Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 174 of 318
Found at i:54028396 original size:40 final size:39
Alignment explanation
Indices: 54028231--54028414 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
54028221 AAATTGAATG
* * *
54028231 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
54028271 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
54028311 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
54028351 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
54028390 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
54028415 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:54028439 original size:80 final size:81
Alignment explanation
Indices: 54028271--54028459 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
54028261 GCTGGAAATT
* * * *
54028271 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
54028336 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
54028352 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
54028415 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
54028431 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
54028460 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:54039113 original size:40 final size:40
Alignment explanation
Indices: 54038972--54039156 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
54038962 TCGAATGATG
* *
54038972 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTTACTAAA
* * * * * *
54039012 TTCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTTACTAAA
54039052 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAA
* * * * *
54039091 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-AA
** *
54039132 -CCGGGCTTCGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54039157 AGCGAGTCGT
Statistics
Matches: 116, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
39 33 0.28
40 74 0.64
41 9 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAA
Found at i:54039136 original size:79 final size:81
Alignment explanation
Indices: 54038972--54039156 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
54038962 TCGAATGATG
* ** *
54038972 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATTCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
54039036 CGTGCGAGTTAATAAA
66 CGTGCGAGTCAATAAA
* **
54039052 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
54039114 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATA-AA
** *
54039132 -CCGGGCTTCGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54039157 AGCGAGTCGT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATAAA
Found at i:54045540 original size:29 final size:28
Alignment explanation
Indices: 54045425--54045543 Score: 105
Period size: 28 Copynumber: 4.2 Consensus size: 28
54045415 ACCCCTACAT
*
54045425 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACT-GGCCCAAATC
** * **
54045453 TTATTCAAATGGCCCATCTGGCCCAGTTC
1 ACATTCATATGGCCCA-CTGGCCCAAATC
* * * *
54045482 ATATTCTTAAGGCCCACTGGCCCAATTC
1 ACATTCATATGGCCCACTGGCCCAAATC
*
54045510 ACATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACT-GGCCCAAATC
54045539 ACATT
1 ACATT
54045544 ATACTCATGC
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
28 42 0.58
29 30 0.42
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (28 bp):
ACATTCATATGGCCCACTGGCCCAAATC
Found at i:54050523 original size:40 final size:40
Alignment explanation
Indices: 54050466--54050691 Score: 291
Period size: 40 Copynumber: 5.7 Consensus size: 40
54050456 TCGAATGATG
* * * *
54050466 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
54050506 TCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54050546 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54050586 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
**
54050626 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
54050667 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGACTAAGAT-CCGAAGGCATTTG
54050692 AATGAGTAGC
Statistics
Matches: 172, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.01
40 162 0.94
41 9 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54053416 original size:2 final size:2
Alignment explanation
Indices: 54053409--54053437 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54053399 CTGATTGGAG
54053409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54053438 GAGTACGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54053533 original size:29 final size:29
Alignment explanation
Indices: 54053501--54053600 Score: 191
Period size: 29 Copynumber: 3.4 Consensus size: 29
54053491 ATTTAAGCCC
*
54053501 GCACACATAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54053530 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54053559 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54053588 GCACACTTAGTGC
1 GCACACTTAGTGC
54053601 TAATCTCGTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:54053542 original size:58 final size:58
Alignment explanation
Indices: 54053472--54053600 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
54053462 ACTCGATTTC
* *
54053472 GCACACTTAGTGCCATGCGATTT-AAGCCCGCACACATAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCAT-AGATTTCAAGCACGCACACATAGTGCCATATATTTCCAGCAT
* * * *
54053530 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATAGATTTCAAGCACGCACACATAGTGCCATATATTTCCAGCAT
54053588 GCACACTTAGTGC
1 GCACACTTAGTGC
54053601 TAATCTCGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 4 0.06
58 60 0.94
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (58 bp):
GCACACTTAGTGCCATAGATTTCAAGCACGCACACATAGTGCCATATATTTCCAGCAT
Found at i:54061204 original size:2 final size:2
Alignment explanation
Indices: 54061197--54061227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54061187 CCGATTGGAG
54061197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54061228 GAGTACGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54061295 original size:29 final size:29
Alignment explanation
Indices: 54061261--54061365 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 29
54061251 TACTCGATTT
* * *
54061261 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * * *
54061290 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
54061319 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
54061348 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
54061366 TATTTCCAGC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:54061366 original size:29 final size:29
Alignment explanation
Indices: 54061320--54061390 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
54061310 CTTCGAGCTC
54061320 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54061349 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54061378 GCACACTTAGTGC
1 GCACACTTAGTGC
54061391 TAATCTCGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:54069706 original size:79 final size:79
Alignment explanation
Indices: 54069558--54069782 Score: 314
Period size: 79 Copynumber: 2.8 Consensus size: 79
54069548 TCGAATGATG
* * *
54069558 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGG-CTAAGATCCGAAGGCATT
54069622 TGTGCGAGTTACTAAA
64 TGTGCGAGTTACTAAA
*
54069638 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGCTAAGATCCGAAGGCATTT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGCTAAGATCCGAAGGCATTT
54069702 GTGCGAGTTACTAAA
65 GTGCGAGTTACTAAA
* *
54069717 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC-GGCTAAGAT-CCGAAGGCAT
54069780 TTG
63 TTG
54069783 AACGAGTAGC
Statistics
Matches: 132, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
78 1 0.01
79 71 0.54
80 52 0.39
81 8 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGCTAAGATCCGAAGGCATTTG
TGCGAGTTACTAAA
Found at i:54069774 original size:119 final size:119
Alignment explanation
Indices: 54069562--54069782 Score: 299
Period size: 119 Copynumber: 1.9 Consensus size: 119
54069552 ATGATGTCCG
*
54069562 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
54069627 GAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCC
66 GAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCC
* * **
54069681 GGCTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 GGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATTTG
* *
54069743 TGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTG
63 TGCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
54069783 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
118 2 0.02
119 78 0.87
120 10 0.11
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:54069789 original size:40 final size:40
Alignment explanation
Indices: 54069558--54069782 Score: 300
Period size: 40 Copynumber: 5.7 Consensus size: 40
54069548 TCGAATGATG
* * *
54069558 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
54069598 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
54069638 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54069678 TCC-GGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
54069717 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
54069758 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGGCTAAGAT-CCGAAGGCATTTG
54069783 AACGAGTAGC
Statistics
Matches: 172, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
39 39 0.23
40 123 0.72
41 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54069789 original size:119 final size:119
Alignment explanation
Indices: 54069562--54069815 Score: 297
Period size: 119 Copynumber: 2.1 Consensus size: 119
54069552 ATGATGTCCG
*
54069562 GGCTAAG-TCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGCTAAGAT-CCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTG
**
54069626 CGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAATCC
65 CGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAATCC
* * **
54069681 GGCTAAGATCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGT
1 GGCTAAGATCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATTTGT
* * *
54069744 GCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATATCC
64 GCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAATCC
*
54069800 GGTTAA-ACTCCGAAGG
1 GGCTAAGA-TCCGAAGG
54069816 TACGTGATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
118 5 0.04
119 102 0.87
120 10 0.09
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (119 bp):
GGCTAAGATCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAATCC
Found at i:54069813 original size:79 final size:78
Alignment explanation
Indices: 54069571--54069815 Score: 284
Period size: 79 Copynumber: 3.1 Consensus size: 78
54069561 GGGCTAAGTC
* * * *
54069571 CCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACT
*
54069635 AAATCCGGACTAAGAT
65 AAATCCGG-TTAA-AT
54069651 CCGAAGGCATTTGTGCGAGTTACTA-AATCC-GGCTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACT
*
54069714 AAATCCGGGTTAAGT
65 AAATCC-GGTTAAAT
* **
54069729 CCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACGAG-TAG
1 -CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTA-
*
54069792 CTATATCCGGTTAAACT
63 CTAAATCCGGTTAAA-T
54069809 CCGAAGG
1 CCGAAGG
54069816 TACGTGATTC
Statistics
Matches: 145, Mismatches: 11, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
78 1 0.01
79 85 0.59
80 52 0.36
81 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTA
AATCCGGTTAAAT
Found at i:54077740 original size:40 final size:40
Alignment explanation
Indices: 54077683--54077907 Score: 282
Period size: 40 Copynumber: 5.7 Consensus size: 40
54077673 TCGAATGATG
* * * *
54077683 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
54077723 TCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54077763 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54077803 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
**
54077843 T-CGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
54077883 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGACTAAGAT-CCGAAGGCATTTG
54077908 AACGAGTAGC
Statistics
Matches: 170, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 32 0.19
40 130 0.76
41 7 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54077929 original size:79 final size:79
Alignment explanation
Indices: 54077690--54077930 Score: 294
Period size: 79 Copynumber: 3.0 Consensus size: 79
54077680 ATGTCCGGGC
* * * *
54077690 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTCGTGCGA
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGACTAAGATCCGAAGGCATTTGTGCGA
*
54077754 GTTACTAAATCCGGAC
65 GTTACTAAATCCGG-T
54077770 TAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGATCCGAAGGCATTTGTGCG
1 TAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGACTAAGATCCGAAGGCATTTGTGCG
*
54077833 AGTTACTAAATCGGGT
64 AGTTACTAAATCCGGT
* * **
54077849 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACGA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGAT-CCGAAGGCATTTGTGCGA
*
54077913 G-TAGCTATATCCGGT
65 GTTA-CTAAATCCGGT
54077928 TAA
1 TAA
54077931 ACTCCGAAGG
Statistics
Matches: 142, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
78 4 0.03
79 67 0.47
80 63 0.44
81 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (79 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATTTGTGCGAG
TTACTAAATCCGGT
Found at i:54081800 original size:29 final size:29
Alignment explanation
Indices: 54081719--54081833 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
54081709 TGCATACATG
* *
54081719 CATATGACCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* * *
54081747 CAAATGGCCCATCT-GGCCGAGTTCATATT
1 CATATGGCCCA-CTAGGCCCAATTCATATT
* * *
54081776 CTTATTGCCCACTAGGCCCAATTCACATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* * *
54081805 CATACGGCCCAGTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAATTCATATT
54081834 ATACTCATGC
Statistics
Matches: 67, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
28 16 0.24
29 51 0.76
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAATTCATATT
Found at i:54104357 original size:37 final size:37
Alignment explanation
Indices: 54104278--54104360 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
54104268 AACCTTTAGT
* * *
54104278 TCGGGGCTTACCCGGACAAAATCTCCACCCGTGGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
*
54104315 TCGGGTCTTACCCGGACATAATCTCCACACGTAGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
54104352 TCGGGTCTT
1 TCGGGTCTT
54104361 TAGAGCTCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.24
Consensus pattern (37 bp):
TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
Found at i:54104547 original size:47 final size:47
Alignment explanation
Indices: 54104478--54105338 Score: 1328
Period size: 47 Copynumber: 18.3 Consensus size: 47
54104468 CCCTTCGGGA
* * * * *
54104478 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54104525 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATT-AGGC
* *
54104572 CTTATCACATATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
54104619 CTTGTCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
54104666 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54104713 CTTATCACATATATACACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54104760 ATTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
54104807 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54104854 ATTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54104901 CTTGTCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
54104948 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54104995 CTTGTCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105042 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105089 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105136 CTTATCACATATATACACTTTCACCTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105183 CTTATCACATATATACACTTTCACCTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105230 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54105277 CTTATCACATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54105324 CTTATAACATATATA
1 CTTATCACATATATA
54105339 TATCTCATAC
Statistics
Matches: 752, Mismatches: 60, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
46 1 0.00
47 751 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54104556 original size:25 final size:25
Alignment explanation
Indices: 54104528--54104606 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
54104518 ACTCGGCCTT
*
54104528 ATCACATATATACACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
* * *
54104553 ATCACAT-T-GGC-CATTCAGCCTT-
1 ATCACATATATGCACTTTCA-CATTC
54104575 ATCACATATATGCACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
54104600 ATCACAT
1 ATCACAT
54104607 GGGCCATTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 12 0.29
23 5 0.12
24 6 0.14
25 19 0.45
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACTTTCACATTC
Found at i:54105144 original size:22 final size:22
Alignment explanation
Indices: 54105117--54105239 Score: 66
Period size: 22 Copynumber: 5.3 Consensus size: 22
54105107 TTTCACATTC
54105117 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
**** ***
54105139 ATCACATATATACACTTTCACCTT
1 ATCACAT-CGGCCA-TTAGGCCTT
54105163 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
**** ***
54105186 ATCACATATATACACTTTCACCTT
1 ATCACAT-CGGCCA-TTAGGCCTT
54105210 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
54105233 ATCACAT
1 ATCACAT
54105240 ATATACACTT
Statistics
Matches: 67, Mismatches: 28, Indels: 12
0.63 0.26 0.11
Matches are distributed among these distances:
22 21 0.31
23 16 0.24
24 16 0.24
25 14 0.21
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.31
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:54105168 original size:25 final size:24
Alignment explanation
Indices: 54105135--54105217 Score: 71
Period size: 25 Copynumber: 3.5 Consensus size: 24
54105125 GGCCATTAGG
54105135 CCTTATCACATATATACACTTTCA
1 CCTTATCACATATATACACTTTCA
**** ***
54105159 CCTTCATCACAT-CGGCCA-TTAGG
1 CCTT-ATCACATATATACACTTTCA
54105182 CCTTATCACATATATACACTTTCA
1 CCTTATCACATATATACACTTTCA
54105206 CCTTCATCACAT
1 CCTT-ATCACAT
54105218 CGGCCATTAG
Statistics
Matches: 41, Mismatches: 14, Indels: 7
0.66 0.23 0.11
Matches are distributed among these distances:
22 7 0.17
23 8 0.20
24 12 0.29
25 14 0.34
ACGTcount: A:0.29, C:0.33, G:0.05, T:0.34
Consensus pattern (24 bp):
CCTTATCACATATATACACTTTCA
Found at i:54108699 original size:25 final size:25
Alignment explanation
Indices: 54108662--54108712 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
54108652 AAGGAATTCG
54108662 CACACACACAGTGGCTC-TAATCATT
1 CACACACACAGT-GCTCTTAATCATT
* *
54108687 CACACACATAGTGCTCTTATTCATT
1 CACACACACAGTGCTCTTAATCATT
54108712 C
1 C
54108713 GTTATTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (25 bp):
CACACACACAGTGCTCTTAATCATT
Found at i:54108939 original size:40 final size:40
Alignment explanation
Indices: 54108890--54109160 Score: 425
Period size: 40 Copynumber: 6.8 Consensus size: 40
54108880 CCAGCATGAT
* * *
54108890 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
54108930 TGCTCTTCGGGACTTAGTCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
54108970 CGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
54109010 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
54109050 CGCTCTTCGGAACTTAGTCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
54109090 CGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
54109130 TGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TGCTCTTCGGAACTTAGTCCGGATACATCAC
54109161 ACTCAATGCT
Statistics
Matches: 216, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 216 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:54111117 original size:37 final size:37
Alignment explanation
Indices: 54111076--54111148 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
54111066 CTTTAGTTCG
* * *
54111076 GGTCTTACCCGGACAAAATCTCCACCCGTGGTCATCA
1 GGTCTTACCCAGACAAAATCTCCACACGTAGTCATCA
*
54111113 GGTCTTACCCAGACATAATCTCCACACGTAGTCATC
1 GGTCTTACCCAGACAAAATCTCCACACGTAGTCATC
54111149 GACTCTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.23
Consensus pattern (37 bp):
GGTCTTACCCAGACAAAATCTCCACACGTAGTCATCA
Found at i:54111342 original size:47 final size:47
Alignment explanation
Indices: 54111273--54111992 Score: 1116
Period size: 47 Copynumber: 15.3 Consensus size: 47
54111263 ACCTTCGGGA
* * * *
54111273 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54111320 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54111367 CTTATCACATATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
54111414 CTTGTCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54111461 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54111508 CTTATCACATATATACACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54111555 CTTGTCACATATATACACTATCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54111602 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54111649 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54111696 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54111743 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54111790 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54111837 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54111884 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54111931 CTTATCACATATATGCACTTTCACATTCATCACAATGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54111978 CTTATCACATATATA
1 CTTATCACATATATA
54111993 TATCTCATAC
Statistics
Matches: 620, Mismatches: 53, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 620 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:54111351 original size:25 final size:25
Alignment explanation
Indices: 54111323--54111401 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
54111313 ACTCGGCCTT
*
54111323 ATCACATATATACACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
* * * *
54111348 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACTTTC-ACATTC
54111370 ATCACATATATGCACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
54111395 ATCACAT
1 ATCACAT
54111402 GGGCCATTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.12
24 6 0.15
25 18 0.45
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACTTTCACATTC
Found at i:54115652 original size:18 final size:18
Alignment explanation
Indices: 54115629--54115664 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54115619 ATGGAAGTGT
54115629 ATGATTGTTTAAGGGTGA
1 ATGATTGTTTAAGGGTGA
54115647 ATGATTGTTTAAGGGTGA
1 ATGATTGTTTAAGGGTGA
54115665 CCAATGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (18 bp):
ATGATTGTTTAAGGGTGA
Found at i:54116945 original size:25 final size:25
Alignment explanation
Indices: 54116917--54116983 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
54116907 TCCTATACAT
*
54116917 GTATGCTCATATGAGCTATGAATCA
1 GTATGCTCATATGAGCTATAAATCA
54116942 GTATGCTC-TCATGAGCTATAAATCA
1 GTATGCTCAT-ATGAGCTATAAATCA
* *
54116967 ATAAT-CTCATACGAGCT
1 GT-ATGCTCATATGAGCT
54116984 GAGAATCGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 1 0.03
25 32 0.89
26 3 0.08
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAAATCA
Found at i:54116983 original size:50 final size:50
Alignment explanation
Indices: 54116921--54117045 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
54116911 ATACATGTAT
* * * *
54116921 GCTCATATGAGCT-ATGAATCAGTATGCTCTCATGAGCTATAAATCAATAA
1 GCTCATACGAGCTGA-GAATCAGTAAGCTCTCACGAGCTACAAATCAATAA
* * * **
54116971 TCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
1 GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTACAAATCAATAA
54117021 GCTCATACGAGCTGAGAATCAGTAA
1 GCTCATACGAGCTGAGAATCAGTAA
54117046 TCCCTAATGA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 62 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (50 bp):
GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTACAAATCAATAA
Found at i:54116990 original size:25 final size:25
Alignment explanation
Indices: 54116962--54117045 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 25
54116952 ATGAGCTATA
* *
54116962 AATCAATAATCTCATACGAGCTGAG
1 AATCAGTAAGCTCATACGAGCTGAG
*
54116987 AATCGGTAAGCTC-TCACGAGCTGCA-
1 AATCAGTAAGCTCAT-ACGAGCTG-AG
*
54117012 AATCGGTAAGCTCATACGAGCTGAG
1 AATCAGTAAGCTCATACGAGCTGAG
54117037 AATCAGTAA
1 AATCAGTAA
54117046 TCCCTAATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.04
25 47 0.92
26 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (25 bp):
AATCAGTAAGCTCATACGAGCTGAG
Found at i:54131433 original size:21 final size:21
Alignment explanation
Indices: 54131404--54131444 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54131394 TAATTAACTT
*
54131404 ATTTCTTGATTTTTAAATTTA
1 ATTTATTGATTTTTAAATTTA
54131425 ATTTATTGATTTTTAAATTT
1 ATTTATTGATTTTTAAATTT
54131445 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTTATTGATTTTTAAATTTA
Found at i:54131498 original size:13 final size:13
Alignment explanation
Indices: 54131480--54131504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54131470 TAAACTGTAA
54131480 TTAATTAATTTCT
1 TTAATTAATTTCT
54131493 TTAATTAATTTC
1 TTAATTAATTTC
54131505 GATTTTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTAATTTCT
Found at i:54133048 original size:19 final size:18
Alignment explanation
Indices: 54133019--54133198 Score: 95
Period size: 19 Copynumber: 9.5 Consensus size: 18
54133009 CATTTTCTAT
*
54133019 AATTAAATTTGATTTTTA
1 AATTAATTTTGATTTTTA
54133037 AATTTAATTTTGATTTTTTA
1 AA-TTAATTTTGA-TTTTTA
*
54133057 AATTAATTTT-A-TTTAA
1 AATTAATTTTGATTTTTA
*
54133073 AACTGTAATTAACTTG-TTTCTTT
1 AA-T-TAATT---TTGATTT-TTA
*
54133096 AATTAATTTTGATCTTTA
1 AATTAATTTTGATTTTTA
54133114 AATTTAATTTTGATTTTTTA
1 AA-TTAATTTTGA-TTTTTA
*
54133134 AAATAA---T-ATTTTTA
1 AATTAATTTTGATTTTTA
* *
54133148 AATTGTAATTAATTTATTTCTTT
1 AA-T-TAATT--TTGATTT-TTA
*
54133171 AATTAATTTTGAATTTTAA
1 AATTAATTTTG-ATTTTTA
54133190 AATTAATTT
1 AATTAATTT
54133199 CATTTTAATT
Statistics
Matches: 126, Mismatches: 13, Indels: 45
0.68 0.07 0.24
Matches are distributed among these distances:
14 8 0.06
15 1 0.01
16 10 0.08
17 1 0.01
18 15 0.12
19 44 0.35
20 19 0.15
21 13 0.10
22 8 0.06
23 7 0.06
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (18 bp):
AATTAATTTTGATTTTTA
Found at i:54133107 original size:77 final size:75
Alignment explanation
Indices: 54133012--54133198 Score: 266
Period size: 77 Copynumber: 2.5 Consensus size: 75
54133002 GTCATCCCAT
* * * *
54133012 TTTCTATAATTAAATTTGATTTTTAAATTTAATTTTGATTTTTTAAATTAATTTTATTTAAAACT
1 TTTCTTTAATTAATTTTGATTTTTAAATTTAATTTTGATTTTTTAAAATAATATT-TTT-AAACT
*
54133077 GTAATTAACTTG
64 GTAATTAACTTA
* *
54133089 TTTCTTTAATTAATTTTGATCTTTAAATTTAATTTTGATTTTTTAAAATAATATTTTTAAATTGT
1 TTTCTTTAATTAATTTTGATTTTTAAATTTAATTTTGATTTTTTAAAATAATATTTTTAAACTGT
*
54133154 AATTAATTTA
66 AATTAACTTA
* *
54133164 TTTCTTTAATTAATTTTGAATTTTAAAATTAATTT
1 TTTCTTTAATTAATTTTGATTTTTAAATTTAATTT
54133199 CATTTTAATT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 46 0.46
76 3 0.03
77 50 0.51
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (75 bp):
TTTCTTTAATTAATTTTGATTTTTAAATTTAATTTTGATTTTTTAAAATAATATTTTTAAACTGT
AATTAACTTA
Found at i:54133208 original size:15 final size:15
Alignment explanation
Indices: 54133148--54133220 Score: 56
Period size: 17 Copynumber: 4.5 Consensus size: 15
54133138 AATATTTTTA
*
54133148 AATTGTAATTAATTT
1 AATTTTAATTAATTT
*
54133163 ATTTCTTTAATTAATTTT
1 A-AT-TTTAATTAA-TTT
54133181 GAATTTTAAAATTAATTT
1 -AATTTT--AATTAATTT
* *
54133199 CATTTTAATTTATTT
1 AATTTTAATTAATTT
54133214 AATTTTA
1 AATTTTA
54133221 CAACAATAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
15 15 0.33
16 1 0.02
17 16 0.35
18 7 0.15
19 7 0.15
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
AATTTTAATTAATTT
Found at i:54133235 original size:18 final size:18
Alignment explanation
Indices: 54133212--54133275 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
54133202 TTTAATTTAT
*
54133212 TTAATTTTACAACAATAG
1 TTAATTTTACAACAATAA
*
54133230 TTAATTTTA-AA-ATTAA
1 TTAATTTTACAACAATAA
*
54133246 AT-ATTTTACAACAATAA
1 TTAATTTTACAACAATAA
*
54133263 TTAATTATACAAC
1 TTAATTTTACAAC
54133276 CATATTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.16
16 6 0.16
17 7 0.19
18 18 0.49
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAATTTTACAACAATAA
Found at i:54136508 original size:42 final size:41
Alignment explanation
Indices: 54136461--54136612 Score: 137
Period size: 41 Copynumber: 3.7 Consensus size: 41
54136451 AATCATACCA
* *
54136461 ATGCCATATCCCAGATAAGGTCTTACATGGGATCTTATATCG
1 ATGCCATATCCCAGATATGGTCTTACAT-GGATCTCATATCG
* *
54136503 ATGCCAATAGCCCAGCTATGGTCTTACAT-GATTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGGA-TCTCATATCG
* * * * * * * * *
54136545 ATGCCATGTTCCAGACACGGTCCTATA-GAAATCTCATAACA
1 ATGCCATATCCCAGATATGGTCTTACATG-GATCTCATATCG
54136586 ATGCCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
54136613 CGTAAACTCA
Statistics
Matches: 85, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
41 45 0.53
42 20 0.24
43 20 0.24
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACATGGATCTCATATCG
Found at i:54136526 original size:43 final size:42
Alignment explanation
Indices: 54136461--54136550 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
54136451 AATCATACCA
* *
54136461 ATGCC-ATATCCCAGATAAGGTCTTACATGGGA-TCTTATATCG
1 ATGCCAATAGCCCAGATAAGGTCTTACAT--GATTCTCATATCG
* *
54136503 ATGCCAATAGCCCAGCTATGGTCTTACATGATTCTCATATCG
1 ATGCCAATAGCCCAGATAAGGTCTTACATGATTCTCATATCG
54136545 ATGCCA
1 ATGCCA
54136551 TGTTCCAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.05
42 20 0.48
43 20 0.48
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (42 bp):
ATGCCAATAGCCCAGATAAGGTCTTACATGATTCTCATATCG
Found at i:54137514 original size:22 final size:22
Alignment explanation
Indices: 54137488--54137532 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
54137478 GTTCTTTTTA
54137488 CTTATTCATGCTCATTTTTGTC
1 CTTATTCATGCTCATTTTTGTC
*
54137510 CTTATTCATGCTTATTTTTGTC
1 CTTATTCATGCTCATTTTTGTC
54137532 C
1 C
54137533 ATAAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (22 bp):
CTTATTCATGCTCATTTTTGTC
Found at i:54138993 original size:47 final size:47
Alignment explanation
Indices: 54138930--54139323 Score: 644
Period size: 47 Copynumber: 8.4 Consensus size: 47
54138920 CCCTTCGGGA
* *
54138930 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
54138977 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
54139024 CTTATCTCATATATACACTTTCACATTCATCACCTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
54139071 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
54139118 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
54139165 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
54139212 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
54139259 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
54139306 CTTATCACATATACACAC
1 CTTATCACATATATACAC
54139324 CTTGTACATC
Statistics
Matches: 322, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 322 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:54145651 original size:27 final size:27
Alignment explanation
Indices: 54145613--54145748 Score: 166
Period size: 27 Copynumber: 5.0 Consensus size: 27
54145603 CCCAAATCGA
*
54145613 TAAAATGACTATTTTTCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
54145640 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
54145667 TAAAATGACTATTTTGCCCTTATATTG
1 TAAAATGACTATTTTGCCCTTATGTGG
** **
54145694 TAAAATGACTGA-AATGCCCTTACATGG
1 TAAAATGACT-ATTTTGCCCTTATGTGG
* * *
54145721 TAAAATGATTGTTTTGCCCCTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
54145748 T
1 T
54145749 GTATATATGT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
27 92 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:54148841 original size:40 final size:40
Alignment explanation
Indices: 54148797--54148880 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
54148787 TAATTCGACT
*
54148797 ATGTTAAATT-AATGTTTACGATGCTATGTACGTAATGGTG
1 ATGTTAAATTAAATGTTTAC-ATGCTATGTACGTAATGGTA
54148837 ATGTTAAATTAAATGTTTACATGCTATGTACGTAATGGTA
1 ATGTTAAATTAAATGTTTACATGCTATGTACGTAATGGTA
54148877 ATGT
1 ATGT
54148881 ACTCCATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 33 0.79
41 9 0.21
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.40
Consensus pattern (40 bp):
ATGTTAAATTAAATGTTTACATGCTATGTACGTAATGGTA
Found at i:54150520 original size:46 final size:46
Alignment explanation
Indices: 54150418--54150677 Score: 253
Period size: 46 Copynumber: 5.6 Consensus size: 46
54150408 ATATCTGTGT
* *
54150418 CGATGCCATGTCCAAGACATGGTCTTACACTGGC--AC-TCTCGTA-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTTG-AGGC
* *
54150463 CGATACATGTCCTAGACATGTCTTACACTGGCTTACGTCTTGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGC
* *
54150509 CGATGCATGTCCCAAACATGTCTTACACTGGCTTATGTCTTGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGC
* * ** * *
54150555 CGATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCAATGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TTACGTCTTGAGGC
* * ** *
54150601 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCTTGAGGC
*
54150649 CGATGCATGTCCCAGACATGTCGTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
54150678 AGCTCACAAT
Statistics
Matches: 179, Mismatches: 28, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
43 13 0.07
44 13 0.07
45 7 0.04
46 98 0.55
47 27 0.15
48 21 0.12
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGC
Found at i:54150658 original size:94 final size:92
Alignment explanation
Indices: 54150369--54150680 Score: 303
Period size: 94 Copynumber: 3.3 Consensus size: 92
54150359 TGTAGGTGCT
* * * **
54150369 GATGCCATGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTGTGTCGATGCCATGTCCAAG
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-CTA-CGTCTCAATGTCGATGCCATGTCCAAG
* * *
54150434 ACATGGTCTTACACTGGCACTC-TCGTAGCC
62 ACATGGTCTTACACTGGCTCTCATTGTGGCC
* * * * ** * *
54150464 GATACATGTCCTAGACATGTCTTACACTGGCTTACGTCTTGAGGCCGATG-CATGTCCCAA-ACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCCTACGTCTCAATGTCGATGCCATGT-CCAAGACA
* *
54150527 T-GTCTTACACTGGCTTATGTC-TTGAGGCC
65 TGGTCTTACACTGGC---TCTCATTGTGGCC
*
54150556 GATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCAATGTCGATGCCATGTCCTAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CTACGTCTCAATGTCGATGCCATGTCCAAGACA
54150620 TGGTCTTACACTGGCTCTCATAATGTGGCC
65 TGGTCTTACACTGGCTCTCAT--TGTGGCC
*
54150650 GATGCATGTCCCAGACATGTCGTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
54150681 TCACAATAAA
Statistics
Matches: 177, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
89 13 0.07
90 9 0.05
91 16 0.09
92 53 0.30
93 21 0.12
94 62 0.35
95 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCTACGTCTCAATGTCGATGCCATGTCCAAGACAT
GGTCTTACACTGGCTCTCATTGTGGCC
Found at i:54154784 original size:46 final size:46
Alignment explanation
Indices: 54154731--54154903 Score: 215
Period size: 46 Copynumber: 3.7 Consensus size: 46
54154721 TTTAGCATCT
54154731 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * * * *
54154777 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGATATGTA-ACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-ACGTCC
*
54154824 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * *
54154870 GAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54154904 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.01
46 67 0.63
47 37 0.35
48 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:54154834 original size:93 final size:93
Alignment explanation
Indices: 54154725--54154896 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54154715 AAATATTTTA
* * *
54154725 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
54154790 TGAGTCCGAGTTCGTGATATGTAACTAG
66 TGAGTCCGAGTTCGTGATATGTAACTAG
*
54154818 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
54154883 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54154897 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGATATGTAACTAG
Found at i:54158460 original size:158 final size:158
Alignment explanation
Indices: 54158172--54158488 Score: 555
Period size: 158 Copynumber: 2.0 Consensus size: 158
54158162 AATGTGACTA
*
54158172 ATAAATAGACTAAATGTGATATTATAGATCAAATAAAATGAGGTTCAGACCTAGAACAGAGGAAA
1 ATAAATAGACTAAATGTGATATTATAGATCAAAGAAAATGAGGTTCAGACCTAGAACAGAGGAAA
*
54158237 AATAAGAAATTGACAGTTAGGTCCCTTTTTGCCATTTTTGGTATCGAGGTAAGTTCGTGTGATAA
66 AATAAGAAATTGACAGTTAGGTCCCTTTTCGCCATTTTTGGTATCGAGGTAAGTTCGTGTGATAA
*
54158302 TAATAATGCAACGTTATACTTGAATGTT
131 TAATAATGCAACGTTATACTGGAATGTT
* *
54158330 ATAAATAGACTAAATGTGATATTATAGAAT-AAAGAAAATGAGGTTCAGACCTAGAACGGGGGAA
1 ATAAATAGACTAAATGTGATATTATAG-ATCAAAGAAAATGAGGTTCAGACCTAGAACAGAGGAA
*
54158394 AAATAAGAAATTGACGGTTAGGTCCCTTTTCGCCATTTTTGGTATCGAGGTAAGTTCGTGTGATA
65 AAATAAGAAATTGACAGTTAGGTCCCTTTTCGCCATTTTTGGTATCGAGGTAAGTTCGTGTGATA
*
54158459 ATAATAGTGCAACGTTATACTGGAATGTT
130 ATAATAATGCAACGTTATACTGGAATGTT
54158488 A
1 A
54158489 ATGCTTGATA
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
158 149 0.99
159 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (158 bp):
ATAAATAGACTAAATGTGATATTATAGATCAAAGAAAATGAGGTTCAGACCTAGAACAGAGGAAA
AATAAGAAATTGACAGTTAGGTCCCTTTTCGCCATTTTTGGTATCGAGGTAAGTTCGTGTGATAA
TAATAATGCAACGTTATACTGGAATGTT
Found at i:54158814 original size:43 final size:43
Alignment explanation
Indices: 54158766--54158879 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
54158756 TATGATCTGT
* *
54158766 ACTCATTGAGTTGGTCTGAGTTCATGATATATGTGCCA-TCCGA
1 ACTCATTGAGTTGGTCTGAGTTCATGATACATGCGCCACT-CGA
* * *
54158809 ACTCATTGAGCTGGTCTCAGTTCATGATACATGCGCCACTTGA
1 ACTCATTGAGTTGGTCTGAGTTCATGATACATGCGCCACTCGA
* *
54158852 GCTCATTGGGTTGGTCTGAGTTCATGAT
1 ACTCATTGAGTTGGTCTGAGTTCATGAT
54158880 GTACGTGACA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 60 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (43 bp):
ACTCATTGAGTTGGTCTGAGTTCATGATACATGCGCCACTCGA
Found at i:54163431 original size:30 final size:30
Alignment explanation
Indices: 54163376--54163506 Score: 164
Period size: 30 Copynumber: 4.5 Consensus size: 30
54163366 ATAGTGAATC
*
54163376 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
54163405 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
54163435 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * *
54163463 CGCACACTTAGTGCTGTACAATTTTAAAC-
1 CGCACACTTAGTGCTATATAATTTTCAACT
54163492 CTGCACACTTAGTGC
1 C-GCACACTTAGTGC
54163507 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 47 0.51
31 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:54163486 original size:58 final size:57
Alignment explanation
Indices: 54163375--54163506 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 57
54163365 TATAGTGAAT
* * * * *
54163375 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAG
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAA
*
54163433 CTCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAA
1 C-CGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAA
54163491 CCTGCACACTTAGTGC
1 CC-GCACACTTAGTGC
54163507 CAATCTTGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 3 0.05
58 42 0.65
59 20 0.31
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAA
Found at i:54165564 original size:28 final size:27
Alignment explanation
Indices: 54165501--54165570 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54165491 ATAGTGAGTC
*
54165501 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
54165528 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
54165556 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54165571 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54166685 original size:30 final size:30
Alignment explanation
Indices: 54166651--54166715 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
54166641 AACATGCATG
54166651 AATCTCATGGCACAACCTCAAACATACCTT
1 AATCTCATGGCACAACCTCAAACATACCTT
54166681 AATCTCATGGCACAACCTCAAACATACCTT
1 AATCTCATGGCACAACCTCAAACATACCTT
54166711 AATCT
1 AATCT
54166716 TGATGCAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.32, G:0.06, T:0.25
Consensus pattern (30 bp):
AATCTCATGGCACAACCTCAAACATACCTT
Found at i:54169792 original size:33 final size:32
Alignment explanation
Indices: 54169743--54169805 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
54169733 AAAAATTAAA
*
54169743 AAAAATATTTTTAAAATGACTAAAAATTTTGT
1 AAAAATATTTTAAAAATGACTAAAAATTTTGT
*
54169775 AAAAATATTTTAAAAAATGACTACAAATTTT
1 AAAAATATTTT-AAAAATGACTAAAAATTTT
54169806 CAAATCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (32 bp):
AAAAATATTTTAAAAATGACTAAAAATTTTGT
Found at i:54169820 original size:33 final size:32
Alignment explanation
Indices: 54169743--54169824 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
54169733 AAAAATTAAA
** *
54169743 AAAAATATTTTTAAAATGACTAAAAATTTTGT
1 AAAAATATTTAAAAAATGACTAAAAATTTTGC
*
54169775 AAAAATATTTTAAAAAATGACTACAAATTTT-C
1 AAAAATA-TTTAAAAAATGACTAAAAATTTTGC
54169807 AAATCAATATTTAAAAAA
1 AAA--AATATTTAAAAAA
54169825 ATATAGATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
32 10 0.23
33 29 0.67
34 4 0.09
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (32 bp):
AAAAATATTTAAAAAATGACTAAAAATTTTGC
Found at i:54172045 original size:24 final size:24
Alignment explanation
Indices: 54172018--54172110 Score: 150
Period size: 24 Copynumber: 3.9 Consensus size: 24
54172008 AAGGCTGTCA
* *
54172018 GGAGAAGATTTGGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
54172042 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
54172066 AGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
54172090 GGAGAGGATTTAGGAACTGAT
1 GGAGAGGATTTAGGAGCTGAT
54172111 TAGAGAGAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:54172095 original size:48 final size:48
Alignment explanation
Indices: 54172019--54172119 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 48
54172009 AGGCTGTCAG
* *
54172019 GAGAAGATTTGGGAGCTGATAAGGGAGAGGATTTAGGAGCTGATAAGA
1 GAGAAGATTTAGGAGCTGATAAGGGAGAGGATTTAGGAACTGATAAGA
* *
54172067 GAGAGGATTTAGGAGCTGATAAGGGAGAGGATTTAGGAACTGATTAGA
1 GAGAAGATTTAGGAGCTGATAAGGGAGAGGATTTAGGAACTGATAAGA
54172115 GAGAA
1 GAGAA
54172120 CGGTGTTGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.04, G:0.39, T:0.21
Consensus pattern (48 bp):
GAGAAGATTTAGGAGCTGATAAGGGAGAGGATTTAGGAACTGATAAGA
Found at i:54173408 original size:17 final size:18
Alignment explanation
Indices: 54173380--54173413 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54173370 TTAAATTACT
54173380 TAATACCCCTATGTATAA
1 TAATACCCCTATGTATAA
54173398 TAATA-CCCTATGTATA
1 TAATACCCCTATGTATA
54173414 GAAATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (18 bp):
TAATACCCCTATGTATAA
Found at i:54173649 original size:53 final size:52
Alignment explanation
Indices: 54173567--54173671 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 52
54173557 GGAAGCGTCC
*
54173567 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCTGTT
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACAT-TATCTGTT
* * *
54173620 TGGTGGCTCTGCCACAATTATCTGTTCTGGTGACACTGTCACATTATCTGTT
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACATTATCTGTT
54173672 CTGGCAGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
52 8 0.17
53 40 0.83
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (52 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACATTATCTGTT
Found at i:54173672 original size:26 final size:26
Alignment explanation
Indices: 54173566--54173675 Score: 134
Period size: 26 Copynumber: 4.2 Consensus size: 26
54173556 AGGAAGCGTC
*
54173566 CTGGTGGCTA-TGCCACAATTATCTGAT
1 CTGGTGGC-ACTGCCAC-ATTATCTGTT
54173593 CTGGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAT-TATCTGTT
*
54173620 -TGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCACTGCCAC-ATTATCTGTT
* *
54173646 CTGGTGACACTGTCACATTATCTGTT
1 CTGGTGGCACTGCCACATTATCTGTT
54173672 CTGG
1 CTGG
54173676 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
26 39 0.53
27 35 0.47
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCACTGCCACATTATCTGTT
Found at i:54179946 original size:24 final size:24
Alignment explanation
Indices: 54179913--54179966 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54179903 AAGGCTGTCA
*
54179913 GGAGAAGATTTGGGACCTGATAAG
1 GGAGAAGATTTAGGACCTGATAAG
* * *
54179937 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGACCTGATAAG
54179961 GGAGAA
1 GGAGAA
54179967 CGGTGTTGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.41, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGACCTGATAAG
Found at i:54181274 original size:26 final size:27
Alignment explanation
Indices: 54181219--54181292 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
54181209 AAGAATAGTT
* *
54181219 AAATTACTTA-ATACCCCTATGTAAAG
1 AAATTACTAATATACCCCTAGGTAAAG
**
54181245 AAATTACTAATATACCCCTAGGTGCA-
1 AAATTACTAATATACCCCTAGGTAAAG
* *
54181271 AAATTACCATTATACCCCTAGG
1 AAATTACTAATATACCCCTAGG
54181293 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 29 0.71
27 12 0.29
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATTACTAATATACCCCTAGGTAAAG
Found at i:54181489 original size:27 final size:27
Alignment explanation
Indices: 54181396--54181491 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
54181386 AGGAAGCGTC
* *
54181396 CTGGTGGCAATGCCACAATTATCTGATT
1 CTGGTGGCACTGTCACAATTATCTG-TT
* *
54181424 -TAGTGGCACTGCCAC-ATATATCTGTT
1 CTGGTGGCACTGTCACAAT-TATCTGTT
*
54181450 CTGGTGGCTCTGTCACAATTATCTGTT
1 CTGGTGGCACTGTCACAATTATCTGTT
*
54181477 CTGGTGACACTGTCA
1 CTGGTGGCACTGTCA
54181492 TTAGCACCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
26 4 0.07
27 52 0.90
28 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCACTGTCACAATTATCTGTT
Found at i:54184049 original size:26 final size:26
Alignment explanation
Indices: 54184019--54184100 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
54184009 TGAAATTCCC
54184019 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54184045 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54184071 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54184097 ATCA
1 ATCA
54184101 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54191122 original size:26 final size:26
Alignment explanation
Indices: 54191092--54191173 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
54191082 TGAAATTCCC
54191092 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54191118 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54191144 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54191170 ATCA
1 ATCA
54191174 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54193893 original size:71 final size:71
Alignment explanation
Indices: 54193804--54193967 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
54193794 GAGATGTATC
*
54193804 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCATGATTCCAAGTGA
54193869 AGGACA
66 AGGACA
*
54193875 CCATGTTGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCATGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCATGATTCCAAGTGA
54193940 AGGACA
66 AGGACA
54193946 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54193968 AGACAAATCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 90 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCATGATTCCAAGTGA
AGGACA
Found at i:54199945 original size:18 final size:19
Alignment explanation
Indices: 54199902--54199945 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
54199892 TGTAGCAATT
54199902 AATTTGCTTTTAAATTTGA
1 AATTTGCTTTTAAATTTGA
54199921 AATTTTG-TTTTAAA-TTGA
1 AA-TTTGCTTTTAAATTTGA
54199939 AGATTTG
1 A-ATTTG
54199946 AATAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
20 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
AATTTGCTTTTAAATTTGA
Found at i:54200400 original size:130 final size:129
Alignment explanation
Indices: 54200228--54200499 Score: 424
Period size: 130 Copynumber: 2.1 Consensus size: 129
54200218 TAATTTTCTT
*
54200228 AAAAATCAAAACTTTATTTTCAAAATAGTTGAAAAATATCAAAACTTTATTTTAAGAATTTAAAC
1 AAAAATCAAAACTTTATTTTCAAAATAGTTGAAAAAGATCAAAACTTTATTTTAAGAATTTAAAC
* *
54200293 CTTTCCTTTAATATAACTAAAAAGCATATTTTTATTTTAAAAATTTAAACTTTCTCTTTTTTTAA
66 CTTTCCTTTAATATAACTAAAAAACATATTTTTATTTTAAAAATCTAAAC-TT-TCTTTTTTTAA
54200358 A
129 A
* ** *
54200359 AAAAATTAAAACTTTA-TTTCGGAATAGTTGAAAAAGATCAAAACTTTGTTTTAAGAATTTAAAC
1 AAAAATCAAAACTTTATTTTCAAAATAGTTGAAAAAGATCAAAACTTTATTTTAAGAATTTAAAC
* *
54200423 TTTTCCTTTAATATGACTAAAAAACATATTTTTATTTTAAAAATCTAAACTTTCTTTTTTT--A
66 CTTTCCTTTAATATAACTAAAAAACATATTTTTATTTTAAAAATCTAAACTTTCTTTTTTTAAA
54200485 AAAAATCAAAACTTT
1 AAAAATCAAAACTTT
54200500 TCCTAAGATC
Statistics
Matches: 131, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
126 15 0.11
128 9 0.07
129 2 0.02
130 90 0.69
131 15 0.11
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (129 bp):
AAAAATCAAAACTTTATTTTCAAAATAGTTGAAAAAGATCAAAACTTTATTTTAAGAATTTAAAC
CTTTCCTTTAATATAACTAAAAAACATATTTTTATTTTAAAAATCTAAACTTTCTTTTTTTAAA
Found at i:54200817 original size:3 final size:3
Alignment explanation
Indices: 54200811--54200854 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
54200801 GTAAAAAAAG
54200811 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54200855 TTGGGCCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54201300 original size:42 final size:42
Alignment explanation
Indices: 54201229--54201698 Score: 598
Period size: 42 Copynumber: 11.2 Consensus size: 42
54201219 TTGAAATGAG
* * * *
54201229 AATGCAAGGAAAAGTAAATGGACCCCCACACCTGGGACTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * **
54201271 AATACAATGAAAAGTAAACGGACCTCCACACCTAAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
54201313 AATGCAATGAAAAGTCAATGGACCTCCACACCTAGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
54201355 AATGCAATGAAAAGCAAATGGACCTCCACACATGGGTCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
54201397 AATGCAATGAAAATTAAATGAACCTCCACACCTGGGCCCCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
54201439 AATGCAATGAAAAGGAAATGGACATCCACACCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* *
54201481 AATGCAATGAAAAGTAAATGAAACTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
54201523 AATGAAATAAAAAGTAAATGAACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
54201565 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
54201607 AATGCAATAAAAAGTAAATGGACCTCTACGCCTGGGTCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * * * *
54201649 AATGCAATGTAAAGTAAATAGACCTCCACAGCTGAGCATTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
54201691 AATGCAAT
1 AATGCAAT
54201699 AAATGTTTTT
Statistics
Matches: 370, Mismatches: 58, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 370 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:54216307 original size:40 final size:40
Alignment explanation
Indices: 54216262--54216429 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
54216252 CGGAATATAA
54216262 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * *
54216302 CCGGATAGAAT-ATCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCA-CTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
54216342 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54216382 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
54216422 CCGGATAT
1 CCGGATAT
54216430 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 101 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54216412 original size:80 final size:80
Alignment explanation
Indices: 54216278--54216427 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
54216268 ATAATCACGT
*
54216278 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATATCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGAT-TTAGC
54216342 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
54216358 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTC-GCACGAA-TGCCTTCGGGATTTAG
54216421 CCCGGAT
64 CCCGGAT
54216428 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:54221518 original size:19 final size:19
Alignment explanation
Indices: 54221496--54221541 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
54221486 CTCTTTTAAA
54221496 AAAAATCACTATTTTTCTT
1 AAAAATCACTATTTTTCTT
54221515 AAAAATCACTATTTTTCTT
1 AAAAATCACTATTTTTCTT
54221534 AAAAATCA
1 AAAAATCA
54221542 AAACTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATCACTATTTTTCTT
Found at i:54222006 original size:3 final size:3
Alignment explanation
Indices: 54222000--54222053 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
54221990 AAAAAAGAAG
* * * * *
54222000 ATA ATA ATA ATA TTTA ATA ATA GTA GTA GTA ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54222046 ATA ATA AT
1 ATA ATA AT
54222054 TTGGGCCCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:54225031 original size:44 final size:44
Alignment explanation
Indices: 54224978--54225078 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
54224968 TCCGATATGT
* * *
54224978 GATTTCGTGTAAGATAACGTCTGGGACATTGGCATCG-ATTTGA
1 GATTTCGTGTAAGACAACGTCTGGGACATCGACATCGTATTTGA
* *
54225021 GATTTACGTGTAAGACCATGTCTGGGACATCGACATCGTATTT--
1 GATTT-CGTGTAAGACAACGTCTGGGACATCGACATCGTATTTGA
*
54225064 GATTTCGTATAAGAC
1 GATTTCGTGTAAGAC
54225079 CCTGTCTGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 9 0.18
43 10 0.20
44 27 0.54
45 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (44 bp):
GATTTCGTGTAAGACAACGTCTGGGACATCGACATCGTATTTGA
Found at i:54225089 original size:42 final size:43
Alignment explanation
Indices: 54224996--54225089 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
54224986 GTAAGATAAC
* * *
54224996 GTCTGGGACATTGGCATCGATTTGAGATTTACGTGTAAGACCAT
1 GTCTGGGACATCGACATCGATTT-AGATTTACGTATAAGACCAT
*
54225040 GTCTGGGACATCGACATCGTATTT-GATTT-CGTATAAGACCCT
1 GTCTGGGACATCGACATCG-ATTTAGATTTACGTATAAGACCAT
54225082 GTCTGGGA
1 GTCTGGGA
54225090 TAGAAGAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 19 0.42
43 5 0.11
44 17 0.38
45 4 0.09
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
GTCTGGGACATCGACATCGATTTAGATTTACGTATAAGACCAT
Found at i:54225120 original size:43 final size:42
Alignment explanation
Indices: 54225024--54225123 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
54225014 GATTTGAGAT
**
54225024 TTACGTGTAAGACCATGTCTGGGACATCGACATCGTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAAAGACATCGTATTTGA
* * * *
54225066 TTTCGTATAAGACCCTGTCTGGGATAGAAGA-ATCGATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACA-AAGACATCG-TATTTGA
*
54225109 TTACATGTAAGACCA
1 TTACGTGTAAGACCA
54225124 CATCTGGGTC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
42 26 0.57
43 20 0.43
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACAAAGACATCGTATTTGA
Found at i:54231661 original size:18 final size:18
Alignment explanation
Indices: 54231616--54231653 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54231606 CGTACATGAG
* *
54231616 AGAAACAAAAACAAAGAA
1 AGAAAAAAAAAAAAAGAA
54231634 AGAAAAAAAAAAAAAGAA
1 AGAAAAAAAAAAAAAGAA
54231652 AG
1 AG
54231654 GAAGAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAAAAAGAA
Found at i:54232951 original size:40 final size:40
Alignment explanation
Indices: 54232892--54232998 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
54232882 CAATTGAATG
* * * *
54232892 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
54232932 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
54232972 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
54232999 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:54233018 original size:40 final size:39
Alignment explanation
Indices: 54232933--54233059 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
54232923 CTGGAAATTA
* * *
54232933 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTG-AC
1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGTTC
54232971 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
* * *
54233013 TATCCGGGCTAAGACCCGAGGGCATTCGTGCATGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
54233053 TATCCGG
1 TATCCGG
54233060 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 70 0.91
41 1 0.01
42 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTTC
Found at i:54239692 original size:16 final size:18
Alignment explanation
Indices: 54239661--54239696 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
54239651 CGTACATGAG
54239661 AGAAACAAAAACAAAGAA
1 AGAAACAAAAACAAAGAA
54239679 AGAAA-AAAAA-AAAGAA
1 AGAAACAAAAACAAAGAA
54239695 AG
1 AG
54239697 GAAGAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.81, C:0.06, G:0.14, T:0.00
Consensus pattern (18 bp):
AGAAACAAAAACAAAGAA
Found at i:54239696 original size:20 final size:20
Alignment explanation
Indices: 54239667--54239704 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54239657 TGAGAGAAAC
54239667 AAAAACAAAGAAAGAAAAAA
1 AAAAACAAAGAAAGAAAAAA
* *
54239687 AAAAAGAAAGGAAGAAAA
1 AAAAACAAAGAAAGAAAA
54239705 GTGTTCATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAACAAAGAAAGAAAAAA
Found at i:54240994 original size:40 final size:40
Alignment explanation
Indices: 54240935--54241041 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
54240925 CAATTGAATG
* * * *
54240935 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
54240975 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
54241015 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
54241042 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:54241061 original size:40 final size:39
Alignment explanation
Indices: 54240976--54241102 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
54240966 CTGGAAATTA
* * *
54240976 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTG-AC
1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGTTC
54241014 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
* * *
54241056 TATCCGGGCTAAGACCCGAGGGCATTCGTGCATGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
54241096 TATCCGG
1 TATCCGG
54241103 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 70 0.91
41 1 0.01
42 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTTC
Found at i:54245117 original size:40 final size:40
Alignment explanation
Indices: 54245073--54245170 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
54245063 AGAGAGGTTA
* * * *
54245073 GCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATTTGT
1 GCAAGTCGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
*
54245113 GCAAGTCGTTCTATCCGGGCTAAGACCCGAAGGCATTCGT
1 GCAAGTCGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
* *
54245153 GCATGTGGTTATATCCGG
1 GCAAGTCGTTATATCCGG
54245171 TTGTATTCCG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GCAAGTCGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
Found at i:54248007 original size:43 final size:42
Alignment explanation
Indices: 54247959--54248123 Score: 161
Period size: 43 Copynumber: 3.9 Consensus size: 42
54247949 CTTCGATATG
* *
54247959 TGATTTCGTGTAAGACCACGTTTGGGACATTGGCATCGATTT
1 TGATTTCATGTAAGACCACGTCTGGGACATTGGCATCGATTT
* * * ** *
54248001 GAGATTTACATGAAAGACCATGTCTGGGACATCAGCATCGAATT
1 -TGATTT-CATGTAAGACCACGTCTGGGACATTGGCATCGATTT
* ** *
54248045 TGATTTCATATAAGACC-CTGTCTGGGACAGAGGCATCAATATT
1 TGATTTCATGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TT
* *
54248088 TGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TGATTTCATGTAAGACCACGTCTGGGACATTGGCAT
54248124 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 22, Indels: 8
0.76 0.17 0.06
Matches are distributed among these distances:
42 25 0.26
43 41 0.43
44 30 0.31
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (42 bp):
TGATTTCATGTAAGACCACGTCTGGGACATTGGCATCGATTT
Found at i:54248071 original size:42 final size:43
Alignment explanation
Indices: 54248006--54248115 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 43
54247996 GATTTGAGAT
* *
54248006 TTACATGA-AAGACCATGTCTGGGACATCA-GCATCGA-ATTTGA
1 TTACAT-ATAAGACCCTGTCTGGGACA-CAGGCATCAATATTTGA
* *
54248048 TTTCATATAAGACCCTGTCTGGGACAGAGGCATCAATATTTGA
1 TTACATATAAGACCCTGTCTGGGACACAGGCATCAATATTTGA
*
54248091 TTACATGTAAGACCAC-GTCTGGGAC
1 TTACATATAAGACC-CTGTCTGGGAC
54248116 GTTGGCATTG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.03
42 28 0.48
43 27 0.47
44 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TTACATATAAGACCCTGTCTGGGACACAGGCATCAATATTTGA
Found at i:54255615 original size:16 final size:15
Alignment explanation
Indices: 54255589--54255618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54255579 AACTATTTTA
54255589 TTACAAATTTCACTC
1 TTACAAATTTCACTC
54255604 TTACATAATTTCACT
1 TTACA-AATTTCACT
54255619 TGCTACATTC
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:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:54255941 original size:50 final size:50
Alignment explanation
Indices: 54255818--54256056 Score: 214
Period size: 50 Copynumber: 4.8 Consensus size: 50
54255808 AACCGAAGCT
* * * * * *
54255818 ATCTGGTACTCATAGTAG-CTGCACTTAATACTACACATGCGACC-AACA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* *
54255866 ATCTGGTACA-AGTAATAGCCTGCACTTAGTACTACACACGTGACCTAACC
1 ATCTGATACACA-TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * * * * **
54255916 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACAAATGTGATCGAAGTT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CC
* * * *
54255967 GTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACC
* * * *
54256019 GTCTTAAACACATAGTAGCCTGCACATAGTACTACACA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACA
54256057 TGTGTTCTCA
Statistics
Matches: 152, Mismatches: 32, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
47 1 0.01
48 14 0.09
49 23 0.15
50 43 0.28
51 37 0.24
52 32 0.21
53 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:54259926 original size:2 final size:2
Alignment explanation
Indices: 54259919--54259960 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54259909 CACATTCGGC
54259919 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
54259961 AAAATGTATG
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:54260553 original size:28 final size:28
Alignment explanation
Indices: 54260521--54260590 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
54260511 AATGAGATTG
*
54260521 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
54260549 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
54260577 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54260591 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:54260863 original size:12 final size:12
Alignment explanation
Indices: 54260846--54260870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54260836 GTGGAAATGC
54260846 ATCAAATATCAT
1 ATCAAATATCAT
54260858 ATCAAATATCAT
1 ATCAAATATCAT
54260870 A
1 A
54260871 CGAGATGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCAAATATCAT
Found at i:54265570 original size:48 final size:48
Alignment explanation
Indices: 54265503--54265628 Score: 198
Period size: 48 Copynumber: 2.6 Consensus size: 48
54265493 AGGTGTGAAA
54265503 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATC
* * * *
54265551 CCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGTGATT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATC
* *
54265599 TCATGTAAGACCATGTTTGGGACATGGCAT
1 CCATGTAAGACCATGTCTGGGACATGGCAT
54265629 CGATTTGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (48 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATC
Found at i:54271750 original size:48 final size:48
Alignment explanation
Indices: 54271679--54272594 Score: 1517
Period size: 48 Copynumber: 19.0 Consensus size: 48
54271669 TGTTACAACA
* *
54271679 TTCACATTAGCCATTCGGCTTTACCACATATTCATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * *
54271727 TTCACATTCGCCATTCGGCTTTACGACATTTACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54271775 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
54271823 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54271871 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * * *
54271919 TTCACATTCGCCATTCGGCTTTACCACATCTACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54271967 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54272015 TTCACATTAGCCATTCGGCTTTACCATATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * *
54272063 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
54272111 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54272159 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54272207 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54272255 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54272303 TTCACATTAGCCATTCGACTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54272351 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54272399 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATAAAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATAT--CTCATATAT--AT
*
54272451 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
54272499 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
54272547 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
54272595 ATATTTATCT
Statistics
Matches: 806, Mismatches: 58, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
48 753 0.93
50 14 0.02
52 39 0.05
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
Found at i:54278230 original size:65 final size:64
Alignment explanation
Indices: 54278115--54278277 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
54278105 ATATAGCTCG
* * * * * * *
54278115 GACACAAACATAGCTCTTTATAAGTGTCATGTTTATTAATCGGTTATGATCCTGCATATGTTACA
1 GACACAAACACAGCTCTTTATGAGCGTCCTG-TTATCAATCAGTTATGATCCTACATATGTTACA
* * * *
54278180 GACACAAACACAGCTCTTTATGAGCGTCCTGTTATGCGATCAGTTGTGATCCTACATATGTTGCG
1 GACACAAACACAGCTCTTTATGAGCGTCCTGTTAT-CAATCAGTTATGATCCTACATATGTTACA
* *
54278245 GACACAAACGCAGCTCTTTATGAGCGTTCTGTT
1 GACACAAACACAGCTCTTTATGAGCGTCCTGTT
54278278 CCGATGAGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 4 0.05
65 80 0.95
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (64 bp):
GACACAAACACAGCTCTTTATGAGCGTCCTGTTATCAATCAGTTATGATCCTACATATGTTACA
Found at i:54278627 original size:12 final size:12
Alignment explanation
Indices: 54278610--54278634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54278600 TATTGTGTGA
54278610 TATTTGAATTCT
1 TATTTGAATTCT
54278622 TATTTGAATTCT
1 TATTTGAATTCT
54278634 T
1 T
54278635 GTGAAACAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TATTTGAATTCT
Found at i:54286954 original size:46 final size:46
Alignment explanation
Indices: 54286792--54286967 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
54286782 TGTAACTCGC
* * * * *
54286792 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * * *
54286838 CCATGAGTGAACTCAGACTCAACACAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
54286888 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
54286931 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54286968 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 1 0.01
46 59 0.56
47 26 0.25
49 1 0.01
50 6 0.06
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:54286960 original size:93 final size:93
Alignment explanation
Indices: 54286801--54286970 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
54286791 CCCATAAGCG
* * *
54286801 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCAGACTCAACACAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACACAAC
54286866 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
* * * *
54286894 AACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACACAAC
54286959 GAGTTCGGATGC
66 GAGTTCGGATGC
54286971 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACACAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:54298862 original size:19 final size:19
Alignment explanation
Indices: 54298816--54298863 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
54298806 GTATATATTT
54298816 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
54298834 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
54298853 TAAGTTTTATT
1 TAAATTTTATT
54298864 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:54298939 original size:42 final size:42
Alignment explanation
Indices: 54298880--54298968 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
54298870 CTAGGAATAT
* * *
54298880 TTTTATTTTATCTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
* *
54298922 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAATTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
54298964 TTTTC
1 TTTTC
54298969 CCAATTAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.52
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:54300077 original size:38 final size:38
Alignment explanation
Indices: 54300026--54300101 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54300016 TCCATCTCAA
54300026 AAATATAAAGCCTCCAAACCTTTTTCGTTAATTCATAG
1 AAATATAAAGCCTCCAAACCTTTTTCGTTAATTCATAG
54300064 AAATATAAAGCCTCCAAACCTTTTTCGTTAATTCATAG
1 AAATATAAAGCCTCCAAACCTTTTTCGTTAATTCATAG
54300102 TGATGTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (38 bp):
AAATATAAAGCCTCCAAACCTTTTTCGTTAATTCATAG
Found at i:54302934 original size:42 final size:42
Alignment explanation
Indices: 54302875--54302963 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
54302865 CTAGGAATAT
* * *
54302875 TTTTATTTTATCTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
*
54302917 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
54302959 TTTTC
1 TTTTC
54302964 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:54317344 original size:29 final size:29
Alignment explanation
Indices: 54317304--54317406 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
54317294 GTTGAGAGAT
*
54317304 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
54317333 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* **
54317362 TGGCACTAAGTGTGCGAG-TTTAAAGTATA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
54317391 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54317407 CGGCTGATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.07
29 64 0.93
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:54321560 original size:20 final size:19
Alignment explanation
Indices: 54321522--54321578 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
54321512 AATAAAATTA
*
54321522 TAAAAATTATTAAATTTTTAAT
1 TAAAAA-TA-TAAAATTTT-AT
54321544 TAAAAATATAAAATTTTAT
1 TAAAAATATAAAATTTTAT
* *
54321563 TGAAAAT-TAGAATTTT
1 TAAAAATATAAAATTTT
54321579 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.25
19 8 0.25
20 8 0.25
21 2 0.06
22 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TAAAAATATAAAATTTTAT
Found at i:54321579 original size:19 final size:19
Alignment explanation
Indices: 54321530--54321579 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
54321520 TATAAAAATT
54321530 ATTAAATTTTTAATTAAAA
1 ATTAAATTTTTAATTAAAA
* *
54321549 ATATAAAATTTT-ATTGAAA
1 AT-TAAATTTTTAATTAAAA
54321568 ATTAGAATTTTT
1 ATTA-AATTTTT
54321580 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 16 0.62
20 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTAAATTTTTAATTAAAA
Found at i:54321604 original size:20 final size:19
Alignment explanation
Indices: 54321581--54321647 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
54321571 AGAATTTTTT
54321581 TATAAAAATAGTAAAAGAAA
1 TATAAAAATAGTAAAA-AAA
* **
54321601 TATAAAAAATTGTAAAAATT
1 TAT-AAAAATAGTAAAAAAA
*
54321621 TATAAAAATCA-TAAAAAAC
1 TATAAAAAT-AGTAAAAAAA
54321640 TATAAAAA
1 TATAAAAA
54321648 AACATAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 20 0.51
20 7 0.18
21 12 0.31
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.25
Consensus pattern (19 bp):
TATAAAAATAGTAAAAAAA
Found at i:54321618 original size:10 final size:10
Alignment explanation
Indices: 54321580--54321658 Score: 56
Period size: 10 Copynumber: 8.0 Consensus size: 10
54321570 TAGAATTTTT
54321580 TTAT-AAAAA
1 TTATAAAAAA
54321589 -TAGTAAAAGAA
1 TTA-TAAAA-AA
*
54321600 ATATAAAAAA
1 TTATAAAAAA
* *
54321610 TTGTAAAAAT
1 TTATAAAAAA
54321620 TTAT-AAAAA
1 TTATAAAAAA
*
54321629 TCATAAAAAA
1 TTATAAAAAA
*
54321639 CTATAAAAAA
1 TTATAAAAAA
**
54321649 ACATAAAAAA
1 TTATAAAAAA
54321659 ACGTCCTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
8 2 0.04
9 8 0.15
10 36 0.65
11 7 0.13
12 2 0.04
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:54321648 original size:20 final size:20
Alignment explanation
Indices: 54321601--54321658 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
54321591 GTAAAAGAAA
** **
54321601 TATAAAAAATTGTAAAAATT
1 TATAAAAAATCATAAAAAAC
54321621 TAT-AAAAATCATAAAAAAC
1 TATAAAAAATCATAAAAAAC
*
54321640 TATAAAAAAACATAAAAAA
1 TATAAAAAATCATAAAAAA
54321659 ACGTCCTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
TATAAAAAATCATAAAAAAC
Found at i:54321869 original size:21 final size:21
Alignment explanation
Indices: 54321812--54321869 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
54321802 TTGGTACAAT
54321812 AATTTTTATAATTTT-TCTTAC
1 AATTTTTATAATTTTCT-TTAC
* *
54321833 AAATTTTGT-A-TTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
54321852 ACTTTTTATAATTTTCTT
1 AATTTTTATAATTTTCTT
54321870 ACTTTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTATAATTTTCTTTAC
Found at i:54321922 original size:29 final size:30
Alignment explanation
Indices: 54321879--54321947 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
54321869 TACTTTATAA
*
54321879 AATTGTATAATTTTTTTCTAT-ATTTCT-AT
1 AATTTTATAATTTTTTT-TATGATTTCTAAT
*
54321908 ATATTTTATAA-TTTTTTTATGATTTTTAAT
1 A-ATTTTATAATTTTTTTTATGATTTCTAAT
54321938 AATTTTATAA
1 AATTTTATAA
54321948 AATTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 21 0.60
30 11 0.31
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTTTATAATTTTTTTTATGATTTCTAAT
Found at i:54321976 original size:22 final size:21
Alignment explanation
Indices: 54321910--54321983 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
54321900 ATTTCTATAT
*
54321910 ATTTT-ATAATTTTTT-TATGA
1 ATTTTAATAATTTTTTATA-AA
*
54321930 TTTTTAATAA--TTTTATAAA
1 ATTTTAATAATTTTTTATAAA
54321949 ATTTTAAATAATTTTTTATTAAA
1 ATTTT-AATAATTTTTTA-TAAA
54321972 A-TTTAATAATTT
1 ATTTTAATAATTT
54321984 AATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 9 0.20
20 11 0.24
21 12 0.27
22 8 0.18
23 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
ATTTTAATAATTTTTTATAAA
Found at i:54321994 original size:10 final size:10
Alignment explanation
Indices: 54321911--54322010 Score: 61
Period size: 10 Copynumber: 10.4 Consensus size: 10
54321901 TTTCTATATA
54321911 TTTT-ATAATT
1 TTTTAATAA-T
* *
54321921 TTTTTATGAT
1 TTTTAATAAT
54321931 TTTTAATAAT
1 TTTTAATAAT
54321941 TTTATAA-AAT
1 TTT-TAATAAT
*
54321951 TTTAAATAATT
1 TTTTAATAA-T
* *
54321962 TTTTATTAAA
1 TTTTAATAAT
*
54321972 ATTTAATAA-
1 TTTTAATAAT
54321981 -TTTAATAAT
1 TTTTAATAAT
54321990 TTTT-AT--T
1 TTTTAATAAT
*
54321997 TTTTAATTAT
1 TTTTAATAAT
54322007 TTTT
1 TTTT
54322011 TAATCACATG
Statistics
Matches: 72, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
7 5 0.07
8 10 0.14
9 4 0.06
10 39 0.54
11 14 0.19
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:54323368 original size:53 final size:53
Alignment explanation
Indices: 54323284--54323384 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
54323274 CGATCAGATT
54323284 GTTTCATATATGCTAACTGCTTCATTCGCTCTTGAGCTCGCTTCAAGTGGATC
1 GTTTCATATATGCTAACTGCTTCATTCGCTCTTGAGCTCGCTTCAAGTGGATC
* * *
54323337 GTTTCGTATCTGCTAACTGCTTCATTTGCTCTTGAGCTCGCTTCAAGT
1 GTTTCATATATGCTAACTGCTTCATTCGCTCTTGAGCTCGCTTCAAGT
54323385 AAAACCGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (53 bp):
GTTTCATATATGCTAACTGCTTCATTCGCTCTTGAGCTCGCTTCAAGTGGATC
Found at i:54333130 original size:17 final size:16
Alignment explanation
Indices: 54333105--54333138 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54333095 TTCAATTATG
54333105 CTTAAATTTTTATATTT
1 CTTAAATTTTTA-ATTT
*
54333122 CTTATATTTTTAATTT
1 CTTAAATTTTTAATTT
54333138 C
1 C
54333139 CCCCAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTAAATTTTTAATTT
Found at i:54343771 original size:20 final size:21
Alignment explanation
Indices: 54343746--54343785 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54343736 CTCTTGAAAT
*
54343746 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCATGTGGA
*
54343766 AGGGCAACATGCCCATGTGG
1 AGGGCAACACGCCCATGTGG
54343786 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:54345579 original size:46 final size:46
Alignment explanation
Indices: 54345512--54345687 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
54345502 TGTAACCCGC
* *
54345512 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * * *
54345558 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAAATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC---GGAC-ATTTGCAT
* *
54345608 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
54345651 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54345688 TGCTCAATCA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 5 0.05
44 3 0.03
45 2 0.02
46 61 0.57
47 26 0.24
48 2 0.02
49 3 0.03
50 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:54346510 original size:22 final size:22
Alignment explanation
Indices: 54346485--54346537 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
54346475 AAAACGTAAA
54346485 AATCA-TTAAAAACGGGGCTTGG
1 AATCACTT-AAAACGGGGCTTGG
** *
54346507 AATCACTTACTATGGGGCTTGG
1 AATCACTTAAAACGGGGCTTGG
54346529 AATCACTTA
1 AATCACTTA
54346538 CTATGGAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
AATCACTTAAAACGGGGCTTGG
Done.