Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 129 of 253
Found at i:40991321 original size:14 final size:13
Alignment explanation
Indices: 40991298--40991329 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
40991288 GGGATATCAA
40991298 AACAATAATTAAG
1 AACAATAATTAAG
40991311 AACACATAATTAAG
1 AACA-ATAATTAAG
40991325 AACAA
1 AACAA
40991330 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:40992109 original size:42 final size:42
Alignment explanation
Indices: 40992061--40992177 Score: 135
Period size: 43 Copynumber: 2.8 Consensus size: 42
40992051 TGTGTTATCG
**
40992061 TGTAAGACCATGTCTGGGACATTGGCATTGTATATGATTTTA
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATATGATTACA
* * * * *
40992103 TGTAAGACCCTGTCTGGGGCAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATTG-TATATGATTACA
* * *
40992146 TGTAAGATCACGTCTGGGACGTTGGCATTGTA
1 TGTAAGACCATGTCTGGGACATTGGCATTGTA
40992178 CGAGCTTATG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 28 0.47
43 32 0.53
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATATGATTACA
Found at i:40995296 original size:27 final size:27
Alignment explanation
Indices: 40995266--40995572 Score: 225
Period size: 27 Copynumber: 11.4 Consensus size: 27
40995256 GGGTAGAATC
* *
40995266 ACTAAAATACCATTGGTTTACAAAATT
1 ACTAAAATACCCTTGATTTACAAAATT
*
40995293 ACTAAAATACCCTTGATTTAAAAAATT
1 ACTAAAATACCCTTGATTTACAAAATT
* * *
40995320 ACT-AAATACCTTTGGTTTACAATATT
1 ACTAAAATACCCTTGATTTACAAAATT
* * *
40995346 ACCAAAATACCC-TCAATTAGCAAAATT
1 ACTAAAATACCCTTGATTTA-CAAAATT
* **
40995373 ACTAAAATACCC-CGAGTTTGTAAAATT
1 ACTAAAATACCCTTGA-TTTACAAAATT
* ** **
40995400 ACCAAAATACCCTCAATTTGTAAAATT
1 ACTAAAATACCCTTGATTTACAAAATT
* * **
40995427 ACCAAAATACCTTTGATTTGGAAAATT
1 ACTAAAATACCCTTGATTTACAAAATT
* **
40995454 A-TCGAAATACCCTTGATTTGGAAAATT
1 ACT-AAAATACCCTTGATTTACAAAATT
*
40995481 A-TAGAAATACCCCTGATTTACAAAATT
1 ACTA-AAATACCCTTGATTTACAAAATT
40995508 AC-AGAAATACCCTTGACTTT-CAAAAATT
1 ACTA-AAATACCCTTGA-TTTAC-AAAATT
* * *
40995536 A-TAAAAATACCATTGGTTTGCAAAATT
1 ACT-AAAATACCCTTGATTTACAAAATT
*
40995563 ACTGAAATAC
1 ACTAAAATAC
40995573 TCTTAGTTTG
Statistics
Matches: 231, Mismatches: 36, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
26 25 0.11
27 179 0.77
28 26 0.11
29 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (27 bp):
ACTAAAATACCCTTGATTTACAAAATT
Found at i:40996626 original size:27 final size:27
Alignment explanation
Indices: 40996543--40996626 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
40996533 AGCATGGCTG
* *
40996543 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* * *
40996569 CCAAAACCGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
40996596 CCAGAACAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
40996623 CCAG
1 CCAG
40996627 GACGCTTCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
26 11 0.23
27 37 0.77
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:40997065 original size:16 final size:15
Alignment explanation
Indices: 40997044--40997073 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40997034 AAAATACTGA
40997044 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
40997060 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
40997074 CCAATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:40998082 original size:24 final size:24
Alignment explanation
Indices: 40998047--40998123 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
40998037 CCAACACCTT
* *
40998047 TCTCCCTAATCAACTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
40998071 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
40998095 TCTCCCTTATCAGCTCCTAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
40998119 TCTCC
1 TCTCC
40998124 TGATAGCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.22, C:0.42, G:0.03, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:40998777 original size:41 final size:41
Alignment explanation
Indices: 40998732--40998853 Score: 149
Period size: 41 Copynumber: 3.0 Consensus size: 41
40998722 GCAGGAAGAA
*
40998732 ATTGAGGATCGCATGGTTACTTGACAACCGTGGATCCA-CTG
1 ATTGAGGATCGCATGGTTGCTTGACAACCGTGGATCCATC-G
* * *
40998773 ATTGAGGATCACATGGTTGCTTGATGAA-TGTGGATCCATCG
1 ATTGAGGATCGCATGGTTGCTTGA-CAACCGTGGATCCATCG
* **
40998814 ATTAAGGATCGCATGGTTGCTTGATGACCGTGGATCCATC
1 ATTGAGGATCGCATGGTTGCTTGACAACCGTGGATCCATC
40998854 AGTGGCTTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 65 0.94
42 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACAACCGTGGATCCATCG
Found at i:40999036 original size:22 final size:22
Alignment explanation
Indices: 40999011--40999058 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40999001 TGGCTTTGCA
40999011 CCAACCTACA-TATGGATCTGTG
1 CCAACCTA-ATTATGGATCTGTG
* *
40999033 CCAACCTAATTATGGTTGTGTG
1 CCAACCTAATTATGGATCTGTG
40999055 CCAA
1 CCAA
40999059 ACGTATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (22 bp):
CCAACCTAATTATGGATCTGTG
Found at i:40999286 original size:22 final size:22
Alignment explanation
Indices: 40999261--40999307 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
40999251 ATTGATGCGA
* *
40999261 TGTTTACGGTTATGTGCTGTCC
1 TGTTTACGGCTATGTGCTATCC
40999283 TGTTTACGGCTATGTGCTATCC
1 TGTTTACGGCTATGTGCTATCC
40999305 TGT
1 TGT
40999308 CTATGGCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.45
Consensus pattern (22 bp):
TGTTTACGGCTATGTGCTATCC
Found at i:40999437 original size:21 final size:22
Alignment explanation
Indices: 40999396--40999442 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
40999386 GATCCCCACA
40999396 TGGTGTGCTGGTTGGTATGGG-
1 TGGTGTGCTGGTTGGTATGGGC
*
40999417 TGGTGTGTTGGTTGG-ATTGGGC
1 TGGTGTGCTGGTTGGTA-TGGGC
40999439 TGGT
1 TGGT
40999443 AATCTATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.04, C:0.04, G:0.51, T:0.40
Consensus pattern (22 bp):
TGGTGTGCTGGTTGGTATGGGC
Found at i:41003884 original size:44 final size:44
Alignment explanation
Indices: 41003821--41003911 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
41003811 TATTTTCACT
*
41003821 GAGTTCACTCTAGTACAATGGTGTTCGACATTTACGACCTTATA
1 GAGTTCACTCCAGTACAATGGTGTTCGACATTTACGACCTTATA
41003865 GAGTTCACTCCAGTACAATGGTGTTCGACATTTACGACCTTATA
1 GAGTTCACTCCAGTACAATGGTGTTCGACATTTACGACCTTATA
41003909 GAG
1 GAG
41003912 CTTTATACAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
GAGTTCACTCCAGTACAATGGTGTTCGACATTTACGACCTTATA
Found at i:41014419 original size:24 final size:24
Alignment explanation
Indices: 41014387--41014465 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
41014377 GTTAGGACAT
* * *
41014387 ATTAAATTCATCCACCAGTAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
*
41014411 ATTAAATTCGTCAACTAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
* *
41014435 ATTAAATCCGTCAACCAGCAACTC
1 ATTAAATTCGTCAACCAGCAGCTC
41014459 ATTAAAT
1 ATTAAAT
41014466 CTATCTAGGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.28
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:41019117 original size:31 final size:31
Alignment explanation
Indices: 41019079--41019194 Score: 160
Period size: 31 Copynumber: 3.7 Consensus size: 31
41019069 TAATGAAAAT
*
41019079 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
41019110 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
* * ***
41019141 TGAAAGGTGGTAGCACCGAAAACCTGATCAG
1 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
* *
41019172 TGAATAGTGGTAGCTTCGGCTAC
1 TGAAAAGTGGTAGCTCCGGCTAC
41019195 AAGTGACAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
Found at i:41019267 original size:46 final size:43
Alignment explanation
Indices: 41019217--41019374 Score: 153
Period size: 41 Copynumber: 3.7 Consensus size: 43
41019207 ATTTCTGTAC
* * * *
41019217 AAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTTGTGT
1 AAGACCATAGCTGGGCTATGGCATCA--GAGATATG-AATATGTGT
*
41019263 AAGACCATAGCTGGGCTATGGCATC-GATATATGAATATGTGT
1 AAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTGT
** * *
41019305 AAGA-CATAGCTGGGCTATGGCATCA-TTATGTGAAGATGTGT
1 AAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTGT
* **
41019346 AAGACCATAGTTGAACTATGGCATC-GAGA
1 AAGACCATAGCTGGGCTATGGCATCAGAGA
41019375 AAACGAAGTA
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
41 37 0.39
42 29 0.30
43 7 0.07
46 23 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (43 bp):
AAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTGT
Found at i:41019313 original size:41 final size:43
Alignment explanation
Indices: 41019258--41019372 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 43
41019248 ATATGTGATT
*
41019258 TGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATA
1 TGTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGA
*
41019300 TGTGTAAGA-CATAGCTGGGCTATGGCATC-ATTATGTGAAGA
1 TGTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGA
* **
41019341 TGTGTAAGACCATAGTTGAACTATGGCATCGA
1 TGTGTAAGACCATAGCTGGGCTATGGCATCGA
41019373 GAAAACGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
40 1 0.02
41 37 0.57
42 26 0.40
43 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGA
Found at i:41026622 original size:14 final size:14
Alignment explanation
Indices: 41026603--41026632 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41026593 GGTGTAAGAT
41026603 TTTTAAGTAAAATA
1 TTTTAAGTAAAATA
*
41026617 TTTTAAGTATAATA
1 TTTTAAGTAAAATA
41026631 TT
1 TT
41026633 AAATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTTAAGTAAAATA
Found at i:41030802 original size:41 final size:41
Alignment explanation
Indices: 41030674--41030907 Score: 307
Period size: 41 Copynumber: 5.8 Consensus size: 41
41030664 GGATATAGCT
* * * * *
41030674 ACTCGCTC-AATGCCTTCGGGACATAGCTCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
*
41030713 ACTCACACAAATGCCTTCGGGACTTAGCCCGG-ATGTAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
* *
41030753 ACTCGCACAAATGCTTTAGGGACTTAGCCCGGAATGTAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
*
41030794 ACTCGCACAAATGCCTTCAGGACTTAGCCCGGAATGTAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
* * *
41030835 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA-CTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
41030875 ACTAGCGCA-AAATGCCTTCGGGACTTAGCCCGG
1 ACT--CGCACAAATGCCTTCGGGACTTAGCCCGG
41030908 TTATCATCCA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 6 0.03
40 62 0.35
41 103 0.59
42 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (41 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATGTAATA
Found at i:41032771 original size:43 final size:42
Alignment explanation
Indices: 41032706--41032862 Score: 199
Period size: 43 Copynumber: 3.7 Consensus size: 42
41032696 AGCTCGTACA
*
41032706 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATA-CG
* * * *
41032749 GTGCCACTGTCCCAGACATGGTCTTACATGAAATCAAATACG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATACG
* *
41032791 ATGCCAATGTCCCAAACGTGGTCTTACATGTAAATCATAAGT-CA
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATCA-AA-TACG
*
41032835 ATGCCAATGTCCCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
41032863 CGAGAACACA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
42 28 0.29
43 40 0.41
44 29 0.30
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATACG
Found at i:41035481 original size:28 final size:28
Alignment explanation
Indices: 41035421--41035485 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
41035411 ACTTTTCACA
*
41035421 ACATTTAATGCGTTAATGCATTATCCCT
1 ACATTTAATGCGTTAATGCATTATCCAT
* *
41035449 ACATTTAATGCTTTAATGTC-TTTTCCAT
1 ACATTTAATGCGTTAATG-CATTATCCAT
*
41035477 GCATTTAAT
1 ACATTTAAT
41035486 CCCTAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (28 bp):
ACATTTAATGCGTTAATGCATTATCCAT
Found at i:41038111 original size:42 final size:41
Alignment explanation
Indices: 41037990--41038111 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 41
41037980 TACCATACCA
*
41037990 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACAT-GAATCTCATATCG
* * * *
41038032 ATGCCAAGAGCCCAGCTATGGTCTTGCATGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGAA-TCTCATATCG
*
41038075 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACATG-AATCTCA
41038112 ACTAACCCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 31 0.46
43 36 0.54
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACATGAATCTCATATCG
Found at i:41039157 original size:13 final size:13
Alignment explanation
Indices: 41039139--41039163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41039129 GCCCAAACGT
41039139 CAAAATTTTCAAA
1 CAAAATTTTCAAA
41039152 CAAAATTTTCAA
1 CAAAATTTTCAA
41039164 GAAATCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
CAAAATTTTCAAA
Found at i:41044087 original size:43 final size:42
Alignment explanation
Indices: 41044021--41044119 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 42
41044011 AGCTCGTACA
* * ***
41044021 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAATATCCCAGACAAGGTCTTACACAAAATCAAATAT-G
*
41044064 ATGCCACTATCCCAGACAAGGTCTTACACAAAATCAAATATG
1 ATGCCAATATCCCAGACAAGGTCTTACACAAAATCAAATATG
*
41044106 ATGCCAATGTCCCA
1 ATGCCAATATCCCA
41044120 AATGTAACAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 13 0.27
43 35 0.73
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (42 bp):
ATGCCAATATCCCAGACAAGGTCTTACACAAAATCAAATATG
Found at i:41044996 original size:37 final size:37
Alignment explanation
Indices: 41044937--41045008 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
41044927 AGCTCAGACG
*
41044937 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
41044974 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
41045009 ATATATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:41045278 original size:48 final size:48
Alignment explanation
Indices: 41045154--41045338 Score: 309
Period size: 48 Copynumber: 3.8 Consensus size: 48
41045144 GCACATCGCC
*
41045154 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
41045204 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
41045252 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
41045300 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
41045339 TGCATGTTCA
Statistics
Matches: 128, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
48 84 0.66
49 2 0.02
50 42 0.33
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:41045343 original size:98 final size:97
Alignment explanation
Indices: 41045154--41045337 Score: 318
Period size: 98 Copynumber: 1.9 Consensus size: 97
41045144 GCACATCGCC
*
41045154 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA-ATACATATTTCACATT
41045219 GACCATTCGGCTTTACCACATATGCATATCTCA
65 GACCATTCGGCTTTACCACATATGCATATCTCA
*
41045252 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
41045315 AGCCATTCGGCTTTACCACATAT
66 A-CCATTCGGCTTTACCACATAT
41045338 ATGCATGTTC
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
95 1 0.01
96 36 0.43
98 46 0.55
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (97 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
ACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:41045387 original size:47 final size:47
Alignment explanation
Indices: 41045308--41045501 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
41045298 CATACATATT
* * * *
41045308 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAATTCA
* * *
41045355 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCAAATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAATTCA
*
41045402 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAATTCA
* * ** *
41045449 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAATTCA
41045496 TCACAT
1 TCACAT
41045502 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAATTCA
Found at i:41045428 original size:22 final size:22
Alignment explanation
Indices: 41045401--41045472 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
41045391 GCTCAAATTC
41045401 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
41045423 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
41045447 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41045470 ATC
1 ATC
41045473 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41045495 original size:94 final size:94
Alignment explanation
Indices: 41045261--41045501 Score: 281
Period size: 94 Copynumber: 2.6 Consensus size: 94
41045251 ATACATATTT
* * * *
41045261 CACATTAGCCATTCGGCTTTA-C-CACATATACATATCTCATACATAT-TTCACATTAGCCATTC
1 CACATTGGCCATTCGGCCTTATCACACATATACACA-CTCA-A-AT-TCATCACATTAGCCATTC
* *
41045323 GGCTTTACCACATATATGCATGTTCATATTCAC
62 GGCCTTACCACATATATGCATGTTCACATTCAC
* ** *
41045356 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCAAATTCATCACATTGGCCATTCGGCC
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCAAATTCATCACATTAGCCATTCGGCC
* *
41045421 TTATCACATATATGCATGTTCACATTCAT
66 TTACCACATATATGCATGTTCACATTCAC
* * * *
41045450 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCAAATTCATCACAT
41045502 AAAATCCTAA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 90 0.71
95 20 0.16
96 5 0.04
97 10 0.08
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (94 bp):
CACATTGGCCATTCGGCCTTATCACACATATACACACTCAAATTCATCACATTAGCCATTCGGCC
TTACCACATATATGCATGTTCACATTCAC
Found at i:41050804 original size:27 final size:27
Alignment explanation
Indices: 41050774--41050892 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
41050764 AAAGAGATTC
*
41050774 CTTTCAAAGTTTGCCACAAAGGCTATT
1 CTTTCAGAGTTTGCCACAAAGGCTATT
* * *
41050801 CTTTCAGAGTTTCCCACAAGGGTTATT
1 CTTTCAGAGTTTGCCACAAAGGCTATT
* * *
41050828 CTTTTAGAGTTCGCCACAGAGGCTA-T
1 CTTTCAGAGTTTGCCACAAAGGCTATT
*
41050854 CATTTCAGAGTTTGCCACAAAGGCTATC
1 C-TTTCAGAGTTTGCCACAAAGGCTATT
41050882 CTTTCAGAGTT
1 CTTTCAGAGTT
41050893 CACTACGAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.03
27 73 0.96
28 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (27 bp):
CTTTCAGAGTTTGCCACAAAGGCTATT
Found at i:41050893 original size:54 final size:55
Alignment explanation
Indices: 41050732--41050908 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 55
41050722 AATAGAGTAT
* * * * * *
41050732 GCCACTAAGGCGATCCATTTC-GAGTTCACCACAAAGAGAT-TCCTTTCAAAGTTT
1 GCCACAAAGGCTATTCATTTCAGAGTTTACCACAAAG-GATATCCTTTCAGAGTTC
* * * * *
41050786 GCCACAAAGGCTATTC-TTTCAGAGTTTCCCACAAGGGTTATTCTTTTAGAGTTC
1 GCCACAAAGGCTATTCATTTCAGAGTTTACCACAAAGGATATCCTTTCAGAGTTC
* * *
41050840 GCCACAGAGGCTA-TCATTTCAGAGTTTGCCACAAAGGCTATCCTTTCAGAGTTC
1 GCCACAAAGGCTATTCATTTCAGAGTTTACCACAAAGGATATCCTTTCAGAGTTC
* * *
41050894 ACTACGAAGGCTATT
1 GCCACAAAGGCTATT
41050909 TTTTAGCAGT
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
53 8 0.08
54 89 0.91
55 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (55 bp):
GCCACAAAGGCTATTCATTTCAGAGTTTACCACAAAGGATATCCTTTCAGAGTTC
Found at i:41050903 original size:27 final size:27
Alignment explanation
Indices: 41050733--41050907 Score: 117
Period size: 27 Copynumber: 6.5 Consensus size: 27
41050723 ATAGAGTATG
* *
41050733 CCACTAAGGCGATCCATTTC-GAGTTCA
1 CCACAAAGGCTAT-CATTTCAGAGTTCA
* * * **
41050760 CCACAAAGAGAT-TCCTTTCAAAGTTTG
1 CCACAAAG-GCTATCATTTCAGAGTTCA
41050787 CCACAAAGGCTATTC-TTTCAGAGTTTC-
1 CCACAAAGGCTA-TCATTTCAGAG-TTCA
* * * *
41050814 CCACAAGGGTTATTC-TTTTAGAGTTCG
1 CCACAAAGGCTA-TCATTTCAGAGTTCA
* **
41050841 CCACAGAGGCTATCATTTCAGAGTTTG
1 CCACAAAGGCTATCATTTCAGAGTTCA
*
41050868 CCACAAAGGCTATCCTTTCAGAGTTCA
1 CCACAAAGGCTATCATTTCAGAGTTCA
* *
41050895 CTACGAAGGCTAT
1 CCACAAAGGCTAT
41050908 TTTTTAGCAG
Statistics
Matches: 117, Mismatches: 24, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
26 12 0.10
27 100 0.85
28 5 0.04
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (27 bp):
CCACAAAGGCTATCATTTCAGAGTTCA
Found at i:41053958 original size:24 final size:26
Alignment explanation
Indices: 41053931--41053979 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
41053921 AGTTCATGCA
41053931 ATATTAAAGC-ATTTAA-ATACAATT
1 ATATTAAAGCTATTTAACATACAATT
41053955 ATATTAAAGCTTATTTAACATACAA
1 ATATTAAAGC-TATTTAACATACAA
41053980 ACTTACCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACAATT
Found at i:41062803 original size:41 final size:42
Alignment explanation
Indices: 41062756--41062869 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 42
41062746 TGATTTTCTG
* *
41062756 TAAGACCACATCTGGGAAGTTGGCATTGT-TTTGATTTCGTA
1 TAAGACCACATCTGGGAAGTTGGCATTGTATTTGATTACATA
* *
41062797 TAAGACC-CTATCTGGGACAG-TGGCATCGATATTTGATTACATG
1 TAAGACCAC-ATCTGGGA-AGTTGGCATTG-TATTTGATTACATA
* * * *
41062840 CAAGACCACGTCTGGGACGTTGGCGTTGTA
1 TAAGACCACATCTGGGAAGTTGGCATTGTA
41062870 CGAGCTTTCC
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
40 1 0.02
41 22 0.38
42 6 0.10
43 28 0.48
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TAAGACCACATCTGGGAAGTTGGCATTGTATTTGATTACATA
Found at i:41066814 original size:20 final size:20
Alignment explanation
Indices: 41066773--41066817 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41066763 AGCACATGTA
*
41066773 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTAGAACTT
*
41066793 TTCATCAAAATTTT-TAACTT
1 TTCAT-AAAATTTTAGAACTT
41066813 TTCAT
1 TTCAT
41066818 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTTAGAACTT
Found at i:41068754 original size:31 final size:31
Alignment explanation
Indices: 41068706--41068783 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
41068696 TTTTGGAGAG
* * *
41068706 TCACATGCCCGTTTGGGTAGGCCGTGTGGTC
1 TCACACGCCCGTGTGGGTAGGCCGTGTGGCC
*
41068737 TCACACGCCTGTGTGGGTAGGCCGTGTGGCC
1 TCACACGCCCGTGTGGGTAGGCCGTGTGGCC
* *
41068768 TTACACTCCCGTGTGG
1 TCACACGCCCGTGTGG
41068784 CTCTGGACAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.10, C:0.28, G:0.35, T:0.27
Consensus pattern (31 bp):
TCACACGCCCGTGTGGGTAGGCCGTGTGGCC
Found at i:41068798 original size:20 final size:18
Alignment explanation
Indices: 41068758--41068801 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
41068748 TGTGGGTAGG
* *
41068758 CCGTGTGGCCTTACACTC
1 CCGTGTGGCCTGACACAC
41068776 CCGTGTGGCTCTGGACACAC
1 CCGTGTGGC-CT-GACACAC
41068796 CCGTGT
1 CCGTGT
41068802 CCTCAAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.11, C:0.36, G:0.27, T:0.25
Consensus pattern (18 bp):
CCGTGTGGCCTGACACAC
Found at i:41073070 original size:22 final size:22
Alignment explanation
Indices: 41073042--41073085 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41073032 AGAGATAACT
41073042 CTGGTAGAACCTGATGCTCGGG
1 CTGGTAGAACCTGATGCTCGGG
41073064 CTGGTAGAACCTGATGCTCGGG
1 CTGGTAGAACCTGATGCTCGGG
41073086 TTTAATCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (22 bp):
CTGGTAGAACCTGATGCTCGGG
Found at i:41088707 original size:40 final size:40
Alignment explanation
Indices: 41088611--41088794 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
41088601 TTGAATGATG
* * * *
41088611 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
41088651 TCCGGAC-AAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41088690 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41088730 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41088771 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41088795 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
39 37 0.28
40 91 0.70
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41088824 original size:39 final size:40
Alignment explanation
Indices: 41088662--41088827 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
41088652 CCGGACAAGA
*
41088662 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
* *
41088702 CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
* *
41088742 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCT--AT
1 TCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAAT
** *
41088780 GTCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAAT
1 -TCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAAT
41088820 TCCGAAGG
1 TCCGAAGG
41088828 TACGTGATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
38 7 0.06
39 30 0.27
40 73 0.65
41 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
Found at i:41094063 original size:9 final size:9
Alignment explanation
Indices: 41094049--41094170 Score: 109
Period size: 9 Copynumber: 12.9 Consensus size: 9
41094039 ATGTATTAGT
41094049 TAAGTTATG
1 TAAGTTATG
41094058 TAAGTTGTTATG
1 TAA---GTTATG
*
41094070 TACGTTATG
1 TAAGTTATG
*
41094079 TGAGTTATG
1 TAAGTTATG
*
41094088 TAAATTATG
1 TAAGTTATG
41094097 TAAGTTATG
1 TAAGTTATG
*
41094106 TAAATTATG
1 TAAGTTATG
41094115 TAAGTCGTTATG
1 TAA---GTTATG
* *
41094127 TAAATTACG
1 TAAGTTATG
*
41094136 TAAGTTATA
1 TAAGTTATG
*
41094145 TGAGTTATG
1 TAAGTTATG
41094154 TAAGTTATG
1 TAAGTTATG
*
41094163 TAATTTAT
1 TAAGTTAT
41094171 TGAAGTAATG
Statistics
Matches: 90, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
9 74 0.82
12 16 0.18
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:41094125 original size:57 final size:57
Alignment explanation
Indices: 41094053--41094170 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
41094043 ATTAGTTAAG
* ** * * *
41094053 TTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTAAA
1 TTATGTAAGTCGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
* * *
41094110 TTATGTAAGTCGTTATGTAAATTACGTAAGTTATATGAGTTATGTAAGTTATGTAAT
1 TTATGTAAGTCGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
41094167 TTAT
1 TTAT
41094171 TGAAGTAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (57 bp):
TTATGTAAGTCGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
Found at i:41098071 original size:25 final size:25
Alignment explanation
Indices: 41098043--41098097 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
41098033 GAGAGTGACA
*
41098043 GCGAAGGGACGCAGAAGAGACAACG
1 GCGAAGGGACACAGAAGAGACAACG
* *
41098068 GCGAAGGGACACAGAAGAGACGATG
1 GCGAAGGGACACAGAAGAGACAACG
41098093 GCGAA
1 GCGAA
41098098 CAACGATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.40, T:0.02
Consensus pattern (25 bp):
GCGAAGGGACACAGAAGAGACAACG
Found at i:41099657 original size:14 final size:14
Alignment explanation
Indices: 41099637--41099681 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
41099627 TCCTACACCT
41099637 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
41099651 TATACCCTAAA-TCA
1 TAAACCCTAAACT-A
*
41099665 AAAACCCTAAACTA
1 TAAACCCTAAACTA
41099679 TAA
1 TAA
41099682 TGATAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.04
14 23 0.92
15 1 0.04
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:41099966 original size:7 final size:7
Alignment explanation
Indices: 41099954--41100066 Score: 95
Period size: 7 Copynumber: 16.1 Consensus size: 7
41099944 AAAAACGCCA
41099954 CTAAACC
1 CTAAACC
41099961 CTAAACC
1 CTAAACC
*
41099968 CTAAACA
1 CTAAACC
*
41099975 CTAAACT
1 CTAAACC
41099982 CTAAACC
1 CTAAACC
*
41099989 CTTAACC
1 CTAAACC
*
41099996 CTTAACC
1 CTAAACC
*
41100003 CCAAACC
1 CTAAACC
*
41100010 CTTACACC
1 C-TAAACC
*
41100018 TTAAACTC
1 CTAAAC-C
41100026 C--AACC
1 CTAAACC
*
41100031 CTAACCC
1 CTAAACC
41100038 CTAAACC
1 CTAAACC
*
41100045 CTAAATC
1 CTAAACC
* *
41100052 ATAATCC
1 CTAAACC
41100059 CTAAACC
1 CTAAACC
41100066 C
1 C
41100067 ATAATTCATC
Statistics
Matches: 83, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
5 2 0.02
6 3 0.04
7 73 0.88
8 5 0.06
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:41100112 original size:7 final size:7
Alignment explanation
Indices: 41100104--41100155 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
41100094 AGTTAACTCT
*
41100104 TAAACCT
1 TAAACCA
*
41100111 TAAACCC
1 TAAACCA
41100118 TAAACCA
1 TAAACCA
* * *
41100125 TATATCT
1 TAAACCA
41100132 TAAACCA
1 TAAACCA
41100139 TAAACCA
1 TAAACCA
*
41100146 TAAACTA
1 TAAACCA
41100153 TAA
1 TAA
41100156 TGATAATTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCA
Found at i:41100409 original size:41 final size:41
Alignment explanation
Indices: 41100312--41100612 Score: 412
Period size: 41 Copynumber: 7.4 Consensus size: 41
41100302 GTTATATGAC
* *
41100312 TTTTAGTGGCGTTTTTCCAAAAGAGCCGCTAATGCTCTGG-
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
41100352 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
41100393 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
41100434 TTTTAGCGGCGTTTTTACAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
41100475 TTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * * * *
41100516 TTTTAGCGACGTTTTGCTAGAAGCACCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * *
41100556 TTTTTGCAGCGTTTTTTACTAAAA-CGCCGCTATTGCTCT-GT
1 TTTTAGCGGCG-TTTTT-CCAAAAGCGCCGCTAATGCTCTGGT
*
41100597 TTTTAGTGGCGTTTTT
1 TTTTAGCGGCGTTTTT
41100613 GGTAAAACGC
Statistics
Matches: 233, Mismatches: 25, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
40 52 0.22
41 176 0.76
42 5 0.02
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:41100681 original size:12 final size:12
Alignment explanation
Indices: 41100666--41100691 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41100656 GTTTTTTGAT
41100666 AAAACGCCGCTA
1 AAAACGCCGCTA
41100678 AAAACGCCGCTA
1 AAAACGCCGCTA
41100690 AA
1 AA
41100692 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:41101180 original size:30 final size:30
Alignment explanation
Indices: 41101144--41101206 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
41101134 CGAGATGGCC
41101144 TAAAAGCCCTTTTAGTATTTTTATTGACTA
1 TAAAAGCCCTTTTAGTATTTTTATTGACTA
41101174 TAAAAGCCCTTTTAGTATTTTTATTGACTA
1 TAAAAGCCCTTTTAGTATTTTTATTGACTA
41101204 TAA
1 TAA
41101207 CAGAATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (30 bp):
TAAAAGCCCTTTTAGTATTTTTATTGACTA
Found at i:41102974 original size:46 final size:46
Alignment explanation
Indices: 41102921--41103013 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
41102911 GCATAACTTA
41102921 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCGCAT
1 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCGCAT
* **
41102967 GTCTCTATAAAGAAGATCACCTGAGGATTATACATCTTCAGCGCAT
1 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCGCAT
41103013 G
1 G
41103014 CCGAAGTCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (46 bp):
GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCGCAT
Found at i:41104878 original size:29 final size:29
Alignment explanation
Indices: 41104836--41104903 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
41104826 AATTAGCTAC
* *
41104836 TTGATTCACCTTCTGCGTGTAAGGTAAGG
1 TTGAATCACCTTCTGCGTGTAAGATAAGG
*
41104865 TTGAATCACCTTCTGCGTGTAAGATAATG
1 TTGAATCACCTTCTGCGTGTAAGATAAGG
*
41104894 TTGAACCACC
1 TTGAATCACC
41104904 CTTCCCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (29 bp):
TTGAATCACCTTCTGCGTGTAAGATAAGG
Found at i:41105515 original size:20 final size:20
Alignment explanation
Indices: 41105492--41105532 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41105482 CTTTAAATTG
41105492 ATTTGAATAAAAGCAAATCA
1 ATTTGAATAAAAGCAAATCA
* * *
41105512 ATTTGATTGAAATCAAATCA
1 ATTTGAATAAAAGCAAATCA
41105532 A
1 A
41105533 AACGAGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (20 bp):
ATTTGAATAAAAGCAAATCA
Found at i:41109939 original size:33 final size:33
Alignment explanation
Indices: 41109897--41109962 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41109887 AATATATAAT
41109897 AAGTTATTGTTTATGAATAAACAAATAAGGTAG
1 AAGTTATTGTTTATGAATAAACAAATAAGGTAG
41109930 AAGTTATTGTTTATGAATAAACAAATAAGGTAG
1 AAGTTATTGTTTATGAATAAACAAATAAGGTAG
41109963 GTGCTAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (33 bp):
AAGTTATTGTTTATGAATAAACAAATAAGGTAG
Found at i:41111210 original size:16 final size:16
Alignment explanation
Indices: 41111189--41111240 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
41111179 TGTATTTGTA
41111189 AATTTTGATTTTATAT
1 AATTTTGATTTTATAT
* *
41111205 AATTTT-A-TATATAA
1 AATTTTGATTTTATAT
* *
41111219 AATTTTGATTTGATCT
1 AATTTTGATTTTATAT
41111235 AATTTT
1 AATTTT
41111241 TATAGATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
16 15 0.54
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (16 bp):
AATTTTGATTTTATAT
Found at i:41111224 original size:30 final size:29
Alignment explanation
Indices: 41111188--41111244 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
41111178 TTGTATTTGT
*
41111188 AAATTTTGATTTTATATAATTTTATATATA
1 AAATTTTGATTTGATATAATTTT-TATATA
*
41111218 AAATTTTGATTTGATCTAATTTTTATA
1 AAATTTTGATTTGATATAATTTTTATA
41111245 GATTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (29 bp):
AAATTTTGATTTGATATAATTTTTATATA
Found at i:41111543 original size:15 final size:16
Alignment explanation
Indices: 41111513--41111550 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41111503 TTAAAAACTA
41111513 ATTTAAAAAAATATTT
1 ATTTAAAAAAATATTT
41111529 ATTTAAAAATAAT-TTT
1 ATTTAAAAA-AATATTT
*
41111545 TTTTAA
1 ATTTAA
41111551 CTTTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAAAAAATATTT
Found at i:41116378 original size:47 final size:47
Alignment explanation
Indices: 41116271--41116605 Score: 499
Period size: 47 Copynumber: 7.1 Consensus size: 47
41116261 GAAATGATAG
41116271 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
41116320 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41116367 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * *
41116414 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41116461 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41116508 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
41116555 CAAGGCCGAGTGGCCAACGTAATGGATGTGGAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41116602 TAAG
1 TAAG
41116606 TCCCGAAAGG
Statistics
Matches: 263, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 228 0.87
49 35 0.13
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41116780 original size:37 final size:37
Alignment explanation
Indices: 41116724--41116802 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41116714 CCGAGCTCTA
* * *
41116724 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41116761 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41116798 AAGAC
1 AAGAC
41116803 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41120409 original size:47 final size:47
Alignment explanation
Indices: 41120267--41120423 Score: 196
Period size: 47 Copynumber: 3.4 Consensus size: 47
41120257 AATAGCACAA
*
41120267 CCCAGACACGTCTTACACTAGCTATCTGTGTTGAGGCCGATGCATGT
1 CCCAGACACGTCTTACACTAGCTATCTCTGTTGAGGCCGATGCATGT
* * * * * *
41120314 CCTAGACATGTCTTACACTAGC-A-CAACTCTT-A-GTCGATGCGTGT
1 CCCAGACACGTCTTACACTAGCTATC-TCTGTTGAGGCCGATGCATGT
*
41120358 CCCAGACACGTCTTACACTAGCTATCTTTGTTGAGGCCGATGCATGT
1 CCCAGACACGTCTTACACTAGCTATCTCTGTTGAGGCCGATGCATGT
*
41120405 CCCAGACATGTCTTACACT
1 CCCAGACACGTCTTACACT
41120424 GGCTCTCAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
44 30 0.33
45 6 0.07
46 6 0.07
47 48 0.53
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
CCCAGACACGTCTTACACTAGCTATCTCTGTTGAGGCCGATGCATGT
Found at i:41121598 original size:37 final size:37
Alignment explanation
Indices: 41121548--41121626 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41121538 TTATTACGAA
* * *
41121548 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41121585 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41121622 GTCTT
1 GTCTT
41121627 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41121818 original size:47 final size:47
Alignment explanation
Indices: 41121744--41122057 Score: 594
Period size: 47 Copynumber: 6.7 Consensus size: 47
41121734 GCCCTTCGGG
* *
41121744 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41121792 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41121839 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41121886 ACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41121932 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41121979 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41122026 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
41122058 ATACTATCAT
Statistics
Matches: 263, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
46 46 0.17
47 213 0.81
48 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:41122002 original size:140 final size:140
Alignment explanation
Indices: 41121744--41122057 Score: 592
Period size: 140 Copynumber: 2.2 Consensus size: 140
41121734 GCCCTTCGGG
*
41121744 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACTTTCACATTCATCAC
1 ACTT-TCACATTCATCACATCGGCCATTAGG-CCTATCACATATATACACTTTCACATTCATCAC
41121809 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
64 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41121874 TCACATATATAC
129 TCACATATATAC
*
41121886 ACTTTCACATTCATCACATCGGCCATTAGGCTTATCACATATATACACTTTCACATTCATCACAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACTTTCACATTCATCACAT
41121951 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
66 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
41122016 ACATATATAC
131 ACATATATAC
41122026 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
41122058 ATACTATCAT
Statistics
Matches: 169, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
140 139 0.82
141 26 0.15
142 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (140 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
ACATATATAC
Found at i:41125656 original size:40 final size:40
Alignment explanation
Indices: 41125583--41125922 Score: 375
Period size: 40 Copynumber: 8.5 Consensus size: 40
41125573 AGCATGATTA
* * * *
41125583 CTCTTC-GGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* ** * *
41125622 CTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
*
41125662 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* * *
41125702 CTCCTCGGGACTTAGCCCGGATATATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
41125742 CTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
41125782 CTCTTCGGGACTTAGCCCGGATACATCGCTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
** * * *
41125822 CTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATG
1 CTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATG
* ** *
41125863 C-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAATG
41125903 C-CTTCGGGACTTAGCCCGGA
1 CTCTTCGGGACTTAGCCCGGA
41125923 CATCATTCGA
Statistics
Matches: 258, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
39 8 0.03
40 231 0.90
41 19 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
Found at i:41126267 original size:29 final size:29
Alignment explanation
Indices: 41126228--41126306 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
41126218 CTTAATAATC
*
41126228 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
41126258 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
41126287 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41126307 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:41126349 original size:43 final size:43
Alignment explanation
Indices: 41126288--41126390 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
41126278 TGCATTTCAA
41126288 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
41126331 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
41126374 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
41126391 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:41128297 original size:37 final size:37
Alignment explanation
Indices: 41128247--41128325 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41128237 TTATTACGAA
* * *
41128247 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41128284 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41128321 GTCTT
1 GTCTT
41128326 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41128554 original size:47 final size:47
Alignment explanation
Indices: 41128443--41128618 Score: 316
Period size: 47 Copynumber: 3.7 Consensus size: 47
41128433 GCCCTTCGGG
*
41128443 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
41128493 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41128540 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41128587 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
41128619 ATACTATCAT
Statistics
Matches: 125, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
47 87 0.70
49 34 0.27
50 4 0.03
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:41134009 original size:28 final size:29
Alignment explanation
Indices: 41133945--41134009 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
41133935 CTTTTTTTAT
* **
41133945 TAATTTATATTTTTAAATTTTTTAAAATGT
1 TAATATATATTTTTAAA-TTTTTAAAATAA
**
41133975 TTTTATATATTTTTAAA-TTTTAAAATAA
1 TAATATATATTTTTAAATTTTTAAAATAA
41134003 TAATATA
1 TAATATA
41134010 AATAACTTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 14 0.50
30 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
TAATATATATTTTTAAATTTTTAAAATAA
Found at i:41145647 original size:11 final size:12
Alignment explanation
Indices: 41145622--41145649 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41145612 TGAGTGTAGT
41145622 AAAATATTTTAA
1 AAAATATTTTAA
41145634 AAAATATTTTAA
1 AAAATATTTTAA
41145646 AAAA
1 AAAA
41145650 GAGATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:41148758 original size:51 final size:52
Alignment explanation
Indices: 41148637--41148762 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
41148627 ATGTCACTAG
41148637 TGACT-CAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
1 TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
* * *
41148688 TG-GTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTT
1 TGACT-ACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
*
41148739 TGACTACAAGGGTGGTACTATGTG
1 TGACTACAAGTGTGGTACTATGTG
41148763 CAGCCCACCA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.01
51 31 0.46
52 35 0.52
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (52 bp):
TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
Found at i:41150905 original size:40 final size:40
Alignment explanation
Indices: 41150860--41151011 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
41150850 ATAACCACAA
* * *
41150860 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
41150900 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
41150940 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
41150980 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41151012 CATTCAAATG
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41159046 original size:40 final size:40
Alignment explanation
Indices: 41159001--41159152 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
41158991 ATAACCACAA
* * *
41159001 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
41159041 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
41159081 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
41159121 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41159153 CATTCAAATG
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41163107 original size:24 final size:23
Alignment explanation
Indices: 41163065--41163148 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
41163055 GAGATGGAAA
* * *
41163065 TGAAGACGAAAACAGGGGTGGAGG
1 TGAAGATGAAGAC-GGGGTCGAGG
* *
41163089 TGAAGATGAAGACGAGGGTCAAGA
1 TGAAGATGAAGACG-GGGTCGAGG
* *
41163113 TGAAGATGAATATGGGAGTCGAGG
1 TGAAGATGAAGACGGG-GTCGAGG
*
41163137 TAAAGATGAAGA
1 TGAAGATGAAGA
41163149 TGATGATCAT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.40, C:0.06, G:0.39, T:0.14
Consensus pattern (23 bp):
TGAAGATGAAGACGGGGTCGAGG
Found at i:41168795 original size:20 final size:20
Alignment explanation
Indices: 41168745--41168784 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41168735 AATTAGATTA
*
41168745 CAAAAAGTATCGATACCTTT
1 CAAAAAGTATCGATACATTT
*
41168765 CAAAAAATATCGATACATTT
1 CAAAAAGTATCGATACATTT
41168785 TACCAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
CAAAAAGTATCGATACATTT
Found at i:41171753 original size:16 final size:16
Alignment explanation
Indices: 41171732--41171763 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41171722 GAAATGTTAG
41171732 AATTTAAATATACTAT
1 AATTTAAATATACTAT
41171748 AATTTAAATATACTAT
1 AATTTAAATATACTAT
41171764 GGAATATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAATATACTAT
Found at i:41186411 original size:27 final size:27
Alignment explanation
Indices: 41186380--41186556 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
41186370 TAAATTGTAC
*
41186380 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
41186407 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
41186433 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
41186461 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
41186489 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
41186515 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
41186542 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41186557 GACTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.18
27 81 0.64
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:41186526 original size:81 final size:81
Alignment explanation
Indices: 41186381--41186535 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
41186371 AAATTGTACA
* *
41186381 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
41186446 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* *
41186462 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
*
41186525 GTGCGAGTTGA
64 GTGCGAATTGA
41186536 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 41 0.61
82 25 0.37
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41186547 original size:81 final size:81
Alignment explanation
Indices: 41186377--41186556 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
41186367 GATTAAATTG
* *
41186377 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41186442 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * *
41186458 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41186521 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41186539 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41186557 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 58 0.69
82 25 0.30
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41190996 original size:15 final size:15
Alignment explanation
Indices: 41190957--41191035 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
41190947 GTATCTTGGG
*
41190957 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
41190972 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
41190987 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
41191001 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
41191016 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
41191030 TTTCTT
1 TTTCTT
41191036 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:41191020 original size:29 final size:29
Alignment explanation
Indices: 41190948--41191034 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
41190938 CATAGTATCG
* * * *
41190948 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
41190978 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
41191007 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
41191035 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:41193469 original size:46 final size:45
Alignment explanation
Indices: 41193402--41193575 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 45
41193392 TATTTGGGCA
41193402 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
41193448 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
41193495 TCCGAGCTCGTTGAGTTGAGT--GAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
41193539 CCCGAGA-TCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41193576 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 14, Indels: 20
0.75 0.10 0.14
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 1 0.01
44 22 0.21
45 6 0.06
46 42 0.40
47 24 0.23
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:41193555 original size:91 final size:92
Alignment explanation
Indices: 41193398--41193568 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 92
41193388 CGGATATTTG
* *
41193398 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41193463 TTGAGTCCGAGTTCGAGAGATGTAACTA
65 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
41193491 GGCATCCGAGCTCGTTGAGTTGAGT-GAGTTCACTTATGGATGCGAACGCCCGAGA-TCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGA-ACTCGTTGAG
41193554 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
41193569 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
91 49 0.66
92 1 0.01
93 24 0.32
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:41196971 original size:20 final size:19
Alignment explanation
Indices: 41196935--41196985 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
41196925 TAGGGCTATT
*
41196935 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
41196954 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
41196974 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
41196986 GTTTCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:41197727 original size:46 final size:44
Alignment explanation
Indices: 41197637--41197752 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 44
41197627 TATGTGTGCT
*
41197637 AGTGTAAGAAATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTATGAGAGCC
*
41197683 AGTGTAAGACATGTCTGGGACATGCATCGG-CATTGA-GACAAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATT-ATG---AGAGCC
*
41197729 AGTGTAAGACATGTATGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
41197753 TATGGGACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
43 5 0.08
44 1 0.02
46 57 0.90
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.22
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATTATGAGAGCC
Found at i:41197752 original size:11 final size:11
Alignment explanation
Indices: 41197736--41197763 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41197726 GCTAGTGTAA
41197736 GACATGTATGG
1 GACATGTATGG
41197747 GACATGTATGG
1 GACATGTATGG
41197758 GACATG
1 GACATG
41197764 CATCAGCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.36, T:0.25
Consensus pattern (11 bp):
GACATGTATGG
Found at i:41197808 original size:59 final size:57
Alignment explanation
Indices: 41197690--41197811 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 57
41197680 GCCAGTGTAA
* * * *
41197690 GACATGTCTGGGACATGCATCGGCATTGAGACAAGAGCTAGTGTAAGACATGTATGG
1 GACATGTATGGGACATGCATCAGCATCGAGACAAAAGCTAGTGTAAGACATGTATGG
* * * *
41197747 GACATGTATGGGACATGCATCAGCCTCGAGATATACAAGCTAGTGTAAGACCTGTCTGG
1 GACATGTATGGGACATGCATCAGCATCGAGACA-A-AAGCTAGTGTAAGACATGTATGG
41197806 GACATG
1 GACATG
41197812 GCATCGACAC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 28 0.51
58 1 0.02
59 26 0.47
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (57 bp):
GACATGTATGGGACATGCATCAGCATCGAGACAAAAGCTAGTGTAAGACATGTATGG
Found at i:41197857 original size:48 final size:49
Alignment explanation
Indices: 41197755--41197909 Score: 165
Period size: 48 Copynumber: 3.2 Consensus size: 49
41197745 GGGACATGTA
* * * *
41197755 TGGGACAT-GCATCAGCCTCGAGATATACAAGCTAGTGTAAGACCTGTC
1 TGGGACATGGCATCAGCCTCGATAGATAAAAGCCAGTGTAAGACCTGTC
* *
41197803 TGGGACATGGCATC-GACAC-CGATAGATGAGAGCCAGTGTAAGACCTGTC
1 TGGGACATGGCATCAG-C-CTCGATAGATAAAAGCCAGTGTAAGACCTGTC
* * * * *
41197852 T-GGACACGACATCAGCCTCGATATATAAAAGTCAGTGTAAGACCTATC
1 TGGGACATGGCATCAGCCTCGATAGATAAAAGCCAGTGTAAGACCTGTC
41197900 TGGGACATGG
1 TGGGACATGG
41197910 TGTCGGCATC
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
47 1 0.01
48 46 0.53
49 38 0.44
50 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (49 bp):
TGGGACATGGCATCAGCCTCGATAGATAAAAGCCAGTGTAAGACCTGTC
Found at i:41203142 original size:13 final size:14
Alignment explanation
Indices: 41203122--41203191 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 14
41203112 TTTATGTTAT
41203122 ATATATATAATATA
1 ATATATATAATATA
41203136 ATA-ATATAATATA
1 ATATATATAATATA
*
41203149 TTATAATATTAATACCTA
1 ATAT-ATA-TAATA--TA
*
41203167 A-ATAT-TAATTTA
1 ATATATATAATATA
41203179 ATATAT-TAATATA
1 ATATATATAATATA
41203192 TATTTTAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.07
13 22 0.48
14 7 0.15
15 3 0.07
16 7 0.15
17 2 0.04
18 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATAATATA
Found at i:41216619 original size:43 final size:44
Alignment explanation
Indices: 41216499--41216620 Score: 151
Period size: 43 Copynumber: 2.8 Consensus size: 44
41216489 AGCTCATACA
* *
41216499 ATGCCAACGTCCTAGACATGGTCTTACATGT-GATCAAATATTG
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
* * * * * *
41216542 ATGCCATTGTCCCAAATAGGGTCTTACACG-AAATCAAATA-TG
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
41216584 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCA
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCA
41216621 TAAGTCGATG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 26 0.41
43 37 0.59
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
Found at i:41221372 original size:23 final size:23
Alignment explanation
Indices: 41221342--41221386 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
41221332 TTGGAGTGCT
41221342 ATTGGGCTATTTGCACACTTTCG
1 ATTGGGCTATTTGCACACTTTCG
41221365 ATTGGGCTATTTGCACACTTTC
1 ATTGGGCTATTTGCACACTTTC
41221387 ACAAACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (23 bp):
ATTGGGCTATTTGCACACTTTCG
Found at i:41221848 original size:26 final size:27
Alignment explanation
Indices: 41221810--41221875 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
41221800 TTTACCTAGA
*
41221810 GCCCCTA-ATTGATAAAATGACT-TTAT
1 GCCCCTATA-TGATAAAATAACTGTTAT
* *
41221836 GCCCTTATGTGATAAAATAACTGTTAT
1 GCCCCTATATGATAAAATAACTGTTAT
41221863 GCCCCTATATGAT
1 GCCCCTATATGAT
41221876 GTATGATTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.35
Consensus pattern (27 bp):
GCCCCTATATGATAAAATAACTGTTAT
Found at i:41222514 original size:20 final size:20
Alignment explanation
Indices: 41222489--41222536 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
41222479 CCTCTTTGGA
41222489 TTTTATTTTTAATTTGGGAT
1 TTTTATTTTTAATTTGGGAT
*
41222509 TTTTATTTTTAATTTGGGGT
1 TTTTATTTTTAATTTGGGAT
41222529 TTTTATTT
1 TTTTATTT
41222537 GATTCGATTT
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:0.17, C:0.00, G:0.15, T:0.69
Consensus pattern (20 bp):
TTTTATTTTTAATTTGGGAT
Found at i:41222963 original size:42 final size:42
Alignment explanation
Indices: 41222869--41223004 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 42
41222859 GTGTTACACT
* *
41222869 ACGTCTGGGACGTTGGCATCG-ACTTATGATTTACGTGTAAGACC
1 ACGTCTGGGATGTTGGCATCGTAC-T-TGATTT-CATGTAAGACC
41222913 ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
1 ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
* * * *
41222955 -CTGTCTGGGATAG-TGGCATCAATATTTGATTACATATAAGACC
1 AC-GTCTGGGAT-GTTGGCATC-GTACTTGATTTCATGTAAGACC
*
41222998 ACATCTG
1 ACGTCTG
41223005 AGACATTGGC
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.32
43 29 0.36
44 22 0.28
45 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
Found at i:41232933 original size:40 final size:40
Alignment explanation
Indices: 41232771--41232919 Score: 219
Period size: 40 Copynumber: 3.7 Consensus size: 40
41232761 TATTCAGATG
* * *
41232771 ATAACCGGGCTAAGTCCCGTAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41232811 A-ATTCCGGGCTAAGTACCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41232851 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41232891 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41232920 AGCAAGTAGC
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 95 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41236768 original size:21 final size:23
Alignment explanation
Indices: 41236739--41236787 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
41236729 CAACAAATGC
*
41236739 ACAAGATAATGGCACATTTGCAT
1 ACAACATAATGGCACATTTGCAT
41236762 CACATAACATAATGGCACATTTGCAT
1 -AC--AACATAATGGCACATTTGCAT
41236788 CACATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
26 20 0.91
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (23 bp):
ACAACATAATGGCACATTTGCAT
Found at i:41236773 original size:26 final size:26
Alignment explanation
Indices: 41236744--41236798 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
41236734 AATGCACAAG
41236744 ATAATGGCACATTTGCATCACATAAC
1 ATAATGGCACATTTGCATCACATAAC
*
41236770 ATAATGGCACATTTGCATCACATATC
1 ATAATGGCACATTTGCATCACATAAC
41236796 ATA
1 ATA
41236799 TATCAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
ATAATGGCACATTTGCATCACATAAC
Found at i:41237480 original size:43 final size:45
Alignment explanation
Indices: 41237378--41237516 Score: 121
Period size: 43 Copynumber: 3.2 Consensus size: 45
41237368 GTCCCAGACT
**
41237378 TGGTCTTACATGT-AATCAAATATCGATGCCACTGTCCCAAACAG
1 TGGTCTTACATGTAAATCAAATATCGATGCCACCATCCCAAACAG
* * * * *
41237422 -GTTCTTACACG-AAATCAAATAT-GATGTCACCATCCCATA-TG
1 TGGTCTTACATGTAAATCAAATATCGATGCCACCATCCCAAACAG
* * * *
41237463 TGGTCTTACATGTAAATCATAA-GTCGATGCCAACGTCCCACAC-G
1 TGGTCTTACATGTAAATCA-AATATCGATGCCACCATCCCAAACAG
41237507 TGGTCTTACA
1 TGGTCTTACA
41237517 CGATAACACA
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
42 22 0.29
43 26 0.35
44 26 0.35
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (45 bp):
TGGTCTTACATGTAAATCAAATATCGATGCCACCATCCCAAACAG
Found at i:41239434 original size:93 final size:93
Alignment explanation
Indices: 41239325--41239495 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41239315 GCCCCTAAGT
* * *
41239325 GAACTCGGACTGAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41239390 TGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
41239418 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41239483 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41239496 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:41239492 original size:46 final size:46
Alignment explanation
Indices: 41239320--41239492 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
41239310 ATCCCGCCCC
* * * *
41239320 TAAGTGAACTCGGACTGAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
41239366 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
41239414 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
41239459 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41239493 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:41241587 original size:40 final size:40
Alignment explanation
Indices: 41241532--41241715 Score: 237
Period size: 40 Copynumber: 4.6 Consensus size: 40
41241522 ATTTGAATGA
*
41241532 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
41241572 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
41241612 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
41241652 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* *
41241692 TACCCGGGTTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGGCA
41241716 ATTGTGCTTG
Statistics
Matches: 136, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 133 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:41243338 original size:30 final size:30
Alignment explanation
Indices: 41243304--41243363 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41243294 ATTTAATACG
41243304 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
41243334 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
41243364 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:41248862 original size:82 final size:81
Alignment explanation
Indices: 41248746--41248901 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
41248736 AAATTGTACA
* * * *
41248746 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
41248810 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41248827 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
41248892 TGCGAGTTGA
65 TGCGAATTGA
41248902 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41248869 original size:55 final size:52
Alignment explanation
Indices: 41248745--41248898 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
41248735 TAAATTGTAC
* *
41248745 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
41248798 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
41248853 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
41248899 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:41248903 original size:27 final size:27
Alignment explanation
Indices: 41248746--41248901 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
41248736 AAATTGTACA
*
41248746 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
41248773 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
41248800 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
41248827 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
41248855 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
41248882 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
41248902 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:41248912 original size:27 final size:27
Alignment explanation
Indices: 41248738--41248922 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
41248728 GCGGGATTAA
*
41248738 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
41248765 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
41248792 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
41248819 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
41248847 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
41248874 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
41248901 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
41248923 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:41248913 original size:82 final size:81
Alignment explanation
Indices: 41248738--41248922 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
41248728 GCGGGATTAA
* * * *
41248738 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
41248803 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
41248819 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
41248883 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
41248901 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
41248923 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:41256654 original size:27 final size:26
Alignment explanation
Indices: 41256621--41256770 Score: 131
Period size: 27 Copynumber: 5.5 Consensus size: 26
41256611 AAATTGTACA
*
41256621 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* * *
41256648 GCGCTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
41256675 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
* * *
41256702 GCACTAAATGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTG
* *
41256730 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
41256757 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41256771 GGTTGATTGT
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.01
27 74 0.75
28 24 0.24
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:41256739 original size:82 final size:81
Alignment explanation
Indices: 41256621--41256770 Score: 194
Period size: 82 Copynumber: 1.8 Consensus size: 81
41256611 AAATTGTACA
* * * * * *
41256621 GCACTAAGTGTGCGATTCGACTATGTTGCGCTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAATGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
41256685 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41256702 GCACTAAATGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAATGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
41256767 TGCG
65 TGCG
41256771 GGTTGATTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 17 0.29
82 41 0.71
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAATGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41256787 original size:27 final size:27
Alignment explanation
Indices: 41256728--41256799 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
41256718 TCTAACTATG
** *
41256728 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGGGTTGATTACA
* **
41256755 TGGCACTAAGTGTGCGGGTTGATTGTA
1 TAGCACTAAGTGTGCGGGTTGATTACA
*
41256782 TAGCACTGAGTGTGCGGG
1 TAGCACTAAGTGTGCGGG
41256800 CTCAATATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.31
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGGGTTGATTACA
Found at i:41267337 original size:27 final size:26
Alignment explanation
Indices: 41267304--41267455 Score: 126
Period size: 27 Copynumber: 5.5 Consensus size: 26
41267294 AAATTGTACA
*
41267304 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* * *
41267331 GCGCTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
*
41267358 GCACTAAGTGTGCGAATTGACCATGCTCG
1 GCACTAAGTGTGCG-ATTGACTATG-T-G
* * *
41267387 GCACTAAATGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTG
* *
41267415 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
41267442 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41267456 GGTTGATTGT
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
27 61 0.60
28 19 0.19
29 15 0.15
30 6 0.06
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:41267472 original size:27 final size:27
Alignment explanation
Indices: 41267413--41267484 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
41267403 TCTAACTATG
** *
41267413 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGGGTTGATTACA
* **
41267440 TGGCACTAAGTGTGCGGGTTGATTGTA
1 TAGCACTAAGTGTGCGGGTTGATTACA
*
41267467 TAGCACTGAGTGTGCGGG
1 TAGCACTAAGTGTGCGGG
41267485 CTCAATATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.31
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGGGTTGATTACA
Found at i:41270435 original size:42 final size:43
Alignment explanation
Indices: 41270317--41270480 Score: 165
Period size: 43 Copynumber: 3.8 Consensus size: 43
41270307 ACATAGGATC
* * * *
41270317 CGATATGTGTTTTCATGTAAGACGAC-ATCTGGGACATTGGCAT
1 CGATATTTGATTTCATGTAAGAC-CCTGTCTGGGACATTGGCAT
* * *
41270360 CGACT-TATAATTTACATGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TATTTGATTT-CATGTAAGACCCTGTCTGGGACATTGGCAT
* *
41270404 C-ATATTTGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCAT
1 CGATATTTGATTTCATGTAAGACCCTGTCTGGGACATTGGCAT
**
41270446 CGATATTTGATCACATGTAAGACCAC-GTCTGGGAC
1 CGATATTTGATTTCATGTAAGACC-CTGTCTGGGAC
41270481 GTTCGCTTTG
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
42 29 0.29
43 43 0.43
44 29 0.29
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCCTGTCTGGGACATTGGCAT
Found at i:41270466 original size:43 final size:42
Alignment explanation
Indices: 41270373--41270480 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 42
41270363 CTTATAATTT
* * *
41270373 ACATGTAAGACCATGTCTGGGACATTGGCATCATATTTGATT
1 ACATGTAAGACCCTGTCTGGGACAGTGGCATCATATTTGATC
* *
41270415 TCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATC
1 ACATGTAAGACCCTGTCTGGGACAGTGGCATC-ATATTTGATC
41270458 ACATGTAAGACCAC-GTCTGGGAC
1 ACATGTAAGACC-CTGTCTGGGAC
41270481 GTTCGCTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
42 28 0.49
43 28 0.49
44 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (42 bp):
ACATGTAAGACCCTGTCTGGGACAGTGGCATCATATTTGATC
Found at i:41274581 original size:1 final size:1
Alignment explanation
Indices: 41274575--41274659 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
41274565 ACAAGCATAT
* * * * * * * * * *
41274575 AAAAAAAGAAAACAAATAATAAAAAAAAAAAATAAATAAAAAATAAAGAAAAAAAAAAAAATAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
41274640 AATAAATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
41274660 TACAAGAATA
Statistics
Matches: 60, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.86, C:0.01, G:0.02, T:0.11
Consensus pattern (1 bp):
A
Found at i:41274589 original size:21 final size:20
Alignment explanation
Indices: 41274573--41274653 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
41274563 TCACAAGCAT
*
41274573 ATAAAAAAAGAAAACAAATA
1 ATAAAAAAAAAAAACAAATA
*
41274593 ATAAAAAAAAAAAATAAATAAAAA
1 ATAAAAAAAAAAAACAAAT----A
*
41274617 ATAAAGAAAAAAAAAAAAATA
1 ATAAA-AAAAAAAAACAAATA
41274638 ATAATAAATAAAAAAA
1 ATAA-AAA-AAAAAAA
41274654 AAAAAATACA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
20 17 0.33
21 7 0.14
22 8 0.16
24 6 0.12
25 13 0.25
ACGTcount: A:0.84, C:0.01, G:0.02, T:0.12
Consensus pattern (20 bp):
ATAAAAAAAAAAAACAAATA
Found at i:41274593 original size:17 final size:15
Alignment explanation
Indices: 41274573--41274657 Score: 80
Period size: 17 Copynumber: 5.1 Consensus size: 15
41274563 TCACAAGCAT
41274573 ATAAAAAAAGAAAACAA
1 ATAAAAAAA-AAAA-AA
41274590 ATAATAAAAAAAAAAA
1 ATAA-AAAAAAAAAAA
41274606 ATAAATAAAAAATAAAGA
1 ATAAA-AAAAAA-AAA-A
*
41274624 AAAAAAAAAAAATAATA
1 ATAAAAAAAAAA-AA-A
41274641 ATAAATAAAAAAAAAA
1 ATAAA-AAAAAAAAAA
41274657 A
1 A
41274658 AATACAAGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
15 1 0.02
16 15 0.25
17 26 0.44
18 17 0.29
ACGTcount: A:0.85, C:0.01, G:0.02, T:0.12
Consensus pattern (15 bp):
ATAAAAAAAAAAAAA
Found at i:41274598 original size:20 final size:20
Alignment explanation
Indices: 41274573--41274626 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
41274563 TCACAAGCAT
41274573 ATAAAAAAAGAAAACAAATA
1 ATAAAAAAAGAAAACAAATA
* *
41274593 ATAAAAAAAAAAAATAAATA
1 ATAAAAAAAGAAAACAAATA
41274613 A-AAAATAAAGAAAA
1 ATAAAA-AAAGAAAA
41274627 AAAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (20 bp):
ATAAAAAAAGAAAACAAATA
Found at i:41274619 original size:24 final size:23
Alignment explanation
Indices: 41274575--41274659 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 23
41274565 ACAAGCATAT
* * *
41274575 AAAAAAAGAAAACAAATAATAAA
1 AAAAAAAAAAAATAAAAAATAAA
41274598 AAAAAAAAATAAATAAAAAATAAAGA
1 AAAAAAAAA-AAATAAAAAAT-AA-A
41274624 AAAAAAAAAAAATAATAATAAATAAA
1 AAAAAAAAAAAAT-A-AA-AAATAAA
41274650 AAAAAAAAAA
1 AAAAAAAAAA
41274660 TACAAGAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
23 8 0.15
24 9 0.17
25 6 0.11
26 22 0.42
27 4 0.08
28 4 0.08
ACGTcount: A:0.86, C:0.01, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAAAAAAAAAATAAAAAATAAA
Found at i:41274627 original size:28 final size:27
Alignment explanation
Indices: 41274595--41274659 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 27
41274585 AACAAATAAT
41274595 AAAAAAAAAAAATAAATAAAAAATAAAGA
1 AAAAAAAAAAAAT-AATAAAAAATAAA-A
*
41274624 AAAAAAAAAAAATAATAATAAATAAAA
1 AAAAAAAAAAAATAATAAAAAATAAAA
41274651 AAAAAAAAA
1 AAAAAAAAA
41274660 TACAAGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 10 0.29
28 12 0.34
29 13 0.37
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAAAATAATAAAAAATAAAA
Found at i:41274660 original size:24 final size:24
Alignment explanation
Indices: 41274573--41274661 Score: 110
Period size: 24 Copynumber: 3.7 Consensus size: 24
41274563 TCACAAGCAT
*
41274573 ATAAAAAAAGAAAACA-AATAATAA
1 ATAAAAAAA-AAAAAATAATAATAA
* *
41274597 A-AAAAAAAAATAAATAAAAAATAA
1 ATAAAAAAAAAAAAAT-AATAATAA
*
41274621 AGAAAAAAAAAAAAATAATAATAA
1 ATAAAAAAAAAAAAATAATAATAA
41274645 ATAAAAAAAAAAAAATA
1 ATAAAAAAAAAAAAATA
41274662 CAAGAATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.07
23 7 0.12
24 32 0.57
25 13 0.23
ACGTcount: A:0.84, C:0.01, G:0.02, T:0.12
Consensus pattern (24 bp):
ATAAAAAAAAAAAAATAATAATAA
Found at i:41274669 original size:29 final size:27
Alignment explanation
Indices: 41274575--41274672 Score: 110
Period size: 27 Copynumber: 3.6 Consensus size: 27
41274565 ACAAGCATAT
*
41274575 AAAAAAAGAA-AACAAATAATAAAAAAA
1 AAAAAAAGAATAATAAATAA-AAAAAAA
* *
41274602 AAAAATA-AATAAAAAATAAAGAAAAAA
1 AAAAAAAGAATAATAAATAAA-AAAAAA
*
41274629 AAAAAAATAATAATAAATAAAAAAAAA
1 AAAAAAAGAATAATAAATAAAAAAAAA
41274656 AAAATACAAGAATAATA
1 AAAA-A-AAGAATAATA
41274673 TGTCATCAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.05
27 36 0.59
28 13 0.21
29 9 0.15
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (27 bp):
AAAAAAAGAATAATAAATAAAAAAAAA
Done.