Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1511686 original size:16 final size:16
Alignment explanation
Indices: 1511646--1511686 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1511636 TTTTAAAATT
*
1511646 ATTTAAATATGTACAA
1 ATTTAAATTTGTACAA
1511662 ATTTAAATTTGCTA-AA
1 ATTTAAATTTG-TACAA
1511678 ATTTAAATT
1 ATTTAAATT
1511687 GTTAACGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTTAAATTTGTACAA
Found at i:1512463 original size:26 final size:26
Alignment explanation
Indices: 1512427--1512480 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1512417 ATCAATGCTT
1512427 TGGGTTAGACTGTTTTCTCACGTCCA
1 TGGGTTAGACTGTTTTCTCACGTCCA
1512453 TGGGTTAGACTGTTTTCTCACGTCCA
1 TGGGTTAGACTGTTTTCTCACGTCCA
1512479 TG
1 TG
1512481 AGCTGATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (26 bp):
TGGGTTAGACTGTTTTCTCACGTCCA
Found at i:1514649 original size:63 final size:62
Alignment explanation
Indices: 1514540--1514662 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
1514530 TTATATATAT
* *
1514540 TATCTATTTAAATTTGAATATTAAAAGATAATTATATACTTTGAATATTTCAAATTAAAATAA
1 TATCTATTTAAATTTGAATAGTAAAAGAT-ATTAAATACTTTGAATATTTCAAATTAAAATAA
1514603 TATCTATTTAAATTTGAATAGTAAAAGGAGT-TTAAAT-CTTTCGAATATTTCAAATTAAAA
1 TATCTATTTAAATTTGAATAGTAAAA-GA-TATTAAATACTTT-GAATATTTCAAATTAAAA
1514663 GATAATATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
62 4 0.07
63 48 0.87
64 2 0.04
65 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (62 bp):
TATCTATTTAAATTTGAATAGTAAAAGATATTAAATACTTTGAATATTTCAAATTAAAATAA
Found at i:1517284 original size:23 final size:23
Alignment explanation
Indices: 1517250--1517374 Score: 187
Period size: 23 Copynumber: 5.4 Consensus size: 23
1517240 GAGTCGAAGG
* *
1517250 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
* *
1517273 TTCTATGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
1517296 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
1517319 TTGTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
1517342 TTCTATGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
1517365 TTCTACGTGG
1 TTCTACGTGG
1517375 CACTTTGGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:1518766 original size:2 final size:2
Alignment explanation
Indices: 1518759--1518798 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1518749 TATTAAAAGA
1518759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1518799 TAAAATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1521153 original size:29 final size:29
Alignment explanation
Indices: 1521044--1521197 Score: 197
Period size: 29 Copynumber: 5.4 Consensus size: 29
1521034 AACTATTACA
*
1521044 AAAATAACACCTTTTTTGAAATAATTCCC
1 AAAATATCACCTTTTTTGAAATAATTCCC
* * * **
1521073 AAACTATCATC-TTTTTGACATAAAACCC
1 AAAATATCACCTTTTTTGAAATAATTCCC
*
1521101 AAAATATCA-CTTTTCT-AAATAATTCCC
1 AAAATATCACCTTTTTTGAAATAATTCCC
* *
1521128 ATAATATCACTTTTTTTGAAATAATTCCC
1 AAAATATCACCTTTTTTGAAATAATTCCC
*
1521157 AAAATATCACCTTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTTGAAATAATTCCC
1521186 AAAATATCACCT
1 AAAATATCACCT
1521198 AACAACAATT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 17 0.16
28 31 0.30
29 57 0.54
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATATCACCTTTTTTGAAATAATTCCC
Found at i:1528349 original size:29 final size:29
Alignment explanation
Indices: 1528297--1528450 Score: 206
Period size: 29 Copynumber: 5.4 Consensus size: 29
1528287 AACTATTACG
*
1528297 AAAATAACACCTTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
* * * *
1528326 AAACTATTACCTTTTTCGACATAATTCCT
1 AAAATATCACCTTTTTCGAAATAATTCCC
* *
1528355 AAAATATCA-C-TTTTCAAAATAATTTCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
*
1528382 AAAATATCACTTTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
*
1528411 AAAATATCA-CTTTTTTGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1528439 AAAATATCACCT
1 AAAATATCACCT
1528451 AACAACAATT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 22 0.21
28 27 0.25
29 57 0.54
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATATCACCTTTTTCGAAATAATTCCC
Found at i:1528397 original size:56 final size:57
Alignment explanation
Indices: 1528297--1528450 Score: 211
Period size: 56 Copynumber: 2.7 Consensus size: 57
1528287 AACTATTACG
* * * * *
1528297 AAAATAACACCTTTTTCGAAATAATTCCCAAACTATTACCTTTTTCGACATAATTCCT
1 AAAATATCA-CTTTTTCGAAATAATTCCCAAAATATCACCTTTTTCGAAATAATTCCC
* * *
1528355 AAAATATCAC-TTTTCAAAATAATTTCCAAAATATCACTTTTTTCGAAATAATTCCC
1 AAAATATCACTTTTTCGAAATAATTCCCAAAATATCACCTTTTTCGAAATAATTCCC
*
1528411 AAAATATCACTTTTTTGAAATAATTCCCAAAATATCACCT
1 AAAATATCACTTTTTCGAAATAATTCCCAAAATATCACCT
1528451 AACAACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
56 49 0.59
57 26 0.31
58 8 0.10
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATATCACTTTTTCGAAATAATTCCCAAAATATCACCTTTTTCGAAATAATTCCC
Found at i:1528464 original size:57 final size:55
Alignment explanation
Indices: 1528346--1528464 Score: 123
Period size: 57 Copynumber: 2.1 Consensus size: 55
1528336 CTTTTTCGAC
* * * ** *
1528346 ATAATTCCTAAAATATCACTTTTCAAAATAATTTCCAAAATATCACTTTTTTCGAA
1 ATAATTCCCAAAATATCACTTTTCAAAATAATTCCCAAAATATCAC-TCTAACAAA
**
1528402 ATAATTCCCAAAATATCACTTTTTTGAAATAATTCCCAAAATATCAC-CTAACAACA
1 ATAATTCCCAAAATATCAC-TTTTCAAAATAATTCCCAAAATATCACTCTAACAA-A
1528458 ATTAATT
1 A-TAATT
1528465 ACAAATCTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
55 3 0.06
56 20 0.38
57 29 0.56
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (55 bp):
ATAATTCCCAAAATATCACTTTTCAAAATAATTCCCAAAATATCACTCTAACAAA
Found at i:1531759 original size:15 final size:15
Alignment explanation
Indices: 1531739--1531769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1531729 AAGACTGAAA
1531739 CATACTCAAAACGAC
1 CATACTCAAAACGAC
1531754 CATACTCAAAACGAC
1 CATACTCAAAACGAC
1531769 C
1 C
1531770 CTAATGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.35, G:0.06, T:0.13
Consensus pattern (15 bp):
CATACTCAAAACGAC
Found at i:1532895 original size:31 final size:31
Alignment explanation
Indices: 1532857--1532917 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1532847 CTCCATTAGA
* *
1532857 TCTTCGGTTCCTTCCGGTTGGGCATATTTAT
1 TCTTCGGTTCCATCCCGTTGGGCATATTTAT
1532888 TCTTCGGTTCCATCCCGTTGGGCATATTTA
1 TCTTCGGTTCCATCCCGTTGGGCATATTTA
1532918 GAAGGGTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (31 bp):
TCTTCGGTTCCATCCCGTTGGGCATATTTAT
Found at i:1538431 original size:24 final size:26
Alignment explanation
Indices: 1538392--1538439 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1538382 ATATTAAAAA
1538392 TAAACATATAAAATTAAAA-TATACC
1 TAAACATATAAAATTAAAACTATACC
*
1538417 TAAACA-ATGAAATTAAAACTATA
1 TAAACATATAAAATTAAAACTATA
1538440 TATAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAACATATAAAATTAAAACTATACC
Found at i:1538445 original size:25 final size:25
Alignment explanation
Indices: 1538391--1538445 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1538381 TATATTAAAA
1538391 ATAAACATATAAAATTAAAATATAC
1 ATAAACATATAAAATTAAAATATAC
* * *
1538416 CTAAACA-ATGAAATTAAAACTATAT
1 ATAAACATATAAAATTAAAA-TATAC
1538441 ATAAA
1 ATAAA
1538446 AAAATAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAAACATATAAAATTAAAATATAC
Found at i:1540371 original size:112 final size:112
Alignment explanation
Indices: 1540226--1540788 Score: 586
Period size: 112 Copynumber: 4.9 Consensus size: 112
1540216 ATCTCATTTT
1540226 GTGATAGAA-TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
1 GTGAT-GAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
* * **
1540289 ATAAGTTCTTCTTATTACAAACTTTCTCTGGAAAAGTTGATCCATTGA
65 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGA
* * * *
1540337 GTAATGAATTCAAACAAAAGGTTAAACAAATTCTTATCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAG
**
1540402 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTTT
65 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C----C-A-----TTGA
* ** * * *
1540461 GTGAT-AGAGTCATGCAAAAGGTTGAACAAGCTCTTCTGATTATGAACTTCTTCTTTCTCTTCAG
1 GTGATGA-ATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
* *
1540525 ATAAG-TCTTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCATCT-A
65 ATGAGTTC-TTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCAT-TGA
** * * * *
1540573 GTGATGAATTTGAATAAAAGGTTAAACAAGTTCTTCTCATTATGAAATTCTTCTTACTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CCTCTTCAG
* * *
1540638 ATGAGTTCTTCTCATTATGAAC--TCTACTAGAAATGCTGATCCATTGA
65 ATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGTTGATCCATTGA
* * * * *
1540685 ATGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAA
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAG
*
1540750 ATGAGTTCTTCTCATTATGAAC--TCTACTGGAAATGTTGA
65 ATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGTTGA
1540789 AAATACTCTG
Statistics
Matches: 378, Mismatches: 51, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
110 3 0.01
111 15 0.04
112 188 0.50
113 71 0.19
114 3 0.01
117 1 0.00
118 2 0.01
119 1 0.00
122 2 0.01
123 45 0.12
124 47 0.12
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGA
Found at i:1540594 original size:236 final size:236
Alignment explanation
Indices: 1540147--1540660 Score: 732
Period size: 236 Copynumber: 2.2 Consensus size: 236
1540137 AAAGTTGAAC
* * * *
1540147 AAATTCTTC-TCTTTCTTTAGATGTGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGATGATAC
1 AAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGATGATAC
*
1540210 TGATCTATCTCATTTTGTGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
66 TGATCTATCTCATTTTGTGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
1540275 TTCTTCCTCTTCAGATAAGTTCTTCTTATTACAAACTTTCTCTGGAAAAGTTGATCCATTGAGTA
131 TTCTTCCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATTGAGTA
1540340 ATGAATTCAAACAAAAGGTTAAACAAATTCTTATCATTATG
196 ATGAATTCAAACAAAAGGTTAAACAAATTCTTATCATTATG
* * * *
1540381 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGATGC
1 AAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGATGATAC
* * ** *
1540445 TGATCTATCTCCTTTTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTGATTATGAACTT
66 TGATCTATCTCATTTTGTGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTT
* ** *
1540510 CTTCTTTCTCTTCAGATAAG-TCTTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCATCT-A
130 CTTCTTCCTCTTCAGATAAGTTC-TTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCAT-TGA
* ** * * *
1540573 GTGATGAATTTGAATAAAAGGTTAAACAAGTTCTTCTCATTATG
193 GTAATGAATTCAAACAAAAGGTTAAACAAATTCTTATCATTATG
*
1540617 AAATTCTTCTTACTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1540661 CTACTAGAAA
Statistics
Matches: 248, Mismatches: 27, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
234 8 0.03
235 73 0.29
236 166 0.67
237 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (236 bp):
AAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGATGATAC
TGATCTATCTCATTTTGTGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTTCCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATTGAGTA
ATGAATTCAAACAAAAGGTTAAACAAATTCTTATCATTATG
Found at i:1542045 original size:54 final size:54
Alignment explanation
Indices: 1541963--1542124 Score: 193
Period size: 54 Copynumber: 3.0 Consensus size: 54
1541953 ATAATCACTG
* **
1541963 GTTCGTAAAACATATGACAATTCATTCATCCTTTCTCGTGGTTTCTGCATAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCTGCATAGAT
* * * *
1542017 GTTCGTAAAACATTTGATAACACATTCATCCTTTCTTGTGGCTTCTG-ACCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCTGCA-TAGAT
* * * *
1542071 GTTCATAAAGCATTTCACAACACATTCATCATTT-TCTGTGGTTTCTGCATAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTC-GTGGTTTCTGCATAGAT
1542125 TTATGATCAA
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 2 0.02
54 87 0.97
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCTGCATAGAT
Found at i:1543123 original size:75 final size:75
Alignment explanation
Indices: 1542975--1543133 Score: 194
Period size: 75 Copynumber: 2.1 Consensus size: 75
1542965 GTATGATTAT
* * * * **
1542975 ATGGGATTTTAGTATGCCCCAGCATTTGTTAATACAGACGTTCAAAATGCGCCAACATTCTTGAT
1 ATGGGCTTTTAGTATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCTCAAT
1543040 TCTGATTGAA
66 TCTGATTGAA
* * * * *
1543050 ATGGGCTTTTAGTATGCCCCAATATTTGCTGATACAAACGTTCAAAATGTGTCAATATTC-CAAT
1 ATGGGCTTTTAGTATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCTCAA-
*
1543114 TTCTTATTGAA
65 TTCTGATTGAA
1543125 ATGGGCTTT
1 ATGGGCTTT
1543134 CAACATTCCC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 1 0.01
75 70 0.99
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (75 bp):
ATGGGCTTTTAGTATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCGCCAACATTCTCAAT
TCTGATTGAA
Found at i:1548722 original size:23 final size:22
Alignment explanation
Indices: 1548696--1548738 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1548686 TGCAAAAAAT
*
1548696 AAAAATACAAATTTAAAAATGAA
1 AAAAATACAAA-ATAAAAATGAA
*
1548719 AAAAATGCAAAATAAAAATG
1 AAAAATACAAAATAAAAATG
1548739 TAAATATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAAATACAAAATAAAAATGAA
Found at i:1548731 original size:30 final size:29
Alignment explanation
Indices: 1548683--1548742 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1548673 GCAAATATGC
* * *
1548683 AAATGCAAAAAATAAAAATACAAATTTAA
1 AAATGAAAAAAATAAAAATAAAAATGTAA
*
1548712 AAATGAAAAAAATGCAAAATAAAAATGTAA
1 AAATGAAAAAAAT-AAAAATAAAAATGTAA
1548742 A
1 A
1548743 TATGTGAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (29 bp):
AAATGAAAAAAATAAAAATAAAAATGTAA
Found at i:1550427 original size:26 final size:27
Alignment explanation
Indices: 1550389--1550443 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1550379 TAAAAACATT
*
1550389 AATAATATATATATA-AATATTATGAA
1 AATAATATATATATATAAAATTATGAA
*
1550415 AATAATA-AGTATATATAAAATTTTGAA
1 AATAATATA-TATATATAAAATTATGAA
1550442 AA
1 AA
1550444 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 13 0.52
27 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
AATAATATATATATATAAAATTATGAA
Found at i:1550427 original size:28 final size:25
Alignment explanation
Indices: 1550389--1550443 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
1550379 TAAAAACATT
1550389 AATAATATATATATAAATATTATGAA
1 AATAATATATATATAAA-ATTATGAA
*
1550415 AATAATAAGTATATATAAAATTTTGAA
1 AATAAT-A-TATATATAAAATTATGAA
1550442 AA
1 AA
1550444 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 10 0.38
28 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
AATAATATATATATAAAATTATGAA
Found at i:1550455 original size:28 final size:28
Alignment explanation
Indices: 1550396--1550465 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1550386 ATTAATAATA
* *
1550396 TATATATAAATATTATGAAAATAATAAG
1 TATATATAAATATTATGAAAAAAAGAAG
* *
1550424 TATATATAAA-ATTTTGAAAAGAAAGAAT
1 TATATATAAATATTATGAAAA-AAAGAAG
*
1550452 TATAAATTAAATAT
1 TATATA-TAAATAT
1550466 ATGGATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 9 0.26
28 19 0.56
29 4 0.12
30 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (28 bp):
TATATATAAATATTATGAAAAAAAGAAG
Found at i:1550632 original size:15 final size:16
Alignment explanation
Indices: 1550604--1550634 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1550594 AATAATGTAT
1550604 ATAAAAAATGATTTTG
1 ATAAAAAATGATTTTG
1550620 ATAAAAAAT-ATTTTG
1 ATAAAAAATGATTTTG
1550635 GGAGCCGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
ATAAAAAATGATTTTG
Found at i:1552833 original size:3 final size:3
Alignment explanation
Indices: 1552827--1552873 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
1552817 AATAATATTT
1552827 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA T-A TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA
1552873 T
1 T
1552874 CAAATGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1559668 original size:5 final size:5
Alignment explanation
Indices: 1559658--1559684 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1559648 TTTTGTTGCA
1559658 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1559685 CGATCGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1563516 original size:26 final size:26
Alignment explanation
Indices: 1563464--1563531 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
1563454 GGTCTGACGT
*
1563464 GGCAGTTTCTAGAAGGTTCAGTCAGC
1 GGCAGTTTCTAGAAGATTCAGTCAGC
* *
1563490 GGCAGTTTCTAAAAGA-TCTAGTTAGC
1 GGCAGTTTCTAGAAGATTC-AGTCAGC
*
1563516 -GCAGCTTCTAGAAGAT
1 GGCAGTTTCTAGAAGAT
1563532 GGACAGATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (26 bp):
GGCAGTTTCTAGAAGATTCAGTCAGC
Found at i:1565619 original size:14 final size:16
Alignment explanation
Indices: 1565600--1565631 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1565590 TAAGGTCAAT
1565600 ATGGATTA-TA-TGAA
1 ATGGATTAGTATTGAA
1565614 ATGGATTAGTATTGAA
1 ATGGATTAGTATTGAA
1565630 AT
1 AT
1565632 AATTTTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (16 bp):
ATGGATTAGTATTGAA
Found at i:1566514 original size:27 final size:27
Alignment explanation
Indices: 1566458--1566536 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 27
1566448 TGGGCTATTA
* * * *
1566458 AAATAAAAGTGAAT-AGTAAATGTTATG
1 AAATGAAAGTGAATGA-TACATGATACG
1566485 AAATGAAAGTGAATGATACATGATACG
1 AAATGAAAGTGAATGATACATGATACG
*
1566512 AAATGAATTAAATGAATGATACATG
1 AAATG-A--AAGTGAATGATACATG
1566537 CTATGGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 26 0.60
28 2 0.05
30 15 0.35
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.27
Consensus pattern (27 bp):
AAATGAAAGTGAATGATACATGATACG
Found at i:1570782 original size:31 final size:31
Alignment explanation
Indices: 1570747--1570807 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1570737 AATTCGGTGA
*
1570747 ATTCAATATGCCCTTCTCACTAGGAACTCCT
1 ATTCAATATGCCATTCTCACTAGGAACTCCT
* *
1570778 ATTCAATATGTCATTCTCATTAGGAACTCC
1 ATTCAATATGCCATTCTCACTAGGAACTCC
1570808 CAAACTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTCAATATGCCATTCTCACTAGGAACTCCT
Found at i:1577673 original size:58 final size:58
Alignment explanation
Indices: 1577573--1577715 Score: 155
Period size: 59 Copynumber: 2.4 Consensus size: 58
1577563 ATTATACTTG
* * *
1577573 AAGAAAAAGAAAATGAGAGAAAAGAATAAAGAGAAAAGT-AAAAAGGAAATAAACAAAA
1 AAGAAAAA-AAAATGAGAAAAAAGAATAAAGAGAAAAGTAAAAAAAGAAAGAAACAAAA
* * *
1577631 AAGAAAAAACAATGAGAAAAAAGAGATAAAGA-TAAAGATAAAAAAAGAAAGAAAGAAAA
1 AAGAAAAAAAAATGAGAAAAAAGA-ATAAAGAGAAAAG-TAAAAAAAGAAAGAAACAAAA
* * *
1577690 ATGAAAAAAAAAAGTAGGAAAAAGAA
1 AAGAAAAAAAAATG-AGAAAAAAGAA
1577716 AAACAAAGAG
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 18 0.25
58 16 0.23
59 28 0.39
60 9 0.13
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (58 bp):
AAGAAAAAAAAATGAGAAAAAAGAATAAAGAGAAAAGTAAAAAAAGAAAGAAACAAAA
Found at i:1577703 original size:22 final size:22
Alignment explanation
Indices: 1577619--1577734 Score: 78
Period size: 24 Copynumber: 5.0 Consensus size: 22
1577609 AGTAAAAAGG
*
1577619 AAAT-AAACAAAAAAGAAA-AA
1 AAATGAAAAAAAAAAGAAAGAA
* *
1577639 ACAATGAGAAAAAAGAGATAAAGATA
1 A-AATGA-AAAAAA-AAAGAAAGA-A
1577665 AAGAT-AAAAAAAGAAAGAAAGAA
1 AA-ATGAAAAAAA-AAAGAAAGAA
* *
1577688 AAATGAAAAAAAAAAGTAGGAA
1 AAATGAAAAAAAAAAGAAAGAA
1577710 AAA-GAAAAACAAAGAGAGAAAGAA
1 AAATGAAAAA-AAA-A-AGAAAGAA
1577734 A
1 A
1577735 GAAAATGAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.01
21 9 0.12
22 17 0.22
23 16 0.21
24 26 0.34
25 3 0.04
26 4 0.05
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (22 bp):
AAATGAAAAAAAAAAGAAAGAA
Found at i:1577724 original size:46 final size:50
Alignment explanation
Indices: 1577623--1577734 Score: 130
Period size: 48 Copynumber: 2.4 Consensus size: 50
1577613 AAAAGGAAAT
* * *
1577623 AAACAAA-AAAGAAA-AAACAATGAGAAAAAAGAGATAAAGATAAAGATA
1 AAACAAAGAAAGAAAGAAACAATGAAAAAAAAAAGATAAAGAAAAAGATA
*
1577671 AAA-AAAGAAAGAAAGAAA-AATGAAAAAAAAAAG-T-AGGAAAAAGA-A
1 AAACAAAGAAAGAAAGAAACAATGAAAAAAAAAAGATAAAGAAAAAGATA
*
1577716 AAACAAAGAGAGAAAGAAA
1 AAACAAAGAAAGAAAGAAA
1577735 GAAAATGAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.07
46 22 0.39
47 4 0.07
48 23 0.41
49 3 0.05
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (50 bp):
AAACAAAGAAAGAAAGAAACAATGAAAAAAAAAAGATAAAGAAAAAGATA
Found at i:1577735 original size:22 final size:20
Alignment explanation
Indices: 1577672--1577739 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1577662 ATAAAGATAA
* *
1577672 AAAAAGAAAGAAAGAAAAATG
1 AAAAA-AAAGAGAGAAAAAAG
* *
1577693 AAAAAAAAAAGTAGGAAAAAG
1 AAAAAAAAGAG-AGAAAAAAG
1577714 AAAAACAAAGAGAGAAAGAAAG
1 AAAAA-AAAGAGAGAAA-AAAG
1577736 AAAA
1 AAAA
1577740 TGAGTGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.11
21 21 0.55
22 13 0.34
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAAAAAGAGAGAAAAAAG
Found at i:1583537 original size:24 final size:24
Alignment explanation
Indices: 1583510--1583555 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1583500 CTTGACTTGA
1583510 GCCAGCTATGTTACCACGAAATGG
1 GCCAGCTATGTTACCACGAAATGG
* * * *
1583534 GCCATCTGTGTTATCAGGAAAT
1 GCCAGCTATGTTACCACGAAAT
1583556 TGTCTTATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
GCCAGCTATGTTACCACGAAATGG
Found at i:1587368 original size:18 final size:19
Alignment explanation
Indices: 1587342--1587377 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1587332 TTTCTACACA
1587342 ATAAAATAA-AAATTAAAC
1 ATAAAATAATAAATTAAAC
*
1587360 ATAATATAATAAATTAAA
1 ATAAAATAATAAATTAAA
1587378 GTAGATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAATAATAAATTAAAC
Found at i:1587949 original size:13 final size:13
Alignment explanation
Indices: 1587931--1587978 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1587921 CACTATGCTC
1587931 TTTTTTATTTTTA
1 TTTTTTATTTTTA
**
1587944 TTTTTTATTTTGG
1 TTTTTTATTTTTA
* *
1587957 TCTTTT-CTTTTA
1 TTTTTTATTTTTA
1587969 TTTTTTATTT
1 TTTTTTATTT
1587979 CAATTTGGTC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1589975 original size:8 final size:8
Alignment explanation
Indices: 1589962--1590079 Score: 80
Period size: 8 Copynumber: 14.8 Consensus size: 8
1589952 TTAATAACAA
1589962 GAGAGAGG
1 GAGAGAGG
1589970 GAGAGAGAG
1 GAGAGAG-G
1589979 G-GAGA--
1 GAGAGAGG
*
1589984 GAGGGAGG
1 GAGAGAGG
*
1589992 GAGAGAAG
1 GAGAGAGG
* *
1590000 GAGGGAGA
1 GAGAGAGG
*
1590008 GAGGGAGG
1 GAGAGAGG
*
1590016 GAGAGAAG
1 GAGAGAGG
* *
1590024 GAGGGAGA
1 GAGAGAGG
*
1590032 GAGAGGGG
1 GAGAGAGG
1590040 GAGAGAGGGG
1 GAGAGA--GG
1590050 GAGAGAGG
1 GAGAGAGG
* *
1590058 AAGGGAGG
1 GAGAGAGG
*
1590066 GAGAGAGA
1 GAGAGAGG
1590074 GAGAGA
1 GAGAGA
1590080 ATGAAACGCC
Statistics
Matches: 83, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
8 69 0.83
9 2 0.02
10 8 0.10
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:1589978 original size:12 final size:12
Alignment explanation
Indices: 1589961--1590079 Score: 117
Period size: 12 Copynumber: 10.2 Consensus size: 12
1589951 TTTAATAACA
1589961 AGAGAGA-GG-G
1 AGAGAGAGGGAG
1589971 AGAGAGAGGGAG
1 AGAGAGAGGGAG
*
1589983 AGAGGGAGGGAG
1 AGAGAGAGGGAG
1589995 AGA-AGGAGGGAG
1 AGAGA-GAGGGAG
*
1590007 AGAGGGAGGGAG
1 AGAGAGAGGGAG
1590019 AGA-AGGAGGGAG
1 AGAGA-GAGGGAG
1590031 AGAGAG-GGG-G
1 AGAGAGAGGGAG
*
1590041 AGAGAGGGGGAG
1 AGAGAGAGGGAG
1590053 AGAG-GAAGGGAG
1 AGAGAG-AGGGAG
* *
1590065 GGAGAGAGAGAG
1 AGAGAGAGGGAG
1590077 AGA
1 AGA
1590080 ATGAAACGCC
Statistics
Matches: 91, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
10 14 0.15
11 9 0.10
12 66 0.73
13 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (12 bp):
AGAGAGAGGGAG
Found at i:1590003 original size:24 final size:23
Alignment explanation
Indices: 1589961--1590079 Score: 145
Period size: 24 Copynumber: 5.1 Consensus size: 23
1589951 TTTAATAACA
*
1589961 AGAGAGAGGGAGAGA-GAGGGAG
1 AGAGGGAGGGAGAGAGGAGGGAG
1589983 AGAGGGAGGGAGAGAAGGAGGGAG
1 AGAGGGAGGGAGAG-AGGAGGGAG
1590007 AGAGGGAGGGAGAGAAGGAGGGAG
1 AGAGGGAGGGAGAG-AGGAGGGAG
1590031 AGAGAGG-GGGAGAGAGG-GGGAG
1 AGAG-GGAGGGAGAGAGGAGGGAG
* * *
1590053 AGAGGAAGGGAGGGAGAGAGAGAG
1 AGAGGGAGGGAGAGAG-GAGGGAG
1590077 AGA
1 AGA
1590080 ATGAAACGCC
Statistics
Matches: 87, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
21 1 0.01
22 30 0.34
23 5 0.06
24 49 0.56
25 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (23 bp):
AGAGGGAGGGAGAGAGGAGGGAG
Found at i:1595805 original size:20 final size:20
Alignment explanation
Indices: 1595782--1595844 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
1595772 ATCTAAATTC
1595782 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
1595802 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
1595825 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
1595845 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:1596000 original size:24 final size:27
Alignment explanation
Indices: 1595939--1595992 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
1595929 CCAATATATA
*
1595939 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
1595966 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
1595993 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:1596634 original size:9 final size:9
Alignment explanation
Indices: 1596620--1596650 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1596610 CAATACAACC
1596620 ACCACCATT
1 ACCACCATT
*
1596629 ACCACCACT
1 ACCACCATT
1596638 ACCACCATT
1 ACCACCATT
1596647 ACCA
1 ACCA
1596651 TCACCACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (9 bp):
ACCACCATT
Found at i:1596643 original size:18 final size:18
Alignment explanation
Indices: 1596617--1596686 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
1596607 CATCAATACA
1596617 ACCACCACCATTACCACC
1 ACCACCACCATTACCACC
*
1596635 ACTACCACCATTACCATCACC
1 ACCACCACCATTA-C--CACC
* *
1596656 ACCACCACCAGTACTACC
1 ACCACCACCATTACCACC
*
1596674 ATCACCACCATTA
1 ACCACCACCATTA
1596687 TCATTATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 26 0.60
19 1 0.02
20 1 0.02
21 15 0.35
ACGTcount: A:0.34, C:0.49, G:0.01, T:0.16
Consensus pattern (18 bp):
ACCACCACCATTACCACC
Found at i:1596650 original size:24 final size:24
Alignment explanation
Indices: 1596617--1596683 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1596607 CATCAATACA
* * *
1596617 ACCACCACCATTACCACCACTACC
1 ACCACTACCATCACCACCACCACC
*
1596641 ACCATTACCATCACCACCACCACC
1 ACCACTACCATCACCACCACCACC
**
1596665 AGTACTACCATCACCACCA
1 ACCACTACCATCACCACCA
1596684 TTATCATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.51, G:0.01, T:0.13
Consensus pattern (24 bp):
ACCACTACCATCACCACCACCACC
Found at i:1596695 original size:18 final size:17
Alignment explanation
Indices: 1596658--1596716 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
1596648 CCATCACCAC
* *
1596658 CACCACCAGTACTACCAT
1 CACCACCACTAC-ATCAT
* *
1596676 CACCACCATTATCATTAT
1 CACCACCACTA-CATCAT
1596694 CACCACCACTACATCAT
1 CACCACCACTACATCAT
1596711 CACCAC
1 CACCAC
1596717 TTTAATCATC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 11 0.31
18 23 0.66
19 1 0.03
ACGTcount: A:0.34, C:0.44, G:0.02, T:0.20
Consensus pattern (17 bp):
CACCACCACTACATCAT
Found at i:1598995 original size:32 final size:32
Alignment explanation
Indices: 1598954--1599020 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1598944 AAAAAGATAG
1598954 CATGAAATATCAATATAAATTAATCTCTAAAT
1 CATGAAATATCAATATAAATTAATCTCTAAAT
1598986 CATGAAATATCAATATAAATTAATCTCTAAAT
1 CATGAAATATCAATATAAATTAATCTCTAAAT
1599018 CAT
1 CAT
1599021 ATGAAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (32 bp):
CATGAAATATCAATATAAATTAATCTCTAAAT
Found at i:1600250 original size:30 final size:30
Alignment explanation
Indices: 1600191--1600273 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
1600181 TAGGATTGGT
* * *
1600191 GACTAAAAA-GTAAATTTTGAAAGTTTAGA
1 GACTAAAAATATAAATTTTAAAAATTTAGA
* *
1600220 GAC-CAAAGTATAAATTTGTAAAAATTTAGA
1 GACTAAAAATATAAATTT-TAAAAATTTAGA
*
1600250 GACTAAAAATATAAATTTTCAAAA
1 GACTAAAAATATAAATTTTAAAAA
1600274 GTTATATTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 3 0.07
29 10 0.23
30 18 0.42
31 12 0.28
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (30 bp):
GACTAAAAATATAAATTTTAAAAATTTAGA
Found at i:1610313 original size:17 final size:16
Alignment explanation
Indices: 1610282--1610315 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1610272 CATATGAGGA
1610282 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1610298 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1610315 T
1 T
1610316 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1616620 original size:23 final size:23
Alignment explanation
Indices: 1616594--1616668 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
1616584 CTCCCAAATT
1616594 TTTAACTTTTTCTTTTCTCTTTC
1 TTTAACTTTTTCTTTTCTCTTTC
* *
1616617 TTTATTCATTTT-TTTTCTCTTTC
1 TTTA-ACTTTTTCTTTTCTCTTTC
* *
1616640 ATGTTAACTTTTACTTTTTCTCTCTC
1 -T-TTAACTTTTTC-TTTTCTCTTTC
1616666 TTT
1 TTT
1616669 TACTCATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 15 0.37
24 12 0.29
25 4 0.10
26 10 0.24
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTAACTTTTTCTTTTCTCTTTC
Found at i:1620521 original size:17 final size:16
Alignment explanation
Indices: 1620490--1620523 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1620480 CACGTGAGGA
1620490 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1620506 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1620523 T
1 T
1620524 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1623581 original size:20 final size:20
Alignment explanation
Indices: 1623556--1623596 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1623546 TATTTCCACC
* *
1623556 AAATGCAACTTTATGCTCCT
1 AAATGCAACTATATGATCCT
*
1623576 AAATGCATCTATATGATCCT
1 AAATGCAACTATATGATCCT
1623596 A
1 A
1623597 TATGAGCACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (20 bp):
AAATGCAACTATATGATCCT
Found at i:1637685 original size:2 final size:2
Alignment explanation
Indices: 1637678--1637732 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1637668 CTTTTAAAAC
1637678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1637720 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1637733 CCCCCATCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1637956 original size:24 final size:24
Alignment explanation
Indices: 1637929--1638052 Score: 65
Period size: 24 Copynumber: 5.2 Consensus size: 24
1637919 TATATCAAAA
*
1637929 ATCAAAACATAAAT-CAGGTCAATT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
1637953 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
1637977 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
1638001 TTCAGATCAGAA-CCTATGTC-AGAT
1 ATCAAAACAAAATCC-AGGTCAAG-T
* * *
1638025 ATCAGATCAAAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
1638049 ATCA
1 ATCA
1638053 GATCAGAATT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
23 8 0.09
24 73 0.86
25 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:1638053 original size:24 final size:24
Alignment explanation
Indices: 1637946--1638057 Score: 129
Period size: 24 Copynumber: 4.7 Consensus size: 24
1637936 CATAAATCAG
* * *
1637946 GTCAATTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAT
* *
1637970 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
* *
1637994 GTCAAGTTTCAGATCAGAA-CCTAT
1 GTCAAGTATCAGATCAAAATCC-AT
1638018 GTC-AGATATCAGATCAAAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
1638042 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
1638058 GAATTCAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.05
24 68 0.89
25 4 0.05
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:1638077 original size:48 final size:48
Alignment explanation
Indices: 1637977--1638084 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
1637967 CAGGTCAAGT
* * ** *
1637977 ATCAGATCAGAATCCAAGTCAAGTTTCAGATCAGAACCTATGTCAGAT
1 ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAACCTAAATCAGAA
* *
1638025 ATCAGATCAAAATCCATGTCAAGTATCAGATCAGAA-TTCAAATC-GAAA
1 ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAACCT-AAATCAG-AA
1638073 ATCAGAT-AAAAT
1 ATCAGATCAAAAT
1638085 ATTCATGTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
47 7 0.14
48 44 0.86
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (48 bp):
ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAACCTAAATCAGAA
Found at i:1639191 original size:18 final size:18
Alignment explanation
Indices: 1639170--1639205 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1639160 CTTCCATCCG
*
1639170 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1639188 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1639206 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1640539 original size:15 final size:15
Alignment explanation
Indices: 1640519--1640550 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1640509 TCAACGCCGA
1640519 TCAACGATCAACGGG
1 TCAACGATCAACGGG
*
1640534 TCAACGGTCAACGGG
1 TCAACGATCAACGGG
1640549 TC
1 TC
1640551 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (15 bp):
TCAACGATCAACGGG
Found at i:1640557 original size:13 final size:13
Alignment explanation
Indices: 1640539--1640607 Score: 120
Period size: 13 Copynumber: 5.3 Consensus size: 13
1640529 ACGGGTCAAC
*
1640539 GGTCAACGGGTCG
1 GGTCAACAGGTCG
*
1640552 GGTCAACGGGTCG
1 GGTCAACAGGTCG
1640565 GGTCAACAGGTCG
1 GGTCAACAGGTCG
1640578 GGTCAACAGGTCG
1 GGTCAACAGGTCG
1640591 GGTCAACAGGTCG
1 GGTCAACAGGTCG
1640604 GGTC
1 GGTC
1640608 GGGCCAACGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:1640594 original size:18 final size:18
Alignment explanation
Indices: 1640586--1640624 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1640576 CGGGTCAACA
*
1640586 GGTCGGGTCAACAGG-TCG
1 GGTCGGGCCAAC-GGATCG
1640604 GGTCGGGCCAACGGATCG
1 GGTCGGGCCAACGGATCG
1640622 GGT
1 GGT
1640625 AAACGGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (18 bp):
GGTCGGGCCAACGGATCG
Found at i:1640608 original size:31 final size:30
Alignment explanation
Indices: 1640545--1640643 Score: 109
Period size: 31 Copynumber: 3.4 Consensus size: 30
1640535 CAACGGTCAA
1640545 CGGGTCGGGTCAACGGGTCGGGTCAACA---
1 CGGGTCGGGTCAAC-GGTCGGGTCAACAGGT
1640573 --GGTCGGGTCAACAGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAAC-GGTCGGGTCAACAGGT
* * *
1640602 CGGGTCGGGCCAACGGATCGGGTAAACGGGT
1 CGGGTCGGGTCAACGG-TCGGGTCAACAGGT
1640633 CGGGTCGGGTC
1 CGGGTCGGGTC
1640644 GGGTTATGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 25 0.42
30 2 0.03
31 33 0.55
ACGTcount: A:0.17, C:0.23, G:0.44, T:0.15
Consensus pattern (30 bp):
CGGGTCGGGTCAACGGTCGGGTCAACAGGT
Found at i:1640631 original size:26 final size:25
Alignment explanation
Indices: 1640543--1640638 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 25
1640533 GTCAACGGTC
*
1640543 AACGGGTCGGGTCAACGGGTCGGGTC
1 AACGGGTCGGGTCAAC-GGTCGGGTA
*
1640569 AACAGGTCGGGTCAACAGGTCGGGTCA
1 AACGGGTCGGGTCAAC-GGTCGGGT-A
*
1640596 ACAGGTCGGGTCGGGCCAACGGATCGGGTA
1 A-A---CGGGTCGGGTCAACGG-TCGGGTA
1640626 AACGGGTCGGGTC
1 AACGGGTCGGGTC
1640639 GGGTCGGGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 33 0.57
27 1 0.02
28 1 0.02
29 1 0.02
30 4 0.07
31 18 0.31
ACGTcount: A:0.20, C:0.23, G:0.43, T:0.15
Consensus pattern (25 bp):
AACGGGTCGGGTCAACGGTCGGGTA
Found at i:1641632 original size:9 final size:9
Alignment explanation
Indices: 1641618--1641669 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
1641608 AGATATATTA
1641618 AAATAAAAT
1 AAATAAAAT
1641627 AAATAAAAT
1 AAATAAAAT
1641636 AAATAAAA-
1 AAATAAAAT
*
1641644 AAAGAAAAAT
1 AAA-TAAAAT
1641654 AATATAATAAT
1 AA-ATAA-AAT
1641665 AAATA
1 AAATA
1641670 TTAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 21 0.57
10 7 0.19
11 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1641635 original size:14 final size:14
Alignment explanation
Indices: 1641616--1641667 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1641606 AAAGATATAT
1641616 TAAAATAAAATAAA
1 TAAAATAAAATAAA
1641630 TAAAAT-AAATAAA
1 TAAAATAAAATAAA
*
1641643 -AAAAGAAAAATAATA
1 TAAAA-TAAAATAA-A
1641658 TAATAATAAA
1 TAA-AATAAA
1641668 TATTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 12 0.39
15 1 0.03
16 5 0.16
17 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:1641758 original size:21 final size:22
Alignment explanation
Indices: 1641725--1641765 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1641715 GGTTAAAATA
1641725 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
1641747 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
1641766 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:1642500 original size:75 final size:76
Alignment explanation
Indices: 1642413--1642577 Score: 226
Period size: 76 Copynumber: 2.2 Consensus size: 76
1642403 AAGTAATAAT
* **
1642413 ATAATATTCTAAATCCTAATTAAAATACT-AAAACTTATTTAAACTAAAATAAAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCGATTTAAACTAAAATAAAAAGATAAA-AT
1642477 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
1642488 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCGATTTAAACTAAAATAAAAAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCGATTTAAACTAAAATAAAAAGATAAAATA
* * *
1642553 TAATGTTTAAA
66 AAATGATAAAA
*
1642564 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1642578 TTGAGTTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 32 0.41
76 46 0.59
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAACCGATTTAAACTAAAATAAAAAGATAAAATA
AAATGATAAAA
Found at i:1644533 original size:2 final size:2
Alignment explanation
Indices: 1644526--1644550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1644516 TGTTCGAAAG
1644526 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1644551 GCTTTTCTGG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1649219 original size:138 final size:138
Alignment explanation
Indices: 1648967--1649221 Score: 352
Period size: 138 Copynumber: 1.8 Consensus size: 138
1648957 GTTTATACTG
* * ** * *
1648967 GTTATCTATCGATTTTGTTTAATGCATAACGGTGCATTTTTGTATCAGTACTATGTGTACTTTCG
1 GTTATCGATCAATTTTGTTTAATGCATAACGGTGCATTTTCCTATCAGTACTATGAGAACTTTCG
* *
1649032 ACACTAAATGTGCAATCATGGTATTCATAATGAGTTTGTGAATCACCATTTCAATATACATATGT
66 ACACTAAATGTGCAATCATGGAATTCATAATAAGTTTGTGAATCACCATTTCAATATACATATGT
1649097 ATATAAAA
131 ATATAAAA
* * *
1649105 GTTATCGATCAATTTTGTTTAATGCATAACGGTGCATTTTCCTATCAGTATTGTGAGAACTTTTG
1 GTTATCGATCAATTTTGTTTAATGCATAACGGTGCATTTTCCTATCAGTACTATGAGAACTTTCG
* **
1649170 GCAC-AATATGTGC-ATCAATGGAATTCATAATAAGTTTGTGAATTTCCATTTC
66 ACACTAA-ATGTGCAATC-ATGGAATTCATAATAAGTTTGTGAATCACCATTTC
1649222 GGCACTTCAG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.05
138 96 0.95
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (138 bp):
GTTATCGATCAATTTTGTTTAATGCATAACGGTGCATTTTCCTATCAGTACTATGAGAACTTTCG
ACACTAAATGTGCAATCATGGAATTCATAATAAGTTTGTGAATCACCATTTCAATATACATATGT
ATATAAAA
Found at i:1657739 original size:22 final size:23
Alignment explanation
Indices: 1657688--1657740 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
1657678 TCTTTATTAT
1657688 GTTGTCAATAGTCATTCCACGGATA
1 GTTGTCAATAGTCATTCCACGG--A
*
1657713 TGTTGTCAATAGTCATTCCATGG-
1 -GTTGTCAATAGTCATTCCACGGA
1657736 GTTGT
1 GTTGT
1657741 TCCAATCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.19
26 21 0.81
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (23 bp):
GTTGTCAATAGTCATTCCACGGA
Found at i:1669110 original size:20 final size:20
Alignment explanation
Indices: 1669085--1669125 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1669075 TAAGAAAGAT
*
1669085 TCTGAATAGATACTATATTG
1 TCTGAATAGATACTACATTG
1669105 TCTGAATAGATACTACATTG
1 TCTGAATAGATACTACATTG
1669125 T
1 T
1669126 AATCACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (20 bp):
TCTGAATAGATACTACATTG
Found at i:1669807 original size:30 final size:30
Alignment explanation
Indices: 1669773--1669846 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
1669763 GTTCAAACAA
*
1669773 TGAACCAGTTTGACTGAATTGGCCTGACCC
1 TGAACCAGTTTGACTGAACTGGCCTGACCC
1669803 TGAACCAGTTTGACTGAACTGGCCTGACCC
1 TGAACCAGTTTGACTGAACTGGCCTGACCC
1669833 TGAACC-GATTTGAC
1 TGAACCAG-TTTGAC
1669847 CCGACCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (30 bp):
TGAACCAGTTTGACTGAACTGGCCTGACCC
Found at i:1670544 original size:29 final size:29
Alignment explanation
Indices: 1670511--1670573 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1670501 AATGCATACA
*
1670511 TGATTCTAT-ATGAGATTATATCCCCATCC
1 TGATTCT-TCATGAGATTAAATCCCCATCC
* **
1670540 TGATTCTTCATGGGATTAAATCCCTTTCC
1 TGATTCTTCATGAGATTAAATCCCCATCC
1670569 TGATT
1 TGATT
1670574 ATGTTTGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (29 bp):
TGATTCTTCATGAGATTAAATCCCCATCC
Found at i:1670648 original size:51 final size:49
Alignment explanation
Indices: 1670568--1670673 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 49
1670558 AATCCCTTTC
* *
1670568 CTGATTATGTTTGGGATACTCTTTAGAGGGCT-AAATCCTCTATTCTAATTT
1 CTGATTATGTTTGAGATACTCTATAGAGGG-TGAAATCCTC-ATTCTAA-TT
* * * * *
1670619 CTGATTCTGTTTGAGATTCTCTATGGAGGGTGATATCCTCATTCTGATT
1 CTGATTATGTTTGAGATACTCTATAGAGGGTGAAATCCTCATTCTAATT
1670668 CTGATT
1 CTGATT
1670674 GGGATCCTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 8 0.17
50 7 0.15
51 32 0.68
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (49 bp):
CTGATTATGTTTGAGATACTCTATAGAGGGTGAAATCCTCATTCTAATT
Found at i:1678312 original size:29 final size:29
Alignment explanation
Indices: 1678277--1678342 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1678267 GATGCATACA
* * *
1678277 TGATTCTGCATGGGATTATATCCCCTTCC
1 TGATTCTGCATGGCATTAAATCCCCGTCC
* **
1678306 TTATTCTATATGGCATTAAATCCCCGTCC
1 TGATTCTGCATGGCATTAAATCCCCGTCC
1678335 TGATTCTG
1 TGATTCTG
1678343 TTCGAGATCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (29 bp):
TGATTCTGCATGGCATTAAATCCCCGTCC
Found at i:1686323 original size:15 final size:14
Alignment explanation
Indices: 1686299--1686337 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1686289 CTTGAATTGC
*
1686299 ATTTAGATTAGTTTT
1 ATTTATATTAG-TTT
1686314 ATTTATATTAGTTT
1 ATTTATATTAGTTT
1686328 AGTTTATATT
1 A-TTTATATT
1686338 TTCATGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (14 bp):
ATTTATATTAGTTT
Found at i:1694590 original size:2 final size:2
Alignment explanation
Indices: 1694583--1694628 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1694573 ACTTTTTCTT
1694583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1694625 TA TA
1 TA TA
1694629 ATTTTATCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1698594 original size:17 final size:17
Alignment explanation
Indices: 1698572--1698614 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1698562 AGTTAAAATT
1698572 GGATTTAAAAGTTAGAA
1 GGATTTAAAAGTTAGAA
1698589 GGATTTAAAAGTTAGAA
1 GGATTTAAAAGTTAGAA
*
1698606 GGACTTAAA
1 GGATTTAAA
1698615 GAAACAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (17 bp):
GGATTTAAAAGTTAGAA
Found at i:1698784 original size:22 final size:19
Alignment explanation
Indices: 1698742--1698789 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1698732 TGACTCAAAC
*
1698742 TTTAAATTTAAACAAACTT
1 TTTAAATTTAAACAAAATT
*
1698761 TTTAAATAATTAAACAAAAAT
1 TTTAAAT--TTAAACAAAATT
*
1698782 TTTGAATT
1 TTTAAATT
1698790 AACTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (19 bp):
TTTAAATTTAAACAAAATT
Found at i:1702030 original size:3 final size:3
Alignment explanation
Indices: 1701969--1702017 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
1701959 TTCATTTAAA
*
1701969 TAT TAT T-T ATAT TAT TAC TAT TAT TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1702013 TAT TA
1 TAT TA
1702018 ATAAATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 37 0.90
4 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1703720 original size:23 final size:26
Alignment explanation
Indices: 1703688--1703737 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1703678 CATTTTCTGA
*
1703688 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1703711 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1703737 T
1 T
1703738 TTTTCTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1704531 original size:113 final size:113
Alignment explanation
Indices: 1704302--1705440 Score: 1415
Period size: 113 Copynumber: 10.0 Consensus size: 113
1704292 ATAGAATTAT
* ** * *
1704302 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTGAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**** ** * * *
1704363 ATTATGAACTTCTCTAAAAAAAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAA---CTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
*
1704414 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1704479 ATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* *
1704527 GCAAAAGGTTGCACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * * * *
1704592 CTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAA
63 CTCATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* *
1704643 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * ** *
1704708 ATTATGAACT-TGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAA
66 ATTATGAACTCT-AACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* * *
1704756 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TT-CA-GATGAGTTCTT
* * * * *
1704821 CTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAA
63 CTCATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
*
1704872 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1704937 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* * *
1704985 GCAAAAGGTTGAACAAATTTTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * * * *
1705050 CTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAA
63 CTCATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* *
1705101 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * ** *
1705166 ATTTTGAACTCGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAA
66 ATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
* * *
1705214 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TT-CA-GATGAGTTCTT
* * * *
1705279 CTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATAATGAATTTAA
63 CTCATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
*
1705330 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1705395 ATTATGAACTCAAACTGGAAAAGCTGATCCATCAAATGATGGATTT
66 ATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTT
1705441 GAATCTTTGC
Statistics
Matches: 887, Mismatches: 122, Indels: 35
0.85 0.12 0.03
Matches are distributed among these distances:
112 30 0.03
113 421 0.47
114 10 0.01
115 10 0.01
116 415 0.47
117 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTAACTGGAAATGCTGATCCATCAAATGATGAATTTAA
Found at i:1704691 original size:229 final size:228
Alignment explanation
Indices: 1704392--1705442 Score: 1715
Period size: 229 Copynumber: 4.6 Consensus size: 228
1704382 AAAAAAACTG
* * * * * *
1704392 ATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1704457 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAA-TGATGGA
* * *
1704522 TTTGAGCAAAAGGTTGCACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAG
130 TTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAG
1704587 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
195 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
1704621 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * * * *
1704686 CTTCTTCAGATGAGTTCTTCTTATTATGAACTTGAACTGGTAATGCTGGTCCATTGAATGATGAA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCA-TCAATGATGGA
** * *
1704751 TTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGATGAG
130 TTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAG
1704816 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
195 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
1704850 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1704915 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAA-TGATGGA
* * * *
1704980 TTTGAGCAAAAGGTTGAACAAATTTTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAG
130 TTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAG
1705045 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
195 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
1705079 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * * * *
1705144 CTTCTTCAGATGAGTTCTTCTTATTTTGAACTCGAACTGGTAATGCTGGTCCATTGAATGATGAA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCA-TCAATGATGGA
** * *
1705209 TTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGATGAG
130 TTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAG
*
1705274 TTCTTCTCATTATGAACTCTACCTGGCAATGCTA
195 TTCTTCTCATTATGAACTCTACCTGGCAATGTTA
1705308 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1705373 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAATGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATC-AATGATGGA
1705438 TTTGA
130 TTTGA
1705443 ATCTTTGCTA
Statistics
Matches: 756, Mismatches: 62, Indels: 8
0.92 0.08 0.01
Matches are distributed among these distances:
228 4 0.01
229 746 0.99
230 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (228 bp):
ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAATGATGGAT
TTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGT
TCTTCTCATTATGAACTCTACCTGGCAATGTTA
Found at i:1705043 original size:458 final size:458
Alignment explanation
Indices: 1704392--1705442 Score: 1976
Period size: 458 Copynumber: 2.3 Consensus size: 458
1704382 AAAAAAACTG
* * * * * *
1704392 ATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1704457 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
* *
1704522 TTTGAGCAAAAGGTTGCACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAG
131 TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAG
1704587 TTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGT
196 TTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGT
1704652 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
261 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
*
1704717 TTGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCA
326 TCGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCA
1704782 TTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
391 TTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
*
1704847 TTA
456 CTA
1704850 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1704915 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
*
1704980 TTTGAGCAAAAGGTTGAACAAATTTTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAG
131 TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAG
1705045 TTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGT
196 TTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGT
*
1705110 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTTTGAAC
261 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
1705175 TCGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCA
326 TCGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCA
1705240 TTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
391 TTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
1705305 CTA
456 CTA
1705308 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1705373 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAATGATGGA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
1705438 TTTGA
131 TTTGA
1705443 ATCTTTGCTA
Statistics
Matches: 578, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
458 578 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (458 bp):
ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA
TTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGATGAG
TTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGT
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
TCGAACTGGTAATGCTGGTCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCA
TTATGAACTTCTTCTTCCTTCTTTAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
CTA
Found at i:1706274 original size:115 final size:115
Alignment explanation
Indices: 1706145--1706459 Score: 571
Period size: 115 Copynumber: 2.7 Consensus size: 115
1706135 GATCATACAG
* *
1706145 TTCATCTTT-TAATTCCAATGATTGGTTCTGTGG-TTCCTACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATT-CAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
1706208 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
65 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
1706259 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1706324 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
1706374 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
* *
1706439 AACACTTCTAGAAGATACTAT
66 AACACTTCCAGAAGATGCTAT
1706460 GAGCACATTC
Statistics
Matches: 195, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
114 27 0.14
115 168 0.86
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
Found at i:1706469 original size:93 final size:94
Alignment explanation
Indices: 1706363--1706932 Score: 909
Period size: 93 Copynumber: 6.1 Consensus size: 94
1706353 CTTATTTCTA
* * * * * *
1706363 CTATGATCACATTCATCTTTCAAATTCAATGATTGGTTCT-GTGGTTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
* *
1706427 GATAACTCAAAGAACACTTCTAGAAGATA
66 GATAACTCAAAGAACACTTCCAGAAGATG
* * * * *
1706456 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCT-GTGGTTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
*
1706520 GATAACTCAAAGAACACTTCTAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1706549 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGG-TTCATATCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
1706613 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1706642 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCG-GGGTTCATATCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
*
1706706 GATAACTTAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1706735 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGGGGTTT-ATATCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
1706799 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
* * * *
1706828 CTATGAGCACATTCATCTTTTAAATTCAATGATTGGTTTTC-AGGGTTCATATCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
1706892 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1706921 CTATGAGCACAT
1 CTATGAGCACAT
1706933 GGCACTTGTT
Statistics
Matches: 457, Mismatches: 16, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
92 6 0.01
93 444 0.97
94 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (94 bp):
CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGAGGTTTCATATCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1707948 original size:13 final size:13
Alignment explanation
Indices: 1707930--1707998 Score: 79
Period size: 13 Copynumber: 5.1 Consensus size: 13
1707920 CTTGACCCCC
1707930 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
1707943 TTTTTCTTTTCTCT
1 TTTTTCTTTT-TCT
1707957 TTTTT-TTCTTTCTT
1 TTTTTCTT-TTTC-T
1707971 TTTTTCTTTTTTCT
1 TTTTTC-TTTTTCT
1707985 TCTTTT-TTTTTCT
1 T-TTTTCTTTTTCT
1707998 T
1 T
1707999 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
13 22 0.44
14 18 0.36
15 8 0.16
16 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:1707959 original size:20 final size:20
Alignment explanation
Indices: 1707929--1707997 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1707919 TCTTGACCCC
1707929 CTTTT-TCTTTTTCTTTTTT
1 CTTTTCTCTTTTTCTTTTTT
1707948 CTTTTCTCTTTTT-TTTCTTT
1 CTTTTCTCTTTTTCTTT-TTT
*
1707968 CTTTTTTTCTTTTTTCTTCTTTT
1 C-TTTTCTC-TTTTTCTT-TTTT
*
1707991 TTTTTCT
1 CTTTTCT
1707998 TCAAGCATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 8 0.20
20 11 0.27
21 6 0.15
22 10 0.24
23 5 0.12
24 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
CTTTTCTCTTTTTCTTTTTT
Found at i:1707961 original size:28 final size:27
Alignment explanation
Indices: 1707930--1707998 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
1707920 CTTGACCCCC
*
1707930 TTTTTCTTTTTCTTTTTTCTTTTCTCT
1 TTTTTTTTTTTCTTTTTTCTTTTCTCT
* *
1707957 TTTTTTTCTTTCTTTTTTTCTTTTTTCT
1 TTTTTTTTTTTC-TTTTTTCTTTTCTCT
*
1707985 TCTTTTTTTTTCTT
1 TTTTTTTTTTTCTT
1707999 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 12 0.33
28 24 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTTTCTTTTTTCTTTTCTCT
Found at i:1707998 original size:20 final size:20
Alignment explanation
Indices: 1707930--1707998 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 20
1707920 CTTGACCCCC
1707930 TTTTTC-TTTTTCTT-TTTT
1 TTTTTCTTTTTTCTTCTTTT
1707948 CTTTTCTCTTTTTT-TTCTTTCTT
1 -TTTT-TCTTTTTTCTTC-TT-TT
1707971 TTTTTCTTTTTTCTTCTTTT
1 TTTTTCTTTTTTCTTCTTTT
1707991 TTTTTCTT
1 TTTTTCTT
1707999 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.09
20 14 0.32
21 15 0.34
22 9 0.20
23 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTTTCTTCTTTT
Found at i:1707999 original size:13 final size:12
Alignment explanation
Indices: 1707929--1707995 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
1707919 TCTTGACCCC
*
1707929 CTTTTTCTTTTT
1 CTTTTTTTTTTT
*
1707941 CTTTTTTCTTTT
1 CTTTTTTTTTTT
*
1707953 C-TCTTTTTTTT
1 CTTTTTTTTTTT
*
1707964 CTTTCTTTTTTT
1 CTTTTTTTTTTT
*
1707976 C--TTTTTTCTT
1 CTTTTTTTTTTT
1707986 CTTTTTTTTT
1 CTTTTTTTTT
1707996 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
10 8 0.19
11 9 0.21
12 26 0.60
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:1720321 original size:22 final size:22
Alignment explanation
Indices: 1720246--1720314 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
1720236 TCAAATGTTT
*
1720246 ACGGTAAGGGAGTTGGAAAGTG
1 ACGGTAAGGGAGATGGAAAGTG
1720268 ACGGTAAGGGAGATGGAAAGTG
1 ACGGTAAGGGAGATGGAAAGTG
1720290 ACGGTAAGGGAGATGGAAAGTG
1 ACGGTAAGGGAGATGGAAAGTG
1720312 ACG
1 ACG
1720315 TAGAGGGGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.45, T:0.14
Consensus pattern (22 bp):
ACGGTAAGGGAGATGGAAAGTG
Found at i:1720407 original size:22 final size:22
Alignment explanation
Indices: 1720360--1720410 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1720350 GCATCTACTT
* *
1720360 AAAATTTTAAATTATTTTTTTG
1 AAAAGTTTAAATTATCTTTTTG
*
1720382 -AAAGTTTAATTTATCTTTTTG
1 AAAAGTTTAAATTATCTTTTTG
1720403 AAAAGTTT
1 AAAAGTTT
1720411 TAAAGGCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (22 bp):
AAAAGTTTAAATTATCTTTTTG
Found at i:1722609 original size:6 final size:6
Alignment explanation
Indices: 1722598--1722623 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1722588 TGGATCTTCT
1722598 CATTCC CATTCC CATTCC CATTCC CA
1 CATTCC CATTCC CATTCC CATTCC CA
1722624 CCTATCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CATTCC
Found at i:1724606 original size:12 final size:12
Alignment explanation
Indices: 1724589--1724622 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1724579 ATTTTGGTGA
1724589 TTTCTCTCTTTT
1 TTTCTCTCTTTT
*
1724601 TTTCTCTTTTTT
1 TTTCTCTCTTTT
*
1724613 TTTTTCTCTT
1 TTTCTCTCTT
1724623 CCATTGTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTCTCTTTT
Found at i:1724774 original size:35 final size:34
Alignment explanation
Indices: 1724680--1724776 Score: 97
Period size: 35 Copynumber: 2.8 Consensus size: 34
1724670 CTTTTCATGG
* * *
1724680 GAAAATATCTCAAGTGAGAT-TAATTATTTTTCGA
1 GAAAATATCTCAAGTGAGATAAAATT-TATTTAGA
* * *
1724714 GAAAACTGTCTCAAGTGAAACAAAATTTATTTAGA
1 GAAAA-TATCTCAAGTGAGATAAAATTTATTTAGA
*
1724749 GAAAATTATCTCAAGCGAGATAAAATTT
1 GAAAA-TATCTCAAGTGAGATAAAATTT
1724777 TTGTTTCAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
34 5 0.10
35 41 0.82
36 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (34 bp):
GAAAATATCTCAAGTGAGATAAAATTTATTTAGA
Found at i:1724942 original size:73 final size:73
Alignment explanation
Indices: 1724819--1725223 Score: 498
Period size: 72 Copynumber: 5.6 Consensus size: 73
1724809 AAACTTTTCT
*
1724819 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACCGTCTCGAGTG
1 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTG
*
1724884 AGATGAAA
66 AGACGAAA
* * * *
1724892 CTTTTCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTATTCCGAGAGAAACTATCTCGAGTG
1 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTG
*
1724957 AGACAAAA
66 AGACGAAA
* * * *
1724965 CTTTTCAACAGAAAACTAT-TCAAGCGAGATAAAAAATTTGTTCCAAGAGGAACTGTTTCGAGTG
1 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTG
*
1725029 AGACAAAA
66 AGACGAAA
*
1725037 CTTTTCAAGAGAAAACTAT-TCAAGTGAGA-AAAAATTTTGTTCCAAGAGAAACTGTCAT-GAGT
1 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTC-TCGAGT
1725099 GAGACGAAA
65 GAGACGAAA
* * * ** * *
1725108 C-TATCAAGAGAAAACTATCCCAAGCAAGATAAATTTTTTGTTTCAAAAGAAACTGTCTCGAGTG
1 CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTG
* *
1725172 AGATGATA
66 AGACGAAA
* * * * *
1725180 CTTGTTTTAAG-GGAAATTATCTCAAGTGAGATAAAATTTTTGTT
1 C-T-TTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTT
1725224 TTAAGTGAAA
Statistics
Matches: 286, Mismatches: 39, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
70 16 0.06
71 45 0.16
72 109 0.38
73 84 0.29
74 27 0.09
75 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (73 bp):
CTTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTG
AGACGAAA
Found at i:1724951 original size:38 final size:38
Alignment explanation
Indices: 1724746--1725087 Score: 194
Period size: 38 Copynumber: 9.2 Consensus size: 38
1724736 AAATTTATTT
* * *
1724746 AGAGAAAATTATCTCAAGCGAGATAAAATTTTTGTTTCA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTT-TTCCA
* * * * * ** *
1724785 AGAG-AAACTGTCTCGAGTGGGACGAAACTTTTCTCTTTTCA
1 AGAGAAAACTATCTCAAGCGAGA-TAAA-AATT-T-TTTCCA
1724826 AGAGAAAACTATCTCAAGCGAGATAAAAATTTTGTTCCA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTT-TTCCA
** * * * *
1724865 AGAG-AAACCGTCTCGAGTGAGAT-GAAA-CTTTT-CA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTTTTCCA
* *
1724899 AGAGAAAACTATCTCAAGCAAGATAAAAATTTTATTCCG
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTT-TTCCA
* * * *
1724938 AGAG-AAACTATCTCGAGTGAGA-CAAAA-CTTTT-CA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTTTTCCA
* *
1724972 ACAGAAAACTAT-TCAAGCGAGATAAAAAATTTGTTCCA
1 AGAGAAAACTATCTCAAGCGAGAT-AAAAATTTTTTCCA
* * * * * * *
1725010 AGAG-GAACTGTTTCGAGTGAGA-CAAAA-CTTTT-CA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTTTTCCA
*
1725044 AGAGAAAACTAT-TCAAGTGAGA-AAAAATTTTGTTCCA
1 AGAGAAAACTATCTCAAGCGAGATAAAAATTTT-TTCCA
1725081 AGAGAAA
1 AGAGAAA
1725088 CTGTCATGAG
Statistics
Matches: 228, Mismatches: 54, Indels: 44
0.70 0.17 0.13
Matches are distributed among these distances:
34 37 0.16
35 35 0.15
36 17 0.07
37 26 0.11
38 59 0.26
39 21 0.09
40 5 0.02
41 13 0.06
42 15 0.07
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (38 bp):
AGAGAAAACTATCTCAAGCGAGATAAAAATTTTTTCCA
Found at i:1725148 original size:143 final size:146
Alignment explanation
Indices: 1724716--1725174 Score: 498
Period size: 143 Copynumber: 3.1 Consensus size: 146
1724706 TTTTTCGAGA
* * ** * * * *
1724716 AAACTGTCTCAAGTGAAACAAAA-TTTATTTAGAGAAAATTATCTCAAGCGAGATAAAATTTTTG
1 AAACTGTCTCGAGTGAGACAAAACTTT-TCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTA
* * * * *
1724780 TTTCAAGAGAAACTGTCTCGAGTGGGACGAAACTTTTCTCTTTTCAAGAGAAAACTATCTCAAGC
65 TTCCAAGAGAAACTATCTCGAGTGAGAC-AAA------ACTTATCAAGAGAAAACTATCTCAAGC
1724845 GAGATAAAAATTTTGTTCCAAGAG
123 GAGATAAAAATTTTGTTCCAAGAG
* **
1724869 AAACCGTCTCGAGTGAGATGAAACTTTTCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTAT
1 AAACTGTCTCGAGTGAGACAAAACTTTTCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTAT
* * *
1724934 TCCGAGAGAAACTATCTCGAGTGAGACAAAACTTTTCAACAGAAAACTAT-TCAAGCGAGATAAA
66 TCCAAGAGAAACTATCTCGAGTGAGACAAAACTTATCAAGAGAAAACTATCTCAAGCGAGATAAA
*
1724998 AAATTTGTTCCAAGAG
131 AATTTTGTTCCAAGAG
* * ** *
1725014 GAACTGTTTCGAGTGAGACAAAACTTTTCAAGAGAAAACTAT-TCAAGTGAGA-AAAAATTTTGT
1 AAACTGTCTCGAGTGAGACAAAACTTTTCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTAT
* * * *
1725077 TCCAAGAGAAACTGTCAT-GAGTGAGACGAAAC-TATCAAGAGAAAACTATCCCAAGCAAGATAA
66 TCCAAGAGAAACTATC-TCGAGTGAGACAAAACTTATCAAGAGAAAACTATCTCAAGCGAGATAA
** * *
1725140 ATTTTTTGTTTCAAAAG
130 AAATTTTGTTCCAAGAG
1725157 AAACTGTCTCGAGTGAGA
1 AAACTGTCTCGAGTGAGA
1725175 TGATACTTGT
Statistics
Matches: 263, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
142 15 0.06
143 76 0.29
144 9 0.03
145 66 0.25
146 18 0.07
152 3 0.01
153 73 0.28
154 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (146 bp):
AAACTGTCTCGAGTGAGACAAAACTTTTCAAGAGAAAACTATCTCAAGCAAGATAAAAATTTTAT
TCCAAGAGAAACTATCTCGAGTGAGACAAAACTTATCAAGAGAAAACTATCTCAAGCGAGATAAA
AATTTTGTTCCAAGAG
Found at i:1727348 original size:34 final size:34
Alignment explanation
Indices: 1727310--1727421 Score: 93
Period size: 36 Copynumber: 3.2 Consensus size: 34
1727300 AGTGAGACAT
*
1727310 AATTTTTCAAGAGAAAATATCTTAAGTGAGATGA
1 AATTTTTCAAGAGAAAATATCTCAAGTGAGATGA
* * * * *
1727344 AATTTTGTTTCGAG-GAAACTGTGTCAAGTGAGACGA
1 AA--TT-TTTCAAGAGAAAATATCTCAAGTGAGATGA
* *
1727380 AATTTATT-AAAAGAAAACTATCTCAAGTGAGATAA
1 AATTT-TTCAAGAGAAAA-TATCTCAAGTGAGATGA
1727415 AATTTTT
1 AATTTTT
1727422 GTTTCGTGAG
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
33 2 0.03
34 12 0.20
35 18 0.31
36 21 0.36
37 6 0.10
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (34 bp):
AATTTTTCAAGAGAAAATATCTCAAGTGAGATGA
Found at i:1727374 original size:36 final size:36
Alignment explanation
Indices: 1727333--1727441 Score: 103
Period size: 35 Copynumber: 3.0 Consensus size: 36
1727323 AAAATATCTT
*
1727333 AAGTGAGATGAAATTTTGTTTCGAGGAAACTGTGTC
1 AAGTGAGATGAAATTTTGTTTCGAGGAAACTGTCTC
* * *** * *
1727369 AAGTGAGACGAAA-TTTATTAAAAGAAAACTATCTC
1 AAGTGAGATGAAATTTTGTTTCGAGGAAACTGTCTC
* *
1727404 AAGTGAGATAAAATTTTTGTTTCGTGAGAAACTGTCTC
1 AAGTGAGATGAAA-TTTTGTTTCGAG-GAAACTGTCTC
1727442 GAAATGATAT
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
35 26 0.49
36 12 0.23
37 6 0.11
38 9 0.17
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (36 bp):
AAGTGAGATGAAATTTTGTTTCGAGGAAACTGTCTC
Found at i:1729829 original size:26 final size:26
Alignment explanation
Indices: 1729798--1729852 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1729788 TTGATAAATG
1729798 AATGAAAATATTGCATAATATTAAAA
1 AATGAAAATATTGCATAATATTAAAA
1729824 AATGAAAATATTGCATAATATTAAAA
1 AATGAAAATATTGCATAATATTAAAA
1729850 AAT
1 AAT
1729853 AATCATGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (26 bp):
AATGAAAATATTGCATAATATTAAAA
Found at i:1732652 original size:14 final size:14
Alignment explanation
Indices: 1732615--1732665 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1732605 TCAACTTGTT
*
1732615 CGAGTCAACTCATT
1 CGAGTCAACTCATC
** *
1732629 TAAGTTAACTCATC
1 CGAGTCAACTCATC
1732643 CGAGTCAACTCATC
1 CGAGTCAACTCATC
1732657 CGAGTCAAC
1 CGAGTCAAC
1732666 CCCTTGACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (14 bp):
CGAGTCAACTCATC
Found at i:1735736 original size:16 final size:16
Alignment explanation
Indices: 1735711--1735741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1735701 TTATAAGGTG
*
1735711 TATTCGTGCAATAATT
1 TATTCATGCAATAATT
1735727 TATTCATGCAATAAT
1 TATTCATGCAATAAT
1735742 ATGAAAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
TATTCATGCAATAATT
Found at i:1738975 original size:2 final size:2
Alignment explanation
Indices: 1738968--1739013 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1738958 TCGAATACAA
1738968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1739010 AT AT
1 AT AT
1739014 GTATGTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1739018 original size:4 final size:4
Alignment explanation
Indices: 1739011--1739063 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
1739001 TATATATATA
*
1739011 TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1739059 TATG T
1 TATG T
1739064 TTGGTTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1740414 original size:131 final size:131
Alignment explanation
Indices: 1740279--1740621 Score: 375
Period size: 131 Copynumber: 2.6 Consensus size: 131
1740269 AGAAACAATA
* * * ***
1740279 TCTCACACATTAAAGCAATCATTTCTTACTCCAATCAAAATAAAGAAATATTATTATTTCTTTCT
1 TCTCACACATTAAAGCAATCATTTATTACTCCAATCAAAATAAAGAAATATAACTATTTCGCCCT
** *
1740344 AAAATTTGATATTAATTTGAGAGAAAACGATAACATATAATTATTTCCAATCGAGAATAAATGAC
66 AAAATTAAATATTAATTCGAGAGAAAACGATAACATATAATTATTTCCAATCGAGAATAAATGAC
1740409 C
131 C
** * * * * * *
1740410 TCTCATTCCTTAAATCAATCGTTTATTACTCCAATCGAAATGAAGAGATATAACTATTTCGCCCT
1 TCTCACACATTAAAGCAATCATTTATTACTCCAATCAAAATAAAGAAATATAACTATTTCGCCCT
* * *
1740475 AAAATTAAATATTAATTCGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATATATGAC
66 AAAATTAAATATTAATTCGAGAGAAAACGATAACATATAATTATTTCCAATCGAGAATAAATGAC
1740540 C
131 C
** * * * * * * * * *
1740541 TCAT-ATGCCTTAAATCAATAATTTATTACTCCAAT-ATAGATGAAGATATATTACTATTTTGTC
1 TC-TCACACATTAAAGCAATCATTTATTACTCCAATCA-AAATAAAGAAATATAACTATTTCGCC
1740604 CTAAAATTAAATATTAAT
64 CTAAAATTAAATATTAAT
1740622 CCAAGTGTTA
Statistics
Matches: 181, Mismatches: 29, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
131 180 0.99
132 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (131 bp):
TCTCACACATTAAAGCAATCATTTATTACTCCAATCAAAATAAAGAAATATAACTATTTCGCCCT
AAAATTAAATATTAATTCGAGAGAAAACGATAACATATAATTATTTCCAATCGAGAATAAATGAC
C
Found at i:1741631 original size:108 final size:108
Alignment explanation
Indices: 1741494--1741697 Score: 259
Period size: 108 Copynumber: 1.9 Consensus size: 108
1741484 CCTAACTCAG
* * ** ***
1741494 GGGGACTAAACAAGAAATATTCCAAAAAATACATAACGTGCATGAAAATGGGTAAATAACAACTT
1 GGGGACTAAACAAGAAATATCCCAAAAAATACATAACATGCACAAAAACAAGTAAATAACAACTT
1741559 TGGTCTCCACAGGTGACCAACATGA-AAAAATACGCTAACTATA
66 TGGTCTCCACAGGTGACCAACAT-ACAAAAATACGCTAACTATA
* * * * *
1741602 GGGGACTAAA-TAGCAAATATCCCACAAAATATATAGCATGCACAAAAACAAGTAAATAATAACT
1 GGGGACTAAACAAG-AAATATCCCAAAAAATACATAACATGCACAAAAACAAGTAAATAACAACT
*
1741666 TTGGTCTTCACAGGTGACCAACATACAAAAAT
65 TTGGTCTCCACAGGTGACCAACATACAAAAAT
1741698 GTTACTAACT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 3 0.04
108 78 0.96
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (108 bp):
GGGGACTAAACAAGAAATATCCCAAAAAATACATAACATGCACAAAAACAAGTAAATAACAACTT
TGGTCTCCACAGGTGACCAACATACAAAAATACGCTAACTATA
Found at i:1743479 original size:136 final size:136
Alignment explanation
Indices: 1743320--1743643 Score: 452
Period size: 136 Copynumber: 2.4 Consensus size: 136
1743310 TTCAGTATAT
* *
1743320 ATCATATTTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAATATTGAATCGAGGTAGACTTG
1 ATCAGATTTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAATATTGAATCGAGGCAGACTTG
* * * * *
1743385 TTCTATTGCTTCTTCAGGGAAGATCAAATCTGGAAAAAGAAGGGATCTGATCCGCTACTTCTTCA
66 TTCCACTACTTCTTCAGGGAAGATCAAATATGGAAAAAGAAGGGATATGATCCGCTACTTCTTCA
1743450 GGGAAA
131 GGGAAA
* * * * * * * *
1743456 ATTAGATTTGGAAACGTTAATTCATTCCACTGTTCTTCAGGGAACATTAAATCGAGGCATACTTG
1 ATCAGATTTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAATATTGAATCGAGGCAGACTTG
* *
1743521 TTCCACTACTTTTTCAGGGAAGATCAAATATGGAAAAAGAAGGGATATGCTCCGCTACTTCTTCA
66 TTCCACTACTTCTTCAGGGAAGATCAAATATGGAAAAAGAAGGGATATGATCCGCTACTTCTTCA
*
1743586 GGGAAT
131 GGGAAA
* *
1743592 ATCAGATCTGGAAATGTTGATTTATTCCACTATTCTTC-AGGAAATATTGAAT
1 ATCAGATTTGGAAATGTTGATTCATTCCACTATTCTTCAAGG-AATATTGAAT
1743644 TGAGTTCAAT
Statistics
Matches: 160, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
135 2 0.01
136 158 0.99
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (136 bp):
ATCAGATTTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAATATTGAATCGAGGCAGACTTG
TTCCACTACTTCTTCAGGGAAGATCAAATATGGAAAAAGAAGGGATATGATCCGCTACTTCTTCA
GGGAAA
Found at i:1744997 original size:11 final size:10
Alignment explanation
Indices: 1744941--1745010 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
1744931 TTGAACCCCA
*
1744941 TTTT-ATTTA
1 TTTTCATTTT
1744950 TTTT-ATTTT
1 TTTTCATTTT
1744959 ATTTTC-TTTCT
1 -TTTTCATTT-T
*
1744970 TTTTC-TATT
1 TTTTCATTTT
1744979 TTTTCATTTT
1 TTTTCATTTT
1744989 TTCTTCATTTT
1 TT-TTCATTTT
1745000 TCTTTC-TTTT
1 T-TTTCATTTT
1745010 T
1 T
1745011 CATTTTTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
9 14 0.27
10 24 0.46
11 13 0.25
12 1 0.02
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:1745017 original size:17 final size:17
Alignment explanation
Indices: 1744960--1745017 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 17
1744950 TTTTATTTTA
1744960 TTTTCTTTCTTTTTCTATT
1 TTTTCTTTCTTTTTC-A-T
1744979 TTTTCATTT-TTTCTTCAT
1 TTTTC-TTTCTTT-TTCAT
1744997 TTTTCTTTCTTTTTCAT
1 TTTTCTTTCTTTTTCAT
1745014 TTTT
1 TTTT
1745018 AATTTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
17 12 0.33
18 9 0.25
19 9 0.25
20 6 0.17
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTCAT
Found at i:1752707 original size:37 final size:38
Alignment explanation
Indices: 1752663--1752742 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
1752653 ACGAAGGAGA
* * *
1752663 AAAAATACCCAGAGAGATTCA-ATCCACA-AACAAAGAG
1 AAAAATACACAGAGAGATTCAGA-CCAAAGAAAAAAGAG
1752700 AAAAATACACAGAGAGATTCAGACCAAAGAAAAAAGAG
1 AAAAATACACAGAGAGATTCAGACCAAAGAAAAAAGAG
1752738 AAAAA
1 AAAAA
1752743 AAATATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 24 0.63
38 14 0.37
ACGTcount: A:0.60, C:0.16, G:0.15, T:0.09
Consensus pattern (38 bp):
AAAAATACACAGAGAGATTCAGACCAAAGAAAAAAGAG
Found at i:1754460 original size:24 final size:22
Alignment explanation
Indices: 1754433--1754487 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1754423 GAAATTTTCA
1754433 AATAAAAGTCATAATTATTTTTTT
1 AATAAAA-T-ATAATTATTTTTTT
* *
1754457 AATAACATATAATTGTTTTTTT
1 AATAAAATATAATTATTTTTTT
*
1754479 CAAAAAAAT
1 -AATAAAAT
1754488 GGTTATGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.50
23 7 0.27
24 6 0.23
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (22 bp):
AATAAAATATAATTATTTTTTT
Found at i:1754806 original size:19 final size:19
Alignment explanation
Indices: 1754774--1754812 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1754764 CTAGACCCGA
* *
1754774 GCTTCTATCTAAGTAAGTC
1 GCTTCGATCCAAGTAAGTC
1754793 GCTTCGATCCAAGTAAGTC
1 GCTTCGATCCAAGTAAGTC
1754812 G
1 G
1754813 GGGTGAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
GCTTCGATCCAAGTAAGTC
Found at i:1757320 original size:8 final size:8
Alignment explanation
Indices: 1757307--1757363 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
1757297 AAAAGTAAAG
1757307 AAAAAGAA
1 AAAAAGAA
1757315 AAAAAGAA
1 AAAAAGAA
**
1757323 AAAAATCA
1 AAAAAGAA
*
1757331 AAGAA-AA
1 AAAAAGAA
*
1757338 AAAAATAA
1 AAAAAGAA
1757346 AAGAAAGAA
1 AA-AAAGAA
1757355 AGAAAAGAA
1 A-AAAAGAA
1757364 GACAAGAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 5 0.12
8 22 0.55
9 12 0.30
10 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:1757333 original size:13 final size:13
Alignment explanation
Indices: 1757303--1757363 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
1757293 AGATAAAAGT
1757303 AAAGAAAAAGAAAA
1 AAAGAAAAA-AAAA
**
1757317 AAAGAAAAAAATC
1 AAAGAAAAAAAAA
1757330 AAAGAAAAAAAAATA
1 AAAG-AAAAAAAA-A
* *
1757345 AAAGAAAGAAAGA
1 AAAGAAAAAAAAA
1757358 AAAGAA
1 AAAGAA
1757364 GACAAGAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 13 0.33
14 22 0.56
15 4 0.10
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:1757339 original size:15 final size:15
Alignment explanation
Indices: 1757295--1757351 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1757285 CAAGGCGAAG
*
1757295 ATAAAAGTAAAGAAAA
1 ATAAAAG-AAAAAAAA
* *
1757311 AGAAAAAAAGAAAAAA
1 ATAAAAGAA-AAAAAA
*
1757327 ATCAAAGAAAAAAAA
1 ATAAAAGAAAAAAAA
1757342 ATAAAAGAAA
1 ATAAAAGAAA
1757352 GAAAGAAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 17 0.52
16 16 0.48
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.07
Consensus pattern (15 bp):
ATAAAAGAAAAAAAA
Found at i:1757347 original size:23 final size:23
Alignment explanation
Indices: 1757313--1757360 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1757303 AAAGAAAAAG
1757313 AAAAAAAGAAAA-AAATCAAAGAA
1 AAAAAAAGAAAAGAAA-CAAAGAA
* *
1757336 AAAAAAATAAAAGAAAGAAAGAA
1 AAAAAAAGAAAAGAAACAAAGAA
1757359 AA
1 AA
1757361 GAAGACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.04
Consensus pattern (23 bp):
AAAAAAAGAAAAGAAACAAAGAA
Found at i:1757361 original size:28 final size:27
Alignment explanation
Indices: 1757297--1757363 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
1757287 AGGCGAAGAT
* *
1757297 AAAAGTAAAGAAAAAGAAAAAAAGAAA
1 AAAAGAAAAGAAAAAAAAAAAAAGAAA
**
1757324 AAAATCAAAGAAAAAAAAATAAAAGAAA
1 AAAAGAAAAGAAAAAAAAA-AAAAGAAA
*
1757352 GAAAGAAAAGAA
1 AAAAGAAAAGAA
1757364 GACAAGAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.04
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAAAAAAAGAAA
Found at i:1757370 original size:13 final size:13
Alignment explanation
Indices: 1757298--1757372 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
1757288 GGCGAAGATA
1757298 AAAGTAAAGAAAAAG
1 AAAG-AAAG-AAAAG
*
1757313 AAAAAAAGAAAA-
1 AAAGAAAGAAAAG
*
1757325 AAATCAAAG-AAA-
1 AAA-GAAAGAAAAG
*
1757337 AAA-AAATAAAAG
1 AAAGAAAGAAAAG
1757349 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
1757362 -AAGACAAGAAA
1 AAAGA-AAGAAA
1757373 CACATGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 3 0.06
11 3 0.06
12 16 0.31
13 22 0.43
14 4 0.08
15 3 0.06
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.04
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:1758738 original size:99 final size:101
Alignment explanation
Indices: 1758510--1758731 Score: 229
Period size: 101 Copynumber: 2.2 Consensus size: 101
1758500 AAAAAATTTT
* ** * * * *
1758510 TCTCGCTTGAGATAATTTCTCTCAAAACAAATTTTGTCTCACTTGAGACATTTTCCTTTGAGATA
1 TCTCACTTGAGATGGTTTCCCTCAAAACAAACTTTGTCTCACTTGAGACATCTTCCTTTGAGAGA
** **
1758575 CAAATTTTGAGTTTGTTTCACTTGAAACAAAGTTGA
66 CAAACGTTGAAATTGTTTCACTTGAAACAAAGTTGA
* * **
1758611 TGTCACTTGAGATTGTTTTTCTCAAAACAAACTTTGTCTCACTTGAGACAGTCTTCC-TT-A-AG
1 TCTCACTTGAGATGGTTTCCCTCAAAACAAACTTTGTCTCACTTGAGACA-TCTTCCTTTGAGAG
*
1758673 ACAAACGTTGAAATTGTTTCTCTTGAAAC-AAGTTTTG-
65 ACAAACGTTGAAATTGTTTCACTTGAAACAAAG--TTGA
*
1758710 TCTCCCTTGAGATGGTTTCCCT
1 TCTCACTTGAGATGGTTTCCCT
1758732 TGAAACACAA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
98 3 0.03
99 42 0.42
100 4 0.04
101 46 0.46
102 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (101 bp):
TCTCACTTGAGATGGTTTCCCTCAAAACAAACTTTGTCTCACTTGAGACATCTTCCTTTGAGAGA
CAAACGTTGAAATTGTTTCACTTGAAACAAAGTTGA
Found at i:1758783 original size:52 final size:52
Alignment explanation
Indices: 1758727--1758838 Score: 179
Period size: 52 Copynumber: 2.2 Consensus size: 52
1758717 TGAGATGGTT
* *
1758727 TCCCTTGAAACACAAATCTCTGAGTCTGTTTCCCATGAAACAAAGTTTTGTC
1 TCCCTTGAAACACAAATATCTGAGTATGTTTCCCATGAAACAAAGTTTTGTC
* **
1758779 TCCCTTGAAACACAAATATTTGAGTATGTTTCCTTTGAAACAAAGTTTTGTC
1 TCCCTTGAAACACAAATATCTGAGTATGTTTCCCATGAAACAAAGTTTTGTC
1758831 TCCCTTGA
1 TCCCTTGA
1758839 GATAGTTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (52 bp):
TCCCTTGAAACACAAATATCTGAGTATGTTTCCCATGAAACAAAGTTTTGTC
Done.