Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 38 of 218
Found at i:11941601 original size:5 final size:5
Alignment explanation
Indices: 11941591--11941616 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11941581 CTCGAAAATT
11941591 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
11941617 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:11945472 original size:66 final size:66
Alignment explanation
Indices: 11945366--11945499 Score: 223
Period size: 66 Copynumber: 2.0 Consensus size: 66
11945356 GTTTCAACCT
* *
11945366 TTGGATTTATCAAATCAACCTTTCAATCCTCCTAAACCTTCTATGGAGGAACCTCCTACATTAGA
1 TTGGATTTATCAAATCAACCTTTCAATCCTCCTAAACCTTCTATGGAAGAACCTCCTACACTAGA
11945431 G
66 G
* * *
11945432 TTGGATTTATCAAATCAACCTTTCAATCCTTCTAAACCTTCTATGGAAGAACTTCTTACACTAGA
1 TTGGATTTATCAAATCAACCTTTCAATCCTCCTAAACCTTCTATGGAAGAACCTCCTACACTAGA
11945497 G
66 G
11945498 TT
1 TT
11945500 ACAACCTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (66 bp):
TTGGATTTATCAAATCAACCTTTCAATCCTCCTAAACCTTCTATGGAAGAACCTCCTACACTAGA
G
Found at i:11950940 original size:20 final size:21
Alignment explanation
Indices: 11950912--11950954 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
11950902 TTAGTTTAAT
*
11950912 CTAGTAATAAAGTA-AATGAG
1 CTAGAAATAAAGTAGAATGAG
*
11950932 CTAGAAATAAATTAGAATGAG
1 CTAGAAATAAAGTAGAATGAG
11950953 CT
1 CT
11950955 CAAATGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (21 bp):
CTAGAAATAAAGTAGAATGAG
Found at i:11950959 original size:20 final size:20
Alignment explanation
Indices: 11950917--11950959 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11950907 TTAATCTAGT
*
11950917 AATAAAGTAAATGAGCTAGA
1 AATAAAGTAAATGAGCTACA
*
11950937 AATAAATTAGAATGAGCT-CA
1 AATAAAGTA-AATGAGCTACA
11950957 AAT
1 AAT
11950960 GAGCTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (20 bp):
AATAAAGTAAATGAGCTACA
Found at i:11952680 original size:36 final size:36
Alignment explanation
Indices: 11952640--11952731 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 36
11952630 ATTCTCGCTC
*
11952640 TCTTTTTCAATTTGCTTTTCTTGCTCGCA-CTCTTTT
1 TCTTTTTCAATTT-CTTTTCTTGCTCCCACCTCTTTT
* * *
11952676 TCTTTTTCAATCTCATTTGCTTTCTCCCACTCTCTTTT
1 TCTTTTTCAATTTC-TTTTCTTGCTCCCAC-CTCTTTT
*
11952714 TCTTTTTAAATTTCTTTT
1 TCTTTTTCAATTTCTTTT
11952732 TCTTTCATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
35 1 0.02
36 23 0.50
37 3 0.07
38 19 0.41
ACGTcount: A:0.11, C:0.25, G:0.04, T:0.60
Consensus pattern (36 bp):
TCTTTTTCAATTTCTTTTCTTGCTCCCACCTCTTTT
Found at i:11953725 original size:16 final size:16
Alignment explanation
Indices: 11953691--11953725 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11953681 AACTTCGTAA
* *
11953691 AATTTTTTTATACTTC
1 AATTTTTTTAAACTAC
11953707 AATTTTTTTAAACTAC
1 AATTTTTTTAAACTAC
11953723 AAT
1 AAT
11953726 AAGATGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTTTTTTAAACTAC
Found at i:11957582 original size:139 final size:140
Alignment explanation
Indices: 11957376--11957640 Score: 435
Period size: 139 Copynumber: 1.9 Consensus size: 140
11957366 CATGGGATAT
** *
11957376 TTGGATTTACCCTAGGGAAAAAAATTATAAAAAGTCAAAGGAGGAAACCCTAAAGGGGGCAAACA
1 TTGGATTTACCCTAGGGAAAAAAATTATAAAAAACCAAAAGAGGAAACCCTAAAGGGGGCAAACA
* *
11957441 AAAAGAAGAAGAGAGATCCTTAGGTGAACACAAAA-A-AGTGGAGATCCAGAGGCAACAATAAAT
66 AAAA-AAGAAGAAAGATCCTTAGGCGAACACAAAAGAGAGTGGAGATCCAGAGGCAACAATAAAT
11957504 ATCATGAGCAG
130 ATCATGAGCAG
*
11957515 TTGGATTTACCCTAGGGAAAAAGATTATAAAAAACCAAAAGAGGAAACCCTAAAGGGGGCAAACA
1 TTGGATTTACCCTAGGGAAAAAAATTATAAAAAACCAAAAGAGGAAACCCTAAAGGGGGCAAACA
* *
11957580 AAAAAAGAAGAAAGATCCTTAGGCGAACACAAAAGAGTGTGGAGATCCGGAGGCAACAATA
66 AAAAAAGAAGAAAGATCCTTAGGCGAACACAAAAGAGAGTGGAGATCCAGAGGCAACAATA
11957641 GAAGGTAGCA
Statistics
Matches: 116, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
138 28 0.24
139 66 0.57
140 22 0.19
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (140 bp):
TTGGATTTACCCTAGGGAAAAAAATTATAAAAAACCAAAAGAGGAAACCCTAAAGGGGGCAAACA
AAAAAAGAAGAAAGATCCTTAGGCGAACACAAAAGAGAGTGGAGATCCAGAGGCAACAATAAATA
TCATGAGCAG
Found at i:11958098 original size:159 final size:159
Alignment explanation
Indices: 11957809--11958133 Score: 569
Period size: 159 Copynumber: 2.0 Consensus size: 159
11957799 GATCAAAACG
* *
11957809 ATGTGGATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGG
1 ATGTGTATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGA
* * *
11957874 GATTACATGATGGAACTTTTATTTCCTTTAATGGTTGAAGCATATATTTGATTTAATCTACTGTT
66 GATTACATGATGAAACTTTTATTTCCTTTAATAGTTGAAACATATATTTGATTTAATCTACTGTT
11957939 TCATTCAATTGTTTTTATTTCCTAACTGT
131 TCATTCAATTGTTTTTATTTCCTAACTGT
* *
11957968 ATGTGTATACTATTTTGAACTGAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTTA
1 ATGTGTATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGA
11958033 GATTACATGATGAAACTTTTATTTCCTTTAATAGTTGAAACATATATTTGATTTAATCTACTGTT
66 GATTACATGATGAAACTTTTATTTCCTTTAATAGTTGAAACATATATTTGATTTAATCTACTGTT
* *
11958098 TCATTCAATTTTTTTTATTTCGTAACTGT
131 TCATTCAATTGTTTTTATTTCCTAACTGT
11958127 ATGTGTA
1 ATGTGTA
11958134 CATTCTTTAG
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 157 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (159 bp):
ATGTGTATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGA
GATTACATGATGAAACTTTTATTTCCTTTAATAGTTGAAACATATATTTGATTTAATCTACTGTT
TCATTCAATTGTTTTTATTTCCTAACTGT
Found at i:11964747 original size:19 final size:20
Alignment explanation
Indices: 11964715--11964754 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11964705 TTTTTTTTAA
*
11964715 TATTTAATTAATTTTAGTTT
1 TATTTAATTAATTTTAATTT
*
11964735 TATTT-ATTTATTTTAATTT
1 TATTTAATTAATTTTAATTT
11964754 T
1 T
11964755 TTAATTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TATTTAATTAATTTTAATTT
Found at i:11977026 original size:15 final size:16
Alignment explanation
Indices: 11977001--11977032 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11976991 TTATACTTTT
11977001 TAATATTTTTTAAAAA
1 TAATATTTTTTAAAAA
11977017 TAAT-TTTTTTAAAAA
1 TAATATTTTTTAAAAA
11977032 T
1 T
11977033 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTTTTTAAAAA
Found at i:11977452 original size:15 final size:15
Alignment explanation
Indices: 11977432--11977539 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
11977422 TTTATGGAAA
*
11977432 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
11977447 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
11977461 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
11977477 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
11977491 ATTCAAATATATGGGT
1 A-TCAAATATATGGGT
**
11977507 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
11977521 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
11977537 ATC
1 ATC
11977540 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:11977469 original size:30 final size:30
Alignment explanation
Indices: 11977426--11977549 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
11977416 TCCATATTTA
* *
11977426 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
11977456 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
11977486 TGGAAATTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
11977516 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
11977547 TGG
1 TGG
11977550 CATAATAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 76 0.90
31 8 0.10
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:11982144 original size:15 final size:15
Alignment explanation
Indices: 11982124--11982231 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
11982114 TTTATGGAAA
11982124 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
11982139 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
11982153 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
11982169 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
11982183 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
11982199 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
11982213 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
11982229 ATC
1 ATC
11982232 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:11982161 original size:30 final size:30
Alignment explanation
Indices: 11982118--11982241 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
11982108 TCCATATTTA
* *
11982118 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
11982148 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
11982178 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
11982208 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
11982239 TGG
1 TGG
11982242 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:11987455 original size:55 final size:55
Alignment explanation
Indices: 11987376--11987487 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
11987366 ATTTAAAAGA
11987376 TAATTAATTAAAATGGATGGTGGTGATCATAGCCCTCCACTAACCTTGTAATAAT
1 TAATTAATTAAAATGGATGGTGGTGATCATAGCCCTCCACTAACCTTGTAATAAT
11987431 TAATTAATTAAAATGGATGGTGGTGATCATAGCCCTCCACTAACCTTGTAATAAT
1 TAATTAATTAAAATGGATGGTGGTGATCATAGCCCTCCACTAACCTTGTAATAAT
11987486 TA
1 TA
11987488 TGGGTTAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (55 bp):
TAATTAATTAAAATGGATGGTGGTGATCATAGCCCTCCACTAACCTTGTAATAAT
Found at i:11994811 original size:20 final size:20
Alignment explanation
Indices: 11994786--11994823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11994776 TAAAGTTATT
* *
11994786 TATTTTATATTGGATGGATG
1 TATTTTACATTAGATGGATG
11994806 TATTTTACATTAGATGGA
1 TATTTTACATTAGATGGA
11994824 GATGGAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (20 bp):
TATTTTACATTAGATGGATG
Found at i:11995010 original size:40 final size:40
Alignment explanation
Indices: 11994956--11995033 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
11994946 GTTTGTACAA
* *
11994956 AAAAAACGCTGCTAAAAATCGAGCATTAGCGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTTTC
* *
11994996 AAAAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTT
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTT
11995034 CCTAGAAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTTTC
Found at i:11995046 original size:40 final size:40
Alignment explanation
Indices: 11994956--11995053 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 40
11994946 GTTTGTACAA
* * *
11994956 AAAAAACGCTGCTAAAAATCGAGCATTAGCGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTTCC
* *
11994996 AAAAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTTCC
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTTCC
* * * *
11995036 TAGAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
11995054 CCTAAGCCCA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCACTTTCC
Found at i:11995137 original size:41 final size:40
Alignment explanation
Indices: 11995081--11995399 Score: 323
Period size: 41 Copynumber: 7.8 Consensus size: 40
11995071 CCTTTCGAGG
* * * * *
11995081 CTTTAGCGGCATTTTTGAAAAAGCACCGCTAAAGATCGAGA
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC-AGA
* * * * *
11995122 TTTTAGCGGTGTTTTTGGATAAGCGCCACTAATACTCAGA
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* * * * *
11995162 GATTTAGCGGCGTTTTTGAAAAATCGCTGCTAATGCTCAGCG
1 -CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAG-A
* * *
11995204 CTTTAGCGGTGTTTTTGGAGAAGCACCGCTAATGCTCAGA
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* *
11995244 GCTTTAGCTGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGA
1 -CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
*
11995285 GCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
1 -CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* * *
11995326 TCTTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGCTCGGG
1 -CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* ** *
11995367 CTTTTAGCGGCATTTTTAAAAAAGCGCTGCTAA
1 C-TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
11995400 AACATTTTAT
Statistics
Matches: 231, Mismatches: 43, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
40 4 0.02
41 227 0.98
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
Found at i:11995219 original size:82 final size:82
Alignment explanation
Indices: 11995080--11995399 Score: 356
Period size: 82 Copynumber: 3.9 Consensus size: 82
11995070 ACCTTTCGAG
* * * * * * *
11995080 GCTTTAGCGGCATTTTTGAAAAAGCACCGCTAAAGATC-GAGATTTTAGCGGTGTTTTTGGATAA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAG-CTTTAGCGGTGTTTTTGGAAAA
* *
11995144 GCGCCACTAATACTCAGA
65 GCGCCGCTAATGCTCAGA
* * * * * *
11995162 GATTTAGCGGCGTTTTTGAAAAATCGCTGCTAATGCTCAGCGCTTTAGCGGTGTTTTTGGAGAAG
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGTGTTTTTGGAAAAG
*
11995227 CACCGCTAATGCTCAGA
66 CGCCGCTAATGCTCAGA
* * * *
11995244 GCTTTAGCTGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGAGCTTTAGTGGCGTTTTTGGAAAAG
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGTGTTTTTGGAAAAG
11995309 CGCCGCTAATGCTCAGA
66 CGCCGCTAATGCTCAGA
* * * ** **
11995326 TCTTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGCTC-GGGCTTTTAGCGGCATTTTTAAAAAA
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC-TTTAGCGGTGTTTTTGGAAAA
*
11995390 GCGCTGCTAA
65 GCGCCGCTAA
11995400 AACATTTTAT
Statistics
Matches: 202, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
81 3 0.01
82 197 0.98
83 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (82 bp):
GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGTGTTTTTGGAAAAG
CGCCGCTAATGCTCAGA
Found at i:11995392 original size:123 final size:123
Alignment explanation
Indices: 11995080--11995399 Score: 381
Period size: 123 Copynumber: 2.6 Consensus size: 123
11995070 ACCTTTCGAG
* * * * * * *
11995080 GCTTTAGCGGCATTTTTGAAAAAGCACCGCTAAAGATCGAGATTTTAGCGGTGTTTTTGGATAAG
1 GCTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCGAGCTTTTAGCGGCGTTTTTGGAAAAG
* * * *
11995145 CGCCACTAATACTCAGAGATTTAGCGGCGTTTTTGAAAAATCGCTGCTAATGCTCAGC
66 CGCCGCTAATACTCAGAGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* * * *
11995203 GCTTTAGCGGTGTTTTTGGAGAAGCACCGCTAATGCTCAGAGC-TTTAGCTGCGTTTTTGGAGAA
1 GCTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTC-GAGCTTTTAGCGGCGTTTTTGGAAAA
* * * *
11995267 GCGCCGCTAATGCTCAGAGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
65 GCGCCGCTAATACTCAGAGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* * * * * **
11995326 TCTTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGCTCGGGCTTTTAGCGGCATTTTTAAAAAAG
1 GCTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCGAGCTTTTAGCGGCGTTTTTGGAAAAG
*
11995391 CGCTGCTAA
66 CGCCGCTAA
11995400 AACATTTTAT
Statistics
Matches: 165, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
122 3 0.02
123 159 0.96
124 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (123 bp):
GCTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCGAGCTTTTAGCGGCGTTTTTGGAAAAG
CGCCGCTAATACTCAGAGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
Found at i:11995824 original size:14 final size:15
Alignment explanation
Indices: 11995796--11995828 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
11995786 AATGTTTATA
11995796 GATTATGGAATTAGG
1 GATTATGGAATTAGG
11995811 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
11995825 GATT
1 GATT
11995829 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:11996045 original size:21 final size:21
Alignment explanation
Indices: 11995999--11996052 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
11995989 TTAAATAAGG
*
11995999 TTTAGGGGTTAGTAGTTAGGG
1 TTTAGGGGTTAGTAGTTAGGA
* *
11996020 GTTAGGGGTTA-TGAGTTATGA
1 TTTAGGGGTTAGT-AGTTAGGA
*
11996041 TTTAGGGTTTAG
1 TTTAGGGGTTAG
11996053 AGACTCGAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (21 bp):
TTTAGGGGTTAGTAGTTAGGA
Found at i:11996154 original size:7 final size:7
Alignment explanation
Indices: 11996142--11996184 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
11996132 ATTGTAAAAG
11996142 AGGGGTT
1 AGGGGTT
11996149 AGGGGTT
1 AGGGGTT
*
11996156 AGAGGTT
1 AGGGGTT
** *
11996163 AAAGATT
1 AGGGGTT
11996170 AGGGGTT
1 AGGGGTT
11996177 AGGGGTT
1 AGGGGTT
11996184 A
1 A
11996185 TGGATAGGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.47, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:12001560 original size:86 final size:86
Alignment explanation
Indices: 12001467--12001626 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 86
12001457 TGAAAAGCGC
* * * * *
12001467 CGCTAAAGGTTTTTATCTATAGAAGCGTTTGT-GGAACAAGCGCCGCTAAAAGTCCTGATCTATA
1 CGCTAAAGGTCTTGATCTATAGAAGCGTTT-TCGAAAAAAGCGCCGCTAAAAGTCATGATCTATA
12001531 GCGGCATTTTGTGAAAAAGCAT
65 GCGGCATTTTGTGAAAAAGCAT
** * * *
12001553 CGCTAAAGGTCTTGATCTATAGCGGTGTTTTCGAAAAAAGCGCCGCTAAAGGTTATGATCTATAG
1 CGCTAAAGGTCTTGATCTATAGAAGCGTTTTCGAAAAAAGCGCCGCTAAAAGTCATGATCTATAG
*
12001618 CGGCGTTTT
66 CGGCATTTT
12001627 TATTTCAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
85 1 0.02
86 61 0.98
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (86 bp):
CGCTAAAGGTCTTGATCTATAGAAGCGTTTTCGAAAAAAGCGCCGCTAAAAGTCATGATCTATAG
CGGCATTTTGTGAAAAAGCAT
Found at i:12001575 original size:43 final size:43
Alignment explanation
Indices: 12001459--12001626 Score: 153
Period size: 43 Copynumber: 3.9 Consensus size: 43
12001449 CGTTTGTGTG
* * * ** *
12001459 AAAAGCGCCGCTAAAGGTTTTTATCTATAGAAGCGTTTGT-GGA
1 AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTT-TCGAA
* * * * * *
12001502 ACAAGCGCCGCTAAAAGTCCTGATCTATAGCGGCATTTT-GTGA
1 AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTTCG-AA
* *
12001545 AAAAGCATCGCTAAAGGTCTTGATCTATAGCGGTGTTTTCGAA
1 AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTTCGAA
*
12001588 AAAAGCGCCGCTAAAGGT-TATGATCTATAGCGGCGTTTT
1 AAAAGCACCGCTAAAGGTCT-TGATCTATAGCGGCGTTTT
12001627 TATTTCAAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 3 0.03
43 99 0.96
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTTCGAA
Found at i:12010288 original size:14 final size:15
Alignment explanation
Indices: 12010262--12010290 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12010252 TACAAAAGTG
12010262 TTATAATATATTTAT
1 TTATAATATATTTAT
12010277 TTATAA-ATATTTAT
1 TTATAATATATTTAT
12010291 ATAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAATATATTTAT
Found at i:12021455 original size:45 final size:44
Alignment explanation
Indices: 12021357--12021532 Score: 131
Period size: 45 Copynumber: 3.9 Consensus size: 44
12021347 GCTATGCGCC
* * * * * *
12021357 TAAAGATGAGTAAGATCATGGCTGAAAGACGCCATGGCATCA-CA
1 TAAA-ATGAGTAAGAACATAGCTGAAAGATGCTATGACATCATGA
* *
12021401 CTAACAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
1 -TAA-AATGAGTAAGAACATAGCTGAAAGATGCTATGACATCATGA
* * * * *
12021447 TATAAATGAGTAAGATCAT-GACTAAAAGACGCCATGACATCATGG
1 TA-AAATGAGTAAGAACATAG-CTGAAAGATGCTATGACATCATGA
* * * *
12021492 TAAACAAGATTAAAAACATAGTTGAAAGATGCTATGACATC
1 TAAA-ATGAGTAAGAACATAGCTGAAAGATGCTATGACATC
12021533 CTACGAAAGC
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
44 3 0.03
45 97 0.93
46 4 0.04
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (44 bp):
TAAAATGAGTAAGAACATAGCTGAAAGATGCTATGACATCATGA
Found at i:12021518 original size:90 final size:90
Alignment explanation
Indices: 12021362--12021532 Score: 227
Period size: 90 Copynumber: 1.9 Consensus size: 90
12021352 GCGCCTAAAG
* * * * *
12021362 ATGAGTAAGATCATGGCTGAAAGACGCCATGGCATCACACTAACAATGAGTAAGACCATAGCTGA
1 ATGAGTAAGATCATGACTAAAAGACGCCATGACATCACACTAACAATGAGTAAAAACATAGCTGA
*
12021427 AAGATGTTATGACATCATGATATAA
66 AAGATGCTATGACATCATGATATAA
*** * *
12021452 ATGAGTAAGATCATGACTAAAAGACGCCATGACATCATGGTAAACAA-GATTAAAAACATAGTTG
1 ATGAGTAAGATCATGACTAAAAGACGCCATGACATCACACT-AACAATGAGTAAAAACATAGCTG
12021516 AAAGATGCTATGACATC
65 AAAGATGCTATGACATC
12021533 CTACGAAAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
90 64 0.93
91 5 0.07
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (90 bp):
ATGAGTAAGATCATGACTAAAAGACGCCATGACATCACACTAACAATGAGTAAAAACATAGCTGA
AAGATGCTATGACATCATGATATAA
Found at i:12021779 original size:27 final size:27
Alignment explanation
Indices: 12021747--12021820 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
12021737 ATAGTTTGGT
12021747 AGGACGTTAAACATGGGATAGTCCAA-
1 AGGACGTTAAACATGGGATAGTCCAAC
* *
12021773 TGAGACGTTAAACACGGGATAGTCCAAC
1 AG-GACGTTAAACATGGGATAGTCCAAC
12021801 AGGACGTTAAACATGGGATA
1 AGGACGTTAAACATGGGATA
12021821 ATCTGTCGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (27 bp):
AGGACGTTAAACATGGGATAGTCCAAC
Found at i:12025622 original size:35 final size:36
Alignment explanation
Indices: 12025583--12025654 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
12025573 TTAATTTAAG
12025583 TAAGTATCTAAGCCA-TTTTTTTTATGAAAATTGAA
1 TAAGTATCTAAGCCATTTTTTTTTATGAAAATTGAA
12025618 TAAGTATCTAAGCCATTTTTTTTTATGAAAATTGAA
1 TAAGTATCTAAGCCATTTTTTTTTATGAAAATTGAA
12025654 T
1 T
12025655 CATAAGAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 15 0.42
36 21 0.58
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (36 bp):
TAAGTATCTAAGCCATTTTTTTTTATGAAAATTGAA
Found at i:12026414 original size:24 final size:24
Alignment explanation
Indices: 12026387--12026432 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12026377 GAATTGATGA
12026387 TGAAT-TAAAATGAAATTATGAAAT
1 TGAATGTAAAATGAAA-TATGAAAT
* *
12026411 TGAATGTGAAATGATATATGAA
1 TGAATGTAAAATGAAATATGAA
12026433 TTGGATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (24 bp):
TGAATGTAAAATGAAATATGAAAT
Found at i:12031905 original size:31 final size:28
Alignment explanation
Indices: 12031836--12031905 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
12031826 AACAGAGTTT
**
12031836 AACAGAGTGACTAAAACGTAATATTTAA
1 AACAGAGTGACTAAAACGTAATATAGAA
* *
12031864 AACATAAGTGACTAAAATGTAATATGAGACA
1 AACA-GAGTGACTAAAACGTAATAT-AGA-A
12031895 AACAGGAGTGA
1 AACA-GAGTGA
12031906 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.12
29 18 0.55
30 1 0.03
31 10 0.30
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (28 bp):
AACAGAGTGACTAAAACGTAATATAGAA
Found at i:12037474 original size:18 final size:18
Alignment explanation
Indices: 12037447--12037486 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12037437 AATACTTGAG
*
12037447 TAAATCAGAATTAAAAAT
1 TAAATCAGAAATAAAAAT
*
12037465 TAAATTAGAAATAAAAAT
1 TAAATCAGAAATAAAAAT
12037483 TAAA
1 TAAA
12037487 ATTTGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
TAAATCAGAAATAAAAAT
Found at i:12039878 original size:22 final size:22
Alignment explanation
Indices: 12039831--12039884 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12039821 ACAAATGGCT
* * *
12039831 TGTCTCGAGACAATTTGCTCTG
1 TGTCTCGAGACAATCTGATCTA
12039853 TGTCTCGAGACAATCT-ATCGTA
1 TGTCTCGAGACAATCTGATC-TA
12039875 TGTCTCGAGA
1 TGTCTCGAGA
12039885 TTAAGCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (22 bp):
TGTCTCGAGACAATCTGATCTA
Found at i:12043299 original size:23 final size:23
Alignment explanation
Indices: 12043267--12043316 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12043257 AATTCAAAGC
12043267 AAATAAATTATTAAAACAT-TAA
1 AAATAAATTATTAAAACATATAA
12043289 AAATAGAATTATTAAAACATATAA
1 AAATA-AATTATTAAAACATATAA
12043313 AAAT
1 AAAT
12043317 CGGTCCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAAATTATTAAAACATATAA
Found at i:12045932 original size:24 final size:24
Alignment explanation
Indices: 12045885--12045932 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12045875 AGTTTAAATG
****
12045885 TTAGTTTTTGAATATATGGGCTAA
1 TTAGTTTTTGAATATACAAACTAA
12045909 TTAGTTTTTGAATATACAAACTAA
1 TTAGTTTTTGAATATACAAACTAA
12045933 AGTATGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (24 bp):
TTAGTTTTTGAATATACAAACTAA
Found at i:12046414 original size:71 final size:71
Alignment explanation
Indices: 12046296--12046432 Score: 179
Period size: 71 Copynumber: 1.9 Consensus size: 71
12046286 AGTACGAATC
* **
12046296 ATTCTTTATCGATGGCTAAGACACAACATATGTTGTGGATTCGCGACAGCTTGAGTGAACAACAT
1 ATTCTTTATCGATGGCTAAGACACAACATATATTGCAGATTCGCGACAGCTTGAGTGAACAACAT
12046361 CAAATT
66 CAAATT
* * * *
12046367 ATTCTTTATCGATGGTTGAGATC-CAACATATATTGCAGATGT-TCGACAGCTTGAGTGAGCAAC
1 ATTCTTTATCGATGGCTAAGA-CACAACATATATTGCAGAT-TCGCGACAGCTTGAGTGAACAAC
12046430 ATC
64 ATC
12046433 GAATAAAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 55 0.96
72 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (71 bp):
ATTCTTTATCGATGGCTAAGACACAACATATATTGCAGATTCGCGACAGCTTGAGTGAACAACAT
CAAATT
Found at i:12051287 original size:28 final size:27
Alignment explanation
Indices: 12051256--12051311 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
12051246 TTTTTCCTTC
*
12051256 ACATTACTTATCTTATACTTTTATATAT
1 ACATTACTTATCTTAT-CTTATATATAT
* *
12051284 ACATTATTTATTTTATCTTATATATAT
1 ACATTACTTATCTTATCTTATATATAT
12051311 A
1 A
12051312 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (27 bp):
ACATTACTTATCTTATCTTATATATAT
Found at i:12054056 original size:33 final size:33
Alignment explanation
Indices: 12054019--12054092 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
12054009 AGTCTGTTAT
* * *
12054019 GACAGTAAATAAAGAACATAAATAGTCCACTGG
1 GACAGTAAACAAAGAACAGAAATAGTCCACTAG
* * *
12054052 GACAGTAAACACAGAATAGAGATAGTCCACTAG
1 GACAGTAAACAAAGAACAGAAATAGTCCACTAG
12054085 GACAGTAA
1 GACAGTAA
12054093 CCACAGATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.16
Consensus pattern (33 bp):
GACAGTAAACAAAGAACAGAAATAGTCCACTAG
Found at i:12054098 original size:33 final size:32
Alignment explanation
Indices: 12054040--12054104 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
12054030 AAGAACATAA
*
12054040 ATAGTCCACTGGGACAGTAAACACAGAATAGAG
1 ATAGTCCACTAGGACAGTAAACACAG-ATAGAG
*
12054073 ATAGTCCACTAGGACAGTAACCACAGATAGAG
1 ATAGTCCACTAGGACAGTAAACACAGATAGAG
12054105 TATGTGGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (32 bp):
ATAGTCCACTAGGACAGTAAACACAGATAGAG
Found at i:12054724 original size:9 final size:9
Alignment explanation
Indices: 12054710--12054749 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
12054700 TTTGGTTAAA
12054710 AATTAACCG
1 AATTAACCG
12054719 AATTAACCG
1 AATTAACCG
*
12054728 AATTACCCG
1 AATTAACCG
12054737 AATTAACCG
1 AATTAACCG
12054746 AATT
1 AATT
12054750 GAATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:12065317 original size:49 final size:49
Alignment explanation
Indices: 12065225--12065318 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
12065215 ATTCAAACAC
** * *
12065225 CATTTTAAAGTTATGTACACTAAGGAGTGTCCTAGAAACAAGGTTTTTG
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAAAAACAAGGTTTTTG
*
12065274 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAAAAATAAGGTT
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAAAAACAAGGTT
12065319 CTTACATATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (49 bp):
CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAAAAACAAGGTTTTTG
Found at i:12067548 original size:95 final size:91
Alignment explanation
Indices: 12067398--12067567 Score: 243
Period size: 95 Copynumber: 1.8 Consensus size: 91
12067388 AATTTAATTT
*
12067398 CTCGTTTTGGAAATAAAATAAAAAAGGAATAAAATCCGCTGCACGGCGGGAATAAATCCCAAAAC
1 CTCGTTTTGGAAATAAAATAAAAAAGGAATAAAATCCGCTGAACGGCGGGAATAAAT-CCAAAAC
12067463 AGATTTTATTCTATTTTTAAAAAGAAA
65 AGATTTTATTCTATTTTTAAAAAGAAA
** * *
12067490 CTCGTTTTTGGAAATAAAAATCAAAATTGGAATAAAATCCGTTGAACGGCAGGG-ATAAATCCGA
1 CTCG-TTTTGGAAAT-AAAAT-AAAAAAGGAATAAAATCCGCTGAACGGC-GGGAATAAATCCAA
12067554 AACAGATTTTATTC
62 AACAGATTTTATTC
12067568 ACCTTTGTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
92 4 0.06
93 10 0.14
94 22 0.32
95 30 0.43
96 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (91 bp):
CTCGTTTTGGAAATAAAATAAAAAAGGAATAAAATCCGCTGAACGGCGGGAATAAATCCAAAACA
GATTTTATTCTATTTTTAAAAAGAAA
Found at i:12070006 original size:31 final size:32
Alignment explanation
Indices: 12069948--12070011 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12069938 AGAGATAGAG
* *
12069948 ATCCCATGTATATCCCTTGTTTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
12069980 ATCCCAGGTATATCCCATG-TTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
12070011 A
1 A
12070012 ATATAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (32 bp):
ATCCCAGGTATATCCCATGTTTTTTTATGCTT
Found at i:12072156 original size:28 final size:28
Alignment explanation
Indices: 12072102--12072157 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
12072092 AATTAGTATT
* * *
12072102 TTTATATTTTTAAAGATTTTTTTAAAAA
1 TTTATATATTTAAAGATTTTATGAAAAA
12072130 TTTATATATTTATAA-ATTTTATGAAAAA
1 TTTATATATTTA-AAGATTTTATGAAAAA
12072158 ATATCTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTATATATTTAAAGATTTTATGAAAAA
Found at i:12088104 original size:21 final size:21
Alignment explanation
Indices: 12088078--12088118 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12088068 ATCTGCTCAA
* *
12088078 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
12088099 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
12088119 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:12089890 original size:26 final size:26
Alignment explanation
Indices: 12089854--12089909 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
12089844 CAGCAAATCA
12089854 GTGACTAACTGATTAAATTTGGTGAT
1 GTGACTAACTGATTAAATTTGGTGAT
12089880 GTGACTAACTGATTAAATTTGGTGAT
1 GTGACTAACTGATTAAATTTGGTGAT
12089906 GTGA
1 GTGA
12089910 TCATTCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
GTGACTAACTGATTAAATTTGGTGAT
Found at i:12099035 original size:41 final size:41
Alignment explanation
Indices: 12098978--12099171 Score: 280
Period size: 41 Copynumber: 4.7 Consensus size: 41
12098968 GACTTTTTAA
* * *
12098978 GCTTTAGCGGCGTTTTTGGAGAAGTGCCGCTAATGCTCCGG
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGG
* * *
12099019 GCTTTAGCGGCATTTTTGGAGAAGCGCCGCTAATGCTCCGG
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGG
*
12099060 GCTTTAGCGGCGTTTTTGGAAAACCGCCGCTAATGCTCAGG
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGG
* **
12099101 GCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCAAT
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGG
* *
12099142 GCTTTAGCGGCGTTTTTGAAAAAGCTCCGC
1 GCTTTAGCGGCGTTTTTGGAAAAGCGCCGC
12099172 AAAAGCATTT
Statistics
Matches: 140, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 140 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.28
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGG
Found at i:12099605 original size:14 final size:14
Alignment explanation
Indices: 12099573--12099617 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
12099563 GTTTTATATA
12099573 TTATGGAATT-AGGG
1 TTATGG-ATTAAGGG
12099587 ATTATGGATTAAGGG
1 -TTATGGATTAAGGG
*
12099602 TTATGGTTTAAGGG
1 TTATGGATTAAGGG
12099616 TT
1 TT
12099618 GTGATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (14 bp):
TTATGGATTAAGGG
Found at i:12099791 original size:79 final size:82
Alignment explanation
Indices: 12099683--12099833 Score: 236
Period size: 79 Copynumber: 1.9 Consensus size: 82
12099673 TCAGTGTCAG
*
12099683 GTTAGGATTTAGGGTTTAGATTAATTAGTGTGCTTTAA-TT-TATATTAAATAAGGTTTA-GGGT
1 GTTAGGATTTAGGGTTGAGATTAATTAGTGTGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
12099745 TAGGGGTAGGGATTCGA
66 TAGGGGTAGGGATTCGA
* * **
12099762 GTTAGGGTTTATGGTTGAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGT
1 GTTAGGATTTAGGGTTGAGATTAATTAGTGTGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
12099827 TAGGGGT
66 TAGGGGT
12099834 TTGTGGTTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
79 33 0.52
80 2 0.03
81 18 0.28
82 11 0.17
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.43
Consensus pattern (82 bp):
GTTAGGATTTAGGGTTGAGATTAATTAGTGTGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
TAGGGGTAGGGATTCGA
Found at i:12101178 original size:16 final size:16
Alignment explanation
Indices: 12101157--12101188 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12101147 TTTACTTTTA
12101157 TTTGGGGTTCTTTTCT
1 TTTGGGGTTCTTTTCT
12101173 TTTGGGGTTCTTTTCT
1 TTTGGGGTTCTTTTCT
12101189 GGGTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.25, T:0.62
Consensus pattern (16 bp):
TTTGGGGTTCTTTTCT
Found at i:12105257 original size:43 final size:43
Alignment explanation
Indices: 12105034--12105260 Score: 233
Period size: 43 Copynumber: 5.3 Consensus size: 43
12105024 GCATGATGTT
* * * * * *
12105034 TTTAGCGGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
* ** *
12105076 TTTAGCGGCGTTTGT-GATAAAAGCACCGCTAAAGGTTGTAGTC
1 TTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
12105119 TTTAGCAGCATTTGTGGGAAAAGCGTCGCTAAAGGTTATGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
12105162 TATAGCGGCATTTGTGGGAAAAGCGCTGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
* *
12105205 TTTAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
*
12105248 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
12105261 ATTTCTAAAA
Statistics
Matches: 155, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.01
42 29 0.19
43 124 0.80
44 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:12113279 original size:108 final size:108
Alignment explanation
Indices: 12113085--12113403 Score: 503
Period size: 108 Copynumber: 3.0 Consensus size: 108
12113075 ATTGGTTGTG
* * * * *
12113085 GAACCATGAGAACTTTAAATAGATGACGCATGAACTTGAGTTGATGATTGGCATAACAGAGCATA
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
12113150 GTGGTCATAATCACTATCGGAGACAATTTTTGCATTTTCCCTA
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * *
12113193 GAACCATGAGAGCTTTAAATGGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAAAGCACG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
12113258 GTGGTCATACTCACTACCGGAGACAATTTTTGCATTTTCCCTA
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * *
12113301 GAACCATGAGAACTTTAAATAGACGAAACTTGAACTTGAATTGATGATTGGCATGATAGAGCTTG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
12113366 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTT
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTT
12113404 TTAAAAAGTA
Statistics
Matches: 191, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 191 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (108 bp):
GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
Found at i:12113557 original size:17 final size:17
Alignment explanation
Indices: 12113535--12113568 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12113525 ATTTTGGTCA
12113535 TCAAAAAATAAAATTTG
1 TCAAAAAATAAAATTTG
12113552 TCAAAAAATAAAATTTG
1 TCAAAAAATAAAATTTG
12113569 AAACTAGGGC
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:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
TCAAAAAATAAAATTTG
Found at i:12117109 original size:2 final size:2
Alignment explanation
Indices: 12117102--12117131 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12117092 TTCTTATAAG
12117102 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12117132 AATATACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12120738 original size:30 final size:31
Alignment explanation
Indices: 12120702--12120765 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12120692 ACTTATTTTA
12120702 TTGTTAA-TTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
* *
12120732 TTGTTAATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
12120763 TTG
1 TTG
12120766 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGACAT
Found at i:12122859 original size:17 final size:18
Alignment explanation
Indices: 12122834--12122869 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12122824 TACCCTCAAA
*
12122834 ATAATATAATT-TATTTT
1 ATAAAATAATTATATTTT
12122851 ATAAAATAATTATATTTT
1 ATAAAATAATTATATTTT
12122869 A
1 A
12122870 ATCATTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAAATAATTATATTTT
Found at i:12123414 original size:3 final size:3
Alignment explanation
Indices: 12123401--12123450 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
12123391 CAACCTAGCT
* * *
12123401 GAA GGA GAA GAA GAA GAA GAGA GAT GAA GGA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA
12123447 GAA G
1 GAA G
12123451 GTGGTGCGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:12123722 original size:79 final size:81
Alignment explanation
Indices: 12123629--12123820 Score: 214
Period size: 82 Copynumber: 2.4 Consensus size: 81
12123619 TTTTAGTTAG
* * * * *
12123629 TATTATTATTGTTAGTTTTTAGGGTTTAGT-TA-TTAATAATTATTGTTACTTAGTATTATTATT
1 TATTATTATGGTTAGTTATTAGGGATTAGTAAACCTAATAATTATTGTTACTTAGTATTATT-TT
*
12123692 -AGTAAAAAATTAATAT
65 GAGTAAAAAACTAATAT
* *
12123708 TATTATTATGGTTAGTTATTA-GGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATTATTT
1 TATTATTATGGTTAGTTATTAGGGATTAGT-AAA-CCTAATAATTATTGTTACTTAGTATTATTT
*
12123772 TGAGTAAAAAACTATTAT
64 TGAGTAAAAAACTAATAT
*
12123790 TATTGTTATTGTGTTAGTTATTA-GGATTAGT
1 TATTATTA-TG-GTTAGTTATTAGGGATTAGT
12123821 GGTTAAACGT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 7 0.07
79 19 0.20
80 1 0.01
81 2 0.02
82 46 0.48
83 2 0.02
84 19 0.20
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.51
Consensus pattern (81 bp):
TATTATTATGGTTAGTTATTAGGGATTAGTAAACCTAATAATTATTGTTACTTAGTATTATTTTG
AGTAAAAAACTAATAT
Found at i:12123778 original size:82 final size:84
Alignment explanation
Indices: 12123662--12123820 Score: 243
Period size: 82 Copynumber: 1.9 Consensus size: 84
12123652 GTTTAGTTAT
*
12123662 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAATTAATATTATTATTA-TG-GTTAGTT
1 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAACTAATATTATTATTATTGTGTTAGTT
12123725 ATTAGGATTAGTAAAACCC
66 ATTAGGATTAGTAAAACCC
* * * *
12123744 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTGTTATTGTGTTAGT
1 TAATAATTATTGTTACTTAGTATTATTATT-AGTAAAAAACTAATATTATTATTATTGTGTTAGT
12123808 TATTAGGATTAGT
65 TATTAGGATTAGT
12123821 GGTTAAACGT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
81 2 0.03
82 46 0.67
83 2 0.03
84 19 0.28
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (84 bp):
TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAACTAATATTATTATTATTGTGTTAGTT
ATTAGGATTAGTAAAACCC
Found at i:12129387 original size:314 final size:313
Alignment explanation
Indices: 12128974--12129882 Score: 1297
Period size: 314 Copynumber: 2.9 Consensus size: 313
12128964 ATTTAGTAAA
* * *
12128974 AACCTTTATTTCGGCCCTTTGTTCGTATTTTTTCCCCG-ATTTTATTACTTT--A-AAAAATAT-
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATA
* *
12129034 TCTATTTTCTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
66 T-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
12129099 TGTATTTTTAAAATCAATTTTAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCC
130 TGTATTTTTTAAATAAATTTTAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCC
* *
12129163 GGATTTTATTACTTTCAATAAAAATATATTATATTCTAATTTTATTATTTTACATTATTTTAGTA
195 GAATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTA
*
12129228 CATTATGTTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTCAAAAATT
260 CATTATGTTTGAAATGTATTAATTTAGTGT-TTTTTAAAATAAATTTCAAAAATT
* * *
12129283 AACTCTTATTTCGGCCATTTATTCGTATTTTTCTTCTCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTCTCGAATTTTATTACTTTCAATAAAAATAT
* *
12129348 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAT
65 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* * * * *
12129413 TGTGTTTTTTAAATAAATTTCAAAAATTAAC-CCTTATTTCGGTCATTTGTTCGTATTTTTCTTC
130 TGTATTTTTTAAATAAATTTTAAAAA-AAACTCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTC
* *
12129477 TCGAATTTTATTACTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAG
193 CCGAATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAG
*
12129542 TACATTATGTTTGAAATGTATTAATTTAGTGTTTTTTAAAATAAATTTTAAAAATT
258 TACATTATGTTTGAAATGTATTAATTTAGTGTTTTTTAAAATAAATTTCAAAAATT
* *
12129598 AACCCTTATTTCGGCCCTTTGTTCGCATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATA
* * *
12129663 TTATTTT-TGTATTTTATTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAG
66 TTATTTTCT-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
12129727 TGTATTTTTTAAATAAATTTTGTAAAAAAACT-CTTATTTCGGCCCTTTGTTCGTATTTTTTTAC
130 TGTATTTTTTAAATAAATTTT-AAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCC
** * * * *
12129791 CGAAGCCTCATT-GTTTC-A-AAAAATATATTATTTTCGT-ATTTTATCATTTTA-AGCTATTTT
194 CGAA-TTTTATTACTTTCAATAAAAATATATTATTTTC-TAATTTTATTATTTTACA-TTATTTT
*
12129851 AGTACATTATGTTTGAAATGCATTAATTTAGT
256 AGTACATTATGTTTGAAATGTATTAATTTAGT
12129883 AAAAAAACCC
Statistics
Matches: 536, Mismatches: 49, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
309 28 0.05
310 5 0.01
311 79 0.15
312 2 0.00
313 12 0.02
314 252 0.47
315 62 0.12
316 96 0.18
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (313 bp):
AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATA
TTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
GTATTTTTTAAATAAATTTTAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCG
AATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTAC
ATTATGTTTGAAATGTATTAATTTAGTGTTTTTTAAAATAAATTTCAAAAATT
Found at i:12129421 original size:158 final size:157
Alignment explanation
Indices: 12128979--12129882 Score: 1275
Period size: 158 Copynumber: 5.8 Consensus size: 157
12128969 GTAAAAACCT
* *
12128979 TTATTTCGGCCCTTTGTTCGTATTTTTTCCCCG-ATTTTATTACTTT--A-AAAAATAT-TCTAT
1 TTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATAT-TAT
* *
12129039 TTTCTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTAT
65 TTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTAT
* * *
12129104 TTTTAAAATCAATTTTAAAAA-AAACTCC
130 TTTTTAAATAAATTTTAAAAATTAACT-C
* * *
12129132 TTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATA
1 TTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATATTATT
12129196 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTATT
66 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTATT
*
12129261 TTTTAAATAAATTTCAAAAATTAACTC
131 TTTTAAATAAATTTTAAAAATTAACTC
* *
12129288 TTATTTCGGCCATTTATTCGTATTTTTCTTCTCGAATTTTATTACTTTCAATAAAAATATATTAT
1 TTATTTCGGCCCTTTGTTCGTATTTTT-TTCTCGAATTTTATTACTTTCAATAAAAATATATTAT
* * *
12129353 TTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTATTGTGT
65 TTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTAT
* *
12129418 TTTTTAAATAAATTTCAAAAATTAACCC
130 TTTTTAAATAAATTTTAAAAATTAACTC
* *
12129446 TTATTTCGGTCATTTGTTCGTATTTTTCTTCTCGAATTTTATTACTTTCAATAAAAATATATTAT
1 TTATTTCGGCCCTTTGTTCGTATTTTT-TTCTCGAATTTTATTACTTTCAATAAAAATATATTAT
*
12129511 TTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGT-T
65 TTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTAT
* *
12129575 TTTTAAAATAAATTTTAAAAATTAACCC
130 TTTTTAAATAAATTTTAAAAATTAACTC
* *
12129603 TTATTTCGGCCCTTTGTTCGCATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATATTATT
1 TTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATATTATT
* * *
12129668 TT-TGTATTTTATTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAGTGTAT
66 TTCT-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTAT
12129732 TTTTTAAATAAATTTTGTAAAAA--AACTC
130 TTTTTAAATAAA-TTT-TAAAAATTAACTC
** * *
12129760 TTATTTCGGCCCTTTGTTCGTATTTTTTTAC-CGAAGCCTCATT-GTTTC-A-AAAAATATATTA
1 TTATTTCGGCCCTTTGTTCGTATTTTTTT-CTCGAA-TTTTATTACTTTCAATAAAAATATATTA
* * *
12129821 TTTTCGT-ATTTTATCATTTTA-AGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTAGT
64 TTTTC-TAATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
12129883 AAAAAAACCC
Statistics
Matches: 690, Mismatches: 44, Indels: 32
0.90 0.06 0.04
Matches are distributed among these distances:
152 9 0.01
153 35 0.05
154 1 0.00
155 66 0.10
156 207 0.30
157 112 0.16
158 254 0.37
159 6 0.01
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (157 bp):
TTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTCAATAAAAATATATTATT
TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTATT
TTTTAAATAAATTTTAAAAATTAACTC
Found at i:12130237 original size:19 final size:19
Alignment explanation
Indices: 12130209--12130246 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12130199 TTTTTTACAT
*
12130209 AAATATTACAAAAAAATTA
1 AAATAATACAAAAAAATTA
12130228 AAATAATACAAAAAAATTA
1 AAATAATACAAAAAAATTA
12130247 TCTTTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAATACAAAAAAATTA
Found at i:12130273 original size:10 final size:10
Alignment explanation
Indices: 12130260--12130360 Score: 58
Period size: 10 Copynumber: 9.2 Consensus size: 10
12130250 TTACTTATTT
12130260 TTTTTCTTTC
1 TTTTTCTTTC
*
12130270 TTTTTCCTTC
1 TTTTTCTTTC
* *
12130280 TCTTCCTCTTC
1 TTTTTCT-TTC
12130291 TTCTTCTCCTTTC
1 TT-TT-T-CTTTC
*
12130304 CTTTTCTTTC
1 TTTTTCTTTC
*
12130314 TTTTCCTTTC
1 TTTTTCTTTC
*
12130324 TTCTCCTTTCCTTCC
1 -T-T--TTT-CTTTC
*
12130339 CTTTTCTTTC
1 TTTTTCTTTC
12130349 TTTTTCTTTC
1 TTTTTCTTTC
12130359 TT
1 TT
12130361 ATCCTTCTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
10 41 0.60
11 9 0.13
12 5 0.07
13 5 0.07
14 4 0.06
15 4 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:12130307 original size:5 final size:5
Alignment explanation
Indices: 12130297--12130358 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
12130287 CTTCTTCTTC
* * * *
12130297 TCCTT TCCTT TTCTT TCTTT TCCTT T-CTT CTCCTT TCCTT CCCTT TTCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT -TCCTT TCCTT TCCTT TCCTT
* *
12130347 TCTTT TTCTT TC
1 TCCTT TCCTT TC
12130359 TTATCCTTCT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
4 3 0.07
5 37 0.86
6 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TCCTT
Found at i:12130336 original size:35 final size:35
Alignment explanation
Indices: 12130265--12130366 Score: 118
Period size: 35 Copynumber: 2.9 Consensus size: 35
12130255 TATTTTTTTT
* * * *
12130265 CTTTCTTTTTCCTTCTCTTCCTCTTCTTCT--TCTC
1 CTTTCCTTTTCTTTCTTTTCCT-TTCTTCTCCTTTC
12130299 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
1 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
* * *
12130334 CTTCCCTTTTCTTTCTTTTTCTTTCTTATCCTT
1 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTT
12130367 CTTTCTTCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 7 0.12
34 19 0.32
35 33 0.56
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (35 bp):
CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
Found at i:12130701 original size:26 final size:26
Alignment explanation
Indices: 12130653--12130702 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12130643 GTATTTTATT
*
12130653 TTTATTATTTTTAATTTTCTTTAAGG
1 TTTATTATTTTTAAATTTCTTTAAGG
12130679 TTTATTATTTTTATAATTT-TTTAA
1 TTTATTATTTTTA-AATTTCTTTAA
12130703 ATGATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTATTATTTTTAAATTTCTTTAAGG
Found at i:12134571 original size:30 final size:31
Alignment explanation
Indices: 12134511--12134568 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
12134501 GGGTTGGGAG
12134511 GGGAAGAGAGTAAAAGTTTTGGAGGGAAAGT
1 GGGAAGAGAGTAAAAGTTTTGGAGGGAAAGT
12134542 GGGAAG-GAGTAAAAGTTTT-GAGGGAAA
1 GGGAAGAGAGTAAAAGTTTTGGAGGGAAA
12134569 AGTAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.30
30 13 0.48
31 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.41, T:0.19
Consensus pattern (31 bp):
GGGAAGAGAGTAAAAGTTTTGGAGGGAAAGT
Found at i:12134634 original size:9 final size:9
Alignment explanation
Indices: 12134620--12134683 Score: 101
Period size: 9 Copynumber: 7.1 Consensus size: 9
12134610 TATAGTTTGA
12134620 TATTCGAAT
1 TATTCGAAT
12134629 TATTCGAAT
1 TATTCGAAT
*
12134638 TATTCGAGT
1 TATTCGAAT
*
12134647 TATTTGAAT
1 TATTCGAAT
12134656 TATTCGAAT
1 TATTCGAAT
*
12134665 TATTCGAGT
1 TATTCGAAT
12134674 TATTCGAAT
1 TATTCGAAT
12134683 T
1 T
12134684 CGAAAACTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12134655 original size:27 final size:27
Alignment explanation
Indices: 12134620--12134683 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
12134610 TATAGTTTGA
12134620 TATTCGAATTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
*
12134647 TATTTGAATTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
12134674 TATTCGAATT
1 TATTCGAATT
12134684 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (27 bp):
TATTCGAATTATTCGAATTATTCGAGT
Found at i:12135707 original size:23 final size:24
Alignment explanation
Indices: 12135681--12135731 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12135671 AAAAATCAAA
* *
12135681 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
12135704 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
12135727 ATATG
1 ATATG
12135732 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:12135885 original size:185 final size:185
Alignment explanation
Indices: 12135614--12135951 Score: 608
Period size: 185 Copynumber: 1.8 Consensus size: 185
12135604 ACAAATAATC
12135614 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
1 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
12135679 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
66 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
**
12135744 TGAAATAAATAA-A-TATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
131 CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
*
12135797 AATAAATACTATGTGAAATGATAATATCAAAATGAATTTTCAAAGTAAATATTGTATAAAAAAAT
1 AATAAATACTATATGAAATGATAATATCAAAATGAA-TTTCAAAGTAAATATTGTAT-AAAAAAT
12135862 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
64 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
*
12135927 TTCCAAATAGATAATATTATATATA
129 TTCCAAATAAATAATATTATATATA
12135952 TATATAAAGA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
183 35 0.24
184 20 0.14
185 83 0.56
186 1 0.01
187 8 0.05
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (185 bp):
AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
Found at i:12135892 original size:23 final size:24
Alignment explanation
Indices: 12135866--12135916 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12135856 AAAAATCAAA
* *
12135866 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
12135889 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
12135912 ATATG
1 ATATG
12135917 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:12136200 original size:20 final size:18
Alignment explanation
Indices: 12136177--12136224 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
12136167 GAATTTGAAT
12136177 AATAATACATGAAAACTTAA
1 AATAATACA--AAAACTTAA
12136197 AATATATGAACAAAAACTTAA
1 AATA-AT--ACAAAAACTTAA
12136218 AATAATA
1 AATAATA
12136225 ATGTACGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.04
20 6 0.24
21 15 0.60
23 3 0.12
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.25
Consensus pattern (18 bp):
AATAATACAAAAACTTAA
Found at i:12138071 original size:45 final size:44
Alignment explanation
Indices: 12137996--12138123 Score: 134
Period size: 44 Copynumber: 2.9 Consensus size: 44
12137986 GCTGCCTTCA
* *
12137996 GCTTTAATCTGTTCCACTGCAA-TGCGAGGGAAATAAGATTCGCTG
1 GCTTTAATCTGCTCCACTGCAACTTC-AGGGAAATAAGATT-GCTG
* * * ** *
12138041 TCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTG
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTG
*
12138085 GCTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGAT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGAT
12138124 CCGCCATAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 3 0.04
44 32 0.48
45 30 0.45
46 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (44 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTG
Found at i:12138219 original size:51 final size:51
Alignment explanation
Indices: 12138138--12138588 Score: 713
Period size: 51 Copynumber: 8.8 Consensus size: 51
12138128 CATAATTTGT
** * *
12138138 AGCTTTAATCTGTTCTGCTGTAACGTCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12138189 AGCTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGTTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
** *
12138240 AGCTTTAATCTACTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12138291 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAAATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12138342 AGCTTTAATCTGCTCCACTGCAACGCCAGGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12138393 AACTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
12138444 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12138495 AGTTTTAATCTGTTCCACTGCAACTCTAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
12138546 AGCTTTAATATGTTCCACTGCAACGCCAGGGAAATAAGATTCG
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCG
12138589 ATATAATGAC
Statistics
Matches: 365, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 365 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:12140518 original size:19 final size:20
Alignment explanation
Indices: 12140494--12140540 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
12140484 TGGTAGACTT
* *
12140494 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
12140513 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
12140533 -AATGCAAA
1 TAATGCAAA
12140541 AAGGTGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:12142841 original size:20 final size:21
Alignment explanation
Indices: 12142792--12142841 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
12142782 TAAAAATATA
* *
12142792 TAAAATAATGCATGATGAATT
1 TAAAATAATGCATGATAAACT
12142813 TGAATAATAATGCATGA-AAACT
1 T-AA-AATAATGCATGATAAACT
12142835 TAAAATA
1 TAAAATA
12142842 TATGAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 3 0.12
22 6 0.24
23 12 0.48
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (21 bp):
TAAAATAATGCATGATAAACT
Found at i:12143158 original size:22 final size:22
Alignment explanation
Indices: 12143133--12143194 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
12143123 CTCAATTTCA
12143133 TTCAAAAATTCTCTTAAATTCC
1 TTCAAAAATTCTCTTAAATTCC
* *
12143155 TTCAAAAATTCTCTCAATTTCC
1 TTCAAAAATTCTCTTAAATTCC
*
12143177 TTCCAAAATTCTCTTAAA
1 TTCAAAAATTCTCTTAAA
12143195 CTCTCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCAAAAATTCTCTTAAATTCC
Found at i:12143225 original size:21 final size:21
Alignment explanation
Indices: 12143197--12143245 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
12143187 CTCTTAAACT
*
12143197 CTCAAA-TTCCTTCCAAAATC
1 CTCAAATTTCCTTCAAAAATC
12143217 CTCACAATTTCCTTCAAAAAATC
1 CTCA-AATTTCCTTC-AAAAATC
12143240 TCTCAA
1 -CTCAA
12143246 CTCCATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 2 0.08
22 7 0.29
23 7 0.29
24 4 0.17
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.31
Consensus pattern (21 bp):
CTCAAATTTCCTTCAAAAATC
Found at i:12143226 original size:52 final size:52
Alignment explanation
Indices: 12143143--12143242 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
12143133 TTCAAAAATT
* * * * *
12143143 CTCTTAAATTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTTAAA
*
12143195 CTCTCAAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCT
12143243 CAACTCCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (52 bp):
CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTTAAA
Found at i:12143332 original size:28 final size:29
Alignment explanation
Indices: 12143280--12143335 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
12143270 TTCAATTTCA
12143280 TTTTTTAAGAAAATTTTAAATATTTTTAT
1 TTTTTTAAGAAAATTTTAAATATTTTTAT
12143309 TTTTTTAA-AATAATTTTAAA-ATTTTTA
1 TTTTTTAAGAA-AATTTTAAATATTTTTA
12143336 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTTAAGAAAATTTTAAATATTTTTAT
Found at i:12143342 original size:29 final size:29
Alignment explanation
Indices: 12143281--12143342 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
12143271 TCAATTTCAT
*
12143281 TTTTTAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAGAAAATTTTAAATATTTTTATA
12143310 TTTTTAA-AATAATTTTAAA-ATTTTTAATA
1 TTTTTAAGAA-AATTTTAAATATTTTT-ATA
12143339 TTTT
1 TTTT
12143343 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAATATTTTTATA
Found at i:12147995 original size:126 final size:125
Alignment explanation
Indices: 12147771--12148052 Score: 401
Period size: 126 Copynumber: 2.2 Consensus size: 125
12147761 CACGAGGGCA
* * * * * *
12147771 CGATTTGACACTATTTGCTCAAAAACGTCAACAAATAATTATTTCCTACATGACCAATTGTAGCG
1 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * **
12147836 AAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
66 AAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
12147896 CGATTTTATACTATTTGCTCAGAAAGCGTCAAAAAAAAATTATTT-CTGACATGACCAACTGT-G
1 CGATTTTATACTATTTGCTCAGAAA-CGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTAG
12147959 CCGAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
64 -CGAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
12148022 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTATACTATTTG-CTCAGAAACGTCAA
12148053 CTCGAAATAA
Statistics
Matches: 142, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
125 32 0.23
126 109 0.77
127 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
Found at i:12148332 original size:28 final size:28
Alignment explanation
Indices: 12148273--12148331 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
12148263 GATTTCGGGG
12148273 AAAATGGCCCATTTCGGTAAATAATTAA
1 AAAATGGCCCATTTCGGTAAATAATTAA
* *
12148301 AAAATTGGCCTATTTCGG-AAA-ATTTAA
1 AAAA-TGGCCCATTTCGGTAAATAATTAA
12148328 AAAA
1 AAAA
12148332 AAGGGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.32
28 7 0.25
29 12 0.43
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (28 bp):
AAAATGGCCCATTTCGGTAAATAATTAA
Found at i:12154828 original size:2 final size:2
Alignment explanation
Indices: 12154821--12154845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12154811 TTCCTGAACA
12154821 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12154846 ATCCGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12168261 original size:31 final size:31
Alignment explanation
Indices: 12168226--12168289 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
12168216 TATAATTAAT
* *
12168226 TATATTAACAATTTTATTTA-AAATCAATCAC
1 TATATCAACAATTTTA-ATAGAAATCAATCAC
* *
12168257 TATATCAATAATTTTAATAGGAATCAATCAC
1 TATATCAACAATTTTAATAGAAATCAATCAC
12168288 TA
1 TA
12168290 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (31 bp):
TATATCAACAATTTTAATAGAAATCAATCAC
Found at i:12169723 original size:125 final size:126
Alignment explanation
Indices: 12169508--12170041 Score: 711
Period size: 125 Copynumber: 4.3 Consensus size: 126
12169498 ATTTTTGCAG
* * * * *
12169508 TCGCGCCCACGT-GTACGCGCTTTTGTTATAGTAGGTCCTGGAA-AAATAATGTCAATTTGACGT
1 TCGCGCCCACGTAG-ACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGT
* * *
12169571 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCGGGATGCTATATGCGAAGAATTTGTGAAA
65 TTCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * ** *
12169633 TCGCGCCCTCCTAGACGCGCTTTTGCTACAGTTTGTCCTGGAAGAAATAATTTCGAGTTAACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * * *
12169698 TCTGAGCAAATAGTAT-AAAATCGCTTCTACCAAGATACTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * *
12169758 TCGCACCCACGTAGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTCGAGTTGACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * *
12169822 TCTGAGCAAATAATATAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * *
12169883 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *
12169948 TCTGAGCAAATAGTAT-AAAATCGCTT-ATACCAGGATGCTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCA-ACCAGGATGCTATATGAGAAGAATTTGTGAAA
* *
12170008 TCGCGCCCACGTGGATGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAG
12170042 CATGTTTGTG
Statistics
Matches: 353, Mismatches: 51, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
124 38 0.11
125 243 0.69
126 72 0.20
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (126 bp):
TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:12169954 original size:250 final size:249
Alignment explanation
Indices: 12169508--12170041 Score: 843
Period size: 250 Copynumber: 2.1 Consensus size: 249
12169498 ATTTTTGCAG
* * * *
12169508 TCGCGCCCACGTGTACGCGCTTTTGTTATAGTAGGTCCTGGAAAAATAATGTCAATTTGACGTTT
1 TCGCGCCCACGTG-ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGTTGACGTTT
* * * *
12169573 CTGAGCAAATAGTATAAAAAACGCTTCAAGCGGGATGCTATATGCGAAGAATTTGTGAAATCGCG
65 CTGAGCAAATAATATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
*
12169638 CCCTCCTAGACGCGCTTTTGCTACAGTTTGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
130 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
*
12169703 GCAAATAGTATAAAATCGCTTCTACCAAGATACTTTATGAGAAGAATTTGTGAAA
195 GCAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
* * * *
12169758 TCGCACCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
1 TCGCGCCCACGT-GACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGTTGACGTTT
*
12169823 CTGAGCAAATAATATAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAATCGCG
65 CTGAGCAAATAATATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
* * * *
12169888 CCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
130 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
* *
12169953 GCAAATAGTATAAAATCGCTTATACCAGGATGCTTTATGAGAAGAATTTGTGAAA
195 GCAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
*
12170008 TCGCGCCCACGTGGATGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGT-GACGCGCTTTTGCTACAGTAG
12170042 CATGTTTGTG
Statistics
Matches: 259, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
250 258 1.00
251 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (249 bp):
TCGCGCCCACGTGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGTTGACGTTTC
TGAGCAAATAATATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGC
CCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAG
CAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
Found at i:12173283 original size:44 final size:44
Alignment explanation
Indices: 12173224--12173363 Score: 110
Period size: 44 Copynumber: 3.2 Consensus size: 44
12173214 AACTTAAGGG
* *
12173224 TTAGGGTTTTA-AAGTTA-ATGTTTTAGTGTTT-AAGGTTTTTAAGT
1 TTAGGG-TTTAGAAGTTATA-GCTTTAGGGTTTGAA-GTTTTTAAGT
* *
12173268 TTAGGGTTTAGAAGTTTTAGCTTTAGGGTTTGTAGTTTTTAAGT
1 TTAGGGTTTAGAAGTTATAGCTTTAGGGTTTGAAGTTTTTAAGT
* * * * *
12173312 TTAAGGTTTAG-GGTTTTTAAG-TTTAAGGTTTGAGGTTTTTAAGT
1 TTAGGGTTTAGAAG-TTAT-AGCTTTAGGGTTTGAAGTTTTTAAGT
*
12173356 TAAGGGTT
1 TTAGGGTT
12173364 AGGGTTTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
43 5 0.06
44 71 0.89
45 4 0.05
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (44 bp):
TTAGGGTTTAGAAGTTATAGCTTTAGGGTTTGAAGTTTTTAAGT
Found at i:12173305 original size:29 final size:30
Alignment explanation
Indices: 12173273--12173336 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
12173263 TAAGTTTAGG
*
12173273 GTTTAGAAGTTTTAGCTTTAGGGTTTGT-A
1 GTTTAGAAGTTTAAGCTTTAGGGTTTGTAA
** * *
12173302 GTTTTTAAGTTTAAGGTTTAGGGTTTTTAA
1 GTTTAGAAGTTTAAGCTTTAGGGTTTGTAA
12173332 GTTTA
1 GTTTA
12173337 AGGTTTGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.22, C:0.02, G:0.25, T:0.52
Consensus pattern (30 bp):
GTTTAGAAGTTTAAGCTTTAGGGTTTGTAA
Found at i:12173320 original size:7 final size:7
Alignment explanation
Indices: 12173305--12173427 Score: 51
Period size: 7 Copynumber: 17.4 Consensus size: 7
12173295 GTTTGTAGTT
12173305 TTTAA-G
1 TTTAAGG
12173311 TTTAAGG
1 TTTAAGG
*
12173318 TTTAGGG
1 TTTAAGG
12173325 TTTTTAA-G
1 --TTTAAGG
12173333 TTTAAGG
1 TTTAAGG
*
12173340 TTTGAGG
1 TTTAAGG
12173347 TTTTTAA-G
1 --TTTAAGG
12173355 -TTAAGG
1 TTTAAGG
* *
12173361 GTTAGGG
1 TTTAAGG
*
12173368 TTTTTAGG
1 -TTTAAGG
12173376 TTTAAGG
1 TTTAAGG
12173383 --TAAGGG
1 TTTAA-GG
*
12173389 TTTTTAGG
1 -TTTAAGG
*
12173397 TTTAGGG
1 TTTAAGG
*
12173404 TTTTAGG
1 TTTAAGG
*
12173411 TTTATGG
1 TTTAAGG
*
12173418 TTTAGGG
1 TTTAAGG
12173425 TTT
1 TTT
12173428 TAAGTTTGGG
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
5 7 0.08
6 13 0.15
7 49 0.56
8 8 0.09
9 10 0.11
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:12173388 original size:21 final size:21
Alignment explanation
Indices: 12173302--12173405 Score: 129
Period size: 21 Copynumber: 4.9 Consensus size: 21
12173292 AGGGTTTGTA
12173302 GTTTTTAAGTTTAAGGTTTAGG
1 GTTTTTAAGTTTAAGG-TTAGG
*
12173324 GTTTTTAAGTTTAAGGTTTGAG
1 GTTTTTAAGTTTAAGGTTAG-G
12173346 GTTTTTAAG-TTAAGGGTTAGG
1 GTTTTTAAGTTTAA-GGTTAGG
* *
12173367 GTTTTTAGGTTTAAGGTAAGG
1 GTTTTTAAGTTTAAGGTTAGG
* *
12173388 GTTTTTAGGTTTAGGGTT
1 GTTTTTAAGTTTAAGGTT
12173406 TTAGGTTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
21 38 0.52
22 35 0.48
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
GTTTTTAAGTTTAAGGTTAGG
Found at i:12173414 original size:35 final size:35
Alignment explanation
Indices: 12173362--12173442 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
12173352 AAGTTAAGGG
*
12173362 TTAGGGTTTTTAGGTTTAAGG-TAAGGGTTTTTAGGT
1 TTAGGG-TTTTAGGTTTAAGGTTAAGGG-TTTTAAGT
* *
12173398 TTAGGGTTTTAGGTTTATGGTTTAGGGTTTTAAGT
1 TTAGGGTTTTAGGTTTAAGGTTAAGGGTTTTAAGT
*
12173433 TTGGGGTTTT
1 TTAGGGTTTT
12173443 TATATTTAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 29 0.73
36 11 0.28
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (35 bp):
TTAGGGTTTTAGGTTTAAGGTTAAGGGTTTTAAGT
Found at i:12173419 original size:21 final size:20
Alignment explanation
Indices: 12173245--12174308 Score: 184
Period size: 22 Copynumber: 49.8 Consensus size: 20
12173235 AAGTTAATGT
*
12173245 TTTAGTGTTTAAGGTTTTTAAG
1 TTTAG-GTTT-AGGGTTTTAAG
*
12173267 TTTAGGGTTTAGAAGTTTT-AG
1 TTTA-GGTTTAG-GGTTTTAAG
*
12173288 CTTTAGGGTTT-GTAGTTTTTAAG
1 -TTTA-GGTTTAG--GGTTTTAAG
12173311 TTTAAGGTTTAGGGTTTTTAAG
1 TTT-AGGTTTAGGG-TTTTAAG
*
12173333 TTTAAGGTTTGAGGTTTTTAAG
1 TTT-AGGTTT-AGGGTTTTAAG
* * *
12173355 TTAAGGGTTAGGGTTTTTAGG
1 TTTAGGTTTAGGG-TTTTAAG
*
12173376 TTTAAGG-TAAGGG--TT---
1 TTT-AGGTTTAGGGTTTTAAG
*
12173391 TTTAGGTTTAGGGTTTTAGG
1 TTTAGGTTTAGGGTTTTAAG
12173411 TTTATGGTTTAGGGTTTTAAG
1 TTTA-GGTTTAGGGTTTTAAG
*
12173432 TTT-GG----GGTTTTTATA-
1 TTTAGGTTTAGGGTTTTA-AG
*
12173447 TTTAGGGCTT-GGAGTTTTAAG
1 TTTA-GGTTTAGG-GTTTTAAG
* *
12173468 TTAATGG-TTAGTGTTTTTAA-
1 TTTA-GGTTTAG-GGTTTTAAG
*
12173488 TTTAAGGGTTAGGGTTTTTAAG
1 TTT-AGGTTTAGGG-TTTTAAG
* * * *
12173510 TTAAGGGTTA-GG-ATTAGGG
1 TTTAGGTTTAGGGTTTTA-AG
* ** ***
12173529 TTATAGTTTTAAAG-CCAAAG
1 TT-TAGGTTTAGGGTTTTAAG
**
12173549 TTTTAGGGTTTATAGTTTTAAG
1 -TTTA-GGTTTAGGGTTTTAAG
*
12173571 TTTAGTGTTTATGGTTTTTAAG
1 TTTAG-GTTTA-GGGTTTTAAG
12173593 TTTAGGGTTTAGGGTTTTAATTTTAAAG
1 TTTA-GGTTTAGGG------TTTT-AAG
*
12173621 TTTAGGGTTTAAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
*
12173643 TTTAGGATTTAAGGTTTTTAAG
1 TTTAGG-TTT-AGGGTTTTAAG
* *
12173665 -TTAGGGGTTAGGGTTTTTAGG
1 TTTA-GGTTTAGGG-TTTTAAG
* * * *
12173686 TTAAGGGTTA-GG-ATTAGG
1 TTTAGGTTTAGGGTTTTAAG
**
12173704 TTTAGGGTTTTAAAG--TTAATG
1 TTTA-GG-TTTAGGGTTTTAA-G
12173725 TTTTAGGGTTTAGAGGTTTTAAG
1 -TTTA-GGTTTAG-GGTTTTAAG
* * *
12173748 CTTAAGGTTTATGGTTTTTAGG
1 -TTTAGGTTTA-GGGTTTTAAG
*
12173770 TTTATGGTTTATGGTTTTTAAG
1 TTTA-GGTTTA-GGGTTTTAAG
** *
12173792 TTTATGGTTTAATGTTGTTAGG
1 TTTA-GGTTTAGGGTT-TTAAG
*
12173814 TTTAGGGTTTAAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
* * *
12173836 TTTAAAGTTTATGGTTTTTAGG
1 TTT-AGGTTTA-GGGTTTTAAG
12173858 TTTAGGGTTTAGGGTTTTAAG
1 TTTA-GGTTTAGGGTTTTAAG
* * *
12173879 TTTAAGGCTTATGGTTTTTAGG
1 TTT-AGGTTTA-GGGTTTTAAG
* *
12173901 TTTTGGGTTTCTA-GTTTTTAAG
1 -TTTAGG-TT-TAGGGTTTTAAG
* * **
12173923 TTAAGGATTAGCATTTTTAA-
1 TTTAGGTTTAG-GGTTTTAAG
*
12173943 TTTAAGGGTTAGGGTTTTAAG
1 TTT-AGGTTTAGGGTTTTAAG
* * * *
12173964 TTAAGGGTTA-GG-ATTAGG
1 TTTAGGTTTAGGGTTTTAAG
* **
12173982 GTTATGGTTTTAAAG--TTAAG
1 TTTA-GG-TTTAGGGTTTTAAG
*
12174002 TTTTTAGGGTTTAAGGTTTTTAAG
1 --TTTA-GGTTT-AGGGTTTTAAG
*
12174026 TTTAAGGTTTGGGGTTTTAAAG
1 TTT-AGGTTTAGGGTTTT-AAG
12174048 TTTGAGGTTTAGGGTTTGGGGTTTTAAG
1 TTT-AGGTTTA-------GGGTTTTAAG
* * *
12174076 TTAAGAG-TTAGTGTTTTTAGG
1 TTTAG-GTTTAG-GGTTTTAAG
*
12174097 TTTAGGCTTTGAGGTTTTTAAG
1 TTTAGG-TTT-AGGGTTTTAAG
* * *
12174119 TTAATGG-TTATGGTTTTTAGG
1 TTTA-GGTTTA-GGGTTTTAAG
*
12174140 TTTAGGGTTTGAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
12174162 TTTAGGGTTTAGGGTTTTAAAG
1 TTTA-GGTTTAGGGTTTT-AAG
* *
12174184 TTTA-GTATTTGGATTTTTTAAG
1 TTTAGGT-TTAGG--GTTTTAAG
12174206 TTTAGGGTTTAGGGTTTTTAAG
1 TTTA-GGTTTAGGG-TTTTAAG
*
12174228 TTTATGGTTTGAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
* *
12174250 TTAAGAG-TTAGCGTTTTTAA-
1 TTTAG-GTTTAG-GGTTTTAAG
* *
12174270 TTTAAGGGTTAAGGTTTTTAAG
1 TTT-A-GGTTTAGGGTTTTAAG
* *
12174292 TTAAGGGTTTATGGTTT
1 TTTA-GGTTTAGGGTTT
12174309 GTCAATTAAA
Statistics
Matches: 797, Mismatches: 128, Indels: 235
0.69 0.11 0.20
Matches are distributed among these distances:
14 3 0.00
15 18 0.02
16 1 0.00
17 4 0.01
18 19 0.02
19 13 0.02
20 71 0.09
21 247 0.31
22 327 0.41
23 43 0.05
24 13 0.02
27 9 0.01
28 19 0.02
29 10 0.01
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (20 bp):
TTTAGGTTTAGGGTTTTAAG
Found at i:12173571 original size:22 final size:21
Alignment explanation
Indices: 12173550--12174308 Score: 204
Period size: 22 Copynumber: 34.8 Consensus size: 21
12173540 AAGCCAAAGT
*
12173550 TTTAGGGTTTATAGTTTTAAG
1 TTTAGGGTTTATGGTTTTAAG
*
12173571 TTTAGTGTTTATGGTTTTTAAG
1 TTTAGGGTTTATGG-TTTTAAG
* *
12173593 TTTAGGGTTTAGGGTTTTAAT
1 TTTAGGGTTTATGGTTTTAAG
** *
12173614 TTTAAAGTTTA-GGGTTTAAGG
1 TTTAGGGTTTATGGTTTTAA-G
* * *
12173635 TTTTTAAGTTTAGGATTTAAGGTTTTTAA
1 --TTT-AG----GG-TTTATGGTTTTAAG
* * * *
12173664 GTTAGGGGTTAGGGTTTTTAGG
1 TTTAGGGTTTATGGTTT-TAAG
* * *
12173686 TTAAGGG-TTA-GG-ATTAGG
1 TTTAGGGTTTATGGTTTTAAG
**
12173704 TTTAGGGTTTTAAAG--TTAATG
1 TTTAGGG-TTTATGGTTTTAA-G
*
12173725 TTTTAGGGTTTAGAGGTTTTAAG
1 -TTTAGGGTTTA-TGGTTTTAAG
* * *
12173748 CTTAAGGTTTATGGTTTTTAGG
1 TTTAGGGTTTATGG-TTTTAAG
*
12173770 TTTATGGTTTATGGTTTTTAAG
1 TTTAGGGTTTATGG-TTTTAAG
* *
12173792 TTTATGGTTTAAT-GTTGTTAGG
1 TTTAGGGTTT-ATGGTT-TTAAG
*
12173814 TTTAGGGTTTAAGGTTTTTAAG
1 TTTAGGGTTTATGG-TTTTAAG
** *
12173836 TTTAAAGTTTATGGTTTTTAGG
1 TTTAGGGTTTATGG-TTTTAAG
*
12173858 TTTAGGGTTTAGGGTTTTAAG
1 TTTAGGGTTTATGGTTTTAAG
* * *
12173879 TTTAAGGCTTATGGTTTTTAGG
1 TTTAGGGTTTATGG-TTTTAAG
* * *
12173901 TTTTGGGTTTCTAGTTTTTAAG
1 TTTAGGGTTTAT-GGTTTTAAG
* * *
12173923 -TTAAGGATTA-GCATTTTTAA-
1 TTTAGGGTTTATG--GTTTTAAG
*
12173943 TTTAAGGG-TTAGGGTTTTAAG
1 TTT-AGGGTTTATGGTTTTAAG
* * *
12173964 TTAAGGG-TTA-GG-ATTAGG
1 TTTAGGGTTTATGGTTTTAAG
* * **
12173982 GTTATGGTTTTAAAG--TTAAG
1 TTTA-GGGTTTATGGTTTTAAG
*
12174002 TTTTTAGGGTTTAAGGTTTTTAAG
1 --TTTAGGGTTTATGG-TTTTAAG
* **
12174026 TTTAAGGTTTGGGGTTTTAAAG
1 TTTAGGGTTTATGGTTTT-AAG
12174048 TTT-GAGGTTTAGGGTTTGGGGTTTTAAG
1 TTTAG-GGTTTA-----T--GGTTTTAAG
* * * *
12174076 TTAAGAG-TTAGTGTTTTTAGG
1 TTTAGGGTTTA-TGGTTTTAAG
*
12174097 TTTAGGCTTTGA-GGTTTTTAAG
1 TTTAGGGTTT-ATGG-TTTTAAG
* * *
12174119 TTAATGG-TTATGGTTTTTAGG
1 TTTAGGGTTTATGG-TTTTAAG
12174140 TTTAGGGTTTGA-GGTTTTTAAG
1 TTTAGGGTTT-ATGG-TTTTAAG
*
12174162 TTTAGGGTTTAGGGTTTTAAAG
1 TTTAGGGTTTATGGTTTT-AAG
** *
12174184 TTTAGTATTTGGAT-TTTTTAAG
1 TTTAGGGTTT--ATGGTTTTAAG
*
12174206 TTTAGGGTTTAGGGTTTTTAAG
1 TTTAGGGTTTATGG-TTTTAAG
*
12174228 TTTATGGTTTGA-GGTTTTTAAG
1 TTTAGGGTTT-ATGG-TTTTAAG
* *
12174250 TTAAGAG-TTA-GCGTTTTTAA-
1 TTTAGGGTTTATG-G-TTTTAAG
*
12174270 TTTAAGGG-TTAAGGTTTTTAAG
1 TTT-AGGGTTTATGG-TTTTAAG
*
12174292 TTAAGGGTTTATGGTTT
1 TTTAGGGTTTATGGTTT
12174309 GTCAATTAAA
Statistics
Matches: 557, Mismatches: 112, Indels: 138
0.69 0.14 0.17
Matches are distributed among these distances:
18 16 0.03
19 6 0.01
20 41 0.07
21 163 0.29
22 272 0.49
23 17 0.03
24 11 0.02
26 2 0.00
27 5 0.01
28 7 0.01
29 11 0.02
30 6 0.01
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTATGGTTTTAAG
Found at i:12173581 original size:28 final size:26
Alignment explanation
Indices: 12173550--12173638 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 26
12173540 AAGCCAAAGT
*
12173550 TTTAGGGTTTATAGTTTTAAGTTTAGTG
1 TTTAGGGTTT-TA-TTTTAAGTTTAGGG
*
12173578 TTTATGG---T-TTTTAAGTTTAGGG
1 TTTAGGGTTTTATTTTAAGTTTAGGG
12173600 TTTAGGGTTTTAATTTTAAAGTTTAGGG
1 TTTAGGGTTTT-ATTTT-AAGTTTAGGG
*
12173628 TTTAAGGTTTT
1 TTTAGGGTTTT
12173639 TAAGTTTAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
22 19 0.37
24 1 0.02
25 1 0.02
27 4 0.08
28 26 0.51
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (26 bp):
TTTAGGGTTTTATTTTAAGTTTAGGG
Found at i:12173595 original size:44 final size:44
Alignment explanation
Indices: 12173550--12173924 Score: 226
Period size: 44 Copynumber: 8.5 Consensus size: 44
12173540 AAGCCAAAGT
*
12173550 TTTAGGGTTTATAGTTTTAAGTTTAGTGTTTATGGTTTTTAA-G
1 TTTAGGGTTTATAGTTTTAAGTTTAGGGTTTATGGTTTTTAAGG
* *
12173593 TTTAGGGTTTAGGGTTTTAATTTTAAAGTTTAGGGTTTAAGGTTTTTAA-G
1 TTTAGGGTTTA------TAGTTTT-AAGTTTAGGGTTTATGGTTTTTAAGG
* * *
12173643 TTTAGGATTTA-AGGTTTTTAAG-TTAGGGGTTAGGGTTTTT-AGG
1 TTTAGGGTTTATA-G-TTTTAAGTTTAGGGTTTATGGTTTTTAAGG
* ** * ** *
12173686 TTAAGGG--T-TAGGATTAGGTTTAGGGTTTTAAAG---TTAATGT
1 TTTAGGGTTTATAGTTTTAAGTTTAGGG-TTTATGGTTTTTAA-GG
* * *
12173726 TTTAGGGTTTAGAGGTTTTAAGCTTAAGGTTTATGGTTTTT-AGG
1 TTTAGGGTTTATA-GTTTTAAGTTTAGGGTTTATGGTTTTTAAGG
* * * *
12173770 TTTATGGTTTATGGTTTTTAAGTTTATGGTTTAAT-GTTGTT-AGG
1 TTTAGGGTTTATAG-TTTTAAGTTTAGGGTTT-ATGGTTTTTAAGG
**
12173814 TTTAGGGTTTA-AGGTTTTTAAGTTTAAAGTTTATGGTTTTT-AGG
1 TTTAGGGTTTATA-G-TTTTAAGTTTAGGGTTTATGGTTTTTAAGG
** * *
12173858 TTTAGGGTTTAGGGTTTTAAGTTTAAGGCTTATGGTTTTT-AGG
1 TTTAGGGTTTATAGTTTTAAGTTTAGGGTTTATGGTTTTTAAGG
* *
12173901 TTTTGGGTTTCTAGTTTTTAAGTT
1 TTTAGGGTTTATAG-TTTTAAGTT
12173925 AAGGATTAGC
Statistics
Matches: 260, Mismatches: 44, Indels: 55
0.72 0.12 0.15
Matches are distributed among these distances:
38 2 0.01
39 5 0.02
40 14 0.05
41 6 0.02
42 2 0.01
43 80 0.31
44 103 0.40
45 7 0.03
46 2 0.01
49 6 0.02
50 33 0.13
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.51
Consensus pattern (44 bp):
TTTAGGGTTTATAGTTTTAAGTTTAGGGTTTATGGTTTTTAAGG
Found at i:12173604 original size:50 final size:50
Alignment explanation
Indices: 12173550--12173660 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
12173540 AAGCCAAAGT
* * * *
12173550 TTTAGGGTTTATAGTTTT-AAGTTTAGTGTTTATGGTTTTTAAGTTTAGGG
1 TTTAGGGTTT-TAATTTTAAAGTTTAGGGTTTAAGGTTTTTAAGTTTAGGA
12173600 TTTAGGGTTTTAATTTTAAAGTTTAGGGTTTAAGGTTTTTAAGTTTAGGA
1 TTTAGGGTTTTAATTTTAAAGTTTAGGGTTTAAGGTTTTTAAGTTTAGGA
*
12173650 TTTAAGGTTTT
1 TTTAGGGTTTT
12173661 TAAGTTAGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 6 0.11
50 49 0.89
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (50 bp):
TTTAGGGTTTTAATTTTAAAGTTTAGGGTTTAAGGTTTTTAAGTTTAGGA
Found at i:12173636 original size:7 final size:7
Alignment explanation
Indices: 12173587--12173895 Score: 70
Period size: 7 Copynumber: 43.4 Consensus size: 7
12173577 GTTTATGGTT
12173587 TTTAA-G
1 TTTAAGG
*
12173593 TTTAGGG
1 TTTAAGG
*
12173600 TTTAGGG
1 TTTAAGG
*
12173607 TTTTAA-T
1 -TTTAAGG
*
12173614 TTTAAAG
1 TTTAAGG
*
12173621 TTTAGGG
1 TTTAAGG
12173628 TTTAAGG
1 TTTAAGG
12173635 TTTTTAA-G
1 --TTTAAGG
12173643 TTT-AGG
1 TTTAAGG
12173649 ATTTAAGG
1 -TTTAAGG
12173657 TTTTTAA-G
1 --TTTAAGG
*
12173665 -TTAGGG
1 TTTAAGG
* *
12173671 GTTAGGG
1 TTTAAGG
*
12173678 TTTTTAGG
1 -TTTAAGG
12173686 -TTAAGG
1 TTTAAGG
*
12173692 GTT-AGG
1 TTTAAGG
*
12173698 ATT-AGG
1 TTTAAGG
*
12173704 TTTAGGG
1 TTTAAGG
*
12173711 TTTTAAAG
1 -TTTAAGG
*
12173719 -TTAATGT
1 TTTAA-GG
*
12173726 TTTAGGG
1 TTTAAGG
12173733 TTTAGAGG
1 TTTA-AGG
12173741 TTTTAA-G
1 -TTTAAGG
*
12173748 CTTAAGG
1 TTTAAGG
*
12173755 TTTATGG
1 TTTAAGG
*
12173762 TTTTTAGG
1 -TTTAAGG
*
12173770 TTTATGG
1 TTTAAGG
*
12173777 TTTATGG
1 TTTAAGG
12173784 TTTTTAA-G
1 --TTTAAGG
*
12173792 TTTATGG
1 TTTAAGG
*
12173799 TTTAATG
1 TTTAAGG
*
12173806 TTGTTAGG
1 TT-TAAGG
*
12173814 TTTAGGG
1 TTTAAGG
12173821 TTTAAGG
1 TTTAAGG
12173828 TTTTTAA-G
1 --TTTAAGG
*
12173836 TTTAAAG
1 TTTAAGG
*
12173843 TTTATGG
1 TTTAAGG
*
12173850 TTTTTAGG
1 -TTTAAGG
*
12173858 TTTAGGG
1 TTTAAGG
*
12173865 TTTAGGG
1 TTTAAGG
12173872 TTTTAA-G
1 -TTTAAGG
12173879 TTTAAGG
1 TTTAAGG
* *
12173886 CTTATGG
1 TTTAAGG
12173893 TTT
1 TTT
12173896 TTAGGTTTTG
Statistics
Matches: 223, Mismatches: 49, Indels: 61
0.67 0.15 0.18
Matches are distributed among these distances:
5 4 0.02
6 51 0.23
7 100 0.45
8 45 0.20
9 23 0.10
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:12173676 original size:50 final size:50
Alignment explanation
Indices: 12173550--12173680 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
12173540 AAGCCAAAGT
* * * * * *
12173550 TTTAGGGTTTATAGT-TTTAAGTTTAGTGTTTATGGTTTTTAAGTTTAGGG
1 TTTAGGGTTT-TAATGTTAAAGGTTAGGGTTTAAGGTTTTTAAGTTTAGGA
* *
12173600 TTTAGGGTTTTAATTTTAAAGTTTAGGGTTTAAGGTTTTTAAGTTTAGGA
1 TTTAGGGTTTTAATGTTAAAGGTTAGGGTTTAAGGTTTTTAAGTTTAGGA
* **
12173650 TTTAAGGTTTTTAA-GTTAGGGGTTAGGGTTT
1 TTT-AGGGTTTTAATGTTAAAGGTTAGGGTTT
12173681 TTAGGTTAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 3 0.04
50 57 0.83
51 9 0.13
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (50 bp):
TTTAGGGTTTTAATGTTAAAGGTTAGGGTTTAAGGTTTTTAAGTTTAGGA
Found at i:12173758 original size:29 final size:29
Alignment explanation
Indices: 12173702--12173764 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
12173692 GTTAGGATTA
*
12173702 GGTTTAGGGTTTTAAAGTTAATGTTTTAG
1 GGTTTAGGGTTTTAAAGTTAATGGTTTAG
*
12173731 GGTTTAGAGGTTTT-AAGCTTAA-GGTTTAT
1 GGTTTAG-GGTTTTAAAG-TTAATGGTTTAG
12173760 GGTTT
1 GGTTT
12173765 TTAGGTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.48
Consensus pattern (29 bp):
GGTTTAGGGTTTTAAAGTTAATGGTTTAG
Found at i:12173772 original size:15 final size:15
Alignment explanation
Indices: 12173752--12173867 Score: 62
Period size: 15 Copynumber: 7.9 Consensus size: 15
12173742 TTTAAGCTTA
12173752 AGGTTTATGGTTTTT
1 AGGTTTATGGTTTTT
*
12173767 AGGTTTATGGTTTAT
1 AGGTTTATGGTTTTT
* * *
12173782 -GGTTTTTAAGTTTAT
1 AGGTTTAT-GGTTTTT
*
12173797 -GGTTTAAT-GTTGTT
1 AGGTTT-ATGGTTTTT
* *
12173811 AGGTTTA-GGGTTTA
1 AGGTTTATGGTTTTT
* * *
12173825 AGGTTTTTAAG-TTTA
1 AGGTTTAT-GGTTTTT
*
12173840 AAGTTTATGGTTTTT
1 AGGTTTATGGTTTTT
*
12173855 AGGTTTAGGGTTT
1 AGGTTTATGGTTT
12173868 AGGGTTTTAA
Statistics
Matches: 77, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
14 21 0.27
15 54 0.70
16 2 0.03
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (15 bp):
AGGTTTATGGTTTTT
Found at i:12173962 original size:20 final size:20
Alignment explanation
Indices: 12173916--12173975 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
12173906 GGTTTCTAGT
* **
12173916 TTTTAAGTTAAGGATTAGCAT
1 TTTTAAGTTAAGGGTTAG-GG
*
12173937 TTTTAATTTAAGGGTTAGGG
1 TTTTAAGTTAAGGGTTAGGG
12173957 TTTTAAGTTAAGGGTTAGG
1 TTTTAAGTTAAGGGTTAGG
12173976 ATTAGGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (20 bp):
TTTTAAGTTAAGGGTTAGGG
Found at i:12174040 original size:29 final size:28
Alignment explanation
Indices: 12174008--12174077 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
12173998 TAAGTTTTTA
* *
12174008 GGGTTTAAGGTTTTTAAGTTTAAGGTTTG
1 GGGTTTAAAG-TTTGAAGTTTAAGGTTTG
* *
12174037 GGGTTTTAAAGTTTGAGGTTTAGGGTTTG
1 GGG-TTTAAAGTTTGAAGTTTAAGGTTTG
*
12174066 GGGTTTTAAGTT
1 GGGTTTAAAGTT
12174078 AAGAGTTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 8 0.23
29 21 0.60
30 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (28 bp):
GGGTTTAAAGTTTGAAGTTTAAGGTTTG
Found at i:12174874 original size:18 final size:18
Alignment explanation
Indices: 12174851--12174890 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12174841 GACTCGAAAA
* *
12174851 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
12174869 AGGATATATAAAAGGGCT
1 AGGATACATAAAAGGGCT
12174887 AGGA
1 AGGA
12174891 AACGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:12176828 original size:12 final size:12
Alignment explanation
Indices: 12176787--12176830 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
12176777 ATTAAAAATG
12176787 AATTTGAG-GGA
1 AATTTGAGAGGA
*
12176798 AATTTGAAAGGA
1 AATTTGAGAGGA
12176810 AA-TTGAGAGGA
1 AATTTGAGAGGA
12176821 AATTTGAGAG
1 AATTTGAGAG
12176831 AGGATTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:12178720 original size:26 final size:26
Alignment explanation
Indices: 12178689--12178749 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
12178679 TTGAATTATG
*
12178689 AAATTGTTTTTGTGTGGTTGTAATTT
1 AAATTGTTTTTGTGTGGTTATAATTT
12178715 AAATTGTTTTTGTGTGGTTATAATTT
1 AAATTGTTTTTGTGTGGTTATAATTT
*
12178741 GAATTGTTT
1 AAATTGTTT
12178750 ACAATTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (26 bp):
AAATTGTTTTTGTGTGGTTATAATTT
Found at i:12179989 original size:16 final size:16
Alignment explanation
Indices: 12179968--12180006 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12179958 TTTTAATAAA
12179968 ATTAAAACTAATTATT
1 ATTAAAACTAATTATT
* *
12179984 ATTAAAATTAATTGTT
1 ATTAAAACTAATTATT
*
12180000 AGTAAAA
1 ATTAAAA
12180007 TCATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTATT
Found at i:12179992 original size:22 final size:23
Alignment explanation
Indices: 12179939--12179994 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
12179929 CCCGTTTTTA
* *
12179939 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTATT
*
12179962 AATAAAATTAAAACTA-ATTATT
1 ATTAAAATTAAAACTATATTATT
12179984 ATTAAAATTAA
1 ATTAAAATTAA
12179995 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTATT
Found at i:12181362 original size:19 final size:19
Alignment explanation
Indices: 12181338--12181391 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
12181328 AACCATATCT
12181338 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12181357 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
12181376 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
12181392 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12185704 original size:11 final size:12
Alignment explanation
Indices: 12185664--12185706 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
12185654 CCTATTTGAA
12185664 AAGTGATGCTTGG
1 AAGT-ATGCTTGG
12185677 AAGTATGCTTGG
1 AAGTATGCTTGG
12185689 AAGTATGCTT-G
1 AAGTATGCTTGG
12185700 AAGTATG
1 AAGTATG
12185707 TTTGTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.27
12 18 0.60
13 4 0.13
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (12 bp):
AAGTATGCTTGG
Found at i:12187605 original size:24 final size:24
Alignment explanation
Indices: 12187578--12187692 Score: 83
Period size: 24 Copynumber: 4.7 Consensus size: 24
12187568 GTTGTATAAT
12187578 GGAAGCTCATAAGAGCCATAATCG
1 GGAAGCTCATAAGAGCCATAATCG
* *
12187602 GGAAGCTCATGCAAG-TCAATAAT-G
1 GGAAGCTCAT--AAGAGCCATAATCG
* *
12187626 GGTAGCT-TTGAAGAGCCATTAATCG
1 GGAAGCTCAT-AAGAGCCA-TAATCG
* *
12187651 GGAAGCTCACGAAGAGCCATATAACG
1 GGAAGCTCA-TAAGAGCCATA-ATCG
* *
12187677 GGATGTTCATAAGAGC
1 GGAAGCTCATAAGAGC
12187693 TGCGGTGTGT
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
22 3 0.04
23 3 0.04
24 21 0.30
25 21 0.30
26 21 0.30
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCG
Found at i:12191336 original size:25 final size:26
Alignment explanation
Indices: 12191289--12191337 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
12191279 AAGGCACCTT
12191289 ATAAATTCTTTAAGGGTTACAAGAGC
1 ATAAATTCTTTAAGGGTTACAAGAGC
*
12191315 ATAAATTC-TTAGGGGTTACAAGA
1 ATAAATTCTTTAAGGGTTACAAGA
12191338 CTTGTATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (26 bp):
ATAAATTCTTTAAGGGTTACAAGAGC
Found at i:12195385 original size:3 final size:3
Alignment explanation
Indices: 12195377--12195405 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12195367 AGTAGAAAGG
12195377 TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12195406 AAAACCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:12199563 original size:221 final size:221
Alignment explanation
Indices: 12199180--12199622 Score: 850
Period size: 221 Copynumber: 2.0 Consensus size: 221
12199170 TAGTGCAAGA
*
12199180 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCAAGAGAGACGAGCC
1 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCAAGAGAAACGAGCC
12199245 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
66 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
*
12199310 ATGCCCTAACTATATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
131 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
12199375 GTTGTTTACCTTGATGATATTGTGGT
196 GTTGTTTACCTTGATGATATTGTGGT
*
12199401 TGGTTTACCAAGTTGGATTTGAGATCGGGGCACCATCAAGTTTGGGTAGTCAAGAGAAACGAGCC
1 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCAAGAGAAACGAGCC
12199466 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
66 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
*
12199531 ATGCCCTAACTACATTCTGTACCTTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
131 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
12199596 GTTGTTTACCTTGATGATATTGTGGT
196 GTTGTTTACCTTGATGATATTGTGGT
12199622 T
1 T
12199623 TATAGTAAGT
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
221 218 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (221 bp):
TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCAAGAGAAACGAGCC
AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
GTTGTTTACCTTGATGATATTGTGGT
Found at i:12203206 original size:29 final size:29
Alignment explanation
Indices: 12203166--12203224 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
12203156 GAATATAAAC
*
12203166 TATATTTTTTATTTTTAAAATACACCACA
1 TATATTTTTTATTTTTAAAAAACACCACA
*
12203195 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACCACA
12203224 T
1 T
12203225 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACCACA
Found at i:12207766 original size:5 final size:5
Alignment explanation
Indices: 12207758--12207805 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
12207748 CGAACAAATA
* *
12207758 ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG AT
12207806 AAAACTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:12211338 original size:3 final size:3
Alignment explanation
Indices: 12211330--12211370 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12211320 ATGTTTCCAC
*
12211330 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12211371 GTTTTTTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Done.