Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:1387084 original size:4 final size:4
Alignment explanation
Indices: 1387075--1387132 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
1387065 AACGAAATTG
1387075 GAAA GAAA GAAA GAAA G-AA -AAA GAAA -AAA GGAAA GAAA -AAGA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAA-A GAAA
1387121 G-AA GAAA GAAA G
1 GAAA GAAA GAAA G
1387133 CCACGGCCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
3 12 0.26
4 30 0.64
5 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1387097 original size:18 final size:17
Alignment explanation
Indices: 1387076--1387131 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 17
1387066 ACGAAATTGG
1387076 AAAGAAAGAAAGAAAGAA
1 AAAGAAA-AAAGAAAGAA
1387094 AAAGAAAAAAGGAAAGAA
1 AAAGAAAAAA-GAAAGAA
1387112 AAAGAGAAAGAAGAAAGAA
1 AAAGA-AAA-AAGAAAGAA
1387131 A
1 A
1387132 GCCACGGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.09
18 19 0.54
19 11 0.31
20 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAAAGAA
Found at i:1388047 original size:41 final size:40
Alignment explanation
Indices: 1387999--1388117 Score: 145
Period size: 41 Copynumber: 3.0 Consensus size: 40
1387989 TTCGACTTCG
1387999 AGTCGATGAGACACTGGGTGTCAATTTACTACTTCGAATTA
1 AGTCGATGAGACACTGGGTGTCAATTTA-TACTTCGAATTA
* ** * *
1388040 ATTCGATGAGGTACTGGGTGTCAA-TT-TACTTCG-GTTT
1 AGTCGATGAGACACTGGGTGTCAATTTATACTTCGAATTA
*
1388077 AGCCGATGAGACACTGGGTGTCAATTTATTACTTCGAATTA
1 AGTCGATGAGACACTGGGTGTCAATTTA-TACTTCGAATTA
1388118 TCCGATCAGG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 22 0.35
38 9 0.14
40 9 0.14
41 23 0.37
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
AGTCGATGAGACACTGGGTGTCAATTTATACTTCGAATTA
Found at i:1388093 original size:37 final size:38
Alignment explanation
Indices: 1388002--1388104 Score: 118
Period size: 37 Copynumber: 2.7 Consensus size: 38
1387992 GACTTCGAGT
**
1388002 CGATGAGACACTGGGTGTCAATTTACTACTTCGAATTAATT
1 CGATGAGACACTGGGTGTCAA-TT--TACTTCGAATTAAGC
** * *
1388043 CGATGAGGTACTGGGTGTCAATTTACTTCG-GTTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTTCGAATTAAGC
1388080 CGATGAGACACTGGGTGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
1388105 TTACTTCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 26 0.48
38 7 0.13
40 2 0.04
41 19 0.35
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAATTTACTTCGAATTAAGC
Found at i:1393124 original size:12 final size:11
Alignment explanation
Indices: 1393107--1393153 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1393097 ATCACGAATA
1393107 TTTTTTATATAT
1 TTTTTTATA-AT
*
1393119 TTTTTTAGAAT
1 TTTTTTATAAT
*
1393130 TTTTTTATAAA
1 TTTTTTATAAT
*
1393141 TTTTATA-AAT
1 TTTTTTATAAT
1393151 TTT
1 TTT
1393154 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 5 0.17
11 17 0.57
12 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:1394919 original size:16 final size:16
Alignment explanation
Indices: 1394898--1394931 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1394888 TTTTAATTTT
* *
1394898 AAATATTGTTATATCA
1 AAATATTGATAAATCA
1394914 AAATATTGATAAATCA
1 AAATATTGATAAATCA
1394930 AA
1 AA
1394932 TTTAGACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATATTGATAAATCA
Found at i:1397075 original size:74 final size:74
Alignment explanation
Indices: 1396996--1397140 Score: 206
Period size: 74 Copynumber: 1.9 Consensus size: 74
1396986 TCCCCTATTC
* *
1396996 CATTTCCTATACTTTTTTGAAATTT-TTCCTTTATTTTATTTCCT-TCTTTTTTTTTTTTTGCA-
1 CATTTCCTATAC---TTAGAAATTTCTTCCTTCATTTTATTTCCTATCTTTTTTTTTTTTTGCAT
1397058 TTTTCCTTGTTT
63 TTTTCCTTGTTT
*
1397070 CATTTCCTATACTTAGCAATTTCTTCCTTCATTTTATTTCCTACTCTTTTTTTTTTTTTGCATTT
1 CATTTCCTATACTTAGAAATTTCTTCCTTCATTTTATTTCCTA-TCTTTTTTTTTTTTTGCATTT
1397135 TTCCTT
65 TTCCTT
1397141 TATTTTATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
71 8 0.12
72 18 0.28
74 30 0.47
75 8 0.12
ACGTcount: A:0.13, C:0.19, G:0.03, T:0.64
Consensus pattern (74 bp):
CATTTCCTATACTTAGAAATTTCTTCCTTCATTTTATTTCCTATCTTTTTTTTTTTTTGCATTTT
TCCTTGTTT
Found at i:1404090 original size:30 final size:30
Alignment explanation
Indices: 1404054--1404113 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1404044 CTTGAGGGAA
*
1404054 GAGCGGGAGCTTGTTGAGTTTACGCCAAGC
1 GAGCGGGAGCATGTTGAGTTTACGCCAAGC
1404084 GAGCGGGAGCATGTTGAGTTTACGCCAAGC
1 GAGCGGGAGCATGTTGAGTTTACGCCAAGC
1404114 TGAAACCGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (30 bp):
GAGCGGGAGCATGTTGAGTTTACGCCAAGC
Found at i:1405135 original size:2 final size:2
Alignment explanation
Indices: 1405128--1405154 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1405118 GAACAAATAA
1405128 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1405155 AGAAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1406953 original size:31 final size:32
Alignment explanation
Indices: 1406907--1406967 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
1406897 CTAACTAATA
1406907 ACATTATAAAAAGTATAAAGATCAAATTATTG
1 ACATTATAAAAAGTATAAAGATCAAATTATTG
1406939 ACATTAT-AAAAGTATAAAGATCAAATTAT
1 ACATTATAAAAAGTATAAAGATCAAATTAT
1406968 GTCAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.54, C:0.07, G:0.08, T:0.31
Consensus pattern (32 bp):
ACATTATAAAAAGTATAAAGATCAAATTATTG
Found at i:1406982 original size:31 final size:31
Alignment explanation
Indices: 1406915--1406995 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1406905 TAACATTATA
* * **
1406915 AAAAGTATAAAGATCAAATTATTGACATTAT
1 AAAAGTATAAAGATCAAATTATTCAAAAAAT
1406946 AAAAGTATAAAGATCAAATTATGTCAAAAAAT
1 AAAAGTATAAAGATCAAATTAT-TCAAAAAAT
* *
1406978 -AAAGTATATAGATTAAAT
1 AAAAGTATAAAGATCAAAT
1406996 CTCAAGTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 38 0.88
32 5 0.12
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.30
Consensus pattern (31 bp):
AAAAGTATAAAGATCAAATTATTCAAAAAAT
Found at i:1408570 original size:13 final size:14
Alignment explanation
Indices: 1408552--1408586 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1408542 AGTGTGCATA
1408552 ATAAAATTA-AAAT
1 ATAAAATTATAAAT
*
1408565 ATAAAATTATCAAT
1 ATAAAATTATAAAT
1408579 ATAAAATT
1 ATAAAATT
1408587 TTAGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAATTATAAAT
Found at i:1410620 original size:15 final size:16
Alignment explanation
Indices: 1410602--1410631 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1410592 TGACAATAAT
1410602 ACTAATA-TCAATCGA
1 ACTAATACTCAATCGA
1410617 ACTAATACTCAATCG
1 ACTAATACTCAATCG
1410632 GCAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (16 bp):
ACTAATACTCAATCGA
Found at i:1414383 original size:31 final size:32
Alignment explanation
Indices: 1414340--1414409 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
1414330 TTATTTATCA
* *
1414340 AAAT-GGTACGTTTTG-TACAAATGAATTACCG
1 AAATGGGTACG-TTTGCTACAAAAGAAATACCG
1414371 AAATGGGT-CGTTTGCTACAAAAGAAATACCG
1 AAATGGGTACGTTTGCTACAAAAGAAATACCG
1414402 AAATGGGT
1 AAATGGGT
1414410 TATTTGCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 4 0.11
31 28 0.80
32 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (32 bp):
AAATGGGTACGTTTGCTACAAAAGAAATACCG
Found at i:1414416 original size:31 final size:31
Alignment explanation
Indices: 1414351--1414422 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
1414341 AATGGTACGT
* * *
1414351 TTTG-TACAAATGAATTACCGAAATGGGTCG
1 TTTGCTACAAAAGAAATACCGAAATGGGTCA
*
1414381 TTTGCTACAAAAGAAATACCGAAATGGGTTA
1 TTTGCTACAAAAGAAATACCGAAATGGGTCA
*
1414412 TTTGCTTCAAA
1 TTTGCTACAAA
1414423 TTTTTACGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (31 bp):
TTTGCTACAAAAGAAATACCGAAATGGGTCA
Found at i:1418180 original size:116 final size:116
Alignment explanation
Indices: 1418052--1418285 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 116
1418042 AAAATGAAAT
1418052 AAATAAATGAATAAGACTATAAAAAAGTAAAAAGGTACATGTATACTTAAAAAAATTAAAAACGT
1 AAATAAATGAATAAGACTATAAAAAAGTAAAAAGGTACATGTATACTTAAAAAAATTAAAAACGT
1418117 ATATTGATATATGCATTAAAAATATGTGTATGAACTATAAAATATGATACA
66 ATATTGATATATGCATTAAAAATATGTGTATGAACTATAAAATATGATACA
*
1418168 AAATAAATGAATAAGACTATAAAAAAGTAAAAAGGTACATGTATACTTATAAAAATTAAAAACGT
1 AAATAAATGAATAAGACTATAAAAAAGTAAAAAGGTACATGTATACTTAAAAAAATTAAAAACGT
1418233 ATATTGATATATGCATTAAAAATATGTGTATGAACTATAAAATATGATACA
66 ATATTGATATATGCATTAAAAATATGTGTATGAACTATAAAATATGATACA
1418284 AA
1 AA
1418286 TATATATATA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (116 bp):
AAATAAATGAATAAGACTATAAAAAAGTAAAAAGGTACATGTATACTTAAAAAAATTAAAAACGT
ATATTGATATATGCATTAAAAATATGTGTATGAACTATAAAATATGATACA
Found at i:1418916 original size:80 final size:80
Alignment explanation
Indices: 1418818--1418974 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
1418808 GCGGATCCCC
*
1418818 CCTGGAGCGGGTCGGATCGCGCGCGGGTCATGTTGGACTAAACGGCGCCGTTTCATTTCTTATAT
1 CCTGGAGCGGGTCGGATCGCGCGCGGGTCATGTTGGACTAAACGGCGCCATTTCATTTCTTATAT
1418883 AAATAGCAAAATGAA
66 AAATAGCAAAATGAA
1418898 CCTGGAGCGGGTCGGATCGCGCGCGGGTCATGTTGGACTAAACGGCGCCATTTCATTTCTTATAT
1 CCTGGAGCGGGTCGGATCGCGCGCGGGTCATGTTGGACTAAACGGCGCCATTTCATTTCTTATAT
1418963 AAATAGCAAAAT
66 AAATAGCAAAAT
1418975 AAACAAAAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
CCTGGAGCGGGTCGGATCGCGCGCGGGTCATGTTGGACTAAACGGCGCCATTTCATTTCTTATAT
AAATAGCAAAATGAA
Found at i:1419592 original size:189 final size:189
Alignment explanation
Indices: 1419272--1419648 Score: 720
Period size: 189 Copynumber: 2.0 Consensus size: 189
1419262 GGCCTTCGAA
*
1419272 ACAAATAGGTACTTTTCTTTTCCTTTTTTTCTTTTGTTTAAAAGAGTAGTGAAACAAACAAAAAT
1 ACAAATAGGTACTTTTCTTTTCCTTTTTTTCTTTTGTTTAAAAGAGTAATGAAACAAACAAAAAT
1419337 AAATAAAGAAAAAAGGAAAATAGAAAACGCCAGAACAGAAAAGAAAAAATAGAATCTACCTTTTC
66 AAATAAAGAAAAAAGGAAAATAGAAAACGCCAGAACAGAAAAGAAAAAATAGAATCTACCTTTTC
1419402 AATTTTTCTTCTTTTTATTAAGTTGTTTTTTTTTACCCTCAATCGAAAA-AAAGACCCCC
131 AATTTTTCTTCTTTTTATTAAGTTGTTTTTTTTTACCCTCAATCGAAAAGAAA-ACCCCC
1419461 ACAAATAGGTACTTTTCTTTTCCTTTTTTTCTTTTGTTTAAAAGAGTAATGAAACAAACAAAAAT
1 ACAAATAGGTACTTTTCTTTTCCTTTTTTTCTTTTGTTTAAAAGAGTAATGAAACAAACAAAAAT
*
1419526 AAATAAAGAAAAAAGGAAAATAGAAAACGCCAGAACAGAAAAGAAAAAATGGAATCTACCTTTTC
66 AAATAAAGAAAAAAGGAAAATAGAAAACGCCAGAACAGAAAAGAAAAAATAGAATCTACCTTTTC
1419591 AATTTTTCTTCTTTTTATTAAGTTGTTTTTTTTTACCCTCAATCGAAAAGAAAACCCC
131 AATTTTTCTTCTTTTTATTAAGTTGTTTTTTTTTACCCTCAATCGAAAAGAAAACCCC
1419649 TGTTACATTT
Statistics
Matches: 185, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
189 182 0.98
190 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (189 bp):
ACAAATAGGTACTTTTCTTTTCCTTTTTTTCTTTTGTTTAAAAGAGTAATGAAACAAACAAAAAT
AAATAAAGAAAAAAGGAAAATAGAAAACGCCAGAACAGAAAAGAAAAAATAGAATCTACCTTTTC
AATTTTTCTTCTTTTTATTAAGTTGTTTTTTTTTACCCTCAATCGAAAAGAAAACCCCC
Found at i:1420473 original size:130 final size:130
Alignment explanation
Indices: 1420232--1420543 Score: 425
Period size: 130 Copynumber: 2.4 Consensus size: 130
1420222 ACATCAGGGG
* * * *
1420232 GATAAGACCTGACACGATCTCCTCTACTGTAACTTCAAAGAGATAAGAT-CCTTTATTTTAATCC
1 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
*
1420296 ACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCA-AGG
66 ACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA-G
1420360 A
130 A
1420361 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
1 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
*
1420426 GCTCCACTGTAA-CTTCAGAG-AGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA
66 ACTCCACTGTAATC-TCAG-GCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA
1420489 GA
129 GA
* * * * * * *
1420491 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 GATAAGA-C-CT-GATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1420544 TGAAATTCTT
Statistics
Matches: 163, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
129 47 0.29
130 78 0.48
131 3 0.02
132 2 0.01
133 33 0.20
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (130 bp):
GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
ACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGA
Found at i:1420508 original size:44 final size:44
Alignment explanation
Indices: 1420248--1420719 Score: 258
Period size: 44 Copynumber: 10.8 Consensus size: 44
1420238 ACCTGACACG
* * * * * *
1420248 ATCTCCTCTACTGTAA-CTTCAAAGAGATAAGATCCTTTA-TTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGAT-CTCTAGCTTCA
* * *
1420292 ATCCACTCCACTGTAATCTCAG-GCAGATAGGAT-TACTATCTTCA
1 ATCTACTCCACTGTAATCTCAGAG-AGATAAGATCT-CTAGCTTCA
* * * *
1420336 ATCTACTCCGCTGTAATCTCA-AGGAGATAAGA-C-CT-GATACG
1 ATCTACTCCACTGTAATCTCAGA-GAGATAAGATCTCTAGCTTCA
* * ** *
1420377 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCCTTAATTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCTC-TAGCTTCA
** *
1420422 ATCCGCTCCACTGTAA-CTTCAGAGAGATAGGAT-TACTAGCTTCA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCT-CTAGCTTCA
* *
1420466 ATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTGGCTTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
* * * ** * *
1420510 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT-CTA-GCTTCA
* * * * * * * *
1420556 GTCTACTCCACTGTAACCTCAGGGTGATGAGA-C-CT-GATGCG
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
** * * *
1420597 ATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGAT-CTCTAGCTTCA
** * *
1420641 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT-CTAGCTTCA
**
1420685 ATCTACTCCGTTGTAATCTCAGAGAGATAAGATCT
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT
1420720 GAAATTCTTT
Statistics
Matches: 322, Mismatches: 79, Indels: 53
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.01
41 55 0.17
42 6 0.02
43 7 0.02
44 182 0.57
45 38 0.12
46 32 0.10
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
Found at i:1420661 original size:175 final size:174
Alignment explanation
Indices: 1420213--1420766 Score: 575
Period size: 175 Copynumber: 3.2 Consensus size: 174
1420203 TTCAGTCTGT
* * * * * *
1420213 TCCACTGCAACATCAGGGGGATAAGACCTGACACGATCTCCTCTACTGTAACTTCAAAGAGATAA
1 TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
*
1420278 GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACT
66 GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGG-AGATAGGATTACTAGCTTCAATCTACT
* * * *
1420343 CCGCTGTAATCTCAAGGAGATAAGACCTG--A---TACGATCTAC
130 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
* * * * *** ** *
1420383 TCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCCGCTCCACTGTAACTTCAGAGAG
1 TCCACTGTAACCTCAGGGAGATAAGA--CC-TGA-TACGATCTACTCTACTGTAACTTCAGAGAG
* * * * * * * *
1420448 ATAGGAT--TACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTCA
62 ATAAGATCCT-TTA-TTTTAATCCACTCCACTGTAATCTCAG-GAGATAGGAT-TACTAGCTTCA
* * *
1420510 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
123 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
* * * *
1420562 TCCACTGTAACCTCAGGGTGATGAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
*
1420627 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACT
66 GATCCTTTATTTTAATCCACTCCACTGTAATCTCA-GGAGATAGGATTACTAGCTTCAATCTACT
* * * **
1420692 CCGTTGTAATCTCAGAGAGATAAGATCTGAAATTCTTTGGTCTGT
130 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
*
1420737 TCCACTGTAATCTCAGGGAGATAAGACCTG
1 TCCACTGTAACCTCAGGGAGATAAGACCTG
1420767 TATAATAAAC
Statistics
Matches: 304, Mismatches: 63, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
170 21 0.07
172 3 0.01
173 4 0.01
174 98 0.32
175 140 0.46
176 6 0.02
177 3 0.01
179 29 0.10
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (174 bp):
TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGAGATAGGATTACTAGCTTCAATCTACTC
CGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
Found at i:1432273 original size:89 final size:89
Alignment explanation
Indices: 1432122--1432299 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
1432112 AAAATAAAAA
*
1432122 ACGAAAATGGAAGTCACCACCAATCCTTTTTAAAGAGGTGTGATTGGATCACCTCGAAAAGTGGT
1 ACGAAAATGAAAGTCACCACCAATCCTTTTTAAAGAGGTGTGATTGGATCACCTCGAAAAGTGGT
1432187 TGTTTTTAATAAACAGTTTGATTT
66 TGTTTTTAATAAACAGTTTGATTT
*
1432211 ACGAAAATGAAAGTCGCCACCAATCCTTTTTAAAGAGGTGTGATTGGATCACCTCGAAAAGTGGT
1 ACGAAAATGAAAGTCACCACCAATCCTTTTTAAAGAGGTGTGATTGGATCACCTCGAAAAGTGGT
1432276 TGTTTTTAATAAACAGTTTGATTT
66 TGTTTTTAATAAACAGTTTGATTT
1432300 TATTAAAACA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (89 bp):
ACGAAAATGAAAGTCACCACCAATCCTTTTTAAAGAGGTGTGATTGGATCACCTCGAAAAGTGGT
TGTTTTTAATAAACAGTTTGATTT
Found at i:1433547 original size:14 final size:14
Alignment explanation
Indices: 1433528--1433555 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1433518 GCCAAGGACC
1433528 CGATTGAAAACGAA
1 CGATTGAAAACGAA
1433542 CGATTGAAAACGAA
1 CGATTGAAAACGAA
1433556 ATAAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
CGATTGAAAACGAA
Found at i:1433862 original size:70 final size:70
Alignment explanation
Indices: 1433728--1433868 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 70
1433718 AACGGCGCCG
*
1433728 TTTCATTTCTTATATAAATAGCAAAATGAACAAAAAAACAGTTTTAAAAACATTTTCTCAAAAAA
1 TTTCATTTCTTATATAAATAGCAAAATAAACAAAAAAACAGTTTTAAAAACATTTTCTCAAAAAA
1433793 AAGAA
66 AAGAA
1433798 TTTCATTTCTTATATAAATAGCAAAATAAACAAAAAAAACAGTTTTAAAAACATTTTCTCAAAAA
1 TTTCATTTCTTATATAAATAGCAAAATAAAC-AAAAAAACAGTTTTAAAAACATTTTCTCAAAAA
1433863 AAAGAA
65 AAAGAA
1433869 AAGAGCTCTT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 30 0.43
71 39 0.57
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (70 bp):
TTTCATTTCTTATATAAATAGCAAAATAAACAAAAAAACAGTTTTAAAAACATTTTCTCAAAAAA
AAGAA
Found at i:1435134 original size:130 final size:130
Alignment explanation
Indices: 1434893--1435204 Score: 425
Period size: 130 Copynumber: 2.4 Consensus size: 130
1434883 ACATCAGGGG
* * * *
1434893 GATAAGACCTGACACGATCTCCTCTACTGTAACTTCAAAGAGATAAGAT-CCTTTATTTTAATCC
1 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
*
1434957 ACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCA-AGG
66 ACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA-G
1435021 A
130 A
1435022 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
1 GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
*
1435087 GCTCCACTGTAA-CTTCAGAG-AGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA
66 ACTCCACTGTAATC-TCAG-GCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGA
1435150 GA
129 GA
* * * * * * *
1435152 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 GATAAGA-C-CT-GATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1435205 TGAAATTCTT
Statistics
Matches: 163, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
129 47 0.29
130 78 0.48
131 3 0.02
132 2 0.01
133 33 0.20
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (130 bp):
GATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCC
ACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGA
Found at i:1435169 original size:44 final size:44
Alignment explanation
Indices: 1434909--1435380 Score: 258
Period size: 44 Copynumber: 10.8 Consensus size: 44
1434899 ACCTGACACG
* * * * * *
1434909 ATCTCCTCTACTGTAA-CTTCAAAGAGATAAGATCCTTTA-TTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGAT-CTCTAGCTTCA
* * *
1434953 ATCCACTCCACTGTAATCTCAG-GCAGATAGGAT-TACTATCTTCA
1 ATCTACTCCACTGTAATCTCAGAG-AGATAAGATCT-CTAGCTTCA
* * * *
1434997 ATCTACTCCGCTGTAATCTCA-AGGAGATAAGA-C-CT-GATACG
1 ATCTACTCCACTGTAATCTCAGA-GAGATAAGATCTCTAGCTTCA
* * ** *
1435038 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCCTTAATTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCTC-TAGCTTCA
** *
1435083 ATCCGCTCCACTGTAA-CTTCAGAGAGATAGGAT-TACTAGCTTCA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCT-CTAGCTTCA
* *
1435127 ATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTGGCTTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
* * * ** * *
1435171 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT-CTA-GCTTCA
* * * * * * * *
1435217 GTCTACTCCACTGTAACCTCAGGGTGATGAGA-C-CT-GATGCG
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
** * * *
1435258 ATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTTA
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGAT-CTCTAGCTTCA
** * *
1435302 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT-CTAGCTTCA
**
1435346 ATCTACTCCGTTGTAATCTCAGAGAGATAAGATCT
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCT
1435381 GAAATTCTTT
Statistics
Matches: 322, Mismatches: 79, Indels: 53
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.01
41 55 0.17
42 6 0.02
43 7 0.02
44 182 0.57
45 38 0.12
46 32 0.10
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
ATCTACTCCACTGTAATCTCAGAGAGATAAGATCTCTAGCTTCA
Found at i:1435322 original size:175 final size:174
Alignment explanation
Indices: 1434874--1435427 Score: 575
Period size: 175 Copynumber: 3.2 Consensus size: 174
1434864 TTCAGTCTGT
* * * * * *
1434874 TCCACTGCAACATCAGGGGGATAAGACCTGACACGATCTCCTCTACTGTAACTTCAAAGAGATAA
1 TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
*
1434939 GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACT
66 GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGG-AGATAGGATTACTAGCTTCAATCTACT
* * * *
1435004 CCGCTGTAATCTCAAGGAGATAAGACCTG--A---TACGATCTAC
130 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
* * * * *** ** *
1435044 TCTACTGTAACTTCAGAGAGATAAGATCCCTTAATTTTAATCCGCTCCACTGTAACTTCAGAGAG
1 TCCACTGTAACCTCAGGGAGATAAGA--CC-TGA-TACGATCTACTCTACTGTAACTTCAGAGAG
* * * * * * * *
1435109 ATAGGAT--TACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTCA
62 ATAAGATCCT-TTA-TTTTAATCCACTCCACTGTAATCTCAG-GAGATAGGAT-TACTAGCTTCA
* * *
1435171 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
123 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
* * * *
1435223 TCCACTGTAACCTCAGGGTGATGAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
*
1435288 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACT
66 GATCCTTTATTTTAATCCACTCCACTGTAATCTCA-GGAGATAGGATTACTAGCTTCAATCTACT
* * * **
1435353 CCGTTGTAATCTCAGAGAGATAAGATCTGAAATTCTTTGGTCTGT
130 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
*
1435398 TCCACTGTAATCTCAGGGAGATAAGACCTG
1 TCCACTGTAACCTCAGGGAGATAAGACCTG
1435428 TATAATAAAC
Statistics
Matches: 304, Mismatches: 63, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
170 21 0.07
172 3 0.01
173 4 0.01
174 98 0.32
175 140 0.46
176 6 0.02
177 3 0.01
179 29 0.10
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (174 bp):
TCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGAGATAGGATTACTAGCTTCAATCTACTC
CGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
Found at i:1450522 original size:12 final size:12
Alignment explanation
Indices: 1450500--1450534 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1450490 AATATAAATA
1450500 AATAGGTAATAAT
1 AATA-GTAATAAT
1450513 AATAGTAATAAT
1 AATAGTAATAAT
*
1450525 AATAATAATA
1 AATAGTAATA
1450535 GGACTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:1452903 original size:22 final size:20
Alignment explanation
Indices: 1452867--1452925 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
1452857 AGCCCGGCCC
1452867 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
1452889 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
1452910 AAATATTTTAAAAATA
1 ATTTATTTTAAAAATA
1452926 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:1452934 original size:10 final size:11
Alignment explanation
Indices: 1452908--1452933 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1452898 AAAAATTAAA
1452908 AAAAATATTTT
1 AAAAATATTTT
1452919 AAAAATATTTT
1 AAAAATATTTT
1452930 AAAA
1 AAAA
1452934 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1452939 original size:17 final size:17
Alignment explanation
Indices: 1452917--1452992 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 17
1452907 AAAAAATATT
1452917 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
**
1452934 TTAAAAA-ATAAT-AAA
1 TTAAAAATATTTTAAAA
*
1452949 --AAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
1452964 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTTAAAA
* *
1452981 ATAAATATATTT
1 TTAAAAATATTT
1452993 ATTATATCTG
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
13 4 0.09
14 3 0.07
15 6 0.14
16 3 0.07
17 28 0.64
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:1456473 original size:61 final size:61
Alignment explanation
Indices: 1456378--1456498 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
1456368 CAAAGTTGCT
* * * *
1456378 CTTTTAATTTAATTCCCCAAACAGTGAAACAAAACGTTACCTGGTGTGTCAATTAGTTTCC
1 CTTTTAACTTAATTCCCCAAACAATGAAACAAAACGATACCTGGTATGTCAATTAGTTTCC
* **
1456439 CTTTTAACTTAATTCCCCCAACAATGAAACAAAACGATAGTTGGTATGTCAATTAGTTTC
1 CTTTTAACTTAATTCCCCAAACAATGAAACAAAACGATACCTGGTATGTCAATTAGTTTC
1456499 ACTTCCCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (61 bp):
CTTTTAACTTAATTCCCCAAACAATGAAACAAAACGATACCTGGTATGTCAATTAGTTTCC
Found at i:1466623 original size:5 final size:5
Alignment explanation
Indices: 1466613--1466659 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
1466603 AAAATTACAC
*
1466613 ATTTT ATTTT ATTTTT ATTTT -TTCTT CTTTCT ATTTT ATTTT ATTTT
1 ATTTT ATTTT A-TTTT ATTTT ATT-TT ATTT-T ATTTT ATTTT ATTTT
1466660 GCAGGTAGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
4 2 0.05
5 24 0.65
6 11 0.30
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:1473621 original size:28 final size:31
Alignment explanation
Indices: 1473589--1473647 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
1473579 TGATGCCTAG
*
1473589 TTGAAATG-GTAT-AATTTG-ATTGATATGC
1 TTGAAATGTGTATGAATATGAATTGATATGC
1473617 TTGAAATGTGTATGGAATATGAATTGATATG
1 TTGAAATGTGTAT-GAATATGAATTGATATG
1473648 AAATAAGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.31
29 4 0.15
31 5 0.19
32 9 0.35
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.41
Consensus pattern (31 bp):
TTGAAATGTGTATGAATATGAATTGATATGC
Found at i:1474002 original size:23 final size:25
Alignment explanation
Indices: 1473977--1474024 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1473967 ATAAATAAGA
1473977 AAAAT-ATCTC-TAGA-AATTTTCT
1 AAAATAATCTCTTAGATAATTTTCT
1473999 AAAATAATCTCTTTAGATAATTTTCT
1 AAAATAATCTC-TTAGATAATTTTCT
1474025 CTTTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
25 4 0.18
26 8 0.36
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (25 bp):
AAAATAATCTCTTAGATAATTTTCT
Found at i:1479995 original size:25 final size:25
Alignment explanation
Indices: 1479944--1479997 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1479934 GCTCTTATGG
** *
1479944 GCTTCTCGTTAATCAGCTCGCATGA
1 GCTTCTCGTTAATCAGCTCAAAAGA
*
1479969 GCTTCTCGTTATTCAGCTCAAAAGA
1 GCTTCTCGTTAATCAGCTCAAAAGA
1479994 GCTT
1 GCTT
1479998 AATATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
GCTTCTCGTTAATCAGCTCAAAAGA
Found at i:1480953 original size:30 final size:30
Alignment explanation
Indices: 1480919--1480988 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
1480909 GTGTATCTCA
*
1480919 ACCGTGTGTGACACACGGCCAAGTGATACG
1 ACCGTGTGTGACACACGGCCAAGTGACACG
** *
1480949 ACCGTACGTGACACACGGCCAGGTGACACG
1 ACCGTGTGTGACACACGGCCAAGTGACACG
**
1480979 GTCGTGTGTG
1 ACCGTGTGTG
1480989 TAACAACTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (30 bp):
ACCGTGTGTGACACACGGCCAAGTGACACG
Found at i:1482407 original size:26 final size:26
Alignment explanation
Indices: 1482388--1482461 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 26
1482378 GGCTTTTCTG
1482388 GAGCTTCTCGATTAAAGGCTCTTTGT
1 GAGCTTCTCGATTAAAGGCTCTTTGT
* * ***
1482414 GAGCTTCTTGATTAATGGCTC-TCCA
1 GAGCTTCTCGATTAAAGGCTCTTTGT
* *
1482439 GAGCTTCCCGATTAATGGCTCTT
1 GAGCTTCTCGATTAAAGGCTCTT
1482462 CGGAGGTACC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 20 0.50
26 20 0.50
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
GAGCTTCTCGATTAAAGGCTCTTTGT
Found at i:1482473 original size:25 final size:25
Alignment explanation
Indices: 1482423--1482483 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
1482413 TGAGCTTCTT
*
1482423 GATTAATGGCTCTCCAGAGCTTCCC
1 GATTAATGGCTCTCCAGAGCTACCC
* * *
1482448 GATTAATGGCTCTTCGGAGGTACCC
1 GATTAATGGCTCTCCAGAGCTACCC
*
1482473 G-TTATTGGCTC
1 GATTAATGGCTC
1482484 ACATGAGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (25 bp):
GATTAATGGCTCTCCAGAGCTACCC
Found at i:1482505 original size:24 final size:23
Alignment explanation
Indices: 1482473--1482525 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
1482463 GGAGGTACCC
1482473 GTTATTGGCTCACATGAGCTTCTT
1 GTTA-TGGCTCACATGAGCTTCTT
**
1482497 GATTATGGCTCTTATGAGCTTCTT
1 G-TTATGGCTCACATGAGCTTCTT
1482521 GTTAT
1 GTTAT
1482526 ACAACCTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 19 0.73
25 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (23 bp):
GTTATGGCTCACATGAGCTTCTT
Found at i:1488743 original size:25 final size:25
Alignment explanation
Indices: 1488715--1488786 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
1488705 CTCATTATAT
1488715 GGCTCTTCGGAGCTTCCCGATTAAA
1 GGCTCTTCGGAGCTTCCCGATTAAA
* * * * *
1488740 GGCTTTTTGTGAGCTTTCTGATTAAT
1 GGCTCTTCG-GAGCTTCCCGATTAAA
* *
1488766 GGCTCTCCGGAGCTTCTCGAT
1 GGCTCTTCGGAGCTTCCCGAT
1488787 ATGGCTCGCT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCGATTAAA
Found at i:1488792 original size:23 final size:24
Alignment explanation
Indices: 1488713--1488840 Score: 71
Period size: 25 Copynumber: 5.2 Consensus size: 24
1488703 GTCTCATTAT
* *
1488713 ATGGCTCTTCGGAGCTTCCCGATTA
1 ATGGCTCTCCGGAGCTTCTCGA-TA
* * **
1488738 AAGGCTTTTTGTGAGCTT-TCTGATTA
1 ATGGCTCTCCG-GAGCTTCTC-GA-TA
1488764 ATGGCTCTCCGGAGCTTCTCGAT-
1 ATGGCTCTCCGGAGCTTCTCGATA
* ** * *
1488787 ATGGCTCGCTTGAACTTCCCGATA
1 ATGGCTCTCCGGAGCTTCTCGATA
* *
1488811 CATGGTTATCCGGAGCTTCTCGATTA
1 -ATGGCTCTCCGGAGCTTCTCGA-TA
1488837 ATGG
1 ATGG
1488841 ATTTTCGCAG
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
23 18 0.23
24 1 0.01
25 36 0.47
26 22 0.29
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (24 bp):
ATGGCTCTCCGGAGCTTCTCGATA
Found at i:1490586 original size:78 final size:78
Alignment explanation
Indices: 1490457--1490612 Score: 224
Period size: 78 Copynumber: 2.0 Consensus size: 78
1490447 TAAACTATGT
** * * *
1490457 CATTTGTTTGAGTTAGGTACCTAAATATTTTTTTGGTCAAAACGGGTACCTAAACTTTATTCCAT
1 CATTTGTTTGAGTTAGCAACCTAAACATTTTTTTGGTCAAAACGAGCACCTAAACTTTATTCCAT
1490522 AATT-AGAATTGAC
66 AATTGA-AATTGAC
* * *
1490535 CATTTGTTTGAGTTATCAACCTAAACATTTTTTTGGTCGAAATGAGCACCTAAACTTTATTCCAT
1 CATTTGTTTGAGTTAGCAACCTAAACATTTTTTTGGTCAAAACGAGCACCTAAACTTTATTCCAT
1490600 AATTGAAATTGAC
66 AATTGAAATTGAC
1490613 ACTTATCGCT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 68 0.99
79 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (78 bp):
CATTTGTTTGAGTTAGCAACCTAAACATTTTTTTGGTCAAAACGAGCACCTAAACTTTATTCCAT
AATTGAAATTGAC
Found at i:1491075 original size:28 final size:27
Alignment explanation
Indices: 1491043--1491100 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1491033 ATTTTTAAAA
1491043 TTTAAAAGAA-TAAAAAATTATCAATTTT
1 TTTAAAA-AAGTAAAAAATTAT-AATTTT
*
1491071 TTTAAAAAAGGTATAAAATTATAATTTT
1 TTTAAAAAA-GTAAAAAATTATAATTTT
1491099 TT
1 TT
1491101 AATATCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 15 0.56
29 10 0.37
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (27 bp):
TTTAAAAAAGTAAAAAATTATAATTTT
Found at i:1495135 original size:29 final size:30
Alignment explanation
Indices: 1495081--1495154 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 30
1495071 TTAATACCAC
*
1495081 ATTTGGTACCTAAATTTGACATTTTTT-TA
1 ATTTGGTACCTAAACTTGACATTTTTTCTA
*
1495110 ATTTGGTACTTAAACTTGAC-TCTTTTTCCTA
1 ATTTGGTACCTAAACTTGACAT-TTTTT-CTA
1495141 ATTTTGGTACCTAA
1 A-TTTGGTACCTAA
1495155 TCTTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.61
31 3 0.08
32 11 0.29
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACATTTTTTCTA
Found at i:1495646 original size:59 final size:59
Alignment explanation
Indices: 1495579--1495797 Score: 195
Period size: 59 Copynumber: 3.8 Consensus size: 59
1495569 AAAAAATGCC
*
1495579 AAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGGGCTCAAAA
1 AAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGGGCACAAAA
** * * *
1495638 AAGTTTAGGTATTAAATTAGGAAAAAGTGTCAAGTTTAGGTA-CTAAATTGGGCCCAAAAA
1 AAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATC-AAATTGGGCAC-AAAA
* * * * ** *
1495698 AAGTATAGATATCAAATTA-GAAAAAAGTGTCAAGATC--G--T---ATTACGCAAAAAA
1 AAGTTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTCAGGTATCAAATTGGGCACAAAA
* * * *
1495750 AAGTTTAGGTACTAAATTAGGAAAAAGTGTCAAGCTCAGGTACCAAAT
1 AAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAAT
1495798 GTTATATTAA
Statistics
Matches: 126, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
52 28 0.22
53 11 0.09
54 1 0.01
58 2 0.02
59 56 0.44
60 28 0.22
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (59 bp):
AAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGGGCACAAAA
Found at i:1495676 original size:31 final size:31
Alignment explanation
Indices: 1495555--1495686 Score: 128
Period size: 31 Copynumber: 4.4 Consensus size: 31
1495545 AAAAAGCTTT
* *
1495555 GGTACCAAATTAGAAAAAAATGCCAAGTTTA
1 GGTACCAAATTAGGAAAAAATGTCAAGTTTA
*
1495586 GGTACCAAATTAGGAAAAAATGTCAAGTTCA
1 GGTACCAAATTAGGAAAAAATGTCAAGTTTA
* * **
1495617 GGTATCAAATTGGGCTCAAAA----AAGTTTA
1 GGTACCAAATTAGG-AAAAAATGTCAAGTTTA
** *
1495645 GGTATTAAATTAGGAAAAAGTGTCAAGTTTA
1 GGTACCAAATTAGGAAAAAATGTCAAGTTTA
*
1495676 GGTACTAAATT
1 GGTACCAAATT
1495687 GGGCCCAAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
27 3 0.04
28 18 0.22
31 57 0.70
32 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (31 bp):
GGTACCAAATTAGGAAAAAATGTCAAGTTTA
Found at i:1495727 original size:60 final size:59
Alignment explanation
Indices: 1495591--1495731 Score: 187
Period size: 60 Copynumber: 2.4 Consensus size: 59
1495581 GTTTAGGTAC
* * *
1495591 CAAATTAGGAAAAAA-TGTCAAGTTCAGGTATCAAATTGGGCTCAAAAAAGTTTAGGTAT
1 CAAATTA-GAAAAAAGTGTCAAGTTCAGGTATCAAATTGGGCCCAAAAAAGTATAGATAT
* * *
1495650 TAAATTAGGAAAAAGTGTCAAGTTTAGGTA-CTAAATTGGGCCCAAAAAAAGTATAGATAT
1 CAAATTAGAAAAAAGTGTCAAGTTCAGGTATC-AAATTGGGCCC-AAAAAAGTATAGATAT
1495710 CAAATTAGAAAAAAGTGTCAAG
1 CAAATTAGAAAAAAGTGTCAAG
1495732 ATCGTATTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
58 7 0.10
59 30 0.42
60 34 0.48
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (59 bp):
CAAATTAGAAAAAAGTGTCAAGTTCAGGTATCAAATTGGGCCCAAAAAAGTATAGATAT
Found at i:1501671 original size:24 final size:24
Alignment explanation
Indices: 1501643--1501693 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1501633 CCTCAACTTC
1501643 TTTAGATTCTTG-TTTGGCTTCTGG
1 TTTAGATTCTTGCTTT-GCTTCTGG
*
1501667 TTTAGATTCTTGCTTTGTTTCTGG
1 TTTAGATTCTTGCTTTGCTTCTGG
1501691 TTT
1 TTT
1501694 TCCATCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.59
Consensus pattern (24 bp):
TTTAGATTCTTGCTTTGCTTCTGG
Found at i:1502644 original size:15 final size:16
Alignment explanation
Indices: 1502624--1502653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1502614 CTGATATGAC
1502624 ATTATTTTT-ATTTGT
1 ATTATTTTTAATTTGT
1502639 ATTATTTTTAATTTG
1 ATTATTTTTAATTTG
1502654 GGTTAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
ATTATTTTTAATTTGT
Found at i:1502824 original size:21 final size:21
Alignment explanation
Indices: 1502798--1502841 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1502788 TACCAAAACA
1502798 AGGTTT-TAGCGGCGCTTTTTT
1 AGGTTTATAGCGGCG-TTTTTT
1502819 AGGTTTATAGCGGCGTTTTTT
1 AGGTTTATAGCGGCGTTTTTT
1502840 AG
1 AG
1502842 CGCCGCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.14, C:0.11, G:0.30, T:0.45
Consensus pattern (21 bp):
AGGTTTATAGCGGCGTTTTTT
Found at i:1503024 original size:43 final size:42
Alignment explanation
Indices: 1502976--1503238 Score: 411
Period size: 43 Copynumber: 6.1 Consensus size: 42
1502966 TTTTCTTTGC
1502976 AACGCCGA-TATAGACCATGGTCTTTAGCGGCGCTTAGCCACAA
1 AACGCC-ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCA-AA
1503019 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCACAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCA-AA
**
1503062 AACGCCACTATAGACCATGGTCTTTAATGGCGCTTAGCCAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAA
* * *
1503104 AAAGCCACTATAGACCATGGTATTTAGCGGCGCTTAGACGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAG-CCAAA
1503147 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCC-AAA
*
1503190 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTATCCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCC-AAA
1503233 AACGCC
1 AACGCC
1503239 GCTAATTTTG
Statistics
Matches: 206, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
42 37 0.18
43 169 0.82
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (42 bp):
AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAA
Found at i:1503140 original size:128 final size:128
Alignment explanation
Indices: 1502984--1503234 Score: 432
Period size: 128 Copynumber: 2.0 Consensus size: 128
1502974 GCAACGCCGA
*
1502984 TATAGACCATGGTCTTTAGCGGCGCTTAG-CCACAAAACGCCACTATAGACCATGGTCTTTAGCG
1 TATAGACCATGGTATTTAGCGGCGCTTAGACCA-AAAACGCCACTATAGACCATGGTCTTTAGCG
* *
1503048 GCGCTTAGCCACAAAACGCCACTATAGACCATGGTCTTTAATGGCGCTTAGCCAAAAAAGCCAC
65 GCGCTTAGCCAAAAAACGCCACTATAGACCATGGTCTTTAACGGCGCTTAGCCAAAAAAGCCAC
*
1503112 TATAGACCATGGTATTTAGCGGCGCTTAGACGAAAAACGCCACTATAGACCATGGTCTTTAGCGG
1 TATAGACCATGGTATTTAGCGGCGCTTAGACCAAAAACGCCACTATAGACCATGGTCTTTAGCGG
* *
1503177 CGCTTAGCCAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCTTATCCAAAAAA
66 CGCTTAGCCAAAAAACGCCACTATAGACCATGGTCTTTAACGGCGCTTAGCCAAAAAA
1503235 CGCCGCTAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
128 114 0.98
129 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (128 bp):
TATAGACCATGGTATTTAGCGGCGCTTAGACCAAAAACGCCACTATAGACCATGGTCTTTAGCGG
CGCTTAGCCAAAAAACGCCACTATAGACCATGGTCTTTAACGGCGCTTAGCCAAAAAAGCCAC
Found at i:1503557 original size:21 final size:21
Alignment explanation
Indices: 1503531--1503585 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1503521 TGCTGTTCTG
* *
1503531 CTTCCCTCGCTGTAGCCTCTA
1 CTTCCCTCGCTGCAGCCGCTA
*
1503552 CTTCCCTCGCTGCAGCCGCTG
1 CTTCCCTCGCTGCAGCCGCTA
*
1503573 CTTCTCTCGCTGC
1 CTTCCCTCGCTGC
1503586 CGCATCTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.45, G:0.18, T:0.31
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCGCTA
Found at i:1503656 original size:21 final size:21
Alignment explanation
Indices: 1503632--1503672 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1503622 CTTTCGTTGA
1503632 ACCTCAGCTTCTCTCGCTGCT
1 ACCTCAGCTTCTCTCGCTGCT
*
1503653 ACCTCTGCTTCTCTCGCTGC
1 ACCTCAGCTTCTCTCGCTGC
1503673 CGCATCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.44, G:0.15, T:0.34
Consensus pattern (21 bp):
ACCTCAGCTTCTCTCGCTGCT
Found at i:1503665 original size:87 final size:87
Alignment explanation
Indices: 1503552--1503734 Score: 248
Period size: 87 Copynumber: 2.1 Consensus size: 87
1503542 GTAGCCTCTA
* *
1503552 CTTCCCTCGCTGCAGCCGCTGCTTCTCTCGCTGCCGCATCTTCTTTAAGCTGCT-GCTGCAGTTG
1 CTTCTCTCGCTGCAGCCGCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGCAGTT-
1503616 C-TCATA-CTTTCGTTGAACCTCAG
64 CTTCATATCTTT-GTTGAACCTCAG
* * *
1503639 CTTCTCTCGCTGCTA-CCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTC
1 CTTCTCTCGCTGC-AGCCGCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGCAGTTC
*
1503703 TTCATATCTTTTTTGAACCTCAG
65 TTCATATCTTTGTTGAACCTCAG
1503726 CTTCTCTCG
1 CTTCTCTCG
1503735 ATGTTGCCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
86 2 0.02
87 79 0.92
88 5 0.06
ACGTcount: A:0.11, C:0.33, G:0.18, T:0.37
Consensus pattern (87 bp):
CTTCTCTCGCTGCAGCCGCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGCAGTTCT
TCATATCTTTGTTGAACCTCAG
Found at i:1503680 original size:21 final size:21
Alignment explanation
Indices: 1503638--1503683 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1503628 TTGAACCTCA
* *
1503638 GCTTCTCTCGCTGCTACCTCT
1 GCTTCTCTCGCTGCCACATCT
*
1503659 GCTTCTCTCGCTGCCGCATCT
1 GCTTCTCTCGCTGCCACATCT
1503680 GCTT
1 GCTT
1503684 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.41, G:0.17, T:0.37
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCACATCT
Found at i:1509701 original size:14 final size:14
Alignment explanation
Indices: 1509678--1509712 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1509668 GTGTTTAAAA
*
1509678 TTAAACTTTAATGT
1 TTAAAATTTAATGT
*
1509692 TTAAAATTTATTGT
1 TTAAAATTTAATGT
1509706 TTAAAAT
1 TTAAAAT
1509713 ATATTTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (14 bp):
TTAAAATTTAATGT
Found at i:1510133 original size:28 final size:28
Alignment explanation
Indices: 1510102--1510160 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
1510092 AAAATAATGT
*
1510102 AATTTTTAAAAATTGTTAATACAATTAA
1 AATTTTTAAAAATTGTTAATACAAATAA
1510130 AA-TTTTAAAAATTGTTAATACAAATAA
1 AATTTTTAAAAATTGTTAATACAAATAA
1510157 AATT
1 AATT
1510161 ATCTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
AATTTTTAAAAATTGTTAATACAAATAA
Found at i:1512130 original size:23 final size:23
Alignment explanation
Indices: 1512087--1512131 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1512077 TGGTTTTGTA
*
1512087 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
1512110 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
1512132 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:1512919 original size:23 final size:23
Alignment explanation
Indices: 1512876--1512920 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1512866 TGCTTTTGTA
*
1512876 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
1512899 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
1512921 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:1513900 original size:41 final size:41
Alignment explanation
Indices: 1513823--1513902 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
1513813 TTTTTACACA
* *
1513823 AACGCCGCTATAGACCCAAGAGTTACCGGCGTTTCTCCAGG
1 AACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAGG
* * *
1513864 AACGCCGCTATAGACCAGAACA-TTAGCGGTGATTCTCCA
1 AACGCCGCTATAGACC-CAACAGTTACCGGCGATTCTCCA
1513903 TAAACGCTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 30 0.91
42 3 0.09
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (41 bp):
AACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAGG
Found at i:1513909 original size:41 final size:41
Alignment explanation
Indices: 1513822--1513918 Score: 97
Period size: 41 Copynumber: 2.4 Consensus size: 41
1513812 ATTTTTACAC
* *
1513822 AAACGCCGCTATAGACCCAAGAGTTACCGGCGTTTCTCCAG
1 AAACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAG
* * * * *
1513863 GAACGCCGCTATAGACCAGAACA-TTAGCGGTGATTCTCCAT
1 AAACGCCGCTATAGACC-CAACAGTTACCGGCGATTCTCCAG
* *
1513904 AAACGCTGCTTTAGA
1 AAACGCCGCTATAGA
1513919 GCGGAGCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
41 42 0.93
42 3 0.07
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (41 bp):
AAACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAG
Found at i:1514227 original size:114 final size:113
Alignment explanation
Indices: 1514029--1514374 Score: 541
Period size: 112 Copynumber: 3.1 Consensus size: 113
1514019 GCTTAACGCC
* * * *
1514029 AAACGCCACTGAAGAACGGATTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAAT
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGC-AAAACCGCCACTAATGTTCCCAAAT
*
1514094 ATATGAAAACGGCGTCGTTCTGTGTTACTCTATTTGCGACGCTTTTTGTA
65 ATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGGCGCTTTTTGTA
*
1514144 AAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
1514209 TATGAAAACGGCGTCGTTCTGTGTTACTCCATTGCGGCGCTTTTTATA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
* * * *
1514257 AAACGCCGTTG-AGAACGGAGTTTTAGCCGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
1514321 TATGAAAACGGCGTCGTTCTTTGTGACTCTATTGCGGCGCTTTTTGTA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
1514369 AAACGC
1 AAACGC
1514375 TGCTAATGCT
Statistics
Matches: 214, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
112 99 0.46
113 25 0.12
114 55 0.26
115 35 0.16
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (113 bp):
AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
Found at i:1514500 original size:41 final size:39
Alignment explanation
Indices: 1514361--1514500 Score: 106
Period size: 40 Copynumber: 3.5 Consensus size: 39
1514351 ATTGCGGCGC
* * *
1514361 TTTTTGTAAAACGCTGCTAATGCTTGGT-TT-TAGCAGCGT
1 TTTTTGTAAAACGCCGCTAATGCTCGATATTGT-GC-GCGT
* ** * *
1514400 TTTTTATGTAGCGCCGCTAATGCTCGATATTTTGCTGCGT
1 TTTTTGTAAAACGCCGCTAATGCTCGATATTGTGC-GCGT
* *
1514440 TTTTTGTAAAATGCGGCTAATGCTCGATTATTAGTG-GCGT
1 TTTTTGTAAAACGCCGCTAATGCTCGA-TATT-GTGCGCGT
*
1514480 TTTTTGTCCAAACGCCGCTAA
1 TTTTTGT-AAAACGCCGCTAA
1514501 AAGCGCCGCT
Statistics
Matches: 78, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
39 21 0.27
40 40 0.51
41 15 0.19
42 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (39 bp):
TTTTTGTAAAACGCCGCTAATGCTCGATATTGTGCGCGT
Found at i:1515179 original size:20 final size:22
Alignment explanation
Indices: 1515138--1515179 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1515128 TTCAACCTAA
*
1515138 TCATTAAAATTGTATGTAATTT
1 TCATCAAAATTGTATGTAATTT
1515160 TCATCAAAATT-TAT-TAATTT
1 TCATCAAAATTGTATGTAATTT
1515180 GATATGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
TCATCAAAATTGTATGTAATTT
Found at i:1521646 original size:31 final size:29
Alignment explanation
Indices: 1521611--1521674 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1521601 TGACCACTTC
1521611 GTAACAAAACAATAACATAAGTGACTAAAAT
1 GTAACAAAAC-A-AACATAAGTGACTAAAAT
*** *
1521642 GTAACATTTCAAACATAAGTGTCTAAAAT
1 GTAACAAAACAAACATAAGTGACTAAAAT
1521671 GTAA
1 GTAA
1521675 TCTGAGATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.72
30 1 0.03
31 7 0.24
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (29 bp):
GTAACAAAACAAACATAAGTGACTAAAAT
Found at i:1527468 original size:31 final size:31
Alignment explanation
Indices: 1527420--1527478 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1527410 GCAGTAGTTA
*
1527420 TATACATTAAAATTTGATTTTAGTTCAAATG
1 TATACATTAAAATTTGATTTTAATTCAAATG
1527451 TATACA-TAAAATATTGATTTTAATTCAA
1 TATACATTAAAAT-TTGATTTTAATTCAA
1527479 TTCTACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
TATACATTAAAATTTGATTTTAATTCAAATG
Found at i:1528827 original size:24 final size:24
Alignment explanation
Indices: 1528800--1528851 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1528790 TTAGTAAGTC
*
1528800 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1528824 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1528848 AAAT
1 AAAT
1528852 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1530796 original size:24 final size:24
Alignment explanation
Indices: 1530769--1530820 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1530759 TTAGTAAGTC
*
1530769 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1530793 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1530817 AAAT
1 AAAT
1530821 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1533460 original size:31 final size:31
Alignment explanation
Indices: 1533425--1533494 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
1533415 AACTTAACAA
* *
1533425 TTTAGTGACTTAAATAAAAATTTTCGAATAG
1 TTTAGTGACTTAAATAAAAACTTTCAAATAG
*
1533456 TTTAGTGACTTGAATAAAAACTTTCAAATAG
1 TTTAGTGACTTAAATAAAAACTTTCAAATAG
1533487 TTTAGTGA
1 TTTAGTGA
1533495 TCATTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTAGTGACTTAAATAAAAACTTTCAAATAG
Found at i:1537167 original size:42 final size:42
Alignment explanation
Indices: 1537116--1537360 Score: 377
Period size: 42 Copynumber: 5.8 Consensus size: 42
1537106 GTTTACAAAC
* *
1537116 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1537158 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1537200 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-GTAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AA
* * * *
1537242 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
1537284 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A
*
1537326 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1537361 TTTTTTTTCT
Statistics
Matches: 187, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.01
42 185 0.99
43 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:1537268 original size:126 final size:126
Alignment explanation
Indices: 1537127--1537360 Score: 416
Period size: 126 Copynumber: 1.9 Consensus size: 126
1537117 AAAACGCCGT
*
1537127 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1537192 GCTT-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
66 GCTTAAG-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
*
1537253 TAAAGACCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
**
1537318 GCTTAAGGGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
66 GCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1537361 TTTTTTTTCT
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
126 101 0.98
127 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (126 bp):
TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
GCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
Found at i:1537416 original size:84 final size:83
Alignment explanation
Indices: 1537116--1537447 Score: 369
Period size: 84 Copynumber: 4.0 Consensus size: 83
1537106 GTTTACAAAC
* * *
1537116 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-TAAAAAACGCCGCTAAAGATCATGT
1537181 TCTTTAGCGGCGCTTAGAA
65 TCTTTAGCGGCGCTTAGAA
* * * * *
1537200 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCACTAAAGACCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAT-AAAAAACGCCGCTAAAGATCATGT
*
1537265 TCTTTAGCGGCGCTTAGGA
65 TCTTTAGCGGCGCTTAGAA
*
1537284 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGGGAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATA--AAAAACGCCGCTAAAGATCATG
* ****
1537348 TTCTTTAGCGGCGTTTTTTTT
64 TTCTTTAGCGGCG-CTTAGAA
** * * ** * * * * *
1537369 CTAATCGCCGCTAAAGAACATGTTCTTTAGTGGCATTTTTTACAAACGCCGCAAAAGAACATGTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAAAAAACGCCGCTAAAGATCATGTT
*
1537434 CTTTAGTGGCGCTT
66 CTTTAGCGGCGCTT
1537448 TTATACAAAA
Statistics
Matches: 210, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
82 1 0.00
83 2 0.01
84 173 0.82
85 34 0.16
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (83 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAAAAAACGCCGCTAAAGATCATGTT
CTTTAGCGGCGCTTAGAA
Found at i:1537416 original size:126 final size:126
Alignment explanation
Indices: 1537127--1537447 Score: 394
Period size: 126 Copynumber: 2.5 Consensus size: 126
1537117 AAAACGCCGT
* * * *
1537127 TAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1537192 GCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
66 GCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
* *
1537253 TAAAGACCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
** * * ***** *
1537318 GCTTA-AGGGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTCTAATCGCCGC
66 GCTTAGA-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAAT-GCCAC
* **** * * *
1537380 TAAAGAACATGTTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAAAGAACATGTTCTTTAGTGGC
1 TAAAGAACATGTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1537444 GCTT
66 GCTT
1537448 TTATACAAAA
Statistics
Matches: 171, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
125 1 0.01
126 145 0.85
127 25 0.15
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (126 bp):
TAAAGAACATGTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
GCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCAC
Found at i:1537841 original size:21 final size:21
Alignment explanation
Indices: 1537773--1537843 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1537763 TTTTGCTCTG
* *
1537773 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
1537794 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
1537815 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
1537836 CTCTGCTT
1 CTCTGCTT
1537844 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:1543317 original size:18 final size:18
Alignment explanation
Indices: 1543294--1543484 Score: 73
Period size: 18 Copynumber: 11.0 Consensus size: 18
1543284 AATTGCAATG
1543294 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
1543312 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
1543330 GTAAGTTAAATGTAAG-T-T
1 GTAAGTT--ATGTAAGTTAT
*
1543348 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
1543367 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
*
1543385 GT-A-TTGTGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
1543399 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
1543417 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
*
1543433 -TATGTATTATGTAAG-T-T
1 GTAAG--TTATGTAAGTTAT
*
1543450 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
1543469 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
1543485 TATGTATTGT
Statistics
Matches: 135, Mismatches: 7, Indels: 64
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.04
15 11 0.08
16 18 0.13
17 9 0.07
18 66 0.49
19 21 0.16
20 4 0.03
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:1543342 original size:11 final size:9
Alignment explanation
Indices: 1543294--1543484 Score: 73
Period size: 7 Copynumber: 22.0 Consensus size: 9
1543284 AATTGCAATG
1543294 GTAAGTTAT
1 GTAAGTTAT
1543303 GTAAGTTAT
1 GTAAGTTAT
1543312 GTAAGTTAAAT
1 GTAAGTT--AT
1543323 GT-A-TTAT
1 GTAAGTTAT
1543330 GTAAGTTAAAT
1 GTAAGTT--AT
1543341 GTAAG-T-T
1 GTAAGTTAT
1543348 GTAAGTTAT
1 GTAAGTTAT
*
1543357 -TATGTATTAT
1 GTAAG--TTAT
1543367 GTAAG-T-T
1 GTAAGTTAT
1543374 GTAAGTTAAAT
1 GTAAGTT--AT
*
1543385 GT-A-TTGT
1 GTAAGTTAT
1543392 GTAAG-T-T
1 GTAAGTTAT
1543399 GTAAGTTAAAT
1 GTAAGTT--AT
1543410 GT-A-TTAT
1 GTAAGTTAT
1543417 GTAAG-T-T
1 GTAAGTTAT
1543424 GTAAGTTAT
1 GTAAGTTAT
*
1543433 -TATGTATTAT
1 GTAAG--TTAT
1543443 GTAAG-T-T
1 GTAAGTTAT
1543450 GTAAGTTAT
1 GTAAGTTAT
*
1543459 -TATGTATTAT
1 GTAAG--TTAT
1543469 GTAAG-T-T
1 GTAAGTTAT
1543476 GTAAGTTAT
1 GTAAGTTAT
1543485 TATGTATTGT
Statistics
Matches: 140, Mismatches: 7, Indels: 70
0.65 0.03 0.32
Matches are distributed among these distances:
7 47 0.34
8 23 0.16
9 28 0.20
10 16 0.11
11 26 0.19
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:1543373 original size:26 final size:26
Alignment explanation
Indices: 1543339--1543693 Score: 502
Period size: 26 Copynumber: 14.1 Consensus size: 26
1543329 TGTAAGTTAA
1543339 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
1543365 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
1543390 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
1543415 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
1543441 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
1543467 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
1543493 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
1543519 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
1543545 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
1543570 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
1543588 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
1543613 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
1543639 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
1543666 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
1543692 AT
1 AT
1543694 TTAATAAAAT
Statistics
Matches: 303, Mismatches: 14, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 91 0.30
26 168 0.55
27 15 0.05
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:1543617 original size:18 final size:18
Alignment explanation
Indices: 1543553--1543674 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
1543543 TTGTGTAAGT
1543553 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
* *
1543571 TGTCAGTCAAATGTATTATGTAA
1 TGTAAGTTAAATG---TAT-T-A
1543594 GTTGTAAGTTAAATGTATTA
1 --TGTAAGTTAAATGTATTA
*
1543614 TGTAAGTTGTAA-GTTATTA
1 TGTAAGTT-AAATG-TATTA
*
1543633 TGT-A-TT--ATGTAAGTAA
1 TGTAAGTTAAATGT-A-TTA
1543649 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
1543667 TGTAAGTT
1 TGTAAGTT
1543675 GTAAGTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 32
0.68 0.06 0.27
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 5 0.06
17 3 0.04
18 33 0.41
19 11 0.14
20 5 0.06
21 4 0.05
22 4 0.05
23 1 0.01
25 11 0.14
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:1543812 original size:73 final size:73
Alignment explanation
Indices: 1543729--1543953 Score: 423
Period size: 73 Copynumber: 3.1 Consensus size: 73
1543719 AACATTACTA
1543729 ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1 ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1543794 ATATTTTT
66 ATATTTTT
1543802 ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1 ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1543867 ATATTTTTT
66 ATA-TTTTT
*
1543876 TTATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1 ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
1543941 ATATTTTT
66 ATATTTTT
*
1543949 TTATA
1 ATATA
1543954 TTTTATTTTA
Statistics
Matches: 150, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
73 78 0.52
74 72 0.48
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (73 bp):
ATATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCAC
ATATTTTT
Found at i:1543862 original size:41 final size:41
Alignment explanation
Indices: 1543815--1543936 Score: 118
Period size: 41 Copynumber: 3.2 Consensus size: 41
1543805 TAATTATTAA
1543815 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
1 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
** * * * *
1543856 TAATA-TT--CCACAT---ATTTT-TTTT-ATAAT-TATTAA
1 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATT-T
1543889 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
1 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
1543930 TAATATT
1 TAATATT
1543937 CCACATATTT
Statistics
Matches: 59, Mismatches: 12, Indels: 20
0.65 0.13 0.22
Matches are distributed among these distances:
32 3 0.05
33 9 0.15
34 6 0.10
35 5 0.08
36 3 0.05
38 3 0.05
39 5 0.08
40 6 0.10
41 16 0.27
42 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (41 bp):
TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
Found at i:1543918 original size:74 final size:74
Alignment explanation
Indices: 1543730--1543950 Score: 426
Period size: 74 Copynumber: 3.0 Consensus size: 74
1543720 ACATTACTAA
1543730 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
*
1543795 TA-TTTTTA
66 TATTTTTTT
1543803 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1543868 TATTTTTTT
66 TATTTTTTT
1543877 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1543942 TATTTTTTT
66 TATTTTTTT
1543951 ATATTTTATT
Statistics
Matches: 146, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
73 67 0.46
74 79 0.54
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (74 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTTT
Found at i:1544118 original size:13 final size:13
Alignment explanation
Indices: 1544100--1544170 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
1544090 ATTTATAATT
1544100 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
1544113 ATTTAAGTAACAT
1 ATTTAAGTAATAA
1544126 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
1544139 ATTTAAGTAACAT
1 ATTTAAGTAATAA
1544152 ATTTAAGTAATAA
1 ATTTAAGTAATAA
1544165 ATTTAA
1 ATTTAA
1544171 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:1544129 original size:26 final size:26
Alignment explanation
Indices: 1544099--1544170 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
1544089 TATTTATAAT
1544099 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
1544125 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
1544151 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
1544171 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:1544197 original size:17 final size:17
Alignment explanation
Indices: 1544175--1544473 Score: 161
Period size: 17 Copynumber: 16.6 Consensus size: 17
1544165 ATTTAAACAA
1544175 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
1544192 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
1544209 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
1544226 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* * *
1544249 ATTTAAGTAATTAAT-A
1 ATTTTAGTAAGTAATGT
* *
1544265 AATTTA--AA-CAA---
1 ATTTTAGTAAGTAATGT
1544276 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
1544293 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
1544310 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
1544327 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* *
1544350 ATTTTAG-AAATAAATTT
1 ATTTTAGTAAGT-AATGT
*
1544367 AAACAAATTTATGTAAGTAATGT
1 -----ATTTTA-GTAAGTAATGT
1544390 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
1544407 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
1544424 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
1544447 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
1544464 ATTTTAGTAA
1 ATTTTAGTAA
1544474 TAAATTTAAC
Statistics
Matches: 224, Mismatches: 20, Indels: 76
0.70 0.06 0.24
Matches are distributed among these distances:
11 5 0.02
13 4 0.02
14 4 0.02
16 10 0.04
17 137 0.61
18 5 0.02
22 5 0.02
23 48 0.21
24 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:1544221 original size:57 final size:57
Alignment explanation
Indices: 1544142--1544482 Score: 375
Period size: 57 Copynumber: 6.5 Consensus size: 57
1544132 GTAATAAATT
** *
1544142 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1544199 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTA--TT--
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
* * *
1544252 TAAGTAAT-TA----A-T-A-AATTTAAACA-AATTTT-AGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAA-ACAAATTTTAGTAAGTAATGTATTTTAG
1544300 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
* *
1544357 -AAATAA---A-TTTA--AACAAATTT-----A----T-GTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
*
1544397 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1544454 TAAGTAATGTATTTTAGTAATAAATTTAA
1 TAAGTAATGTATTTTAGTAATAAATTTAA
1544483 CATTCAATCG
Statistics
Matches: 238, Mismatches: 14, Indels: 64
0.75 0.04 0.20
Matches are distributed among these distances:
40 18 0.08
41 6 0.03
44 14 0.06
45 16 0.07
46 4 0.02
47 9 0.04
48 9 0.04
49 2 0.01
50 8 0.03
52 7 0.03
53 10 0.04
54 1 0.00
55 4 0.02
56 17 0.07
57 113 0.47
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (57 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
Found at i:1544236 original size:40 final size:40
Alignment explanation
Indices: 1544192--1544302 Score: 177
Period size: 44 Copynumber: 2.7 Consensus size: 40
1544182 TAAGTAATGT
1544192 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
1544232 ATTTTAGTAAGTAATGTATTTAAGTAATTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTT---T-AGTAATAAATTTAAACAA
1544276 ATTTTAGTAAGTAATGTATTTTAGTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAA
1544303 GTAATGTATT
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
40 25 0.38
41 1 0.02
43 1 0.02
44 38 0.58
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:1544278 original size:101 final size:100
Alignment explanation
Indices: 1544159--1544461 Score: 533
Period size: 101 Copynumber: 3.0 Consensus size: 100
1544149 CATATTTAAG
1544159 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
1 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
*
1544224 TTAAACAAATTTTAGTAAGTAATGTATTTAAGTAA
66 TTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
1544259 TTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1 -TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1544324 TTTAAACAAATTTTAGTAAGTAATGTATTTTAG--A
65 TTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
1544358 -AATAAATTTAAACAAA-TTTATGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1 TAATAAATTTAAACAAATTTTA-GTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
*
1544421 TTTAAACAAATTTTAGTAAGTAATTTATTTTAGTAA
65 TTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
1544457 GTAAT
1 -TAAT
1544462 GTATTTTAGT
Statistics
Matches: 195, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
96 4 0.02
97 90 0.46
99 2 0.01
101 99 0.51
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (100 bp):
TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
TTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
Found at i:1544340 original size:40 final size:40
Alignment explanation
Indices: 1544293--1544399 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
1544283 TAAGTAATGT
1544293 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
1544333 ATTTTAGTAAGTAATGTATTTTAGAAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1544373 A-TTTATGTAAGTAATGTATTTTAGTAA
1 ATTTTA-GTAAGTAATGTATTTTAGTAA
1544400 GTAATGTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 4 0.06
40 60 0.94
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:1544453 original size:97 final size:97
Alignment explanation
Indices: 1544142--1544450 Score: 521
Period size: 97 Copynumber: 3.1 Consensus size: 97
1544132 GTAATAAATT
** *
1544142 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
1 TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
1544207 GTATTTTAGTAATAAATTTAAACAAATTTTAG
66 GTATTTTAGTAATAAATTTAAACAAATTTTAG
1544239 TAAGTAATGTATTTAAGTAATTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAG
1 TAAGTAATGTATTTAAG--A--AATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAG
1544304 TAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
62 TAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
*
1544340 TAAGTAATGTATTTTAGAAATAAATTTAAACAAA-TTTATGTAAGTAATGTATTTTAGTAAGTAA
1 TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTA-GTAAGTAATGTATTTTAGTAAGTAA
1544404 TGTATTTTAGTAATAAATTTAAACAAATTTTAG
65 TGTATTTTAGTAATAAATTTAAACAAATTTTAG
*
1544437 TAAGTAATTTATTT
1 TAAGTAATGTATTT
1544451 TAGTAAGTAA
Statistics
Matches: 202, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
96 4 0.02
97 102 0.50
99 1 0.00
101 95 0.47
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (97 bp):
TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
GTATTTTAGTAATAAATTTAAACAAATTTTAG
Found at i:1545832 original size:11 final size:11
Alignment explanation
Indices: 1545816--1545855 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1545806 GATGATAATA
1545816 CATTAGTTACC
1 CATTAGTTACC
1545827 CATTAGTTACC
1 CATTAGTTACC
*
1545838 CACTAGTTACC
1 CATTAGTTACC
1545849 CA-TAGTT
1 CATTAGTT
1545856 TGAGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:1547300 original size:14 final size:14
Alignment explanation
Indices: 1547281--1547310 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1547271 CACGAACAGC
1547281 AAGATGATTAACTA
1 AAGATGATTAACTA
1547295 AAGATGATTAACTA
1 AAGATGATTAACTA
1547309 AA
1 AA
1547311 AACCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:1547539 original size:36 final size:36
Alignment explanation
Indices: 1547498--1547613 Score: 116
Period size: 36 Copynumber: 3.2 Consensus size: 36
1547488 AAAAACAAAT
1547498 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
* ** *
1547534 TATTTCAGAACAT-AACAACA-TA-ATCAAAAACAAA--T
1 TATTTCAG-AC-TCAA-AA-ATTATTTCAAATCCAAAGCA
*
1547569 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
1547605 TATTTCAGA
1 TATTTCAGA
1547614 ACATAACAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
32 1 0.02
33 5 0.08
34 12 0.19
35 8 0.13
36 17 0.27
37 13 0.21
38 5 0.08
39 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (36 bp):
TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
Found at i:1547562 original size:71 final size:71
Alignment explanation
Indices: 1547446--1547646 Score: 368
Period size: 71 Copynumber: 2.8 Consensus size: 71
1547436 CCAGATCCAG
*
1547446 ATTTCAGAA-CCAAAGCATAATTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTC
1 ATTTCA-AATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTC
1547510 AAAAATT
65 AAAAATT
1547517 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
*
1547582 GAAATT
66 AAAATT
1547588 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
1547647 AATCCACTCA
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
70 2 0.02
71 125 0.98
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (71 bp):
ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
AAAATT
Found at i:1547981 original size:22 final size:22
Alignment explanation
Indices: 1547953--1547999 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1547943 GTGGCTGTAA
*
1547953 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
1547975 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
1547997 TAA
1 TAA
1548000 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:1549175 original size:14 final size:14
Alignment explanation
Indices: 1549156--1549226 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 14
1549146 ACCCCAGACT
1549156 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
*
1549170 CCTAAACACCCTAATAC
1 CCT-AA-ACCTTAA-AC
1549187 CCT-AACCTTAAA-
1 CCTAAACCTTAAAC
* * *
1549199 CCTACATCGTAAAC
1 CCTAAACCTTAAAC
*
1549213 CCTAAACTTTAAAC
1 CCTAAACCTTAAAC
1549227 TTTACACTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
12 3 0.07
13 7 0.16
14 19 0.44
15 3 0.07
16 6 0.14
17 5 0.12
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.23
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:1549661 original size:113 final size:115
Alignment explanation
Indices: 1549463--1549668 Score: 290
Period size: 113 Copynumber: 1.8 Consensus size: 115
1549453 ATCAACAAAT
* * * *
1549463 CGCCGCTAATACTATGCTTTAGCGGCGTTTTACCGAAATCGCCACTAAATCAAGTATACATCAAG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACCGAAAGCGCCACTAAATCAACTATACATCAAG
*
1549528 ACCAAAACGATGCGTTTTGGTTCAGATACTTGGTGGCGCTTTTATCCAAG
66 ACCAAAACGATGCGTTTTGGTTAAGATACTTGGTGGCGCTTTTATCCAAG
* * * *
1549578 CGCCGCTAATACTATGCTTTAACGGCGTTTCA-C-TAAGCGCCACTAATTCTACTATACATCGAG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACCGAAAGCGCCACTAAATCAACTATACATCAAG
* **
1549641 GCCAAAATTATGCGTTTTGGTTAAGATA
66 ACCAAAACGATGCGTTTTGGTTAAGATA
1549669 TTTTGCTGCT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
113 48 0.61
114 1 0.01
115 30 0.38
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (115 bp):
CGCCGCTAATACTATGCTTTAACGGCGTTTCACCGAAAGCGCCACTAAATCAACTATACATCAAG
ACCAAAACGATGCGTTTTGGTTAAGATACTTGGTGGCGCTTTTATCCAAG
Found at i:1549838 original size:208 final size:209
Alignment explanation
Indices: 1549479--1550111 Score: 741
Period size: 208 Copynumber: 2.9 Consensus size: 209
1549469 TAATACTATG
* * * * ** * *
1549479 CTTTAGCGGCGTTTTACCGAAATCGCCACTAAATCAAGTATACATCAAGACCAAAACGA-TGCGT
1 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTA-TATACATTAAGATCAAAAC-ACTGCGT
* * * * ** * *
1549543 TTTGGTTCAGATACTTGGTGGCGCT-TTTATCCAAGCGCCGCTAATACTATGCTTTAACGGCGTT
64 TTTTGTTAAGATATTTTGTGGCGCTAGCTA-CAAATCGCCGCTAATACTATGCTTTAACGGCGTT
1549607 TCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTT
128 TCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTT
1549672 TGCT-GCTATTAATATT
193 TGCTCGCTATTAATATT
1549688 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTT
1 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTT
*
1549753 TTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCGTTTCA
66 TTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCGTTTCA
1549818 CTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTTGC
131 CTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTT--
1549883 GGCGCTTCTCACAAAGCGCCGCTATTAATATT
194 ---G---CT----------CGCTATTAATATT
*
1549915 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
1 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTT
* * *
1549980 TTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTATTCTTTAGCGGCGTTTGA
66 TTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCGTTTCA
* * * * * * ** * * * *
1550045 CCATATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTGTTTCGCTTAAGATAGTTT
131 -C-TAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTT
1550110 GC
194 GC
1550112 GGCGCTTCCA
Statistics
Matches: 367, Mismatches: 34, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
207 1 0.00
208 140 0.38
209 33 0.09
213 1 0.00
216 2 0.01
221 1 0.00
224 1 0.00
227 137 0.37
228 1 0.00
229 50 0.14
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (209 bp):
CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTT
TTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCGTTTCA
CTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTTGC
TCGCTATTAATATT
Found at i:1550001 original size:114 final size:112
Alignment explanation
Indices: 1549676--1550342 Score: 605
Period size: 113 Copynumber: 5.9 Consensus size: 112
1549666 ATATTTTGCT
* * *
1549676 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTACTATTCTTTAACGGC-GTTTACCGTAAGCGCCACTAATTTTATATACATCAAGA-CAA
* * *
1549741 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCT-ACAAATCGCC
64 AACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT-TCTCACAAAGCGCC
* * * * *
1549790 GCTAATACTATGCTTTAACGGCGTTT-CAC-TAAGCGCCACTAATTCTACTATACATCGAGGCCA
1 GCTATTACTATTCTTTAACGGCGTTTAC-CGTAAGCGCCACTAATTTTA-TATACATC-AAGACA
*
1549853 AAATTA-TGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
63 AAA-CACTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
* * *
1549903 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTACTATTCTTTAACGGC-GTTTACCGTAAGCGCCACTAATTTTATATACATCAAGA-CAA
* * * * *
1549968 AACGCTGCGTTTTTGTTAAGATATTTTGTGGCGCTAGCT-ACAAATCGCC
64 AACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT-TCTCACAAAGCGCC
* * * * * * *
1550017 GCTAATACTATTCTTTAGCGGCGTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCA
1 GCTATTACTATTCTTTAACGGCGTTT-ACCGTAAGCGCCACTAATTTTA-TATACATCAAGA-CA
* * * * * *
1550082 AAACGA-TGTGTTTCGCTTAAGATAGTTTGCGGCGCTTC-CATAAAGCGTC
63 AAAC-ACTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
* * * * * * * * *
1550131 GCTATTACTGTACTTTAACGGCGTTTTCCTATAAACGCCACTAATTCTAAGATACCTCAAGACCA
1 GCTATTACTATTCTTTAACGGCGTTTACC-GTAAGCGCCACTAATT-TTATATACATCAAGACAA
* * * *
1550196 AACTCTGCGTTTTGGTTAAGCTATTTTGCGGCGTTTC-CAGAAAGCGCC
64 AACACTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
* * * * * *
1550244 GCTATTACTGTCCTTTAATGGCGTTT-CGCGTAAACGCCACTACTTTTAAGATACATCAAGACGA
1 GCTATTACTATTCTTTAACGGCGTTTAC-CGTAAGCGCCACTAATTTT-ATATACATCAAGAC-A
* * *
1550308 AAACACAGCGTTTTGGTTAAGAGATTTCGCGGCGC
63 AAACACTGCGTTTTGGTTAAGATATTTTGCGGCGC
1550343 ATTGTGGTAA
Statistics
Matches: 450, Mismatches: 82, Indels: 43
0.78 0.14 0.07
Matches are distributed among these distances:
111 1 0.00
112 48 0.11
113 175 0.39
114 165 0.37
115 61 0.14
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (112 bp):
GCTATTACTATTCTTTAACGGCGTTTACCGTAAGCGCCACTAATTTTATATACATCAAGACAAAA
CACTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
Found at i:1550247 original size:227 final size:227
Alignment explanation
Indices: 1549676--1550228 Score: 680
Period size: 227 Copynumber: 2.4 Consensus size: 227
1549666 ATATTTTGCT
* * * * * * *
1549676 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
1549741 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
66 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
* * * ** * *
1549806 AACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTT
131 AACGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGCTT
*
1549871 AAGATATTTTGCGGCGCTTCTCACAAAGCGCC
196 AAGATAGTTTGCGGCGCTTCTCACAAAGCGCC
* * * * * * *
1549903 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
* * *
1549968 AACGCTGCGTTTTTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTATTCTTT
66 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
* * * * * *
1550033 AGCGGCGTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTGTTTCGC
131 AACGGCGTTTCA-C-TAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGC
* *
1550098 TTAAGATAGTTTGCGGCGCTTC-CATAAAGCGTC
194 TTAAGATAGTTTGCGGCGCTTCTCACAAAGCGCC
* * * *
1550131 GCTATTACTGTACTTTAACGGC-GTTTTCCTATAAACGCCACTAATTCTAAGATACCTCAAGA-C
1 GCTATTAATATACTTTAACGGCGGTTTACC-ATAAACGCCACTAATT-TAAGATACATCAAGATC
* * * *
1550194 CAAACTCTGCGTTTTGGTTAAGCTATTTTGCGGCG
64 AAAACACTGCGTTTTTGTTAAGATATTTTGCGGCG
1550229 TTTCCAGAAA
Statistics
Matches: 287, Mismatches: 35, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
227 143 0.50
228 73 0.25
229 71 0.25
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (227 bp):
GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
AACGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGCTT
AAGATAGTTTGCGGCGCTTCTCACAAAGCGCC
Found at i:1551861 original size:27 final size:27
Alignment explanation
Indices: 1551824--1551895 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
1551814 GGTGGAGGGC
* *
1551824 CTGCCACAGGCGGCACTAGAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
* * * *
1551851 GTGGCAGAGGCGGCACCAAATGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
1551878 CTGCCACAGGCGGCACCA
1 CTGCCACAGGCGGCACCA
1551896 CCTTGGGGGA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.10
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAAAGGTGCCA
Found at i:1551965 original size:20 final size:20
Alignment explanation
Indices: 1551940--1551982 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1551930 ACTTCGGCAG
* *
1551940 AAGGAGGAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGA
1551960 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGAAAAAGA
1551980 AAG
1 AAG
1551983 AAAAGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAAGA
Found at i:1551991 original size:10 final size:10
Alignment explanation
Indices: 1551948--1551991 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1551938 AGAAGGAGGA
1551948 GAAAGAAAAG
1 GAAAGAAAAG
*
1551958 GAAAGGAGAA-
1 GAAA-GAAAAG
*
1551968 GAAAGAAAAA
1 GAAAGAAAAG
1551978 GAAAGAAAAG
1 GAAAGAAAAG
1551988 GAAA
1 GAAA
1551992 TGAGAAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 4 0.14
10 21 0.72
11 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:1552010 original size:45 final size:43
Alignment explanation
Indices: 1551961--1552079 Score: 105
Period size: 48 Copynumber: 2.6 Consensus size: 43
1551951 AGAAAAGGAA
*
1551961 AGGAGAAGAAAGAAAAAGAAAGAAAAGGAAATGAGAAGAAGAAGG
1 AGGAGAAGAAGGAAAAAGAAAGAAAAGGAAA--AGAAGAAGAAGG
* * * * *
1552006 AGGAGGAGGCGCAGGAAAAAGAGAAAGAGAAGGAGAAGAAGAAGAGGG
1 AGGA-GA--AGAAGG-AAAA-AGAAAGAAAAGGAAAAGAAGAAGAAGG
1552054 AGG-GAAGGAAGGAAAAAGAAAGAAAA
1 AGGAGAA-GAAGGAAAAAGAAAGAAAA
1552080 AAAAAAGGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
43 9 0.15
44 4 0.07
45 8 0.14
46 4 0.07
48 17 0.29
49 4 0.07
50 13 0.22
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.01
Consensus pattern (43 bp):
AGGAGAAGAAGGAAAAAGAAAGAAAAGGAAAAGAAGAAGAAGG
Found at i:1552331 original size:16 final size:16
Alignment explanation
Indices: 1552310--1552359 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1552300 AAATAGCATT
1552310 AAAAATAAAATACTGA
1 AAAAATAAAATACTGA
***
1552326 AAAAATATGTTTA-TGA
1 AAAAATA-AAATACTGA
1552342 AAAAATAAAATAC-GA
1 AAAAATAAAATACTGA
1552357 AAA
1 AAA
1552360 GAAATAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATACTGA
Found at i:1552510 original size:158 final size:157
Alignment explanation
Indices: 1552362--1553413 Score: 1619
Period size: 160 Copynumber: 6.6 Consensus size: 157
1552352 TACGAAAAGA
* * * *
1552362 AATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTC-GAAAATAAGAAAATTACGAA
1 AATAAAATACGAAAATAGTATATTT-TTGAAAGTAATAAAATTCGGAAAA-AAGAAAAATACGAA
* *
1552426 CAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACTCACACTAAAATAATACATTT
64 CAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAA-ACACACTAAATTAATACATTT
* *
1552491 CAAACATTATGTATTAAAATAATACAAAAT
128 CAAACATTATGTACTAAAATAATATAAAAT
* *
1552521 AATAAAATACGAAAATAGTATATTTTTTATAGTAATAAAATTCGGAAAAAAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTGAAAGTAATAAAATTCGG-AAAAAAGAAAAATACGAAC
*
1552586 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTTA
65 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCA
1552651 AACATTATGTACTAAAATAATATAAAAT
130 AACATTATGTACTAAAATAATATAAAAT
*
1552679 AATAAAATAC-AAAATAGTATATTTTTTGAAAGTCATAAAATTCGGGAAAAAAGAAAAATACGAA
1 AATAAAATACGAAAATAGTATA-TTTTTGAAAGTAATAAAATTC-GGAAAAAAGAAAAATACGAA
*
1552743 TAAA-GTGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTT
64 CAAATG-GCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTT
1552807 CAAACATTATGTACTAAAATAATATAAAAT
128 CAAACATTATGTACTAAAATAATATAAAAT
* * * *
1552837 AATAAAATACGAAAATAGCATATTGTTTGAAAGTAATAAAATCCGAGCAAAAAGAAAAATATGAA
1 AATAAAATACGAAAATAGTATATT-TTTGAAAGTAATAAAATTCG-GAAAAAAGAAAAATACGAA
* *
1552902 CAAAGGGCCAAAATAAAGGTTTTTTTACTAAATTTATATAAAAAACCACACTAAATTAATACATT
64 CAAATGGCCAAAAT-AAGGGTTTTTTACTAAATTTATATAAAAAA-CACACTAAATTAATACATT
*
1552967 TCAAACATTGTGTACTAAAATAATATAAAAT
127 TCAAACATTATGTACTAAAATAATATAAAAT
*
1552998 AATAAAATAC-AAAATAGTATATTTTTTGAAAGTCATAAAATTCGGAAAAAAAGAAAAATACGAA
1 AATAAAATACGAAAATAGTATA-TTTTTGAAAGTAATAAAATTCGG-AAAAAAGAAAAATACGAA
1553062 CAAA-GTGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
64 CAAATG-GCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
1553126 TCAAACATTATGTACTAAAATAATATAAAAT
127 TCAAACATTATGTACTAAAATAATATAAAAT
* * * *
1553157 AATAAAATACGAAAATAGCATATTGTTTGAAAGTAATAAAATCCGAGCAAAAAGAAAAATATGAA
1 AATAAAATACGAAAATAGTATATT-TTTGAAAGTAATAAAATTCG-GAAAAAAGAAAAATACGAA
* *
1553222 CAAAGGGCCAAAATAAAGGTTTTTTTACTAAATTTATATAAAAAACCACACTAAATTAATACATT
64 CAAATGGCCAAAAT-AAGGGTTTTTTACTAAATTTATATAAAAAA-CACACTAAATTAATACATT
1553287 TCAAACATTATGTACTAAAATAATATAAAAT
127 TCAAACATTATGTACTAAAATAATATAAAAT
* *
1553318 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAACAAAATCCAGGAAAAAAGAAAAATACGAA
1 AATAAAATACGAAAATAGTATA-TTTTTGAAAGTAATAAAATTC-GGAAAAAAGAAAAATACGAA
1553383 CAAATGGCCAAAATAAGGGTTTTTTACTAAA
64 CAAATGGCCAAAATAAGGGTTTTTTACTAAA
1553414 ATTGTTTTGA
Statistics
Matches: 827, Mismatches: 43, Indels: 45
0.90 0.05 0.05
Matches are distributed among these distances:
157 12 0.01
158 210 0.25
159 204 0.25
160 212 0.26
161 186 0.22
162 3 0.00
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (157 bp):
AATAAAATACGAAAATAGTATATTTTTGAAAGTAATAAAATTCGGAAAAAAGAAAAATACGAACA
AATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAA
ACATTATGTACTAAAATAATATAAAAT
Found at i:1552575 original size:159 final size:158
Alignment explanation
Indices: 1552362--1553413 Score: 1598
Period size: 158 Copynumber: 6.6 Consensus size: 158
1552352 TACGAAAAGA
* * * * * *
1552362 AATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTC-GAAAATAAGAAAATTACGAA
1 AATAAAATACGAAAATAGTATATTT-TTTAAAGTAATAAAATTCGGAAAAAAAGAAAAATACGAA
* *
1552426 CAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACTCACACTAAAATAATACATTT
65 CAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAA-ACACACTAAATTAATACATTT
* *
1552491 CAAACATTATGTATTAAAATAATACAAAAT
129 CAAACATTATGTACTAAAATAATATAAAAT
*
1552521 AATAAAATACGAAAATAGTATATTTTTTATAGTAATAAAATTCGGAAAAAAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGAAAAAAAGAAAAATACGAAC
*
1552586 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTTA
66 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCA
1552651 AACATTATGTACTAAAATAATATAAAAT
131 AACATTATGTACTAAAATAATATAAAAT
* *
1552679 AATAAAATAC-AAAATAGTATATTTTTTGAAAGTCATAAAATTCGGGAAAAAAGAAAAATACGAA
1 AATAAAATACGAAAATAGTATATTTTTT-AAAGTAATAAAATTCGGAAAAAAAGAAAAATACGAA
*
1552743 TAAA-GTGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTT
65 CAAATG-GCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTT
1552807 CAAACATTATGTACTAAAATAATATAAAAT
129 CAAACATTATGTACTAAAATAATATAAAAT
* * * * *
1552837 AATAAAATACGAAAATAGCATATTGTTTGAAAGTAATAAAA-TCCGAGCAAAAAGAAAAATATGA
1 AATAAAATACGAAAATAGTATATT-TTTTAAAGTAATAAAATTCGGA-AAAAAAGAAAAATACGA
* *
1552901 ACAAAGGGCCAAAATAAAGGTTTTTTTACTAAATTTATATAAAAAACCACACTAAATTAATACAT
64 ACAAATGGCCAAAAT-AAGGGTTTTTTACTAAATTTATATAAAAAA-CACACTAAATTAATACAT
*
1552966 TTCAAACATTGTGTACTAAAATAATATAAAAT
127 TTCAAACATTATGTACTAAAATAATATAAAAT
*
1552998 AATAAAATAC-AAAATAGTATATTTTTTGAAAGTCATAAAATTCGGAAAAAAAGAAAAATACGAA
1 AATAAAATACGAAAATAGTATATTTTTT-AAAGTAATAAAATTCGGAAAAAAAGAAAAATACGAA
1553062 CAAA-GTGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
65 CAAATG-GCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
1553126 TCAAACATTATGTACTAAAATAATATAAAAT
128 TCAAACATTATGTACTAAAATAATATAAAAT
* * * * *
1553157 AATAAAATACGAAAATAGCATATTGTTTGAAAGTAATAAAA-TCCGAGCAAAAAGAAAAATATGA
1 AATAAAATACGAAAATAGTATATT-TTTTAAAGTAATAAAATTCGGA-AAAAAAGAAAAATACGA
* *
1553221 ACAAAGGGCCAAAATAAAGGTTTTTTTACTAAATTTATATAAAAAACCACACTAAATTAATACAT
64 ACAAATGGCCAAAAT-AAGGGTTTTTTACTAAATTTATATAAAAAA-CACACTAAATTAATACAT
1553286 TTCAAACATTATGTACTAAAATAATATAAAAT
127 TTCAAACATTATGTACTAAAATAATATAAAAT
* *
1553318 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAACAAAATCCAGG-AAAAAAGAAAAATACGA
1 AATAAAATACGAAAATAGTATATTTTTT-AAAGTAATAAAATTC-GGAAAAAAAGAAAAATACGA
1553382 ACAAATGGCCAAAATAAGGGTTTTTTACTAAA
64 ACAAATGGCCAAAATAAGGGTTTTTTACTAAA
1553414 ATTGTTTTGA
Statistics
Matches: 820, Mismatches: 51, Indels: 43
0.90 0.06 0.05
Matches are distributed among these distances:
157 18 0.02
158 207 0.25
159 205 0.25
160 204 0.25
161 184 0.22
162 1 0.00
163 1 0.00
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (158 bp):
AATAAAATACGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGAAAAAAAGAAAAATACGAAC
AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCA
AACATTATGTACTAAAATAATATAAAAT
Found at i:1555743 original size:8 final size:8
Alignment explanation
Indices: 1555730--1555771 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1555720 GGGTGTTACA
1555730 ACAACATT
1 ACAACATT
1555738 ACAACATT
1 ACAACATT
1555746 ACAACATT
1 ACAACATT
*
1555754 AC-ACATA
1 ACAACATT
*
1555761 ACAACTTT
1 ACAACATT
1555769 ACA
1 ACA
1555772 GCCTAAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (8 bp):
ACAACATT
Found at i:1559071 original size:17 final size:17
Alignment explanation
Indices: 1559041--1559082 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1559031 ATTTTTTCTA
1559041 TTTTT-TTC-TTCTCT-
1 TTTTTCTTCTTTCTCTC
1559055 TTCTTTCTTCTTTCTCTC
1 TT-TTTCTTCTTTCTCTC
1559073 TTTTTCTTCT
1 TTTTTCTTCT
1559083 CTTTGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 3 0.12
17 14 0.58
18 2 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCTTCTTTCTCTC
Found at i:1559086 original size:11 final size:11
Alignment explanation
Indices: 1559043--1559086 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1559033 TTTTTCTATT
1559043 TTTTTCTTCTC
1 TTTTTCTTCTC
1559054 --TTTCTT-TC
1 TTTTTCTTCTC
1559062 TTCTTTC-TCTC
1 TT-TTTCTTCTC
1559073 TTTTTCTTCTC
1 TTTTTCTTCTC
1559084 TTT
1 TTT
1559087 GTTCGGCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 2 0.07
9 6 0.21
10 5 0.18
11 15 0.54
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:1563702 original size:23 final size:23
Alignment explanation
Indices: 1563652--1563706 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1563642 GGAAAATAAT
1563652 GAAAAAAGTTAAATGAACATAAAA
1 GAAAAAA-TTAAATGAACATAAAA
* *
1563676 GAAAAAATTAAAT-AGCTTAAAA
1 GAAAAAATTAAATGAACATAAAA
1563698 CGAAAAAAT
1 -GAAAAAAT
1563707 ATGAAGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 7 0.25
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.18
Consensus pattern (23 bp):
GAAAAAATTAAATGAACATAAAA
Found at i:1571615 original size:51 final size:51
Alignment explanation
Indices: 1571560--1571696 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
1571550 TATGGTAACT
*
1571560 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * ** * * **
1571611 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* *
1571662 AATCATAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
1571697 TTGATGGTAG
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:1573446 original size:42 final size:40
Alignment explanation
Indices: 1573392--1573534 Score: 196
Period size: 42 Copynumber: 3.5 Consensus size: 40
1573382 ATTATATATA
* *
1573392 TTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA-TT
1573433 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATT
1 TTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTAATT
* *
1573474 TTTTTTAATTTAAAAATATTTTAAAAATACTTTTTTTAATT
1 TTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAATT
*
1573515 TTTTTAAAATTTTTAAAATA
1 TTTTT-TAA-TTTTAAAATA
1573535 AAAATGGGCC
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
40 22 0.24
41 29 0.32
42 32 0.35
43 9 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATT
Found at i:1574174 original size:19 final size:19
Alignment explanation
Indices: 1574150--1574213 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
1574140 TTATAATTAA
1574150 TTAATTTTTAATCATATAT
1 TTAATTTTTAATCATATAT
*
1574169 TTAATTATTT-ATTATATA-
1 TTAATT-TTTAATCATATAT
* *
1574187 TT-ATTTTTAAACATACAT
1 TTAATTTTTAATCATATAT
1574205 TTATATTTT
1 TTA-ATTTT
1574214 AAATATATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 3 0.08
17 8 0.22
18 4 0.11
19 13 0.36
20 8 0.22
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATTTTTAATCATATAT
Found at i:1574221 original size:36 final size:36
Alignment explanation
Indices: 1574136--1574221 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
1574126 TATTTTATAT
* *
1574136 ATTATTATAAT-TA-ATTAATTTTTAATCATATATTTA
1 ATTATTA-AATATATATT-ATTTTTAAACATACATTTA
* *
1574172 ATTATTTATTATATATTATTTTTAAACATACATTTA
1 ATTATTAAATATATATTATTTTTAAACATACATTTA
1574208 TATT-TTAAATATAT
1 -ATTATTAAATATAT
1574222 GCTTCCCACG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
35 2 0.05
36 33 0.80
37 6 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (36 bp):
ATTATTAAATATATATTATTTTTAAACATACATTTA
Found at i:1578295 original size:22 final size:22
Alignment explanation
Indices: 1578270--1578324 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1578260 GATAATGCTG
* *
1578270 AATCTGCTTTTGTTTGCTTTGC
1 AATCTGCTTCTGTTTGCTCTGC
*
1578292 AATCTTCTTCTGTTTGCTCTGC
1 AATCTGCTTCTGTTTGCTCTGC
*
1578314 AATCTTCTTCT
1 AATCTGCTTCT
1578325 CTGTTTAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.11, C:0.24, G:0.13, T:0.53
Consensus pattern (22 bp):
AATCTGCTTCTGTTTGCTCTGC
Found at i:1587846 original size:9 final size:9
Alignment explanation
Indices: 1587828--1587893 Score: 80
Period size: 9 Copynumber: 7.2 Consensus size: 9
1587818 TTTGGTTAAA
1587828 AATTACCCG
1 AATTACCCG
*
1587837 AATTATCCG
1 AATTACCCG
*
1587846 -ATTAACCG
1 AATTACCCG
*
1587854 AATTAACCG
1 AATTACCCG
1587863 AATTACCCG
1 AATTACCCG
1587872 AAAATTACCCG
1 --AATTACCCG
1587883 AATTACCCG
1 AATTACCCG
1587892 AA
1 AA
1587894 AATTACCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.14
9 35 0.69
11 9 0.18
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:1587854 original size:17 final size:18
Alignment explanation
Indices: 1587828--1587893 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 18
1587818 TTTGGTTAAA
*
1587828 AATTACCCGAATTATCCG
1 AATTACCCGAATTAACCG
*
1587846 -ATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
*
1587863 AATTACCCGAAAATTACCCG
1 AATTACCCG--AATTAACCG
1587883 AATTACCCGAA
1 AATTACCCGAA
1587894 AATTACCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.37
18 9 0.22
20 17 0.41
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:1587883 original size:20 final size:20
Alignment explanation
Indices: 1587854--1587901 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1587844 CGATTAACCG
*
1587854 AATTAACCGAATTACCCGAA
1 AATTACCCGAATTACCCGAA
1587874 AATTACCCGAATTACCCGAA
1 AATTACCCGAATTACCCGAA
1587894 AATTACCC
1 AATTACCC
1587902 AAAAAGTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (20 bp):
AATTACCCGAATTACCCGAA
Done.