Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 31 of 208
Found at i:8825164 original size:43 final size:44
Alignment explanation
Indices: 8825115--8825305 Score: 124
Period size: 43 Copynumber: 4.4 Consensus size: 44
8825105 CCTGAGGTTA
*
8825115 CAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
* * * **
8825158 CAGTGGAATAGATTGAAG--ATTACAGATCTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTACA-TTCTATCTCCCTGGGCAG
* * ** *** * * * *
8825201 TAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGTACATTCTATCTCCCTG-GG-CAG
* *
8825246 CAGT-GAGTACATTGAAGCCAGTA-ATTCTATCTCCCTGGGCAA
1 CAGTGGAGTAGATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
* *
8825288 TAGTGGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
8825306 ATTACAGATC
Statistics
Matches: 106, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
41 4 0.04
42 6 0.06
43 67 0.63
44 21 0.20
45 7 0.07
46 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGTGGAGTAGATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
Found at i:8825311 original size:130 final size:131
Alignment explanation
Indices: 8825034--8825363 Score: 563
Period size: 130 Copynumber: 2.5 Consensus size: 131
8825024 TGGCGTGAAG
* ** * *
8825034 TAGATCGAAGATTACAGATCTTATCTCGATAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
1 TAGATTGAAGATTACAGATC-TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
*
8825099 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
8825164 AA
130 AA
*
8825166 TAGATTGAAGATTACAGATCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTT
1 TAGATTGAAGATTACAGATCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTT
*
8825231 ACCTCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAATAGTGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGA
8825295 A
131 A
*
8825296 TAGATTGAAGATTACAGATCTATCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTT
1 TAGATTGAAGATTACAGATCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTT
8825361 ACC
66 ACC
8825364 ATTTTCTTCG
Statistics
Matches: 188, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
130 110 0.59
131 59 0.31
132 19 0.10
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (131 bp):
TAGATTGAAGATTACAGATCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTT
ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGA
A
Found at i:8825318 original size:43 final size:43
Alignment explanation
Indices: 8825141--8825324 Score: 113
Period size: 43 Copynumber: 4.3 Consensus size: 43
8825131 AGCCAGTAAT
*
8825141 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGA
1 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGA
** ** ** ** ***
8825184 TCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGA
1 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGA
* * ** * * * *
8825227 TTTTACCTCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTA-A-T
1 -TCTATCTCCCTG-GGCAACAGTGGAATAGATTGAAG--ATTACAGA
*
8825271 TCTATCTCCCTGGGCAATAGTGGAATAGATTGAAGATTACAGA
1 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGA
*
8825314 TCTATCACCCT
1 TCTATCTCCCT
8825325 AAGCAGTAGT
Statistics
Matches: 98, Mismatches: 36, Indels: 14
0.66 0.24 0.09
Matches are distributed among these distances:
41 3 0.03
42 7 0.07
43 64 0.65
44 18 0.18
45 5 0.05
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGA
Found at i:8825970 original size:3 final size:3
Alignment explanation
Indices: 8825964--8826014 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
8825954 TTTAACATTG
*
8825964 TAT TAT TAT TAT TATT TAT TTT TAT TAT TAT T-T TCAT T-T TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
*
8826009 TTT TAT
1 TAT TAT
8826015 ATCCATATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:8825988 original size:16 final size:16
Alignment explanation
Indices: 8825964--8826014 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
8825954 TTTAACATTG
*
8825964 TATTATTATTATTATT
1 TATTTTTATTATTATT
8825980 TATTTTTATTATTATT
1 TATTTTTATTATTATT
8825996 T-TCATTTTATTATT-TT
1 TAT--TTTTATTATTATT
8826012 TAT
1 TAT
8826015 ATCCATATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 1 0.03
16 19 0.61
17 11 0.35
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTATTATTATT
Found at i:8829213 original size:24 final size:24
Alignment explanation
Indices: 8829198--8829249 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
8829188 AATCAAAGTC
8829198 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
8829222 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
8829246 AAAT
1 AAAT
8829250 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:8833537 original size:24 final size:24
Alignment explanation
Indices: 8833494--8833545 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
8833484 AATCAAAGTC
* *
8833494 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
**
8833518 AAATATATTATACTCGTAAATACT
1 AAATATATTATACTAATAAATACT
8833542 AAAT
1 AAAT
8833546 CTTATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:8838974 original size:97 final size:99
Alignment explanation
Indices: 8838844--8839075 Score: 362
Period size: 97 Copynumber: 2.4 Consensus size: 99
8838834 TAAAATTAGA
* * *
8838844 TTTATGGTTTTTAAGGAAAAAATCAATTAAATTAGGGTTTAAGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAAGATTACTTGAGTAAATTAATTAT
*
8838909 AATTTTTTT-TAAAAATTAGATTAGGGTTTAGTG
66 AATTTTTTTAAAAAAATTAGATTAGGGTTTAGTG
* *
8838942 -TTACGGGTTTTTAA-GAAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 TTTA-GGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAAGATTACTTGAGTAAATTAATTA
*
8839005 TAATTTTTTTAAAAAAATTAGGTTAGGGTTTAGTG
65 TAATTTTTTTAAAAAAATTAGATTAGGGTTTAGTG
*
8839040 TTTAGGGTTTTTAAGGAAAAATTAAAATAAATTAGG
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGG
8839076 ATTTGGGGTT
Statistics
Matches: 122, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
97 58 0.48
98 41 0.34
99 23 0.19
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (99 bp):
TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAAGATTACTTGAGTAAATTAATTAT
AATTTTTTTAAAAAAATTAGATTAGGGTTTAGTG
Found at i:8839356 original size:126 final size:126
Alignment explanation
Indices: 8839122--8839412 Score: 465
Period size: 126 Copynumber: 2.3 Consensus size: 126
8839112 TAATTTAAAA
* * * *
8839122 AAGCTCCCACGTGGACACTTTTTTGCTACAGAAGTTACTGAAAAAATAATTTTGAGAAGATGTTT
1 AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
* *
8839187 CTGAGAAAATAGTGTCAAAAACGCTTTAAGTAGGATGCATTGTCAGCGAAAGTAATGAAAG
66 CTGAGAAAATAGTGTCAAAAACGCTTTAAGTAGAATGCATTGTCAGCAAAAGTAATGAAAG
* *
8839248 AAGCTCCCACGTGGATACTTTTTTCCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * *
8839313 CTGAGTAAATAGTGTCAAAAACGCTTTAAGTAGAATGCTTTGTCAGCAAAAGTACTGAAAG
66 CTGAGAAAATAGTGTCAAAAACGCTTTAAGTAGAATGCATTGTCAGCAAAAGTAATGAAAG
* *
8839374 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
1 AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTCCT
8839413 ATTTGGCCTG
Statistics
Matches: 150, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 150 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (126 bp):
AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
CTGAGAAAATAGTGTCAAAAACGCTTTAAGTAGAATGCATTGTCAGCAAAAGTAATGAAAG
Found at i:8842135 original size:18 final size:18
Alignment explanation
Indices: 8842114--8842148 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8842104 AAAAAGGAAA
* *
8842114 CATATAAGGGTTAGGATG
1 CATAAAAGGGCTAGGATG
8842132 CATAAAAGGGCTAGGAT
1 CATAAAAGGGCTAGGAT
8842149 ACGCACCTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (18 bp):
CATAAAAGGGCTAGGATG
Found at i:8842268 original size:30 final size:30
Alignment explanation
Indices: 8842211--8842269 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
8842201 TGTTGGGTCA
* **
8842211 GGTGACTGTGTCGGTGCTGTTGCTGGGCCC
1 GGTGACTGTGTCGGCGCTGTTAATGGGCCC
* *
8842241 GGTGATTGTGTGGGCGCTGTTAATGGGCC
1 GGTGACTGTGTCGGCGCTGTTAATGGGCC
8842270 TGCGTCATCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.07, C:0.19, G:0.44, T:0.31
Consensus pattern (30 bp):
GGTGACTGTGTCGGCGCTGTTAATGGGCCC
Found at i:8844212 original size:40 final size:41
Alignment explanation
Indices: 8844132--8844213 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 41
8844122 GGAAGTGCTT
* *
8844132 TGTCCACGTGGACACAAAGCGCCCCCTTAAGGACGTGTTTTC
1 TGTCCACGTGGA-ACAAAGCGCCCCCTTAAGGAAGCGTTTTC
* ** *
8844174 TGTCCACGTGG-ATAAAGCGCTTCCTTGAGGAAGCGTTTTC
1 TGTCCACGTGGAACAAAGCGCCCCCTTAAGGAAGCGTTTTC
8844214 CTGCTTTGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 23 0.68
42 11 0.32
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.27
Consensus pattern (41 bp):
TGTCCACGTGGAACAAAGCGCCCCCTTAAGGAAGCGTTTTC
Found at i:8849588 original size:45 final size:45
Alignment explanation
Indices: 8849539--8849648 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
8849529 CTTCCTGATC
* *
8849539 TAATGTCATAGTGTCTTTCAACCATGGTCTTACAAATTTGAATCG
1 TAATGCCATAGCGTCTTTCAACCATGGTCTTACAAATTTGAATCG
* * ***
8849584 TAATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGAATCG
1 TAATGCCATAGCGTCTTTCAACCATGGTCTTACAAATTTGAATCG
* *
8849629 TGATGCCATAACGTCTTTCA
1 TAATGCCATAGCGTCTTTCA
8849649 GCTTTAGTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (45 bp):
TAATGCCATAGCGTCTTTCAACCATGGTCTTACAAATTTGAATCG
Found at i:8849649 original size:45 final size:45
Alignment explanation
Indices: 8849551--8849712 Score: 225
Period size: 45 Copynumber: 3.6 Consensus size: 45
8849541 ATGTCATAGT
* * *** * *
8849551 GTCTTTCAACCATGGTCTTACAAATTTGAATCGTAATGCCATAGC
1 GTCTTTCAGCTATGGTCTTACTCGTTTGAATCGTGATGCCATAAC
8849596 GTCTTTCAGCTATGGTCTTACTCGTTTGAATCGTGATGCCATAAC
1 GTCTTTCAGCTATGGTCTTACTCGTTTGAATCGTGATGCCATAAC
* * * *
8849641 GTCTTTCAGCTTTAGTCTTACTCGTTTGTATCGTGATGCCACAAC
1 GTCTTTCAGCTATGGTCTTACTCGTTTGAATCGTGATGCCATAAC
8849686 GTCTTTCAGCTATGGTCTTACTCGTTT
1 GTCTTTCAGCTATGGTCTTACTCGTTT
8849713 TCAACCAACG
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (45 bp):
GTCTTTCAGCTATGGTCTTACTCGTTTGAATCGTGATGCCATAAC
Found at i:8852903 original size:31 final size:32
Alignment explanation
Indices: 8852853--8852915 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
8852843 CAAGAGAACC
8852853 CATTGAAAAATAGAGTGAATCTCCTAGATAAA
1 CATTGAAAAATAGAGTGAATCTCCTAGATAAA
* *
8852885 CATTGACAATTAG-GTGAATCTCCTAGATAAA
1 CATTGAAAAATAGAGTGAATCTCCTAGATAAA
8852916 ACCATATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (32 bp):
CATTGAAAAATAGAGTGAATCTCCTAGATAAA
Found at i:8853667 original size:25 final size:27
Alignment explanation
Indices: 8853637--8853704 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
8853627 AAAATTGGTA
8853637 AGACATTTTCCATTCT-TCTCTAAGCA-
1 AGACATTTTCCATTCTCT-TCTAAGCAC
8853663 A-ACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAAGCA-C
8853690 AGACATTTTCCATTC
1 AGACATTTTCCATTC
8853705 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 13 0.34
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAC
Found at i:8858080 original size:35 final size:36
Alignment explanation
Indices: 8858032--8858100 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
8858022 ATTTGTTAGA
8858032 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
8858068 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
8858101 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:8859162 original size:71 final size:72
Alignment explanation
Indices: 8859043--8859185 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 72
8859033 TTGATACATT
*
8859043 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
8859108 TTGGATA
66 TTGGATA
*
8859115 TATGTGGTGTAATATTATGCAC-TAGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
8859179 TTGGATA
66 TTGGATA
8859186 ATATTATTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 47 0.68
72 22 0.32
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:8859397 original size:14 final size:14
Alignment explanation
Indices: 8859378--8859405 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8859368 ACAATTTATT
8859378 AATATATATTAATA
1 AATATATATTAATA
8859392 AATATATATTAATA
1 AATATATATTAATA
8859406 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:8859479 original size:32 final size:33
Alignment explanation
Indices: 8859438--8859522 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
8859428 AACTTTTCTG
* * *
8859438 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
8859470 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
8859502 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
8859523 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:8859521 original size:14 final size:15
Alignment explanation
Indices: 8859499--8859575 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
8859489 TTACCAAACA
8859499 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
8859513 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
8859528 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
8859548 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
8859562 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
8859576 ATTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:8859540 original size:20 final size:20
Alignment explanation
Indices: 8859515--8859554 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8859505 AATATTTTCC
*
8859515 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
8859535 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
8859555 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:8859560 original size:34 final size:35
Alignment explanation
Indices: 8859503--8859569 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
8859493 CAAACACCAG
*
8859503 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
8859538 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
8859570 CATTTTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:8867706 original size:19 final size:19
Alignment explanation
Indices: 8867682--8867734 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
8867672 TAAATAATTT
8867682 AAAAATTATAAAAATATTC
1 AAAAATTATAAAAATATTC
*
8867701 AAAAATTA-AAAATAAATTC
1 AAAAATTATAAAA-ATATTC
*
8867720 --AAATTTTAAAAATAT
1 AAAAATTATAAAAATAT
8867735 AAAATGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
19 13 0.45
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAATATTC
Found at i:8874181 original size:20 final size:19
Alignment explanation
Indices: 8874152--8874190 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
8874142 GGCGTTACAG
*
8874152 AATATCTTTCAAATCACAAT
1 AATATATTTCAAAT-ACAAT
*
8874172 AATATATTTCCAATACAAT
1 AATATATTTCAAATACAAT
8874191 TCCTATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATATTTCAAATACAAT
Found at i:8877509 original size:8 final size:8
Alignment explanation
Indices: 8877496--8877523 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
8877486 TATACTAAAC
8877496 AATAAAAT
1 AATAAAAT
8877504 AATAAAAT
1 AATAAAAT
8877512 AATAAAAT
1 AATAAAAT
8877520 AATA
1 AATA
8877524 TTTAAAAATC
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:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:8884729 original size:21 final size:22
Alignment explanation
Indices: 8884683--8884729 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
8884673 TATTAAACAT
*
8884683 TTAATTTTTTTAGTATGTTTAA
1 TTAATTTTATTAGTATGTTTAA
*
8884705 -TAATTTTATTAGT-TTTTTAA
1 TTAATTTTATTAGTATGTTTAA
8884725 TTAAT
1 TTAAT
8884730 AAAAGATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (22 bp):
TTAATTTTATTAGTATGTTTAA
Found at i:8887165 original size:22 final size:21
Alignment explanation
Indices: 8887119--8887169 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
8887109 TGGACTAGTG
8887119 GTTTAATATAAATATATATAA
1 GTTTAATATAAATATATATAA
* *
8887140 --TTAATATAATATTTTTATAA
1 GTTTAATATAA-ATATATATAA
8887160 GTTTAATATA
1 GTTTAATATA
8887170 TTCGGACTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
22 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
GTTTAATATAAATATATATAA
Found at i:8895197 original size:9 final size:9
Alignment explanation
Indices: 8895185--8895252 Score: 75
Period size: 9 Copynumber: 7.4 Consensus size: 9
8895175 AAAATAAAAA
8895185 AATTCGGGT
1 AATTCGGGT
8895194 AATTCGGGT
1 AATTCGGGT
*
8895203 ATTTTTC-GGT
1 A--ATTCGGGT
*
8895213 AATTCGGTT
1 AATTCGGGT
*
8895222 AATTCGGTT
1 AATTCGGGT
8895231 AATTCGGGT
1 AATTCGGGT
*
8895240 AATTCAGGT
1 AATTCGGGT
8895249 AATT
1 AATT
8895253 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.06
9 41 0.80
10 4 0.08
11 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:8898699 original size:2 final size:2
Alignment explanation
Indices: 8898692--8898726 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8898682 CATATAATTA
*
8898692 AT AT AT AT AT AT AT AT CT 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
8898727 GGCTTGCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8900130 original size:33 final size:32
Alignment explanation
Indices: 8900093--8900170 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
8900083 TGGCCCTACC
** * **
8900093 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATCAG-AATGCCATAACCCAACT
*
8900126 ATGGTCTTATCATCAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAACT
8900159 ATGGTCTTACAT
1 ATGGTCTTACAT
8900171 ATAAACACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.82
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAACT
Found at i:8900218 original size:101 final size:99
Alignment explanation
Indices: 8900045--8900237 Score: 278
Period size: 101 Copynumber: 1.9 Consensus size: 99
8900035 GTTCTTTTTG
* * * * **
8900045 TGCCATAGTCCAACTATGGTCTTACACATGCATTGCCATGGCCCTACCATGGTCTTACATTTGTA
1 TGCCATAGCCCAACTATGGTCTTACACATACACTGCCATGGCCCAACCATGGTCTTACATTCATA
8900110 GTGCCATAACCCAGTTATGGTCTTATCATCAGAA
66 GTGCCATAACCCAGTTATGGTCTTATCATCAGAA
* * *
8900144 TGCCATAGCCCAACTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTTCA
1 TGCCATAGCCCAACTATGGTCTTACACAT--ACACTGCCATGGCCCAACCATGGTCTTACATTCA
*
8900209 TAGTGCCATAACCTAGTTATGGTCTTATC
64 TAGTGCCATAACCCAGTTATGGTCTTATC
8900238 CGTCAATTCA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 27 0.33
101 55 0.67
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (99 bp):
TGCCATAGCCCAACTATGGTCTTACACATACACTGCCATGGCCCAACCATGGTCTTACATTCATA
GTGCCATAACCCAGTTATGGTCTTATCATCAGAA
Found at i:8903396 original size:15 final size:15
Alignment explanation
Indices: 8903345--8903390 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
8903335 CGCGATAATG
*
8903345 TAAGTGACTAAAACA
1 TAAGTAACTAAAACA
*
8903360 TAA--AATTTAAAACA
1 TAAGTAA-CTAAAACA
8903374 TAAGTAACTAAAACA
1 TAAGTAACTAAAACA
8903389 TA
1 TA
8903391 TATAACCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 12 0.48
16 2 0.08
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.24
Consensus pattern (15 bp):
TAAGTAACTAAAACA
Found at i:8918251 original size:23 final size:23
Alignment explanation
Indices: 8918225--8918300 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
8918215 ATAAGTGCCA
*
8918225 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
8918248 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
8918271 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
8918294 CACTGAT
1 CACTGAT
8918301 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:8918400 original size:8 final size:8
Alignment explanation
Indices: 8918387--8918415 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
8918377 ACCCGGGACT
8918387 CACTGTAA
1 CACTGTAA
8918395 CACTGTAA
1 CACTGTAA
8918403 CACTGTAA
1 CACTGTAA
8918411 CACTG
1 CACTG
8918416 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:8918546 original size:18 final size:17
Alignment explanation
Indices: 8918520--8918558 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
8918510 ATTTTCCTTC
8918520 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
8918537 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
8918555 CACA
1 CACA
8918559 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:8932618 original size:23 final size:24
Alignment explanation
Indices: 8932578--8932626 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
8932568 TTTTGTTCTC
8932578 TGCTGGTACTGTTGTTCCTCTGCT
1 TGCTGGTACTGTTGTTCCTCTGCT
*
8932602 TGCTGGTTCT-TTGTTCCTCTGCT
1 TGCTGGTACTGTTGTTCCTCTGCT
8932625 TG
1 TG
8932627 TTCTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.02, C:0.24, G:0.24, T:0.49
Consensus pattern (24 bp):
TGCTGGTACTGTTGTTCCTCTGCT
Found at i:8932629 original size:19 final size:19
Alignment explanation
Indices: 8932569--8932630 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 19
8932559 TCCTCCAAAT
* *
8932569 TTTGTT-CTCTGCTGGTAC
1 TTTGTTCCTCTGCTTGTTC
8932587 TGTTGTTCCTCTGCTTGCTGGTTC
1 T-TTGTTCCTCTGC-T--T-GTTC
8932611 TTTGTTCCTCTGCTTGTTC
1 TTTGTTCCTCTGCTTGTTC
8932630 T
1 T
8932631 AATTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
18 1 0.03
19 10 0.28
20 7 0.19
21 1 0.03
22 1 0.03
23 12 0.33
24 4 0.11
ACGTcount: A:0.02, C:0.24, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTGTTCCTCTGCTTGTTC
Found at i:8932893 original size:13 final size:13
Alignment explanation
Indices: 8932870--8932920 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
8932860 ATACTTAAAT
*
8932870 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
8932883 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* **
8932896 TTTTCCACGGCAC
1 TTTTCAAAAGCAC
8932909 TTTTCAAAAGCA
1 TTTTCAAAAGCA
8932921 ACGAAGAACT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:8934772 original size:16 final size:16
Alignment explanation
Indices: 8934751--8934787 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
8934741 CACTCCGCAG
8934751 CGCCGCCGTAGCCGGT
1 CGCCGCCGTAGCCGGT
8934767 CGCCGCCGTAGCCGGT
1 CGCCGCCGTAGCCGGT
*
8934783 GGCCG
1 CGCCG
8934788 GCGTTGCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.43, G:0.41, T:0.11
Consensus pattern (16 bp):
CGCCGCCGTAGCCGGT
Found at i:8935739 original size:42 final size:41
Alignment explanation
Indices: 8935692--8936130 Score: 292
Period size: 40 Copynumber: 10.7 Consensus size: 41
8935682 GTGTCTTCAA
*
8935692 TCTGCTCCACTGCTGCTTAGGGAGATAAGGTCTGTTGTTCTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCT-TTGTTCTG
* ** *
8935734 TCTGCTCCACTACTGCTTAGGGAGATAA-GACTTAATGC-G
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTGTTCTG
* * * *
8935773 ATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAGTTTTG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGGTCT-TTGTTCTG
* *
8935816 TCTGCTCCACTACTGCTTAGGGAGATAA-GAC-TTGATGC-G
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTG-TTCTG
* *
8935855 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGCTT-TG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGGTCT-TTG-TTCTG
** * * *
8935898 TCTGCTCTGCTACTGCTTAGGGAGATAA-GAC-TTGATGTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTGTTCTG
* * * * *
8935937 ATCTGATCTATTACTGCTTAGGGAGATAAGATCTGTGGCTT-TG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGGTCT-TTG-TTCTG
* ** * * * *
8935980 TCCGCTCCGTTACTGCTTAAGGAGATAA-GAC-TTGATGTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTGTTCTG
* * * * *
8936019 ATCTGATCTACTACTGCTTAGGGAGATAAGATCTGTGGTTTTG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGGTCT-TTGTTCTG
* * * * *
8936062 TCCGCTCCGCTACTGCTTAGGGAGATAA-GAC-TTGATGTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTGTTCTG
* *
8936101 ATCTGCTCCACTACTTCATAGGGAGATAAG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAG
8936131 ATCTGTAATC
Statistics
Matches: 306, Mismatches: 68, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
38 2 0.01
39 17 0.06
40 130 0.42
41 12 0.04
42 130 0.42
43 14 0.05
44 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTTTGTTCTG
Found at i:8935828 original size:82 final size:82
Alignment explanation
Indices: 8935691--8936136 Score: 658
Period size: 82 Copynumber: 5.4 Consensus size: 82
8935681 TGTGTCTTCA
* * * * *
8935691 ATCTGCTCCACTGCTGCTTAGGGAGATAAGGTCTGTTGTTCTGTCTGCTCCACTACTGCTTAGGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
* *
8935756 AGATAAGACTTAATGCG
66 AGATAAGACTTGATGTG
* * *
8935773 ATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAGTTTTGTCTGCTCCACTACTGCTTAGGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
*
8935838 AGATAAGACTTGATGCG
66 AGATAAGACTTGATGTG
* * *
8935855 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGCTTTGTCTGCTCTGCTACTGCTTAGGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
8935920 AGATAAGACTTGATGTG
66 AGATAAGACTTGATGTG
* * * * * * *
8935937 ATCTGATCTATTACTGCTTAGGGAGATAAGATCTGTGGCTTTGTCCGCTCCGTTACTGCTTAAGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
8936002 AGATAAGACTTGATGTG
66 AGATAAGACTTGATGTG
* * *
8936019 ATCTGATCTACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
8936084 AGATAAGACTTGATGTG
66 AGATAAGACTTGATGTG
* *
8936101 ATCTGCTCCACTACTTCATAGGGAGATAAGATCTGT
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
8936137 AATCTTCAAT
Statistics
Matches: 335, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 335 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (82 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGG
AGATAAGACTTGATGTG
Found at i:8936468 original size:15 final size:15
Alignment explanation
Indices: 8936431--8936468 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
8936421 CTAGATGTGT
*
8936431 ATGAACGATATTTGC
1 ATGAATGATATTTGC
8936446 ATTGAATGATATTTGC
1 A-TGAATGATATTTGC
8936462 ATGAATG
1 ATGAATG
8936469 CGAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (15 bp):
ATGAATGATATTTGC
Found at i:8950335 original size:7 final size:7
Alignment explanation
Indices: 8950270--8950336 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
8950260 AAAAGAACGT
*
8950270 AAAATAT
1 AAAATAA
*
8950277 AAAATATT
1 AAAATA-A
8950285 AAAATAA
1 AAAATAA
*
8950292 AAAATGA
1 AAAATAA
8950299 AAAA-AA
1 AAAATAA
* **
8950305 TAAACGA
1 AAAATAA
*
8950312 TAAATAA
1 AAAATAA
8950319 AAAATAA
1 AAAATAA
8950326 AAAATAA
1 AAAATAA
8950333 AAAA
1 AAAA
8950337 ATCGGTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 4 0.08
7 39 0.78
8 7 0.14
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:8955055 original size:66 final size:66
Alignment explanation
Indices: 8954949--8955074 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
8954939 TAAAAGTTAG
* *
8954949 AACTTTGAAGAATGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
1 AACTTAGAAGAATGCTTTAGGATGCATGGATGTACGTTGACTAAGACCAAAACTGAATAAATGTG
8955014 A
66 A
* * *
8955015 AACTTAGAAGAGTGCTTTAGGATGCATGGATGTACTTTGACTAGGACCAAAACTGAATAA
1 AACTTAGAAGAATGCTTTAGGATGCATGGATGTACGTTGACTAAGACCAAAACTGAATAA
8955075 TAGGATGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (66 bp):
AACTTAGAAGAATGCTTTAGGATGCATGGATGTACGTTGACTAAGACCAAAACTGAATAAATGTG
A
Found at i:8960511 original size:8 final size:9
Alignment explanation
Indices: 8960488--8960547 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
8960478 GTATTTAATT
8960488 AATTTTAAA
1 AATTTTAAA
8960497 AATTTTAAA
1 AATTTTAAA
*
8960506 AATTTAAAAAA
1 AATTT--TAAA
8960517 ACATTTTAAA
1 A-ATTTTAAA
* *
8960527 TATTTT-TA
1 AATTTTAAA
*
8960535 AATTTAAAA
1 AATTTTAAA
8960544 AATT
1 AATT
8960548 AACTAAATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
8 5 0.12
9 24 0.60
10 3 0.08
11 4 0.10
12 4 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTTTAAA
Found at i:8960524 original size:30 final size:29
Alignment explanation
Indices: 8960489--8960545 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
8960479 TATTTAATTA
8960489 ATTTTAAAAATTTTAAAAATTTAAAAAAAC
1 ATTTTAAAAATTTT-AAAATTTAAAAAAAC
* *
8960519 ATTTTAAATATTTTTAAATTTAAAAAA
1 ATTTTAAAAATTTTAAAATTTAAAAAA
8960546 TTAACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTTAAAAATTTTAAAATTTAAAAAAAC
Found at i:8965368 original size:11 final size:11
Alignment explanation
Indices: 8965348--8965407 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
8965338 CTTTTCTTTC
8965348 TATTATATTAG
1 TATTATATTAG
*
8965359 TATTAAATTAG
1 TATTATATTAG
*
8965370 TATTATATT-C
1 TATTATATTAG
8965380 TATTAATATTAG
1 TATT-ATATTAG
8965392 -ATTAGTATTAG
1 TATTA-TATTAG
8965403 TATTA
1 TATTA
8965408 GTTAGTGATC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 5 0.12
11 32 0.78
12 4 0.10
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (11 bp):
TATTATATTAG
Found at i:8965374 original size:6 final size:6
Alignment explanation
Indices: 8965348--8965409 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
8965338 CTTTTCTTTC
* * *
8965348 TATTA- TATTAG TATTA- AATTAG TATTA- TATT-C TATTAA TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
8965392 -ATTAG TATTAG TATTAG T
1 TATTAG TATTAG TATTAG T
8965410 TAGTGATCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
5 22 0.46
6 26 0.54
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (6 bp):
TATTAG
Found at i:8965389 original size:27 final size:28
Alignment explanation
Indices: 8965348--8965407 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
8965338 CTTTTCTTTC
*
8965348 TATTATATTAGTATTAAATTAGTATTA-
1 TATTATATTAATATTAAATTAGTATTAG
* *
8965375 TATTCTATTAATATTAGATTAGTATTAG
1 TATTATATTAATATTAAATTAGTATTAG
8965403 TATTA
1 TATTA
8965408 GTTAGTGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (28 bp):
TATTATATTAATATTAAATTAGTATTAG
Found at i:8969456 original size:2 final size:2
Alignment explanation
Indices: 8969443--8969472 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8969433 TAAAAGTTAA
*
8969443 AT AT AA 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
8969473 TTACTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8970492 original size:2 final size:2
Alignment explanation
Indices: 8970487--8970517 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8970477 TAAAATACAC
8970487 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8970518 TTGAGACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8976167 original size:2 final size:2
Alignment explanation
Indices: 8976160--8976193 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8976150 ATTTTCTACT
8976160 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8976194 TCACATATTT
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):
TA
Found at i:8976593 original size:27 final size:25
Alignment explanation
Indices: 8976552--8976602 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
8976542 ATAGATTAAA
8976552 TGTTGTTAATAATAAATT-AAAATT
1 TGTTGTTAATAATAAATTGAAAATT
8976576 TGTTGTTAATAAATATAATTTGAAAAT
1 TGTTGTTAAT-AATA-AA-TTGAAAAT
8976603 ATTAAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.43
25 4 0.17
26 2 0.09
27 2 0.09
28 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (25 bp):
TGTTGTTAATAATAAATTGAAAATT
Found at i:8982284 original size:14 final size:15
Alignment explanation
Indices: 8982257--8982286 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
8982247 AAAAAGAGAG
8982257 TAAAATATGAAAAGT
1 TAAAATATGAAAAGT
8982272 TAAAATA-GAAAAGT
1 TAAAATATGAAAAGT
8982286 T
1 T
8982287 GACTGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAAATATGAAAAGT
Found at i:8997981 original size:23 final size:22
Alignment explanation
Indices: 8997911--8997992 Score: 98
Period size: 21 Copynumber: 3.8 Consensus size: 22
8997901 CCTGATCAGT
*
8997911 ATACGACACAT-AAGTGCCTGT
1 ATACGACACATAAAGTGCCTGG
** *
8997932 A-ACGACACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTGG
8997952 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTG-G
8997975 ATACGACACATAAAGTGC
1 ATACGACACATAAAGTGC
8997993 TTGATCGGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.18
21 23 0.45
23 19 0.37
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGG
Found at i:8999282 original size:15 final size:16
Alignment explanation
Indices: 8999264--8999295 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8999254 TTAATTAATA
8999264 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
8999279 TAATTTAATAATATTT
1 TAATTTAATAATATTT
8999295 T
1 T
8999296 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:8999286 original size:25 final size:26
Alignment explanation
Indices: 8999251--8999303 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
8999241 TATTATCTTA
8999251 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
8999275 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
8999302 AT
1 AT
8999304 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:9011892 original size:21 final size:21
Alignment explanation
Indices: 9011845--9011892 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
9011835 CTGTTGAAGT
* *
9011845 TAGTTAAAAGGAGTTAGTTAG
1 TAGTTAAAAGGAATTAGTTAA
*
9011866 TTGTTAAACA-GAATTAGTTAA
1 TAGTTAAA-AGGAATTAGTTAA
9011887 TAGTTA
1 TAGTTA
9011893 GCTATTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (21 bp):
TAGTTAAAAGGAATTAGTTAA
Found at i:9016750 original size:16 final size:17
Alignment explanation
Indices: 9016723--9016757 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
9016713 GCATTTGGAT
9016723 TAAAATTTTTAAAAATA
1 TAAAATTTTTAAAAATA
9016740 TAAAA-TTTTAAAAATA
1 TAAAATTTTTAAAAATA
9016756 TA
1 TA
9016758 CCAAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTTTAAAAATA
Found at i:9018904 original size:24 final size:24
Alignment explanation
Indices: 9018876--9018925 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
9018866 CATTTTTGGA
9018876 AATCGAATTTTTATTTTAAATACG
1 AATCGAATTTTTATTTTAAATACG
*
9018900 AATCGAGTTTTTATTTTAAATACG
1 AATCGAATTTTTATTTTAAATACG
9018924 AA
1 AA
9018926 GATGGAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
AATCGAATTTTTATTTTAAATACG
Found at i:9019597 original size:28 final size:28
Alignment explanation
Indices: 9019566--9019620 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
9019556 CAACATAAAT
9019566 AATAAAATAA-AACGACAATAAT-ATAATG
1 AATAAAATAATAA-GA-AATAATAATAATG
*
9019594 AATACAATAATAAGAAATAATAATAAT
1 AATAAAATAATAAGAAATAATAATAAT
9019621 TATTCAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 16 0.67
29 2 0.08
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (28 bp):
AATAAAATAATAAGAAATAATAATAATG
Found at i:9025917 original size:29 final size:28
Alignment explanation
Indices: 9025849--9025920 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
9025839 TCTTTTCTTA
**
9025849 CTCGTATTCTTTTTCTTTCTCTTTTTTTT
1 CTCGT-TTCTTTTTCTTTCAATTTTTTTT
** *
9025878 CAAGCTCTCTTTTTCTTTCAATTTTTTTCT
1 CTCG-TTTCTTTTTCTTTCAATTTTTTT-T
9025908 CTCGTTTCTTTTT
1 CTCGTTTCTTTTT
9025921 TTCTTCTCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (28 bp):
CTCGTTTCTTTTTCTTTCAATTTTTTTT
Found at i:9025938 original size:21 final size:19
Alignment explanation
Indices: 9025899--9025957 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 19
9025889 TTTCTTTCAA
*
9025899 TTTTTTTCTCTCGTTTCTT
1 TTTTTTTCTCTCATTTCTT
9025918 TTTTTCTTCTCTCAATTTCTT
1 TTTTT-TTCTCTC-ATTTCTT
*
9025939 TTATTTTTCGCTCATTTCT
1 TT-TTTTTCTCTCATTTCT
9025958 CTCATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 14 0.40
22 3 0.09
ACGTcount: A:0.07, C:0.22, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTTTCTCTCATTTCTT
Found at i:9028264 original size:39 final size:38
Alignment explanation
Indices: 9028188--9028277 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 38
9028178 TTAAAACACT
* *
9028188 TAATTAAA-ACACATATTAGTGAGTTCAAAATAAGACA
1 TAATTAAAGACATATATTAATGAGTTCAAAATAAGACA
* * *
9028225 TAATTAAAGACATATATTAATGGTGTTCAAACTACGACA
1 TAATTAAAGACATATATTAAT-GAGTTCAAAATAAGACA
*
9028264 TAATTAAGGACATA
1 TAATTAAAGACATA
9028278 ACTAAGACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 8 0.18
38 10 0.22
39 27 0.60
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (38 bp):
TAATTAAAGACATATATTAATGAGTTCAAAATAAGACA
Found at i:9028277 original size:12 final size:12
Alignment explanation
Indices: 9028260--9028299 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
9028250 TTCAAACTAC
9028260 GACATAATTAAG
1 GACATAATTAAG
*
9028272 GACATAACTAA-
1 GACATAATTAAG
9028283 GACATAATTAAG
1 GACATAATTAAG
9028295 GACAT
1 GACAT
9028300 GAACTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (12 bp):
GACATAATTAAG
Found at i:9028281 original size:23 final size:24
Alignment explanation
Indices: 9028254--9028306 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
9028244 ATGGTGTTCA
*
9028254 AACTACGACATAATTAAGGACAT-
1 AACTAAGACATAATTAAGGACATG
9028277 AACTAAGACATAATTAAGGACATG
1 AACTAAGACATAATTAAGGACATG
9028301 AACTAA
1 AACTAA
9028307 AATAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (24 bp):
AACTAAGACATAATTAAGGACATG
Found at i:9028315 original size:9 final size:9
Alignment explanation
Indices: 9028301--9028327 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9028291 TAAGGACATG
9028301 AACTAAAAT
1 AACTAAAAT
9028310 AACTAAAAT
1 AACTAAAAT
9028319 AACTAAAAT
1 AACTAAAAT
9028328 GGATTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
AACTAAAAT
Found at i:9029143 original size:10 final size:10
Alignment explanation
Indices: 9029128--9029159 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
9029118 CCTTGACCTT
9029128 CTCCTTGCTC
1 CTCCTTGCTC
9029138 CTCCTTGCTC
1 CTCCTTGCTC
9029148 CTCCTTGC-C
1 CTCCTTGCTC
9029157 CTC
1 CTC
9029160 TTCCCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.53, G:0.09, T:0.38
Consensus pattern (10 bp):
CTCCTTGCTC
Found at i:9033522 original size:16 final size:16
Alignment explanation
Indices: 9033501--9033539 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
9033491 TTATTAAATT
*
9033501 ATATATTTTAATTATA
1 ATATATTTTAATAATA
9033517 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
9033532 ATTATATT
1 A-TATATT
9033540 AAAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 9 0.45
17 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:9033766 original size:45 final size:44
Alignment explanation
Indices: 9033667--9033776 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
9033657 TTTTCTATTA
9033667 TGCTATTACACCTCTATT-C--T--ATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
9033706 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
9033751 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
9033777 CATCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
42 1 0.02
44 15 0.26
45 25 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:9033776 original size:16 final size:16
Alignment explanation
Indices: 9033757--9033808 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
9033747 GATTTGCTAT
* *
9033757 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
9033773 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
9033789 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
9033805 TACA
1 TACA
9033809 GCGAACTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:9039028 original size:14 final size:14
Alignment explanation
Indices: 9039011--9039053 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
9039001 TCATTTAAGA
9039011 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
9039025 TTTAATTTTTA-AC
1 TTTAATTTTTATAT
*
9039038 TTTGA-TTTTATAT
1 TTTAATTTTTATAT
9039051 TTT
1 TTT
9039054 TATAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 11 0.44
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:9049698 original size:25 final size:25
Alignment explanation
Indices: 9049670--9049720 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9049660 AAAGACTTGA
9049670 GCCTATTACAGAAGAATGTTAGGAT
1 GCCTATTACAGAAGAATGTTAGGAT
9049695 GCCTATTACAGAAGAATGTTAGGAT
1 GCCTATTACAGAAGAATGTTAGGAT
9049720 G
1 G
9049721 ACATACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (25 bp):
GCCTATTACAGAAGAATGTTAGGAT
Found at i:9051440 original size:11 final size:11
Alignment explanation
Indices: 9051422--9051454 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9051412 CACATATATC
9051422 TCTTTTC-TTT
1 TCTTTTCTTTT
9051432 TCTTTTTCTTTT
1 TC-TTTTCTTTT
9051444 TCTTTTCTTTT
1 TCTTTTCTTTT
9051455 ATCTCATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 14 0.67
12 5 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:9053117 original size:29 final size:31
Alignment explanation
Indices: 9053072--9053143 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
9053062 TAGCTTATAT
9053072 ACTTAATTAATATTTAATTAA-TCTAAT-TTA
1 ACTTAATTAATATTTAATTAAGT-TAATCTTA
9053102 ACTT-ATTAA-ATCTTAATTAAGTTAATCTTA
1 ACTTAATTAATAT-TTAATTAAGTTAATCTTA
9053132 ACTTTAATTAAT
1 AC-TTAATTAAT
9053144 CAATTTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
30 10 0.28
31 2 0.06
32 5 0.14
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (31 bp):
ACTTAATTAATATTTAATTAAGTTAATCTTA
Found at i:9058536 original size:29 final size:30
Alignment explanation
Indices: 9058499--9058571 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
9058489 CAGCCAAAGT
* *
9058499 TTCATGTATATAATTACAC-CAAATTAAAA
1 TTCAAGTATATAATTACACACAAATCAAAA
*
9058528 TTCAAGTAT-TATATTACACATTAAATCAAAA
1 TTCAAGTATATA-ATTACACA-CAAATCAAAA
9058559 TTC-A-TATATAATT
1 TTCAAGTATATAATT
9058572 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 21 0.57
30 3 0.08
31 11 0.30
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (30 bp):
TTCAAGTATATAATTACACACAAATCAAAA
Found at i:9069896 original size:16 final size:16
Alignment explanation
Indices: 9069875--9069924 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
9069865 GAAATTTAAT
9069875 TATTTTATTGAA-ATAA
1 TATTTTATT-AATATAA
9069891 TATTTTAATTAATATAA
1 TATTTT-ATTAATATAA
9069908 T-TTTTATTTAATA-AA
1 TATTTTA-TTAATATAA
9069923 TA
1 TA
9069925 ATAATTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
16 18 0.60
17 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTTTATTAATATAA
Found at i:9083380 original size:44 final size:46
Alignment explanation
Indices: 9083294--9083386 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
9083284 ATAGGGCTGT
*
9083294 AATGGAATAGAGTTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
*
9083340 AATGGAATAGAGCTGTAAT-AG-AATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGAATGG
9083384 AAT
1 AAT
9083387 AGATGTTGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 2 0.05
46 18 0.41
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:9083618 original size:21 final size:20
Alignment explanation
Indices: 9083594--9083643 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
9083584 TAATTATTAT
9083594 TATATGAAT-TAAAAAATATAA
1 TATAT-AATATAAAAAA-ATAA
*
9083615 TATATAATACTATAAAAATAA
1 TATATAATA-TAAAAAAATAA
9083636 TATATAAT
1 TATATAAT
9083644 CTACTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 6 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TATATAATATAAAAAAATAA
Found at i:9086888 original size:14 final size:14
Alignment explanation
Indices: 9086869--9086898 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9086859 ATCACCCAAA
9086869 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
9086883 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
9086897 AA
1 AA
9086899 TGTGTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:9089775 original size:9 final size:9
Alignment explanation
Indices: 9089761--9089844 Score: 114
Period size: 9 Copynumber: 9.3 Consensus size: 9
9089751 TTTGGTTAAA
9089761 AATTAACCG
1 AATTAACCG
9089770 AATTAACCG
1 AATTAACCG
*
9089779 AATTAACCA
1 AATTAACCG
* *
9089788 AATTATCCA
1 AATTAACCG
9089797 AATTAACCG
1 AATTAACCG
*
9089806 AATTACCCG
1 AATTAACCG
*
9089815 AATTACCCG
1 AATTAACCG
9089824 AATTAACCG
1 AATTAACCG
*
9089833 AATTACCCG
1 AATTAACCG
9089842 AAT
1 AAT
9089845 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 68 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:9096561 original size:13 final size:13
Alignment explanation
Indices: 9096540--9096603 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
9096530 ACACTCAAAT
9096540 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
9096553 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
9096566 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
9096579 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
9096592 TTTTCAAAAGCA
1 TTTTCAAAAGCA
9096604 ATAAAGAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 5 0.12
13 34 0.79
14 4 0.09
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:9104228 original size:5 final size:6
Alignment explanation
Indices: 9104213--9104237 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9104203 ATATGAAACA
9104213 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
9104238 TGATATTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9105928 original size:27 final size:27
Alignment explanation
Indices: 9105897--9105948 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9105887 ACAAACAACA
*
9105897 AAATTCAAAACAAAGGAAAACAGAAGC
1 AAATTCAAAAAAAAGGAAAACAGAAGC
* *
9105924 AAATTCAAAAAAAATGATAACAGAA
1 AAATTCAAAAAAAAGGAAAACAGAA
9105949 AATTTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (27 bp):
AAATTCAAAAAAAAGGAAAACAGAAGC
Found at i:9109101 original size:27 final size:28
Alignment explanation
Indices: 9109068--9109161 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 28
9109058 AAACAAACAA
*
9109068 CAAAATTCAAAACAAAGGAAAACAGCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
* * *
9109096 C-AAATTCAAAATAAATGATAACACCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
*
9109123 CAAAATTC-AAATAAA-GAATAACACCAG
1 CAAAATTCAAAACAAAGGAA-AACACCAG
*
9109150 -AAAGTT-AAAACA
1 CAAAATTCAAAACA
9109162 CATGATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 11 0.20
27 38 0.68
28 7 0.12
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.14
Consensus pattern (28 bp):
CAAAATTCAAAACAAAGGAAAACACCAG
Found at i:9109927 original size:27 final size:27
Alignment explanation
Indices: 9109900--9109959 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
9109890 AACAAAAAAA
* *
9109900 TTCAAAATAAATGATAACACCAGCAAAT
1 TTCAAAATAAAGGATAACACCAG-AAAG
*
9109928 TTC-AAATAAAGGATAACCCCAGAAAG
1 TTCAAAATAAAGGATAACACCAGAAAG
9109954 TTCAAA
1 TTCAAA
9109960 CACATTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 19 0.68
28 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (27 bp):
TTCAAAATAAAGGATAACACCAGAAAG
Found at i:9113645 original size:181 final size:181
Alignment explanation
Indices: 9113341--9113783 Score: 868
Period size: 181 Copynumber: 2.4 Consensus size: 181
9113331 TAGCTCTTAC
*
9113341 CACACCACCAACAATAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
1 CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
9113406 AGAGAGAGAGAAGCAGATTTCCTCGGGTTTCATTGAGCTCCTATTGCATTTTACCCAATGATGGA
66 AGAGAGAGAGAAGCAGATTTCCTCGGGTTTCATTGAGCTCCTATTGCATTTTACCCAATGATGGA
9113471 AACTTGGTTTTGATTGAATGGTTTTGGTTTTCAATTTATCTTTAGCTTTTT
131 AACTTGGTTTTGATTGAATGGTTTTGGTTTTCAATTTATCTTTAGCTTTTT
9113522 CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
1 CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
9113587 AGAGAGAGAGAAGCAGATTTCCTCGGGTTTCATTGAGCTCCTATTGCATTTTACCCAATGATGGA
66 AGAGAGAGAGAAGCAGATTTCCTCGGGTTTCATTGAGCTCCTATTGCATTTTACCCAATGATGGA
9113652 AACTTGGTTTTGATTGAATGGTTTTGGTTTTCAATTTATCTTTAGCTTTTT
131 AACTTGGTTTTGATTGAATGGTTTTGGTTTTCAATTTATCTTTAGCTTTTT
9113703 CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
1 CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
*
9113768 AGAGACAGAGAAGCAG
66 AGAGAGAGAGAAGCAG
9113784 GCGGTGTGAA
Statistics
Matches: 260, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 260 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (181 bp):
CACACCACCAACACTAATAAATAAAATAACTAAACAAACAAACATACACACATAATATGCATGAG
AGAGAGAGAGAAGCAGATTTCCTCGGGTTTCATTGAGCTCCTATTGCATTTTACCCAATGATGGA
AACTTGGTTTTGATTGAATGGTTTTGGTTTTCAATTTATCTTTAGCTTTTT
Found at i:9118385 original size:40 final size:40
Alignment explanation
Indices: 9118330--9118407 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
9118320 GATGTCAGGG
* * * *
9118330 GACGTGTCAGCAAATCGCGTCCACATCAGCGTGGTTTGCT
1 GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTGCT
*
9118370 GACGTGGCAGCAAATCCCGTCCACGTAAGCGCGGTTTG
1 GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTG
9118408 TGTCCACGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (40 bp):
GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTGCT
Found at i:9118608 original size:11 final size:11
Alignment explanation
Indices: 9118586--9118643 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
9118576 AACTAATCCT
9118586 CTCTCAAATTTC
1 CTCTC-AATTTC
9118598 CTCTCAATTTC
1 CTCTCAATTTC
*
9118609 CTCTAAATTTC
1 CTCTCAATTTC
*
9118620 CTCTCAATTTG
1 CTCTCAATTTC
*
9118631 CTCTCAAATTC
1 CTCTCAATTTC
9118642 CT
1 CT
9118644 TCCAAACTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:9118643 original size:22 final size:23
Alignment explanation
Indices: 9118586--9118640 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
9118576 AACTAATCCT
9118586 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
9118609 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
9118631 CTCTCAAATT
1 CTCTCAAATT
9118641 CCTTCCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:9118657 original size:33 final size:32
Alignment explanation
Indices: 9118585--9118659 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
9118575 AAACTAATCC
* * *
9118585 TCTCTCAAATTTCCTCTCAATTTCCTCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTCCAAACT
*
9118618 TCCTCTCAATTTGCTCTCAAATTCCTTCCAAACT
1 T-CTCTCAATTTCCTCTCAAATTCC-TCCAAACT
9118652 TCTCTCAA
1 TCTCTCAA
9118660 ATCCATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 24 0.67
34 12 0.33
ACGTcount: A:0.24, C:0.33, G:0.01, T:0.41
Consensus pattern (32 bp):
TCTCTCAATTTCCTCTCAAATTCCTCCAAACT
Found at i:9118679 original size:51 final size:51
Alignment explanation
Indices: 9118621--9118720 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
9118611 CTAAATTTCC
9118621 TCTCAATTTGCTCTCAAATTCCT-TCCAAACTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAACTTCTCTCAAATCCATATTTAA
* * * * * *
9118672 TCTCAATTTTCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAACTTCTCTCAAATCCATATTT
9118721 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAACTTCTCTCAAATCCATATTTAA
Found at i:9118756 original size:18 final size:19
Alignment explanation
Indices: 9118726--9118772 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
9118716 TATTTTTAAA
*
9118726 TAATTTTTAAAAAAATTAT
1 TAATTTTTAAAAAATTTAT
9118745 TAATTTTTAAAAAATTTAT
1 TAATTTTTAAAAAATTTAT
9118764 T--TTTTTAAA
1 TAATTTTTAAA
9118773 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
19 19 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTTTTAAAAAATTTAT
Found at i:9119881 original size:7 final size:7
Alignment explanation
Indices: 9119869--9119894 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9119859 TAGTCAATTG
9119869 GTATTTA
1 GTATTTA
9119876 GTATTTA
1 GTATTTA
9119883 GTATTTA
1 GTATTTA
9119890 GTATT
1 GTATT
9119895 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:9122309 original size:22 final size:22
Alignment explanation
Indices: 9122280--9122551 Score: 297
Period size: 22 Copynumber: 12.6 Consensus size: 22
9122270 NNNNNNNNNN
*
9122280 ACCCTTAAATTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
*
9122302 ACCTTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
* *
9122323 ACCTTTAACTTTAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
*
9122345 CCCCTTAACTTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
* * *
9122367 ACACTTAAATTAAAAACCCAAA
1 ACCCTTAACTTAAAAACCCTAA
** * *
9122389 ACTTTTAAGTTATAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
*
9122410 ACCCTTAACTTTAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
*
9122432 ACACTTAACTTAAAAA--CTATA
1 ACCCTTAACTTAAAAACCCTA-A
*
9122453 ACCCTTAAATTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
* **
9122475 ACCCTTAACTTTAAAACTGT-A
1 ACCCTTAACTTAAAAACCCTAA
* *
9122496 ACCCTTAAATAAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
*
9122517 ACACTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
9122538 ACCCTTAACTTAAA
1 ACCCTTAACTTAAA
9122552 TATAATTTGA
Statistics
Matches: 208, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
20 3 0.01
21 99 0.48
22 103 0.50
23 3 0.01
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (22 bp):
ACCCTTAACTTAAAAACCCTAA
Found at i:9122353 original size:43 final size:43
Alignment explanation
Indices: 9122280--9122551 Score: 330
Period size: 43 Copynumber: 6.3 Consensus size: 43
9122270 NNNNNNNNNN
*
9122280 ACCCTTAAATTAAAAACCCTAAACCTTTAACTTAAAAACCCTA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * *
9122323 ACCTTTAACTTTAAAACCCTAACCCCTTAACTTAAAAACCCTAA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCT-A
* * ** * *
9122367 ACACTTAAATTAAAAACCCAAAACTTTTAAGTTATAAACCCTA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * **
9122410 ACCCTTAACTTTAAAACCCTAAACACTTAACTTAAAAACTATA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* **
9122453 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTTAAAACTGTA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* *
9122496 ACCCTTAAATAAAAAACCCT-AACACTTAACTTAAAAACCCTA
1 ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
*
9122538 ACCCTTAACTTAAA
1 ACCCTTAAATTAAA
9122552 TATAATTTGA
Statistics
Matches: 191, Mismatches: 37, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
42 30 0.16
43 128 0.67
44 33 0.17
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (43 bp):
ACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
Found at i:9122528 original size:26 final size:26
Alignment explanation
Indices: 9122499--9122553 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 26
9122489 AACTGTAACC
9122499 CTTAAATAAAAAACCCTAACACTTAA
1 CTTAAATAAAAAACCCTAACACTTAA
*
9122525 C-T---T-AAAAACCCTAACCCTTAA
1 CTTAAATAAAAAACCCTAACACTTAA
9122546 CTTAAATA
1 CTTAAATA
9122554 TAATTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 10
0.68 0.03 0.29
Matches are distributed among these distances:
21 18 0.78
22 2 0.09
25 2 0.09
26 1 0.04
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (26 bp):
CTTAAATAAAAAACCCTAACACTTAA
Found at i:9126011 original size:127 final size:125
Alignment explanation
Indices: 9125727--9126058 Score: 452
Period size: 127 Copynumber: 2.6 Consensus size: 125
9125717 AACATGCTAT
* * * * *
9125727 TGTAACAAAAACGCGTCCACGTGGGCGCGATTTCACAAATTCTTTTCATAAAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* * * *
9125792 AGCG-ATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGTACCTAC
66 AGCGTTTTTTATACTACTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCAAC
*
9125851 TGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTG
* * *
9125915 CAGCGTTGTTTTATACTACTTGCTTAGAAATGTCAAGTCGAAATTATTTTTTCCAGGACCAAC
65 AAGCGTT-TTTTATACTACTTGCTCAGAAACGTCAAGTCGAAATTA-TTTTTCCAGGACCAAC
* * * * *
9125978 TGTAGCAAAAGCGCATCCACGAGGGCGCAATTTCACAAATTTTTCTCATAAAGCATCTTGTTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
*
9126043 AGCGTTTTTTAAACTA
66 AGCGTTTTTTATACTA
9126059 TTTTCCAGGA
Statistics
Matches: 182, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
123 2 0.01
124 59 0.32
126 44 0.24
127 75 0.41
128 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (125 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
AGCGTTTTTTATACTACTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCAAC
Found at i:9126557 original size:12 final size:13
Alignment explanation
Indices: 9126529--9126558 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9126519 TAATTGTTAA
9126529 TATTATTAAATTT
1 TATTATTAAATTT
9126542 TATTATTAAA-TT
1 TATTATTAAATTT
9126554 TATTA
1 TATTA
9126559 GATGTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTAAATTT
Found at i:9139162 original size:17 final size:17
Alignment explanation
Indices: 9139140--9139203 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
9139130 AATCTTAGAG
9139140 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
9139157 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
9139176 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
9139193 TTTTAATTGTA
1 TTCTAATTGTA
9139204 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:9139179 original size:36 final size:36
Alignment explanation
Indices: 9139132--9139202 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
9139122 GATTATGTAA
9139132 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
9139168 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
9139203 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:9139181 original size:19 final size:19
Alignment explanation
Indices: 9139131--9139187 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
9139121 AGATTATGTA
9139131 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
9139150 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
9139167 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
9139186 AT
1 AT
9139188 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:9139483 original size:48 final size:48
Alignment explanation
Indices: 9139411--9139502 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
9139401 GGAAATTCTG
*
9139411 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTGCTT
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTGCTT
* * *
9139459 TTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTT
9139503 TAAGCAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (48 bp):
TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTGCTT
Found at i:9144325 original size:36 final size:36
Alignment explanation
Indices: 9144273--9144343 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
9144263 GATTATGTAA
*
9144273 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* *
9144309 TCTTGGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
9144344 AGCCTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:9144623 original size:48 final size:48
Alignment explanation
Indices: 9144548--9144642 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
9144538 TGAGGGAATT
*
9144548 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTTG
*
9144596 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTT
9144643 TAAGCAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTTG
Found at i:9147214 original size:42 final size:42
Alignment explanation
Indices: 9147156--9147279 Score: 239
Period size: 42 Copynumber: 3.0 Consensus size: 42
9147146 GATGCAAGGG
9147156 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
*
9147198 ACACACGGCCAAACCACACGTTCGTGTGCATGATCGTGTGTC
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
9147240 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTG
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTG
9147280 GATGAAAATA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (42 bp):
ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
Found at i:9147901 original size:25 final size:25
Alignment explanation
Indices: 9147872--9147957 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
9147862 GCCCTCTCTC
9147872 GAGCCATATAACAAGAAGCTCATGT
1 GAGCCATATAACAAGAAGCTCATGT
* ** *
9147897 GAGCCATGTAACGGGAAGCTTATCCG-
1 GAGCCATATAACAAGAAGCTCAT--GT
** *
9147923 GA-CTGTATAACAAGAAGCTCATAT
1 GAGCCATATAACAAGAAGCTCATGT
9147947 GAGCCA-ATAAC
1 GAGCCATATAAC
9147958 GGGTAGCTCC
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
24 7 0.16
25 34 0.77
26 2 0.05
27 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAAGAAGCTCATGT
Found at i:9148150 original size:24 final size:25
Alignment explanation
Indices: 9148123--9148170 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
9148113 GGATGCTCCG
*
9148123 AAGAACTAT-TAACGAGAAGCTCGC
1 AAGAACCATATAACGAGAAGCTCGC
9148147 AAGAACCATATAACGAGAAGCTCG
1 AAGAACCATATAACGAGAAGCTCG
9148171 AGAGGGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (25 bp):
AAGAACCATATAACGAGAAGCTCGC
Found at i:9150525 original size:58 final size:58
Alignment explanation
Indices: 9150463--9150605 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 58
9150453 AAATTAGAAA
* * ** *
9150463 AAAAAGTGTCAAGTT-TAGATACCACATTGGACCGAAAAAACTAATGTA-ATAAATTAAG
1 AAAAAGTGTCAAGTTCAAG-TACCAAATTGGACAAAAAAAACTAATATATATAAA-TAAG
* *
9150521 AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTTATATATCTAAATAAG
1 AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTAATATATATAAATAAG
* *
9150579 AAAAAGTGTCAAATTCATGTACCAAAT
1 AAAAAGTGTCAAGTTCAAGTACCAAAT
9150606 ACTATATTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 68 0.92
59 6 0.08
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (58 bp):
AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTAATATATATAAATAAG
Found at i:9151501 original size:18 final size:18
Alignment explanation
Indices: 9151463--9151498 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9151453 TTATTATTTT
*
9151463 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
9151481 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
9151499 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:9154375 original size:37 final size:36
Alignment explanation
Indices: 9154274--9154375 Score: 89
Period size: 37 Copynumber: 2.7 Consensus size: 36
9154264 CGACCTTGAG
9154274 TCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA-AC--TTACTTCGGAT--AT
** ** *
9154315 TCGATGAGGTACTGGGTACCAACTTACTTCGGCT-T
1 TCGATGAGACACTGGGTGTCAACTTACTTCGGATAT
9154350 TGCCGATGAGACACTGGGTGTCAACT
1 T--CGATGAGACACTGGGTGTCAACT
9154376 ATTGCTTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.04
37 19 0.38
38 10 0.20
40 2 0.04
41 17 0.34
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (36 bp):
TCGATGAGACACTGGGTGTCAACTTACTTCGGATAT
Found at i:9157734 original size:35 final size:35
Alignment explanation
Indices: 9157688--9157756 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
9157678 AAGGGACTAA
*
9157688 ATTGAAATAGGGGTAAAAGTTTAATAATAGATTAC
1 ATTGAAATAGGGGTAAAAGTTGAATAATAGATTAC
9157723 ATTGAAATAGGGGTAAAAGTTGAATAATAGATTA
1 ATTGAAATAGGGGTAAAAGTTGAATAATAGATTA
9157757 AAGAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.30
Consensus pattern (35 bp):
ATTGAAATAGGGGTAAAAGTTGAATAATAGATTAC
Found at i:9157910 original size:14 final size:14
Alignment explanation
Indices: 9157844--9157903 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
9157834 GATATTTTAG
9157844 TTAATATATATTATA
1 TTAAT-TATATTATA
*
9157859 TTTATT-TACTTA-A
1 TTAATTATA-TTATA
* *
9157872 TAAATAAGTATTATA
1 TTAATTA-TATTATA
9157887 TTAATTATATTATA
1 TTAATTATATTATA
9157901 TTA
1 TTA
9157904 TATATATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
13 6 0.17
14 17 0.49
15 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAATTATATTATA
Found at i:9159243 original size:18 final size:17
Alignment explanation
Indices: 9159185--9159243 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
9159175 TTTTTTTGAG
*
9159185 AACACGAAAAATTTTTAA
1 AACACG-AAAATTCTTAA
**
9159203 AACACGAGGA-TCTTAGA
1 AACACGAAAATTCTTA-A
9159220 AACACGAAAATTCTTAA
1 AACACGAAAATTCTTAA
9159237 AAGCACG
1 AA-CACG
9159244 GGGATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 15 0.45
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (17 bp):
AACACGAAAATTCTTAA
Found at i:9159267 original size:38 final size:38
Alignment explanation
Indices: 9159218--9159291 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
9159208 GAGGATCTTA
*
9159218 GAAACACGAAAATTCTT-AAAAGCACGGGGATTTTTTTT
1 GAAACACGAAAATTCTTGAAAA-CACGGGAATTTTTTTT
* * *
9159256 GAAACATGAAAATTTTTGAAAACACGGTAATTTTTT
1 GAAACACGAAAATTCTTGAAAACACGGGAATTTTTT
9159292 AAAACACGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (38 bp):
GAAACACGAAAATTCTTGAAAACACGGGAATTTTTTTT
Found at i:9159278 original size:18 final size:18
Alignment explanation
Indices: 9159251--9159608 Score: 103
Period size: 18 Copynumber: 19.9 Consensus size: 18
9159241 ACGGGGATTT
*
9159251 TTTTTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
**
9159268 TTTTTGAAAACACGGTAA
1 TTTTTGAAAACACGAAAA
* **
9159286 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
9159304 TTTTTGGAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
9159322 -TTTTG-AAACACCG-AAG
1 TTTTTGAAAACA-CGAAAA
9159338 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*** * * ***
9159356 TTTTTTTTATCGCCTGAA
1 TTTTTGAAAACACGAAAA
* * *
9159374 TTTTTGGAAACGCGGAAA
1 TTTTTGAAAACACGAAAA
*
9159392 TTTTTG-AAACACCGAAATTT
1 TTTTTGAAAACA-CGAAA--A
* *
9159412 TTTTTAAAAAAACACGAAGA
1 TTTTT--GAAAACACGAAAA
* **
9159432 TTTTTG-AAACACAGTATT
1 TTTTTGAAAACAC-GAAAA
9159450 TTTTTG-AAACACAGAAAA
1 TTTTTGAAAACAC-GAAAA
*** **
9159468 -TTTTGAAAATTTGAATTTT
1 TTTTTGAAAACACGAA--AA
* * *
9159487 TTTTATGAAAATACGGGAAT
1 TTTT-TGAAAACAC-GAAAA
* *
9159507 TTTTTGAAAAAATGAAAA
1 TTTTTGAAAACACGAAAA
* *
9159525 ATTTTG-AAACACG--AG
1 TTTTTGAAAACACGAAAA
*
9159540 TTTTTGAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
9159558 TTTTTTAAAACGCAAAAA
1 TTTTTGAAAACACGAAAA
**
9159576 TTTTT--AAACACGAGATT
1 TTTTTGAAAACACGA-AAA
*
9159593 TTTTTTAAAACACGAA
1 TTTTTGAAAACACGAA
9159609 TATATTTTTT
Statistics
Matches: 248, Mismatches: 69, Indels: 47
0.68 0.19 0.13
Matches are distributed among these distances:
15 6 0.02
16 19 0.08
17 48 0.19
18 124 0.50
19 15 0.06
20 18 0.07
21 7 0.03
22 6 0.02
23 5 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:9159342 original size:70 final size:71
Alignment explanation
Indices: 9159252--9159413 Score: 184
Period size: 70 Copynumber: 2.3 Consensus size: 71
9159242 CGGGGATTTT
* ** *
9159252 TTTTGAAACA-TGAAAATTTTTGAAAACACGGTAATTTTTTAAAACACGGGAATTTTTGGAAAC-
1 TTTTGAAACACCG-AAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACG
*
9159315 ATGAAAA
65 AGGAAAA
* ** * * * *
9159322 TTTTGAAACACCGAAGTTTTTGAAAACACGAAAATTTTTTTTATCGCCTGAATTTTTGGAAACGC
1 TTTTGAAACACCGAAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACGA
*
9159387 GGAAAT
66 GGAAAA
9159393 TTTTGAAACACCGAAATTTTT
1 TTTTGAAACACCGAAATTTTT
9159414 TTTAAAAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
70 51 0.67
71 25 0.33
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (71 bp):
TTTTGAAACACCGAAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACGA
GGAAAA
Found at i:9159413 original size:17 final size:17
Alignment explanation
Indices: 9159251--9159413 Score: 82
Period size: 17 Copynumber: 9.3 Consensus size: 17
9159241 ACGGGGATTT
*
9159251 TTTTTGAAACA-TGAAAA
1 TTTTTGAAACACCG-AAA
* *
9159268 TTTTTGAAAACACGGTAAT
1 TTTTTG-AAACACCG-AAA
* * *
9159287 TTTTTAAAACACGGGAA
1 TTTTTGAAACACCGAAA
*
9159304 TTTTTGGAAACA-TGAAA
1 TTTTT-GAAACACCGAAA
* *
9159321 ATTTTGAAACACCGAAG
1 TTTTTGAAACACCGAAA
9159338 TTTTTGAAA-ACACGAAAA
1 TTTTTGAAACAC-CG-AAA
** * *
9159356 TTTTTTTTATCGCCTG-AA
1 -TTTTTGAAACACC-GAAA
* *
9159374 TTTTTGGAAACGCGGAAA
1 TTTTT-GAAACACCGAAA
9159392 TTTTTGAAACACCGAAA
1 TTTTTGAAACACCGAAA
9159409 TTTTT
1 TTTTT
9159414 TTTAAAAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.07
17 53 0.48
18 33 0.30
19 15 0.14
20 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACCGAAA
Found at i:9159443 original size:17 final size:17
Alignment explanation
Indices: 9159421--9159475 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
9159411 TTTTTTAAAA
9159421 AAACAC-GAAGATTTTTG
1 AAACACAGAA-ATTTTTG
**
9159438 AAACACAGTATTTTTTTG
1 AAACACAG-AAATTTTTG
*
9159456 AAACACAGAAAATTTTG
1 AAACACAGAAATTTTTG
9159473 AAA
1 AAA
9159476 ATTTGAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 15 0.48
18 15 0.48
19 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
AAACACAGAAATTTTTG
Done.