTTTT
* * *
85217818 CGTGTAAGATCACGTCTGGGACGTTGGCATCG-ACTTATGACTTA
1 CGTGTAAGACCACATCTAGGACGTTGGCATCGTA-TT-TGA-TTA
*
85217862 CGTGTAAGACCACATCTAGGACGTTGGCATCGTATTTGATTT
1 CGTGTAAGACCACATCTAGGACGTTGGCATCGTATTTGATTA
85217904 CGTGTAAGACC-CTATCT-GAGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-ATCTAG-GAC-GTTGGCATCG-TATTTGATTA
*
85217947 CATGTAAGACCA
1 CGTGTAAGACCA
85217959 TGTATGGGAC
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
41 2 0.02
42 28 0.33
43 23 0.27
44 31 0.36
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCACATCTAGGACGTTGGCATCGTATTTGATTA
Found at i:85217932 original size:42 final size:43
Alignment explanation
Indices: 85217818--85217958 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 43
85217808 TATGTGTTTT
* * * *
85217818 CGTGTAAGATCACGTCTGGGACGTTGGCATCGACT-TATGACTTA
1 CGTGTAAGACCACATCTAGGACGTTGGCATCGA-TATTTGA-TTA
*
85217862 CGTGTAAGACCACATCTAGGACGTTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACATCTAGGACGTTGGCATCGATATTTGATTA
85217904 CGTGTAAGACC-CTATCT-GAGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-ATCTAG-GAC-GTTGGCATCGATATTTGATTA
*
85217947 CATGTAAGACCA
1 CGTGTAAGACCA
85217959 TGTATGGGAC
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.35
43 24 0.29
44 29 0.35
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACATCTAGGACGTTGGCATCGATATTTGATTA
Found at i:85217975 original size:43 final size:43
Alignment explanation
Indices: 85217818--85217976 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
85217808 TATGTGTTTT
* * * *
85217818 CGTGTAAGATCACGTCTGGGACGTTGGCATCGACT-TATGACTTA
1 CGTGTAAGACCACATCTGGGACATTGGCATCGA-TATTTGA-TTA
* * *
85217862 CGTGTAAGACCACATCTAGGACGTTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
* *
85217904 CGTGTAAGACC-CTATCTGAGACAGTGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-ATCTGGGACATTGGCATCGATATTTGATTA
* ** *
85217947 CATGTAAGACCATGTATGGGACATTGGCAT
1 CGTGTAAGACCACATCTGGGACATTGGCAT
85217977 GGTACGAGCT
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.31
43 36 0.38
44 29 0.31
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
Found at i:85223812 original size:19 final size:18
Alignment explanation
Indices: 85223790--85223841 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
85223780 ATAAAAAATA
*
85223790 TTTTTATATTGTTTATACTT
1 TTTTTATATT-TTTA-ACAT
*
85223810 TTTTTAATAATTTTAACAT
1 TTTTT-ATATTTTTAACAT
85223829 TTTTTATATTTTT
1 TTTTTATATTTTT
85223842 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 9 0.32
21 4 0.14
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTATATTTTTAACAT
Found at i:85223842 original size:19 final size:19
Alignment explanation
Indices: 85223790--85223850 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
85223780 ATAAAAAATA
* *
85223790 TTTTTATATTGTTTATACTT
1 TTTTTATATTTTTTA-ACAT
*
85223810 TTTTTA-ATAATTTTAACAT
1 TTTTTATAT-TTTTTAACAT
*
85223829 TTTTTATATTTTTTAAAAT
1 TTTTTATATTTTTTAACAT
85223848 TTT
1 TTT
85223851 ATAATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTATATTTTTTAACAT
Found at i:85224648 original size:3 final size:3
Alignment explanation
Indices: 85224640--85224664 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
85224630 TCTTAAATCG
85224640 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
85224665 TATGTTTAAG
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:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:85225341 original size:23 final size:23
Alignment explanation
Indices: 85225315--85225359 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
85225305 AGTGATTTGA
*
85225315 TAAAAAA-AGATAAATTTAAATAT
1 TAAAAAACAGA-AAAATTAAATAT
85225338 TAAAAAACAGAAAAATTAAATA
1 TAAAAAACAGAAAAATTAAATA
85225360 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
TAAAAAACAGAAAAATTAAATAT
Found at i:85240117 original size:26 final size:26
Alignment explanation
Indices: 85240080--85240147 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
85240070 CCATATTGGG
85240080 AAGCTC-CAAAGAGCCACTAATCAGA
1 AAGCTCACAAAGAGCCACTAATCAGA
** * *
85240105 AAGCTCACAAAGAGCCTTTAATCGGG
1 AAGCTCACAAAGAGCCACTAATCAGA
* *
85240131 AAGTTCACGAAGAGCCA
1 AAGCTCACAAAGAGCCA
85240148 TATATAGGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (26 bp):
AAGCTCACAAAGAGCCACTAATCAGA
Found at i:85240447 original size:2 final size:2
Alignment explanation
Indices: 85240440--85240482 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
85240430 TACACAATTC
85240440 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
85240482 A
1 A
85240483 CAACATTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85242488 original size:11 final size:11
Alignment explanation
Indices: 85242472--85242499 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
85242462 CCACCAAAAC
85242472 AAATTACATAT
1 AAATTACATAT
85242483 AAATTACATAT
1 AAATTACATAT
85242494 AAATTA
1 AAATTA
85242500 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATTACATAT
Found at i:85242768 original size:16 final size:16
Alignment explanation
Indices: 85242742--85242790 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
85242732 GTAAAGTGGA
85242742 AAAAAACTTGAAAAGAT
1 AAAAAA-TTGAAAAGAT
* *
85242759 AAAAAATTGAAAGGGT
1 AAAAAATTGAAAAGAT
* *
85242775 AGAAAAGTGAAAAGAT
1 AAAAAATTGAAAAGAT
85242791 GGAAAATAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (16 bp):
AAAAAATTGAAAAGAT
Found at i:85244226 original size:33 final size:34
Alignment explanation
Indices: 85244165--85244232 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
85244155 AATATATTAT
*
85244165 TCTTATGTTCTTTGCATTATTATTATTTTATAACAG
1 TCTTATGTTCTTTGC--TATTATCATTTTATAACAG
*
85244201 TCTTGTGTTCTTTGC-ATTATCATTTTATAACA
1 TCTTATGTTCTTTGCTATTATCATTTTATAACA
85244233 CATTATCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 16 0.53
36 14 0.47
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (34 bp):
TCTTATGTTCTTTGCTATTATCATTTTATAACAG
Found at i:85253629 original size:169 final size:169
Alignment explanation
Indices: 85253343--85253679 Score: 629
Period size: 169 Copynumber: 2.0 Consensus size: 169
85253333 TAATATATTC
* *
85253343 TTAGTTTGTGTCAAAATTTTGTTGGAATCCAAGCATTAAATTTAATTGTTTGGTTGAAGAATCAT
1 TTAGTTGGTGTCAAAAATTTGTTGGAATCCAAGCATTAAATTTAATTGTTTGGTTGAAGAATCAT
85253408 TAGAATCAATAGCTATTTGATATTTGCTTGGGGATGATCTATTTCACTTCATTACAAAGGATGCT
66 TAGAATCAATAGCTATTTGATATTTGCTTGGGGATGATCTATTTCACTTCATTACAAAGGATGCT
*
85253473 TATAATCCTTACTTCCCATCTATGGTAACCTAAGTCAAA
131 TATAATCCTTACTTCCCATCCATGGTAACCTAAGTCAAA
* *
85253512 TTAGTTGGTGTCAAAAATTTGTTGGAATCCAAGCATTAAATTTAGTTGTTTGGTTTAAGAATCAT
1 TTAGTTGGTGTCAAAAATTTGTTGGAATCCAAGCATTAAATTTAATTGTTTGGTTGAAGAATCAT
85253577 TAGAATCAATAGCTATTTGATATTTGCTTGGGGATGATCTATTTCACTTCATTACAAAGGATGCT
66 TAGAATCAATAGCTATTTGATATTTGCTTGGGGATGATCTATTTCACTTCATTACAAAGGATGCT
85253642 TATAATCCTTACTTCCCATCCATGGTAACCTAAGTCAA
131 TATAATCCTTACTTCCCATCCATGGTAACCTAAGTCAA
85253680 TTTAATCAAC
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
169 163 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (169 bp):
TTAGTTGGTGTCAAAAATTTGTTGGAATCCAAGCATTAAATTTAATTGTTTGGTTGAAGAATCAT
TAGAATCAATAGCTATTTGATATTTGCTTGGGGATGATCTATTTCACTTCATTACAAAGGATGCT
TATAATCCTTACTTCCCATCCATGGTAACCTAAGTCAAA
Found at i:85255255 original size:27 final size:27
Alignment explanation
Indices: 85255217--85255428 Score: 186
Period size: 27 Copynumber: 7.9 Consensus size: 27
85255207 GCGAGGGTGC
*
85255217 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGACAG-AGCCACCAGATA
85255244 CAGATATTGTGACAGAGCCACCAGA-A
1 CAGATATTGTGACAGAGCCACCAGATA
*
85255270 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
* * *
85255297 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGACAGAGCCACCAGATA
* *
85255324 CAGTTATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
* * *
85255351 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGACAGAGCCACCAGATA
* *
85255378 CAGTTATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
* *
85255405 CAGATAATTGTGGCATAGCCACCA
1 CAGAT-ATTGTGACAGAGCCACCA
85255429 AGACGCTTCC
Statistics
Matches: 158, Mismatches: 15, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
26 12 0.08
27 139 0.88
28 7 0.04
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGACAGAGCCACCAGATA
Found at i:85255307 original size:54 final size:54
Alignment explanation
Indices: 85255235--85255428 Score: 336
Period size: 54 Copynumber: 3.6 Consensus size: 54
85255225 GTGACGAAGT
* * * *
85255235 CACCAGATACAGAT-ATTGTGACAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
85255289 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
85255343 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
85255397 CACCAGATCAGATAATTGTGGCATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
85255429 AGACGCTTCC
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
53 5 0.04
54 130 0.96
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGTTATATGTGGCAGAGC
Found at i:85257050 original size:26 final size:26
Alignment explanation
Indices: 85257019--85257126 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
85257009 TGAAATGCCC
*
85257019 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
85257045 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
85257071 ATCATGGAAAATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
85257097 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
85257123 ATCA
1 ATCA
85257127 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:85259663 original size:42 final size:43
Alignment explanation
Indices: 85259565--85259685 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 43
85259555 AACAAGTACA
* * *
85259565 ATGTCGACGTCCCGGAC-GTGGTCTTACATGTAATTCAATATCG
1 ATGTCGATGTCCCAGACAG-GGTCTTACATGTAAATCAATATCG
* **
85259608 ATGCCTCTGTCCCAGACAGGGTCTTACATG-AAATCAGATA-CG
1 ATGTCGATGTCCCAGACAGGGTCTTACATGTAAATCA-ATATCG
* * *
85259650 ATGTCGATGTCCCAGACATGGTCTTATACGTAAATC
1 ATGTCGATGTCCCAGACAGGGTCTTACATGTAAATC
85259686 TCAATCGAGG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 31 0.49
43 31 0.49
44 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
ATGTCGATGTCCCAGACAGGGTCTTACATGTAAATCAATATCG
Found at i:85259809 original size:85 final size:85
Alignment explanation
Indices: 85259604--85259812 Score: 267
Period size: 85 Copynumber: 2.5 Consensus size: 85
85259594 GTAATTCAAT
* * * * * * * *
85259604 ATCGATGCCTCTGTCCCAGACAGGGTCTTACATGAAATCAGATACGATGTCGATGTCCCAGACAT
1 ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATCAGATACGATGTCAATATCCCAAACAT
*
85259669 GGTCTTATACGTAAATCTCA
66 GGTCATATACGTAAATCTCA
* * ** *
85259689 ATCGAGGCTTGTGTTCCAGACACAATCTTACACGATATCAGATATGATAG-CAATATCCCAAACA
1 ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATCAGATACGAT-GTCAATATCCCAAACA
85259753 TGGTCATATACGTAAATCTCA
65 TGGTCATATACGTAAATCTCA
*
85259774 ATCGAGGCCTGTGTCCCAAACACGGTCTTACACGATATC
1 ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATC
85259813 TCAGACAGAT
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 103 0.99
86 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (85 bp):
ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATCAGATACGATGTCAATATCCCAAACAT
GGTCATATACGTAAATCTCA
Found at i:85273157 original size:17 final size:18
Alignment explanation
Indices: 85273137--85273170 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
85273127 TTGTTTGCTA
85273137 TTTGCTGCAATT-TGTTG
1 TTTGCTGCAATTCTGTTG
85273154 TTTGCTGCAATTCTGTT
1 TTTGCTGCAATTCTGTT
85273171 AATAATCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.12, C:0.15, G:0.21, T:0.53
Consensus pattern (18 bp):
TTTGCTGCAATTCTGTTG
Found at i:85275538 original size:13 final size:13
Alignment explanation
Indices: 85275520--85275545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
85275510 AATTCAAATT
85275520 TATTATTAGGATA
1 TATTATTAGGATA
85275533 TATTATTAGGATA
1 TATTATTAGGATA
85275546 GGATAATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TATTATTAGGATA
Found at i:85276617 original size:46 final size:46
Alignment explanation
Indices: 85276550--85276640 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
85276540 TCAGTTTTAG
85276550 CTTTTGGGGCTCTTTGGATTAAAAAATTAAAAACTAGGAAGGAAAA
1 CTTTTGGGGCTCTTTGGATTAAAAAATTAAAAACTAGGAAGGAAAA
85276596 CTTTTGGGGCTCTTTGGATTAAAAAATTAAAAACTAGGAAGGAAA
1 CTTTTGGGGCTCTTTGGATTAAAAAATTAAAAACTAGGAAGGAAA
85276641 TTGCTTCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (46 bp):
CTTTTGGGGCTCTTTGGATTAAAAAATTAAAAACTAGGAAGGAAAA
Found at i:85281700 original size:21 final size:21
Alignment explanation
Indices: 85281625--85281690 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
85281615 GTCTTGAATT
85281625 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTA
* *
85281646 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
85281671 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
85281691 TGGTTGGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 4 0.11
24 2 0.05
25 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:85283022 original size:28 final size:28
Alignment explanation
Indices: 85282952--85283023 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
85282942 AAATCATTGC
*
85282952 AATATATGTAAAAACAATTTAAAGTATA
1 AATATATGTAAAAACAATTTAAAATATA
*
85282980 AATTTAT-TAAAAAACAATTTAAAATATA
1 AATATATGT-AAAAACAATTTAAAATATA
85283008 AATATATGTAAAAACA
1 AATATATGTAAAAACA
85283024 GCTTTTCCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 1 0.03
28 37 0.95
29 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (28 bp):
AATATATGTAAAAACAATTTAAAATATA
Found at i:85283142 original size:14 final size:15
Alignment explanation
Indices: 85283123--85283160 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
85283113 TCCAGAAAGT
*
85283123 AAATCATTTTTCA-A
1 AAATCATTTTCCAGA
85283137 AAATCATTTTCCAGA
1 AAATCATTTTCCAGA
85283152 AAAT-ATTTT
1 AAATCATTTT
85283161 ACTGGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (15 bp):
AAATCATTTTCCAGA
Found at i:85289506 original size:7 final size:7
Alignment explanation
Indices: 85289494--85289520 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
85289484 TATGTGAGGC
85289494 AAAAAAG
1 AAAAAAG
85289501 AAAAAAG
1 AAAAAAG
85289508 AAAAAAG
1 AAAAAAG
85289515 AAAAAA
1 AAAAAA
85289521 AAAGAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:85289673 original size:25 final size:26
Alignment explanation
Indices: 85289624--85289674 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
85289614 AATGGCTTAT
*
85289624 AATCCCCACTCCACATTACATGACAA
1 AATCCCAACTCCACATTACATGACAA
85289650 AATCCCAACTCCCACA-TACA-GACAA
1 AATCCCAACT-CCACATTACATGACAA
85289675 TCCCATGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 13 0.57
27 5 0.22
ACGTcount: A:0.41, C:0.39, G:0.04, T:0.16
Consensus pattern (26 bp):
AATCCCAACTCCACATTACATGACAA
Found at i:85292046 original size:26 final size:26
Alignment explanation
Indices: 85292009--85292059 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
85291999 TTAATTTTTT
*
85292009 ATTTTATATTTTTTAATAGTGATTTG
1 ATTTTATATTTTTTAATAGTAATTTG
*
85292035 ATTTT-TAGTTTTTTTATAGTAATTT
1 ATTTTATA-TTTTTTAATAGTAATTT
85292060 TGAATTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTTATATTTTTTAATAGTAATTTG
Found at i:85292061 original size:27 final size:26
Alignment explanation
Indices: 85292004--85292067 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
85291994 GTTTGTTAAT
* *
85292004 TTTTTATTTTATATTTTTTAATAGTGA
1 TTTTGATTTT-TATTTTTTAATAGTAA
*
85292031 -TTTGATTTTTAGTTTTTTTATAGTAA
1 TTTTGATTTTTA-TTTTTTAATAGTAA
*
85292057 TTTTGAATTTT
1 TTTTGATTTTT
85292068 GGGTTTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 20 0.65
27 9 0.29
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (26 bp):
TTTTGATTTTTATTTTTTAATAGTAA
Found at i:85292074 original size:27 final size:27
Alignment explanation
Indices: 85292017--85292075 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
85292007 TTATTTTATA
* *
85292017 TTTTTTAATAGTGATTTGATTTTTA-G
1 TTTTTTAATAGTAATTTGAATTTTAGG
* *
85292043 TTTTTTTATAGTAATTTTGAATTTTGGG
1 TTTTTTAATAGTAA-TTTGAATTTTAGG
85292071 TTTTT
1 TTTTT
85292076 AGATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.44
27 9 0.33
28 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.64
Consensus pattern (27 bp):
TTTTTTAATAGTAATTTGAATTTTAGG
Found at i:85292566 original size:2 final size:2
Alignment explanation
Indices: 85292559--85292600 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
85292549 TTCCCCCAAT
85292559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85292601 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85292605 original size:2 final size:2
Alignment explanation
Indices: 85292600--85292636 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
85292590 ATATATATAT
*
85292600 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
85292637 AAAGTGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:85292810 original size:37 final size:36
Alignment explanation
Indices: 85292769--85292839 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
85292759 TTAAATTATA
*
85292769 TTTAAATA-GTTTAATATAATTATATATAAAATATGTT
1 TTTAAATACGTTTAA-ATAATTA-ATAAAAAATATGTT
*
85292806 TTTAAATATCTTTTAAATAATTAATAAAAAATAT
1 TTTAAATA-CGTTTAAATAATTAATAAAAAATAT
85292840 TTATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
37 18 0.60
38 7 0.23
39 5 0.17
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTAAATACGTTTAAATAATTAATAAAAAATATGTT
Found at i:85292873 original size:26 final size:26
Alignment explanation
Indices: 85292820--85292891 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
85292810 AATATCTTTT
*
85292820 AAAT-AAT-TAATAAAAAATATTTATA
1 AAATAAATATAATGAAAAAT-TTTATA
*
85292845 AAATTAATAGTACAT-AAAAATTTTA-A
1 AAATAAATA-TA-ATGAAAAATTTTATA
85292871 AAATAAATATAATGAAAAATT
1 AAATAAATATAATGAAAAATT
85292892 ATATTTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
24 2 0.05
25 13 0.32
26 12 0.29
27 4 0.10
28 8 0.20
29 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (26 bp):
AAATAAATATAATGAAAAATTTTATA
Found at i:85317308 original size:40 final size:40
Alignment explanation
Indices: 85317146--85317347 Score: 148
Period size: 40 Copynumber: 5.1 Consensus size: 40
85317136 CGAATGATGT
*
85317146 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTCG-CTATAA
* * * * ***
85317186 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTCGCTATAA
**
85317225 TCCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTA-AA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
* *
85317263 CCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
** * * * *
85317304 CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
85317344 CCGG
1 CCGG
85317348 TTAAATTCCG
Statistics
Matches: 129, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
38 24 0.19
39 19 0.15
40 77 0.60
41 9 0.07
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
Found at i:85317310 original size:78 final size:79
Alignment explanation
Indices: 85317145--85317296 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 79
85317135 TCGAATGATG
* * *
85317145 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
* *
85317210 GTGCGAGTTAATAAA
65 GTGCAAGTCAATAAA
* **
85317225 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATTC
1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATTC
85317288 GTGCAAGTC
65 GTGCAAGTC
85317297 GCTATAACCG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.02
78 35 0.56
79 17 0.27
80 10 0.16
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG
TGCAAGTCAATAAA
Found at i:85319133 original size:49 final size:50
Alignment explanation
Indices: 85319066--85319312 Score: 266
Period size: 49 Copynumber: 5.0 Consensus size: 50
85319056 AGCTATTGTA
* *
85319066 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * * *
85319116 -GGTCGCATGTGTAGTACTAAGTTCAGGCTACTATGCGTACCTGATAGCTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG-TT
* * * * * *
85319166 CGATCACGTGTGTAGTACTGAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * *
85319216 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGCACC-GAATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAGTT
* * **
85319266 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATAG
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
85319313 CTTCGGCTAC
Statistics
Matches: 160, Mismatches: 33, Indels: 9
0.79 0.16 0.04
Matches are distributed among these distances:
49 78 0.49
50 45 0.28
51 37 0.23
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
Found at i:85325729 original size:46 final size:46
Alignment explanation
Indices: 85325662--85326027 Score: 464
Period size: 46 Copynumber: 8.0 Consensus size: 46
85325652 ACTTTCTGAA
** * * *
85325662 ATGAAATGTGTAAGACCATGGTTGAAAGATAACATGGAAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
85325708 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
85325754 ATGAAATGTGTAAGACCATGGTTGAAAGATAACATGGAAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
85325800 ATGAAAAGAATAAGACCATAGTTAAAAGATACCATGGCAACGTTAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
85325846 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
85325892 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
85325938 AGGAAATGAATAAGACCATGGTTGAAAGATACCACGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
85325984 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
85326028 TCGAAGATAA
Statistics
Matches: 292, Mismatches: 27, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 291 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:85331808 original size:2 final size:2
Alignment explanation
Indices: 85331798--85331838 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
85331788 TTTTGGTTTG
85331798 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85331839 CGTCAATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85339060 original size:93 final size:93
Alignment explanation
Indices: 85338948--85339119 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
85338938 GCCCATAAGT
* *
85338948 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
85339013 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
85339041 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
85339106 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
85339120 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:85339115 original size:46 final size:46
Alignment explanation
Indices: 85338940--85339115 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
85338930 TGTAACCCGC
* * *
85338940 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
85338986 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
85339036 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
85339079 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
85339116 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:85340675 original size:16 final size:16
Alignment explanation
Indices: 85340654--85340684 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85340644 TGTTCATCCG
*
85340654 ATTAAAATGGTAAGTT
1 ATTAAAAAGGTAAGTT
85340670 ATTAAAAAGGTAAGT
1 ATTAAAAAGGTAAGT
85340685 CCTTAGGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
ATTAAAAAGGTAAGTT
Done.