Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 173 of 410
Found at i:53137996 original size:20 final size:20
Alignment explanation
Indices: 53137957--53137996 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53137947 AAACTTCTTC
* *
53137957 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
53137977 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
53137997 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:53138311 original size:53 final size:54
Alignment explanation
Indices: 53138182--53138436 Score: 265
Period size: 55 Copynumber: 4.8 Consensus size: 54
53138172 ACACGGGTAC
* * * *
53138182 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
53138231 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
53138284 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * *
53138339 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
53138392 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
53138437 AAACCCTAAT
Statistics
Matches: 172, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 71 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:53138373 original size:108 final size:110
Alignment explanation
Indices: 53138229--53138426 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 110
53138219 ATCCTTTTGA
* *
53138229 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTA-GAAACCTCACCAA
53138292 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* ** *
53138337 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
53138402 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
53138427 CGGTATCCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 25 0.31
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:53140325 original size:678 final size:675
Alignment explanation
Indices: 53139031--53140383 Score: 2501
Period size: 678 Copynumber: 2.0 Consensus size: 675
53139021 CCTCAGATTC
53139031 TATCATAAAACACCAAAATACACAAATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGT
1 TATCATAAAACACCAAAATACACAAATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGT
53139096 TGAATTATTGCTAGAATAAGCTTAATCAAGTTATCGGGACTCCAAAAACGTAAAGATCATTAAAA
66 TGAATTATTGCTAGAATAAGCTTAATCAAGTTATCGGGACTCCAAAAACGTAAAGATCATTAAAA
** *
53139161 ATGGGGCTTGGAATCACTTACTATGGAGTTTAAAGCTTGAAACAAACCCTAGCTATGGAGAACCC
131 ACAGGGCTTGGAATCACTTACTATGGAGTTTAAAGCTTGAAACAAACCCTAGCTATGGAAAACCC
**
53139226 TTGAAATTTTGTCCTAATGAAGAAGATGGAAAAAATTGGCTTTTAATTTTGTTTTTAATCATTTT
196 TTGAAATTTCATCCTAATGAAGAAGATGGAAAAAATTGGCTTTTAATTTTGTTTTTAATCATTTT
*
53139291 AATAACTAACTGACCAAAATGCCCTTACTACTAAACTTTCCAAAAATTCCATCCATGTCCAACTT
261 AATAACTAAATGACCAAAATGCCCTTACTACTAAACTTTCCAAAAATTCCATCCATGTCCAACTT
*
53139356 TTGTCCATAGACTTAGAAATTGGTCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAGCA
326 TTGTCCATAGACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTCCAAAGCA
*
53139421 ATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTTGATTTAGTCCCTAATCTCAA
391 ATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTCGATTTAGTCCCTAATCTCAA
*
53139486 CTTAAGCACTTTATGCATAGAATTTCATCACGAAATTTTCACACATCATGCAATCATATCATGAA
456 CTTAAGCACTTTATGCATAGAATTTCATCACGAAAATTTCACACATCATGCAATCATATCATGAA
53139551 CCTAAAAATAATAATAAAATAAATTTTCTACCTCAGATTTGTGGTTTCGCAACCACTGTTCCATT
521 CCTAAAAATAATAATAAAATAAATTTTCTACCTCAGATTTGTGGTTTCGCAACCACTGTTCCATT
53139616 TAGGCCCTATTTCGGGATGTTACAACAATCACAGATTGGGACCTCTATCGAATAGCCAGAGACTC
586 TAGGCCCTATTTCGGGATGTTACAACAATCACAGATTGGGACCTCTATCGAATAGCCAGAGACTC
*
53139681 TGTTCTCCAGCAAAGAATTGAAGAG
651 TATTCTCCAGCAAAGAATTGAAGAG
53139706 TATCATAAAACACCAAAATACACAAATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGT
1 TATCATAAAACACCAAAATACACAAATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGT
53139771 TGAATTATTGCTAGAATAAGCTTAATCAAGTTATCGGGACTCCAAAAACGTAAAGATCATTAAAA
66 TGAATTATTGCTAGAATAAGCTTAATCAAGTTATCGGGACTCCAAAAACGTAAAGATCATTAAAA
*
53139836 ACAGGGCTTGGAATCACTTACTATGGAGTTTAAAAGCTTGAAATAAACCCTAGCTATGGAAAACC
131 ACAGGGCTTGGAATCACTTACTATGGAGTTT-AAAGCTTGAAACAAACCCTAGCTATGGAAAACC
* *
53139901 GTTGAAATTTCATCCTAATGAAGAAGATGGACAAAATTTGGCTTTTAATTTTGTTTTTAATTCAT
195 CTTGAAATTTCATCCTAATGAAGAAGATGGA-AAAAATTGGCTTTTAATTTTGTTTTTAA-TCAT
53139966 TTTAATAACTAAATGACCAAAATGCCCTTACTACTAAACTTTCCAAAAATTCCATCCATGTCCAA
258 TTTAATAACTAAATGACCAAAATGCCCTTACTACTAAACTTTCCAAAAATTCCATCCATGTCCAA
53140031 CTTTTGTCCATAGACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTCCAAA
323 CTTTTGTCCATAGACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTCCAAA
53140096 GCAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTCGATTTAGTCCCTAATCT
388 GCAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTCGATTTAGTCCCTAATCT
* *
53140161 CAACTTAAGCACTTTATGTATAGAATTTCATCACGAAAATTTCACACCATTATGCAATCATATCA
453 CAACTTAAGCACTTTATGCATAGAATTTCATCACGAAAATTTCACA-CATCATGCAATCATATCA
*
53140226 TGAA-CTCAAAATAATAATAAAATAAATTTTCTACCTCAGATTTGTGGTTTCGCAACCACTGTTC
517 TGAACCTAAAAATAATAATAAAATAAATTTTCTACCTCAGATTTGTGGTTTCGCAACCACTGTTC
*
53140290 CGTTTAGGCCCTATTTCGGGATGTTACAACAATCACAGATTGGGACCTCTATCGAATAGCCAGAG
582 CATTTAGGCCCTATTTCGGGATGTTACAACAATCACAGATTGGGACCTCTATCGAATAGCCAGAG
*
53140355 ACTCTATTCTCCAGCAAAGAGTTGAAGAG
647 ACTCTATTCTCCAGCAAAGAATTGAAGAG
53140384 AGCGAGGATC
Statistics
Matches: 656, Mismatches: 18, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
675 159 0.24
676 59 0.09
677 27 0.04
678 390 0.59
679 21 0.03
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (675 bp):
TATCATAAAACACCAAAATACACAAATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGGT
TGAATTATTGCTAGAATAAGCTTAATCAAGTTATCGGGACTCCAAAAACGTAAAGATCATTAAAA
ACAGGGCTTGGAATCACTTACTATGGAGTTTAAAGCTTGAAACAAACCCTAGCTATGGAAAACCC
TTGAAATTTCATCCTAATGAAGAAGATGGAAAAAATTGGCTTTTAATTTTGTTTTTAATCATTTT
AATAACTAAATGACCAAAATGCCCTTACTACTAAACTTTCCAAAAATTCCATCCATGTCCAACTT
TTGTCCATAGACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTCCAAAGCA
ATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTCGATTTAGTCCCTAATCTCAA
CTTAAGCACTTTATGCATAGAATTTCATCACGAAAATTTCACACATCATGCAATCATATCATGAA
CCTAAAAATAATAATAAAATAAATTTTCTACCTCAGATTTGTGGTTTCGCAACCACTGTTCCATT
TAGGCCCTATTTCGGGATGTTACAACAATCACAGATTGGGACCTCTATCGAATAGCCAGAGACTC
TATTCTCCAGCAAAGAATTGAAGAG
Found at i:53141707 original size:9 final size:9
Alignment explanation
Indices: 53141694--53141723 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
53141684 CTCGTGAAGA
53141694 AAAAAAAGAG
1 AAAAAAA-AG
53141704 AAAAAAAAG
1 AAAAAAAAG
53141713 AAAAAAAAG
1 AAAAAAAAG
53141722 AA
1 AA
53141724 GAGCATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:53141707 original size:11 final size:11
Alignment explanation
Indices: 53141691--53141726 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
53141681 ATGCTCGTGA
53141691 AGAAAAAAAAG
1 AGAAAAAAAAG
53141702 AGAAAAAAAAG
1 AGAAAAAAAAG
*
53141713 AAAAAAAAGAAG
1 AGAAAAAA-AAG
53141725 AG
1 AG
53141727 CATATGTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:53147167 original size:27 final size:27
Alignment explanation
Indices: 53147144--53147278 Score: 180
Period size: 27 Copynumber: 5.0 Consensus size: 27
53147134 TAAAATTATT
*
53147144 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
53147171 GAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
53147198 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
53147225 AAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
53147252 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
53147279 ATTTTGCCCC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:53147843 original size:22 final size:22
Alignment explanation
Indices: 53147791--53147853 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
53147781 GCAAATTATT
*
53147791 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
* *
53147813 CT-ACATATGGATTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
53147835 CTGATTATGGCTGTGTGCC
1 CTGATTATGGCTTTGTGCC
53147854 GTTATTGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:53148120 original size:6 final size:6
Alignment explanation
Indices: 53148111--53148216 Score: 83
Period size: 6 Copynumber: 17.3 Consensus size: 6
53148101 TTGCATTCAC
* * * * *
53148111 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTA ATTCTA ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* *
53148161 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT-
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
53148208 AGTTCTG AT
1 A-TTCTG AT
53148217 AATGTTTCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.05
6 68 0.85
7 6 0.08
8 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:53148145 original size:25 final size:25
Alignment explanation
Indices: 53148117--53148178 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
53148107 TCACATTCTG
* *
53148117 ATTCTGATTCTGTTACCTGATACTA
1 ATTCTGATTCTGTCACCTAATACTA
* * *
53148142 ATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGTCACCTAATACTA
53148167 ATTCTGATTCTG
1 ATTCTGATTCTG
53148179 ATTCTGATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (25 bp):
ATTCTGATTCTGTCACCTAATACTA
Found at i:53154052 original size:30 final size:30
Alignment explanation
Indices: 53154018--53154075 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53154008 ATTTAATACG
53154018 AACTTTGGCAAAATTACA-TGTTTGCCCCCA
1 AACTTTGGCAAAATTACACT-TTTGCCCCCA
* *
53154048 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGCAAAATTACACTTTTGCCCC
53154076 TAGGCTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCCA
Found at i:53156572 original size:40 final size:40
Alignment explanation
Indices: 53156514--53156797 Score: 399
Period size: 40 Copynumber: 7.1 Consensus size: 40
53156504 TGAATGATAC
* * * *
53156514 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
53156554 CCGGGTTAAGACCTGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
53156594 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
53156634 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
53156674 CCAGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
53156714 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* ** *
53156754 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
53156794 CCGG
1 CCGG
53156798 CTAAATTCCG
Statistics
Matches: 217, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
40 215 0.99
41 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:53165005 original size:46 final size:46
Alignment explanation
Indices: 53164947--53165214 Score: 267
Period size: 47 Copynumber: 5.7 Consensus size: 46
53164937 ATTCGTGTGT
*
53164947 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGA
* * *
53164993 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGAGATGA
* *
53165041 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATG-A
* * *
53165088 -AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGA
* * * **
53165133 TAGTTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGAT-A
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGAGATGA
* *
53165179 TGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC
1 -GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
53165215 AGCACCTTAC
Statistics
Matches: 187, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 75 0.40
47 82 0.44
48 28 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGA
Found at i:53165199 original size:140 final size:140
Alignment explanation
Indices: 53164952--53165209 Score: 378
Period size: 140 Copynumber: 1.8 Consensus size: 140
53164942 TGTGTGAGCT
* *
53164952 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
* * *
53165017 GACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGA
66 GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGCATTGGCCTCGA
53165082 GATGTAAGCC
131 GATGTAAGCC
* * **
53165092 AGTGTAAGACATGTCTAGGACATGCATCGGCTACGA-GATGATAGTTAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATGATGAGAGCCAGTGTAAGACCATGTCTG
*
53165156 GGACATGGCATCGAC-TTGAGA-TATGAGCCAGTGTAAGACCATGTCTAGGACATG
65 GGACATGGCATCGACATTGAGACGA-GAGCCAGTGTAAGA-CATGTCTAGGACATG
53165210 GCATCAGCAC
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
138 1 0.01
139 19 0.18
140 84 0.80
141 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGCATTGGCCTCGA
GATGTAAGCC
Found at i:53166350 original size:21 final size:22
Alignment explanation
Indices: 53166311--53166351 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53166301 TTGGAATGCT
*
53166311 CACATGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
53166333 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
53166352 GTGTCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.10, C:0.41, G:0.29, T:0.20
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:53166654 original size:58 final size:58
Alignment explanation
Indices: 53166564--53166680 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
53166554 CGAAGGATAC
*
53166564 ATGTATGGGGTGTTACATTTAGTGGTATCAGAGCTATGGTTTAGTTAGTTCTAGGACT
1 ATGTATGGGGTGTTACATTTAGTGGTATCAGAGCTATGGTTTAGTCAGTTCTAGGACT
53166622 ATGTATGGGGTGTTACATTTAGTGGTATCAGAGCTATGGTTTAGTCAGTTCTAGGACT
1 ATGTATGGGGTGTTACATTTAGTGGTATCAGAGCTATGGTTTAGTCAGTTCTAGGACT
53166680 A
1 A
53166681 ACCTAGCGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.38
Consensus pattern (58 bp):
ATGTATGGGGTGTTACATTTAGTGGTATCAGAGCTATGGTTTAGTCAGTTCTAGGACT
Found at i:53170091 original size:26 final size:26
Alignment explanation
Indices: 53170054--53170106 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
53170044 ACTCTAAATT
*
53170054 TTGTATTGGTACCGATGGTTGTATAA
1 TTGTATTAGTACCGATGGTTGTATAA
53170080 TTGTATTAGTACCGATGGTTGTATAA
1 TTGTATTAGTACCGATGGTTGTATAA
53170106 T
1 T
53170107 GTTCAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.43
Consensus pattern (26 bp):
TTGTATTAGTACCGATGGTTGTATAA
Found at i:53172733 original size:47 final size:45
Alignment explanation
Indices: 53172662--53172793 Score: 151
Period size: 47 Copynumber: 2.8 Consensus size: 45
53172652 CATTCGTTTG
* * *
53172662 TGAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGC-CAGATTG
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTCAGA-TA
*
53172706 TGAAAGCCAGTGTAAGACCATGTCTGGGACATGACATCGACTTGAGATA
1 TG--AGCCAGTGTAAGACCATGTCTGGGACATG-CATCGAC-TCAGATA
*
53172755 TGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC
1 TGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGAC
53172794 ACCTTACCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
44 2 0.03
46 12 0.16
47 49 0.64
48 7 0.09
49 3 0.04
50 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTCAGATA
Found at i:53178015 original size:2 final size:2
Alignment explanation
Indices: 53178008--53178033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53177998 TGAAATTTGA
53178008 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53178034 TTTGAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53179190 original size:37 final size:38
Alignment explanation
Indices: 53179082--53179260 Score: 229
Period size: 38 Copynumber: 4.7 Consensus size: 38
53179072 GGCCTAAAGA
*
53179082 CCCGCAGGCTAT-ATGCTGG-AATTATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGGTAA-TATATCCGGGTTAAAT
* *
53179120 TCTGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
*
53179158 CCCGCAGGCTTCGTGCT-GTAATATATCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
* *
53179195 CCCGCAGGCTTCGTGCTGGTAACATATCCGGGTTAAGT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
* * *
53179233 CCGCGCAGGCCTAGTGCTGGTACTATAT
1 CC-CGCAGGCTTCGTGCTGGTAATATAT
53179261 TCGAGCCTTC
Statistics
Matches: 124, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.30
38 64 0.52
39 23 0.19
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
Found at i:53179206 original size:75 final size:74
Alignment explanation
Indices: 53179082--53179260 Score: 223
Period size: 75 Copynumber: 2.3 Consensus size: 74
53179072 GGCCTAAAGA
* * * * *
53179082 CCCGCAGGCTATATGCTGGAATTATATCCGGGTTAAATTCTGCAGGCTTCGTGCTGGTAATATAT
1 CCCGCAGGCT-TGTGCTGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAACATAT
53179147 CCGGGTTAAAT
64 CCGGGTTAAAT
*
53179158 CCCGCAGGCTTCGTGCTGTAATATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTAACATATC
1 CCCGCAGGCTT-GTGCTGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAACATATC
*
53179223 CGGGTTAAGT
65 CGGGTTAAAT
* *
53179233 CCGCGCAGGCCTAGTGCTGGTACTATAT
1 CC-CGCAGG-CTTGTGCT-GTAATATAT
53179261 TCGAGCCTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
75 52 0.58
76 28 0.31
77 10 0.11
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (74 bp):
CCCGCAGGCTTGTGCTGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAACATATCC
GGGTTAAAT
Found at i:53179374 original size:44 final size:43
Alignment explanation
Indices: 53179258--53179387 Score: 208
Period size: 43 Copynumber: 3.0 Consensus size: 43
53179248 GCTGGTACTA
*
53179258 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCAGATGATGTG
* *
53179301 TATTCGGGCCTTCGTGCCCAGCAGGCTTCGTGCAGATGATGTG
1 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCAGATGATGTG
53179344 TATTCGAGCCTTTCGTGCCTAGCAGGCTTCGTGCCAG-TGATGTG
1 TATTCGAGCC-TTCGTGCCTAGCAGGCTTCGTG-CAGATGATGTG
53179388 CAGTCCTAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
43 49 0.61
44 28 0.35
45 3 0.04
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.30
Consensus pattern (43 bp):
TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCAGATGATGTG
Found at i:53181253 original size:94 final size:94
Alignment explanation
Indices: 53180976--53181253 Score: 493
Period size: 94 Copynumber: 3.0 Consensus size: 94
53180966 TGACCGTATG
* *
53180976 TGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
1 TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
* * *
53181041 TAAATATCACTTTGTGTGTAGATTATATA
66 TAAATGTCACTTTGTGTGCAGATTTTATA
53181070 TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
1 TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
53181135 TAAATGTCACTTTGTGTGCAGATTTTATA
66 TAAATGTCACTTTGTGTGCAGATTTTATA
53181164 TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
1 TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
* *
53181229 TAAATGGCACTATGTGTGCAGATTT
66 TAAATGTCACTTTGTGTGCAGATTT
53181254 GAATGTCGAT
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 177 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (94 bp):
TGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCGGAAT
TAAATGTCACTTTGTGTGCAGATTTTATA
Found at i:53181314 original size:24 final size:24
Alignment explanation
Indices: 53181282--53181345 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
53181272 GAAAATTTCA
* *
53181282 GGCACTATGTGTGCG-GTTTAGTAT
1 GGCACTATGTGTGCGAGCTTAAT-T
53181306 GGCACTATGTGTGCGAGCTTAATT
1 GGCACTATGTGTGCGAGCTTAATT
*
53181330 AGCACTATGTGTGCGA
1 GGCACTATGTGTGCGA
53181346 ATTTGGTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (24 bp):
GGCACTATGTGTGCGAGCTTAATT
Found at i:53189114 original size:95 final size:94
Alignment explanation
Indices: 53188810--53189186 Score: 648
Period size: 94 Copynumber: 4.0 Consensus size: 94
53188800 AATGTGACCG
* *
53188810 TATATGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
53188875 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
* *
53188904 TATATGCTATTTGAATTAAGTAAATTGCCTTATTACAATGAGTTAACATTGGCATTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
53188969 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
53188998 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACAATTGGCACTATGTGTGC
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAAC-ATTGGCACTATGTGTGC
*
53189063 GGAATTAAATGTCACTTTGTGTGCAAATTT
65 GGAATTAAATGTCACTTTGTGTGCAGATTT
* *
53189093 TATATGCTATTTGAATTAAGTAAATTGCCTTACTATAACGAGTTAACATTGGCACTATGTGT-CT
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGC-
* *
53189157 GGAATTAAATGGCACTATGTGTGCAGATTT
65 GGAATTAAATGTCACTTTGTGTGCAGATTT
53189187 GAATGTCGAT
Statistics
Matches: 269, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
93 1 0.00
94 178 0.66
95 90 0.33
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (94 bp):
TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATGTCACTTTGTGTGCAGATTT
Found at i:53189138 original size:189 final size:188
Alignment explanation
Indices: 53188810--53189186 Score: 648
Period size: 189 Copynumber: 2.0 Consensus size: 188
53188800 AATGTGACCG
*
53188810 TATATGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCG
* *
53188875 GAATTAAATGTCACTTTGTGTGCAGATTTTATATGCTATTTGAATTAAGTAAATTGCCTTATTAC
66 GAATTAAATGTCACTTTGTGTGCAAATTTTATATGCTATTTGAATTAAGTAAATTGCCTTACTAC
* * * *
53188940 AATGAGTTAACATTGGCATTATGTGTGC-GGAATTAAATGTCACTTTGTGTGCAGATTT
131 AACGAGTTAACATTGGCACTATGTGT-CTGGAATTAAATGGCACTATGTGTGCAGATTT
*
53188998 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACAATTGGCACTATGTGTGC
1 TATATGCTATTTGAATTAAGTAAATTGCCATATTATAATGAGTTAAC-ATTGGCACTATGTGTGC
53189063 GGAATTAAATGTCACTTTGTGTGCAAATTTTATATGCTATTTGAATTAAGTAAATTGCCTTACTA
65 GGAATTAAATGTCACTTTGTGTGCAAATTTTATATGCTATTTGAATTAAGTAAATTGCCTTACTA
*
53189128 TAACGAGTTAACATTGGCACTATGTGTCTGGAATTAAATGGCACTATGTGTGCAGATTT
130 CAACGAGTTAACATTGGCACTATGTGTCTGGAATTAAATGGCACTATGTGTGCAGATTT
53189187 GAATGTCGAT
Statistics
Matches: 178, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
188 46 0.26
189 132 0.74
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (188 bp):
TATATGCTATTTGAATTAAGTAAATTGCCATATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATGTCACTTTGTGTGCAAATTTTATATGCTATTTGAATTAAGTAAATTGCCTTACTAC
AACGAGTTAACATTGGCACTATGTGTCTGGAATTAAATGGCACTATGTGTGCAGATTT
Found at i:53190979 original size:10 final size:10
Alignment explanation
Indices: 53190964--53190998 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
53190954 CGGGTCAGGG
53190964 TGTGAAAGTA
1 TGTGAAAGTA
53190974 TGTGAAAGTA
1 TGTGAAAGTA
53190984 TGTGAAAGTA
1 TGTGAAAGTA
53190994 TGTGA
1 TGTGA
53190999 TTTAATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
TGTGAAAGTA
Found at i:53193742 original size:17 final size:19
Alignment explanation
Indices: 53193700--53193743 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53193690 ATGAAATTTT
*
53193700 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53193719 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53193737 AA-TATTA
1 AATTATTA
53193744 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53195597 original size:28 final size:28
Alignment explanation
Indices: 53195565--53195633 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
53195555 GCGTAGATCA
53195565 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
53195593 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
53195621 CGATA-TACCCCTA
1 CGAAATTACCCCTA
53195634 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:53198055 original size:17 final size:19
Alignment explanation
Indices: 53198013--53198056 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53198003 ATGAAATTTT
*
53198013 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53198032 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53198050 AA-TATTA
1 AATTATTA
53198057 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53199900 original size:28 final size:28
Alignment explanation
Indices: 53199868--53199936 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
53199858 GCGTAGATCA
53199868 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
53199896 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
53199924 CGATA-TACCCCTA
1 CGAAATTACCCCTA
53199937 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:53202359 original size:17 final size:19
Alignment explanation
Indices: 53202317--53202360 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53202307 ATGAAATTTT
*
53202317 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53202336 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53202354 AA-TATTA
1 AATTATTA
53202361 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53203177 original size:15 final size:16
Alignment explanation
Indices: 53203157--53203186 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53203147 TTCTTCAAAA
53203157 CTATTCATC-ATACTG
1 CTATTCATCAATACTG
53203172 CTATTCATCAATACT
1 CTATTCATCAATACT
53203187 TTTGCCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (16 bp):
CTATTCATCAATACTG
Found at i:53204211 original size:28 final size:27
Alignment explanation
Indices: 53204175--53204246 Score: 119
Period size: 28 Copynumber: 2.7 Consensus size: 27
53204165 AGTAGCGTAG
53204175 ATTACGAAATTACCCCTAAAGAGCAAA
1 ATTACGAAATTACCCCTAAAGAGCAAA
53204202 ATTACCGAAATTACCCCTAAAGAGCAAA
1 ATTA-CGAAATTACCCCTAAAGAGCAAA
*
53204230 ATTACGATA-TACCCCTA
1 ATTACGAAATTACCCCTA
53204247 GGGTTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
26 8 0.19
27 8 0.19
28 27 0.63
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (27 bp):
ATTACGAAATTACCCCTAAAGAGCAAA
Found at i:53207810 original size:37 final size:37
Alignment explanation
Indices: 53207702--53207883 Score: 224
Period size: 38 Copynumber: 4.8 Consensus size: 37
53207692 GGCCTAAAGA
* *
53207702 CCCGCAGGCTAT-ATGCTGGAATTATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGTAA-TATATCCGGGTTAAAT
**
53207740 TTCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCT-GTAATATATCCGGGTTAAAT
*
53207778 CCCGCAGGCTTCGTGCTGTAATATATCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGTAATATATCCGGGTTAAAT
53207815 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCT-GTAATATATCCGGGTTAAAT
* * * *
53207853 CCTGCAGGC-CCAGTGCTGTATTATATTCGGG
1 CCCGCAGGCTTC-GTGCTGTAATATATCCGGG
53207884 CCTTCGTGCC
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
37 50 0.39
38 75 0.59
39 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (37 bp):
CCCGCAGGCTTCGTGCTGTAATATATCCGGGTTAAAT
Found at i:53207814 original size:75 final size:75
Alignment explanation
Indices: 53207702--53207883 Score: 242
Period size: 75 Copynumber: 2.4 Consensus size: 75
53207692 GGCCTAAAGA
* * **
53207702 CCCGCAGGCTAT-ATGCTGGAATTATATCCGGGTTAAATTTCGCAGGCTTCGTGCTGGTAATATA
1 CCCGCAGGCT-TCGTGCTGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATA
53207766 TCCGGGTTAAAT
64 TCCGGGTTAAAT
*
53207778 CCCGCAGGCTTCGTGCTGTAATATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATC
1 CCCGCAGGCTTCGTGCTGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATC
53207843 CGGGTTAAAT
66 CGGGTTAAAT
* * * *
53207853 CCTGCAGGC-CCAGTGCTGTATTATATTCGGG
1 CCCGCAGGCTTC-GTGCTGTAATATATCCGGG
53207884 CCTTCGTGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
74 1 0.01
75 76 0.81
76 17 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (75 bp):
CCCGCAGGCTTCGTGCTGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATC
CGGGTTAAAT
Found at i:53207870 original size:38 final size:38
Alignment explanation
Indices: 53207702--53207861 Score: 236
Period size: 38 Copynumber: 4.2 Consensus size: 38
53207692 GGCCTAAAGA
*
53207702 CCCGCAGGCTAT-ATGCTGG-AATTATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGGTAA-TATATCCGGGTTAAAT
**
53207740 TTCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
*
53207778 CCCGCAGGCTTCGTGCT-GTAATATATCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
53207815 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
*
53207853 CCTGCAGGC
1 CCCGCAGGC
53207862 CCAGTGCTGT
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
37 37 0.33
38 72 0.65
39 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
Found at i:53207953 original size:43 final size:43
Alignment explanation
Indices: 53207876--53207957 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
53207866 TGCTGTATTA
* **
53207876 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
53207919 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
53207958 AATGATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.12, C:0.26, G:0.34, T:0.28
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
Found at i:53208567 original size:10 final size:10
Alignment explanation
Indices: 53208552--53208586 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
53208542 CGGGTCAGGG
53208552 TGTGAAAGTA
1 TGTGAAAGTA
53208562 TGTGAAAGTA
1 TGTGAAAGTA
53208572 TGTGAAAGTA
1 TGTGAAAGTA
53208582 TGTGA
1 TGTGA
53208587 TTTAATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
TGTGAAAGTA
Found at i:53213142 original size:43 final size:43
Alignment explanation
Indices: 53213082--53213167 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
53213072 GATATATGTG
** *
53213082 GCATCCGAGCTCGTTGAGTAGTTTGAGTTCATTATGGATGCGA
1 GCATCCGAGCTCGTTGAGTAGTCCGAGTTCATAATGGATGCGA
* * *
53213125 GCATCTGAGCTTGTTGAGTGGTCCGAGTTCATAATGGATGCGA
1 GCATCCGAGCTCGTTGAGTAGTCCGAGTTCATAATGGATGCGA
53213168 TACATTTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGTAGTCCGAGTTCATAATGGATGCGA
Found at i:53214757 original size:19 final size:20
Alignment explanation
Indices: 53214733--53214781 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
53214723 TTATACAGCT
53214733 AGAGGACACAGG-CGTGTCG
1 AGAGGACACAGGACGTGTCG
*
53214752 AGAGGACAC-GGACGTGTTG
1 AGAGGACACAGGACGTGTCG
53214771 AGAGGACACAG
1 AGAGGACACAG
53214782 ACATGTCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.07
19 24 0.89
20 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.41, T:0.10
Consensus pattern (20 bp):
AGAGGACACAGGACGTGTCG
Found at i:53221514 original size:40 final size:40
Alignment explanation
Indices: 53221469--53221635 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
53221459 CGGAATATAA
53221469 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53221509 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53221549 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53221589 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53221628 CCGGATAT
1 CCGGATAT
53221636 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53221619 original size:80 final size:79
Alignment explanation
Indices: 53221469--53221635 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
53221459 CGGAATATAA
* *
53221469 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
53221534 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
53221549 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
53221611 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
53221628 CCGGATAT
1 CCGGATAT
53221636 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:53222484 original size:17 final size:19
Alignment explanation
Indices: 53222461--53222506 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53222451 AAGAAGCATG
53222461 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53222479 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53222497 AATCATGCTC
1 AATCATGCTC
53222507 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53229521 original size:40 final size:40
Alignment explanation
Indices: 53229476--53229642 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
53229466 CGGAATATAA
53229476 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53229516 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53229556 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53229596 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53229635 CCGGATAT
1 CCGGATAT
53229643 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53229626 original size:80 final size:79
Alignment explanation
Indices: 53229476--53229642 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
53229466 CGGAATATAA
* *
53229476 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
53229541 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
53229556 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
53229618 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
53229635 CCGGATAT
1 CCGGATAT
53229643 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:53230491 original size:17 final size:19
Alignment explanation
Indices: 53230468--53230513 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53230458 AAGAAGCATG
53230468 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53230486 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53230504 AATCATGCTC
1 AATCATGCTC
53230514 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53243942 original size:49 final size:49
Alignment explanation
Indices: 53243873--53244123 Score: 457
Period size: 49 Copynumber: 5.1 Consensus size: 49
53243863 GTACATAATA
53243873 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
53243922 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
53243971 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
* *
53244020 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
* * *
53244069 ACATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
53244118 ATATAT
1 ATATAT
53244124 ATGTGGTAAA
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 198 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
Found at i:53244247 original size:37 final size:36
Alignment explanation
Indices: 53244197--53244278 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 36
53244187 AGAAATATGT
53244197 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTACG
1 TCCGGGT-AGACCCGATGACTACGTGTGGAGATTACG
*
53244234 TCCGGGTATGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTA-GACCCGATGACTACGTGTGGAGATTACG
53244271 TCCGGGTA
1 TCCGGGTA
53244279 AGACTTCGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (36 bp):
TCCGGGTAGACCCGATGACTACGTGTGGAGATTACG
Found at i:53246527 original size:42 final size:43
Alignment explanation
Indices: 53246419--53246617 Score: 240
Period size: 42 Copynumber: 4.7 Consensus size: 43
53246409 TGTGTTATCG
* * * *
53246419 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTTTGATTTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTT-CA
53246463 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCA
* * *
53246505 TGTAAGACCCTGTTTGGAACATTGGCATCG-TATATGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCA
* * * * *
53246547 TGTAAGACCCTATCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCA
* * *
53246590 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
53246618 TGTACGAGCT
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 66 0.49
43 40 0.30
44 29 0.21
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCA
Found at i:53252600 original size:46 final size:46
Alignment explanation
Indices: 53252547--53252719 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
53252537 TAGTTGAGCA
*
53252547 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
53252593 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
53252638 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
53252686 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53252720 AGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 4 0.04
45 4 0.04
46 60 0.57
47 29 0.27
48 4 0.04
50 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:53252703 original size:93 final size:93
Alignment explanation
Indices: 53252544--53252715 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
53252534 GGATAGTTGA
* * * *
53252544 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
53252609 TGAGTCCGAGTTCATGAAATGTAACTAG
66 TGAGTCCGAGTTCATGAAATGTAACTAG
*
53252637 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
53252702 TGAGTCTGAGTTCA
66 TGAGTCCGAGTTCA
53252716 CTTAAGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAAATGTAACTAG
Found at i:53266408 original size:42 final size:42
Alignment explanation
Indices: 53266302--53266458 Score: 188
Period size: 43 Copynumber: 3.7 Consensus size: 42
53266292 TGTGTTATCC
* * * *
53266302 TGTAAGACCATGTCTGGGACATTGGCATTGGTTTGTCATTTACA
1 TGTAAGACCATGTCTGGGACATTGGCA-TCGTATATGATTT-CA
53266346 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCA
* * * * * *
53266388 TGGAAGACCCTGTCTGGGACAGTGGCATCGATATTTGACTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTTCA
*
53266431 TGTAAGACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
53266459 TGTACGAGTT
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 29 0.30
43 42 0.43
44 27 0.28
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCA
Found at i:53269180 original size:40 final size:40
Alignment explanation
Indices: 53269125--53269334 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
53269115 AACATTGGAA
53269125 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53269165 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53269205 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
53269245 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
53269284 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
53269325 CTATATCCGG
1 ATATATCCGG
53269335 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:53277520 original size:40 final size:40
Alignment explanation
Indices: 53277475--53277641 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
53277465 CGGAATATAA
53277475 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
53277515 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53277555 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
53277595 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
53277634 CCGGATAT
1 CCGGATAT
53277642 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.13
40 90 0.87
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53285522 original size:40 final size:40
Alignment explanation
Indices: 53285477--53285644 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
53285467 CGGAATATAA
53285477 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
53285517 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53285557 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
53285597 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
53285637 CCGGATAT
1 CCGGATAT
53285645 CATTCAATTT
Statistics
Matches: 102, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 101 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53285627 original size:80 final size:80
Alignment explanation
Indices: 53285493--53285642 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
53285483 ATAACCACGT
* *
53285493 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
53285558 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * * * *
53285573 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG
53285636 CCCGGAT
64 CCCGGAT
53285643 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 3 0.05
80 58 0.95
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:53288285 original size:2 final size:2
Alignment explanation
Indices: 53288273--53288301 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53288263 CACTTTCAAA
53288273 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53288302 TCAACTACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53290794 original size:17 final size:17
Alignment explanation
Indices: 53290772--53290805 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53290762 TTTAATGCAC
53290772 ACATATTCTTCAAGAGG
1 ACATATTCTTCAAGAGG
53290789 ACATATTCTTCAAGAGG
1 ACATATTCTTCAAGAGG
53290806 CTCGATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
ACATATTCTTCAAGAGG
Found at i:53313082 original size:31 final size:31
Alignment explanation
Indices: 53313044--53313107 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
53313034 CCTTTTCATA
53313044 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
53313075 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
53313106 TT
1 TT
53313108 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:53313345 original size:24 final size:24
Alignment explanation
Indices: 53313299--53313441 Score: 184
Period size: 24 Copynumber: 6.0 Consensus size: 24
53313289 GCTTTATCAT
*
53313299 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
53313324 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
53313348 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53313371 ATAGCTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53313395 ATAACTAGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
53313419 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53313442 TCACTTCCTC
Statistics
Matches: 107, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
23 24 0.22
24 70 0.65
25 13 0.12
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53313388 original size:47 final size:48
Alignment explanation
Indices: 53313299--53313440 Score: 182
Period size: 47 Copynumber: 3.0 Consensus size: 48
53313289 GCTTTATCAT
*
53313299 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
* **
53313348 ATAACTGGGGCATAAGCCCTTTT-ATAGCTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
* *
53313395 ATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
53313441 TTCACTTCCT
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
46 2 0.02
47 40 0.48
48 30 0.36
49 12 0.14
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:53313517 original size:20 final size:20
Alignment explanation
Indices: 53313492--53313555 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
53313482 TATGATTACC
*
53313492 TCATGTGCATATCATCCATA
1 TCATGTGCATATCATACATA
* *
53313512 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
53313532 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
53313552 TCAT
1 TCAT
53313556 ATTTATCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:53313626 original size:25 final size:25
Alignment explanation
Indices: 53313594--53313641 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53313584 ATACATAAAC
* * *
53313594 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
53313619 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53313642 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:53316540 original size:27 final size:27
Alignment explanation
Indices: 53316472--53316542 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
53316462 CGACTTGTAA
* *
53316472 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAATAC-CCTCAATTTACAG
****
53316499 AATTACCGTTTTACCCTCAATTTACAG
1 AATTACCAAAATACCCTCAATTTACAG
53316526 AATTACCAAAATACCCT
1 AATTACCAAAATACCCT
53316543 TGGTTTATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTACAG
Found at i:53316549 original size:27 final size:27
Alignment explanation
Indices: 53316526--53316703 Score: 232
Period size: 27 Copynumber: 6.6 Consensus size: 27
53316516 CAATTTACAG
53316526 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
53316553 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
53316580 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
53316607 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
53316634 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
53316661 AATTACCAAAATACCCATGGTTTGA-AA
1 AATTACCAAAATACCCTTGGTTT-ATAA
**
53316688 AATTACTGAAATACCC
1 AATTACCAAAATACCC
53316704 CTGTAGGGTA
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:53316568 original size:54 final size:54
Alignment explanation
Indices: 53316526--53316703 Score: 302
Period size: 54 Copynumber: 3.3 Consensus size: 54
53316516 CAATTTACAG
*
53316526 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
53316580 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
* * * *
53316634 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCATGGTTTGAAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
*
53316688 AATTACTGAAATACCC
1 AATTACTAAAATACCC
53316704 CTGTAGGGTA
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 118 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
Found at i:53316682 original size:81 final size:81
Alignment explanation
Indices: 53316530--53316733 Score: 241
Period size: 81 Copynumber: 2.5 Consensus size: 81
53316520 TTACAGAATT
* * * * * * *
53316530 ACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACC
1 ACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACC
*
53316595 CTTGGTTT-ATAAAATC
66 CATGGTTTGA-AAAATC
*
53316611 ACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACC
1 ACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACC
*
53316676 CATGGTTTGAAAAATT
66 CATGGTTTGAAAAATC
** ** *
53316692 ACTGAAATACCCCT-GTAGGGTAAAATTACTGAAATACCCTTG
1 ACCAAAATACCCCTGGT-TTGTAAAATTACTAAAATACCCTTG
53316734 TGGGGTAAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 102 0.97
82 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (81 bp):
ACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACC
CATGGTTTGAAAAATC
Found at i:53316716 original size:27 final size:27
Alignment explanation
Indices: 53316686--53316747 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
53316676 CATGGTTTGA
53316686 AAAATTACTGAAATACCCCTGTAGGGT
1 AAAATTACTGAAATACCCCTGTAGGGT
* *
53316713 AAAATTACTGAAATACCCTTGTGGGGT
1 AAAATTACTGAAATACCCCTGTAGGGT
53316740 AAAATTAC
1 AAAATTAC
53316748 CATTTTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (27 bp):
AAAATTACTGAAATACCCCTGTAGGGT
Found at i:53317401 original size:28 final size:28
Alignment explanation
Indices: 53317369--53317437 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
53317359 GCGTAGATCA
53317369 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
53317397 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
53317425 CGATA-TACCCCTA
1 CGAAATTACCCCTA
53317438 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:53320767 original size:19 final size:18
Alignment explanation
Indices: 53320732--53320767 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53320722 AATCTGGGCC
*
53320732 ATAAAAAAAATTTTTCAA
1 ATAAAAAAAATTATTCAA
53320750 ATAAAAAAAATTCATTCA
1 ATAAAAAAAATT-ATTCA
53320768 TATTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAAAAATTATTCAA
Found at i:53320906 original size:358 final size:358
Alignment explanation
Indices: 53320240--53320916 Score: 1135
Period size: 358 Copynumber: 1.9 Consensus size: 358
53320230 ACATAAACAA
*
53320240 AGATGAAAAATGAAAAACGATGACCCTTGAGTAGGTATGGTACAAGTTGTAACACCACTTACCCG
1 AGATGAAAAATGAAAAACGATGACCCTTGAGCAGGTATGGTACAAGTTGTAACACCACTTACCCG
53320305 AGTTCGAGGCCGAGACAGGGTACAAGGCATTACCAGACTTAAACATACACAACTATGTAAAATCG
66 AGTTCGAGGCCGAGACAGGGTACAAGGCATTACCAGACTTAAACATACACAACTATGTAAAATCG
* * * *
53320370 AGCCATAAAAAATTTTATTCAAATTAAAAACATTCATTCATATTCATAATGTTCCTTATACGGGC
131 AGCCATAAAAAAATTTATTCAAATAAAAAAAATTCATTCATATTCATAATGTCCCTTATACGGGC
*
53320435 TTACGAGGCCCAAAACATACATCGAGGGTGGTTCGGGACTAAACCAAGAACTTACGAACTTTTTA
196 TTACGAGGCCCAAAACATACATCGAGGGTGGTTCGGGACTAAACCAAGAACTTACAAACTTTTTA
*
53320500 CAATGCTTAGAAAATTTTCTAGTTTTGGAGAGTCACACGCTCGTGTGGGTAGGCCGTGTCGTCAC
261 CAACGCTTAGAAAATTTTCTAGTTTTGGAGAGTCACACGCTCGTGTGGGTAGGCCGTGTCGTCAC
53320565 ACACGCCCGCGTGGCTCGGACATGCCCGTGTAC
326 ACACGCCCGCGTGGCTCGGACATGCCCGTGTAC
* * * *
53320598 AGATGGAAAATGAAAAATGATGATCCTTGAGCAGGTATGGTACAAGTTGTAACACCCCTTACCCG
1 AGATGAAAAATGAAAAACGATGACCCTTGAGCAGGTATGGTACAAGTTGTAACACCACTTACCCG
* * * ***
53320663 AGTTCGAGGCTGGGACAGGGTACAAGGTATTATTGGACTTAAACATACACAACTATGT-AAATCT
66 AGTTCGAGGCCGAGACAGGGTACAAGGCATTACCAGACTTAAACATACACAACTATGTAAAATC-
*
53320727 GGGCCATAAAAAAAATTT-TTCAAATAAAAAAAATTCATTCATATTCATAATGTCCCTTATACGG
130 GAGCCAT-AAAAAAATTTATTCAAATAAAAAAAATTCATTCATATTCATAATGTCCCTTATACGG
*
53320791 GCTTACGAGGCCCAAAACATACATCGGGGGTGGTTCGGGACTAAACCAAGAACTTACAAACTTTT
194 GCTTACGAGGCCCAAAACATACATCGAGGGTGGTTCGGGACTAAACCAAGAACTTACAAACTTTT
53320856 TACAACGCTTAGAAAATTTTCTAGTTTTGGAGAGTCACACGC-CAGTGTGGGTAGGCCGTGT
259 TACAACGCTTAGAAAATTTTCTAGTTTTGGAGAGTCACACGCTC-GTGTGGGTAGGCCGTGT
53320917 GGCTCGGACA
Statistics
Matches: 297, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
357 6 0.02
358 282 0.95
359 9 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (358 bp):
AGATGAAAAATGAAAAACGATGACCCTTGAGCAGGTATGGTACAAGTTGTAACACCACTTACCCG
AGTTCGAGGCCGAGACAGGGTACAAGGCATTACCAGACTTAAACATACACAACTATGTAAAATCG
AGCCATAAAAAAATTTATTCAAATAAAAAAAATTCATTCATATTCATAATGTCCCTTATACGGGC
TTACGAGGCCCAAAACATACATCGAGGGTGGTTCGGGACTAAACCAAGAACTTACAAACTTTTTA
CAACGCTTAGAAAATTTTCTAGTTTTGGAGAGTCACACGCTCGTGTGGGTAGGCCGTGTCGTCAC
ACACGCCCGCGTGGCTCGGACATGCCCGTGTAC
Found at i:53322799 original size:48 final size:48
Alignment explanation
Indices: 53322712--53323038 Score: 230
Period size: 48 Copynumber: 6.8 Consensus size: 48
53322702 TTCTCACATT
* * * * *
53322712 GATGCCAATAGCCC-AACTATGGTCTTACAC-GAAGTCTCATAACGGTGTC
1 GATGCC-ATATCCCAAAC-ATGGTCTTATACGGGA-TCTCATAACGATGCC
* * * *
53322761 GATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATCGATGCC
1 GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAACGATGCC
* * * * *
53322809 AATGCCATATTCCAAATATGGTCTTACATGGGATCTCAT-ACTGATGCC
1 GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAAC-GATGCC
* * * * * **
53322857 GATGCCATGTCCCAAACGTGGTCTTATACAGGATCTCTTATCGATGTT
1 GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAACGATGCC
* * * *** *
53322905 GATGCCATATCCCAAATATGGTCTTACATGGGATCTCATCTTGATGCT
1 GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAACGATGCC
* * * * * ** *
53322953 GATGCCATATCACAGATATGGTCTTAAACGAGATCTCATTTCAATGCC
1 GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAACGATGCC
* **
53323001 GATGCCATAT-CCAAGATATGGTCTTATATTGGATCTCA
1 GATGCCATATCCCAA-ACATGGTCTTATACGGGATCTCA
53323039 ATACTCACAT
Statistics
Matches: 218, Mismatches: 55, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
47 3 0.01
48 204 0.94
49 11 0.05
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (48 bp):
GATGCCATATCCCAAACATGGTCTTATACGGGATCTCATAACGATGCC
Found at i:53322868 original size:96 final size:96
Alignment explanation
Indices: 53322760--53323043 Score: 356
Period size: 96 Copynumber: 2.9 Consensus size: 96
53322750 ATAACGGTGT
* *
53322760 CGATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATCGATGCCAATGCCATATTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATTCCAAA
53322825 TATGGTCTTACATGGGATCTCATACTGATGC
66 TATGGTCTTACATGGGATCTCATACTGATGC
* * * * ** *
53322856 CGATGCCATGTCCCAAACGTGGTCTTATACAGGATCTCTTATCGATGTTGATGCCATATCCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATTCCAAA
53322921 TATGGTCTTACATGGGATCTCAT-CTTGATGC
66 TATGGTCTTACATGGGATCTCATAC-TGATGC
* * * * * * * *
53322952 TGATGCCATATCACAGATATGGTCTTAAACGAGATCTCATTTCAATGCCGATGCCATA-TCCAAG
1 CGATGCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATTCCAA-
* *
53323016 ATATGGTCTTATATTGGATCTCAATACT
65 ATATGGTCTTACATGGGATCTC-ATACT
53323044 CACATGTCGT
Statistics
Matches: 158, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
95 5 0.03
96 149 0.94
97 3 0.02
98 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATTCCAAA
TATGGTCTTACATGGGATCTCATACTGATGC
Found at i:53323023 original size:144 final size:144
Alignment explanation
Indices: 53322761--53323037 Score: 317
Period size: 144 Copynumber: 1.9 Consensus size: 144
53322751 TAACGGTGTC
* * *
53322761 GATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATCGATGCCAATGCCATATTCCAAAT
1 GATGCCATATCCCAAACATGGTCTTACACGGGACCTCATATCGATGCCAATGCCATATTCCAAAT
* * * * * *
53322826 ATGGTCTTACATGGGATCTCATACTGATGCCGATGCCATGTCCCAAACGTGGTCTTATACAGGAT
66 ATGGTCTTAAACGAGATCTCATACTAATGCCGATGCCATATCCCAAACATGGTCTTATACAGGAT
53322891 CTCTTATCGATGTT
131 CTCTTATCGATGTT
* * * * * ** *
53322905 GATGCCATATCCCAAATATGGTCTTACATGGGATCTCATCTTGATGCTGATGCCATA-TCACAGA
1 GATGCCATATCCCAAACATGGTCTTACACGGGACCTCATATCGATGCCAATGCCATATTC-CAAA
* * **
53322969 TATGGTCTTAAACGAGATCTCAT-TTCAATGCCGATGCCATAT-CCAAGATATGGTCTTATATTG
65 TATGGTCTTAAACGAGATCTCATACT-AATGCCGATGCCATATCCCAA-ACATGGTCTTATACAG
53323032 GATCTC
128 GATCTC
53323038 AATACTCACA
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
143 7 0.06
144 102 0.94
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (144 bp):
GATGCCATATCCCAAACATGGTCTTACACGGGACCTCATATCGATGCCAATGCCATATTCCAAAT
ATGGTCTTAAACGAGATCTCATACTAATGCCGATGCCATATCCCAAACATGGTCTTATACAGGAT
CTCTTATCGATGTT
Found at i:53328131 original size:11 final size:11
Alignment explanation
Indices: 53328115--53328140 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53328105 GGAAGCCGAC
53328115 ATCACAATAAT
1 ATCACAATAAT
53328126 ATCACAATAAT
1 ATCACAATAAT
53328137 ATCA
1 ATCA
53328141 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:53328631 original size:27 final size:27
Alignment explanation
Indices: 53328601--53328770 Score: 148
Period size: 27 Copynumber: 6.3 Consensus size: 27
53328591 CAAAACAGTT
* * *
53328601 ATTTTACCCTACAAGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
**
53328628 ATTTTACACTACAAATGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
53328655 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * * *
53328682 ATTTTACAAATA-AGGGGTGTTTCTGTA
1 ATTTTAC-ACTACAAGGGTATTTCGGTA
* * *
53328709 ATTTTACA-AATCGAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
53328736 ATTTTACA-AATCGAGGGTATTTCAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
53328763 ATTTTACA
1 ATTTTACA
53328771 AATCGAGGGT
Statistics
Matches: 119, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 114 0.96
28 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:53328771 original size:27 final size:27
Alignment explanation
Indices: 53328644--53328927 Score: 301
Period size: 27 Copynumber: 10.6 Consensus size: 27
53328634 CACTACAAAT
* * *
53328644 GTATTTCGGTAATTTTAC-ACTACAAGG
1 GTATTTCAGTAATTTTACAAAT-CGAGG
*
53328671 GTATTTC-GATAATTTTACAAAT-AAGGG
1 GTATTTCAG-TAATTTTACAAATCGA-GG
* *
53328698 GTGTTTCTGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
53328725 GTATTTC-GATAATTTTACAAATCGAGG
1 GTATTTCAG-TAATTTTACAAATCGAGG
53328752 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * * * *
53328779 GTGTTTCAGTAATTTCAAAAATTGGGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* *
53328806 GTATTTCGGTAATTTTACAAATCGAAG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
53328833 GTACTTCAGTAATTTCAC-AATTGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
53328859 GTATTTCGGTAATTTTACAAATTGGGGG
1 GTATTTCAGTAATTTTACAAA-TCGAGG
*
53328887 GTATTT-TGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
53328913 GTATTTCAGTAATTT
1 GTATTTCAGTAATTT
53328928 CTCTTTATTA
Statistics
Matches: 217, Mismatches: 30, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
26 35 0.16
27 167 0.77
28 15 0.07
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:53329264 original size:29 final size:28
Alignment explanation
Indices: 53329222--53329305 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
53329212 CAGATCCACA
* * *
53329222 CTTATTCATTTGGCCCTTTTAGGCCCAAT
1 CTTATTCATATGGCCC-ATCAGGCCCAAT
*
53329251 CTTATTCACATGGCCCATCAGGCCCAAT
1 CTTATTCATATGGCCCATCAGGCCCAAT
**
53329279 CACATTCATATGGCCCATCAGGCCCAA
1 CTTATTCATATGGCCCATCAGGCCCAA
53329306 CTACTTCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 34 0.71
29 14 0.29
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (28 bp):
CTTATTCATATGGCCCATCAGGCCCAAT
Found at i:53334031 original size:80 final size:80
Alignment explanation
Indices: 53333947--53334095 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
53333937 TATGGTAACC
* * * *
53333947 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
53334011 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
53334027 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
53334092 CCGG
66 CCGG
53334096 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:53334037 original size:40 final size:38
Alignment explanation
Indices: 53333988--53334095 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
53333978 ATCACGATTT
*
53333988 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
53334028 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
53334068 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
53334096 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:53341335 original size:80 final size:80
Alignment explanation
Indices: 53341251--53341399 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
53341241 TATGGTAACC
* * * *
53341251 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
53341315 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
53341331 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
53341396 CCGG
66 CCGG
53341400 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:53341341 original size:40 final size:38
Alignment explanation
Indices: 53341292--53341399 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
53341282 ATCACGATTT
*
53341292 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
53341332 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
53341372 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
53341400 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:53347094 original size:40 final size:40
Alignment explanation
Indices: 53347034--53347242 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
53347024 GTTAATTATA
* * * *
53347034 CCTGAATTGCATATACGTGCCCTTGTTTGTACTTCGGTACC
1 CCTG-ATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
* * *
53347075 CTTGATTGCACACACGTGCCCCTGGTTGTACTTCAATACC
1 CCTGATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
* *
53347115 CCTGATTGCACTCAGGTGCCCCTGTTTGTACTTCAGTACC
1 CCTGATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
** *
53347155 CCTGATTGCACA-TTGTGCCCCTTTTTGTACTTCAGTA-C
1 CCTGATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
* * * * *
53347193 CCTGATTGCACATACTTGCCCCAGTTTGTACTTTAGGACC
1 CCTGATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
*
53347233 CCTAATTGCA
1 CCTGATTGCA
53347243 TATGTTAAGT
Statistics
Matches: 142, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
38 13 0.09
39 40 0.28
40 86 0.61
41 3 0.02
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (40 bp):
CCTGATTGCACACACGTGCCCCTGTTTGTACTTCAGTACC
Found at i:53347118 original size:20 final size:20
Alignment explanation
Indices: 53347060--53347200 Score: 94
Period size: 20 Copynumber: 7.2 Consensus size: 20
53347050 GTGCCCTTGT
* *
53347060 TTGTACTTCGGTACCCTTGA
1 TTGTACTTCAGTACCCCTGA
* * * *
53347080 TTGCAC-ACACGTGCCCCTGG
1 TTGTACTTCA-GTACCCCTGA
*
53347100 TTGTACTTCAATACCCCTGA
1 TTGTACTTCAGTACCCCTGA
* * *
53347120 TTGCAC-TCAGGTGCCCCTGT
1 TTGTACTTCA-GTACCCCTGA
53347140 TTGTACTTCAGTACCCCTGA
1 TTGTACTTCAGTACCCCTGA
* * **
53347160 TTGCACATT--GTGCCCCTTT
1 TTGTAC-TTCAGTACCCCTGA
53347179 TTGTACTTCAGTA-CCCTGA
1 TTGTACTTCAGTACCCCTGA
53347198 TTG
1 TTG
53347201 CACATACTTG
Statistics
Matches: 88, Mismatches: 26, Indels: 15
0.68 0.20 0.12
Matches are distributed among these distances:
18 2 0.02
19 23 0.26
20 56 0.64
21 7 0.08
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTACTTCAGTACCCCTGA
Found at i:53349788 original size:39 final size:39
Alignment explanation
Indices: 53349657--53349861 Score: 238
Period size: 39 Copynumber: 5.3 Consensus size: 39
53349647 CGGGATTTAA
* * * *
53349657 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGA-TGCCTTCGGGTCTTAGC
* * * * * * *
53349697 CCGGATTTGGT-GACTTGCACAAAGGCTTCGGGTCTTAG-
1 CCGGATAT-ATCAACTCGCACGATGCCTTCGGGTCTTAGC
53349735 CCGGATATATCAACTCGCACGATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGATGCCTTCGGGTCTTAGC
53349774 CCGGATATATCAACTCGCA-GAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACG-ATGCCTTCGGGTCTTAGC
*
53349813 CCGGATATAT-AACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATATCAACTCGCACG-ATGCCTTCGGGTCTTAGC
53349852 CCGGATATAT
1 CCGGATATAT
53349862 TTCCAATGTT
Statistics
Matches: 143, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
37 1 0.01
38 38 0.27
39 88 0.62
40 16 0.11
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (39 bp):
CCGGATATATCAACTCGCACGATGCCTTCGGGTCTTAGC
Found at i:53353126 original size:29 final size:29
Alignment explanation
Indices: 53353025--53353118 Score: 170
Period size: 29 Copynumber: 3.2 Consensus size: 29
53353015 GTGACGAGAT
53353025 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53353054 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
53353083 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
53353112 CGGCACT
1 TGGCACT
53353119 GGGTGTGCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53353143 original size:58 final size:58
Alignment explanation
Indices: 53353021--53353155 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 58
53353011 TACGGTGACG
* * *
53353021 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
53353078 ATATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
53353136 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53353156 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
57 3 0.05
58 62 0.94
59 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53360973 original size:29 final size:29
Alignment explanation
Indices: 53360940--53361022 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
53360930 GTGACGAGAT
53360940 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53360969 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53360998 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
53361023 AAATACGGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53361058 original size:58 final size:58
Alignment explanation
Indices: 53360936--53361070 Score: 159
Period size: 58 Copynumber: 2.3 Consensus size: 58
53360926 TACGGTGACG
* * *
53360936 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
53360993 ATATATGGCACTAAGTGTGCATGCTGGAAAAAATACGGCACTGGGTGTGCGA-GCTCG-A
1 AGATATGGCACTAAGTGTGCATGCTGG-AAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* *
53361051 AGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
53361071 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
57 3 0.05
58 40 0.61
59 22 0.33
60 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:53367665 original size:30 final size:30
Alignment explanation
Indices: 53367631--53367690 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53367621 ATTTAATACG
53367631 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53367661 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53367691 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:53378639 original size:48 final size:48
Alignment explanation
Indices: 53378584--53378715 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
53378574 GTGAAATTGT
* * * *
53378584 CGATGCCATGTCCCAAACATGGTCTTACACCGGCTCTCA-TGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACCAGCTCT-AGTCTCAAGGC
* *
53378632 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTAGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACCAGCTCTAGTCTCAAGGC
* * *
53378680 CGATGCCATGTCCTAGACATAGTCTTACACTAGCTC
1 CGATGCCATGTCCCAGACATGGTCTTACACCAGCTC
53378716 ACATAAGGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
47 1 0.01
48 74 0.99
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACCAGCTCTAGTCTCAAGGC
Found at i:53382216 original size:27 final size:26
Alignment explanation
Indices: 53382178--53382229 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
53382168 CTCATTGCAA
*
53382178 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
53382205 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACTTCGCCACAATATCTG
53382230 GCAACCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:53392550 original size:27 final size:28
Alignment explanation
Indices: 53392485--53392553 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
53392475 AAATTTGTAC
*
53392485 AGCACTAAGTGTGCGAGTTGGATCATAT
1 AGCACTAAGTGTGCAAGTTGGATCATAT
*
53392513 AGCACTAAGTGTGCAAGTT-GATTATAT
1 AGCACTAAGTGTGCAAGTTGGATCATAT
*
53392540 AGCACTGAGTGTGC
1 AGCACTAAGTGTGC
53392554 GGACTCACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCAAGTTGGATCATAT
Found at i:53397257 original size:11 final size:11
Alignment explanation
Indices: 53397242--53397283 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
53397232 TTCAAGTCAT
*
53397242 CAGAAAAGTGT
1 CAGAAAAGTGC
53397253 CAGAAAAGTGC
1 CAGAAAAGTGC
*
53397264 CAAAAAAGTGC
1 CAGAAAAGTGC
*
53397275 CAGTAAAGT
1 CAGAAAAGT
53397284 TTTGATCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (11 bp):
CAGAAAAGTGC
Found at i:53400422 original size:40 final size:41
Alignment explanation
Indices: 53400377--53400543 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 41
53400367 CGGAATATAA
*
53400377 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
53400417 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53400457 CCGGATAT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53400497 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
53400536 CCGGATAT
1 CCGGATAT
53400544 CATTCAATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 17 0.16
40 89 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53400527 original size:80 final size:79
Alignment explanation
Indices: 53400393--53400543 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
53400383 ATAATCAAGT
*
53400393 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
53400458 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
53400473 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
53400536 CCGGATAT
64 CCGGATAT
53400544 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:53401387 original size:17 final size:19
Alignment explanation
Indices: 53401364--53401409 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53401354 AAGAAGCATG
53401364 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53401382 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53401400 AATCATGCTC
1 AATCATGCTC
53401410 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53411701 original size:40 final size:40
Alignment explanation
Indices: 53411656--53411822 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
53411646 CGGAATATAA
53411656 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53411696 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
53411736 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53411776 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53411815 CCGGATAT
1 CCGGATAT
53411823 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53419697 original size:40 final size:40
Alignment explanation
Indices: 53419652--53419818 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
53419642 CGGAATATAA
53419652 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53419692 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
53419732 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
53419772 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53419811 CCGGATAT
1 CCGGATAT
53419819 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53420661 original size:17 final size:19
Alignment explanation
Indices: 53420638--53420683 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
53420628 AAGAAGCATG
53420638 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
53420656 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
53420674 AATCATGCTC
1 AATCATGCTC
53420684 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:53421738 original size:46 final size:46
Alignment explanation
Indices: 53421671--53421840 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
53421661 TGTAACCCGC
*
53421671 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCATTCGCAT
* *
53421717 CCATAAGTGAACTCGAACTCAACTCAACGAGC-TGGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCATTCGC-A--T
* *** * *
53421763 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTTGGGCATTCGCAT
53421810 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
53421841 TTCGGATGCC
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 59 0.58
47 27 0.26
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCATTCGCAT
Found at i:53421791 original size:93 final size:93
Alignment explanation
Indices: 53421679--53421852 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
53421669 GCCCATAAGT
* *
53421679 GAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
53421744 CGAGCTGGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
53421772 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
53421837 CGAGTTCGGATGCCTA
66 CGAGCTCGGATGCCTA
53421853 AATATTCTAG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:53424070 original size:15 final size:15
Alignment explanation
Indices: 53424041--53424090 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
53424031 CAAAGATAAC
*
53424041 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
53424055 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
53424070 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
53424085 AAGAAA
1 AAGAAA
53424091 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:53424099 original size:15 final size:15
Alignment explanation
Indices: 53424052--53424099 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
53424042 AGAAAACCGA
53424052 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
53424066 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
53424082 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
53424097 ATA
1 ATA
53424100 CGATATTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:53427131 original size:93 final size:93
Alignment explanation
Indices: 53427025--53427196 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
53427015 GCCCATAAGT
* *
53427025 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
53427089 ACGAGCTGGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
53427118 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
53427183 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
53427197 CAAATATTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:53427192 original size:46 final size:45
Alignment explanation
Indices: 53427017--53427191 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
53427007 TGTAACCCGC
* *
53427017 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
53427063 CCATAAGTGAACTCGGACTCAACTCAACGAGCT-GGGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
53427109 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
53427156 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
53427192 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 66 0.62
47 29 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:53427211 original size:46 final size:45
Alignment explanation
Indices: 53427068--53427211 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 45
53427058 TGCATCCATA
* * * * *
53427068 AGTGAACTCGGACTCAACTCAACGAGCTGGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--AATATCT
* * * *** *
53427115 -CTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 AGT-GAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATATCT
53427161 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATA-TCT
53427207 AGTGA
1 AGTGA
53427212 CATGTCACTT
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
44 6 0.08
45 1 0.01
46 34 0.45
47 31 0.41
49 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCT
Found at i:53435285 original size:48 final size:48
Alignment explanation
Indices: 53435230--53435453 Score: 243
Period size: 48 Copynumber: 4.7 Consensus size: 48
53435220 GTGAAATTGT
* *
53435230 CAATGCCATGTCCTAGACATGGTCTTACACTGGCT-TACATGTCGAGGC
1 CAATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATGTCGAGGC
*
53435278 CAATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATGTCGAGGC
1 CAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATGTCGAGGC
* * * * * * *
53435326 CGATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGT
1 CAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATGTCGAGGC
* * * * *** * *
53435374 CGATGCCATGTCCCAAACATGGTCCTACACTGGCTCTCATAAGGTGGT
1 CAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATGTCGAGGC
* *
53435422 CGATGCCATGTCCCAGACATGGTCTTAAACTA
1 CAATGCCATGTCCCAGACATGGTCTTACACTA
53435454 ACACACATAT
Statistics
Matches: 149, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
48 148 0.99
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
CAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATGTCGAGGC
Found at i:53444401 original size:41 final size:41
Alignment explanation
Indices: 53444332--53444409 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
53444322 GTTAGTGGAT
* * *
53444332 TATGTAGAAAGAATAAAGAAATGAAAAAAAAAAGAAAGAGAA
1 TATGAAGAAAGAACAAAGAAAAGAAAAAAAAAA-AAAGAGAA
*
53444374 TATGAAGAAA-AACAAAGAAAAGGAAAAAAAAAAAAG
1 TATGAAGAAAGAACAAAGAAAAGAAAAAAAAAAAAAG
53444410 TGTTCATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 4 0.12
41 19 0.59
42 9 0.28
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (41 bp):
TATGAAGAAAGAACAAAGAAAAGAAAAAAAAAAAAAGAGAA
Found at i:53445932 original size:17 final size:18
Alignment explanation
Indices: 53445890--53445938 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
53445880 AGTTGAAAAG
53445890 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
53445909 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
53445926 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
53445939 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:53446825 original size:40 final size:40
Alignment explanation
Indices: 53446759--53446925 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
53446749 AAATTGAATG
* * *
53446759 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53446798 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
53446838 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53446878 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53446918 ATATCCGG
1 ATATCCGG
53446926 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53453946 original size:17 final size:18
Alignment explanation
Indices: 53453904--53453952 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
53453894 AGTTGAAAAG
53453904 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
53453923 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
53453940 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
53453953 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:53454837 original size:40 final size:40
Alignment explanation
Indices: 53454771--53454921 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
53454761 AAATTGAATG
* * *
53454771 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53454810 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
53454850 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
53454890 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
53454922 ACTGATTATA
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53466054 original size:38 final size:37
Alignment explanation
Indices: 53465962--53466069 Score: 121
Period size: 40 Copynumber: 2.8 Consensus size: 37
53465952 CTGGAAATTA
* *
53465962 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGGC
*
53466000 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT-TC
1 T--ATCCGGGCTAAGACCCGAAGGCATT-GTGCGAG-TGGC
53466040 TATCCGGGCTAAGA-CCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCA-TTGTGC
53466070 ACGTGATTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
37 13 0.21
38 16 0.26
39 3 0.05
40 29 0.47
41 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (37 bp):
TATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGGC
Found at i:53471196 original size:19 final size:19
Alignment explanation
Indices: 53471172--53471209 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53471162 GTTTTGGTGG
53471172 GTTCTATTAATGTATAATT
1 GTTCTATTAATGTATAATT
53471191 GTTCTATTAATGTATAATT
1 GTTCTATTAATGTATAATT
53471210 TTAGTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
GTTCTATTAATGTATAATT
Found at i:53472626 original size:11 final size:11
Alignment explanation
Indices: 53472594--53472620 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53472584 TAAAACATGC
53472594 CAAACATACTT
1 CAAACATACTT
53472605 CAAACATACTT
1 CAAACATACTT
53472616 CAAAC
1 CAAAC
53472621 TAACTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (11 bp):
CAAACATACTT
Found at i:53481994 original size:39 final size:40
Alignment explanation
Indices: 53481894--53482075 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
53481884 TCGAATGATG
* * *
53481894 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
53481934 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
53481974 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
53482012 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
53482053 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53482076 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:53482039 original size:78 final size:80
Alignment explanation
Indices: 53481894--53482075 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
53481884 TCGAATGATG
* * * *
53481894 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
53481959 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
53481974 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
53482036 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
53482053 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53482076 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:53497195 original size:21 final size:21
Alignment explanation
Indices: 53497169--53497209 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53497159 AATTTTGAAA
*
53497169 GAAAGGCCTGAAGGGCATTTT
1 GAAAGGCCTGAAAGGCATTTT
*
53497190 GAAAGGCCTTAAAGGCATTT
1 GAAAGGCCTGAAAGGCATTT
53497210 GGGTCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (21 bp):
GAAAGGCCTGAAAGGCATTTT
Done.